Embed Size (px)
Citation preview
1
Comparing the utility of different multilocus sequence typing 1
schemes for identifying outbreak strains of Mycobacterium 2
abscessus subspecies massiliense 3
Aristine Cheng, M.B.B.Chir.1,2, Hsin-Yun Sun, M.D1,2, Yi-Tzu Tsai, M.S.1, Shu-Yuan 4
Chang, B.A.1, Un-In Wu, M.D.1,2, Po-ren Hsueh, M.D. PhD1-3, Wang-Huei Sheng, 5
M.D1,2, Yee-Chun Chen* M.D.Ph.D.1,2,4, Shan-Chwen Chang M.D. Ph.D.1,2 6
1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-7
Shan South Road, Taipei, Taiwan. 8
2Department of Medicine, National Taiwan University College of Medicine, No.1 Jen 9
Ai Road Section 1, Taipei 100 Taiwan , Taipei, Taiwan. 10
3Department of Laboratory Medicine, National Taiwan University Hospital, No. 7 11
Chung-Shan South Road, Taipei, Taiwan. 12
4Center for Infection Control, National Taiwan University Hospital, No. 7 Chung-Shan 13
South Road, Taipei, Taiwan. 14
15
* Corresponding author 16
Running title: Multilocus sequencing typing schemes for Mycobacterium abscessus 17
Yee-Chun Chen, M.D. PhD. 18
Professor, National Taiwan University College of Medicine 19
Division of Infectious Diseases, Department of Internal Medicine, National Taiwan 20
University Hospital, 7 Chung-Shan South Road, Taipei 100, Taiwan 21
Tel: (+886) 2-2312-3456 Ext. 65054 Fax: (+886) 2-2397-1412 22
Email: [email protected] 23
Abstract words: 158 Main text: 2989 24
JCM Accepted Manuscript Posted Online 16 October 2019J. Clin. Microbiol. doi:10.1128/JCM.01304-19Copyright © 2019 American Society for Microbiology. All Rights Reserved.
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
2
ABSTRACT 25
Outbreaks of infections by Mycobacterium abscessus, particularly subspecies 26
massiliense, are increasingly reported worldwide. Several multilocus sequence 27
typing (MLST) protocols for grouping international outbreak strains have been 28
developed but not yet directly compared. Using the 3-gene (hsp65, rpoB, secA1), 7-29
gene (argH, cya, glpK, gnd, murC, pta, and purH) and 13-gene (all above plus gdhA, 30
pgm, pknA) MLST schemes, we identified 22, 38 and 40 unique sequence types 31
(STs), respectively, among a total of 139 non-duplicated M. abscessus isolates. 32
Among subspecies massiliense, the 3-gene MLST, not only clustered all outbreak 33
strains together (in 100% agreement with the 7-gene and 13-gene schemes), it also 34
distinguished between two new STs that would have been grouped together by the 35
7-gene MLST, but were distinct by the 13-gene MLST owing to differences in hsp65, 36
rpoB and pknA. Here, we show that an abbreviated MLST may be useful for 37
simultaneous subspeciation of M. abscessus and for screening M. abscessus subsp. 38
massiliense isolates with outbreak potential. 39
40
41
42
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
3
INTRODUCTION 43
The Mycobacterium abscessus complex comprises three closely related 44
genomospecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense 45
and M. abcessus subsp. bolletti that cannot be reliably discriminated by single gene 46
sequencing (1-3). Previous studies have indicated great diversity within M. 47
abscessus among cystic fibrosis patients, suggesting independent acquisitions from 48
the environment (4, 5). However, suspicion of patient-to-patient transmission arose 49
after two reports of respiratory outbreaks with M. abscessus subsp. massiliense at 50
different cystic fibrosis centers across the Atlantic (6-8). One outbreak occurred in 51
Seattle, Washington, USA, wherein the index case-patient and 4 additional patients 52
were infected with near identical M. abscessus subsp. massiliense isolates with 53
resistance to amikacin and clarithromycin, and indistinguishable by repetitive unit 54
sequence–based PCR (rep-PCR) patterns and pulsed field gel electrophoresis 55
(PFGE) analysis (9). The second outbreak occurred in Cambridge, UK, involving 11 56
patients who all had M. abscessus subsp. massiliense infections sharing the same 57
constitutive resistance to amikacin and clarithromycin, despite some individuals 58
being naive to long-term macrolide or aminoglycoside therapy (6). 59
By whole-genome sequencing (WGS), isolates from these two cystic fibrosis 60
centers, were subsequently found to be highly related, belonging to sequence type 61
23 (ST23) and clonal cluster 3 (CC3) according to a multilocus sequence typing 62
(MLST) protocol (7). Meanwhile, an epidemic of at least 2032 post-surgical infections 63
between 2004-2011 across Brazil was also due to M. abscessus subsp. massiliense 64
ST23 (CC3), thereafter referred to as the "globally successful clone" (10, 11). Other 65
outbreaks occurring after ultrasound-guided procedures, acupuncture, injections, 66
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
4
dental, ophthalmological, cardiac, obstetric, and cosmetic surgeries, due to M. 67
abscessus continue to be reported worldwide (12-20). 68
However, outbreak investigations and comparisons of inter-relatedness of 69
outbreak strains by WGS and PFGE are too costly, lengthy and labor intensive for 70
routine infection control surveillance. Hence the aim of this study was to identify a 71
molecular typing method for M. abscessus which would be feasible in the context of 72
epidemiology, post-outbreak surveillance and in validation of new infection control 73
measures. Although the optimal research method may be in evolution such as 65 74
kDa heat shock protein analysis, MALDI-TOF, next-generation sequencing, and 75
WGS, in this study we chose to characterize MLST, since the MLST approach has 76
been validated for subspeciation of the M. abscessus complex (11, 21, 22). Three 77
different MLST schemes, with 3-gene, 7-gene, and 13-gene targets have been 78
proposed in the recent decade by different investigators for typing collections of 79
clinical and environmental isolates of the M. abscessus complex but they have not 80
been directly compared (7, 11, 21). 81
The 3-gene MLST scheme was developed in 2011 for accurate subspeciation 82
of M. abscessus after the failure of single gene targets such as 16srRNA to reliably 83
distinguish between M. chelonae and M. abscessus, followed by the failure of rpoB, 84
hsp65 and secA1 individual gene sequencing to reliably distinguish between 85
subspecies due to the inferred horizontal transfer of genes between the closely 86
related subspecies, especially from the more ancestral M. abscessus subsp. 87
abscessus to the more recently emerged, M. abscessus subsp. massiliense (22-24). 88
Shortly after publication, we used this 3-gene MLST to identify a clone of M. 89
abscessus subsp. massiliense, TPE 101, that was identical by PFGE and rep-PCR 90
as the cause of a multi-center outbreak of post-procedural infections related to the 91
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
5
use of contaminated ultrasonography gel between 2010-2012 island-wide across 92
Taiwan (12, 25). 93
The more usual 7-gene MLST scheme in bacterial taxonomy was developed 94
to delineate microbial species within various taxonomic groups, including groups of 95
highly recombinant bacteria, like Neisseria spp. and to allow the assignment of 96
unknown strains to species clusters over the internet in a global collective electronic 97
taxonomy (26). Typically, the 7-gene MLST scheme concatenated the sequences of 98
between six to eight housekeeping genes that are present as a single copy within the 99
genome, and are not subject to selective pressure (26). For the M. abscessus 100
complex, the 7-gene approach using the housekeeping genes: argH, cya, glpK, gnd, 101
murC, pta and purH was published for non-outbreak molecular epidemiological 102
studies of M. abscessus subsp. abscessus and M. abscessus subsp. massiliense in 103
2014 (with different numbering systems and protocols in two different databases 104
(https://bigsdb.pasteur.fr/mycoabscessus/mycoabscessus.html and 105
https://pubmlst.org/mabscessus/) (11, 27). Notably, no strains of M. abscessus 106
subsp. bolletii were included in these MLST databases. Following the publication of 107
this MLST scheme, we used the same set of primers and conditions to identify our 108
TPE 101 outbreak strain as ST48 by the former Pasteur Institute's system, which 109
differed by only one of 7 MLST loci (MurC gene) from ST23. 110
However, due to the recognized differences between mycobacteria and more 111
rapidly evolving bacteria, investigators studying the trans-Atlantic cystic fibrosis 112
outbreaks proposed simultaneously in 2014 an extended 13-gene MLST approach 113
(incorporating the loci cya, gdhA, argH, glpK, gnd, murC, pgm, pknA, pta, pur, rpoB, 114
hsp65, and secA1) alongside WGS to better characterize strains similar to the 115
Seattle and Papworth outbreak strains (7). As far as we know, the merits of 116
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
6
increasing the number of loci in the MLST approach from 3 mycobacterial specific 117
genes, 7-generic housekeeping genes, and 3 mycobacterial and 10 housekeeping 118
genes, have not been directly compared. In this study, our aim is to study the 119
discriminatory power of these three MLST schemes in discerning isolates from our 120
previous outbreak, clustering within the "globally successful clonal cluster 3" from 121
sporadic clinical and environmental isolates. 122
123
METHODS 124
Mycobacterial isolates 125
A total of 139 M. abscessus non-duplicated isolates were included in this 126
study, comprising 121 clinical isolates, 16 environmental isolates and 2 reference 127
isolates, M. abscessus subsp. abscessus ATCC19977 and M. abscessus subsp. 128
massiliense BCRC 16916. Fifty-seven M. abscessus isolates were outbreak strains 129
of M. abscessus subsp. massiliense ST48 (CC3) as reported previously, and 81 M. 130
abscessus isolates were sporadic isolates that were confirmed to be unrelated to the 131
outbreak by epidemiological investigation, pulse-field gel electrophoresis and rep-132
PCR (12, 25). Of the 121 clinical isolates, 65 were pulmonary isolates, cultured from 133
sputum (61), bronchoalveolar lavage (2), pleural effusion (1) and biopsied lung tissue 134
(1); and 56 were extrapulmonary isolates, cultured from the blood (10), surgical 135
wound (21), cerebrospinal fluid (1), ascites (2), cornea (5), endocervical swab (1), 136
biopsied lymph node (2), ear (4), and other skin and soft tissue (10). Of the 16 137
environmental isolates, 13 were obtained from contaminated ultrasonography 138
transmission gel (different batches and lot numbers) implicated in the nationwide 139
outbreak, and 3 were obtained from routine infection control surveillance of hospital 140
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
7
water at the National Taiwan University Hospital, a 2500-bed teaching hospital in 141
Taipei, Taiwan. 142
143
Multilocus sequence typing (MLST) 144
As described previously, molecular typing of the M. abscessus isolates was 145
done by concatenating the partial sequences of 3-genes (hsp65, rpoB, secA1) 146
according to Zelazny et al. (21, 25), 7-gene (argH, cya, glpK, gnd, murC, pta, and 147
purH) according to the primers and conditions pioneered by Macheras et al. and 148
publicly available at http://bigsdb.pasteur.fr/mycoabscessus/mycoabscessus.html) 149
(11, 25), and 13-gene (the above 10 genes plus gdhA, pgm, pknA) according to 150
Tettelin et al. (7). Subspeciation was secondarily confirmed by Matrix-Assisted Laser 151
Desorption/Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF-MS) (28). 152
Briefly, the mycobacterial strains were stored at -80°C in GermBank (Creative 153
Life Sciences, New Taipei City, Taiwan). Prior to use, the strains were sub-cultured 154
onto sheep blood agar at 30°C (Creative Life Sciences). Mycobacterial DNA was 155
extracted using Tris-EDTA, lysozyme and proteinase K (UNI-ONWARD Corp., New 156
Taipei City, Taiwan). PCRs using the primers listed in the Table 1 were performed to 157
amplify fragments of the 13 genes. Sequences were analysed for their similarity with 158
sequences in the GenBank database using the Basic Local Alignment Tool (BLAST; 159
http://www.ncbi.nlm.nih.gov/BLAST) and compared to type strains of M. abscessus 160
subsp. abscessus (ATCC 19977) and M. abscesus subsp. massiliense (CIP 108297). 161
Phylogenetic analysis conducted by the minimum spanning tree algorithms based on 162
p－distance of concatenated sequence data was performed using BioNumerics v6.6 163
(Applied Maths, Austin, Texas, USA). 164
165
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
8
RESULTS 166
Of the 139 M. abscessus isolates characterized in the previously published 167
outbreak and case-control studies, 54 belonged to the subspecies abscessus and 85 168
belonged to the subspecies massiliense (Table 2). Figures 1 and 2, and Table 2 169
show the results of the 139 isolates discriminated based on the 3-gene, 7-gene, and 170
13-gene MLST schemes. The 54 M. abscessus subsp. abscessus isolates were 171
grouped into ten sequence types, MAB1-10 by the 3-gene scheme, and 24 and 25 172
sequence types, respectively, by the 7-gene and 13-gene schemes. Forty isolates 173
clustered together by the 3-gene scheme (MAB 1). Of these 40 MAB1 isolates, there 174
were 22 isolates including the ATCC 19977 reference strain, belonging to ST1 175
according to the 7-gene MLST database of the Pasteur Institute (Table 3). These 176
MAB1/ST1 isolates exhibited different PFGE/rep-PCR patterns and were not 177
epidemiologically linked (published previously) (12, 25). There was one ST1 isolate 178
based on 7-gene scheme that did not fall into the MAB1 main cluster, due to a 179
difference in internal sequencing of the secA1 gene alone (labelled MAB5 for the 3-180
gene and ST1a for the 13-gene) (Table 4). This was the only 1 additional sequence 181
type gained from extending the MLST schemes from 7- to 13-genes (Figs. 1 & 2). 182
For the remaining isolates there was full agreement between the 7-gene and 13-183
gene schemes, i.e. the addition of gdhA, pgm, pknA to the latter, did not increase the 184
discriminatory power. Overall for M. abscessus subsp. abscessus, the agreement 185
between the 3-gene and 7-gene MLST schemes was 75%, the 3-gene and 13-gene 186
MLST was 77.5% and the 7-gene and 13-gene MLST was 97.5%. 187
The 85 M. abscessus subsp. massiliense isolates were grouped into twelve 188
sequence types, MMA1-12 by the 3-gene scheme, and consisted of 14 and 15 189
sequence types, respectively, by the 7-gene and 13-gene schemes. Of 85 isolates 190
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
9
evaluated, 57 isolates belonged to MMA1/ST48 with 100% agreement between the 191
three MLST schemes (Table 3). Clear epidemiological links to the 2010-2012 192
outbreak by case definition of contaminated ultranography gel or invasive 193
procedures were established for 51 of these MMA1/ST48 isolates (as published 194
previously) (12, 25, 29). The remaining 6 MMA1/ST48 isolates exhibited identical 195
PFGE patterns but did not fit the case definition of contaminated ultrasonography gel 196
or invasive procedures (Table 3). 197
Ten of the eleven isolates grouped together in the second largest subspecies 198
massiliense group (MMA2) by the 3-gene scheme, belonged to ST117 based on 7-199
gene and 13-gene schemes (Figs. 1 amd 2). The remaining one isolate differed from 200
ST117 in the glpK loci (Tables 2 and 3). The reference strain, M. abscessus subsp. 201
massiliense BCRC 16916, was typed as MMA12/ST37 and was closely related to 202
MMA2/ST117 (Figs. 1 and 2). 203
The overall rates of agreement between the 3-gene and 7-gene, the 3-gene 204
and 13-gene, and the 7-gene and 13-gene MLST schemes for M. abscessus subsp. 205
massiliense were 95.3%, 96.5%, and 98.8%, respectively. Two isolates of a new 206
sequence type (ST 273) based on the 7-gene scheme were discriminated into two 207
clones by the 3-gene scheme (MMA9 and 11) and by the 13-gene scheme (ST 273 208
and ST 273a) owing to single nucleotide polymorphisms (SNPs) in hsp65, rpoB and 209
pknA (Table 4). 210
In addition, the hotspots for genetic variation within the internal sequences of 211
the 10 housekeeping genes differed between subspecies (Table 4). For subspecies 212
abscessus the maximum sequence divergence was observed at the pta, purH, gdhA 213
loci (11 different allelic types). In contrast, the glpK loci was highly conserved and 53 214
of 54 subspecies abscessus had the same allelic type for glpK loci. For the 215
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
10
subspecies massiliense, there were fewer sequence divergences overall, and 216
greatest for purH loci (7 allelic types) followed by gdhA (6 allelic types). Unlike the 217
subspecies abscessus, there was also significant variation at the murC (6 allelic 218
types) glpK and pknA loci (5 allelic types each). 219
In summary, among the subspecies abscessus, the 3-gene scheme was only 220
modestly discriminative compared to the standard 7-gene MLST (agreement rates of 221
75%), however for the subspecies massiliense with identical PFGE and outbreak 222
potential, the 3-gene scheme yielded very high agreement rates with the standard 7-223
gene scheme (95.3%) and the extended 13-gene scheme (96.5%). 224
225
DISCUSSION 226
Since the last decade, most experts recommend identifying isolates of M. 227
abscessus complex to the subspecies level due to differences in antimicrobial 228
susceptibility and prognosis (30). However, there is even greater pressure on clinical 229
laboratories to fully identify M. abscessus subsp. massiliense following the 230
emergence of a globally successful clone, ST23 or CC3, causing outbreaks among 231
cystic fibrosis patients and soft tissue infections in Brazilian patients, and a closely 232
related clone, ST48 also CC3, causing outbreaks among Taiwanese patients 233
following invasive procedures (7, 8, 12, 25). Despite the emphasis in recent 234
guidelines on the necessity of screening all isolates of subspecies massiliense 235
recovered from patients with cystic fibrosis for relatedness to outbreak strains in an 236
effort to prevent future outbreaks and patient-to-patient transmission, there has been 237
little practical advice on how to do so within the limits of clinical, and not, research 238
facilities (31). 239
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
11
Our study is the first to compare the use of three different MLST schemes for 240
a very well characterized collection of M. abscessus isolates, notably including both 241
outbreak and sporadic isolates. We showed that for the newly emerged subspecies 242
massiliense, with potentially higher virulence and transmissibility (7, 8, 32), the 3-243
gene MLST using the partial sequences of the hsp65, rpoB and secA1 genes (1578 244
bp) was sufficiently discriminatory. This mycobacteria specific 3-gene MLST 245
identified subspecies, and accurately delineated dominant clusters to >95% 246
agreement with the 7-gene MLST (3576 bp) and 13-gene MLST (6712 bp) schemes. 247
A limitation of this study is the lack of WGS for full genomic comparison. 248
However, the clonality of the isolates clustered together by the 3-gene MLST had 249
previously been validated by PFGE and rep-PCR using the DiversiLab 250
Mycobacterium Typing kit (12, 25). Another limitation of this study is the lack of M. 251
abscessus subsp. bolletii isolates, hence we cannot make any comparisons for this 252
subspecies. However, in most clinical reports, M. abscessus subsp. bolletii appears 253
to be less frequently encountered as a human pathogen and this subspecies is not 254
included in the publicly available MLST databases, nor has it been implicated in 255
outbreaks (27, 33, 34). Misidentification of subspecies using the 3-gene scheme 256
might have led to the absence of M. abscessus subsp. bolletii, however we have 257
attempted to exclude this possibility by cross-checking subspecies identity using 258
MALDI-TOF (28). As the latter technique is fine-tuned, this limitation would be less 259
prominent in the future. 260
The sensitivity and specificity of the 3-gene scheme for simultaneous sub-261
typing and screening of M. abscessus subsp. massiliense cannot be established by 262
this preliminary study. Validation using larger collections of known outbreak versus 263
sporadic collections is warranted. However, our collection was sufficiently diverse, 264
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
12
including 21 novel sequence types submitted to the Pasteur Institute, each were 265
recently assigned a new number from ST271 to ST291. 266
The 3-gene MLST approach may offer time, costs, and labor savings over the 267
7-gene MLST scheme. In addition, accurate subspeciation (either by 3-gene MLST 268
scheme or by MALDI-TOF mass spectrometry) is required as an initial step before 269
sequences can be compared to publicly available MLST database at the Institute of 270
Pasteur. Due to the minimal gains of extending the MLST scheme from 7- to 13-271
genes (only two additional sequence types were identified without a significant 272
impact on the phylogenetic tree), our study supports the omission of gdhA, pgm, 273
pknA from current MLST schemes for M. abscessus. For confirmation of clonality or 274
dominant clusters, the 13-gene MLST did not perform better than the 7-gene MLST. 275
This may be possible due to extensive horizonal gene transfer of genomic blocks of 276
housekeeping genes through distributive conjugal transfer (35). Taking into account 277
the slow mutation rate of M. abscessus, only WGS or PFGE are recognized as 278
having sufficient resolution to confirm an outbreak or person-to-person transmission. 279
Tettlin et al. previously identified signature SNPs in rpoB and secA1 genes 280
that were typical but not exclusive to the globally successful clonal cluster of 281
subspecies massiliense outbreak strains (4). By using the rpoB gene MAB_3869c 282
from the subspecies abscessus type strain described in the BRA-00 outbreak from 283
Brazil, they showed that the Seattle and Papworth cystic fibrosis isolates carried a 2 284
rpoB SNPs (C→T at position 2569 and T→C at position 2760) signature and a 285
secA1 SNP signature (G→T substitution at position 820) by using the secA1 gene 286
MAB_3580c from the M. abscessus subsp. abscessus type strain). Similar to our 287
findings wherein MMA1 by the 3-gene MLST clustered all outbreak strains but also 288
included 6 strains without clear epidemiological links but exhibiting the same PFGE 289
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
13
patterns, the SNPs described for rpoB and secA1 were not 100% specific markers 290
for the outbreak strains, and were found in 4 unrelated M. abscessus subsp. 291
massiliense strains. Hence, we are in agreement over the value of the rpoB and 292
secA1 genes over other housekeeping genes for first-level identification of newly 293
isolated strains as possibly being related to cystic fibrosis clusters or soft tissue 294
outbreak strains, to be confirmed by a second assay. 295
While Tettelin et al. suggest that partial sequencing of rpoB and secA1 genes, 296
should be followed by the 13-target MLST analysis to rule out isolates as belonging 297
to these 2 cystic fibrosis clusters, we have shown that a second assay based on 298
another MLST approach with more routine loci targets did not outperform the first 299
approach with mycobacterial specific targets. Further studies are needed to elucidate 300
a more appropriate second confirmatory assay that offers labor, time, and cost-301
savings over WGS and PFGE. 302
In conclusion, this preliminary study supports the utility of the 3-gene MLST 303
based on the partial sequences of the hsp65, rpoB and secA1 genes as a screening 304
tool for the routine microbiology laboratory struggling to implement the 305
recommendations of recent guidelines recognizing the outbreak and person-to-306
person transmission potential of M. abscessus subsp massiliense. The next step 307
would require development of a publicly available 3-gene MLST database to 308
corroborate previously identified signature SNPs and to identify new patterns. With 309
our collective efforts, accurate identification of M. abscessus subsp. massiliense with 310
potentially higher transmissibility, might soon fall within the scope of clinical practice 311
in many more parts of the world. 312
313
314
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
14
Figure 1. Minimum spanning tree of 139 Mycobacterium abscessus complex 315
isolates based on the 3-gene and 7-gene multilocus sequencing typing schemes. 316
Strains clustered together by the 3-gene scheme was depicted as circles, segments 317
within the circles depict more than one isolate clustered together by the 7-gene 318
schemes. Different colors within one circle represent different sequence types by the 319
7-gene MLST that were indistinguishable by the 3-gene MLST. 320
321
Figure 2. Minimum spanning tree of 139 Mycobacterium abscessus complex 322
isolates based on the 3-gene and 13-gene multilocus sequencing typing schemes. 323
Strains clustered together by the 3-gene scheme was depicted as circles, segments 324
within the circles depict more than one isolate clustered together by the 13-gene 325
schemes. Different colors within one circle represent different sequence type by the 326
13-gene MLST that were indistinguishable by the 3-gene MLST. 327
328
Table 1. Primers used to amplify each gene in the multi-locus sequence typing 329
schemes. 330
Table 2. The source and subspecies distribution of 139 Mycobacterium abscessus 331
isolates included in this study. 332
Table 3. Comparing the results of the 139 isolates of Mycobacterium abscessus 333
complex discriminated based on the 3-gene, 7-gene, and 13-gene multilocus typing 334
schemes 335
Table 4. The allele types of the 139 isolates of Mycobacterium abscessus complex 336
discriminated based on the 3-gene, 7-gene, and 13-gene multilocus typing schemes 337
338
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
15
• Conflict of interest: There are no conflicts of interests to declare for the authors. 339
340
• Funding: This study was funded by Taiwan’s Ministry of Science and Technology 341
(grant no.105-2628-B-002-019-MY3) and the Taiwan's Ministry of Health and 342
Welfare (MOHW107-521 TDU-B-211-113002). 343
344
• Acknowledgments: We thank Po-ren Hsueh and the Department of Laboratory 345
Medicine, National Taiwan University Hospital for storage and access to the 346
mycobacterial isolates. 347
348
• Contributions: A.C. designed the study, analyzed the results, wrote the 349
manuscript. H.Y.S. provided critical analysis and review of the manuscript. Y.T.T. 350
conducted the experiments, analyzed the results. S.Y.C. collected the mycobacterial 351
isolates and helped execute the study. U.I.W. helped collect mycobacterial isolates 352
and execution of the study. P.R.H. helped collect, analyzed the mycobacterial 353
isolates and critically reviewed the manuscript. W.H.S. provided technical expertise, 354
critique and review of the manuscript. Y.C.C. conceived the study, coordinated the 355
infection prevention and control program, clinical and laboratory research teams, 356
provided technical expertise, critique, funding, research assistance and reviewed the 357
manuscript. S.C.C. provided technical expertise, critique and review of the 358
manuscript. 359
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
16
References 360
1. Adekambi T, Sassi M, van Ingen J, Drancourt M. 2017. Reinstating Mycobacterium 361
massiliense and Mycobacterium bolletii as species of the Mycobacterium abscessus 362
complex. Int J Syst Evol Microbiol 67:2726-2730. 363
2. Sassi M, Drancourt M. 2014. Genome analysis reveals three genomospecies in 364
Mycobacterium abscessus. BMC Genomics 15:359. 365
3. Macheras E, Roux AL, Ripoll F, Sivadon-Tardy V, Gutierrez C, Gaillard JL, Heym B. 366
2009. Inaccuracy of single-target sequencing for discriminating species of the 367
Mycobacterium abscessus group. J Clin Microbiol 47:2596-600. 368
4. Bange FC, Brown BA, Smaczny C, Wallace RJ, Jr., Bottger EC. 2001. Lack of 369
transmission of Mycobacterium abscessus among patients with cystic fibrosis 370
attending a single clinic. Clin Infect Dis 32:1648-50. 371
5. Harris KA, Underwood A, Kenna DT, Brooks A, Kavaliunaite E, Kapatai G, Tewolde R, 372
Aurora P, Dixon G. 2015. Whole-genome sequencing and epidemiological analysis do 373
not provide evidence for cross-transmission of Mycobacterium abscessus in a cohort 374
of pediatric cystic fibrosis patients. Clin Infect Dis 60:1007-16. 375
6. Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, 376
Haworth CS, Curran MD, Harris SR, Peacock SJ, Parkhill J, Floto RA. 2013. Whole-377
genome sequencing to identify transmission of Mycobacterium abscessus between 378
patients with cystic fibrosis: a retrospective cohort study. Lancet 381:1551-60. 379
7. Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, Strong M, de 380
Moura VC, De Groote MA, Duarte RS, Hine E, Parankush S, Su Q, Daugherty SC, 381
Fraser CM, Brown-Elliott BA, Wallace RJ, Jr., Holland SM, Sampaio EP, Olivier KN, 382
Jackson M, Zelazny AM. 2014. High-level relatedness among Mycobacterium 383
abscessus subsp. massiliense strains from widely separated outbreaks. Emerg Infect 384
Dis 20:364-71. 385
8. Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma 386
D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, 387
Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, 388
Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, 389
Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen 390
M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb 391
J, Humphrey H, Isalska B, Jensen-Fangel S, Jonsson B, Jones AM, et al. 2016. 392
Emergence and spread of a human-transmissible multidrug-resistant nontuberculous 393
mycobacterium. Science 354:751-757. 394
9. Aitken ML, Limaye A, Pottinger P, Whimbey E, Goss CH, Tonelli MR, Cangelosi GA, 395
Dirac MA, Olivier KN, Brown-Elliott BA, McNulty S, Wallace RJ, Jr. 2012. Respiratory 396
outbreak of Mycobacterium abscessus subspecies massiliense in a lung transplant 397
and cystic fibrosis center. Am J Respir Crit Care Med 185:231-2. 398
10. Nunes Lde S, Baethgen LF, Ribeiro MO, Cardoso CM, de Paris F, De David SM, da Silva 399
MG, Duarte RS, Barth AL. 2014. Outbreaks due to Mycobacterium abscessus subsp. 400
bolletii in southern Brazil: persistence of a single clone from 2007 to 2011. J Med 401
Microbiol 63:1288-93. 402
11. Macheras E, Konjek J, Roux AL, Thiberge JM, Bastian S, Leao SC, Palaci M, Sivadon-403
Tardy V, Gutierrez C, Richter E, Rusch-Gerdes S, Pfyffer GE, Bodmer T, Jarlier V, 404
Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B. 2014. Multilocus 405
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
17
sequence typing scheme for the Mycobacterium abscessus complex. Res Microbiol 406
165:82-90. 407
12. Cheng A, Sheng WH, Huang YC, Sun HY, Tsai YT, Chen ML, Liu YC, Chuang YC, Huang 408
SC, Chang CI, Chang LY, Huang WC, Hsueh PR, Hung CC, Chen YC, Chang SC. 2016. 409
Prolonged postprocedural outbreak of Mycobacterium massiliense infections 410
associated with ultrasound transmission gel. Clin Microbiol Infect 22:382 e1-382 e11. 411
13. Koh SJ, Song T, Kang YA, Choi JW, Chang KJ, Chu CS, Jeong JG, Lee JY, Song MK, Sung 412
HY, Kang YH, Yim JJ. 2010. An outbreak of skin and soft tissue infection caused by 413
Mycobacterium abscessus following acupuncture. Clin Microbiol Infect 16:895-901. 414
14. Jung SY, Kim BG, Kwon D, Park JH, Youn SK, Jeon S, Um HY, Kwon KE, Kim HJ, Jung HJ, 415
Choi E, Park BJ. 2015. An outbreak of joint and cutaneous infections caused by non-416
tuberculous mycobacteria after corticosteroid injection. Int J Infect Dis 36:62-9. 417
15. Hatzenbuehler LA, Tobin-D'Angelo M, Drenzek C, Peralta G, Cranmer LC, Anderson EJ, 418
Milla SS, Abramowicz S, Yi J, Hilinski J, Rajan R, Whitley MK, Gower V, Berkowitz F, 419
Shapiro CA, Williams JK, Harmon P, Shane AL. 2017. Pediatric Dental Clinic-420
Associated Outbreak of Mycobacterium abscessus Infection. J Pediatric Infect Dis Soc 421
6:e116-e122. 422
16. Baker AW, Lewis SS, Alexander BD, Chen LF, Wallace RJ, Jr., Brown-Elliott BA, Isaacs 423
PJ, Pickett LC, Patel CB, Smith PK, Reynolds JM, Engel J, Wolfe CR, Milano CA, 424
Schroder JN, Davis RD, Hartwig MG, Stout JE, Strittholt N, Maziarz EK, Saullo JH, 425
Hazen KC, Walczak RJ, Jr., Vasireddy R, Vasireddy S, McKnight CM, Anderson DJ, 426
Sexton DJ. 2017. Two-Phase Hospital-Associated Outbreak of Mycobacterium 427
abscessus: Investigation and Mitigation. Clin Infect Dis 64:902-911. 428
17. Tsao SM, Liu KS, Liao HH, Huang TL, Shen GH, Tsao TC, Lee YT. 2014. The clinical 429
management of cesarean section-acquired Mycobacterium abscessus surgical site 430
infections. J Infect Dev Ctries 8:184-92. 431
18. Hofling-Lima AL, de Freitas D, Sampaio JL, Leao SC, Contarini P. 2005. In vitro activity 432
of fluoroquinolones against Mycobacterium abscessus and Mycobacterium chelonae 433
causing infectious keratitis after LASIK in Brazil. Cornea 24:730-4. 434
19. Hung JH, Huang YH, Chang TC, Tseng SH, Shih MH, Wu JJ, Huang FC. 2016. A cluster 435
of endophthalmitis caused by Mycobacterium abscessus after cataract surgery. J 436
Microbiol Immunol Infect 49:799-803. 437
20. Cai SS, Chopra K, Lifchez SD. 2016. Management of Mycobacterium abscessus 438
Infection After Medical Tourism in Cosmetic Surgery and a Review of Literature. Ann 439
Plast Surg 77:678-682. 440
21. Zelazny AM, Root JM, Shea YR, Colombo RE, Shamputa IC, Stock F, Conlan S, McNulty 441
S, Brown-Elliott BA, Wallace RJ, Jr., Olivier KN, Holland SM, Sampaio EP. 2009. Cohort 442
study of molecular identification and typing of Mycobacterium abscessus, 443
Mycobacterium massiliense, and Mycobacterium bolletii. J Clin Microbiol 47:1985-95. 444
22. Macheras E, Roux AL, Bastian S, Leao SC, Palaci M, Sivadon-Tardy V, Gutierrez C, 445
Richter E, Rusch-Gerdes S, Pfyffer G, Bodmer T, Cambau E, Gaillard JL, Heym B. 2011. 446
Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus 447
(sensu lato) strains. J Clin Microbiol 49:491-9. 448
23. Leao SC, Tortoli E, Viana-Niero C, Ueki SY, Lima KV, Lopes ML, Yubero J, Menendez 449
MC, Garcia MJ. 2009. Characterization of mycobacteria from a major Brazilian 450
outbreak suggests that revision of the taxonomic status of members of the 451
Mycobacterium chelonae-M. abscessus group is needed. J Clin Microbiol 47:2691-8. 452
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
18
24. Leao SC, Tortoli E, Euzeby JP, Garcia MJ. 2011. Proposal that Mycobacterium 453
massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium 454
abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. 455
abscessus subsp. nov. and emended description of Mycobacterium abscessus. Int J 456
Syst Evol Microbiol 61:2311-3. 457
25. Cheng A, Liu YC, Chen ML, Hung CC, Tsai YT, Sheng WH, Liao CH, Hsueh PR, Chen YC, 458
Chang SC. 2013. Extrapulmonary infections caused by a dominant strain of 459
Mycobacterium massiliense (Mycobacterium abscessus subspecies bolletii). Clin 460
Microbiol Infect 19:E473-82. 461
26. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. 2009. The bacterial species 462
challenge: making sense of genetic and ecological diversity. Science 323:741-6. 463
27. Kim SY, Kang YA, Bae IK, Yim JJ, Park MS, Kim YS, Kim SK, Chang J, Jeong SH. 2013. 464
Standardization of multilocus sequence typing scheme for Mycobacterium abscessus 465
and Mycobacterium massiliense. Diagn Microbiol Infect Dis 77:143-9. 466
28. Kehrmann J, Wessel S, Murali R, Hampel A, Bange FC, Buer J, Mosel F. 2016. Principal 467
component analysis of MALDI TOF MS mass spectra separates M. abscessus (sensu 468
stricto) from M. massiliense isolates. BMC Microbiol 16:24. 469
29. Cheng A, Sun HY, Tsai YT, Wu UI, Chuang YC, Wang JT, Sheng WH, Hsueh PR, Chen YC, 470
Chang SC. 2018. In Vitro Evaluation of Povidone-Iodine and Chlorhexidine against 471
Outbreak and Nonoutbreak Strains of Mycobacterium abscessus Using Standard 472
Quantitative Suspension and Carrier Testing. Antimicrob Agents Chemother 62. 473
30. Koh WJ, Jeon K, Lee NY, Kim BJ, Kook YH, Lee SH, Park YK, Kim CK, Shin SJ, Huitt GA, 474
Daley CL, Kwon OJ. 2011. Clinical significance of differentiation of Mycobacterium 475
massiliense from Mycobacterium abscessus. Am J Respir Crit Care Med 183:405-10. 476
31. Haworth CS, Banks J, Capstick T, Fisher AJ, Gorsuch T, Laurenson IF, Leitch A, 477
Loebinger MR, Milburn HJ, Nightingale M, Ormerod P, Shingadia D, Smith D, 478
Whitehead N, Wilson R, Floto RA. 2017. British Thoracic Society Guideline for the 479
management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). BMJ 480
Open Respir Res 4:e000242. 481
32. Shang S, Gibbs S, Henao-Tamayo M, Shanley CA, McDonnell G, Duarte RS, Ordway DJ, 482
Jackson M. 2011. Increased virulence of an epidemic strain of Mycobacterium 483
massiliense in mice. PLoS One 6:e24726. 484
33. Tortoli E, Kohl TA, Brown-Elliott BA, Trovato A, Leao SC, Garcia MJ, Vasireddy S, 485
Turenne CY, Griffith DE, Philley JV, Baldan R, Campana S, Cariani L, Colombo C, 486
Taccetti G, Teri A, Niemann S, Wallace RJ, Jr., Cirillo DM. 2016. Emended description 487
of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and 488
Mycobacteriumabscessus subsp. bolletii and designation of Mycobacteriumabscessus 489
subsp. massiliense comb. nov. Int J Syst Evol Microbiol 66:4471-4479. 490
34. Koh WJ, Jeong BH, Kim SY, Jeon K, Park KU, Jhun BW, Lee H, Park HY, Kim DH, Huh HJ, 491
Ki CS, Lee NY, Kim HK, Choi YS, Kim J, Lee SH, Kim CK, Shin SJ, Daley CL, Kim H, Kwon 492
OJ. 2017. Mycobacterial Characteristics and Treatment Outcomes in Mycobacterium 493
abscessus Lung Disease. Clin Infect Dis 64:309-316. 494
35. Sapriel G, Konjek J, Orgeur M, Bouri L, Frezal L, Roux AL, Dumas E, Brosch R, Bouchier 495
C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, 496
Gaillard JL, Heym B, Wirth T. 2016. Genome-wide mosaicism within Mycobacterium 497
abscessus: evolutionary and epidemiological implications. BMC Genomics 17:118. 498
499
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
Table 1. Primers used to amplify each gene in the multi-locus sequence typing schemes.
Gene locus
Primer name and sequence Bases (bp)
Analysed fragment Ref.
hsp65 HSP65-F 5'-ACCAACGATGGTGTGTCCAT-3'
HSP65-R 5'-CTTGTCGAACCGCATACCCT-3'
401 5'-CGCCAAGGAG…GAGCTCACCG-3'
21
rpoB RPOB-F 5'-GGCAAGGTCACCCCGAAGGG-3'
RPOB-R 5'-AGCGGCTGCTGGGTGATCATC-3'
711 5'-TGARACCGAG…GBCCGTACTC-3'
21
secA1 SECA1-F 5'-
GACAGYGAGTGGATGGGYCGSGTGCACCG-
3'
SECA1-R 5'-
GCGGACGATGTARTCCTTGTCSCG-3'
466 5'-CTTCCTVGGS…RCTRTTCMMS-3'
21
argH ARGHF: GACGAGGGCGACAGCTTC
ARGHSR1: GTGCGCGAGCAGATGATG
480 5'-
GTGAGCACYAACGAA
GGCTC…CGATCATGCCGGGCA
AGACT-3'
11
cya ACF: GTGAAGCGGGCCAAGAAG
ACSR1: AACTGGGAGGCCAGGAGC
510 5'-
CTGGTGGGGTCCACC
CAGTT…TKGCGCGCCCGCGTC
ACGGC-3'
11
glpK GLPKSF1: AATCTCACCGGCGGTGTC
GLPKSR2: GGACAGACCCACGATGGC
534 5'-
GTGACAAATGCCAGTC
GCAC…TGTTCGCGCCGTACTG
GCGR-3'
11
gnd GNDF: GTGACGTCGGAGTGGTTGG
GNDSR1: CTTCGCCTCAGGTCAGCTC
480 5'-
CARTTCRTTGAAGAYG
TGCG…WCCGYAACGAAGTWG
AGGCG-3'
11
murC MURCSF1: CGGACGAAAGCGACGGCT
MURCSR2: CCAAAACCCTGCTGAGCC
537 5'-
CCGAACCTGATCRTCG
TSAC…AGGTGCGYACRGTGC
TGCAG-3'
11
pta PTASF1: GATCGGGCGTCATGCCCT
PTASR2: ACGAGGCACTGCTCTCCC
486 5'-
GACGTMCTACTSGCC
GTGGC…AAATCCGYTCCCGTGC
YGCC-3'
11
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
purH PURHSF1: CGGAGGCTTCACCCTGGA
PURHSR2: CAGGCCACCGCTGATCTG
549 5'-
AAGGTTYTRGCTGCCA
AGGC…GCAAGAAGAACGTGC
GGCTG-3'
11
gdhA
GDHAF: GTCAGTGCCCCGATCGCT
GDHASR1: GGCTCTCGGAGTACGTCGA
542 5'
GTCGACGGGDCMGAAG
GGTC...
GAGCTCCCCCGCCGTGTT
YT-3'
7
pgm PGMSF1: CCATTTGAACCCGACCGG
PGMSR2: GTGCCAACGAGATCCTGCG
559 5'
TACCTCGATCAGCGTCCG
GC...
TCACCGAGCGCCAGCCGT
CG-3'
7
pknA PKNAF: CAGGTGGACCTCGGACATG
PKNASR1: AACCAGGCGCCCACCATC
457 5'
CCGCCATAGCCGAGGATC
TC...
GCAGCCGGCGTCGCSCGG
CT-3'
7
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
Table 2. The source and subspecies distribution of 139 Mycobacterium abscessus isolates
included in this study.
* M. abscessus subsp. abscessus ATCC 19977 and M. abscessus subsp. massiliense BCRC
16916
Source Subspecies
n (%)
M. abscessus
subsp. abscessus
54 (38.8)
M. abscessus
subsp. massiliense
85 (61.2)
Clinical isolates 121 (87.1)
Pulmonary 65 (50.4) 40 (61.5) 25 (38.4)
Extrapulmonary 56 (46.2) 12 (21.4) 44 (78.6)
Environmental isolates 16 (11.5)
Ultrasonography gel 13 (81.3) 0 (0.0) 16 (100)
Hospital water 3 (18.7) 1 (33.3) 2 (66.7)
Reference standard isolates* 2 (1.4) 1 (50.0) 1 (50.0)
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
Table 3. Comparing the 3-gene, 7-gene, 13 genes multilocus typing schemes (MLST) for
139 isolates of Mycobacterium abscessus
Subspecies 3-gene
(n)
7-gene
(n)
13-gene
(n)
M. abscessus subsp.
abscessus (54)
MAB 1 (40) ST 1 (22)
ST 22 (1)
ST 40 (1)
ST 63 (3)
ST 127 (5)
ST 276 (1)
ST 280 (1)
ST 272 (1)
ST 289 (1)
ST 277 (1)
ST 283 (1)
ST 284 (1)
ST 288 (1)
ST 1 (22)
ST 22 (1)
ST 40 (1)
ST 63 (3)
ST 127 (5)
ST 276 (1)
ST 280 (1)
ST 272 (1)
ST 2 (1)
ST 277 (1)
ST 283 (1)
ST 284 (1)
ST 288 (1)
MAB 2 (2) ST 126 (2) ST 126 (2)
MAB 3 (4) ST 33 (1)
ST 49 (2)
ST 286 (1)
ST 33 (1)
ST 49 (2)
ST 286 (1)
MAB 4 (2) ST 137 (1)
ST 278 (1)
ST 137 (1)
ST 278 (1)
MAB 5 (1) ST 1* (1) ST 1a* (1)
MAB 6 (1) ST 61 (1) ST 61 (1)
MAB 7 (1) ST 282 (1) ST 282 (1)
MAB 8 (1) ST 281 (1) ST 281 (1)
MAB 9 (1) ST 290 (1) ST 290 (1)
MAB 10 (1) ST 274 (1) ST 274 (1)
M. abscessus subsp.
massiliense (85)
MMA 1 (57) ST 48 (57) ST 48 (57)
MMA 2 (11) ST 117 (10)
ST 275 (1)
ST 117 (10)
ST 275 (1)
MMA 3 (1) ST 271 (1) ST 271 (1)
MMA 4 (4) ST 23 (4) ST 23 (4)
MMA 5 (3) ST 176 (2)
ST 287 (1)
ST 176 (2)
ST 287 (1)
MMA 6 (3) ST 115 (2)
ST 285 (1)
ST 115 (2)
ST 2 5 (1)
MMA 7 (1) ST 279 (1) ST 279 (1)
MMA 8 (1) ST 34 (1) ST 34 (1)
MMA 9 (1) ST 273 (1) ST 273 (1)
MMA 10 (1) ST 291 (1) ST 291 (1)
MMA 11 (1) ST 279 * (1) ST 279a* (1)
MMA 12 (1) ST 37 (1) ST 37 (1)
* Denotes where typing by the 7 and 13-gene MLST were not in agreement.
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
MMA 1/ST48, all 57 outbreak isolates shared the same PFGE, rep-PCR patterns. Of the 57
isolates, 51 were obtained from contaminated ultrasonography or patients with
documented exposure to invasive procedures following ultrasonography. Two isolates were
from hospital water supplying two bronchoscopic units, three from three patients' sputum
and one from a patient's wound without documented exposure to contaminated
ultrasonography gel.
All new sequence types from this study that had been submitted to the Pasteur Institute
and were assigned a new sequence number (ST 271-291).
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
Table 4. The key divergent loci for strains clustered together by the 3-gene scheme with
the maximum sequence divergence observed in the pta, purH, gdhA genes for M.
abscessus subsp. abscessus and in the murC, purH, and gdhA genes for M. abscessus subsp.
massiliense. The least sequence divergence was observed in the glpK gene for M.
abscessus subsp. abscessus and in the argH, cya, and pgm genes for M. abscessus subsp.
massiliense.
hsp65 rpoB secA argH cya glpK gnd murC pta purH gdhA pgm pknA
MAB 1 ST 1 1 1 1 1 1 1 1 1 1 1 7 2 6
MAB 5 ST 1 1 1 3 1 1 1 1 1 1 1 7 2 6
MAB 1 ST 22 1 1 1 3 1 1 3 5 15 1 15 7 7
MAB 1 ST 40 1 1 1 3 11 1 3 3 18 3 11 9 8
MAB 1 ST 63 1 1 1 3 11 1 3 3 3 3 11 5 8
MAB 1 ST 127 1 1 1 3 23 1 3 3 3 3 11 5 8
MAB 1 ST 276 1 1 1 3 1 1 3 3 12 35 10 5 7
MAB 1 ST 280 1 1 1 3 14 7 3 3 6 36 11 5 8
MAB 1 ST 272 1 1 1 18 1 1 8 5 1 1 11 2 7
MAB 1 ST 289 1 1 1 18 32 1 3 5 1 1 17 9 7
MAB 1 ST 277 1 1 1 20 12 1 8 3 37 9 16 2 7
MAB 1 ST 283 1 1 1 18 32 1 1 5 1 1 17 9 7
MAB 1 ST 284 1 1 1 3 11 1 3 3 3 20 11 5 8
MAB 1 ST 288 1 1 1 3 11 1 3 3 32 3 11 5 8
MAB 3 ST 33 1 1 2 7 5 1 8 5 6 1 10 6 7
MAB 3 ST 49 1 1 2 3 11 1 3 3 5 10 11 8 8
MAB 3 ST 286 1 1 2 38 1 1 3 5 1 1 12 7 7
MAB 4 ST 137 1 2 2 3 12 1 3 5 1 10 9 2 7
MAB 4 ST 278 1 2 2 13 12 1 3 3 3 9 11 7 7
MMA2 ST 117 m1 m2 m2 11 14 4 24 6 2 16 2 1 1
MMA2 ST 275 m1 m2 m2 11 14 30 24 6 2 16 2 1 1
MMA5 ST 176 m2 m4 m1 21 13 4 10 6 11 7 4 1 3
MMA5 ST 287 m2 m4 m1 21 13 4 10 8 11 7 4 1 3
MMA6 ST 115 m1 m4 m2 24 20 1 9 8 8 27 3 2 2
MMA6 ST 285 m1 m4 m2 24 20 1 9 6 8 27 3 2 2
MMA9 ST 273 m1 1 m2 11 20 1 9 8 8 27 3 2 2
MMA11 ST273a 1 m4 m2 11 20 1 9 8 8 27 3 2 1
Small "m" e.g. m1, m2, m2, m4 denote allelic types numbering for M. abscessus subsp.
massiliense.
on May 27, 2021 by guest
http://jcm.asm
.org/D
ownloaded from
