Colorado Cystic Fibrosis Research & Development Program

Colorado CF RDP Molecular and Genomics Core

The ability to identify, analyze, and compare isolates within the same subspecies of M. abscessus or MAC is central to understanding the diversity of infectious disease pathogens and identifying the occurrence of possible patient-to-patient transmission within CF Centers. Analysis is also needed to identify the possibility of a shared source of environmental exposure, or to rule-out such an environmental source. Thus, genomic sequencing and phylogenomic analysis of isolates is essential to identify outbreaks and limit their occurrence and spread.

The Molecular Core accepts samples from the NTM Culture, Biorepository, and Coordinating Core. Samples are analyzed using whole genome sequencing (WGS) and comparative phylogenomic methods. These results are communicated back to the NTM Culture, Biorepository, and Coordinating Core, for dissemination to the referring Centers. The primary goal of the Molecular Core is to characterize the diversity and prevalence of NTM species affecting the CF community, and to accurately identify and limit potential instances of patient-to-patient transmission or nosocomial acquisition events in CF Centers. Click here to submit a CF patient NTM sample.

This work is the culmination of contributions from members of the Colorado Cystic Fibrosis Research Develpment Program (CF RDP) and collaborators, including Nabeeh A. Hasan, Rebecca M. Davidson, L. Elaine Epperson, Sara Kammlade, Rachael Rodger, Adrah Levin, Alyssa Sherwood, Scott Sagel, Stacey Martiniano. Charles L. Daley, Max Salfinger, Jerry A. Nick, and Michael Strong.

 

The Colorado Cystic Fibrosis RDP has sequenced hundreds of NTM isolates from CF patients across the United States.

A summary analysis of the first 341 NTM isolates is available in our BioRxiv preprint:

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients.​
Nabeeh A. Hasan*, Rebecca M. Davidson*, L. Elaine Epperson, Sara M. Kammlade, Rachael R. Rodger, Adrah R. Levin, Alyssa Sherwood, Scott D. Sagel, Stacey L. Martiniano. Charles L. Daley, Max Salfinger, Jerry A. Nick, Michael Strong. BioRxiv DOI 10.1101/663559 (2019)

 

First 341 CF NTM Isolates Sequenced, Shown by Adjusted State of Origin.

341 CF NTM Isolates Sequenced by State of Origin

 

Of the first 341 sequenced NTM isolates, 60% are Mycobacterium abscessus species and 38% are Mycobacterium avium complex

Pie chart of NTM Isolates

 

 
 

 

 

References:

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients.
Nabeeh A. Hasan*, Rebecca M. Davidson*, L. Elaine Epperson, Sara M. Kammlade, Rachael R. Rodger, Adrah R. Levin, Alyssa Sherwood, Scott D. Sagel, Stacey L. Martiniano. Charles L. Daley, Max Salfinger, Jerry A. Nick, Michael Strong. bioRxiv doi: 10.1101/663559 (2019) .

Pathogen Surveillance and Characterization using Whole Genome Sequencing: The Colorado Cystic Fibrosis Research and Development Program - Molecular and Genomics Core.

Michael Strong, Nabeeh A. Hasan, L. Elaine Epperson. NTM-TB Insights. September Issue (2016).

Microbiology: Bacterial transmission tactics
Michael Strong and Rebecca M. Davidson. Nature, 543: 495-496 (2017).

Complete Genome Sequence of Mycobacterium chimaera Strain AH16
Nabeeh Hasan, Jennifer Honda, Rebecca Davidson, L. Epperson, Matthew Bankowski, Edward Chan, and Michael Strong. Genome Announcements, 4:e01276-16 (2016).

Environmental Nontuberculous Mycobacteria in the Hawaiian Islands
Jennifer R. Honda, Nabeeh A. Hasan, Rebecca M. Davidson, Myra D. Williams, L. Elaine Epperson, Paul R. Reynolds, Terry R. Smith, Elena Iakhiaeva, Matthew J. Bankowski, Richard J. Wallace Jr., Edward D. Chan, Joseph O. Falkinham III, Michael Strong. PLOS Neglected Tropical Diseases, 10(10): e0005068. (2016).

Notes from the Field: Mycobacterium chimaera Contamination of Heater-Cooler Devices Used in Cardiac Surgery - United States.
Kiran M. Perkins, Adrian Lawsin, Nabeeh A. Hasan, Michael Strong, Alison L. Halpin, Rachael R. Rodger, Heather Moulton-Meissner, Matthew B. Crist, Suzanne Schwartz, Julia Marders, Charles L Daley, Max Salfinger, Joseph F. Perz. Morbidity and Mortality Weekly Report (MMWR) , 65(40);1117-1118 (2016).

Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections
Ettie Lipner, Benjamin J. Garcia, Michael Strong. PLOS ONE. 11: e0146585, (2016).

MycoBASE: expanding the functional annotation coverage of mycobacterial genomes.
Benjamin J. Garcia, Gargi Datta, Rebecca M. Davidson, Michael Strong. BMC Genomics 16:1102, (2015).

Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752.
Nabeeh A. Hasan, Rebecca M. Davidson, Vinicius Calado Nogueira de Moura, Benjamin J. Garcia, Paul R. Reynolds, L. Elaine Epperson, Eveline Farias-Hesson, Mary Ann DeGroote, Mary Jackson, Michael Strong. Genome Announcements, e00536. (2015).

Genome sequencing of Mycobacterium abscessus isolates from patients in the United States and comparisons to globally diverse clinical strains.
Rebecca M. Davidson, Nabeeh A. Hasan, Paul R. Reynolds, Sarah Totten, Benjamin Garcia, Adrah Levin, Preveen Ramamoorthy, Leonid Heifets, Charles L. Daley, and Michael Strong. Journal of Clinical Microbiology, 52:3573-3582 (2014).

High Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Geographically Distant Outbreaks.
Herve 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 Jr., Steven M. Holland, Elizabeth P. Sampaio, Kenneth N. Olivier, Mary Jackson, Adrian M. Zelazny. Emerging Infectious Diseases, 20:3 (2014).

Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains.
Rebecca M. Davidson, Nabeeh A Hasan, Vinicius Calado Nogueira de Moura, Rafael Silva Duarte, Mary Jackson, Michael Strong. Infection, Genetics, and Evolution 20C: 292-297. (2013).

Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.
Rebecca M. Davidson, Paul R. Reynolds, Eveline Farias-Hesson, Rafael Silva Duarte, Mary Jackson, Michael Strong. Genome Announcements 1:4 e00617-13. (2013).

Copyright © 2019 Michael Strong and Sara Kammlade