1
|
Genome sequencing of Mycobacterium abscessus isolates from patients in the united states and comparisons to globally diverse clinical strains. J Clin Microbiol 2014; 52:3573-82. [PMID: 25056330 DOI: 10.1128/jcm.01144-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacterial infections caused by Mycobacterium abscessus are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical M. abscessus isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical M. abscessus isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M. abscessus subsp. abscessus isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977(T). Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical M. abscessus strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen.
Collapse
|
2
|
Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential. Sci Rep 2014; 4:4061. [PMID: 24515248 PMCID: PMC3920477 DOI: 10.1038/srep04061] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/23/2014] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients of wide geographical origin. We found a high proportion of accessory strain-specific genes indicating an open, non-conservative pan-genome structure, and clear evidence of rapid phage-mediated evolution. Although we found fewer virulence factors in Ma compared to M. tuberculosis, our data indicated that Ma evolves rapidly and therefore should be monitored closely for the acquisition of more pathogenic traits. This comparative study provides a better understanding of Ma and forms the basis for future functional work on this important pathogen.
Collapse
|
3
|
Heydari H, Wee WY, Lokanathan N, Hari R, Mohamed Yusoff A, Beh CY, Yazdi AH, Wong GJ, Ngeow YF, Choo SW. MabsBase: a Mycobacterium abscessus genome and annotation database. PLoS One 2013; 8:e62443. [PMID: 23658631 PMCID: PMC3639173 DOI: 10.1371/journal.pone.0062443] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/21/2013] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.
Collapse
Affiliation(s)
- Hamed Heydari
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Software Engineering, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Yee Wee
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Naline Lokanathan
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ranjeev Hari
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Aini Mohamed Yusoff
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ching Yew Beh
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Amir Hessam Yazdi
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Computer System & Technology, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia
| | - Guat Jah Wong
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| |
Collapse
|