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Maranha A, Alarico S, Nunes-Costa D, Melo-Marques I, Roxo I, Castanheira P, Caramelo O, Empadinhas N. Drinking Water Microbiota, Entero-Mammary Pathways, and Breast Cancer: Focus on Nontuberculous Mycobacteria. Microorganisms 2024; 12:1425. [PMID: 39065193 PMCID: PMC11279143 DOI: 10.3390/microorganisms12071425] [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: 05/29/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The prospect of drinking water serving as a conduit for gut bacteria, artificially selected by disinfection strategies and a lack of monitoring at the point of use, is concerning. Certain opportunistic pathogens, notably some nontuberculous mycobacteria (NTM), often exceed coliform bacteria levels in drinking water, posing safety risks. NTM and other microbiota resist chlorination and thrive in plumbing systems. When inhaled, opportunistic NTM can infect the lungs of immunocompromised or chronically ill patients and the elderly, primarily postmenopausal women. When ingested with drinking water, NTM often survive stomach acidity, reach the intestines, and migrate to other organs using immune cells as vehicles, potentially colonizing tumor tissue, including in breast cancer. The link between the microbiome and cancer is not new, yet the recognition of intratumoral microbiomes is a recent development. Breast cancer risk rises with age, and NTM infections have emerged as a concern among breast cancer patients. In addition to studies hinting at a potential association between chronic NTM infections and lung cancer, NTM have also been detected in breast tumors at levels higher than normal adjacent tissue. Evaluating the risks of continued ingestion of contaminated drinking water is paramount, especially given the ability of various bacteria to migrate from the gut to breast tissue via entero-mammary pathways. This underscores a pressing need to revise water safety monitoring guidelines and delve into hormonal factors, including addressing the disproportionate impact of NTM infections and breast cancer on women and examining the potential health risks posed by the cryptic and unchecked microbiota from drinking water.
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Affiliation(s)
- Ana Maranha
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Susana Alarico
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Daniela Nunes-Costa
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Melo-Marques
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Roxo
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Ph.D. Programme in Biomedicine and Experimental Biology (PDBEB), Institute for Interdisciplinary Research, University of Coimbra, 3004-504 Coimbra, Portugal
| | | | - Olga Caramelo
- Gynecology Department, Coimbra Hospital and University Centre (CHUC), 3004-561 Coimbra, Portugal;
| | - Nuno Empadinhas
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
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Donohue MJ, Mistry JH. Building size and disinfectant type influence the detection and concentration of Mycobacterium spp. in hot water plumbing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172112. [PMID: 38556005 DOI: 10.1016/j.scitotenv.2024.172112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
The number of nontuberculous mycobacteria (NTM) lung disease cases is increasing in the United States (US). This respiratory disease is primarily caused by three NTM species: Mycobacterium avium, M. intracellulare, and M. abscessus. Since disease transmission could occur through water aerosolization, this study investigated these three species' occurrence (sporadic and persistent) in hot water samples collected from residences (n = 70) and office buildings (n = 30) across the US. A longitudinal survey design was used. Three quantitative Polymerase Chain Reaction (qPCR) assays were used to measure the mycobacterial species in the water samples. Additionally, the water's disinfectant residual was measured. A structure's age and square footage were evaluated to predict mycobacterial contamination. Also, the seasonal occurrence of each species was assessed by structure type. Residences had a 43 % (30/70), and office buildings had a 77 % (23/30) detection frequency of one or more Mycobacterium spp. in their hot water. The age of the structure influenced M. intracellulare detection frequency but not M. avium and M. abscessus. The structure's square footage affected M. avium and M. intracellulare detection frequency but not M. abscessus. In chlorinated water, M. intracellulare was detected 1.4× more often in office buildings' hot water than in chloraminated water. In chloraminated water, the Mycobacterium spp. were detected 2-2.5× more often in residences, while M. avium and M. abscessus were detected 1.5-2.3× more often in office buildings, compared to chlorinated water. Each Mycobacterium spp. had a different trend associated with the type of structure and disinfectant. Further research is needed to better understand NTM occurrence in the built environment to improve public health.
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Affiliation(s)
- Maura J Donohue
- United States Environmental Protection Agency, Cincinnati, OH 45268, United States of America.
| | - Jatin H Mistry
- United States Environmental Protection Agency, Region 6, Dallas, TX 75270, United States of America
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Zhang L, Lin TY, Liu WT, Ling F. Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification. ACS ENVIRONMENTAL AU 2024; 4:127-141. [PMID: 38765059 PMCID: PMC11100324 DOI: 10.1021/acsenvironau.3c00074] [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: 12/01/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 05/21/2024]
Abstract
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
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Affiliation(s)
- Lin Zhang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tzu-Yu Lin
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Mullen B, Houpt ER, Colston J, Becker L, Johnson S, Young L, Hearn J, Falkinham J, Heysell SK. Geographic Variation and Environmental Predictors of Nontuberculous Mycobacteria in Laboratory Surveillance, Virginia, USA, 2021-2023 1. Emerg Infect Dis 2024; 30:548-554. [PMID: 38407146 PMCID: PMC10902533 DOI: 10.3201/eid3003.231162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Because epidemiologic and environmental risk factors for nontuberculous mycobacteria (NTM) have been reported only infrequently, little information exists about those factors. The state of Virginia, USA, requires certain ecologic features to be included in reports to the Virginia Department of Health, presenting a unique opportunity to study those variables. We analyzed laboratory reports of Mycobacterium avium complex (MAC) and M. abscessus infections in Virginia during 2021-2023. MAC/M. abscessus was isolated from 6.19/100,000 persons, and 2.37/100,000 persons had MAC/M. abscessus lung disease. M. abscessus accounted for 17.4% and MAC for 82.6% of cases. Saturated vapor pressure was associated with MAC/M. abscessus prevalence (prevalence ratio 1.414, 95% CI 1.011-1.980; p = 0.043). Self-supplied water use was a protective factor (incidence rate ratio 0.304, 95% CI 0.098-0.950; p = 0.041). Our findings suggest that a better understanding of geographic clustering and environmental water exposures could help develop future targeted prevention and control efforts.
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Barandiaran S, Ponce L, Piras I, Rosas AC, Peña Martinez J, Marfil MJ. Detection of non-tuberculous mycobacteria in native wildlife species at conservation risk of Argentina. Front Vet Sci 2024; 11:1346514. [PMID: 38420209 PMCID: PMC10899436 DOI: 10.3389/fvets.2024.1346514] [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: 11/29/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Non-tuberculous Mycobacteria (NTM) are mainly environmental but can cause opportunistic infections and diseases in humans and animals. Livestock and wild animals can be infected with NTM. In Argentina, there are native wild species facing conservation risks, and they are the focus of protection and reintroduction projects designed to preserve biodiversity in various ecoregions. The aim of this study was to report the presence of NTM in samples collected from four endangered native wild species from nine Argentine provinces, as part of their pre-release health assessment. Methods A total of 165 samples from giant anteater, peccary, tapir and pampas deer were obtained, these included either bronchoalveolar or endotracheal lavages, or oropharyngeal, nasopharyngeal or tracheal swabs. Bacteriological culture followed by molecular identification and sequencing were performed. Results A total of 27 NTM were detected, including Mycobacterium avium subsp. hominissuis, M. intracellulare, M. terrae, M. gordonense, M. kumamotonense, M. fortuitum, M. saskatchewanense, and M. genavense. Results revealed a 16,36% NTM recovery rate, with the giant anteater showing the highest prevalence among the mammals under study. Discussion In Argentina, due to extensive production systems, the interaction between domestic and wild species sharing the same environment is frequent, increasing the exposure of all the species to these NTM. In this way, the transmission of infectious agents from one to another is feasible. Moreover, NTMs might interfere with the diagnosis of bovine tuberculosis and paratuberculosis. These findings emphasize the importance of active health surveillance in conservation programs. It highlights the need to address NTM epidemiology in wildlife and its impact on conservation and public health.
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Affiliation(s)
- Soledad Barandiaran
- Laboratorio de Tuberculosis, Instituto de Investigaciones en Producción Animal (INPA), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Loreana Ponce
- Laboratorio de Tuberculosis, Instituto de Investigaciones en Producción Animal (INPA), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Indiana Piras
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - María Jimena Marfil
- Laboratorio de Tuberculosis, Instituto de Investigaciones en Producción Animal (INPA), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
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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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Honda JR. Environmental Sources and Transmission of Nontuberculous Mycobacteria. Clin Chest Med 2023; 44:661-674. [PMID: 37890909 DOI: 10.1016/j.ccm.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
The field of environmental nontuberculous mycobacteria (NTM) is benefiting from a new era of genomics that has catapulted our understanding of preferred niches, transmission, and outbreak investigations. The ability to forecast environmental features that promote or reduce environmental NTM prevalence will greatly improve with coordinated environmental sampling and by elevating the necessity for uniform disease notifications. Studies that synergize environmental biology, isolate notifications, and comparative genomics in prospective, longitudinal studies, particularly during climate changes and weather events, will be useful to solve longstanding NTM public health quandaries.
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Affiliation(s)
- Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, BMR Building, Tyler, TX 75708, USA.
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van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WOC. M ycobacterium avium complex genomics and transmission in a London hospital. Eur Respir J 2023; 61:2201237. [PMID: 36517182 PMCID: PMC10116071 DOI: 10.1183/13993003.01237-2022] [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: 06/22/2022] [Accepted: 10/23/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Non-tuberculous mycobacteria (NTM) are environmental microorganisms and opportunistic pathogens in individuals with pre-existing lung conditions such as cystic fibrosis (CF) and non-CF bronchiectasis. While recent studies of Mycobacterium abscessus have identified transmission within single CF centres as well as nationally and globally, transmission of other NTM species is less well studied. METHODS To investigate the potential for transmission of the Mycobacterium avium complex (MAC) we sequenced 996 isolates from 354 CF and non-CF patients at the Royal Brompton Hospital (London, UK; collected 2013-2016) and analysed them in a global context. Epidemiological links were identified from patient records. Previously published genomes were used to characterise global population structures. RESULTS We identified putative transmission clusters in three MAC species, although few epidemiological links could be identified. For M. avium, lineages were largely limited to single countries, while for Mycobacterium chimaera, global transmission clusters previously associated with heater-cooler units (HCUs) were found. However, the immediate ancestor of the lineage causing the major HCU-associated outbreak was a lineage already circulating in patients. CONCLUSIONS CF and non-CF patients shared transmission chains, although the lack of epidemiological links suggested that most transmission is indirect and may involve environmental intermediates or asymptomatic carriage in the wider population.
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Affiliation(s)
| | - Huw C Ellis
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kartik Kumar
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Newara Ramadan
- Department of Microbiology, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Susan Benson
- Department of Microbiology, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
| | - Michael R Loebinger
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
| | - William O C Cookson
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
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Abstract
Nontuberculous mycobacteria (NTM) are important pathogens, with a longitudinal prevalence of up to 20% within the cystic fibrosis (CF) population. Diagnosis of NTM pulmonary disease in people with CF (pwCF) is challenging, as a majority have NTM infection that is transient or indolent, without evidence of clinical consequence. In addition, the radiographic and clinical manifestations of chronic coinfections with typical CF pathogens can overlap those of NTM, making diagnosis difficult. Comprehensive care of pwCF must be optimized to assess the true clinical impact of NTM and to improve response to treatment. Treatment requires prolonged, multidrug therapy that varies depending on NTM species, resistance pattern, and extent of disease. With a widespread use of highly effective modulator therapy (HEMT), clinical signs and symptoms of NTM disease may be less apparent, and sensitivity of sputum cultures further reduced. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in pwCF is a research priority, as a lifelong strategy is needed for this high-risk population.
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Misawa K, Nishimura T, Kashimura S, Enoki Y, Taguchi K, Uno S, Uwamino Y, Matsumoto K, Hasegawa N. In vitro effects of diazabicyclooctane β-lactamase inhibitors relebactam and nacubactam against three subspecies of Mycobacterium abscessus complex. Int J Antimicrob Agents 2022; 60:106669. [PMID: 36064079 DOI: 10.1016/j.ijantimicag.2022.106669] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/20/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mycobacterium abscessus complex (MABC) pulmonary disease is notoriously difficult to treat due to intrinsic resistance to many common antibiotics. MABC is β-lactam-resistant as it produces class A β-lactamases, such as blaMab, which are inhibited by diazabicyclooctane (DBO) β-lactamase inhibitors. OBJECTIVES To investigate the microbiological effects of the combination of β-lactam and DBO β-lactamase inhibitors (relebactam and nacubactam) against MABC and determine if the effects are associated with the MABC subspecies and colony morphotype. METHODS The antimicrobial susceptibility of three type strains and 20 clinical isolates of MABC to the combination of seven β-lactams with relebactam or nacubactam was evaluated using broth microdilution checkerboard assays. For these strains, expression levels of blaMab were assessed using quantitative real-time polymerase chain reaction and genotypic diversity was evaluated using 18-locus variable number tandem repeat assay. RESULTS Relebactam and nacubactam lowered the minimum inhibitory concentrations of β-lactams, particularly imipenem, meropenem, and tebipenem, against MABC. There was no difference in efficacy of combination treatment between three subspecies, but rough morphotypes tended to be less susceptible than smooth morphotypes. There were no differences in blaMab expression levels and genotypic diversity between the morphotypes. CONCLUSIONS The combination of β-lactam with relebactam or nacubactam improved the efficacy of β-lactams against all MABC subspecies, but higher concentrations of β-lactams were needed for rough morphotypes.
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Affiliation(s)
- Kana Misawa
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, Minato-ku, Tokyo, Japan; Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Tomoyasu Nishimura
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan; Keio University Health Center, Shinjuku-ku, Tokyo, Japan.
| | - Shoko Kashimura
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yuki Enoki
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, Minato-ku, Tokyo, Japan
| | - Kazuaki Taguchi
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, Minato-ku, Tokyo, Japan
| | - Shunsuke Uno
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yoshifumi Uwamino
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan; Department of Laboratory Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kazuaki Matsumoto
- Division of Pharmacodynamics, Keio University Faculty of Pharmacy, Minato-ku, Tokyo, Japan
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
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11
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Jin P, Dai J, Guo Y, Wang X, Lu J, Zhu Y, Yu F. Genomic Analysis of Mycobacterium abscessus Complex Isolates from Patients with Pulmonary Infection in China. Microbiol Spectr 2022; 10:e0011822. [PMID: 35863029 PMCID: PMC9430165 DOI: 10.1128/spectrum.00118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/19/2022] [Indexed: 11/20/2022] Open
Abstract
Members of the Mycobacterium abscessus complex (MABC) are multidrug-resistant nontuberculous mycobacteria and increasingly cause opportunistic pulmonary infections. However, the genetic typing of MABC isolates remains largely unclear in China. Genomic analyses were conducted for 69 MABC clinical isolates obtained from patients with lower respiratory tract infections in Shanghai Pulmonary Hospital between 2014 and 2016. The draft genomes of the 69 clinical strains were assembled, with a total length of 4.5 to 5.6 Mb, a percent GC content (GC%) ranging from 63.9 to 68.1%, and 4,492 to 5,404 genes per genome. Susceptibility test shows that most isolates are resistant to many antimicrobials, including clarithromycin, but susceptible to tigecycline. Analyses revealed the presence of genes conferring resistance to antibiotics, including macrolides, aminoglycosides, rifampicin, and tetracyclines. Furthermore, 80 to 114 virulence genes were identified per genome, including those related to the invasion of macrophages, iron incorporation, and avoidance of immune clearance. Mobile genetic elements, including insertion sequences, transposons, and genomic islands, were discovered in the genomes. Phylogenetic analyses of all MABC isolates with another 41 complete MABC genomes identified three clades; 46 isolates were clustered in clade I, corresponding to M. abscessus subsp. abscessus, and 25 strains belonged to existing clonal complexes. Overall, this is the first comparative genomic analysis of MABC clinical isolates in China. These results show significant intraspecies variations in genetic determinants encoding antimicrobial resistance, virulence, and mobile elements and controversial subspecies classification using current marker gene combinations. This information will be useful in understanding the evolution, antimicrobial resistance, and pathogenesis of MABC strains and facilitating future vaccine development and drug design. IMPORTANCE Over the past decade, infections by Mycobacterium abscessus complex (MABC) isolates have been increasingly reported worldwide. MABC strains often show a high incidence in cystic fibrosis (CF) patients, whereas in Asia, these strains are frequently recovered from non-CF patients with significant genomic diversity. The present work involves analyses of the antimicrobial resistance, virulence, and phylogeny of 69 selected MABC isolates from non-CF pulmonary patients in Shanghai Pulmonary Hospital by whole-genome sequencing; it represents the first comprehensive investigation of MABC strains in China at the genomic level. These findings highlight the diversity of this group of nontuberculous mycobacteria and provide a mechanistic understanding of evolution and pathogenesis, which is valuable for the development of novel and effective antimicrobial therapies for deadly MABC infections in China.
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Affiliation(s)
- Peipei Jin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Dai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinjuan Guo
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Lu
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yan Zhu
- Immunity and Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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12
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Reduced phagocytic activity of human alveolar macrophages infected with Mycobacterium avium complex. J Infect Chemother 2022; 28:1506-1512. [DOI: 10.1016/j.jiac.2022.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/22/2022]
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13
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Raats D, Brode SK, Mehrabi M, Marras TK. Increasing and More Commonly Refractory Mycobacterium avium Pulmonary Disease, Toronto, Ontario, Canada. Emerg Infect Dis 2022; 28:1589-1596. [PMID: 35876492 PMCID: PMC9328931 DOI: 10.3201/eid2808.220464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In mid-2014, Public Health Ontario Laboratories identified coincident increasing Mycobacterium avium isolation and falling M. xenopi isolation in the Toronto, Ontario, Canada, area. We performed a retrospective cohort of all patients in a Toronto clinic who began treatment for either M. avium or M. xenopi pulmonary disease during 2009–2012 (early period) or 2015–2018 (late period), studying their relative proportions and sputum culture conversion. We conducted a subgroup analysis among patients who lived in the Toronto-York region. The proportion of patients with M. avium was higher in the late period (138/146 [94.5%] vs. 82/106 [77.4%]; p<0.001). Among M. avium patients, conversion was lower in the late period (26.1% vs. 39.0%; p = 0.05). The increase in the proportion of patients with M. avium pulmonary disease and the reduction in the frequency of sputum culture conversion is unexplained but could suggest an increase in environmental M. avium exposure.
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14
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Nontuberculous Mycobacteria: Ecology and Impact on Animal and Human Health. Microorganisms 2022; 10:microorganisms10081516. [PMID: 35893574 PMCID: PMC9332762 DOI: 10.3390/microorganisms10081516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) represent an important group of environmentally saprophytic and potentially pathogenic bacteria that can cause serious mycobacterioses in humans and animals. The sources of infections often remain undetected except for soil- or water-borne, water-washed, water-based, or water-related infections caused by groups of the Mycobacterium (M.) avium complex; M. fortuitum; and other NTM species, including M. marinum infection, known as fish tank granuloma, and M. ulcerans infection, which is described as a Buruli ulcer. NTM could be considered as water-borne, air-borne, and soil-borne pathogens (sapronoses). A lot of clinically relevant NTM species could be considered due to the enormity of published data on permanent, periodic, transient, and incidental sapronoses. Interest is currently increasing in mycobacterioses diagnosed in humans and husbandry animals (esp. pigs) caused by NTM species present in peat bogs, potting soil, garden peat, bat and bird guano, and other matrices used as garden fertilizers. NTM are present in dust particles and in water aerosols, which represent certain factors during aerogenous infection in immunosuppressed host organisms during hospitalization, speleotherapy, and leisure activities. For this Special Issue, a collection of articles providing a current view of the research on NTM-including the clinical relevance, therapy, prevention of mycobacterioses, epidemiology, and ecology-are addressed.
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15
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Ito M, Koga Y, Hachisu Y, Murata K, Sunaga N, Maeno T, Hisada T. Treatment strategies with alternative treatment options for patients with Mycobacterium avium complex pulmonary disease. Respir Investig 2022; 60:613-624. [PMID: 35781424 DOI: 10.1016/j.resinv.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/06/2022] [Accepted: 05/29/2022] [Indexed: 10/17/2022]
Abstract
Diseases caused by Mycobacterium avium complex (MAC) infection in the lungs are increasing worldwide. The recurrence rate of MAC-pulmonary disease (PD) has been reported to be as high as 25-45%. A significant percentage of recurrences occurs because of reinfection with a new genotype from the environment. A focus on reducing exposure to MAC organisms from the environment is therefore an essential component of the management of this disease as well as standard MAC-PD treatment. A macrolide-containing three-drug regimen is recommended over a two-drug regimen as a standard treatment, and azithromycin is recommended rather than clarithromycin. Both the 2007 and 2020 guidelines recommend a treatment duration of MAC-PD of at least one year after the culture conversion. Previous clinical studies have reported that ethambutol could prevent macrolide resistance. Furthermore, the concomitant use of aminoglycoside, amikacin liposomal inhalation, clofazimine, linezolid, bedaquiline, and fluoroquinolone with modification of guideline-based therapy has been studied. Long-term management of MAC-PD remains challenging because of the discontinuation of multi-drug regimens and the acquisition of macrolide resistance. Moreover, the poor compliance of guideline-based therapy for MAC-PD treatment worldwide is concerning since it causes macrolide resistance. Therefore, in this review, we focus on MAC-PD treatment and summarize various treatment options when standard treatment cannot be maintained, with reference to the latest ATS/ERS/ESCMID/IDSA clinical practice guidelines revised in 2020.
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Affiliation(s)
- Masashi Ito
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Yasuhiko Koga
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan.
| | - Yoshimasa Hachisu
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan; Department of Respiratory Medicine, Maebashi Red Cross Hospital, Gunma 371-0813, Japan
| | - Keisuke Murata
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan; Department of Respiratory Medicine, Shibukawa Medical Center, Gunma 377-0280, Japan
| | - Noriaki Sunaga
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Toshitaka Maeno
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Takeshi Hisada
- Gunma University Graduate School of Health Sciences, Gunma 371-8514, Japan
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16
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Falkinham JO, Williams MD. Desiccation-Tolerance of Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium abscessus and Mycobacterium chelonae. Pathogens 2022; 11:pathogens11040463. [PMID: 35456138 PMCID: PMC9028797 DOI: 10.3390/pathogens11040463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Desiccation-tolerance of cells of four strains of Mycobacterium chimaera and individual strains of Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium abscessus, and Mycobacterium chelonae were measured by two methods. The survival of water-acclimated cells both in filter paper and on the surface of stainless-steel coupons were measured. In filter paper at 40% relative humidity at 25 °C, survival of patient isolates of M. avium and M. chimaera cells was 28% and 34% after 21 days of incubation, whereas it was 100% for the Sorin 3T isolate of M. chimaera. On stainless-steel biofilms after 42 days of incubation at 40% relative humidity at 25 °C, survival of water-acclimated cells of M. intracellulare was above 100%, while M. chelonae cells did not survive beyond 21 days, and survival of water-acclimated cells of M. avium and M. abscessus was 18% and 14%, respectively. On stainless-steel coupons, survival of patient and Sorin 3T isolates of M. chimaera was quite similar, specifically between 14% and 28% survival, after 42 days of incubation at 40% relative humidity at 25 °C. The experiments would support the hypothesis that some nontuberculous mycobacterial species are relatively desiccation-tolerant, whereas others are not. Further, long-term survival of the two M. chimaera strains is consistent with the presence of that species in Sorin 3T heater-coolers shipped throughout the world.
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The Presence of Opportunistic Premise Plumbing Pathogens in Residential Buildings: A Literature Review. WATER 2022. [DOI: 10.3390/w14071129] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Opportunistic premise plumbing pathogens (OPPP) are microorganisms that are native to the plumbing environment and that present an emerging infectious disease problem. They share characteristics, such as disinfectant resistance, thermal tolerance, and biofilm formation. The colonisation of domestic water systems presents an elevated health risk for immune-compromised individuals who receive healthcare at home. The literature that has identified the previously described OPPPs (Aeromonas spp., Acinetobacter spp., Helicobacter spp., Legionella spp., Methylobacterium spp., Mycobacteria spp., Pseudomonas spp., and Stenotrophomonas spp.) in residential drinking water systems were systematically reviewed. By applying the Preferred reporting items for systematic reviews and meta-analyses guidelines, 214 studies were identified from the Scopus and Web of Science databases, which included 30 clinical case investigations. Tap components and showerheads were the most frequently identified sources of OPPPs. Sixty-four of these studies detected additional clinically relevant pathogens that are not classified as OPPPs in these reservoirs. There was considerable variation in the detection methods, which included traditional culturing and molecular approaches. These identified studies demonstrate that the current drinking water treatment methods are ineffective against many waterborne pathogens. It is critical that, as at-home healthcare services continue to be promoted, we understand the emergent risks that are posed by OPPPs in residential drinking water. Future research is needed in order to provide consistent data on the prevalence of OPPPs in residential water, and on the incidence of waterborne homecare-associated infections. This will enable the identification of the contributing risk factors, and the development of effective controls.
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18
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Proctor C, Garner E, Hamilton KA, Ashbolt NJ, Caverly LJ, Falkinham JO, Haas CN, Prevost M, Prevots DR, Pruden A, Raskin L, Stout J, Haig SJ. Tenets of a holistic approach to drinking water-associated pathogen research, management, and communication. WATER RESEARCH 2022; 211:117997. [PMID: 34999316 PMCID: PMC8821414 DOI: 10.1016/j.watres.2021.117997] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 05/10/2023]
Abstract
In recent years, drinking water-associated pathogens that can cause infections in immunocompromised or otherwise susceptible individuals (henceforth referred to as DWPI), sometimes referred to as opportunistic pathogens or opportunistic premise plumbing pathogens, have received considerable attention. DWPI research has largely been conducted by experts focusing on specific microorganisms or within silos of expertise. The resulting mitigation approaches optimized for a single microorganism may have unintended consequences and trade-offs for other DWPI or other interests (e.g., energy costs and conservation). For example, the ecological and epidemiological issues characteristic of Legionella pneumophila diverge from those relevant for Mycobacterium avium and other nontuberculous mycobacteria. Recent advances in understanding DWPI as part of a complex microbial ecosystem inhabiting drinking water systems continues to reveal additional challenges: namely, how can all microorganisms of concern be managed simultaneously? In order to protect public health, we must take a more holistic approach in all aspects of the field, including basic research, monitoring methods, risk-based mitigation techniques, and policy. A holistic approach will (i) target multiple microorganisms simultaneously, (ii) involve experts across several disciplines, and (iii) communicate results across disciplines and more broadly, proactively addressing source water-to-customer system management.
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Affiliation(s)
- Caitlin Proctor
- Department of Agricultural and Biological Engineering, Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, IN, USA
| | - Emily Garner
- Wadsworth Department of Civil & Environmental Engineering, West Virginia University, Morgantown, WV, USA
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Centre for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Gold Coast. Queensland, Australia
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Charles N Haas
- Department of Civil, Architectural & Environmental Engineering, Drexel University, Philadelphia, PA, USA
| | - Michele Prevost
- Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - Lutgarde Raskin
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Janet Stout
- Department of Civil & Environmental Engineering, University of Pittsburgh, and Special Pathogens Laboratory, Pittsburgh, PA, USA
| | - Sarah-Jane Haig
- Department of Civil & Environmental Engineering, and Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
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19
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Lari N, Rindi L. High genetic heterogeneity of Mycobacterium intracellulare isolated from respiratory specimens. BMC Microbiol 2022; 22:5. [PMID: 34979921 PMCID: PMC8722163 DOI: 10.1186/s12866-021-02426-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022] Open
Abstract
Background M. intracellulare is a frequent causative pathogen of nontuberculous mycobacteria infection that causes infections in the respiratory tract, whose incidence is increasing in many countries. This study aimed at determining the VNTR-based genetic diversity of a collection of 39 M. intracellulare human strains isolated from respiratory specimens over the last 5 years. Results The VNTR analysis showed that M. intracellulare strains displayed a high genetic diversity, indicating that the M. intracellulare genotypes are quite heterogeneous in our geographical area. Moreover, a comparison with VNTR profiles of strains from other countries confirmed that genotypes of clinical strains of M. intracellulare are not related to geographical origin. Conclusions VNTR typing has proved to be a highly discriminatory method for better understanding the molecular epidemiology of M. intracellulare.
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Affiliation(s)
- Nicoletta Lari
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 35/39, I-56127, Pisa, Italy
| | - Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 35/39, I-56127, Pisa, Italy.
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20
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Nick JA, Daley CL, Lenhart-Pendergrass PM, Davidson RM. Nontuberculous mycobacteria in cystic fibrosis. Curr Opin Pulm Med 2021; 27:586-592. [PMID: 34431787 DOI: 10.1097/mcp.0000000000000816] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW Nontuberculous mycobacteria (NTM) are challenging infections among people with cystic fibrosis (pwCF) as the source, modes of transmission, and best practices for diagnosis and treatment are not known. Investigators have defined aspects of NTM infection that are unique to the CF population, as well as features shared with other conditions at risk. This review describes recent advances in our understanding of NTM infection among pwCF. RECENT FINDINGS The presence of dominant circulating clones of Mycobacterium abscessus within the CF community worldwide continue to be described, as well as pathogen phenotypes that could evoke greater environmental fitness and infectivity. The risk of direct or indirect transmission between pwCF remains an active focus of investigation, with divergent findings and conclusions reached in a site-specific fashion. Derived largely from studies in non-CF populations, new clinical guidelines are now available. A wide variety of agents are in preclinical development or early phase trials with promising findings, and new therapeutic targets have been identified as our understanding of the complex biology of NTM continues to expand. SUMMARY Significant challenges remain in the fight against NTM, however, recent advances in our understanding of the genetics, epidemiology and pathophysiology of pulmonary NTM infection in pwCF are leading efforts to improve clinical care.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver
- University of Colorado Denver, School of Medicine
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver
- University of Colorado Denver, School of Medicine
| | | | - Rebecca M Davidson
- Center for Genes, Environment and Health and Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
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21
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Falkinham JO. Ecology of Nontuberculous Mycobacteria. Microorganisms 2021; 9:microorganisms9112262. [PMID: 34835388 PMCID: PMC8625734 DOI: 10.3390/microorganisms9112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/26/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic human pathogens that are widespread in the human environment. In fact, NTM surround humans. The basis for their widespread presence in soils and natural and human-engineered waters lies primarily in their disinfectant resistance, biofilm formation, and adaptability to fluctuating environmental conditions. As NTM in drinking water surround humans, a major route of infection is through aerosols. The characteristics of NTM, including resistance to disinfection, adherence to surfaces and biofilm formation, present challenges to contemporary water treatment processes developed for control of Escherichia coli and fecal coliforms.
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Affiliation(s)
- Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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22
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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23
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Gardini G, Ori M, Codecasa LR, Matteelli A. Pulmonary nontuberculous mycobacterial infections and environmental factors: A review of the literature. Respir Med 2021; 189:106660. [PMID: 34715617 DOI: 10.1016/j.rmed.2021.106660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/19/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Pulmonary nontuberculous mycobacterial (pNTM) infection is mainly acquired through the inhalation of bioaerosols. Nevertheless, behavioural restrictions are rarely given by clinicians to susceptible populations, in part because the available guidelines for pNTM management emphasize more diagnosis and treatment than prevention. Aim of this review is to clarify if pNTM prevention should routinely include recommendations about risk reducing behaviors. METHODS We used PubMed as biomedical database. We limited our search to the publication period 2000 to 2020 with selected keyword combinations including "nontuberculous mycobacteria", "water", "soil", and "exposure". Titles and abstract of selected articles were systematically screened. Articles were included in the analysis if they were published under free access through the digital library of the University of Brescia (Italy), and provided full text either in English, French, German or Italian. Articles were excluded if the topic was beyond the aim of our study. Finally, we selected 20 articles. RESULTS Studies disagree in identifying the type of aerosol posing the highest risk for the development of pNTM infection. In the retrieved publications the colonization of household niches has been associated with a higher risk of pNTM disease, such as in the exposure to shower aerosols. Considering the non-household settings, the exposure to aerosols in indoor swimming and the higher soil exposure (>2 h/week) seem to correlate with a higher risk to develop pNTM disease. According to our findings, randomized behavioural intervention studies are missing. CONCLUSIONS Stringent scientific evidence is missing to formulate recommendations on behavioural risk reduction for pNTM.
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Affiliation(s)
- Giulia Gardini
- University of Brescia, Division of Tropical and Infectious Diseases, Spedali Civili Hospital, Brescia, Italy.
| | - Margherita Ori
- Division of Pneumology, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Luigi Ruffo Codecasa
- Regional TB Reference Centre, Istituto Villa Marelli, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
| | - Alberto Matteelli
- University of Brescia, Division of Tropical and Infectious Diseases, Spedali Civili Hospital, Brescia, Italy.
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24
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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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25
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Baker AW, Stout JE, Anderson DJ, Sexton DJ, Smith B, Moehring RW, Huslage K, Hostler CJ, Lewis SS. Tap Water Avoidance Decreases Rates of Hospital-onset Pulmonary Nontuberculous Mycobacteria. Clin Infect Dis 2021; 73:524-527. [PMID: 32829397 DOI: 10.1093/cid/ciaa1237] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Indexed: 11/15/2022] Open
Abstract
We analyzed the impact of a hospital tap water avoidance protocol on respiratory isolation of nontuberculous mycobacteria (NTM). After protocol implementation, hospital-onset episodes of respiratory NTM isolation on high-risk units decreased from 41.0 to 9.9 episodes per 10 000 patient-days (incidence rate ratio, 0.24; 95% confidence interval, .17-.34; P < .0001).
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Affiliation(s)
- Arthur W Baker
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Jason E Stout
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Deverick J Anderson
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Daniel J Sexton
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Becky Smith
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rebekah W Moehring
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Kirk Huslage
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Christopher J Hostler
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
- Durham VA Health Care System, Durham, North Carolina, USA
| | - Sarah S Lewis
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
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26
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Park Y, Kwak SH, Yong SH, Lee SH, Leem AY, Kim SY, Lee SH, Chung K, Kim EY, Jung JY, Park MS, Kim YS, Chang J, Kang YA. The Association between Behavioral Risk Factors and Nontuberculous Mycobacterial Pulmonary Disease. Yonsei Med J 2021; 62:702-707. [PMID: 34296547 PMCID: PMC8298869 DOI: 10.3349/ymj.2021.62.8.702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 11/27/2022] Open
Abstract
PURPOSE We aimed to determine the relationship between environmental exposure and nontuberculous mycobacterial pulmonary disease (NTM-PD) in Korea. MATERIALS AND METHODS A group of 150 patients with NTM-PD and a control group of 217 patients with other respiratory diseases were prospectively enrolled between June 2018 and December 2020 in Seoul, Korea. They were surveyed with a standardized questionnaire, and their medical records were reviewed. Odds ratio (OR) and 95% confidence intervals (CI) were calculated with multivariate logistic regression analysis. RESULTS The mean ages of the NTM-PD and control groups were similar (63.8±9.2 years vs. 63.5±10.0 years; p=0.737), and most patients were female (76.0% vs. 68.7%; p=0.157) and nonsmokers (82.0% vs. 72.8%; p=0.021). Mycobacterium avium (49.3%) was the most commonly identified strain among NTM-PD patients, followed by M. intracellulare (32.0%) and M. abscessus subspecies massiliense (12.7%). There were no differences in housing type or frequency of soil- or pet-related exposure between the case and the control groups. However, in subgroup analysis excluding patients with M. intracellulare infection, more case patients frequently visited public baths ≥1 time/week (35.3% vs. 19.4%, p=0.003); this remained significant after multivariate analysis (OR, 2.84; 95% CI, 1.58-5.17). CONCLUSION Frequent exposure to water at public baths might affect the odds of contracting NTM-PD, excluding individuals infected with M. intracellulare strains.
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Affiliation(s)
- Youngmok Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Se Hyun Kwak
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Hyun Yong
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Su Hwan Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ah Young Leem
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Song Yee Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungsoo Chung
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Ye Jung
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Moo Suk Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Sam Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Joon Chang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Ae Kang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea.
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Turner NA, Sweeney MI, Xet-Mull AM, Storm J, Mithani SK, Jones DB, Miles JJ, Tobin DM, Stout JE. A Cluster of Nontuberculous Mycobacterial Tenosynovitis Following Hurricane Relief Efforts. Clin Infect Dis 2021; 72:e931-e937. [PMID: 33136139 DOI: 10.1093/cid/ciaa1665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are a rare cause of infectious tenosynovitis of the upper extremity. Using molecular methods, clinical microbiology laboratories are increasingly reporting identification down to the species level. Improved methods for speciation are revealing new insights into the clinical and epidemiologic features of rare NTM infections. METHODS We encountered 3 cases of epidemiologically linked upper extremity NTM tenosynovitis associated with exposure to hurricane-damaged wood. We conducted whole-genome sequencing to assess isolate relatedness followed by a literature review of NTM infections that involved the upper extremity. RESULTS Despite shared epidemiologic risk, the cases were caused by 3 distinct organisms. Two cases were rare infections caused by closely related but distinct species within the Mycobacterium terrae complex that could not be differentiated by traditional methods. The third case was caused by Mycobacterium intracellulare. An updated literature review that focused on research that used modern molecular speciation methods found that several species within the M. terrae complex are increasingly reported as a cause of upper extremity tenosynovitis, often in association with environmental exposures. CONCLUSIONS These cases illustrate the importance of molecular methods for speciating phenotypically similar NTM, as well as the limitations of laboratory-based surveillance in detecting point-source outbreaks when the source is environmental and may involve multiple organisms.
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Affiliation(s)
- Nicholas A Turner
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Mollie I Sweeney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ana M Xet-Mull
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Suhail K Mithani
- Department of Surgery, Division of Plastic, Oral and Maxillofacial Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - David B Jones
- Orthopedic Institute, Sioux Falls, South Dakota, USA
| | | | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jason E Stout
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
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Lecorche E, Daniau C, La K, Mougari F, Benmansour H, Kumanski S, Robert J, Fournier S, Lebreton G, Carbonne A, Cambau E. Mycobacterium chimaera Genomics With Regard to Epidemiological and Clinical Investigations Conducted for an Open Chest Postsurgical Mycobacterium chimaera Infection Outbreak. Open Forum Infect Dis 2021; 8:ofab192. [PMID: 34189167 PMCID: PMC8231370 DOI: 10.1093/ofid/ofab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
Background Postsurgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole-genome sequencing comparison of patient and heater-cooler unit isolates. Methods We sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in health care facilities performing cardiopulmonary bypass, together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and heater-cooler unit isolates were subjected to whole-genome sequencing analyzed with regard to the reference outbreak strain Zuerich-1. Results Only 2 clinical cases were shown to be related to the outbreak, although 23% (41/175) of heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) of health care facilities, although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole-genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5–9 nonsynonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene was observed in a clinical isolate obtained for 1 patient on antimicrobial treatment. Conclusions Cases of postsurgical M. chimaera infections have been declared to be rare in France, although heater-cooler units were contaminated, as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including 1 suggesting fitness evolution in vivo.
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Affiliation(s)
- Emmanuel Lecorche
- Université de Paris, INSERM, IAME, Paris, France.,APHP-GHU Nord, Service de Mycobactériologie Spécialisée et de Référence, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Côme Daniau
- Santé Publique France, Saint-Maurice, France
| | - Kevin La
- Université de Paris, INSERM, IAME, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Faiza Mougari
- APHP-GHU Nord, Service de Mycobactériologie Spécialisée et de Référence, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Hanaa Benmansour
- APHP-GHU Nord, Service de Mycobactériologie Spécialisée et de Référence, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Sylvain Kumanski
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Jérôme Robert
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Centre d'Immunologie et des Maladies Infectieuses-CIMI-Paris, Sorbonne-Université, INSERM, Paris, France.,Bactériologie-Hygiène, AP-HP, Sorbonne Université, Site Pitié, Paris, France
| | - Sandra Fournier
- Centre d'Immunologie et des Maladies Infectieuses, Sorbonne - Université, INSERM (U1135 - E2), Paris, France
| | - Guillaume Lebreton
- Service de Chirurgie Cardiaque et Thoracique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Emmanuelle Cambau
- Université de Paris, INSERM, IAME, Paris, France.,APHP-GHU Nord, Service de Mycobactériologie Spécialisée et de Référence, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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30
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Association between Mycobacterium avium Complex Pulmonary Disease and Mycobacteria in Home Water and Soil. Ann Am Thorac Soc 2021; 17:57-62. [PMID: 31644315 PMCID: PMC6944351 DOI: 10.1513/annalsats.201812-915oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rationale: Nontuberculous mycobacteria (NTM), including Mycobacterium avium complex (MAC), are emerging pathogens that can opportunistically cause debilitating pulmonary disease in susceptible human hosts. Potential sources of exposure in homes include point-of-use water sources, such as taps and showerheads, as well as gardening soils. The relative human health impacts of NTM in these home environments remain poorly understood.Objectives: This study tested associations between MAC pulmonary disease and NTM colonization of five potential point-of-use sources of pathogen exposure in homes.Methods: A case-control study was conducted of Washington and Oregon residents who had been diagnosed with MAC pulmonary disease, and population controls were matched by age, sex, and geography. Samples were collected from bathroom faucets, kitchen faucets, shower aerosols, indoor soil, and outdoor soil. Mycobacteria in environmental samples were identified in a blinded fashion by using bacteriological culture combined with polymerase chain reaction. The isolation of NTM from case homes (n = 56) versus control homes (n = 51) was quantitatively compared using conditional logistic regression models with adjustment for potential confounding variables.Results: NTM were isolated from shower aerosols collected in case homes more often than in control homes. An adjusted conditional logistic regression analysis showed that NTM isolation from shower aerosols had a high odds ratio associated with disease (odds ratio, 4.0; 95% confidence interval, 1.2-13). Other home environmental samples (tap water, soils) did not exhibit this association.Conclusions: The results implicate shower aerosols as uniquely significant sources of NTM exposure in homes.
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31
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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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Falkinham JO. Living with Legionella and Other Waterborne Pathogens. Microorganisms 2020; 8:E2026. [PMID: 33352932 PMCID: PMC7766883 DOI: 10.3390/microorganisms8122026] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Legionella spp. and other opportunistic premise plumbing pathogens (OPPPs), including Pseudomonas aeruginosa, Mycobacterium avium, Stenotrophomonas maltophilia, and Acinetobacter baumannii, are normal inhabitants of natural waters, drinking water distribution systems and premise plumbing. Thus, humans are regularly exposed to these pathogens. Unfortunately, Legionella spp. and the other OPPPs share a number of features that allow them to grow and persist in premise plumbing. They form biofilms and are also relatively disinfectant-resistant, able to grow at low organic matter concentrations, and able to grow under stagnant conditions. Infections have been traced to exposure to premise plumbing or aerosols generated in showers. A number of measures can lead to reduction in OPPP numbers in premise plumbing, including elevation of water heater temperatures.
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Affiliation(s)
- Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Gu CH, Zhao C, Hofstaedter C, Tebas P, Glaser L, Baldassano R, Bittinger K, Mattei LM, Bushman FD. Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly. PLoS One 2020; 15:e0236533. [PMID: 33166284 PMCID: PMC7652343 DOI: 10.1371/journal.pone.0236533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.
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Affiliation(s)
- Christopher H. Gu
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Casey Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Pablo Tebas
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Growth Temperature, Trehalose, and Susceptibility to Heat in Mycobacterium avium. Pathogens 2020; 9:pathogens9080657. [PMID: 32824162 PMCID: PMC7459632 DOI: 10.3390/pathogens9080657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium avium is capable of an adaptive, reversible response to high-temperature survival depending on its growth temperature. Trehalose concentrations of M. avium cells grown at 42 °C were significantly higher compared to those of cells grown at 25 °C. Further, the survival of cells of M. avium grown at 42 °C and exposed to 65 °C were significantly higher than the survival of cells grown at 25 °C. This adaptive response to growth temperature may play a role in the persistence of M. avium in premise plumbing.
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Lipner EM, French J, Bern CR, Walton-Day K, Knox D, Strong M, Prevots DR, Crooks JL. Nontuberculous Mycobacterial Disease and Molybdenum in Colorado Watersheds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17113854. [PMID: 32485845 PMCID: PMC7312647 DOI: 10.3390/ijerph17113854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
Nontuberculous mycobacteria (NTM) are environmental bacteria that may cause chronic lung disease. Environmental factors that favor NTM growth likely increase the risk of NTM exposure within specific environments. We aimed to identify water-quality constituents (Al, As, Cd, Ca, Cu, Fe, Pb, Mg, Mn, Mo, Ni, K, Se, Na, Zn, and pH) associated with NTM disease across Colorado watersheds. We conducted a geospatial, ecological study, associating data from patients with NTM disease treated at National Jewish Health and water-quality data from the Water Quality Portal. Water-quality constituents associated with disease risk were identified using generalized linear models with Poisson-distributed discrete responses. We observed a highly robust association between molybdenum (Mo) in the source water and disease risk. For every 1- unit increase in the log concentration of molybdenum in the source water, disease risk increased by 17.0%. We also observed a statistically significant association between calcium (Ca) in the source water and disease risk. The risk of NTM varied by watershed and was associated with watershed-specific water-quality constituents. These findings may inform mitigation strategies to decrease the overall risk of exposure.
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Affiliation(s)
- Ettie M. Lipner
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
- Correspondence:
| | - Joshua French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA;
| | - Carleton R. Bern
- U.S. Geological Survey, Colorado Water Science Center, Denver, CO 80225, USA; (C.R.B.); (K.W.-D.)
| | - Katherine Walton-Day
- U.S. Geological Survey, Colorado Water Science Center, Denver, CO 80225, USA; (C.R.B.); (K.W.-D.)
| | - David Knox
- Department of Computer Science, University of Colorado-Boulder, Boulder, CO 80309, USA;
| | - Michael Strong
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
| | - D. Rebecca Prevots
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA;
| | - James L. Crooks
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
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Wang C, Sun R, Wang C, Qian A, Jiang X. M.neoaurum infection increased the inhibitory function of Tregs and the death rate associated with Salmonella coinfection. Res Vet Sci 2020; 132:108-115. [PMID: 32544633 DOI: 10.1016/j.rvsc.2020.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 11/29/2022]
Abstract
Mycobacterium neoaurum belongs to the nontuberculous mycobacteria (NTM) and is ubiquitously present in the environment. However, the changes in Treg percentages and suppressive properties in mice infected with M. neoaurum are still not elucidated. In this study, mice were intraperitoneally injected with M. neoaurum. The change in the CD4+CD25+ Treg cell percentage in the spleen was analyzed using flow cytometry. There was a significant increase in the number of CD4+CD25+ cells by week 6 postinfection, with a peak proportion of approximately 2%. The Foxp3 and IL-10 mRNA expression in CD4+CD25+ cells from the spleens of M.neoaurum-infected mice was higher than that in CD4+CD25+ cells from the spleens of noninfected controls. Proliferation suppression assay results indicated that CD4+CD25+ cells suppressed the proliferation of CD4+CD25- cells at week 6 after M.neoaurum infection, and the suppression rate reached 89.8%. However, CD4+CD25+ cells from the noninfected control group did not suppress the proliferation of CD4+CD25- cells. Based on the above results, mice were subjected to oral administration of S. Typhimurium at 6 weeks postinfection with M. neoaurum, and we found that the mortality of the M.neoaurum-S. Typhimurium infection group was higher than that of the S. Typhimurium infection group. In addition, serious pathological changes appeared in the liver and cecum of the M.neoaurum-S.Typhimurium infection group compared with those of the S. Typhimurium infection group. M. neoaurum increased Treg percentages and suppressed spleen function in mice. These results revealed the possibility that persistent M.neoaurum infection could increase the occurrence of secondary infection.
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Affiliation(s)
- Chunfang Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Rongkuan Sun
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunfeng Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Aidong Qian
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Xiuyun Jiang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China.
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Yoon JK, Kim TS, Kim JI, Yim JJ. Whole genome sequencing of Nontuberculous Mycobacterium (NTM) isolates from sputum specimens of co-habiting patients with NTM pulmonary disease and NTM isolates from their environment. BMC Genomics 2020; 21:322. [PMID: 32326890 PMCID: PMC7181514 DOI: 10.1186/s12864-020-6738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/15/2020] [Indexed: 11/24/2022] Open
Abstract
Background Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis. Results We investigated NTM genomes through NGS to examine transmission patterns in three pairs of co-habiting patients with NTM-PD who were suspected of patient-to-patient transmission. Three pairs of patients with NTM-PD co-habiting for at least 15 years were enrolled: a mother and a daughter with M. avium-PD, a couple with M. intracellulare-PD, and a second couple, one of whom was infected with M. intracellulare and the other of whom was infected with M. abscessus. Whole genome sequencing was performed using patients’ NTM isolates as well as environmental specimens. Genetic distances were estimated based on single nucleotide polymorphisms (SNPs). By comparison with the genetic distances among 78 publicly available NTM genomes, NTM isolates derived from the two pairs of patients infected with the same NTM species were not closely related to each other. In phylogenetic analysis, the NTM isolates from patients with M. avium-PD clustered with isolates from different environmental sources. Conclusions In conclusion, considering the genetic distances between NTM strains, the likelihood of patient-to-patient transmission in pairs of co-habiting NTM-PD patients without overt immune deficiency is minimal.
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Affiliation(s)
- Jung-Ki Yoon
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.,Genomic Medicine Institute, Medical Research Center, Seoul National University School, Seoul, Republic of Korea
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Hasse B, Hannan MM, Keller PM, Maurer FP, Sommerstein R, Mertz D, Wagner D, Fernández-Hidalgo N, Nomura J, Manfrin V, Bettex D, Hernandez Conte A, Durante-Mangoni E, Tang THC, Stuart RL, Lundgren J, Gordon S, Jarashow MC, Schreiber PW, Niemann S, Kohl TA, Daley CL, Stewardson AJ, Whitener CJ, Perkins K, Plachouras D, Lamagni T, Chand M, Freiberger T, Zweifel S, Sander P, Schulthess B, Scriven JE, Sax H, van Ingen J, Mestres CA, Diekema D, Brown-Elliott BA, Wallace RJ, Baddour LM, Miro JM, Hoen B, Athan E, Bayer A, Barsic B, Corey GR, Chu VH, Durack DT, Fortes CQ, Fowler V, Hoen B, Krachmer AW, Durante-Magnoni E, Miro JM, Wilson WR. International Society of Cardiovascular Infectious Diseases Guidelines for the Diagnosis, Treatment and Prevention of Disseminated Mycobacterium chimaera Infection Following Cardiac Surgery with Cardiopulmonary Bypass. J Hosp Infect 2019; 104:214-235. [PMID: 31715282 DOI: 10.1016/j.jhin.2019.10.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/08/2019] [Indexed: 02/09/2023]
Abstract
Mycobacterial infection-related morbidity and mortality in patients following cardiopulmonary bypass surgery is high and there is a growing need for a consensus-based expert opinion to provide international guidance for diagnosing, preventing and treating in these patients. In this document the International Society for Cardiovascular Infectious Diseases (ISCVID) covers aspects of prevention (field of hospital epidemiology), clinical management (infectious disease specialists, cardiac surgeons, ophthalmologists, others), laboratory diagnostics (microbiologists, molecular diagnostics), device management (perfusionists, cardiac surgeons) and public health aspects.
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Affiliation(s)
- B Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland.
| | - M M Hannan
- Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - P M Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - F P Maurer
- Diagnostic Mycobacteriology Group, National and WHO Supranational Reference Center for Mycobacteria, Research Center, Borstel, Germany
| | - R Sommerstein
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - D Mertz
- Departments of Medicine, Health Research Methods, Evidence and Impact, and Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - D Wagner
- Department of Internal Medicine II, Division of Infectious Diseases, Medical Center - University of Freiburg, Freiburg i.Br, Germany
| | - N Fernández-Hidalgo
- Servei de Malalties Infeccioses, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Nomura
- Kaiser Permanente Infectious Diseases, Los Angeles Medical Center, CA, USA
| | - V Manfrin
- Infectious and Tropical Diseases Department, San Bortolo Hospital, Vincenca, Italy
| | - D Bettex
- Institute of Anesthesiology, University Hospital Zurich, Switzerland
| | - A Hernandez Conte
- Department of Anaesthesiology, Kaiser Permanente, Los Angeles Medical Center, CA, USA
| | - E Durante-Mangoni
- Infectious and Transplant Medicine, University of Campania 'L. Vanvitelli', Monaldi Hospital, Naples, Italy
| | - T H-C Tang
- Division of Infectious Diseases, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - R L Stuart
- Monash Infectious Diseases, Monash Health, Australia
| | - J Lundgren
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - S Gordon
- Department of Infectious Diseases, Cleveland Clinic, OH, USA
| | - M C Jarashow
- Acute Communicable Disease Control, Los Angeles Department of Public Health, LA, USA
| | - P W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland
| | - S Niemann
- Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany and German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Borstel, Germany
| | - T A Kohl
- Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany and German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Borstel, Germany
| | - C L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, CO, USA
| | - A J Stewardson
- Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, Australia
| | - C J Whitener
- Penn State Health, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - K Perkins
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - D Plachouras
- Healthcare-associated Infections, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - T Lamagni
- National Infection Service, Public Health England, London, UK
| | - M Chand
- National Infection Service, Public Health England, London, UK; Guy's and St Thomas' NHS Foundation Trust, Imperial College London, UK
| | - T Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - S Zweifel
- Ophthalmology Unit, University of Zurich, Switzerland
| | - P Sander
- National Center for Mycobacteria, Zurich, Switzerland, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - B Schulthess
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - J E Scriven
- Department of Infection and Tropical Medicine, University Hospitals Birmingham, Birmingham, UK
| | - H Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland
| | - J van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - C A Mestres
- Clinic for Cardiovascular Surgery, University Hospital and University of Zurich, Switzerland
| | - D Diekema
- Division of Infectious Diseases, University of Iowa, Carver College of Medicine, IA, USA
| | - B A Brown-Elliott
- Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - R J Wallace
- Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - L M Baddour
- Division of Infectious Diseases, Departments of Medicine and Cardiovascular Diseases, Mayo Clinic, College of Medicine and Science, Rochester, MN, USA
| | - J M Miro
- Infectious Diseases Service at the Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - B Hoen
- Department of Infectious Diseases and Tropical Medicine, University Medical Center of Nancy, Vandoeuvre Cedex, France.
| | | | | | - E Athan
- Infectious Diseases Department at Barwon Health, University of Melbourne and Deakin University, Australia
| | - A Bayer
- Geffen School of Medicine at UCLA Senior Investigator - LA Biomedical Research Institute at Harbor-UCLA, USA
| | - B Barsic
- Department for Infectious Diseases, School of Medicine, University of Zagreb, Croatia
| | - G R Corey
- Duke University Medical Center, Hubert-Yeargan Center for Global Health, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - V H Chu
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - D T Durack
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - C Q Fortes
- Division of Infectious Diseases, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - V Fowler
- Departments of Medicine and Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - B Hoen
- Department of Infectious Diseases and Tropical Medicine, University Medical Center of Nancy, Vandoeuvre Cedex, France
| | - A W Krachmer
- Harvard Medical School, Division of Infectious Diseases at the Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - E Durante-Magnoni
- Infectious and Transplant Medicine of the 'V. Monaldi' Teaching Hospital in Naples, University of Campania 'L. Vanvitelli', Italy
| | - J M Miro
- Infectious Diseases at the Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - W R Wilson
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, College of Medicine and Science, Rochester, MN, USA
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Dewi DNSS, Mertaniasih NM, Soedarsono, Ozeki Y, Artama WT, Fihiruddin, Niki M, Tateishi Y, Ato M, Matsumoto S. Characteristic profile of antibody responses to PPD, ESAT-6, and CFP-10 of Mycobacterium tuberculosis in pulmonary tuberculosis suspected cases in Surabaya, Indonesia. Braz J Infect Dis 2019; 23:246-253. [PMID: 31421107 PMCID: PMC9428029 DOI: 10.1016/j.bjid.2019.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/02/2019] [Accepted: 07/14/2019] [Indexed: 12/23/2022] Open
Abstract
Accurate and rapid diagnostic tools are important aspects of managing tuberculosis (TB) cases appropriately. However, the sensitivity and specificity of diagnostic kits based on immune response such as the tuberculin skin test (TST) and interferon gamma release assay (IGRA) are still debated. Thus, the exploration and assessment of specific biomarker-targeted antibodies are needed for the development of an accurate and rapid diagnostic tool. The present study was conducted in patients with a respiratory problem suspected to be TB at Dr. Soetomo Hospital, Surabaya, Indonesia. Among 102 patients tested by GeneXpert and AFB, 59 serum samples were from cases retrospectively determined to have active TB. A total of 102 serum of healthy controls (HC) was also collected. The PPD antigen and the recombinant CFP-10 and ESAT-6 proteins were prepared. Antibody responses against these proteins were evaluated by ELISA. All samples were also screened for the possibility of Mycobacterium avium-intracellulare complex (MAC) infection using Capilla MaC kit. The results showed that TB patients had a significantly higher concentration of IgG antibody in response to PPD than the HC. In addition, the receiver operating characteristic (ROC) curve analysis showed that PPD was acceptable for diagnostic purposes with an AUC value of 0.835 (95% CI 0.770-0.900, p < 0.0001). However, ESAT-6 and CFP-10 had low AUCs, and 32 samples from both groups showed a low concentration of IgA antibody against all antigens. The MAC detection results also showed that the concentration of IgA in the HC group was the highest. The current results indicate that PPD is a better antigen for antibody-based detection of TB than ESAT-6 and CFP-10. Based on the MAC detection assay, 53 people in the HC group were probably infected with rapidly growing nontuberculous mycobacteria (NTM), although antibody response to PPD was low.
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Affiliation(s)
| | - Ni Made Mertaniasih
- Universitas Airlangga, Faculty of Medicine, Department of Medical Microbiology, Surabaya, Indonesia; Universitas Airlangga, Institute of Tropical Disease, Laboratory of Tuberculosis, Surabaya, Indonesia.
| | - Soedarsono
- Universitas Airlangga, Faculty of Medicine, Department of Pulmonology and Respiratory Medicine, Surabaya, Indonesia.
| | - Yuriko Ozeki
- Niigata University, School of Medicine, Department of Bacteriology, Niigata, Japan.
| | - Wayan Tunas Artama
- Universitas Gadjah Mada, Faculty of Veterinary Medicine, Department of Biochemistry, Yogyakarta, Indonesia; Universitas Gadjah Mada, One Health/Eco-health Resource Center, Yogyakarta, Indonesia.
| | - Fihiruddin
- Universitas Gadjah Mada, Doctoral Program, Research Center of Biotechnology, Yogyakarta, Indonesia; Politeknik Kesehatan Mataram, Department of Medical Laboratory Technology, Mataram, Indonesia.
| | - Mamiko Niki
- Osaka City University Graduate School of Medicine, Department of Bacteriology, Osaka, Japan.
| | - Yoshitaka Tateishi
- Niigata University, School of Medicine, Department of Bacteriology, Niigata, Japan.
| | - Manabu Ato
- National Institute of Infectious Diseases, Department of Mycobacteriology, Leprosy Research Center, Tokyo, Japan.
| | - Sohkichi Matsumoto
- Niigata University, School of Medicine, Department of Bacteriology, Niigata, Japan; Universitas Airlangga, Faculty of Medicine, Department of Medical Microbiology, Surabaya, Indonesia.
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Dowdell K, Haig SJ, Caverly LJ, Shen Y, LiPuma JJ, Raskin L. Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation. Curr Opin Biotechnol 2019; 57:127-136. [PMID: 31003169 DOI: 10.1016/j.copbio.2019.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) pulmonary infections are a growing concern worldwide, with a disproportionate incidence in persons with pre-existing health conditions. NTM have frequently been found in municipally-treated drinking water and building plumbing, leading to the hypothesis that an important source of NTM exposure is drinking water. The identification and quantification of NTM in environmental samples are complicated by genetic variability among NTM species, making it challenging to determine if clinically relevant NTM are present. Additionally, their unique cellular features and lifestyles make NTM and their nucleic acids difficult to recover. This review highlights a recent work focused on quantification and characterization of NTM and on understanding the influence of source water, treatment plants, distribution systems, and building plumbing on the abundance of NTM in drinking water.
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Affiliation(s)
- Katherine Dowdell
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Yun Shen
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA.
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