Ahead of Print -High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks - Volume 20, Number 3—March 2014 - Emerging Infectious Disease journal - CDC

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Ahead of Print -High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks - Volume 20, Number 3—March 2014 - Emerging Infectious Disease journal - CDC

Volume 20, Number 3—March 2014

Research

High-level Relatedness among Mycobacterium abscessussubsp. massiliense Strains from Widely Separated Outbreaks

Article Contents

• Materials and Methods
• Results
• Discussion
• Acknowledgments
• References
• Figure 1
• Figure 2
• Figure 3
• Table 1
• Table 2
• Technical Appendix - 100 KB 
• Suggested Citation

Hervé Tettelin, Rebecca M. Davidson, Sonia Agrawal, Moira L. Aitken, Shamira Shallom, Nabeeh A. Hasan, Michael Strong, Vinicius Calado Nogueira de Moura, Mary Ann De Groote, Rafael S. Duarte, Erin Hine, Sushma Parankush, Qi Su, Sean C. Daugherty, Claire M. Fraser, Barbara A. Brown-Elliott, Richard J. Wallace, Steven M. Holland, Elizabeth P. Sampaio, Kenneth N. Olivier, Mary Jackson, and Adrian M. Zelazny 

Author affiliations: University of Maryland School of Medicine, Baltimore, Maryland, USA (H. Tettelin, S. Agrawal, E. Hine, S. Parankush, Q. Su, S.C. Daugherty, C.M. Fraser); National Jewish Health, Denver, Colorado, USA (R.M. Davidson, N.A. Hasan, M. Strong); University of Washington, Seattle, Washington, USA (M.L. Aitken); National Institutes of Health, Bethesda, Maryland, USA (S. Shallom, S. M. Holland, E.P. Sampaio, K.N. Olivier, A.M. Zelazny);University of Colorado Denver, Aurora, Colorado, USA (N.A. Hasan, M. Strong); Colorado State University, Fort Collins, Colorado, USA (V. Calado Nogueira de Moura, M.A. De Groote, M. Jackson); Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (R.S. Duarte); University of Texas Health Northeast, Tyler, Texas, USA (B.A. Brown-Elliott, R.J. Wallace Jr.)

Suggested citation for this article

Abstract

Three recently sequenced strains isolated from patients during an outbreak ofMycobacterium abscessus subsp. massiliense infections at a cystic fibrosis center in the United States were compared with 6 strains from an outbreak at a cystic fibrosis center in the United Kingdom and worldwide strains. Strains from the 2 cystic fibrosis outbreaks showed high-level relatedness with each other and major-level relatedness with strains that caused soft tissue infections during an epidemic in Brazil. We identified unique single-nucleotide polymorphisms in cystic fibrosis and soft tissue outbreak strains, separate single-nucleotide polymorphisms only in cystic fibrosis outbreak strains, and unique genomic traits for each subset of isolates. Our findings highlight the necessity of identifying M. abscessusto the subspecies level and screening all cystic fibrosis isolates for relatedness to these outbreak strains. We propose 2 diagnostic strategies that use partial sequencing of rpoBand secA1 genes and a multilocus sequence typing protocol.

Nontuberculous mycobacteria (NTM) and, in particular, the Mycobacterium abscessus group are recognized as emerging respiratory pathogens among patients with cystic fibrosis. Reports from the United States, France, and Israel have shown that the M. abscessus group accounts for a major proportion of NTM infections in patients with cystic fibrosis; prevalence rates range from 16% to 48% (1–3).

Previous studies have indicated great diversity within M. abscessus group strains among cystic fibrosis patients, suggesting independent acquisitions of NTM from the environment (2,4). However, suspicion of patient-to-patient transmission arose with the recent report of an outbreak of respiratory infection with M. abscessus subsp. massiliense at a cystic fibrosis center in Seattle, Washington, USA (5). The index case-patient and 4 additional patients all had multidrug-resistant isolates with resistance to amikacin and clarithromycin. All 5 strains were indistinguishable by repetitive unit sequence–based PCR patterns and pulsed-field gel electrophoresis analysis, which led to initiation of whole-genome sequencing. In a separate, recent study, whole-genome sequencing and epidemiologic analysis provided strong support for patient-to-patient transmission in 2 clustered outbreaks of M. abscessus subsp. massiliense at the Papworth Hospital Cystic Fibrosis Centre (Cambridge, UK) (6). Isolates from both clusters showed resistance to clarithromycin, and isolates from one of the clusters also had mutations conferring resistance to amikacin.

The availability of whole-genome sequences from different M. abscessus subsp. massilienseoutbreaks, as well as unrelated strains, provides an unprecedented opportunity for multigenome comparisons. We conducted a genomic study of 3 recently sequenced strains from the Seattle cystic fibrosis outbreak, including the index strain, and compared them with representative strains from the Papworth cystic fibrosis outbreak, as well as with available strains from the United Kingdom, the United States, Brazil, South Korea, France, and Malaysia (Table 1). We found high-level relatedness among strains from the 2 geographically distant outbreaks in Seattle and Papworth. We also identified shared and unique genomic traits for strains from both cystic fibrosis outbreaks and for those from an outbreak of soft tissue infections in Brazil.

Addendum

Recent whole-genome data show deep genetic separation of 3 subspecies, ruling against grouping M. massiliense and M. bolletii under M. abscessus subsp. bolletii.

Dr Tettelin is an associate professor at the Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore. His primary research interests are the use of comparative and functional genomics to understand bacterial diversity and virulence, study host-pathogen interactions, and identify vaccine candidates and drug targets to cure disease.

Acknowledgments

We thank Josephine Bryant, Dorothy Grogono, Julian Parkhill, and Andres Floto for their help and for providing sample identification and accession numbers for the Papworth outbreak isolates.

This study was supported in part by the National Institute of Allergy and Infectious Diseases (NIAID), the National Institutes of Health (NIH), the Department of Health and Human Services (contract no. HHSN272200900009C to C.M.F), and the Intramural Research Program (NIAID, NIH, Department of Health and Human Services). R.M.D, N.A.H, and M.S. were supported by the Amon G. Carter Foundation, the Colorado Bioscience Program, the Eppley Foundation, and the Boettcher Foundation. N.A.H. was supported by NIH Biomedical Informatics training grant 2T15LM009451-06. M.J. was supported by NIH/NIAID grant AI089718. B.B.-E. and R.J.W. were supported by Amon G. Carter Foundation.

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Figures

• Figure 1. . Neighbor-joining phylogenetic tree based on whole-genome multiple alignment of 24Mycobacterium abscessus group genomes. Genomes in Table 1 were aligned by using Mugsy (22), core...
• Figure 2. . Venn diagram of core single-nucleotide polymorphisms (SNPs) shared by outbreak localities. Core segments of the Mugsy (22) alignment of the 20 Mycobacterium abscessussubsp. massiliense genomes (
• Figure 3. . Neighbor-joining phylogenetic tree based on 13-target multilocus sequences types from 20 Mycobacterium abscessus subsp. massiliense genomes. Electronic PCR was performed on the M. abscessus subsp. massiliense genomes listed...

Tables

• Table 1. Twenty-four Mycobacterium abscessus group strain genomes analyzed for genetic relatedness
• Table 2. Detection of rpoB and secA1 SNP signature in the Mycobacterium abscessus group and rapidly growing mycobacteria

Technical Appendix

• Technical Appendix. . Table. Single nucleotide polymorphisms shared and unique for subsets ofMycobacterium abscessus isolates from cystic fibrosis and soft tissue outbreak localities.  100 KB 

Suggested citation for this article: Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, et al. High-level relatedness among Mycobacterium abscessus subsp. massiliensestrains from widely separated outbreaks. Emerg Infect Dis [Internet]. 2014 Mar [date cited].http://dx.doi.org/10.3201/eid2003.131106

DOI: 10.3201/eid2003.131106