Original article
Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method
Evaluación comparativa de la identificación de micobacterias no tuberculosas de crecimiento rápido mediante espectrometría de masas (MALDI-TOF MS), GenoType® Mycobacterium CM/AS assay y la secuenciación parcial del gen rpoβ con análisis filogenético como método de referencia
José Javier Costa-Alcaldea,
, Gema Barbeito-Castiñeirasb, José María González-Albac,d,e, Antonio Aguileraa,f, Juan Carlos Galánc,d,e, María Luisa Pérez-del-Molinoa
Corresponding author
a Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
b Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela – Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
c Servicio de Microbiología Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
d CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
e Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
f Departamento de Microbioloxía, Universidad de Santiago de Compostela, A Coruña, Spain
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array:6 [ 0 => array:3 [ "entidad" => "Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain" "etiqueta" => "a" "identificador" => "aff0005" ] 1 => array:3 [ "entidad" => "Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela – Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain" "etiqueta" => "b" "identificador" => "aff0010" ] 2 => array:3 [ "entidad" => "Servicio de Microbiología Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain" "etiqueta" => "c" "identificador" => "aff0015" ] 3 => array:3 [ "entidad" => "CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain" "etiqueta" => "d" "identificador" => "aff0020" ] 4 => array:3 [ "entidad" => "Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain" "etiqueta" => "e" "identificador" => "aff0025" ] 5 => array:3 [ "entidad" => "Departamento de Microbioloxía, Universidad de Santiago de Compostela, A Coruña, Spain" "etiqueta" => "f" "identificador" => "aff0030" ] ] "correspondencia" => array:1 [ 0 => array:3 [ "identificador" => "cor0005" "etiqueta" => "⁎" "correspondencia" => "Corresponding author." ] ] ] ] "titulosAlternativos" => array:1 [ "es" => array:1 [ "titulo" => "Evaluación comparativa de la identificación de micobacterias no tuberculosas de crecimiento rápido mediante espectrometría de masas (MALDI-TOF MS), GenoType<span class="elsevierStyleSup">®</span> Mycobacterium CM/AS assay y la secuenciación parcial del gen <span class="elsevierStyleItalic">rpoβ</span> con análisis filogenético como método de referencia" ] ] "resumenGrafico" => array:2 [ "original" => 0 "multimedia" => array:7 [ "identificador" => "fig0005" "etiqueta" => "Fig. 1" "tipo" => "MULTIMEDIAFIGURA" "mostrarFloat" => true "mostrarDisplay" => false "figura" => array:1 [ 0 => array:4 [ "imagen" => "gr1.jpeg" "Alto" => 1762 "Ancho" => 2283 "Tamanyo" => 299699 ] ] "descripcion" => array:1 [ "en" => "<p id="spar0045" class="elsevierStyleSimplePara elsevierViewall">Maximum-likelihood tree (GTR plus I plus G; aLRT<span class="elsevierStyleHsp" style=""></span>><span class="elsevierStyleHsp" style=""></span>90%) <span class="elsevierStyleItalic">Mycobacterium rpoβ</span> partial gene 495 nucleotides.</p>" ] ] ] "textoCompleto" => "<span class="elsevierStyleSections"><span id="sec0005" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0065">Introduction</span><p id="par0005" class="elsevierStylePara elsevierViewall">The last twenty years have been characterized by an extraordinary increase of new <span class="elsevierStyleItalic">Mycobacterium</span> spp. Among over 150 officially recognized nontuberculous mycobacteria (NTM), only a few tens are familiar to clinicians.<a class="elsevierStyleCrossRef" href="#bib0130"><span class="elsevierStyleSup">1</span></a> NTM are widely present in the environment and commonly inhabit soil and water. This group of microorganisms are considered to be opportunistic pathogens which can cause pulmonary, skin, soft tissue, lymphatic and disseminated infections, as well as nosocomial outbreaks related to inadequate disinfection/sterilization of medical equipment. The incidence of diseases caused by NTM is on the rise due to, among other reasons, an increase in immunocompromised patients.<a class="elsevierStyleCrossRef" href="#bib0135"><span class="elsevierStyleSup">2</span></a> The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant NTM should be identified to the species level in order to determine their clinical significance and select appropriate treatments.<a class="elsevierStyleCrossRef" href="#bib0140"><span class="elsevierStyleSup">3</span></a></p><p id="par0010" class="elsevierStylePara elsevierViewall">Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) allows the identification of organisms on the basis of unique spectral fingerprints produced by extracted proteins. In recent years, MALDI-TOF MS has irrupted as a rapid, powerful and relatively inexpensive tool for the identification of bacteria and yeast in the clinical laboratory setting.<a class="elsevierStyleCrossRefs" href="#bib0130"><span class="elsevierStyleSup">1,4</span></a></p><p id="par0015" class="elsevierStylePara elsevierViewall">The molecular approach, using both in-house and commercial systems, is the most frequently used method worldwide for the identification of mycobacterial species. In this work, two molecular approaches for mycobacterial identification are used: a molecular commercial system and partial RNA polymerase beta-subunit gene sequencing (<span class="elsevierStyleItalic">rpoβ</span>).<a class="elsevierStyleCrossRef" href="#bib0150"><span class="elsevierStyleSup">5</span></a></p><p id="par0020" class="elsevierStylePara elsevierViewall">Genetic sequencing of conserved genes is the referent method for the identification of mycobacteria.<a class="elsevierStyleCrossRef" href="#bib0130"><span class="elsevierStyleSup">1</span></a> A number of targets useful for identification purposes have been detected within the genome of mycobacteria. Several studies have indicated that the hypervariable region of the <span class="elsevierStyleItalic">rpoβ</span> gene, located between 2300 and 3300<span class="elsevierStyleHsp" style=""></span>bp, is required for suitable identification at species level and this region is recommended as a starting point for identification.<a class="elsevierStyleCrossRef" href="#bib0155"><span class="elsevierStyleSup">6</span></a></p><p id="par0025" class="elsevierStylePara elsevierViewall">The aim of this study was to evaluate rapidly growing mycobacteria (RGM) identification from clinical samples by using MALDI-TOF MS technology and a molecular commercial system, both methodologies are used in the routine practice of our laboratory. For this purpose, we compared the results obtained by using the routine methodology with the results obtained by using gold standard methodology (partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing phylogenetic analysis).</p></span><span id="sec0010" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0070">Material and methods</span><span id="sec0015" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0075">Clinical isolates</span><p id="par0030" class="elsevierStylePara elsevierViewall">From January 2007 to April 2015, a total of 46 clinical isolates of RGM were obtained from patients belonging to the health area of Santiago de Compostela (458.759 inhabitants), Galicia, Northwest of Spain. Only 15 of these patients presented diagnosis criteria according to the American Thoracic Society (ATS).<a class="elsevierStyleCrossRef" href="#bib0140"><span class="elsevierStyleSup">3</span></a> These mycobacterial isolates were firstly identified by using the molecular commercial system GenoType<span class="elsevierStyleSup">®</span> CM/AS, Hain Lifescience, Nehren, Germany. Clinical isolates were preserved at −20<span class="elsevierStyleHsp" style=""></span>°C in skimmed milk until they were used. Thereafter, each strain was inoculated into agar blood medium (Columbia-blood agar base, Becton Dickinson, New Jersey, USA) and incubated at 37<span class="elsevierStyleHsp" style=""></span>°C in a 10% CO<span class="elsevierStyleInf">2</span> incubator. After 5–7 days the growth achieved was enough to carry out the corresponding studies.</p><p id="par0035" class="elsevierStylePara elsevierViewall">Clinical isolates were obtained as part of the routine activity of the Department of Microbiology and they were analyzed anonymously in a retrospective manner. Thus, ethical approval and informed consent were not required.</p></span><span id="sec0020" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0080">GenoType<span class="elsevierStyleSup">®</span><span class="elsevierStyleItalic">Mycobacterium</span> CM/AS (Hain, Lifescience, Germany) (GenoType<span class="elsevierStyleSup">®</span>)</span><p id="par0040" class="elsevierStylePara elsevierViewall">The GenoType<span class="elsevierStyleSup">®</span> includes a multiplex PCR followed by reverse hybridization and line probe technology. This assay targets the 23S rRNA gene and is available as two kits: CM, which identifies 22 of the most frequently isolated species, and AS, which identifies an additional 13 species. The GenoType<span class="elsevierStyleSup">®</span> assay was performed according to the manufacturer's instructions. The final identification was obtained by comparison between the line probe patterns and the evaluation sheet provided by manufacturers.</p></span><span id="sec0025" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0085">MALDI-TOF MS protein extraction protocol</span><p id="par0045" class="elsevierStylePara elsevierViewall">It was used the inactivated mycobacteria bead preparation method provided by Bruker Daltonics GmbH (Bremen, Germany). With a sterile 10<span class="elsevierStyleHsp" style=""></span>μL loop, mycobacterial colonies growing on solid medium (agar blood) were transferred into a 1.5<span class="elsevierStyleHsp" style=""></span>mL screw-cap microcentrifuge tub which contained 300<span class="elsevierStyleHsp" style=""></span>μL of sterile water. Then, it was heated for 30<span class="elsevierStyleHsp" style=""></span>min at 100<span class="elsevierStyleHsp" style=""></span>°C in a thermoblock to inactivate the RGM. On average, colonies were 5–7 days old, depending on the growth rate of the mycobacteria. The tubes were allowed to cool at room temperature for 2<span class="elsevierStyleHsp" style=""></span>min. Then, 900<span class="elsevierStyleHsp" style=""></span>μL of 100% ethanol were added. After vortexing, the tubs were centrifuged at 13,000<span class="elsevierStyleHsp" style=""></span>rpm for 2<span class="elsevierStyleHsp" style=""></span>min and the supernatant was discarded. The tubes were centrifuged again at 13,000<span class="elsevierStyleHsp" style=""></span>rpm for 2<span class="elsevierStyleHsp" style=""></span>min and all residual liquid were completely removed. The pellet was allowed to dry at room temperature for 5<span class="elsevierStyleHsp" style=""></span>min. The pellet was suspended in 25<span class="elsevierStyleHsp" style=""></span>μL of acetonitrile, and approximately a volume of 50<span class="elsevierStyleHsp" style=""></span>μL of 0.5<span class="elsevierStyleHsp" style=""></span>mm diameter glass beds was added to the pellet. The tubes were vortexed for 1<span class="elsevierStyleHsp" style=""></span>min, 25<span class="elsevierStyleHsp" style=""></span>μL of 70% formic acid were added, and the samples were vortexed again for 1<span class="elsevierStyleHsp" style=""></span>min. The tubes were centrifuged at 13,000<span class="elsevierStyleHsp" style=""></span>rpm for 2<span class="elsevierStyleHsp" style=""></span>min, and the supernatant was used for analysis with MALDI-TOF MS.</p><p id="par0050" class="elsevierStylePara elsevierViewall">All steps requiring open manipulation of mycobacteria before heat inactivation were performed inside a biological safety cabinet in a biosafety level 2 setup.</p></span><span id="sec0030" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0090">MALDI-TOF MS analysis</span><p id="par0055" class="elsevierStylePara elsevierViewall">Strains were processed using a MALDI-TOF MS microflex LT (Brucker Daltonics GmbH, Bremen, Germany). Analyses were performed according to the manufacturer's instructions.</p><p id="par0060" class="elsevierStylePara elsevierViewall">One microliter of supernatant was spotted in duplicate onto a steel target (MTP 384 polished steel target plate BC; Brucker Daltonics GmbH, Bremen, Germany) and air dried at room temperature. One microliter of matrix solution (saturate solution of alfa-cyano-4-hydroxycinnamic acid in 50% acetonitrile and 2.5% trifluoroacetic acid) was pipetted onto each of the spotted samples. After drying, the target was inserted into the MALDI-TOF MS. MALDI-TOF MS analysis was performed in automatic mode. Spectra were acquired at a laser frequency of 60<span class="elsevierStyleHsp" style=""></span>Hz across a mass/charge ratio (<span class="elsevierStyleItalic">m</span>/<span class="elsevierStyleItalic">z</span>) of 2000–20,000<span class="elsevierStyleHsp" style=""></span>Da.</p><p id="par0065" class="elsevierStylePara elsevierViewall">The protein profile was obtained by the software FlexControl 3.4 (Brucker Daltonics GmbH, Bremen, Germany). Spectra were analyzed against those in the Brucker database Maldi Biotyper Mycobacteria Library 3.0 (853 references from 149 <span class="elsevierStyleItalic">Mycobacterium</span> species) using the Maldi Biotyper software (v 3.1; Bruker Daltonics). This assigned a logarithmic score ranging from 0 to 3 and determined the best match based on the <span class="elsevierStyleItalic">m</span>/<span class="elsevierStyleItalic">z</span> ratio and relative peak size of each ionized protein.</p></span><span id="sec0035" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0095">Partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing</span><span id="sec0040" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0100">DNA extraction</span><p id="par0070" class="elsevierStylePara elsevierViewall">It was performed using the DNA extraction method for solid culture included in the Anyplex™ MTB/NTM Real-time Detection V2.0 (Seegene, Seoul, Korea) according to the manufacturer's instructions.</p></span><span id="sec0045" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0105"><span class="elsevierStyleItalic">rpoβ</span> amplification</span><p id="par0075" class="elsevierStylePara elsevierViewall">5<span class="elsevierStyleHsp" style=""></span>μL of extracted DNA were used for PCR in a 25<span class="elsevierStyleHsp" style=""></span>μL final reaction volume by using the reagents provided by the GoTaq<span class="elsevierStyleSup">®</span> PCR Core Systems I (Promega) kit: 5<span class="elsevierStyleHsp" style=""></span>U/μL GoTaq<span class="elsevierStyleSup">®</span> DNA Polymerase, 5X Colorless GoTaq<span class="elsevierStyleSup">®</span> Flexi Buffer (Mg-Free), 25<span class="elsevierStyleHsp" style=""></span>mM MgCl<span class="elsevierStyleInf">2</span> and 10<span class="elsevierStyleHsp" style=""></span>mM PCR Nucleotide Mix. The direct and reverse primers were 10<span class="elsevierStyleHsp" style=""></span>μM. The final concentrations were 0.025<span class="elsevierStyleHsp" style=""></span>U/μL GoTaq<span class="elsevierStyleSup">®</span> DNA Polymerase, 4<span class="elsevierStyleHsp" style=""></span>mM MgCl<span class="elsevierStyleInf">2</span>, 0.2<span class="elsevierStyleHsp" style=""></span>mM dNTPs (each nucleotide), 0.2<span class="elsevierStyleHsp" style=""></span>μM each primer. All the clinical strains were identified by partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing using a previously described method.<a class="elsevierStyleCrossRef" href="#bib0150"><span class="elsevierStyleSup">5</span></a> Briefly, flanking the most variable <span class="elsevierStyleItalic">rpoβ</span> region, PCR primers MycoF (5′-GGCAAGGTCACCCCGAAGGG-3′; base positions 2573–2592, the nucleotides have been numbered according to the <span class="elsevierStyleItalic">M. smegmatis</span> ATCC 14468 <span class="elsevierStyleItalic">rpoβ</span> gene sequence) and MycoR (5′-AGCGGCTGCGGGTGATCATC-3′; base positions 3316–3337) amplified a 764-bp fragment from the <span class="elsevierStyleItalic">rpoβ</span> gene region in clinical isolates. Conditions for <span class="elsevierStyleItalic">rpoβ</span> gene amplification were pre-heated at 95<span class="elsevierStyleHsp" style=""></span>°C for 10<span class="elsevierStyleHsp" style=""></span>min, 35 cycles of 95<span class="elsevierStyleHsp" style=""></span>°C for 30<span class="elsevierStyleHsp" style=""></span>s, 55<span class="elsevierStyleHsp" style=""></span>°C for 30<span class="elsevierStyleHsp" style=""></span>s and 72<span class="elsevierStyleHsp" style=""></span>°C for 90<span class="elsevierStyleHsp" style=""></span>s; finally, an elongation step of 72<span class="elsevierStyleHsp" style=""></span>°C for 7<span class="elsevierStyleHsp" style=""></span>min. Five microliters of PCR product were analyzed by ultraviolet fluorescence after having been stained with ethidium bromide in a 1% agarose gel.</p></span><span id="sec0050" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0110"><span class="elsevierStyleItalic">rpoβ</span> partial sequencing</span><p id="par0080" class="elsevierStylePara elsevierViewall">PCR products were purified by using Qiagen columns (Qiagen, Germany). Purified amplicons were sequenced by using the GenomeLab™ Dye Terminator Cycle Sequencing with the Quick Start kit according to the manufacturer's instructions (Beckman Coulter<span class="elsevierStyleSup">®</span>) with the following program: 30 cycles of denaturation at 96<span class="elsevierStyleHsp" style=""></span>°C for 20<span class="elsevierStyleHsp" style=""></span>s, primer annealing at 50<span class="elsevierStyleHsp" style=""></span>°C for 20<span class="elsevierStyleHsp" style=""></span>s and extension at 60<span class="elsevierStyleHsp" style=""></span>°C for 4<span class="elsevierStyleHsp" style=""></span>min. The sequencing primers were the same as in the amplification. Products of sequencing reactions were read in an automatic sequencer (CEQ™ 8000 Genetic Analysis System, Beckman Coulter<span class="elsevierStyleSup">®</span>) by following the standard protocol of the supplier.</p><p id="par0085" class="elsevierStylePara elsevierViewall">Those partial <span class="elsevierStyleItalic">rpoβ</span> gene sequences obtained in that way were compared to those available in the GeneBank using BLAST software (NCBI) (<a id="intr0005" class="elsevierStyleInterRef" href="http://blast.ncbi.nim.nihgov/Blast.cgi-">http://blast.ncbi.nim.nihgov/Blast.cgi-</a>). After that, the most probable bacterial species were selected. Partial <span class="elsevierStyleItalic">rpoβ</span> gene sequences that displayed at least 98% sequence identity when compared to those in the GeneBank were considered as identified species.<a class="elsevierStyleCrossRef" href="#bib0150"><span class="elsevierStyleSup">5</span></a></p></span></span><span id="sec0055" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0115">Phylogenetic analysis</span><p id="par0090" class="elsevierStylePara elsevierViewall">Phylogenetic analysis was carried out to improve the accuracy of partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing. The partial <span class="elsevierStyleItalic">rpoβ</span> gene sequence length ranged between 278 and 710 nucleotides. A set of reference sequences of Mycobacterium's rpo<span class="elsevierStyleItalic">β</span> gene available in the GeneBank was obtained by using BLAST (<a class="elsevierStyleCrossRef" href="#sec0100">Table S1 included as Supplementary material</a>). The reference data set including 1093 sequences and nucleotide sequences were translated and aligned using the ClustalW algorithm implemented in MEGA. The sequences were divided according to the sequenced fragment for analysis. Phylogenetic trees were reconstructed by means of ML with PhyML<a class="elsevierStyleCrossRef" href="#bib0160"><span class="elsevierStyleSup">7</span></a> 3.0 by using the general time reversible plus proportion of invariable sites plus gamma distribution parameter (GTR) plus I plus G evolutionary model selected with jModeltest<a class="elsevierStyleCrossRef" href="#bib0165"><span class="elsevierStyleSup">8</span></a> 0.1 and a BIONJ starting tree. Heuristic tree searches under the ML optimality criterion were performed using the nearest neighbor interchange (NNI) branch-swapping algorithm. The approximate likelihood ratio test (aLRT) based on a Shimodaira–Hasegawa-like procedure was used as a statistical test to calculate branch support.<a class="elsevierStyleCrossRef" href="#bib0170"><span class="elsevierStyleSup">9</span></a> Only aLRT support values of >90% were considered statistically significant and displayed at the tree nodes.</p></span><span id="sec0060" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0120">Statistical analysis</span><p id="par0095" class="elsevierStylePara elsevierViewall">The Kappa coefficient was used to study the degree of concordance between methods. Fisher's exact test was used to evaluate the agreement between GenoType<span class="elsevierStyleSup">®</span> and MALDI-TOF. A <span class="elsevierStyleItalic">p</span> value <0.05 was considered statistically significant. The analyses were done with STATA 13.1 (StataCorp, USA).</p></span></span><span id="sec0065" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0125">Results</span><p id="par0100" class="elsevierStylePara elsevierViewall">The results obtained are shown in <a class="elsevierStyleCrossRef" href="#tbl0005">Table 1</a> and <a class="elsevierStyleCrossRef" href="#fig0005">Fig. 1</a> (<a class="elsevierStyleCrossRef" href="#sec0100">Figures 2–8 are included as Supplementary material</a>).</p><elsevierMultimedia ident="tbl0005"></elsevierMultimedia><elsevierMultimedia ident="fig0005"></elsevierMultimedia><p id="par0105" class="elsevierStylePara elsevierViewall">Phylogenetic and BLAST analyses were in agreement, but in 2 strains, phylogenetic analysis found no significant differences between at least two species of <span class="elsevierStyleItalic">Mycobacterium</span> spp<span class="elsevierStyleItalic">.</span> (<a class="elsevierStyleCrossRef" href="#tbl0005">Table 1</a>: strains 29 and 45). Strains were considered correctly classified if any of these results were obtained.</p><p id="par0110" class="elsevierStylePara elsevierViewall">By using BLAST, samples 42 and 45 displayed a sequence identity less than 98%, when they were compared to those available in the GeneBank. The identification was in accordance with phylogenetic analysis. For sample 45, phylogenetic analysis found no significant differences between <span class="elsevierStyleItalic">M. duvalii</span> and <span class="elsevierStyleItalic">M. monacense</span>.</p><p id="par0115" class="elsevierStylePara elsevierViewall">Three strains (6.5%) were not identified using partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing (BLAST and phylogeny) because it was not possible to amplify them by PCR.</p><p id="par0120" class="elsevierStylePara elsevierViewall">Eight strains were identified by partial <span class="elsevierStyleItalic">rpoβ</span> gene sequence as <span class="elsevierStyleItalic">M. abscessus</span>. It was not possible classified these <span class="elsevierStyleItalic">M. abscessus</span> at subspecies level.</p><span id="sec0070" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0130">GenoType<span class="elsevierStyleSup">®</span> and partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing</span><p id="par0125" class="elsevierStylePara elsevierViewall">Agreement between GenoType<span class="elsevierStyleSup">®</span> and partial <span class="elsevierStyleItalic">rpoβ</span> sequencing methods was observed in 27 of 43 cases (62.8%), Kappa value 0.534 (<span class="elsevierStyleItalic">p</span><span class="elsevierStyleHsp" style=""></span><<span class="elsevierStyleHsp" style=""></span>0.001).</p></span><span id="sec0075" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0135">MALDI-TOF MS and partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing</span><p id="par0130" class="elsevierStylePara elsevierViewall">Agreement between MALDI-TOF MS and partial <span class="elsevierStyleItalic">rpoβ</span> sequencing methods was observed in 38 of 43 cases (88.3%), Kappa value 0.854 (<span class="elsevierStyleItalic">p</span><span class="elsevierStyleHsp" style=""></span><<span class="elsevierStyleHsp" style=""></span>0.001).</p><p id="par0135" class="elsevierStylePara elsevierViewall">When only MALDI-TOF scores >1.85 were considered, the agreement was 100% (36 of 36). For MALDI-TOF scores <1.85, only 2 of 7 (28.6%) results were in accordance (<a class="elsevierStyleCrossRef" href="#tbl0005">Table 1</a>).</p></span><span id="sec0080" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0140">GenoType<span class="elsevierStyleSup">®</span> and MALDI-TOF MS</span><p id="par0140" class="elsevierStylePara elsevierViewall">All the strains correctly classified by GenoType<span class="elsevierStyleSup">®</span> were also well identified when using MALDI-TOF MS (27/27). However, MALDI-TOF MS detected correctly a 68.75% (11/16) of the strains that GenoType<span class="elsevierStyleSup">®</span> misclassified (<span class="elsevierStyleItalic">p</span><span class="elsevierStyleHsp" style=""></span>=<span class="elsevierStyleHsp" style=""></span>0.005).</p></span></span><span id="sec0085" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0145">Discussion</span><p id="par0145" class="elsevierStylePara elsevierViewall">In this work, the identification of RGM using the routine methodology (GenoType<span class="elsevierStyleSup">®</span> and MALDI-TOF MS) and a reference methodology (partial <span class="elsevierStyleItalic">rpo</span>β gene sequencing and phylogenetic analysis) were compared.</p><p id="par0150" class="elsevierStylePara elsevierViewall">Procedures for the identification of mycobacteria have greatly changed in the last years, and conventional biochemical and cultural methods are nowadays used only by a few laboratories worldwide. These methods have been abandoned because, in addition to relying on tests that are poorly reproducible and unbearably time consuming, they lack sufficient discriminative power (1). Even the HPLC methods based on analysis of cell wall lipids now seem to be in trouble because of the steady increment in the number of species within the genus <span class="elsevierStyleItalic">Mycobacterium</span>.<a class="elsevierStyleCrossRef" href="#bib0175"><span class="elsevierStyleSup">10</span></a> In the last few years, the emergence of new species sharing common HPLC profiles has steadily diminished the discriminatory capacity of this method.<a class="elsevierStyleCrossRef" href="#bib0130"><span class="elsevierStyleSup">1</span></a></p><p id="par0155" class="elsevierStylePara elsevierViewall">There are some works which support MALDI-TOF MS technology to identify <span class="elsevierStyleItalic">Mycobacterium</span> spp.<a class="elsevierStyleCrossRefs" href="#bib0145"><span class="elsevierStyleSup">4,11</span></a> Clark et al. conclude that these studies demonstrate the feasibility and strong accuracy associated to MALDI-TOF MS for mycobacterial identification.<a class="elsevierStyleCrossRef" href="#bib0145"><span class="elsevierStyleSup">4</span></a> Nevertheless, other authors believe that the accuracy of the identification achievable at present with genetic approaches is out of reach for MALDI-TOF MS technology.<a class="elsevierStyleCrossRef" href="#bib0130"><span class="elsevierStyleSup">1</span></a> In this work, we have found that it is necessary to reach a specific MALDI-TOF MS score value (1.85) so that the identifications obtained with MALDI-TOF MS are correct with respect to the reference method<a class="elsevierStyleCrossRef" href="#bib0185"><span class="elsevierStyleSup">12</span></a> which was used. However, it must be taken into account the limited number of isolates and varieties of RGM species which were used in our study.</p><p id="par0160" class="elsevierStylePara elsevierViewall">From the point of view of cost-effectiveness, the results were obtained within 2<span class="elsevierStyleHsp" style=""></span>h with MALDI-TOF MS while it took at least 4<span class="elsevierStyleHsp" style=""></span>h with GenoType<span class="elsevierStyleSup">®</span>. Moreover, MALDI-TOF MS methodology is simple, quick and associated with significantly lower consumable costs than GenoType<span class="elsevierStyleSup">®</span>. The MALDI-TOF mass spectrometer and associated software are expensive initially but the continuing consumable costs are inexpensive (less than 1 $, 1.25 €, per isolate).<a class="elsevierStyleCrossRef" href="#bib0180"><span class="elsevierStyleSup">11</span></a> The cost per identification with GenoType<span class="elsevierStyleSup">®</span>GenoType in our laboratory goes up to 49 € each determination, which multiplies several times the cost for each determination obtained with MALDI-TOF MS.</p><p id="par0165" class="elsevierStylePara elsevierViewall"><span class="elsevierStyleItalic">M. abscessus</span> complex comprises a group of multidrug-resistant RGM that has emerged as an important pathogen responsible for a wide spectrum of infections, following its recognition as a different entity from <span class="elsevierStyleItalic">M. chelonae</span> in 1992. In this work these three methods were able to differentiate these species with total accordance.</p><p id="par0170" class="elsevierStylePara elsevierViewall"><span class="elsevierStyleItalic">M. abscessus</span> complex is differentiated into 3 subspecies.<a class="elsevierStyleCrossRef" href="#bib0190"><span class="elsevierStyleSup">13</span></a> These subspecies have clinical relevance because they are related to the response to macrolides. <span class="elsevierStyleItalic">M. abscessus</span> subsp. <span class="elsevierStyleItalic">bolletii</span> infection had a higher response rate (approximately 90%) than patients with <span class="elsevierStyleItalic">M. abscessus</span> subsp. <span class="elsevierStyleItalic">abscessu</span>s infection (approximately 25%).<a class="elsevierStyleCrossRef" href="#bib0195"><span class="elsevierStyleSup">14</span></a> Most <span class="elsevierStyleItalic">M. abscessus</span> subsp. <span class="elsevierStyleItalic">massiliens</span>e strains do not posses inducible macrolide resistance. In contrast with some authors<a class="elsevierStyleCrossRefs" href="#bib0200"><span class="elsevierStyleSup">15,16</span></a> and in agreement with others,<a class="elsevierStyleCrossRefs" href="#bib0210"><span class="elsevierStyleSup">17,18</span></a> we found that the partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing used in our study<a class="elsevierStyleCrossRef" href="#bib0150"><span class="elsevierStyleSup">5</span></a> was unable to classify <span class="elsevierStyleItalic">M. abscessus</span> subspecies. It is widely accepted that several genes, analyzed in a particular way by researches, are necessary to identify the three subspecies: <span class="elsevierStyleItalic">rpoβ</span>, <span class="elsevierStyleItalic">secA</span>, <span class="elsevierStyleItalic">sodA</span> and <span class="elsevierStyleItalic">hsp65</span> genes.<a class="elsevierStyleCrossRefs" href="#bib0210"><span class="elsevierStyleSup">17,18</span></a> The single gene-based approach is sensitive to the evolutionary history of that gene, but not necessarily of the species, and it may be limited by the lack of sufficient variation in a single gene sequence. Therefore, a multiple gene-based approach may lead to an accurate inference of phylogenetic tree for subspecies classification.<a class="elsevierStyleCrossRef" href="#bib0220"><span class="elsevierStyleSup">19</span></a> Nevertheless some authors have described methods in which MALDI-TOF MS is used to differentiate <span class="elsevierStyleItalic">M. abscessus</span> complex at subsp. level.<a class="elsevierStyleCrossRef" href="#bib0225"><span class="elsevierStyleSup">20</span></a> We consider that it would be of great interest to expand the study for the identification of this species of mycobacteria and its subspecies by means of MALDI-TOF MS due to its vital clinical importance.</p><p id="par0175" class="elsevierStylePara elsevierViewall"><span class="elsevierStyleItalic">M. fortuitum</span> complex comprises the following species: <span class="elsevierStyleItalic">M. fortuitum</span>, <span class="elsevierStyleItalic">M. peregrinum</span>, <span class="elsevierStyleItalic">M. senegalense</span>, <span class="elsevierStyleItalic">M. setense</span>, <span class="elsevierStyleItalic">M. mageritense</span>, <span class="elsevierStyleItalic">M. septicum</span>, <span class="elsevierStyleItalic">M. alvei</span>, <span class="elsevierStyleItalic">M. houstonense</span>, <span class="elsevierStyleItalic">M. boenickei</span>, <span class="elsevierStyleItalic">M. conceptionense</span>, <span class="elsevierStyleItalic">M. porcinum</span>, <span class="elsevierStyleItalic">M. neworleansense</span> and <span class="elsevierStyleItalic">M. brisbanense</span>. In our study we found 18 <span class="elsevierStyleItalic">M. fortuitum</span> complex isolates but only six different species. According to the manufacturer's instructions, GenoType<span class="elsevierStyleSup">®</span> differentiates <span class="elsevierStyleItalic">M. fortuitum</span> type 1, <span class="elsevierStyleItalic">M. fortuitum</span> type 2/<span class="elsevierStyleItalic">M. mageritense</span> and <span class="elsevierStyleItalic">M. peregrinum</span>/<span class="elsevierStyleItalic">M. alvei</span>/<span class="elsevierStyleItalic">M. septicum</span> but, in this study, all of them were identified as <span class="elsevierStyleItalic">M. fortuitum</span> by GenoType<span class="elsevierStyleSup">®</span>. Despite the limitation implied by the number and variety of those studied species, when GenoType<span class="elsevierStyleSup">®</span>, MALDI-TOF MS and rpoβ sequencing methods were compared, it was shown that MALDI-TOF MS was superior respect to GenoType<span class="elsevierStyleSup">®</span> method to distinguish <span class="elsevierStyleItalic">M. fortuitum</span> complex species. With our results, GenoType<span class="elsevierStyleSup">®</span> would not be able to distinguish <span class="elsevierStyleItalic">M. fortuitum</span> complex species. However, it would be necessary and interesting to have a greater amount of isolates and species of this complex available in order to be able to verify these results and obtain more solid conclusions. By using MALDI-TOF MS, 4/17 strains of <span class="elsevierStyleItalic">M. fortuitum</span> complex were misidentified. However, it must be pointed out that these four strains showed<a class="elsevierStyleCrossRef" href="#bib0185"><span class="elsevierStyleSup">12</span></a> a MALDI-TOF MS score <1.85.</p><p id="par0180" class="elsevierStylePara elsevierViewall"><span class="elsevierStyleItalic">M. mucogenicum</span> was identified only in one sample with MALDI-TOF MS and partial <span class="elsevierStyleItalic">rpoβ</span> sequencing method, while it was identified as <span class="elsevierStyleItalic">Mycobacterium</span> spp. with GenoType<span class="elsevierStyleSup">®</span>. Han et al.<a class="elsevierStyleCrossRef" href="#bib0230"><span class="elsevierStyleSup">21</span></a> described <span class="elsevierStyleItalic">M. mucogenicum</span> as the dominant RGM species responsible for bloodstream and catheter-related infections.</p><p id="par0185" class="elsevierStylePara elsevierViewall">As we have pointed out previously, one limitation of our work would be the total number of different species included in the study. Another limitation of our study were the two strains with a partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing similarity <98% with respect to the sequences of reference from BLAST. Besides, the phylogenetic analysis found no significant differences between at least two species of <span class="elsevierStyleItalic">Mycobacterium</span> spp.: <span class="elsevierStyleItalic">M. alvei</span>/<span class="elsevierStyleItalic">peregrinum</span> and <span class="elsevierStyleItalic">M. monacense</span>/<span class="elsevierStyleItalic">duvalii</span>. These strains could not be classified correctly due to the short length of the amplified fragment. These strains would be candidates to further study to establish their identification at species level. Interestingly, the 2 strains with partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing with a similarity <98% showed MALDI-TOF MS scores <1.85 and one of them was identified with phylogenetic analysis. The sequencing of additional regions (complete 16S rRNA, <span class="elsevierStyleItalic">hsp</span>65, <span class="elsevierStyleItalic">sod</span>A, <span class="elsevierStyleItalic">dna</span>K genes)<a class="elsevierStyleCrossRefs" href="#bib0235"><span class="elsevierStyleSup">22–24</span></a> would be indicated in these cases. It is known that sequence analysis of DNA isolated from clinical samples has also allowed the discovery of new bacterial pathogens.<a class="elsevierStyleCrossRef" href="#bib0250"><span class="elsevierStyleSup">25</span></a></p><p id="par0190" class="elsevierStylePara elsevierViewall">When MALDI-TOF MS score was <1.85, the revision of these MALDI-TOF MS spectra is proposed with the aim of completing the <span class="elsevierStyleItalic">Mycobacterium</span> spp. MALDI-TOF data base.</p><p id="par0195" class="elsevierStylePara elsevierViewall">Another interesting aspect would be the enlargement of the study with slowly growing NTM. However, this would present a greater difficulty due to the intrinsic characteristics of these NTM, as well as the wide diversity of existing species.</p><p id="par0200" class="elsevierStylePara elsevierViewall">In summary, molecular methods are more costly and time-consuming and they may not be available in some clinical microbiology laboratory. Subsequently, our results, which were obtained with a limited number of rapidly growing mycobacteria species, indicate that the MALDI-TOF MS analysis could be a quick identification method in the future. In addition, to identify new species and subspecies of <span class="elsevierStyleItalic">Mycobacterium</span> spp., as well as to identify correctly all clinically relevant <span class="elsevierStyleItalic">Mycobacterium</span> spp., it will be required the sequencing of additional genes of <span class="elsevierStyleItalic">Mycobacterium</span> spp. or whole genome sequencing and the subsequent phylogenetic analysis.</p></span><span id="sec0090" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0150">Conflict of interest</span><p id="par0205" class="elsevierStylePara elsevierViewall">The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.</p></span></span>" "textoCompletoSecciones" => array:1 [ "secciones" => array:10 [ 0 => array:3 [ "identificador" => "xres1155341" "titulo" => "Abstract" "secciones" => array:4 [ 0 => array:2 [ "identificador" => "abst0005" "titulo" => "Introduction" ] 1 => array:2 [ "identificador" => "abst0010" "titulo" => "Methods" ] 2 => array:2 [ "identificador" => "abst0015" "titulo" => "Results" ] 3 => array:2 [ "identificador" => "abst0020" "titulo" => "Conclusions" ] ] ] 1 => array:2 [ "identificador" => "xpalclavsec1082903" "titulo" => "Keywords" ] 2 => array:3 [ "identificador" => "xres1155340" "titulo" => "Resumen" "secciones" => array:4 [ 0 => array:2 [ "identificador" => "abst0025" "titulo" => "Introducción" ] 1 => array:2 [ "identificador" => "abst0030" "titulo" => "Métodos" ] 2 => array:2 [ "identificador" => "abst0035" "titulo" => "Resultados" ] 3 => array:2 [ "identificador" => "abst0040" "titulo" => "Conclusiones" ] ] ] 3 => array:2 [ "identificador" => "xpalclavsec1082902" "titulo" => "Palabras clave" ] 4 => array:2 [ "identificador" => "sec0005" "titulo" => "Introduction" ] 5 => array:3 [ "identificador" => "sec0010" "titulo" => "Material and methods" "secciones" => array:7 [ 0 => array:2 [ "identificador" => "sec0015" "titulo" => "Clinical isolates" ] 1 => array:2 [ "identificador" => "sec0020" "titulo" => "GenoTypeMycobacterium CM/AS (Hain, Lifescience, Germany) (GenoType)" ] 2 => array:2 [ "identificador" => "sec0025" "titulo" => "MALDI-TOF MS protein extraction protocol" ] 3 => array:2 [ "identificador" => "sec0030" "titulo" => "MALDI-TOF MS analysis" ] 4 => array:3 [ "identificador" => "sec0035" "titulo" => "Partial rpoβ gene sequencing" "secciones" => array:3 [ 0 => array:2 [ "identificador" => "sec0040" "titulo" => "DNA extraction" ] 1 => array:2 [ "identificador" => "sec0045" "titulo" => "rpoβ amplification" ] 2 => array:2 [ "identificador" => "sec0050" "titulo" => "rpoβ partial sequencing" ] ] ] 5 => array:2 [ "identificador" => "sec0055" "titulo" => "Phylogenetic analysis" ] 6 => array:2 [ "identificador" => "sec0060" "titulo" => "Statistical analysis" ] ] ] 6 => array:3 [ "identificador" => "sec0065" "titulo" => "Results" "secciones" => array:3 [ 0 => array:2 [ "identificador" => "sec0070" "titulo" => "GenoType and partial rpoβ gene sequencing" ] 1 => array:2 [ "identificador" => "sec0075" "titulo" => "MALDI-TOF MS and partial rpoβ gene sequencing" ] 2 => array:2 [ "identificador" => "sec0080" "titulo" => "GenoType and MALDI-TOF MS" ] ] ] 7 => array:2 [ "identificador" => "sec0085" "titulo" => "Discussion" ] 8 => array:2 [ "identificador" => "sec0090" "titulo" => "Conflict of interest" ] 9 => array:1 [ "titulo" => "References" ] ] ] "pdfFichero" => "main.pdf" "tienePdf" => true "fechaRecibido" => "2018-01-24" "fechaAceptado" => "2018-04-13" "PalabrasClave" => array:2 [ "en" => array:1 [ 0 => array:4 [ "clase" => "keyword" "titulo" => "Keywords" "identificador" => "xpalclavsec1082903" "palabras" => array:5 [ 0 => "Non-tuberculous mycobacteria" 1 => "MALDI-TOF MS" 2 => "Partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing" 3 => "Phylogenetic analysis" 4 => "Sequence analysis" ] ] ] "es" => array:1 [ 0 => array:4 [ "clase" => "keyword" "titulo" => "Palabras clave" "identificador" => "xpalclavsec1082902" "palabras" => array:5 [ 0 => "Micobacterias no tuberculosas" 1 => "MALDI-TOF MS" 2 => "Secuenciación parcial del gen rpoβ" 3 => "Análisis filogenético" 4 => "Análisis de secuencias" ] ] ] ] "tieneResumen" => true "resumen" => array:2 [ "en" => array:3 [ "titulo" => "Abstract" "resumen" => "<span id="abst0005" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0010">Introduction</span><p id="spar0005" class="elsevierStyleSimplePara elsevierViewall">The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method.</p></span> <span id="abst0010" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0015">Methods</span><p id="spar0010" class="elsevierStyleSimplePara elsevierViewall">We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType<span class="elsevierStyleSup">®</span> CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank.</p></span> <span id="abst0015" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0020">Results</span><p id="spar0015" class="elsevierStyleSimplePara elsevierViewall">The degree of agreement between GenoType<span class="elsevierStyleSup">®</span> and MALDI-TOF MS and the reference method, partial <span class="elsevierStyleItalic">rpoβ</span> sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType<span class="elsevierStyleSup">®</span>, we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType<span class="elsevierStyleSup">®</span> had misclassified (<span class="elsevierStyleItalic">p</span><span class="elsevierStyleHsp" style=""></span>=<span class="elsevierStyleHsp" style=""></span>0.005).</p></span> <span id="abst0020" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0025">Conclusions</span><p id="spar0020" class="elsevierStyleSimplePara elsevierViewall">MALDI-TOF MS classified significantly better than GenoType<span class="elsevierStyleSup">®</span>. When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial <span class="elsevierStyleItalic">rpoβ</span> gene sequencing were equivalent. GenoType<span class="elsevierStyleSup">®</span> was not able to distinguish between species belonging to the <span class="elsevierStyleItalic">M. fortuitum complex</span>. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType<span class="elsevierStyleSup">®</span>. The partial <span class="elsevierStyleItalic">rpoβ s</span>equencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases.</p></span>" "secciones" => array:4 [ 0 => array:2 [ "identificador" => "abst0005" "titulo" => "Introduction" ] 1 => array:2 [ "identificador" => "abst0010" "titulo" => "Methods" ] 2 => array:2 [ "identificador" => "abst0015" "titulo" => "Results" ] 3 => array:2 [ "identificador" => "abst0020" "titulo" => "Conclusions" ] ] ] "es" => array:3 [ "titulo" => "Resumen" "resumen" => "<span id="abst0025" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0035">Introducción</span><p id="spar0025" class="elsevierStyleSimplePara elsevierViewall">La American Thoracic Society y la Infectious Diseases Society of America recomiendan que las micobacterias no tuberculosas (MNT) clínicamente relevantes sean identificadas a nivel de especie para determinar su significado clínico. El propósito de este estudio fue a partir de MNT de crecimiento rápido (MCR) aisladas en muestras clínicas, evaluar su identificación mediante MALDI-TOF MS y un método molecular comercial, comparando estos resultados con la identificación obtenida usando un método de referencia.</p></span> <span id="abst0030" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0040">Métodos</span><p id="spar0030" class="elsevierStyleSimplePara elsevierViewall">Se incluyeron 46 aislados clínicos de MCR. Estos aislados se identificaron mediante el método molecular comercial GenoType<span class="elsevierStyleSup">®</span> Mycobacterium CM/AS (Hain, Lifescience, Alemania), MALDI-TOF MS (Bruker) y, como método de referencia, la secuenciación parcial del gen <span class="elsevierStyleItalic">rpoβ</span> seguido de BLAST y análisis filogenético. Para el análisis filogenético se utilizaron 1.093 secuencias disponibles en el GeneBank.</p></span> <span id="abst0035" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0045">Resultados</span><p id="spar0035" class="elsevierStyleSimplePara elsevierViewall">Entre GenoType<span class="elsevierStyleSup">®</span> o MALDI-TOF MS, la concordancia respecto al método de referencia, secuenciación parcial de <span class="elsevierStyleItalic">rpoB</span>, fue 27/43 (62,8%) y 38/43 casos (88,3%), respectivamente. En todas las muestras que GenoType<span class="elsevierStyleSup">®</span> clasificó correctamente con MALDI-TOF MS se obtuvo el mismo resultado (27/27). Pero además MALDI-TOF MS identificó bien 68,75% (11/16) de las muestras que GenoType<span class="elsevierStyleSup">®</span> no clasificó correctamente (p<span class="elsevierStyleHsp" style=""></span>=<span class="elsevierStyleHsp" style=""></span>0,005).</p></span> <span id="abst0040" class="elsevierStyleSection elsevierViewall"><span class="elsevierStyleSectionTitle" id="sect0050">Conclusiones</span><p id="spar0040" class="elsevierStyleSimplePara elsevierViewall">MALDI-TOF MS clasificó significativamente mejor que GenoType<span class="elsevierStyleSup">®</span>. Cuando MALDI-TOF MS alcanzó una puntuación >1,85, MALDI-TOF y la secuenciación parcial del gen <span class="elsevierStyleItalic">rpoβ</span> fueron equivalentes. GenoType<span class="elsevierStyleSup">®</span> no distinguió dentro del <span class="elsevierStyleItalic">M. fortuitum complex</span>. La metodología MALDI-TOF MS es simple, rápida y se asocia a un menor coste de consumibles que GenoType<span class="elsevierStyleSup">®</span>. La secuenciación parcial del gen <span class="elsevierStyleItalic">rpoβ</span> con BLAST y análisis filogenético no lograron identificar de manera inequívoca algunas MCR. Para estas MCR estaría indicado la secuenciación de regiones adicionales.</p></span>" "secciones" => array:4 [ 0 => array:2 [ "identificador" => "abst0025" "titulo" => "Introducción" ] 1 => array:2 [ "identificador" => "abst0030" "titulo" => "Métodos" ] 2 => array:2 [ "identificador" => "abst0035" "titulo" => "Resultados" ] 3 => array:2 [ "identificador" => "abst0040" "titulo" => "Conclusiones" ] ] ] ] "apendice" => array:1 [ 0 => array:1 [ "seccion" => array:1 [ 0 => array:4 [ "apendice" => "<p id="par0215" class="elsevierStylePara elsevierViewall"><elsevierMultimedia ident="upi0005"></elsevierMultimedia></p>" "etiqueta" => "Appendix A" "titulo" => "Supplementary data" "identificador" => "sec0100" ] ] ] ] "multimedia" => array:3 [ 0 => array:7 [ "identificador" => "fig0005" "etiqueta" => "Fig. 1" "tipo" => "MULTIMEDIAFIGURA" "mostrarFloat" => true "mostrarDisplay" => false "figura" => array:1 [ 0 => array:4 [ "imagen" => "gr1.jpeg" "Alto" => 1762 "Ancho" => 2283 "Tamanyo" => 299699 ] ] "descripcion" => array:1 [ "en" => "<p id="spar0045" class="elsevierStyleSimplePara elsevierViewall">Maximum-likelihood tree (GTR plus I plus G; aLRT<span class="elsevierStyleHsp" style=""></span>><span class="elsevierStyleHsp" style=""></span>90%) <span class="elsevierStyleItalic">Mycobacterium rpoβ</span> partial gene 495 nucleotides.</p>" ] ] 1 => array:8 [ "identificador" => "tbl0005" "etiqueta" => "Table 1" "tipo" => "MULTIMEDIATABLA" "mostrarFloat" => true "mostrarDisplay" => false "detalles" => array:1 [ 0 => array:3 [ "identificador" => "at1" "detalle" => "Table " "rol" => "short" ] ] "tabla" => array:2 [ "tablatextoimagen" => array:1 [ 0 => array:2 [ "tabla" => array:1 [ 0 => """ <table border="0" frame="\n \t\t\t\t\tvoid\n \t\t\t\t" class=""><thead title="thead"><tr title="table-row"><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">N° sample \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">Sample \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">GenoType<span class="elsevierStyleSup">®</span> \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">Phylogenetical \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">BLAST \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">% similarity \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">MALDI-TOF \t\t\t\t\t\t\n \t\t\t\t</th><th class="td" title="table-head " align="left" valign="top" scope="col" style="border-bottom: 2px solid black">MALDI-TOF score \t\t\t\t\t\t\n \t\t\t\t</th></tr></thead><tbody title="tbody"><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">1 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.86 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.019 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">2 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.027 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">3 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Bronchoalveolar lavages \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.162 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">4 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.86 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.169 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">5 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Bronchoalveolar lavages \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.174 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">6 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.191 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">7 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.225 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">8 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Bronchial aspirates \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.273 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">9 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="" valign="top"> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. abscessus</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.011 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">10 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.69 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.87 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">11 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.873 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">12 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.93 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">13 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.993 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">14 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Skin biopsy \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.005 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">15 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Skin biopsy \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.012 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">16 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Skin biopsy \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.69 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.03 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">17 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.041 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">18 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.86 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.043 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">19 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.057 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">20 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.063 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">21 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.098 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">22 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Corneal ulcer exudate \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">98.66 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.117 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">23 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Skin biopsy \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.131 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">24 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.231 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">25 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.86 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.338 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">26 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="" valign="top"> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. chelonae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.112 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">27 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.08 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.717 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">28 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.20 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. boenickei</span>/<span class="elsevierStyleItalic">peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.757 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">29 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei/peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">98.96 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. conceptionense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.781 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">30 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.20 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.046 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">31 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">98.29 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.133 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">32 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.265 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">33 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.56 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.715 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">34 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Urine \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.98 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">35 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.22 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.089 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">36 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Bronchial aspirates \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">99.37 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.125 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">37 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mageritense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.227 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">38 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Bronchial aspirates \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.978 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">39 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">98.92 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.037 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">40 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.269 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">41 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. peregrinum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.269 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">42 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. septicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. septicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">95.01 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. septicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.704 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">43 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. setense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. setense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">98.96 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. alvei</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.843 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">44 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. fortuitum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><a class="elsevierStyleCrossRef" href="#tblfn0005"><span class="elsevierStyleSup">a</span></a> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="" valign="top"> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. conceptionense</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.89 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">45 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Sputum \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">Mycobacterum</span> sp. \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. monacense</span>/<span class="elsevierStyleItalic">duvalii</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. duvalii</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">91.91 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. vaccae</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">1.46 \t\t\t\t\t\t\n \t\t\t\t</td></tr><tr title="table-row"><td class="td" title="table-entry " align="char" valign="top">46 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top">Pleural fluid \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">Mycobacterum</span> sp. \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mucogenicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mucogenicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">100.00 \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="left" valign="top"><span class="elsevierStyleItalic">M. mucogenicum</span> \t\t\t\t\t\t\n \t\t\t\t</td><td class="td" title="table-entry " align="char" valign="top">2.04 \t\t\t\t\t\t\n \t\t\t\t</td></tr></tbody></table> """ ] "imagenFichero" => array:1 [ 0 => "xTab1972348.png" ] ] ] "notaPie" => array:1 [ 0 => array:3 [ "identificador" => "tblfn0005" "etiqueta" => "a" "nota" => "<p class="elsevierStyleNotepara" id="npar0005">Not amplify by PCR.</p>" ] ] ] "descripcion" => array:1 [ "en" => "<p id="spar0050" class="elsevierStyleSimplePara elsevierViewall">Clininal samples, identification with GenoType<span class="elsevierStyleSup">®</span>, phylogenetical analysis, BLAST, % similarity with BLAST, identification with MALDI-TOF and MALDI-TOF score.</p>" ] ] 2 => array:5 [ "identificador" => "upi0005" "tipo" => "MULTIMEDIAECOMPONENTE" "mostrarFloat" => false "mostrarDisplay" => true "Ecomponente" => array:2 [ "fichero" => "mmc1.pdf" "ficheroTamanyo" => 648502 ] ] ] "bibliografia" => array:2 [ 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| Year/Month | Html | Total | |
|---|---|---|---|
| 2024 October | 4 | 1 | 5 |
| 2024 September | 16 | 0 | 16 |
| 2024 August | 20 | 5 | 25 |
| 2024 July | 55 | 5 | 60 |
| 2024 June | 19 | 5 | 24 |
| 2024 May | 10 | 2 | 12 |
| 2024 April | 17 | 7 | 24 |
| 2024 March | 16 | 7 | 23 |
| 2024 February | 23 | 6 | 29 |
| 2024 January | 26 | 4 | 30 |
| 2023 December | 18 | 2 | 20 |
| 2023 November | 32 | 7 | 39 |
| 2023 October | 43 | 8 | 51 |
| 2023 September | 26 | 1 | 27 |
| 2023 August | 18 | 0 | 18 |
| 2023 July | 18 | 2 | 20 |
| 2023 June | 23 | 4 | 27 |
| 2023 May | 49 | 13 | 62 |
| 2023 April | 58 | 16 | 74 |
| 2023 March | 63 | 1 | 64 |
| 2023 February | 34 | 4 | 38 |
| 2023 January | 34 | 6 | 40 |
| 2022 December | 50 | 4 | 54 |
| 2022 November | 41 | 6 | 47 |
| 2022 October | 98 | 11 | 109 |
| 2022 September | 31 | 10 | 41 |
| 2022 August | 42 | 9 | 51 |
| 2022 July | 17 | 3 | 20 |
| 2022 June | 28 | 6 | 34 |
| 2022 May | 19 | 7 | 26 |
| 2022 April | 15 | 4 | 19 |
| 2022 March | 22 | 7 | 29 |
| 2022 February | 21 | 5 | 26 |
| 2022 January | 35 | 3 | 38 |
| 2021 December | 29 | 13 | 42 |
| 2021 November | 24 | 6 | 30 |
| 2021 October | 29 | 10 | 39 |
| 2021 September | 14 | 7 | 21 |
| 2021 August | 22 | 13 | 35 |
| 2021 July | 5 | 5 | 10 |
| 2021 June | 12 | 8 | 20 |
| 2021 May | 15 | 9 | 24 |
| 2021 April | 24 | 11 | 35 |
| 2021 March | 13 | 8 | 21 |
| 2021 February | 15 | 8 | 23 |
| 2021 January | 12 | 8 | 20 |
| 2020 December | 12 | 4 | 16 |
| 2020 November | 15 | 4 | 19 |
| 2020 October | 14 | 3 | 17 |
| 2020 September | 21 | 10 | 31 |
| 2020 August | 18 | 10 | 28 |
| 2020 July | 15 | 3 | 18 |
| 2020 June | 19 | 8 | 27 |
| 2020 May | 12 | 6 | 18 |
| 2020 April | 10 | 4 | 14 |
| 2020 March | 9 | 3 | 12 |
| 2020 February | 14 | 4 | 18 |
| 2020 January | 16 | 5 | 21 |
| 2019 December | 16 | 7 | 23 |
| 2019 November | 5 | 2 | 7 |
| 2019 October | 12 | 0 | 12 |
| 2019 September | 5 | 8 | 13 |
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