@article{Andre2017,
abstract = {The rpoB gene codes for the RNA polymerase $\beta$ subunit, which is the target of rifampicin, an essential drug in the treatment of tuberculosis and other mycobacterial infections. This gene is present in all bacteria, but its length and nucleotide sequence vary between bacterial species, including mycobacteria. Mutations in the rpoB gene alter the structure of this protein and cause drug resistance. To describe the resistance-associated mutations, the scientific and medical communities have been using, since 1993, a numbering system based on the Escherichia coli sequence annotation. Using E. coli reference for describing mutations in mycobacteria leads to misunderstandings, particularly with the increasing use of whole genome sequencing, which brought an alternative numbering system based on the Mycobacterium tuberculosis rpoB sequence. We propose using a consensus numbering system for the reporting of resistance mutations based on the reference genomes from the species interrogated (such as strain H37Rv for M. tuberculosis). This manuscript provides the necessary figures and tables allowing researchers, microbiologists and clinicians to easily convert other annotation systems into one common language.},
author = {Andre, E and Goeminne, L and Cabibbe, A and Beckert, P and {Kabamba Mukadi}, B and Mathys, V and Gagneux, S and Niemann, S and {Van Ingen}, J and Cambau, E},
doi = {10.1016/j.cmi.2016.09.006},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Andre et al. - 2017 - Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.pdf:pdf},
issn = {1469-0691},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
keywords = {Mycobacterium kansasii,Mycobacterium leprae,Mycobacterium tuberculosis,Numbering system,Resistance,Rifampicin,Rifampin,rpoB},
month = {mar},
number = {3},
pages = {167--172},
pmid = {27664776},
publisher = {Elsevier},
title = {{Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27664776},
volume = {23},
year = {2017}
}
@article{Bastian2011,
abstract = {{\textless}p{\textgreater} Clarithromycin was the drug of choice for {\textless}italic{\textgreater}Mycobacterium abscessus{\textless}/italic{\textgreater} infections until inducible resistance due to {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) was described. Because {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} was split into {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} sensu stricto, {\textless}italic{\textgreater}Mycobacterium massiliense{\textless}/italic{\textgreater} , and {\textless}italic{\textgreater}Mycobacterium bolletii{\textless}/italic{\textgreater} , we looked for {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) in the three species and determined their clarithromycin susceptibility levels. Ninety strains were included: 87 clinical strains from cystic fibrosis patients (61{\%}) and others (39{\%}), representing 43 {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} , 30 {\textless}italic{\textgreater}M. massiliense{\textless}/italic{\textgreater} , and 14 {\textless}italic{\textgreater}M. bolletii{\textless}/italic{\textgreater} strains identified on a molecular basis, and 3 reference strains. Clarithromycin and azithromycin MICs were determined by broth microdilution and Etest with a 14-day incubation period. Mutations in {\textless}italic{\textgreater}rrl{\textless}/italic{\textgreater} (23S rRNA gene) known to confer acquired clarithromycin resistance were also sought. {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) was detected in all strains but with two deletions in all {\textless}italic{\textgreater}M. massiliense{\textless}/italic{\textgreater} strains. These strains were indeed susceptible to clarithromycin (MIC {\textless}sub{\textgreater}90{\textless}/sub{\textgreater} of 1 $\mu$g/ml) except for four strains with {\textless}italic{\textgreater}rrl{\textless}/italic{\textgreater} mutations. {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} strains harbored an intact {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) but had a T/C polymorphism at the 28th nucleotide: T28 strains (Trp10 codon) demonstrated inducible clarithromycin resistance (MIC {\textless}sub{\textgreater}90{\textless}/sub{\textgreater} of {\textgreater}16 $\mu$g/ml), while C28 strains (Arg10) were susceptible (MIC {\textless}sub{\textgreater}90{\textless}/sub{\textgreater} of 2 $\mu$g/ml) except for two strains with {\textless}italic{\textgreater}rrl{\textless}/italic{\textgreater} mutations. {\textless}italic{\textgreater}M. bolletii{\textless}/italic{\textgreater} strains had {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) sequences similar to the sequence of the T28 {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} group, associated with inducible clarithromycin resistance (MIC {\textless}sub{\textgreater}90{\textless}/sub{\textgreater} of {\textgreater}16 $\mu$g/ml). {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) sequences appeared species specific within the {\textless}italic{\textgreater}M. abscessus{\textless}/italic{\textgreater} group and were fully concordant with clarithromycin susceptibility when {\textless}italic{\textgreater}erm{\textless}/italic{\textgreater} (41) sequencing was associated with detection of {\textless}italic{\textgreater}rrl{\textless}/italic{\textgreater} mutations. Clarithromycin-resistant strains, including the six {\textless}italic{\textgreater}rrl{\textless}/italic{\textgreater} mutants, were more often isolated in cystic fibrosis patients, but this was not significantly associated with a previous treatment. {\textless}/p{\textgreater}},
author = {Bastian, Sylvaine and Veziris, Nicolas and Roux, Anne-Laure and Brossier, Florence and Gaillard, Jean-Louis and Jarlier, Vincent and Cambau, Emmanuelle},
doi = {10.1128/AAC.00861-10},
issn = {0066-4804},
journal = {Antimicrobial Agents and Chemotherapy},
month = {feb},
number = {2},
pages = {775--781},
pmid = {21135185},
title = {{Assessment of Clarithromycin Susceptibility in Strains Belonging to the {\textless}i{\textgreater}Mycobacterium abscessus{\textless}/i{\textgreater} Group by {\textless}i{\textgreater}erm{\textless}/i{\textgreater} (41) and {\textless}i{\textgreater}rrl{\textless}/i{\textgreater} Sequencing}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21135185 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3028756 http://aac.asm.org/lookup/doi/10.1128/AAC.00861-10},
volume = {55},
year = {2011}
}
@article{Brown-Elliott2002,
abstract = {The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.},
author = {Brown-Elliott, Barbara A and Wallace, Richard J and Jr.},
doi = {10.1128/CMR.15.4.716-746.2002},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Brown-Elliott, Wallace, Jr. - 2002 - Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobac.pdf:pdf},
issn = {0893-8512},
journal = {Clinical microbiology reviews},
month = {oct},
number = {4},
pages = {716--46},
pmid = {12364376},
publisher = {American Society for Microbiology (ASM)},
title = {{Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12364376 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC126856},
volume = {15},
year = {2002}
}
@article{DeMoura2012,
abstract = {Several outbreaks of infections caused by rapidly growing mycobacteria (RGM) were reported in many Brazilian states (2032 notified cases) from 2004 to 2010. Most of the confirmed cases were mainly associated with Mycobacterium massiliense (recently renamed as Mycobacterium abscessus subsp. bolletii) BRA100 clone, recovered from patients who had undergone invasive procedures in which medical instruments had not been properly sterilized and/or disinfected. Since quinolones have been an option for the treatment of general RGM infections and have been suggested for therapeutic schemes for these outbreaks, we evaluated the in vitro activities of all generations of quinolones for clinical and reference RGM by broth microdilution, and analysed the peptide sequences of the quinolone resistance determining regions (QRDRs) of GyrA and GyrB after DNA sequencing followed by amino acid translation. Fifty-four isolates of M. abscessus subsp. bolletii, including clone BRA100, recovered in different states of Brazil, and 19 reference strains of RGM species were characterized. All 54 M. abscessus subsp. bolletii isolates were resistant to all generations of quinolones and showed the same amino acids in the QRDRs, including the Ala-83 in GyrA, and Arg-447 and Asp-464 in GyrB, described as being responsible for an intrinsic low level of resistance to quinolones in mycobacteria. However, other RGM species showed distinct susceptibilities to this class of antimicrobials and patterns of mutations contrary to what has been traditionally defined, suggesting that other mechanisms of resistance, different from gyrA or gyrB mutations, may also be involved in resistance to high levels of quinolones.},
author = {de Moura, V. C. N. and da Silva, M. G. and Gomes, K. M. and Coelho, F. S. and Sampaio, J. L. M. and Mello, F. C. d. Q. and Lourenco, M. C. d. S. and Amorim, E. d. L. T. and Duarte, R. S.},
doi = {10.1099/jmm.0.034942-0},
issn = {0022-2615},
journal = {Journal of Medical Microbiology},
month = {jan},
number = {1},
pages = {115--125},
publisher = {Microbiology Society},
title = {{Phenotypic and molecular characterization of quinolone resistance in Mycobacterium abscessus subsp. bolletii recovered from postsurgical infections}},
url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.034942-0},
volume = {61},
year = {2012}
}
@article{Enright1999,
abstract = {Multilocus sequence typing (MLST) provides a new approach to molecular epidemiology that can identify and track the global spread of virulent or antibiotic-resistant isolates of bacterial pathogens using the Internet. MLST databases, together with interrogation software, are available for Neisseria meningitidis and Streptococcus pneumoniae and databases for Streptococcus pyogenes and Staphylococcus aureus will be released shortly.},
author = {Enright, Mark C. and Spratt, Brian G.},
doi = {10.1016/S0966-842X(99)01609-1},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Enright, Spratt - 1999 - Multilocus sequence typing.pdf:pdf},
issn = {0966-842X},
journal = {Trends in Microbiology},
month = {dec},
number = {12},
pages = {482--487},
publisher = {Elsevier Current Trends},
title = {{Multilocus sequence typing}},
url = {https://www-sciencedirect-com.uml.idm.oclc.org/science/article/pii/S0966842X99016091?via{\%}3Dihub},
volume = {7},
year = {1999}
}
@article{Feijao2018,
abstract = {MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.},
author = {Feijao, Pedro and Yao, Hua-Ting and Fornika, Dan and Gardy, Jennifer and Hsiao, William and Chauve, Cedric and Chindelevitch, Leonid},
doi = {10.1099/mgen.0.000146},
issn = {2057-5858},
journal = {Microbial Genomics},
keywords = {multi-locus sequence typing,next-generation sequencing,pathogen surveillance},
month = {feb},
number = {2},
publisher = {Microbiology Society},
title = {{MentaLiST – A fast MLST caller for large MLST schemes}},
url = {http://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000146},
volume = {4},
year = {2018}
}
@article{Griffith2015,
abstract = {Mycobacterium abscessus is a formidable and difficult-to-treat mycobacterial pathogen with multiple drug-resistance mechanisms. The most important of these mechanisms is the presence of an inducible erythromycin methylase (erm) gene, because it confers macrolide resistance. It has recently been found that “M. abscessus” can be split into three species or subspecies based on gene sequence analysis other than the 16S rRNA gene and the presence or absence of a functional erm(41) gene. Several names have been applied to these three organisms, including M. abscessus or M. abscessus subsp. abscessus, Mycobacterium massiliense or M. abscessus subsp. massiliense, and Mycobacterium bolletii or M. abscessus subsp. bolletii. No universally accepted or recognized species or subspecies designations have emerged, and no names have been universally adopted for these organisms. This uncertainty has led to inconsistencies in the medical literature and understandable confusion by clinicians about the appropriate labels for...},
author = {Griffith, David E. and Brown-Elliott, Barbara A. and {L. Benwill}, Jeana and Wallace, Richard J.},
doi = {10.1513/AnnalsATS.201501-015OI},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Griffith et al. - 2015 - iMycobacterium abscessusi . “Pleased to Meet You, Hope You Guess My Name...”.pdf:pdf},
issn = {2329-6933},
journal = {Annals of the American Thoracic Society},
keywords = {Mycobacterium abscessus,Mycobacterium bolletii,Mycobacterium massiliense},
month = {mar},
number = {3},
pages = {436--439},
publisher = {American Thoracic Society},
title = {{{\textless}i{\textgreater}Mycobacterium abscessus{\textless}/i{\textgreater} . “Pleased to Meet You, Hope You Guess My Name...”}},
url = {http://www.atsjournals.org/doi/10.1513/AnnalsATS.201501-015OI},
volume = {12},
year = {2015}
}
@article{Gupta2017,
abstract = {Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools. AVAILABILITY AND IMPLEMENTATION The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/stringMLST CONTACT: lavanya.rishishwar@gatech.eduSupplementary information: Supplementary data are available at Bioinformatics online.},
author = {Gupta, Anuj and Jordan, I. King and Rishishwar, Lavanya},
doi = {10.1093/bioinformatics/btw586},
issn = {1367-4803},
journal = {Bioinformatics},
month = {jan},
number = {1},
pages = {119--121},
pmid = {27605103},
title = {{stringMLST: a fast k-mer based tool for multilocus sequence typing}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27605103 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw586},
volume = {33},
year = {2017}
}
@article{Han2007,
abstract = {A b s t r a c t We analyzed clinical and microbiologic features of 115 cases involving rapidly growing mycobacteria (RGM) isolated at the University of Texas M.D. Anderson Cancer Center, Houston (2000-2005) and identified by 16S ribosomal RNA gene sequencing analysis. At least 15 RGM species were included: Mycobacterium abscessus (43 strains [37.4{\%}]), Mycobacterium fortuitum complex (33 strains [28.7{\%}]), and Mycobacterium mucogenicum (28 strains [24.3{\%}]) most common, accounting for 90.4{\%}. Most M abscessus (32/43) were isolated from respiratory sources, whereas most M mucogenicum (24/28) were from blood cultures. Antimicrobial susceptibility tests showed that M abscessus was the most resistant species; M mucogenicum was most susceptible. From blood and catheter sources, 46 strains (40.0{\%}) were isolated; 44 represented bacteremia or catheter-related infections. These infections typically manifested high fever (mean temperature, 38.9°C), with a high number of RGM colonies cultured. All infections resolved with catheter removal and antibiotic therapy. Six strains (M abscessus and M fortuitum only) were from skin, soft tissue, and wound infections. There were 59 strains from respiratory sources, and 28 of these represented definitive to probable infections. Prior lung injuries and coisolation of other pathogenic organisms were common. Overall, 78 RGM strains (67.8{\%}) caused true to probable infections without direct deaths. Mycobacterium is probably the best-studied bacterial genus and currently contains more than 100 species. 1,2 Several reasons account for this: Mycobacterium tuberculo-sis is one of the oldest and most common causes of infection and death worldwide; Mycobacterium avium frequently causes bloodstream infection in patients with AIDS 3 ; the spectrum of pathogenicity varies widely across the species, from strict pathogens to essentially nonpathogens 4 ; the nich-es and reservoir are diverse, from human to animal to envi-ronmental 5-7 ; all species are characteristically stained as acid-fast bacilli (AFB); and all disease-causing species elic-it granulomatous tissue reactions. Rapidly growing mycobacteria (RGM) are the Runyon group IV organisms that usually form colonies within 7 days of incubation as opposed to slow-growing mycobacte-ria, ie, Runyon groups I, II, and III and the M tuberculosis complex group, that require longer incubation. RGM have emerged as significant human pathogens, causing various infections in healthy and immunocompromised hosts. Although the general recognition of RGM can be made with confidence, further species identification has been difficult, particularly by biochemical methods, as with many nontu-berculous slow growers. As a result of the widespread use of 16S ribosomal RNA (rRNA) gene sequencing, more than 50 new Mycobacterium species have been described since 1990. 1,2,8 Many clinical and reference laboratories worldwide, including ours, have adopted the 16S sequencing method to routinely identify various mycobacteria 9-15 to improve turnaround time and accuracy. In this study, we analyzed the microbiologic and clinical features of 115 RGM strains.},
author = {Han, Xiang Y and D{\'{e}}, Indra and Jacobson, Kalen L},
doi = {10.1309/1KB2GKYT1BUEYLB5},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Han, D{\'{e}}, Jacobson - 2007 - Rapidly Growing Mycobacteria Clinical and Microbiologic Studies of 115 Cases.pdf:pdf},
journal = {Am J Clin Pathol},
keywords = {16S rRNA gene sequencing,Antimicrobial susceptibility,Catheter infection,Rapidly growing mycobacteria},
pages = {612--621},
title = {{Rapidly Growing Mycobacteria Clinical and Microbiologic Studies of 115 Cases}},
url = {https://academic.oup.com/ajcp/article-abstract/128/4/612/1760214},
volume = {128},
year = {2007}
}
@article{Kim2013,
abstract = {This study aims to develop a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus complex for the typing of stains within each species. A total of 89 clinical isolates of M. abscessus complex from 71 patients of 2 tertiary care hospitals in South Korea were included. Forty-two isolates were identified as M. abscessus, and 29, as Mycobacterium massiliense through sequencing of 8 housekeeping genes and rpoB. The MLST scheme identified 26 different sequence types(STs) and 13 different clonal complexes (CCs) in M. abscessus and 12 different STs and 6 different CCs in M. massiliense. The MLST data showed high concordance with the XbaI-macrorestriction patterns of pulsed-field gel electrophoresis in the duplicated isolates. Our MLST schemes could identify different strains of M. abscessus and M. massiliense, and the schemes also showed a reliable reproducibility. Therefore, our MLST schemes may be useful in studying the epidemiology of M. abscessus and M. massiliense infections.},
author = {Kim, Song Yee and Kang, Young Ae and Bae, Il Kwon and Yim, Jae-Joon and Park, Moo Suk and Kim, Young Sam and Kim, Se Kyu and Chang, Joon and Jeong, Seok Hoon},
doi = {10.1016/J.DIAGMICROBIO.2013.06.023},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Kim et al. - 2013 - Standardization of multilocus sequence typing scheme for Mycobacterium abscessus and Mycobacterium massiliense.pdf:pdf},
issn = {0732-8893},
journal = {Diagnostic Microbiology and Infectious Disease},
month = {oct},
number = {2},
pages = {143--149},
publisher = {Elsevier},
title = {{Standardization of multilocus sequence typing scheme for Mycobacterium abscessus and Mycobacterium massiliense}},
url = {https://www-sciencedirect-com.uml.idm.oclc.org/science/article/pii/S0732889313003787?{\_}rdoc=1{\&}{\_}fmt=high{\&}{\_}origin=gateway{\&}{\_}docanchor={\&}md5=b8429449ccfc9c30159a5f9aeaa92ffb{\#}bb0150},
volume = {77},
year = {2013}
}
@article{Larsson2014,
author = {Larsson, Anders},
doi = {10.1093/bioinformatics/btu531},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Larsson - 2014 - AliView a fast and lightweight alignment viewer and editor for large datasets.pdf:pdf},
issn = {1460-2059},
journal = {Bioinformatics},
month = {nov},
number = {22},
pages = {3276--3278},
publisher = {Oxford University Press},
title = {{AliView: a fast and lightweight alignment viewer and editor for large datasets}},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu531},
volume = {30},
year = {2014}
}
@article{Leao2011,
abstract = {The names 'Mycobacterium abscessus subsp. abscessus' and 'Mycobacterium abscessus subsp. massiliense', proposed by Leao et al. (2009, J Clin Microbiol 47, 2691-2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name 'Mycobacterium abscessus subsp. massiliense' is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.},
author = {Leao, S. C. and Tortoli, E. and Euzeby, J. P. and Garcia, M. J.},
doi = {10.1099/ijs.0.023770-0},
issn = {1466-5026},
journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
month = {sep},
number = {9},
pages = {2311--2313},
pmid = {21037035},
title = {{Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacteri}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21037035 http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.023770-0},
volume = {61},
year = {2011}
}
@article{Lee2015,
abstract = {Mycobacterium abscessus complex comprises a group of rapidly growing, multidrug-resistant, nontuberculous mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, bacteremia, and ocular and other infections. M. abscessus complex is differentiated into 3 subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. The 2 major subspecies, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, have different erm(41) gene patterns. This gene provides intrinsic resistance to macrolides, so the different patterns lead to different treatment outcomes. M. abscessus complex outbreaks associated with cosmetic procedures and nosocomial transmissions are not uncommon. Clarithromycin, amikacin, and cefoxitin are the current antimicrobial drugs of choice for treatment. However, new treatment regimens are urgently needed, as are rapid and inexpensive identification methods and measures to contain nosocomial transmission and outbreaks.},
author = {Lee, Meng-Rui and Sheng, Wang-Huei and Hung, Chien-Ching and Yu, Chong-Jen and Lee, Li-Na and Hsueh, Po-Ren},
doi = {10.3201/2109.141634},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Lee et al. - 2015 - Mycobacterium abscessus Complex Infections in Humans.pdf:pdf},
issn = {1080-6059},
journal = {Emerging infectious diseases},
keywords = {Mycobacterium abscessus,Mycobacterium abscessus complex,Mycobacterium bolletii,Mycobacterium massiliense,bacteria,clinical disease,cosmetic procedures,identification methods,multidrug resistant,mycobacteria,nomenclature,nontuberculous,nosocomial,outbreaks,taxonomy,transmission},
month = {sep},
number = {9},
pages = {1638--46},
pmid = {26295364},
publisher = {Centers for Disease Control and Prevention},
title = {{Mycobacterium abscessus Complex Infections in Humans.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26295364 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4550155},
volume = {21},
year = {2015}
}
@article{Macheras2011,
abstract = {Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3{\%} and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59{\%}. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100{\%} and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61{\%}, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17{\%} (1.13 to 2.58{\%}) between the M. abscessus and M. massiliense clusters, 2.37{\%} (1.5 to 2.85{\%}) between the M. abscessus and M. bolletii clusters, and 2.28{\%} (0.86 to 2.68{\%}) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering of strains. We found 10/120 (8.3{\%}) isolates for which the concatenated MLSA gene sequence and rpoB sequence were discordant (e.g., M. massiliense MLSA sequence and M. abscessus rpoB sequence), suggesting the intergroup lateral transfers of rpoB. In conclusion, our study strongly supports the recent proposal that M. abscessus, M. massiliense, and M. bolletii should constitute a single species. Our findings also indicate that there has been a horizontal transfer of rpoB sequences between these subgroups, precluding the use of rpoB sequencing alone for the accurate identification of the two proposed M. abscessus subspecies.},
author = {Macheras, Edouard and Roux, Anne-Laure and Bastian, Sylvaine and Le{\~{a}}o, Sylvia Cardoso and Palaci, Moises and Sivadon-Tardy, Val{\'{e}}rie and Gutierrez, Cristina and Richter, Elvira and R{\"{u}}sch-Gerdes, Sabine and Pfyffer, Gaby and Bodmer, Thomas and Cambau, Emmanuelle and Gaillard, Jean-Louis and Heym, Beate},
doi = {10.1128/JCM.01274-10},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Macheras et al. - 2011 - Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.pdf:pdf},
issn = {1098-660X},
journal = {Journal of clinical microbiology},
month = {feb},
number = {2},
pages = {491--9},
pmid = {21106786},
publisher = {American Society for Microbiology},
title = {{Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21106786 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3043527},
volume = {49},
year = {2011}
}
@article{Macheras2009,
abstract = {We determined nucleotide sequences of rpoB, hsp65, and sodA in 59 clinical isolates (from 58 patients) of the Mycobacterium abscessus group. Identification to the species level, based on three target genes, was concordant for 44 isolates (25 M. abscessus, 13 Mycobacterium massiliense, and 6 Mycobacterium bolletii isolates) and discordant for 15 isolates which had "interspecific composite patterns." Sequence analysis of five housekeeping genes also showed composite patterns in 8 of these 15 isolates.},
author = {Macheras, Edouard and Roux, Anne-Laure and Ripoll, Fabienne and Sivadon-Tardy, Val{\'{e}}rie and Gutierrez, Cristina and Gaillard, Jean-Louis and Heym, Beate},
doi = {10.1128/JCM.00037-09},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Macheras et al. - 2009 - Inaccuracy of single-target sequencing for discriminating species of the Mycobacterium abscessus group.pdf:pdf},
issn = {1098-660X},
journal = {Journal of clinical microbiology},
month = {aug},
number = {8},
pages = {2596--600},
pmid = {19515839},
publisher = {American Society for Microbiology},
title = {{Inaccuracy of single-target sequencing for discriminating species of the Mycobacterium abscessus group.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19515839 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2725694},
volume = {47},
year = {2009}
}
@article{Monego2012,
abstract = {Fluoroquinolones (FQs) have been increasingly used for effective treatment of infections caused by rapidly growing mycobacteria, and resistance to this drug has been predominantly attributed to gyrA and gyrB mutations. Accordingly, this study investigated a total of 36 Mycobacterium massiliense clinical isolates for their susceptibility to ciprofloxacin and presence of gyrA and gyrB gene mutations. The minimal inhibitory concentration (MIC) values, determined by broth microdilution method, of 35 ciprofloxacin-resistant isolates ranged between 4 and 16 $\mu$g/mL and a single susceptible isolate was obtained. A total of 31 of 35 (88.5{\%}) ciprofloxacin-resistant isolates presented an amino acid substitution at codon 90 (Ala-90→Val) and no isolate presented mutation at position Asp-94. Moreover, 4 of 35 (11.4{\%}) ciprofloxacin-resistant and one susceptible isolate had no mutation in Ala-90 and Asp-94. No gyrB mutation was observed in all tested M. massiliense isolates. In conclusion, our results have shown that mutations of gyrA codon 90 are frequent and may constitute an important mechanism of resistance to FQ in M. massiliense.},
author = {Monego, Fernanda and Duarte, Rafael Silva and Biondo, Alexander Welker},
doi = {10.1089/mdr.2011.0047},
journal = {Microbial Drug Resistance},
month = {feb},
number = {1},
pages = {1--6},
pmid = {21711149},
title = {{gyrA and gyrB Gene Mutation in Ciprofloxacin-Resistant {\textless}i{\textgreater}Mycobacterium massiliense{\textless}/i{\textgreater} Clinical Isolates from Southern Brazil}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21711149},
volume = {18},
year = {2012}
}
@article{Mougari2017,
abstract = {Mycobacterium abscessus is an emerging pathogen against which clarithromycin is the main drug used. Clinical failures are commonly observed and were first attributed to acquired mutations in rrl encoding 23S rRNA but were then attributed to the intrinsic production of the erm(41) 23S RNA methylase. Since strains of M. abscessus were recently distributed into subspecies and erm(41) sequevars, we investigated acquired clarithromycin resistance mechanisms in mutants selected in vitro from four representative strains. Mutants were sequenced for rrl, erm(41), whiB, rpIV, and rplD and studied for seven antibiotic MICs. For mutants obtained from strain M. abscessus subsp. abscessus erm(41) T28 sequevar and strain M. abscessus subsp. bolletii, which are both known to produce effective methylase, rrl was mutated in only 19{\%} (4/21) and 32.5{\%} (13/40) of mutants, respectively, at position 2058 (A2058C, A2058G) or position 2059 (A2059C, A2059G). No mutations were observed in any of the other genes studied, and resistance to other antibiotics (amikacin, cefoxitin, imipenem, tigecycline, linezolid, and ciprofloxacin) was mainly unchanged. For M. abscessus subsp. abscessus erm(41) C28 sequevar and M. abscessus subsp. massiliense, not producing effective methylase, 100{\%} (26/26) and 97.5{\%} (39/40) of mutants had rrl mutations at position 2058 (A2058C, A2058G, A2058T) or position 2059 (A2059C, A2059G). The remaining M. abscessus subsp. massiliense mutant showed an 18-bp repeat insertion in rpIV, encoding the L22 protein. Our results showed that acquisition of clarithromycin resistance is 100{\%} mediated by structural 50S ribosomal subunit mutations for M. abscessus subsp. abscessus erm(41) C28 and M. abscessus subsp. massiliense, whereas it is less common for M. abscessus subsp. abscessus erm(41) T28 sequevar and M. abscessus subsp. bolletii, where other mechanisms may be responsible for failure.},
author = {Mougari, Faiza and Bouziane, Feriel and Crockett, Flora and Nessar, Rachid and Chau, Fran{\c{c}}oise and Veziris, Nicolas and Sapriel, Guillaume and Raskine, Laurent and Cambau, Emmanuelle},
doi = {10.1128/AAC.00943-16},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Mougari et al. - 2017 - Selection of Resistance to Clarithromycin in Mycobacterium abscessus Subspecies.pdf:pdf},
issn = {1098-6596},
journal = {Antimicrobial agents and chemotherapy},
keywords = {ARN23S,Mycobacterium abscessus,antibiotic resistance,clarithromycin,resistant mutants,rrl},
month = {jan},
number = {1},
pages = {e00943--16},
pmid = {27799212},
publisher = {American Society for Microbiology},
title = {{Selection of Resistance to Clarithromycin in Mycobacterium abscessus Subspecies.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27799212 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5192163},
volume = {61},
year = {2017}
}
@article{Nessar2012,
author = {Nessar, R. and Cambau, E. and Reyrat, J. M. and Murray, A. and Gicquel, B.},
doi = {10.1093/jac/dkr578},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Nessar et al. - 2012 - Mycobacterium abscessus a new antibiotic nightmare.pdf:pdf},
issn = {0305-7453},
journal = {Journal of Antimicrobial Chemotherapy},
keywords = {aminoglycosides,antimicrobial susceptibility,mycobacterium,mycobacterium abscessus,nightmare,pathogenic organism},
month = {apr},
number = {4},
pages = {810--818},
publisher = {Oxford University Press},
title = {{Mycobacterium abscessus: a new antibiotic nightmare}},
url = {https://academic.oup.com/jac/article-lookup/doi/10.1093/jac/dkr578},
volume = {67},
year = {2012}
}
@incollection{Perez-Losada2017,
abstract = {Since 1998 multilocus sequence typing (MLST) has been widely used for molecular characterization of bacteria and fungi because of its molecular and technical advantages. MLST data are highly variable and informative, universally comparable, easily validated, accessible through the Internet, and transferable across researchers. MLST data are currently used not only in epidemiological investigations at global and local scales but also in studies of pathogen population dynamics, pathogenicity, and molecular evolution. Here, we review several key aspects of MLST molecular design and development in relation to new sequencing technologies; database submission, storing, access, and management; advantages and disadvantages compared to other typing techniques; statistical methods of analysis with special emphasis on coalescent-based approaches; and their application to population dynamics, epidemiological inferences, species diagnosis, and phylogenetics or phylogenomics. The increasing speed, quantity and quality, and reduced cost of gene and genome nucleotide sequencing, together with improved web-based databases, analytical tools, and rising computer power, will lead to a continued expansion in the use of MLST and its integration with cost-effective pathogen genome sequencing.},
author = {P{\'{e}}rez-Losada, M. and Arenas, M. and Castro-Nallar, E. and Castro-Nallar, E.},
booktitle = {Genetics and Evolution of Infectious Diseases},
doi = {10.1016/B978-0-12-799942-5.00016-0},
isbn = {9780127999425},
pages = {383--404},
publisher = {Elsevier},
title = {{Multilocus Sequence Typing of Pathogens}},
url = {http://linkinghub.elsevier.com/retrieve/pii/B9780127999425000160},
year = {2017}
}
@article{Prammananan1998,
abstract = {Twenty-six clinical isolates of Mycobacterium abscessus resistant to amikacin were identified. Most isolates were from patients with posttympanostomy tube placement otitis media or patients with cystic fibrosis who had received aminoglycoside therapy. Isolates were highly resistant (MICs {\'{u}}1024 mg/mL) to amikacin, kanamycin, gentamicin, tobramycin, and neomycin (all 2-deoxystrep-tamine aminoglycosides) but not to streptomycin. Sequencing of their 16S ribosomal (r) RNA revealed that 16 (94{\%}) of 17 had an AjG mutation at position 1408. In vitro – selected amikacin-resistant mutants of M. abscessus and Mycobacterium chelonae had the same resistance phenotype, and 15 mutants all had the same AjG substitution at position 1408. Introducing an rRNA operon from Mycobacterium smegmatis with a mutated AjG at this position into a single functional allelic rRNA mutant of M. smegmatis produced the same aminoglycoside resistance phenotype. These studies demonstrate this 16S rRNA mutation is responsible for amikacin resistance in M. abscessus, which has only one copy of the rRNA operon.},
author = {Prammananan, Therdsak and Sander, Peter and Brown, Barbara A and Frischkorn, Klaus and Onyi, Grace O and Zhang, Yansheng and B{\"{o}}ttger, Erik C and Wallace, Richard J},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Prammananan et al. - 1998 - A Single 16S Ribosomal RNA Substitution Is Responsible for Resistance to Amikacin and Other 2-Deoxystreptami.pdf:pdf},
journal = {The Journal of Infectious Diseases},
pages = {1573--81},
title = {{A Single 16S Ribosomal RNA Substitution Is Responsible for Resistance to Amikacin and Other 2-Deoxystreptamine Aminoglycosides in Mycobacterium abscessus and Mycobacterium chelonae}},
url = {https://watermark.silverchair.com/177-6-1573.pdf?token=AQECAHi208BE49Ooan9kkhW{\_}Ercy7Dm3ZL{\_}9Cf3qfKAc485ysgAAAaEwggGdBgkqhkiG9w0BBwagggGOMIIBigIBADCCAYMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMtMSV-kl4o1vUdOAvAgEQgIIBVCFRXQ-cxKn{\_}UU4aUDEqHOKp{\_}7D{\_}Njg-yNyIuL8O62pe},
volume = {177},
year = {1998}
}
@article{Ringuet1999,
abstract = {Partial sequencing of the hsp65 gene was used for the identification of rapidly growing mycobacteria (RGM). A 441-bp fragment (A. Telenti, F. Marchesi, M. Balz, F. Bally, E. B{\"{o}}ttger, and T. Bodmer, J. Clin. Microbiol. 31:175-178, 1993) was amplified and sequenced by an automated fluorescence-based method involving capillary electrophoresis. Type strains of 10 RGM species were first studied. Each species had a unique nucleotide sequence, distinguishing it clearly from the other species. A panel of strains from the four main RGM species responsible for human infections, Mycobacterium abscessus, Mycobacterium chelonae, Mycobacterium fortuitum, and Mycobacterium peregrinum, was also studied. There were few sequence differences within each of these species ({\textless}2{\%} of bases were different from the type strain sequence), and they had no effect on species assignment. hsp65 sequencing unambiguously differentiated M. chelonae and M. abscessus, two species difficult to identify by classical methods and 16S rRNA gene sequencing. The devised procedure is a rapid and reliable tool for the identification of RGM species.},
author = {Ringuet, H and Akoua-Koffi, C and Honore, S and Varnerot, A and Vincent, V and Berche, P and Gaillard, J L and Pierre-Audigier, C},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Ringuet et al. - 1999 - hsp65 sequencing for identification of rapidly growing mycobacteria.pdf:pdf},
issn = {0095-1137},
journal = {Journal of clinical microbiology},
month = {mar},
number = {3},
pages = {852--7},
pmid = {9986875},
publisher = {American Society for Microbiology},
title = {hsp65 sequencing for identification of rapidly growing mycobacteria.},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9986875 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC84584},
volume = {37},
year = {1999}
}
@article{Rominski2017,
author = {Rominski, Anna and Roditscheff, Anna and Selchow, Petra and B{\"{o}}ttger, Erik C. and Sander, Peter},
doi = {10.1093/jac/dkw466},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Rominski et al. - 2017 - Intrinsic rifamycin resistance of Mycobacterium abscessus is mediated by ADP-ribosyltransferase MAB{\_}0591.pdf:pdf},
journal = {Journal of Antimicrobial Chemotherapy},
month = {feb},
number = {2},
pages = {376--384},
publisher = {Oxford University Press},
title = {{Intrinsic rifamycin resistance of Mycobacterium abscessus is mediated by ADP-ribosyltransferase MAB{\_}0591}},
url = {https://academic.oup.com/jac/article-lookup/doi/10.1093/jac/dkw466},
volume = {72},
year = {2017}
}
@article{Tortoli2016,
abstract = {The taxonomic position of members of the Mycobacterium abscessus complex has been the subject of intensive investigation and, in some aspects confusion, in recent years as a result of varying approaches to genetic data interpretation. Currently, the former species Mycobacterium massiliense and Mycobacterium bolletii are grouped together as Mycobacterium abscessus subsp. bolletii. They differ greatly, however, as the former M. bolletii has a functional erm(41) gene that confers inducible resistance to macrolides, the primary therapeutic antimicrobials for M. abscessus, while in the former M. massiliense the erm(41) gene is non-functional. Furthermore, previous whole genome studies of the M. abscessus group support the separation of M. bolletii and M. massiliense. To shed further light on the population structure of Mycobacterium abscessus, 43 strains and three genomes retrieved from GenBank were subjected to pairwise comparisons using three computational approaches: verage ucleotide dentity, enome to enome istance and single nucleotide polymorphism analysis. The three methods produced overlapping results, each demonstrating three clusters of strains corresponding to the same number of taxonomic entities. The distances were insufficient to warrant distinction at the species level, but met the criteria for differentiation at the subspecies level. Based on prior erm(41)-related phenotypic data and current genomic data, we conclude that the species M. abscessus encompasses, in adjunct to the presently recognized subspecies M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, a third subspecies for which we suggest the name M. abscessus subsp. massiliense comb. nov. (type strain CCUG 48898T=CIP 108297T=DSM 45103T=KCTC 19086T).},
author = {Tortoli, Enrico and Kohl, Thomas A. and Brown-Elliott, Barbara A. and Trovato, Alberto and Le{\~{a}}o, Sylvia Cardoso and Garcia, Maria Jesus and Vasireddy, Sruthi and Turenne, Christine Y. and Griffith, David E. and Philley, Julie V. and Baldan, Rossella and Campana, Silvia and Cariani, Lisa and Colombo, Carla and Taccetti, Giovanni and Teri, Antonio and Niemann, Stefan and {Wallace Jr.}, Richard J. and Cirillo, Daniela M.},
doi = {10.1099/ijsem.0.001376},
issn = {1466-5026},
journal = {International Journal of Systematic and Evolutionary Microbiology},
month = {nov},
number = {11},
pages = {4471--4479},
pmid = {27499141},
title = {{Emended description of Mycobacterium abscessus, Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. bolletii and designation of Mycobacterium abscessus subsp. massiliense comb. nov.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27499141 http://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001376},
volume = {66},
year = {2016}
}
@article{Zelazny2009,
abstract = {Mycobacterium abscessus is the most common cause of rapidly growing mycobacterial chronic lung disease. Recently, two new M. abscessus-related species, M. massiliense and M. bolletii, have been described. Health care-associated outbreaks have recently been investigated by the use of molecular identification and typing tools; however, very little is known about the natural epidemiology and pathogenicity of M. massiliense or M. bolletii outside of outbreak situations. The differentiation of these two species from M. abscessus is difficult and relies on the sequencing of one or more housekeeping genes. We performed extensive molecular identification and typing of 42 clinical isolates of M. abscessus, M. massiliense, and M. bolletii from patients monitored at the NIH between 1999 and 2007. The corresponding clinical data were also examined. Partial sequencing of rpoB, hsp65, and secA led to the unambiguous identification of 26 M. abscessus isolates, 7 M. massiliense isolates, and 2 M. bolletii isolates. The identification results for seven other isolates were ambiguous and warranted further sequencing and an integrated phylogenetic analysis. Strain relatedness was assessed by repetitive-sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE), which showed the characteristic clonal groups for each species. Five isolates with ambiguous species identities as M. abscessus-M. massiliense by rpoB, hsp65, and secA sequencing clustered as a distinct group by rep-PCR and PFGE together with the M. massiliense type strain. Overall, the clinical manifestations of disease caused by each species were similar. In summary, a multilocus sequencing approach (not just rpoB partial sequencing) is required for division of M. abscessus and closely related species. Molecular typing complements sequence-based identification and provides information on prevalent clones with possible relevant clinical aspects.},
author = {Zelazny, Adrian M and Root, Jeremy M and Shea, Yvonne R and Colombo, Rhonda E and Shamputa, Isdore C and Stock, Frida and Conlan, Sean and McNulty, Steven and Brown-Elliott, Barbara A and Wallace, Richard J and Olivier, Kenneth N and Holland, Steven M and Sampaio, Elizabeth P},
doi = {10.1128/JCM.01688-08},
file = {:Users/michellewuzinski/Library/Application Support/Mendeley Desktop/Downloaded/Zelazny et al. - 2009 - Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and M.pdf:pdf},
issn = {1098-660X},
journal = {Journal of clinical microbiology},
month = {jul},
number = {7},
pages = {1985--95},
pmid = {19420162},
publisher = {American Society for Microbiology},
title = {{Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19420162 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2708513},
volume = {47},
year = {2009}
}
@misc{,
title = {{MLST - Home}},
url = {http://www.mlst.net/},
urldate = {2018-04-12}
}