1
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Gross JE, Finklea JD, Caceres SM, Poch KR, Hasan NA, Jia F, Epperson LE, Lipner EM, Vang CK, Honda JR, Strand MJ, Nogueira de Moura VC, Daley CL, Strong M, Nick JA. Genomic epidemiology of Mycobacterium abscessus at an adult cystic fibrosis programme reveals low potential for healthcare-associated transmission. ERJ Open Res 2024; 10:00165-2024. [PMID: 38978544 PMCID: PMC11228611 DOI: 10.1183/23120541.00165-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 07/10/2024] Open
Abstract
Rationale Nontuberculous mycobacteria (NTM) has been reported to be transmitted between people with cystic fibrosis (CF) attending CF centres. A suspected Mycobacterium abscessus outbreak was investigated at the University of Texas Southwestern (UTSW) Adult CF Program using a combination of pathogen genomic sequencing and epidemiologic methods. The objectives of the present study were to apply the Healthcare-Associated Links in Transmission of NTM (HALT NTM) study to investigate the occurrence of potential healthcare-associated transmission and/or acquisition of NTM among people with CF infected with genetically similar NTM isolates. Methods Whole-genome sequencing of respiratory M. abscessus isolates from 50 people with CF receiving care at UTSW was performed to identify genetically similar isolates. Epidemiologic investigation, comparison of respiratory and environmental isolates, and home residence watershed mapping were studied. Measurements and main results Whole-genome sequencing analysis demonstrated seven clusters of genetically similar M. abscessus (four ssp. abscessus and three ssp. massiliense). Epidemiologic investigation revealed potential opportunities for healthcare-associated transmission within three of these clusters. Healthcare environmental sampling did not recover M. abscessus, but did recover four human disease-causing species of NTM. No subjects having clustered infections lived in the same home residence watershed. Some subjects were infected with more than one M. abscessus genotype, both within and outside of the dominant circulating clones. Conclusions Healthcare-associated person-to-person transmission of M. abscessus appears to be rare at this centre. However, polyclonal infections of M. abscessus species and subspecies, not originating from the endemic hospital environment, suggest multiple shared modes of acquisition outside the healthcare setting.
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Affiliation(s)
- Jane E Gross
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - James D Finklea
- Department of Medicine, University of Texas Southwestern, Dallas, TX, USA
| | | | - Katie R Poch
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Fan Jia
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - L Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Ettie M Lipner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Charmie K Vang
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Matthew J Strand
- Division of Biostatistics, National Jewish Health, Denver, CO, USA
| | | | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, USA
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2
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Glauser KG, Kelley RE, Leonard WJ, Hendrix J, Petri S, Tong EI, Chan YL, Lipner EM, Dawrs SN, Honda JR. Common Features of Environmental Mycobacterium chelonae from Colorado Using Partial and Whole Genomic Sequence Analyses. Curr Microbiol 2024; 81:69. [PMID: 38238596 PMCID: PMC10796651 DOI: 10.1007/s00284-023-03589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024]
Abstract
Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that cause chronic lung disease in susceptible individuals. While presumed to be ubiquitous in built and natural environments, NTM environmental studies are limited. While environmental sampling campaigns have been performed in geographic areas of high NTM disease burden, NTM species diversity is less defined among areas of lower disease burden like Colorado. In Colorado, metals such as molybdenum have been correlated with increased risk for NTM infection, yet environmental NTM species diversity has not yet been widely studied. Based on prior regression modeling, three areas of predicted high, moderate, and low NTM risk were identified for environmental sampling in Colorado. Ice, plumbing biofilms, and sink tap water samples were collected from publicly accessible freshwater sources. All samples were microbiologically cultured and NTM were identified using partial rpoB gene sequencing. From these samples, areas of moderate risk were more likely to be NTM positive. NTM recovery from ice was more common than recovery from plumbing biofilms or tap water. Overall, nine different NTM species were identified, including clinically important Mycobacterium chelonae. MinION technology was used to whole genome sequence and compare mutational differences between six M. chelonae genomes, representing three environmental isolates from this study and three other M. chelonae isolates from other sources. Drug resistance genes and prophages were common findings among environmentally derived M. chelonae, promoting the need for expanded environmental sampling campaigns to improve our current understanding of NTM species abundance while opening new avenues for improved targeted drug therapies.
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Affiliation(s)
- Kayden G Glauser
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Reagan E Kelley
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - William J Leonard
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Jo Hendrix
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Suzanne Petri
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Eric I Tong
- Aina Informatics Network, 'Iolani School, Honolulu, HI, 96826, USA
| | - Yvonne L Chan
- Aina Informatics Network, 'Iolani School, Honolulu, HI, 96826, USA
| | - Ettie M Lipner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stephanie N Dawrs
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX, 75708, USA.
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3
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Dawrs SN, Virdi R, Norton GJ, Elias T, Hasan NA, Robinson S, Matriz J, Epperson LE, Glickman CM, Beagle S, Crooks JL, Nelson ST, Chan ED, Damby DE, Strong M, Honda JR. Hawaiian Volcanic Ash, an Airborne Fomite for Nontuberculous Mycobacteria. GEOHEALTH 2024; 8:e2023GH000889. [PMID: 38161597 PMCID: PMC10757267 DOI: 10.1029/2023gh000889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that can cause chronic lung disease. Within the U.S., Hawai'i shows the highest prevalence rates of NTM lung infections. Here, we investigated a potential role for active volcanism at the Kīlauea Volcano located on Hawai'i Island in promoting NTM growth and diversity. We recovered NTM that are known to cause lung disease from plumbing biofilms and soils collected from the Kīlauea environment. We also discovered viable Mycobacterium avium, Mycobacterium abscessus, and Mycobacterium intracellulare subsp. chimaera on volcanic ash collected during the 2018 Kīlauea eruption. Analysis of soil samples showed that NTM prevalence is positively associated with bulk content of phosphorus, sulfur, and total organic carbon. In growth assays, we showed that phosphorus utilization is essential for proliferation of Kīlauea-derived NTM, and demonstrate that NTM cultured with volcanic ash adhere to ash surfaces and remain viable. Ambient dust collected on O'ahu concurrent with the 2018 eruption contained abundant fresh volcanic glass, suggestive of inter-island ash transport. Phylogenomic analyses using whole genome sequencing revealed that Kīlauea-derived NTM are genetically similar to respiratory isolates identified on other Hawaiian Islands. Consequently, we posit that volcanic eruptions could redistribute environmental microorganisms over large scales. While additional studies are needed to confirm a direct role of ash in NTM dispersal, our results suggest that volcanic particulates harbor and can redistribute NTM and should therefore be studied as a fomite for these burgeoning, environmentally acquired respiratory infections.
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Affiliation(s)
| | - Ravleen Virdi
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
- Now at Corgenix Medical CorporationBroomfieldCOUSA
| | - Grant J. Norton
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
- Now at University of CaliforniaSan DiegoCAUSA
| | - Tamar Elias
- U.S. Geological SurveyVolcano Science CenterHawaiian Volcano ObservatoryHiloHawai'iUSA
| | - Nabeeh A. Hasan
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
| | - Schuyler Robinson
- Department of Geological SciencesBrigham Young UniversityProvoUTUSA
- Now at GSI EnvironmentalHoustonTXUSA
| | - Jobel Matriz
- Department of MicrobiologyUniversity of Hawai'i ManoaHonoluluHawai'iUSA
- Now at National Institutes of HealthBethesdaMDUSA
| | | | - Cody M. Glickman
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
- Now at EndolytixBeverlyMEUSA
| | - Sean Beagle
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
- Now at Lockheed MartinKing of PrussiaPAUSA
| | - James L. Crooks
- Division of Biostatistics and BioinformaticsNational Jewish HealthDenverCOUSA
- Department of EpidemiologyColorado School of Public HealthAuroraCOUSA
| | | | - Edward D. Chan
- Medicine and Academic AffairsNational Jewish HealthDenverCOUSA
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Department of MedicineRocky Mountain Regional Veterans Affairs Medical CenterAuroraCOUSA
| | - David E. Damby
- U.S. Geological SurveyVolcano Science CenterMenlo ParkCAUSA
| | - Michael Strong
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
| | - Jennifer R. Honda
- Center for GenesEnvironmentand HealthNational Jewish HealthDenverCOUSA
- Department of Cellular and Molecular BiologySchool of MedicineUniversity of Texas Health Science Center at TylerTylerTXUSA
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4
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Gross JE, Caceres S, Poch K, Epperson LE, Hasan NA, Jia F, Calado Nogueira de Moura V, Strand M, Lipner EM, Honda JR, Strong M, Davidson RM, Daley CL, Nick JA. Prospective healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (pHALT NTM) study: Rationale and study design. PLoS One 2023; 18:e0291910. [PMID: 38117792 PMCID: PMC10732400 DOI: 10.1371/journal.pone.0291910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Healthcare-associated acquisition and transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been described, and remains a concern for both patients and providers. This report describes the design of a prospective observational study utilizing the standardized epidemiologic investigation toolkit for healthcare-associated links in transmission of NTM among pwCF. METHODS This is a parallel multi-site study of pwCF who have infections with respiratory NTM isolates and receive healthcare within a common CF Care Center. Participants have a history of one or more NTM positive airway cultures and have been identified as having NTM infections suggestive of a possible outbreak within a single Center, based on NTM isolate genomic analysis. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of shared healthcare-associated source(s) among pwCF in a Center, identification of healthcare environmental dust and water biofilm NTM isolates that are genetically highly-related to respiratory isolates, and identification of common home of residence watersheds among pwCF infected with clustered isolates. Secondary endpoints include characterization of healthcare-associated transmission and/or acquisition modes and settings as well as description of incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. DISCUSSION We hypothesize that genetically highly-related isolates of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from health-care environmental dust and/or water biofilms. This study design utilizes a published, standardized, evidence-based epidemiologic toolkit to facilitate confidential, independent healthcare-associated NTM outbreak investigations within CF Care Centers. This study will facilitate real-time, rapid detection and mitigation of healthcare-associated NTM outbreaks to reduce NTM risk, inform infection prevention and control guidelines, and characterize the prevalence and origin of NTM outbreaks from healthcare-associated patient-to-patient transmission and/or environmental acquisition. This study will systematically characterize human disease causing NTM isolates from serial collection of healthcare environmental dust and water biofilms and define the most common healthcare environmental sources harboring NTM biofilms. TRIAL REGISTRATION ClinicalTrials.gov NCT05686837.
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Affiliation(s)
- Jane E. Gross
- Department of Pediatrics, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Fan Jia
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | | | - Matthew Strand
- Division of Biostatistics, National Jewish Health, Denver, CO, United States of America
| | - Ettie M. Lipner
- Epidemiology and Population Studies Unit, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America
| | - Jennifer R. Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Rebecca M. Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Charles L. Daley
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Jerry A. Nick
- Department of Medicine, National Jewish Health, Denver, CO, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
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5
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Tan CG, Oberlag NM, McGowan AE, Dawrs SN, Chan YL, Strong M, Hasan NA, Honda JR. Genomic and microbiological analyses of iron acquisition pathways among respiratory and environmental nontuberculous mycobacteria from Hawai'i. Front Microbiol 2023; 14:1268963. [PMID: 38029173 PMCID: PMC10667711 DOI: 10.3389/fmicb.2023.1268963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
As environmental opportunistic pathogens, nontuberculous mycobacteria (NTM) can cause severe and difficult to treat pulmonary disease. In the United States, Hawai'i has the highest prevalence of infection. Rapid growing mycobacteria (RGM) such as Mycobacterium abscessus and M. porcinum and the slow growing mycobacteria (SGM) including M. intracellulare subspecies chimaera are common environmental NTM species and subspecies in Hawai'i. Although iron acquisition is an essential process of many microorganisms, iron acquisition via siderophores among the NTM is not well-characterized. In this study, we apply genomic and microbiological methodologies to better understand iron acquisition via siderophores for environmental and respiratory isolates of M. abscessus, M. porcinum, and M. intracellulare subspecies chimaera from Hawai'i. Siderophore synthesis and transport genes, including mycobactin (mbt), mmpL/S, and esx-3 were compared among 47 reference isolates, 29 respiratory isolates, and 23 environmental Hawai'i isolates. Among all reference isolates examined, respiratory isolates showed significantly more siderophore pertinent genes compared to environmental isolates. Among the Hawai'i isolates, RGM M. abscessus and M. porcinum had significantly less esx-3 and mbt genes compared to SGM M. chimaera when stratified by growth classification. However, no significant differences were observed between the species when grown on low iron culture agar or siderophore production by the chrome azurol S (CAS) assay in vitro. These results indicate the complex mechanisms involved in iron sequestration and siderophore activity among diverse NTM species.
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Affiliation(s)
| | - Nicole M. Oberlag
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | | | - Stephanie N. Dawrs
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | | | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | - Jennifer R. Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
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6
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Mann BC, Jacobson KR, Ghebrekristos Y, Warren RM, Farhat MR. Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples. J Clin Microbiol 2023; 61:e0038223. [PMID: 37728909 PMCID: PMC10595060 DOI: 10.1128/jcm.00382-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023] Open
Abstract
Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
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Affiliation(s)
- B. C. Mann
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - K. R. Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Y. Ghebrekristos
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Greenpoint Tuberculosis Laboratory, Cape Town, South Africa
| | - R. M. Warren
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M. R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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7
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Hendrix J, Epperson LE, Tong EI, Chan YL, Hasan NA, Dawrs SN, Norton GJ, Virdi R, Crooks JL, Chan ED, Honda JR, Strong M. Complete genome assembly of Hawai'i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria. PLoS One 2023; 18:e0291072. [PMID: 37703253 PMCID: PMC10499228 DOI: 10.1371/journal.pone.0291072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai'i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai'i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai'i, community scientists of Hawai'i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O'ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai'i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai'i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities.
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Affiliation(s)
- Jo Hendrix
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
| | - L. Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Eric I. Tong
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Yvonne L. Chan
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Stephanie N. Dawrs
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Grant J. Norton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Ravleen Virdi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - James L. Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO, United States of America
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States of America
| | - Edward D. Chan
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, CO, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States of America
| | - Jennifer R. Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler, Tyler, TX, United States of America
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
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8
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Lu D, Abudouaini M, Kerimu M, Leng Q, Wu H, Aynazar A, Zhong Z. Clinical Evaluation of Metagenomic Next-Generation Sequencing and Identification of Risk Factors in Patients with Severe Community-Acquired Pneumonia. Infect Drug Resist 2023; 16:5135-5147. [PMID: 37581165 PMCID: PMC10423567 DOI: 10.2147/idr.s421721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/29/2023] [Indexed: 08/16/2023] Open
Abstract
Purpose Severe community-acquired pneumonia (SCAP) is the leading cause of death among patients with infectious diseases worldwide. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) through detecting pathogens in bronchoalveolar lavage fluid (BALF) and identifying risk factors for recovery in SCAP patients. Patients and Methods This prospective study recruited 158 SCAP patients admitted to respiratory intensive care unit that were randomly divided into control and study groups, with receiving conventional tests and the same conventional tests plus mNGS, respectively. The diagnostic efficiency of mNGS was evaluated by comparing with conventional tests. Furthermore, univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for recovery in SCAP patients, and a nomogram prediction model was established based on these factors. Results Within the study group, the pathogen detection rate was significantly higher with mNGS than that with conventional tests (84.81% vs 45.57%, P < 0.001), with a positive coincidence rate of 94.44%. Acinetobacter baumannii (21.52%, 17/79), Candida albicans (17.72%, 14/79), and Klebsiella pneumonia (15.19%, 12/79) were the top three common pathogens detected by mNGS. Of note, the improvement rate of patients in the study group was significantly higher than that in the control group. The further analysis revealed that the increased levels of interleukin-6, blood urea nitrogen, procalcitonin, the longer length of hospital stay, and bacterial infection were independent risk factors for recovery of SCAP patients, while mNGS detection status was a protective factor. The predictive model showed a good performance for the modeling and validation sets. Conclusion Early mNGS exhibited a superior diagnostic efficiency to conventional tests in SCAP patients, which can reduce the risk of death in SCAP patients. Moreover, the clinical factors could also be used for the management and prognosis prediction of SCAP patients.
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Affiliation(s)
- Dongmei Lu
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
| | - Maidina Abudouaini
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
- Department of Public Health, Xinjiang Medical University, Urumqi, People’s Republic of China
| | - Munire Kerimu
- Department of Public Health, Xinjiang Medical University, Urumqi, People’s Republic of China
| | - Qiuping Leng
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
| | - Hongtao Wu
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
| | - Amar Aynazar
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
- Department of Public Health, Xinjiang Medical University, Urumqi, People’s Republic of China
| | - Zhiwei Zhong
- Center of Pulmonary and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, People’s Republic of China
- Department of Public Health, Xinjiang Medical University, Urumqi, People’s Republic of China
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Mvubu NE, Salig A, Moopanar K, Nyide A, Govender D, Mankayi E. A quick, easy and efficient protocol for extracting high-quality RNA from Mycobacterium tuberculosis using a spin column commercial kit. BMC Res Notes 2023; 16:145. [PMID: 37443138 DOI: 10.1186/s13104-023-06424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
RNA extraction from Mycobacterium tuberculosis has been a historically challenging task for researchers due to the thick lipids associated with the cell wall of this "notorious" pathogen that is responsible for Tuberculosis (TB) outbreaks. Several studies have successfully extracted RNA from M. tuberculosis using a Trizol reagent combined with organic solvents. Recently, our laboratory has successfully extracted high quality total RNA using a commercial kit from clinical strains belonging to F15/LAM4/KZN, Beijing and F11 strain families and H37Rv laboratory strain by exploiting high speed homogenizer for cell lysis and spin columns for RNA purification. The quality and integrity of the extracted RNA was analyzed and confirmed through the Nanodrop, Bioanalyzer and RNA 3-(N-morpholino) propanesulfonic acid (MOPS) gel electrophoresis. Furthermore, to confirm the integrity of small RNA (sRNA) molecules due to their vulnerability to degradation, the RNA samples were converted to cDNA and sRNAs were amplified and confirmed through PCR. This detailed RNA extraction protocol proposes to carve a new path into TB transcriptome research without the use of organic solvent for downstream purification steps while yielding high quality RNA that can be used to understand M. tuberculosis transcriptome regulation.
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Affiliation(s)
- N E Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, Medical School, University of KwaZulu Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - A Salig
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - K Moopanar
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - Asg Nyide
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - D Govender
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - E Mankayi
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
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10
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Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P. Characterization of Mycobacterium salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection. Front Microbiol 2022; 13:992610. [PMID: 36299734 PMCID: PMC9589434 DOI: 10.3389/fmicb.2022.992610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water in almost every part of the world. While usually non-pathogenic, they can cause acute respiratory and cutaneous infections under certain circumstances or in patients with underlying medical conditions. Contrary to members of the Mycobacterium tuberculosis complex, documented human-to-human transmissions of NTM have been rarely reported and most cases result from direct environmental exposure. Here we describe the identification of a new NTM species isolated from a hand laceration of a New York State patient after a fall. This new NTM forms rough, orange pigmented colonies and is naturally resistant to doxycycline and tobramycin. Whole genome analysis reveal no close relatives present in public databases, and our findings are in accordance with the recognition of a new taxonomic species of NTM. We propose the name Mycobacterium salfingeri sp. nov. for this new NTM representative. The type strain is 20-157661T (DSM = 113368T, BCCM = ITM 501207T).
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11
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Nick JA, Dedrick RM, Gray AL, Vladar EK, Smith BE, Freeman KG, Malcolm KC, Epperson LE, Hasan NA, Hendrix J, Callahan K, Walton K, Vestal B, Wheeler E, Rysavy NM, Poch K, Caceres S, Lovell VK, Hisert KB, de Moura VC, Chatterjee D, De P, Weakly N, Martiniano SL, Lynch DA, Daley CL, Strong M, Jia F, Hatfull GF, Davidson RM. Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection. Cell 2022; 185:1860-1874.e12. [PMID: 35568033 PMCID: PMC9840467 DOI: 10.1016/j.cell.2022.04.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 04/14/2022] [Indexed: 01/17/2023]
Abstract
Two mycobacteriophages were administered intravenously to a male with treatment-refractory Mycobacterium abscessus pulmonary infection and severe cystic fibrosis lung disease. The phages were engineered to enhance their capacity to lyse M. abscessus and were selected specifically as the most effective against the subject's bacterial isolate. In the setting of compassionate use, the evidence of phage-induced lysis was observed using molecular and metabolic assays combined with clinical assessments. M. abscessus isolates pre and post-phage treatment demonstrated genetic stability, with a general decline in diversity and no increased resistance to phage or antibiotics. The anti-phage neutralizing antibody titers to one phage increased with time but did not prevent clinical improvement throughout the course of treatment. The subject received lung transplantation on day 379, and systematic culturing of the explanted lung did not detect M. abscessus. This study describes the course and associated markers of a successful phage treatment of M. abscessus in advanced lung disease.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alice L Gray
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eszter K Vladar
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Bailey E Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Jo Hendrix
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kimberly Callahan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Kendra Walton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Brian Vestal
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Emily Wheeler
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Natalia Weakly
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO 80206, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
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12
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Gross JE, Caceres S, Poch K, Hasan NA, Jia F, Epperson LE, Lipner E, Vang C, Honda JR, Strand M, Calado Nogueira de Moura V, Daley CL, Strong M, Davidson RM, Nick JA. Investigating Nontuberculous Mycobacteria Transmission at the Colorado Adult Cystic Fibrosis Program. Am J Respir Crit Care Med 2022; 205:1064-1074. [PMID: 35085056 PMCID: PMC9851486 DOI: 10.1164/rccm.202108-1911oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rationale: Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been investigated at CF centers worldwide, with conflicting conclusions. We investigated transmission at the Colorado Adult CF Program. Objectives: To systematically investigate healthcare-associated transmission and/or acquisition of NTM to determine similarity among respiratory and environmental isolates, and to compare home residence watershed mapping among pwCF having genetically similar NTM isolates. Methods: Whole-genome sequencing of NTM isolates from 80 pwCF was conducted to identify genetically similar isolate clusters (⩽30 SNP differences). Epidemiology, comparison of respiratory and environmental isolates, and home residence watershed mapping were analyzed. Measurements and Main Results: Whole-genome sequencing analysis revealed 11 clusters of NTM [6 Mycobacterium abscessus subspecies (ssp.) abscessus, 1 M. abscessus ssp. massiliense, 2 Mycobacterium avium, and 2 Mycobacterium intracellulare] among pwCF. Epidemiologic investigation demonstrated opportunities for healthcare-associated transmission in two M. abscessus and two M. avium clusters. Respiratory and healthcare environmental isolate comparisons revealed no genetic similarity. Individuals comprising one M. abscessus cluster, with no plausible healthcare-associated transmission, resided in the same watershed. Conclusions: This study suggests healthcare-associated transmission of M. abscessus is rare and includes a report of potential healthcare-associated transmission of M. avium among pwCF. One M. abscessus cluster possibly had common acquisition arising from residing in the same watershed. The presence of genetically similar isolates is insufficient to demonstrate healthcare-associated NTM transmission. Standardizing epidemiologic investigation, combined with environmental sampling and watershed analysis, will improve understanding of the frequency and nature of healthcare-associated NTM transmission among pwCF.
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Affiliation(s)
| | | | | | | | - Fan Jia
- Center for Genes, Environment and Health
| | | | | | | | | | | | | | - Charles L. Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado
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13
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Soil Properties and Moisture Synergistically Influence Nontuberculous Mycobacterial Prevalence in Natural Environments of Hawai'i. Appl Environ Microbiol 2022; 88:e0001822. [PMID: 35435715 DOI: 10.1128/aem.00018-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that cause chronic pulmonary disease (PD). NTM infections are thought to be acquired from the environment; however, the basal environmental factors that drive and sustain NTM prevalence are not well understood. The highest prevalence of NTM PD cases in the United States is reported from Hawai'i, which is unique in its climate and soil composition, providing an opportunity to investigate the environmental drivers of NTM prevalence. We used microbiological sampling and spatial logistic regression complemented with fine-scale soil mineralogy to model the probability of NTM presence across the natural landscape of Hawai'i. Over 7 years, we collected and microbiologically cultured 771 samples from 422 geographic sites in natural areas across the Hawaiian Islands for the presence of NTM. NTM were detected in 210 of these samples (27%), with Mycobacterium abscessus being the most frequently isolated species. The probability of NTM presence was highest in expansive soils (those that swell with water) with a high water balance (>1-m difference between rainfall and evapotranspiration) and rich in Fe-oxides/hydroxides. We observed a positive association between NTM presence and iron in wet soils, supporting past studies, but no such association in dry soils. High soil-water balance may facilitate underground movement of NTM into the aquifer system, potentially compounded by expansive capabilities allowing crack formation under drought conditions, representing further possible avenues for aquifer infiltration. These results suggest both precipitation and soil properties are mechanisms by which surface NTM may reach the human water supply. IMPORTANCE Nontuberculous mycobacteria (NTM) are ubiquitous in the environment, being found commonly in soils and natural bodies of freshwater. However, little is known about the environmental niches of NTM and how they relate to NTM prevalence in homes and other human-dominated areas. To characterize NTM environmental associations, we collected and cultured 771 samples from 422 geographic sites in natural areas across Hawai'i, the U.S. state with the highest prevalence of NTM pulmonary disease. We show that the environmental niches of NTM are most associated with highly expansive, moist soils containing high levels of iron oxides/hydroxides. Understanding the factors associated with NTM presence in the natural environment will be crucial for identifying potential mechanisms and risk factors associated with NTM infiltration into water supplies, which are ultimately piped into homes where most exposure risk is thought to occur.
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14
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Healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (HALT NTM) study: Rationale and study design. PLoS One 2021; 16:e0261628. [PMID: 34929010 PMCID: PMC8687591 DOI: 10.1371/journal.pone.0261628] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Background Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been reported and is of increasing concern. No standardized epidemiologic investigation tool has been published for healthcare-associated NTM outbreak investigations. This report describes the design of an ongoing observational study to standardize the approach to NTM outbreak investigation among pwCF. Methods This is a parallel multi-site study of pwCF within a single Center who have respiratory NTM isolates identified as being highly-similar. Participants have a history of positive airway cultures for NTM, receive care within a single Center, and have been identified as part of a possible outbreak based on genomic analysis of NTM isolates. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of a shared healthcare-associated encounter(s) among patients in a Center and identification of environmental isolates that are genetically highly-similar to respiratory isolates recovered from pwCF. Secondary endpoints include characterization of potential transmission modes and settings, as well as incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. Discussion We hypothesize that genetically highly-similar strains of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from environmental sources. This novel study design will establish a standardized, evidence-based epidemiologic investigation tool for healthcare-associated NTM outbreak investigation within CF Care Centers, will broaden the scope of independent outbreak investigations and demonstrate the frequency and nature of healthcare-associated NTM transmission in CF Care Centers nationwide. Furthermore, it will provide valuable insights into modeling risk factors associated with healthcare-associated NTM transmission and better inform future infection prevention and control guidelines. This study will systematically characterize clinically-relevant NTM isolates of CF healthcare environmental dust and water biofilms and set the stage to describe the most common environmental sources within the healthcare setting harboring clinically-relevant NTM isolates. Trial registration ClinicalTrials.gov NCT04024423. Date of registry July 18, 2019.
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15
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Vang CK, Dawrs SN, Oberlag NM, Gilmore AE, Hasan NA, Honda JR. Comparative survival of environmental and clinical Mycobacterium abscessus isolates in a variety of diverse host cells. J Appl Microbiol 2021; 132:3302-3314. [PMID: 34919308 PMCID: PMC9306708 DOI: 10.1111/jam.15416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/12/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
Aims Mycobacterium abscessus subsp. abscessus (MABS) is an emerging, opportunistic pathogen found globally in freshwater biofilms and soil. Typically, isolates are treated as a uniform group of organisms and very little is known about their comparative survival in healthy host cells. We posit that environmentally‐ and clinically derived isolates, show differential infectivity in immune cells and resistance to innate defenses. Methods and Results Six MABS isolates were tested including three water biofilm/soil and three sputum‐derived isolates. A clinical MABS type strain and an environmental isolate of Arthrobacter were also included. MABS counts were significantly higher compared to Arthrobacter after co‐culture with Acanthamoeba lenticulata, BEAS‐2B epithelial cells, alveolar macrophages and the THP‐1 macrophage cell line. A rough sputum‐derived MABS isolate emerged as an isolate with higher virulence compared to others tested, as both a pellicle and cord former, survivor in the human cell models tested, inducer of high and prolonged production of pro‐inflammatory cytokines, and the capacity to evade LL‐37. Conclusions Findings support intraspecies variation between MABS isolates. Significance and Impact of the Study These data indicate subversion of host immune defenses by environmental and clinical MABS isolates is nuanced and maybe isolate dependent, providing new information regarding the pathogenesis of NTM infections.
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Affiliation(s)
- Charmie K Vang
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Stephanie N Dawrs
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Nicole M Oberlag
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Anah E Gilmore
- Professional Biomedical Science Program, University of Denver, Denver, Colorado, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
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16
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Davidson RM, Hasan NA, Epperson LE, Benoit JB, Kammlade SM, Levin AR, Calado de Moura V, Hunkins J, Weakly N, Beagle S, Sagel SD, Martiniano SL, Salfinger M, Daley CL, Nick JA, Strong M. Population Genomics of Mycobacterium abscessus from U.S. Cystic Fibrosis Care Centers. Ann Am Thorac Soc 2021; 18:1960-1969. [PMID: 33856965 PMCID: PMC8641822 DOI: 10.1513/annalsats.202009-1214oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/14/2021] [Indexed: 12/25/2022] Open
Abstract
Rationale:Mycobacterium abscessus is a significant threat to individuals with cystic fibrosis (CF) because of innate drug resistance and potential transmission between patients. Recent studies described global dominant circulating clones of M. abscessus, but detailed genomic surveys have not yet been described for the United States. Objectives: We examined the genetic diversity of respiratory M. abscessus isolates from U.S. patients with CF and evaluated the potential for transmission events within CF Care Centers. Methods: Whole-genome sequencing was performed on 558 M. abscessus isolates from 266 patients with CF attending 48 CF Care Centers in 28 U.S. states as part of a nationwide surveillance program. U.S. isolates were also compared with 64 isolate genomes from 13 previous studies to evaluate the prevalence of recently described dominant circulating clones. Results: More than half of study patients with CF and M. abscessus had isolates within four dominant clones; two clones of M. abscessus subspecies (subsp.) abscessus (MAB) and two clones of M. abscessus subsp. massiliense (MMAS). Acquired drug resistance mutations for aminoglycosides and macrolides were rare in the isolate population, and they were not significantly enriched in dominant clones compared with unclustered isolates. For a subset of 55 patients, there was no relationship between dominant clones and diagnosis of active lung disease (P = 1.0). Twenty-nine clusters of genetically similar MAB isolates and eight clusters of genetically similar MMAS isolates were identified. Overall, 28 of 204 (14%) patients with MAB and 15 of 64 (23%) patients with MMAS had genetically isolates similar to those of at least one other patient at the same CF Care Center. Genetically similar isolates were also found between 60 of 204 (29%) patients with MAB and 19 of 64 (30%) patients with MMAS from different geographic locations. Conclusions: Our study reveals the predominant genotypes of M. abscessus and frequency of shared strains between patients in U.S. CF Care Centers. Integrated epidemiological and environmental studies would help to explain the widespread presence of dominant clones in the United States, including the potential for broad distribution in the environment. Single site studies using systematic, evidence-based approaches will be needed to establish the contributions of health care-associated transmission versus shared environmental exposures.
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Affiliation(s)
| | | | | | | | | | - Adrah R. Levin
- Department of Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Scott D. Sagel
- Department of Pediatrics, Children’s Hospital Colorado–School of Medicine, University of Colorado, Aurora, Colorado; and
| | - Stacey L. Martiniano
- Department of Pediatrics, Children’s Hospital Colorado–School of Medicine, University of Colorado, Aurora, Colorado; and
| | - Max Salfinger
- College of Public Health and
- Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Charles L. Daley
- Department of Medicine, National Jewish Health, Denver, Colorado
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
| | - Jerry A. Nick
- Department of Medicine, National Jewish Health, Denver, Colorado
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
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17
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Genomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission. J Clin Microbiol 2021; 60:e0154721. [PMID: 34705540 DOI: 10.1128/jcm.01547-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus (MABC). Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental MABC isolates. In this study, we retrospectively analyzed the core and accessory genomes of 26 M. abscessus subsp. abscessus (MAA) isolates collected over seven years. Clinical isolates (n=22) were obtained from a large hospital-associated outbreak of MAA, the outbreak hospital before or after the outbreak, a neighboring hospital, and two outside laboratories. Environmental MAA isolates (n=4) were obtained from outbreak hospital water outlets. Phylogenomic analysis of study isolates revealed three clades with pairwise genetic distances ranging from 0-135 single nucleotide polymorphisms (SNPs). Compared to a reference environmental outbreak isolate, all seven clinical outbreak isolates and the remaining three environmental isolates had highly similar core and accessory genomes, differing by up to 7 SNPs and a median of 1.6% accessory genes, respectively. Although genomic comparisons of 15 non-outbreak clinical isolates revealed greater heterogeneity, five (33%) isolates had fewer than 20 SNPs compared to the reference environmental isolate, including two unrelated outside laboratory isolates with less than 4% accessory genome variation. Detailed genomic comparisons confirmed environmental acquisition of outbreak isolates of MAA. SNP distances alone, however, did not clearly differentiate the mechanism of acquisition of outbreak versus non-outbreak isolates. We conclude that successful investigation of MAA clusters requires molecular and epidemiologic components, ideally complemented by environmental sampling.
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18
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Hasan NA, Davidson RM, Epperson LE, Kammlade SM, Beagle S, Levin AR, de Moura VC, Hunkins JJ, Weakly N, Sagel SD, Martiniano SL, Salfinger M, Daley CL, Nick JA, Strong M. Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Care Centers, United States. Emerg Infect Dis 2021; 27:2836-2846. [PMID: 34670648 PMCID: PMC8544995 DOI: 10.3201/eid2711.210124] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium avium complex (MAC) species constitute most mycobacteria infections in persons with cystic fibrosis (CF) in the United States, but little is known about their genomic diversity or transmission. During 2016–2020, we performed whole-genome sequencing on 364 MAC isolates from 186 persons with CF from 42 cystic fibrosis care centers (CFCCs) across 23 states. We compared isolate genomes to identify instances of shared strains between persons with CF. Among persons with multiple isolates sequenced, 15/56 (27%) had >1 MAC strain type. Genomic comparisons revealed 18 clusters of highly similar isolates; 8 of these clusters had patients who shared CFCCs, which included 27/186 (15%) persons with CF. We provide genomic evidence of highly similar MAC strains shared among patients at the same CFCCs. Polyclonal infections and high genetic similarity between MAC isolates are consistent with multiple modes of acquisition for persons with CF to acquire MAC infections.
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19
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Dow CT. Warm, Sweetened Milk at the Twilight of Immunity - Alzheimer's Disease - Inflammaging, Insulin Resistance, M. paratuberculosis and Immunosenescence. Front Immunol 2021; 12:714179. [PMID: 34421917 PMCID: PMC8375433 DOI: 10.3389/fimmu.2021.714179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/09/2021] [Indexed: 01/22/2023] Open
Abstract
This article prosecutes a case against the zoonotic pathogen Mycobacterium avium ss. paratuberculosis (MAP) as a precipitant of Alzheimer’s disease (AD). Like the other major neurodegenerative diseases AD is, at its core, a proteinopathy. Aggregated extracellular amyloid protein plaques and intracellular tau protein tangles are the recognized protein pathologies of AD. Autophagy is the cellular housekeeping process that manages protein quality control and recycling, cellular metabolism, and pathogen elimination. Impaired autophagy and cerebral insulin resistance are invariant features of AD. With a backdrop of age-related low-grade inflammation (inflammaging) and heightened immune risk (immunosenescence), infection with MAP subverts glucose metabolism and further exhausts an already exhausted autophagic capacity. Increasingly, a variety of agents have been found to favorably impact AD; they are agents that promote autophagy and reduce insulin resistance. The potpourri of these therapeutic agents: mTOR inhibitors, SIRT1 activators and vaccines are seemingly random until one recognizes that all these agents also suppress intracellular mycobacterial infection. The zoonotic mycobacterial MAP causes a common fatal enteritis in ruminant animals. Humans are exposed to MAP from contaminated food products and from the environment. The enteritis in animals is called paratuberculosis or Johne’s disease; in humans, it is the putative cause of Crohn’s disease. Beyond Crohn’s, MAP is associated with an increasing number of inflammatory and autoimmune diseases: sarcoidosis, Blau syndrome, autoimmune diabetes, autoimmune thyroiditis, multiple sclerosis, and rheumatoid arthritis. Moreover, MAP has been associated with Parkinson’s disease. India is one county that has extensively studied the human bio-load of MAP; 30% of more than 28,000 tested individuals were found to harbor, or to have harbored, MAP. This article asserts an unfolding realization that MAP infection of humans 1) is widespread in its presence, 2) is wide-ranging in its zoonosis and 3) provides a plausible link connecting MAP to AD.
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Affiliation(s)
- Coad Thomas Dow
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
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20
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Davidson RM, Benoit JB, Kammlade SM, Hasan NA, Epperson LE, Smith T, Vasireddy S, Brown-Elliott BA, Nick JA, Olivier KN, Zelazny AM, Daley CL, Strong M, Wallace RJ. Genomic characterization of sporadic isolates of the dominant clone of Mycobacterium abscessus subspecies massiliense. Sci Rep 2021; 11:15336. [PMID: 34321532 PMCID: PMC8319421 DOI: 10.1038/s41598-021-94789-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Recent studies have characterized a dominant clone (Clone 1) of Mycobacterium abscessus subspecies massiliense (M. massiliense) associated with high prevalence in cystic fibrosis (CF) patients, pulmonary outbreaks in the United States (US) and United Kingdom (UK), and a Brazilian epidemic of skin infections. The prevalence of Clone 1 in non-CF patients in the US and the relationship of sporadic US isolates to outbreak clones are not known. We surveyed a reference US Mycobacteria Laboratory and a US biorepository of CF-associated Mycobacteria isolates for Clone 1. We then compared genomic variation and antimicrobial resistance (AMR) mutations between sporadic non-CF, CF, and outbreak Clone 1 isolates. Among reference lab samples, 57/147 (39%) of patients with M. massiliense had Clone 1, including pulmonary and extrapulmonary infections, compared to 11/64 (17%) in the CF isolate biorepository. Core and pan genome analyses revealed that outbreak isolates had similar numbers of single nucleotide polymorphisms (SNPs) and accessory genes as sporadic US Clone 1 isolates. However, pulmonary outbreak isolates were more likely to have AMR mutations compared to sporadic isolates. Clone 1 isolates are present among non-CF and CF patients across the US, but additional studies will be needed to resolve potential routes of transmission and spread.
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Affiliation(s)
- Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA.
| | - Jeanne B Benoit
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Sara M Kammlade
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - L Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Terry Smith
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Sruthi Vasireddy
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Barbara A Brown-Elliott
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kenneth N Olivier
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Richard J Wallace
- Department of Microbiology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
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21
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Nelson ST, Robinson S, Rey K, Brown L, Jones N, Dawrs SN, Virdi R, Norton GJ, Epperson LE, Hasan NA, Chan ED, Strong M, Honda JR. Exposure Pathways of Nontuberculous Mycobacteria Through Soil, Streams, and Groundwater, Hawai'i, USA. GEOHEALTH 2021; 5:e2020GH000350. [PMID: 33855248 PMCID: PMC8025848 DOI: 10.1029/2020gh000350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/25/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Although uncommon, nontuberculous mycobacterial (NTM) pulmonary infection in the Hawaiian Islands has a relatively high incidence and mortality compared to the mainland U.S. As a result, this study examines the possible geological and hydrological pathways by which NTM patients may become infected, including the environmental conditions that may favor growth and transport. Previously suggested infection routes include the inhalation of NTM attached to micro-droplets from infected home plumbing systems and aerosolized dust from garden soil. In this study, we evaluate the possible routes NTM may take from riparian environments, into groundwater, into public water supplies and then into homes. Because NTM are notoriously hydrophobic and prone to attach to surfaces, mineralogy, and surface chemistry of suspended sediment in streams, soils, and rock scrapings suggest that NTM may especially attach to Fe-oxides/hydroxides, and be transported as particles from losing streams to the aquifer on time-scales of minutes to days. Within the aquifer, flow models indicate that water may be drawn into production wells on time scales (months) that permit NTM to survive and enter domestic water supplies. These processes depend on the presence of interconnected fracture networks with sufficient aperture to preclude complete autofiltration. The common occurrence of NTM in and around streams, in addition to wells, implies that the natural and built environments are capable of introducing a source of NTM into domestic water supplies via groundwater withdrawals. This may produce a persistent source of NTM infection to individuals through the presence of NTM-laden biofilms in home plumbing.
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Affiliation(s)
| | | | - Kevin Rey
- Department of Geological SciencesBrigham Young UniversityProvoUTUSA
| | - Leeza Brown
- Department of Geological SciencesBrigham Young UniversityProvoUTUSA
| | - Norm Jones
- Department of Civil and Environmental EngineeringBrigham Young UniversityProvoUTUSA
| | - Stephanie N. Dawrs
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - Ravleen Virdi
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - Grant J. Norton
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - L. Elaine Epperson
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - Nabeeh A. Hasan
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - Edward D. Chan
- Medicine and Academic AffairsNational Jewish HealthDenverCOUSA
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Department of MedicineRocky Mountain Regional Denver Veterans Affairs Medical CenterAuroraCOUSA
| | - Michael Strong
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
| | - Jennifer R. Honda
- Center for Genes, Environment, and HealthNational Jewish HealthDenverCOUSA
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22
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Measurable genomic changes in Mycobacterium avium subsp. hominissuis after long-term adaptation in Acanthamoeba lenticulata and reduced persistence in macrophages. J Bacteriol 2021; 203:JB.00257-20. [PMID: 33431432 PMCID: PMC8095452 DOI: 10.1128/jb.00257-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Free-living amoebae are ubiquitous in aquatic environments and act as environmental reservoirs for nontuberculous mycobacteria. Mycobacterium avium subsp. hominissuis recovered from Acanthamoeba has been demonstrated to be more virulent in both human and murine models. Here, we investigate the persistence of M. avium subsp. hominissuis after short-term (2 weeks) and long-term (42 weeks) co-culture in Acanthamoeba lenticulata We hypothesize that A. lenticulata-adapted M. avium subsp. hominissuis demonstrate phenotypic and genomic changes facilitating intracellular persistence in naïve Acanthamoeba and human macrophages. M. avium subsp. hominissuis CFU in co-culture with A. lenticulata were recorded every 2 weeks up to 60 weeks. While A. lenticulata-associated M. avium subsp. hominissuis CFU did not significantly change across 60 weeks of co-culture, longer adaptation time in amoebae reduced colony size. Isolates recovered after 2 or 42 weeks of amoebae co-culture were referred as "early-adapted" and "late-adapted" M. avium subsp. hominissuis, respectively. Whole genome sequencing was performed on amoebae-adapted isolates with pan-genome comparisons to the original M. avium subsp. hominissuis isolate. Next, amoebae-adapted isolates were assessed for their persistence in A. lenticulata, A. castellanii, and human THP-1 macrophages. Multiplex cytokine/chemokine analyses were conducted on THP-1 culture supernatants. Compared to the original isolate, counts of late-adapted M. avium subsp. hominissuis were reduced in Acanthamoeba and contrary to expectations, lower counts were also observed in THP-1 macrophages with concomitant decrease in TNFa, IL-6, and MIP-1b suggesting that host adaptation may influence the inflammatory properties of M. avium IMPORTANCE Short-term interaction between Acanthamoeba and M. avium has been demonstrated to increase infectivity in human and murine models of infection, establishing the paradigm that amoebae "train" M. avium in the environment by selecting for phenotypes capable of enduring in human cells. We investigate this phenomenon further by determining the consequence of long-term amoebae adaptation on M. avium subsp. hominissuis persistence in host cells. We monitored genomic changes across long-term Acanthamoeba co-culture and report significant changes to the M. avium subsp. hominissuis genome in response to amoebae-adaptation and reduced colony size. Furthermore, we examined isolates co-cultured with A. lenticulata for 2 or 42 weeks and provide biological evidence that long-term co-culture in amoebae reduces M. avium persistence in human macrophages.
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23
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Vargas R, Freschi L, Marin M, Epperson LE, Smith M, Oussenko I, Durbin D, Strong M, Salfinger M, Farhat MR. In-host population dynamics of Mycobacterium tuberculosis complex during active disease. eLife 2021; 10:61805. [PMID: 33522489 PMCID: PMC7884073 DOI: 10.7554/elife.61805] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of death globally. Understanding the population dynamics of TB’s causative agent Mycobacterium tuberculosis complex (Mtbc) in-host is vital for understanding the efficacy of antibiotic treatment. We use longitudinally collected clinical Mtbc isolates that underwent Whole-Genome Sequencing from the sputa of 200 patients to investigate Mtbc diversity during the course of active TB disease after excluding 107 cases suspected of reinfection, mixed infection or contamination. Of the 178/200 patients with persistent clonal infection >2 months, 27 developed new resistance mutations between sampling with 20/27 occurring in patients with pre-existing resistance. Low abundance resistance variants at a purity of ≥19% in the first isolate predict fixation in the subsequent sample. We identify significant in-host variation in 27 genes, including antibiotic resistance genes, metabolic genes and genes known to modulate host innate immunity and confirm several to be under positive selection by assessing phylogenetic convergence across a genetically diverse sample of 20,352 isolates.
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Affiliation(s)
- Roger Vargas
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Department of Biomedical Informatics, Harvard Medical School, Boston, United States
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, United States
| | - Maximillian Marin
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Department of Biomedical Informatics, Harvard Medical School, Boston, United States
| | - L Elaine Epperson
- Center for Genes, Environment and Health, Center for Genes, National Jewish Health, Denver, United States
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Icahn Institute of Data Sciences and Genomics Technology, New York, United States
| | - Irina Oussenko
- Icahn Institute of Data Sciences and Genomics Technology, New York, United States
| | - David Durbin
- Mycobacteriology Reference Laboratory, Advanced Diagnostic Laboratories, National Jewish Health, Denver, United States
| | - Michael Strong
- Center for Genes, Environment and Health, Center for Genes, National Jewish Health, Denver, United States
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, United States.,Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, United States.,Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, United States
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24
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Virdi R, Lowe ME, Norton GJ, Dawrs SN, Hasan NA, Epperson LE, Glickman CM, Chan ED, Strong M, Crooks JL, Honda JR. Lower Recovery of Nontuberculous Mycobacteria from Outdoor Hawai'i Environmental Water Biofilms Compared to Indoor Samples. Microorganisms 2021; 9:microorganisms9020224. [PMID: 33499212 PMCID: PMC7910870 DOI: 10.3390/microorganisms9020224] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 01/15/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic pulmonary disease with species diversity showing significant regional variation. In the United States, Hawai'i shows the highest rate of NTM pulmonary disease. The need for improved understanding of NTM reservoirs led us to identify NTM from patient respiratory specimens and compare NTM diversity between outdoor and indoor locations in Hawai'i. A total of 545 water biofilm samples were collected from 357 unique locations across Kaua'i (n = 51), O'ahu (n = 202), Maui (n = 159), and Hawai'i Island (n = 133) and divided into outdoor (n = 179) or indoor (n = 366) categories. rpoB sequence analysis was used to determine NTM species and predictive modeling applied to develop NTM risk maps based on geographic characteristics between environments. M. chimaera was frequently identified from respiratory and environmental samples followed by M. chelonae and M. abscessus; yet significantly less NTM were consistently recovered from outdoor compared to indoor biofilms, as exemplified by showerhead biofilm samples. While the frequency of M. chimaera recovery was comparable between outdoor and indoor showerhead biofilms, phylogenetic analyses demonstrate similar rpoB gene sequences between all showerhead and respiratory M. chimaera isolates, supporting outdoor and indoor environments as possible sources for pulmonary M. chimaera infections.
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Affiliation(s)
- Ravleen Virdi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - Melissa E. Lowe
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO 80206, USA; (M.E.L.); (J.L.C.)
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Grant J. Norton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - Stephanie N. Dawrs
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - Nabeeh A. Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - L. Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - Cody M. Glickman
- Computational Biosciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Edward D. Chan
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, CO 80206, USA;
- Division of Pulmonary Science and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Denver, CO 80523, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
| | - James L. Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO 80206, USA; (M.E.L.); (J.L.C.)
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Jennifer R. Honda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; (R.V.); (G.J.N.); (S.N.D.); (N.A.H.); (L.E.E.); (M.S.)
- Correspondence: ; Tel.: +1-303-398-1015
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25
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Hendrix J, Epperson LE, Durbin D, Honda JR, Strong M. Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates. Microb Genom 2021; 7:mgen000497. [PMID: 33355531 PMCID: PMC8115904 DOI: 10.1099/mgen.0.000497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/02/2020] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium, many of the less common but clinically relevant NTM species, including M. kubicae, still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.
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Affiliation(s)
- Jo Hendrix
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - David Durbin
- Advanced Diagnostics Laboratories, National Jewish Health, Denver, CO, USA
| | - Jennifer R. Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
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26
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Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i. Appl Environ Microbiol 2020; 86:AEM.00121-20. [PMID: 32859599 PMCID: PMC7580544 DOI: 10.1128/aem.00121-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 08/25/2020] [Indexed: 11/20/2022] Open
Abstract
Globally and in the United States, the prevalence of NTM pulmonary disease—a potentially life-threatening but underdiagnosed chronic illness—is prominently rising. While NTM are ubiquitous in the environment, including in soil, the specific soil components that promote or inhibit NTM growth have not been elucidated. We hypothesized that NTM culture-positive soil contains minerals that promote NTM growth in vitro. Because Hawai’i is a hot spot for NTM and a unique geographic archipelago, we examined the composition of Hawai’i soil and identified individual clay, iron, and manganese minerals associated with NTM. Next, individual components were evaluated for their ability to directly modulate NTM growth in culture. In general, gibbsite and some manganese oxides were shown to decrease NTM, whereas iron-containing minerals were associated with higher NTM counts. These data provide new information to guide future analyses of soil-associated factors impacting persistence of these soil bacteria. Environmental nontuberculous mycobacteria (NTM), with the potential to cause opportunistic lung infections, can reside in soil. This might be particularly relevant in Hawai’i, a geographic hot spot for NTM infections and whose soil composition differs from many other areas of the world. Soil components are likely to contribute to NTM prevalence in certain niches as food sources or attachment scaffolds, but the particular types of soils, clays, and minerals that impact NTM growth are not well-defined. Hawai’i soil and chemically weathered rock (saprolite) samples were examined to characterize the microbiome and quantify 11 mineralogical features as well as soil pH. Machine learning methods were applied to identify important soil features influencing the presence of NTM. Next, these features were directly tested in vitro by incubating synthetic clays and minerals in the presence of Mycobacteroides abscessus and Mycobacterium chimaera isolates recovered from the Hawai'i environment, and changes in bacterial growth were determined. Of the components examined, synthetic gibbsite, a mineral form of aluminum hydroxide, inhibited the growth of both M. abscessus and M. chimaera, while other minerals tested showed differential effects on each species. For example, M. abscessus (but not M. chimaera) growth was significantly higher in the presence of hematite, an iron oxide mineral. In contrast, M. chimaera (but not M. abscessus) counts were significantly reduced in the presence of birnessite, a manganese-containing mineral. These studies shed new light on the mineralogic features that promote or inhibit the presence of Hawai’i NTM in Hawai’i soil. IMPORTANCE Globally and in the United States, the prevalence of NTM pulmonary disease—a potentially life-threatening but underdiagnosed chronic illness—is prominently rising. While NTM are ubiquitous in the environment, including in soil, the specific soil components that promote or inhibit NTM growth have not been elucidated. We hypothesized that NTM culture-positive soil contains minerals that promote NTM growth in vitro. Because Hawai’i is a hot spot for NTM and a unique geographic archipelago, we examined the composition of Hawai’i soil and identified individual clay, iron, and manganese minerals associated with NTM. Next, individual components were evaluated for their ability to directly modulate NTM growth in culture. In general, gibbsite and some manganese oxides were shown to decrease NTM, whereas iron-containing minerals were associated with higher NTM counts. These data provide new information to guide future analyses of soil-associated factors impacting persistence of these soil bacteria.
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