Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus

PLOS ONE, Dec 2019

Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated.

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Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus

June Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus Byoung-Jun Kim 0 1 Ga-Na Kim 0 1 Bo-Ram Kim 0 1 Tae-Sun Shim 1 Yoon-Hoh Kook 0 1 Bum- Joon Kim 0 1 0 Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, College of Medicine, Seoul National University , Seoul , Korea , 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center , Seoul , Republic of Korea 1 Editor: Seyed Ehtesham Hasnain, Indian Institute of Technology Delhi , INDIA Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work was supported by the National Research Foundation of Korea (NRF), Grant no., NRF-2016R1A2B4011847 (http://ernd.nrf.re.kr). Bo-Ram Kim received a scholarship from the BK21-plus education program provided by the National Research Foundation of Korea. The funders had no role in study design, data collection Introduction Rapidly growing mycobacteria (RGM) are ubiquitous organisms that have gained increasing attention as important human pathogens. Recently, there have been more frequent reports regarding RGM pulmonary infections in many areas including South Korea [ 1, 2 ]. Within and analysis, decision to publish, or preparation of the manuscript. RGM, the Mycobacterium abscessus complex accounts for approximately 65±80% of RGM pulmonary infections [3]. In South Korea, the incidences of M. abscessus lung diseases have also been increasing and account for 70±80% of RGM-induced lung diseases in Korea [4±7]. M. abscessus can cause lung diseases in immunocompetent individuals and shares a number of characteristics with M. tuberculosis, including the ability to induce granulomatous lesions or caseous necrosis [ 8 ]. Together with M. avium, M. abscessus represents the most commonly isolated non-tuberculous mycobacteria (NTM) from cystic fibrosis (CF) patients. Infections with M. abscessus are difficult to treat, due to both natural broad-spectrum resistance and acquired resistance, with disparate antibiotic susceptibility patterns being observed between clinical strains [ 9 ]. The recent advanced taxonomic approach has revealed that the M. abscessus group could be divided into two subspecies, M. abscessus subsp. abscessus (the former species Mycobacterium abscessus) and M. abscessus subsp. bolletii. The M. abscessus subsp. bolletii was proposed to combine the two former species, M. massiliense and M. bolletii [ 10, 11 ]. It was recently reported that M. massiliense can be further subdivided into two genotypes (Type I and Type II) based on hsp65 sequence analysis [12±14]. Hypothesis of lateral gene transfer (LGT) has been acknowledged as a major mechanism by which bacteria can acquire genetic diversity, for their survival under harsh environmental conditions [ 15, 16 ]. Although mycobacteria are assumed to be more recalcitrant to LGT compared to other bacteria, possibly due to the unusual cell wall structure and the relatively scarce exchange of genetic elements such as plasmids and transposable elements between strains within the genus [ 17, 18 ], there is increasing evidence that LGT plays an important role in the mycobacterial evolution from saproph (...truncated)


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Byoung-Jun Kim, Ga-Na Kim, Bo-Ram Kim, Tae-Sun Shim, Yoon-Hoh Kook, Bum-Joon Kim. Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus, PLOS ONE, 2017, Volume 12, Issue 6, DOI: 10.1371/journal.pone.0179237