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Abbas M, Khan MT, Iqbal Z, Ali A, Eddine BT, Yousaf N, Wei D. Sources, transmission and hospital-associated outbreaks of nontuberculous mycobacteria: a review. Future Microbiol 2024; 19:715-740. [PMID: 39015998 PMCID: PMC11259073 DOI: 10.2217/fmb-2023-0279] [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] [Received: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 07/18/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) are widespread environmental organisms found in both natural and man-made settings, such as building plumbing, water distribution networks and hospital water systems. Their ubiquitous presence increases the risk of transmission, leading to a wide range of human infections, particularly in immunocompromised individuals. NTM primarily spreads through environmental exposures, such as inhaling aerosolized particles, ingesting contaminated food and introducing it into wounds. Hospital-associated outbreaks have been linked to contaminated medical devices and water systems. Furthermore, the rising global incidence, prevalence and isolation rates highlight the urgency of addressing NTM infections. Gaining a thorough insight into the sources and epidemiology of NTM infection is crucial for devising novel strategies to prevent and manage NTM transmission and infections.
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Affiliation(s)
- Munawar Abbas
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology & Biotechnology (IMBB), The University of Lahore, 1KM Defense Road, Lahore, 58810, Pakistan
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
| | - Zafar Iqbal
- School of Life Science, Anhui Normal University, Wuhu, Anhui, China
| | - Arif Ali
- Department of Bioinformatics & Biological Statistics, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Benarfa Taki Eddine
- Echahid Cheikh Larbi Tebessi University Faculty of Exact Sciences & Natural & Life Sciences, Département of Microbiology, Algeria
| | - Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Dongqing Wei
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences & School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
- Henan Biological Industry Group, 41, Nongye East Rd, Jinshui, Zhengzhou, Henan, 450008, China
- Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
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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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3
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Clements E, Crank K, Nerenberg R, Atkinson A, Gerrity D, Hannoun D. Quantitative Microbial Risk Assessment Framework Incorporating Water Ages with Legionella pneumophila Growth Rates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6540-6551. [PMID: 38574283 PMCID: PMC11025131 DOI: 10.1021/acs.est.4c01208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
Water age in drinking water systems is often used as a proxy for water quality but is rarely used as a direct input in assessing microbial risk. This study directly linked water ages in a premise plumbing system to concentrations of Legionella pneumophila via a growth model. In turn, the L. pneumophila concentrations were used for a quantitative microbial risk assessment to calculate the associated probabilities of infection (Pinf) and clinically severe illness (Pcsi) due to showering. Risk reductions achieved by purging devices, which reduce water age, were also quantified. The median annual Pinf exceeded the commonly used 1 in 10,000 (10-4) risk benchmark in all scenarios, but the median annual Pcsi was always 1-3 orders of magnitude below 10-4. The median annual Pcsi was lower in homes with two occupants (4.7 × 10-7) than with one occupant (7.5 × 10-7) due to more frequent use of water fixtures, which reduced water ages. The median annual Pcsi for homes with one occupant was reduced by 39-43% with scheduled purging 1-2 times per day. Smart purging devices, which purge only after a certain period of nonuse, maintained these lower annual Pcsi values while reducing additional water consumption by 45-62%.
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Affiliation(s)
- Emily Clements
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas, Nevada 89193, United States
| | - Katherine Crank
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas, Nevada 89193, United States
| | - Robert Nerenberg
- Department
of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre
Dame, Indiana 46556, United States
| | - Ariel Atkinson
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas, Nevada 89193, United States
| | - Daniel Gerrity
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas, Nevada 89193, United States
| | - Deena Hannoun
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas, Nevada 89193, United States
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4
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Healy HG, Ehde A, Bartholow A, Kantor RS, Nelson KL. Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems. NPJ Biofilms Microbiomes 2024; 10:7. [PMID: 38253591 PMCID: PMC10803812 DOI: 10.1038/s41522-023-00473-6] [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] [Received: 07/30/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).
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Affiliation(s)
- Hannah Greenwald Healy
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Aliya Ehde
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, IN, USA
| | - Alma Bartholow
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
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5
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Yang J, Hu Y, Zhang Y, Zhou S, Meng D, Xia S, Wang H. Deciphering the diversity and assemblage mechanisms of nontuberculous mycobacteria community in four drinking water distribution systems with different disinfectants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168176. [PMID: 37907107 DOI: 10.1016/j.scitotenv.2023.168176] [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: 09/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
Nontuberculous mycobacteria (NTM) represent an emerging health concern due to their escalating infections worldwide. Although drinking water distribution systems (DWDSs) have been considered as NTM reservoirs and a potential infection route, NTM community at the species level remain largely elusive in DWDSs. This study employed high-throughput sequencing coupled with qPCR to profile NTM community and estimate their abundances at the species level in water and biofilm samples in four DWDSs using three different disinfectants (i.e. free chlorine, chloramine and chlorine dioxide). Results demonstrated the dominance of Mycobacterium paragordonae and Mycobacterium mucogenicum in both biofilm and water across four DWDSs, whereas Mycobacterium abscessus and Mycobacterium chelonae, the two clinically significant species, exhibited low abundance but high prevalence. Comparable NTM community was observed in biofilm across these four DWDSs. Distinct separation of NTM community between SH-chloramine DWDSs water and other DWDSs highlighted the selective pressure of chloramine on NTM community. Furthermore, the research revealed that biofilm and water exhibited distinct NTM community structures, with biofilm harboring more diverse NTM community. Certain NTM species displayed a preference for biofilm, such as Mycobacterium gordonae, while others, like Mycobacterium mucogenicum, were more abundant in water samples (P < 0.05). In terms of NTM community assembly, stochastic processes dominated biofilm, while comparable role of stochastic and deterministic processes was observed in water. In conclusion, this study offers a pioneering and comprehensive insight into the dynamics and assembly mechanisms of NTM community within four DWDSs treated with three distinct disinfectants. These findings serve as a critical foundation for assessing NTM exposure risks and devising effective management strategies within DWDSs.
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Affiliation(s)
- Jinhao Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yuxing Hu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yue Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Shuang Zhou
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Die Meng
- Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Hong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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6
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Cazals M, Bédard E, Soucy C, Savard P, Prévost M. How clean is your ice machine? Revealing microbial amplification and presence of opportunistic pathogens in hospital ice-water machines. J Hosp Infect 2023; 141:9-16. [PMID: 37604277 DOI: 10.1016/j.jhin.2023.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/18/2023] [Accepted: 08/05/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Ice machines in healthcare facilities have been suspected and even linked to outbreaks and pseudo-outbreaks. Guidelines exist for maintenance of these devices but there is no clear independent infection control standard, and little is known about their microbial contamination. AIM To evaluate the microbial contamination, amplification, and presence of opportunistic pathogens in ice-water machines in a healthcare facility. METHODS Concentrations of general microbial indicators (heterotrophic plate counts (HPC), total and intact cells), faecal indicators (enterococci) and opportunistic pathogens (Pseudomonas aeruginosa, non-tuberculous mycobacteria (NTM), Candida spp.) were measured in 36 ice-water machines on patient wards of a 772-bed hospital. Profile sampling was performed on five ice-water machines and adjacent faucets to identify sites of microbial proliferation. FINDINGS Candida spp. were found in half of ice-water samples while enterococci and P. aeruginosa were present in six and 11 drain inlets respectively. NTM were measured in all ice-water samples and 35 out of 36 biofilms. Pre-filters and ice machines are sites for additional amplification: NTM densities were on average 1.3 log10 higher in water of ice machine flushed 5 min compared to flushed adjacent tap water. CONCLUSION Ice machine design needs to be adapted to reduce microbial proliferation. The absence of correlation between HPC densities (current microbial indicators) and NTM concentrations suggests a need for cleaning efficiency indicators better correlated with opportunistic pathogens. Cleaning and disinfection guidelines of ice machines in healthcare facilities need to be improved, especially when ice is given to the most vulnerable patients, and NTM may be an efficiency indicator.
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Affiliation(s)
- M Cazals
- Civil, Geological and Mining Engineering Department, Polytechnique Montréal, Montreal, Canada.
| | - E Bédard
- Civil, Geological and Mining Engineering Department, Polytechnique Montréal, Montreal, Canada
| | - C Soucy
- Infection Prevention and Control, University of Montreal Hospital Centre (CHUM), Montreal, Canada
| | - P Savard
- Infection Prevention and Control, University of Montreal Hospital Centre (CHUM), Montreal, Canada; Department of Microbiology, Infectious Diseases and Immunology and University of Montreal Hospital Centre Research Centre (CRCHUM), University of Montreal, Canada
| | - M Prévost
- Civil, Geological and Mining Engineering Department, Polytechnique Montréal, Montreal, Canada
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7
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Clements E, Irwin C, Taflanidis A, Bibby K, Nerenberg R. Impact of fixture purging on water age and excess water usage, considering stochastic water demands. WATER RESEARCH 2023; 245:120643. [PMID: 37748346 DOI: 10.1016/j.watres.2023.120643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/27/2023]
Abstract
Higher water ages are linked with water quality decline as chlorine dissipates, temperatures become more favorable for microbial growth, and metals and organic matter leach from the pipes. Water fixtures with automated purging devices can limit water age in premise plumbing systems, but also increase water use. To develop purging strategies that lower age while also minimizing water use, the stochastic nature of water demands must be considered. In this research, a hydraulic plumbing network model, with stochastic demands at fixtures, was used to compare water age and water use for five purging conditions: purging at regular intervals, "smart" purging (considering the time of last use), purging with different volumes of water, purging at different fixtures, and the purging with different levels of home occupancy. Higher purging frequency and volume resulted in lower water ages, but higher water use. Purging greatly reduced the variability in water ages, avoiding extreme ages entirely. Water age was minimized by scheduling the purging around occupancy behavior, such as before the occupants wake up or return from work. Scheduled purging used more water than smart purging. Purging after 12 h of nonuse used only 55% of the additional water required for purging every 12 h. Purging after 24 h of nonuse at the kitchen tap and shower used only 38% of the additional water required for purging every 24 h, while maintaining lower water ages and removing the variability in water ages. While larger purging volumes had a greater impact on water age, there were diminishing returns. Purging has a larger impact on low-occupancy homes because fixtures have less frequent use. Overall, this research provides a methodology to compare purging strategies that minimize both water age and water use. While the numerical results presented here are only valid for the specific layout and usage habits, they provide insights and trends applicable to other cases.
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Affiliation(s)
- Emily Clements
- Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Christopher Irwin
- Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Alexandros Taflanidis
- Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences 156 Fitzpatrick Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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Logan-Jackson AR, Batista MD, Healy W, Ullah T, Whelton AJ, Bartrand TA, Proctor C. A Critical Review on the Factors that Influence Opportunistic Premise Plumbing Pathogens: From Building Entry to Fixtures in Residences. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:6360-6372. [PMID: 37036108 DOI: 10.1021/acs.est.2c04277] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Residential buildings provide unique conditions for opportunistic premise plumbing pathogen (OPPP) exposure via aerosolized water droplets produced by showerheads, faucets, and tubs. The objective of this review was to critically evaluate the existing literature that assessed the impact of potentially enhancing conditions to OPPP occurrence associated with residential plumbing and to point out knowledge gaps. Comprehensive studies on the topic were found to be lacking. Major knowledge gaps identified include the assessment of OPPP growth in the residential plumbing, from building entry to fixtures, and evaluation of the extent of the impact of typical residential plumbing design (e.g., trunk and branch and manifold), components (e.g., valves and fixtures), water heater types and temperature setting of operation, and common pipe materials (copper, PEX, and PVC/CPVC). In addition, impacts of the current plumbing code requirements on OPPP responses have not been assessed by any study and a lack of guidelines for OPPP risk management in residences was identified. Finally, the research required to expand knowledge on OPPP amplification in residences was discussed.
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Affiliation(s)
- Alshae' R Logan-Jackson
- Building Energy and Environment Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Marylia Duarte Batista
- Building Energy and Environment Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - William Healy
- Building Energy and Environment Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Tania Ullah
- Building Energy and Environment Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Andrew J Whelton
- Lyles School of Civil Engineering, Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Timothy A Bartrand
- Environmental Science, Policy, and Research Institute, Bala Cynwyd, Pennsylvania 19004, United States
| | - Caitlin Proctor
- Agricultural and Biological Engineering, Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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9
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Shen Y, Haig SJ, Prussin AJ, LiPuma JJ, Marr LC, Raskin L. Shower water contributes viable nontuberculous mycobacteria to indoor air. PNAS NEXUS 2022; 1:pgac145. [PMID: 36712351 PMCID: PMC9802317 DOI: 10.1093/pnasnexus/pgac145] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Nontuberculous mycobacteria (NTM) are frequently present in municipal drinking water and building plumbing, and some are believed to cause respiratory tract infections through inhalation of NTM-containing aerosols generated during showering. However, the present understanding of NTM transfer from water to air is insufficient to develop NTM risk mitigation strategies. This study aimed to characterize the contribution of shower water to the abundance of viable NTM in indoor air. Shower water and indoor air samples were collected, and 16S rRNA and rpoB genes were sequenced. The sequencing results showed that running the shower impacted the bacterial community structure and NTM species composition in indoor air by transferring certain bacteria from water to air. A mass balance model combined with NTM quantification results revealed that on average 1/132 and 1/254 of NTM cells in water were transferred to air during 1 hour of showering using a rain and massage showerhead, respectively. A large fraction of the bacteria transferred from water to air were membrane-damaged, i.e. they had compromised membranes based on analysis by live/dead staining and flow cytometry. However, the damaged NTM in air were recoverable as shown by growth in a culture medium mimicking the respiratory secretions of people with cystic fibrosis, implying a potential infection risk by NTM introduced to indoor air during shower running. Among the recovered NTM, Mycobacterium mucogenicum was the dominant species as determined by rpoB gene sequencing. Overall, this study lays the groundwork for future pathogen risk management and public health protection in the built environment.
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Affiliation(s)
| | | | - Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg, VA 24061, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, 1500 E. Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg, VA 24061, USA
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10
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Meghdadi H, Khosravi AD, Hashemzadeh M, Tabandeh MR. New design of multilocus sequence analysis of rpoB, ssrA, tuf, atpE, ku, and dnaK for identification of Mycobacterium species. Mol Biol Rep 2022; 49:7967-7977. [PMID: 35717471 DOI: 10.1007/s11033-022-07638-0] [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] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Differentiating Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is very important in the treatment process of patients. According to the American Thoracic Society guideline (ATS), NTM clinical isolates should be identified at the species level proper treatment and patient management. This study aimed to identify NTM clinical isolates by evaluationg rpoB, ssrA, tuf, atpE, ku, and dnaK genes, and use multilocus sequence analysis (MLSA) to concatenate the six genes. METHODS Ninety-six Mycobacterium isolates, including 86 NTM and 10 MTB isolates, from all the patients referred to the certain TB Reference Centres were included. All isolates were evaluated by PCR amplification of rpoB, ssrA, tuf, ku, atpE, and dnaK genes and MLSA. RESULTS Out of 96 isolates, 91 (94.8%), 87 (90.6%), 72 (75%), 84 (87.5%) and 79 (82.3%) were differentiated to the species level by rpoB, tuf, ssrA, dnaK and atpE genes, respectively. The ku gene was able to identify 69 (80.2%) isolates of the 86 NTM isolates to the species level. We could identify 100% of the isolates to the species level by MLSA. CONCLUSIONS None of the PCR targets used in this study were able to completely differentiate all species. The MLSA technique used to concatenate the six genes could increase the identification of clinical Mycobacterium isolates and all 16 species were well-differentiated.
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Affiliation(s)
- Hossein Meghdadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Reza Tabandeh
- Department of Basic Sciences, Division of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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11
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Miao X, Liu C, Liu M, Han X, Zhu L, Bai X. The role of pipe biofilms on dissemination of viral pathogens and virulence factor genes in a full-scale drinking water supply system. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128694. [PMID: 35316639 DOI: 10.1016/j.jhazmat.2022.128694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/24/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Water is an important medium for virus transmission and viral pathogens are increasingly appreciated as a significant water safety issue. However, the effect of pipe biofilms on viral pathogens remains unclear. This research aimed to investigate the dissemination of viruses in a full-scale drinking water supply system (DWSS) and the effect of pipe biofilms on viral pathogens in bulking water. Viral pathogens, pathogenic viral hosts, and viral virulence factors (VFs) were found to disseminate from source water to tap water. The proportion of virus and viral VFs in the biofilm was far less than that in water. The contribution of biofilms in pipe wall to viruses and viral VFs in bulking water was less than 4%, and viruses in the biofilm had no obvious effect on pathogenic viruses in water. Dominant viruses carrying VFs changed from Cyanobacteria virus to Mycobacterium virus after advanced water treatment. Mycobacterium and organics were identified as the key factors influencing composition and abundance of viral VFs, which could explain 41.1% of the variation in viral virulence in the water supply system. Host bacteria and organics may be used as the key targets to control the risk of viruses in DWSSs.
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Affiliation(s)
- Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Chenxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Mingkun Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xue Han
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lingling Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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12
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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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13
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Rahmatika I, Kurisu F, Furumai H, Kasuga I. Dynamics of the Microbial Community and Opportunistic Pathogens after Water Stagnation in the Premise Plumbing of a Building. Microbes Environ 2022; 37. [PMID: 35321996 PMCID: PMC8958293 DOI: 10.1264/jsme2.me21065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In premise plumbing, microbial water quality may deteriorate under certain conditions, such as stagnation. Stagnation results in a loss of disinfectant residual, which may lead to the regrowth of microorganisms, including opportunistic pathogens. In the present study, microbial regrowth was investigated at eight faucets in a building over four seasons in one year. Water samples were obtained before and after 24 h of stagnation. In the first 100 mL after stagnation, total cell counts measured by flow cytometry increased 14- to 220-fold with a simultaneous decrease in free chlorine from 0.17–0.36 mg L–1 to <0.02 mg L–1. After stagnation, total cell counts were not significantly different among seasons; however, the composition of the microbial community varied seasonally. The relative abundance of Pseudomonas spp. was dominant in winter, whereas Sphingomonas spp. were dominant in most faucets after stagnation in other seasons. Opportunistic pathogens, such as Legionella pneumophila, Mycobacterium avium, Pseudomonas aeruginosa, and Acanthamoeba spp., were below the quantification limit for real-time quantitative PCR in all samples. However, sequences related to other opportunistic pathogens, including L. feeleii, L. maceachernii, L. micdadei, M. paragordonae, M. gordonae, and M. haemophilum, were detected. These results indicate that health risks may increase after stagnation due to the regrowth of opportunistic pathogens.
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Affiliation(s)
- Iftita Rahmatika
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo
| | - Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo
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14
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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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15
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Ye C, Xian X, Bao R, Zhang Y, Feng M, Lin W, Yu X. Recovery of microbiological quality of long-term stagnant tap water in university buildings during the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150616. [PMID: 34592279 PMCID: PMC9752782 DOI: 10.1016/j.scitotenv.2021.150616] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 05/10/2023]
Abstract
Stagnant water can cause water quality deterioration and, in particular, microbiological contaminations, posing potential health risks to occupants. University buildings were unoccupied with little water usage during the COVID-19 pandemic. It's an opportunity to study microbiological quality of long-term stagnant water (LTSW) in university buildings. The tap water samples were collected for three months from four types of campus buildings to monitor water quality and microbial risks after long-term stagnation. Specifically, the residual chlorine, turbidity, and iron/zinc were disqualified, and the heterotrophic plate counts (HPC) exceeded the Chinese national standard above 100 times. It took 4-54 days for these parameters to recover to the routine levels. Six species of pathogens were detected with high frequency and levels (101-105 copies/100 mL). Remarkably, L. pneumophilia occurred in 91% of samples with turbidity > 1 NTU. The absence of the culturable cells for these bacteria possibly implied their occurrence in a viable but non-culturable (VBNC) status. The bacterial community of the stagnant tap water differed significantly and reached a steady state in more than 50 days. Furthermore, a high concentration of endotoxin (>10 EU/mL) was found in LTSW, which was in accordance with the high proportion of dead bacteria. The results suggested that the increased microbiological risks require more attention and the countermeasures before the building reopens should be taken.
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Affiliation(s)
- Chengsong Ye
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Xuanxuan Xian
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Ruihan Bao
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Yiting Zhang
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Mingbao Feng
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wenfang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xin Yu
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China.
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16
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The Pathway towards Photoelectrocatalytic Water Disinfection: Review and Prospects of a Powerful Sustainable Tool. Catalysts 2021. [DOI: 10.3390/catal11080921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Photoelectrocatalysis is a hybrid photon/electron-driven process that benefits from the synergistic effects of both processes to enhance and stabilize the generation of disinfecting oxidants. Photoelectrocatalysis is an easy to operate technology that can be scaled-up or scaled-down for various water treatment applications as low-cost decentralized systems. This review article describes the fundamentals of photoelectrocatalysis, applied to water disinfection to ensure access to clean water for all as a sustainable development goal. Advances in reactor engineering design that integrate light-delivery and electrochemical system requirements are presented, with a description of photo-electrode material advances, including doping, nano-decoration, and nanostructure control. Disinfection and cell inactivation are described using different model microorganisms such as E. coli, Mycobacteria, Legionella, etc., as well the fungus Candida parapsilosis, with relevant figures of merit. The key advances in the elucidation of bacterial inactivation mechanisms by photoelectrocatalytic treatments are presented and knowledge gaps identified. Finally, prospects and further research needs are outlined, to define the pathway towards the future of photoelectrocatalytic disinfection technologies.
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17
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Zhou W, Li W, Chen J, Zhou Y, Wei Z, Gong L. Microbial diversity in full-scale water supply systems through sequencing technology: a review. RSC Adv 2021; 11:25484-25496. [PMID: 35478887 PMCID: PMC9037190 DOI: 10.1039/d1ra03680g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/10/2021] [Indexed: 01/07/2023] Open
Abstract
The prevalence of microorganisms in full-scale water supply systems raises concerns about their pathogenicity and threats to public health. Clean tap water is essential for public health safety. The conditions of the water treatment process from the source water to tap water, including source water quality, water treatment processes, the drinking water distribution system (DWDS), and building water supply systems (BWSSs) in buildings, greatly influence the bacterial community in tap water. Given the importance of drinking water biosafety, the study of microbial diversity from source water to tap water is essential. With the development of molecular biology methods and bioinformatics in recent years, sequencing technology has been applied to study bacterial communities in full-scale water supply systems. In this paper, changes in the bacterial community and the influence of each treatment stage on microbial diversity in full-scale water supply systems are classified and analyzed. Microbial traceability analysis and control are discussed, and suggestions for future drinking water biosafety research and its prospects are proposed.
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Affiliation(s)
- Wei Zhou
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University Shanghai 200092 China
| | - Weiying Li
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University Shanghai 200092 China
| | - Jiping Chen
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
| | - Yu Zhou
- College of Environmental Science and Engineering, Tongji University Shanghai 200092 China
| | - Zhongqing Wei
- Fuzhou Water Affairs Investment Development Co., Ltd. Fuzhou 350000 Fujian China
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18
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Kitajima M, Cruz MC, Williams RBH, Wuertz S, Whittle AJ. Microbial abundance and community composition in biofilms on in-pipe sensors in a drinking water distribution system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142314. [PMID: 33077212 DOI: 10.1016/j.scitotenv.2020.142314] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Collecting biofilm samples from drinking water distribution systems (DWDSs) is challenging due to limited access to the pipes during regular operations. We report here the analysis of microbial communities in biofilm and water samples collected from sensors installed in a DWDS where monochloramine is used as a residual disinfectant. A total of 52 biofilm samples and 14 bulk water samples were collected from 17 pipe sections representing different water ages. Prokaryotic genome copies (bacterial and archaeal 16S rRNA genes, Mycobacterium spp., ammonia-oxidizing bacteria (AOB), and cyanobacteria) were quantified with droplet digital PCR, which revealed the abundance of these genes in both biofilm and water samples. Prokaryotic 16S rRNA gene sequencing analysis was carried out for a subset of the samples (12 samples from four sites). Mycobacterium and AOB species were dominant in the DWDS sections with low water age and sufficient residual monochloramine, whereas Nitrospira species (nitrite-oxidizing bacteria) dominated in the sections with higher water age and depleted monochloramine level, suggesting the occurrence of nitrification in the studied DWDS. The present study provides novel information on the abundance and identity of prokaryotes in biofilms and water in a full-scale operational DWDS.
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Affiliation(s)
- Masaaki Kitajima
- Center for Environmental Sensing and Modeling, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.
| | - Mercedes C Cruz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore.
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117456, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Andrew J Whittle
- Center for Environmental Sensing and Modeling, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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19
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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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20
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Evaluation of a new culture medium for isolation of nontuberculous mycobacteria from environmental water samples. PLoS One 2021; 16:e0247166. [PMID: 33657154 PMCID: PMC7928522 DOI: 10.1371/journal.pone.0247166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/03/2021] [Indexed: 11/29/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are waterborne pathogens commonly found in building water systems where they are a primary concern to vulnerable patient populations and can cause severe disease. The recovery of NTM from environmental samples can be a laborious undertaking and current pre-treatment methods and selective media lack sensitivity. We explored the use of the highly selective Rapidly Growing Mycobacteria (RGM) medium for culturing NTM from environmental water samples compared to existing methods. In total, 223 environmental water samples, including potable and non-potable water, were cultured for NTM using three culture media. In addition to direct culture on RGM medium, each sample was cultured on Middlebrook 7H10 medium and Mitchison 7H11 medium after pre-treatment with 0.2M KCl-HCl. Additionally, 33 distinct species of NTM were inoculated onto RGM medium and 7H10 medium in parallel to directly compare their growth. The use of RGM medium alone without pre-treatment provided a sensitivity (91%) comparable to that offered by culture on both 7H10 and 7H11 with acid pretreatment (combined sensitivity; 86%) with significantly less overgrowth and interference from other organisms on RGM medium. The average concentration of NTM observed on RGM medium alone was comparable to or greater than the NTM concentration on either medium alone or combined. Thirty-three species were examined in parallel and all tested strains of 27 of these species successfully grew on RGM medium, including 19 of 21 from the CDC’s healthcare-associated infections species list. RGM medium was successful at recovering environmental NTM without a pre-treatment, greatly reducing labor and materials required to process samples. Simplification of culture processing for environmental NTM will allow for a better assessment of their presence in building water systems and the potential for reduced exposure of susceptible populations.
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21
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Abstract
qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume. We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.
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22
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Hozalski RM, LaPara TM, Zhao X, Kim T, Waak MB, Burch T, McCarty M. Flushing of Stagnant Premise Water Systems after the COVID-19 Shutdown Can Reduce Infection Risk by Legionella and Mycobacterium spp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15914-15924. [PMID: 33232602 DOI: 10.1021/acs.est.0c06357] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There is concern about potential exposure to opportunistic pathogens when reopening buildings closed due to the COVID-19 pandemic. In this study, water samples were collected before, during, and after flushing showers in five unoccupied (i.e., for ∼2 months) university buildings with quantification of opportunists via a cultivation-based assay (Legionella pneumophila only) and quantitative PCR. L. pneumophila were not detected by either method; Legionella spp., nontuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC), however, were widespread. Using quantitative microbial risk assessment (QMRA), the estimated risks of illness from exposure to L. pneumophila and MAC via showering were generally low (i.e., less than a 10-7 daily risk threshold), with the exception of systemic infection risk from MAC exposure in some buildings. Flushing rapidly restored the total chlorine (as chloramine) residual and decreased bacterial gene targets to building inlet concentrations within 30 min. During the postflush stagnation period, the residual chlorine dissipated within a few days and bacteria rebounded, approaching preflush concentrations after 6-7 days. These results suggest that flushing can quickly improve water quality in unoccupied buildings, but the improvement may only last a few days.
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Affiliation(s)
- Raymond M Hozalski
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Xiaotian Zhao
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Michael B Waak
- Norwegian University of Science and Technology, Trondheim 7031, Norway
- Department of Infrastructure, SINTEF Community, Trondheim 7031, Norway
| | - Tucker Burch
- Agricultural Research Service, U.S. Department of Agriculture, Marshfield, Wisconsin 54449, United States
| | - Michael McCarty
- School of Public Health, University of Minnesota, Minneapolis 55455, Minnesota, United States
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23
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Cullom AC, Martin RL, Song Y, Williams K, Williams A, Pruden A, Edwards MA. Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens. Pathogens 2020; 9:E957. [PMID: 33212943 PMCID: PMC7698398 DOI: 10.3390/pathogens9110957] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
Growth of Legionella pneumophila and other opportunistic pathogens (OPs) in drinking water premise plumbing poses an increasing public health concern. Premise plumbing is constructed of a variety of materials, creating complex environments that vary chemically, microbiologically, spatially, and temporally in a manner likely to influence survival and growth of OPs. Here we systematically review the literature to critically examine the varied effects of common metallic (copper, iron) and plastic (PVC, cross-linked polyethylene (PEX)) pipe materials on factors influencing OP growth in drinking water, including nutrient availability, disinfectant levels, and the composition of the broader microbiome. Plastic pipes can leach organic carbon, but demonstrate a lower disinfectant demand and fewer water chemistry interactions. Iron pipes may provide OPs with nutrients directly or indirectly, exhibiting a high disinfectant demand and potential to form scales with high surface areas suitable for biofilm colonization. While copper pipes are known for their antimicrobial properties, evidence of their efficacy for OP control is inconsistent. Under some circumstances, copper's interactions with premise plumbing water chemistry and resident microbes can encourage growth of OPs. Plumbing design, configuration, and operation can be manipulated to control such interactions and health outcomes. Influences of pipe materials on OP physiology should also be considered, including the possibility of influencing virulence and antibiotic resistance. In conclusion, all known pipe materials have a potential to either stimulate or inhibit OP growth, depending on the circumstances. This review delineates some of these circumstances and informs future research and guidance towards effective deployment of pipe materials for control of OPs.
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Affiliation(s)
- Abraham C. Cullom
- Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA; (A.C.C.); (R.L.M.); (Y.S.); (A.P.)
| | - Rebekah L. Martin
- Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA; (A.C.C.); (R.L.M.); (Y.S.); (A.P.)
- Civil and Environmental Engineering, Virginia Military Institute, Lexington, VA 24450, USA
| | - Yang Song
- Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA; (A.C.C.); (R.L.M.); (Y.S.); (A.P.)
| | | | - Amanda Williams
- c/o Marc Edwards, Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA;
| | - Amy Pruden
- Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA; (A.C.C.); (R.L.M.); (Y.S.); (A.P.)
| | - Marc A. Edwards
- Civil and Environmental Engineering, Virginia Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, VA 24061, USA; (A.C.C.); (R.L.M.); (Y.S.); (A.P.)
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Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
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Asaava LLA, Githui WA, Mwangi M, Mwangi E, Juma E, Moraa R, Halakhe A, Gicheru MM. Isolation, identification and associated risk factors of non-tuberculous mycobacteria infection in humans and dromedary camels in Samburu County, Kenya. Zoonoses Public Health 2020; 67:713-731. [PMID: 32697047 DOI: 10.1111/zph.12754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Non-tuberculous mycobacteria are of public health significance, and zoonotic infection is attributed to the sociocultural practice of consumption of raw milk and the close human-livestock contact in pastoral communities. This study aimed at isolation, identification of mycobacteria from human sputum and camel milk and risk factors assessment in Samburu East, Kenya. Six hundred and twelve camels and 48 people presumed to have tuberculosis (TB) from 86 households in Wamba and Waso regions were screened. Camels were categorized into Somali, Turkana and Rendile breeds. Single intradermal comparative tuberculin test (SICTT) was used as a herd-screening test on lactating camels and a milk sample collected from reactive camels. Sputum samples were collected from eligible members of participating households. A standard questionnaire on possible risk factors for both humans and camels was administered to respective household heads or their representatives. Total camel skin test reactors were 238/612 (38.9%). Milk and sputum samples were analysed at KEMRI/TB research laboratory for microscopy, GeneXpert® , culture and identification. Isolates were identified using 16S rRNA gene sequencing at Inqaba biotec in South Africa. Sixty-four isolates were acid-fast bacilli (AFB) positive of which M. fortuitum (3), M. szulgai (20), M. monacense (5), M. lehmanni (4), M. litorale (4), M. elephantis (3), M. duvalii (3), M. brasiliensis (1), M. arcueilense (1) and M. lentiflavum (1) were from milk; M. fortuitum (1), M. szulgai (2) and M. litorale (1) were from humans. Risk factors included the following: Turkana breed (OR = 3.4; 95% CI: 1.2-9.3), replacements from outside the County (OR = 2.1; 95% CI: 0.3-12.3), presence of other domestic species (small stock; OR = 4.6) and replacement from within the herd (OR = 3.2; 95% CI: 0.7-14.7). Zoonotic risk practices included raw milk consumption, shared housing and handling camels. Monitoring of zoonotic NTM through surveillance and notification systems is required.
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Affiliation(s)
- Lucas L A Asaava
- School of Pure and Applied Sciences, Department of Zoological Sciences, Kenyatta University, Nairobi, Kenya
| | - Willie A Githui
- Tuberculosis Research Laboratory, Center for Respiratory Diseases Research (CRDR), Kenya Medical Research Institute (KEMRI), Kenyatta National Hospital Grounds, Nairobi, Kenya
| | - Moses Mwangi
- Center for Public Health Research (CPHR), Kenya Medical Research Institute (KEMRI), Kenyatta National Hospital Grounds, Nairobi, Kenya
| | - Edwin Mwangi
- Tuberculosis Research Laboratory, Center for Respiratory Diseases Research (CRDR), Kenya Medical Research Institute (KEMRI), Kenyatta National Hospital Grounds, Nairobi, Kenya
| | - Ernest Juma
- Tuberculosis Research Laboratory, Center for Respiratory Diseases Research (CRDR), Kenya Medical Research Institute (KEMRI), Kenyatta National Hospital Grounds, Nairobi, Kenya
| | - Ruth Moraa
- Tuberculosis Research Laboratory, Center for Respiratory Diseases Research (CRDR), Kenya Medical Research Institute (KEMRI), Kenyatta National Hospital Grounds, Nairobi, Kenya
| | - Adan Halakhe
- School of Pure and Applied Sciences, Department of Zoological Sciences, Kenyatta University, Nairobi, Kenya
| | - Michael M Gicheru
- School of Pure and Applied Sciences, Department of Zoological Sciences, Kenyatta University, Nairobi, Kenya
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26
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Feeding the Building Plumbing Microbiome: The Importance of Synthetic Polymeric Materials for Biofilm Formation and Management. WATER 2020. [DOI: 10.3390/w12061774] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The environmental conditions in building plumbing systems differ considerably from the larger distribution system and, as a consequence, uncontrolled changes in the drinking water microbiome through selective growth can occur. In this regard, synthetic polymeric plumbing materials are of particular relevance, since they leach assimilable organic carbon that can be utilized for bacterial growth. Here, we discuss the complexity of building plumbing in relation to microbial ecology, especially in the context of low-quality synthetic polymeric materials (i.e., plastics) and highlight the major knowledge gaps in the field. We furthermore show how knowledge on the interaction between material properties (e.g., carbon migration) and microbiology (e.g., growth rate) allows for the quantification of initial biofilm development in buildings. Hence, research towards a comprehensive understanding of these processes and interactions will enable the implementation of knowledge-based management strategies. We argue that the exclusive use of high-quality materials in new building plumbing systems poses a straightforward strategy towards managing the building plumbing microbiome. This can be achieved through comprehensive material testing and knowledge sharing between all stakeholders including architects, planners, plumbers, material producers, home owners, and scientists.
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Brumfield KD, Hasan NA, Leddy MB, Cotruvo JA, Rashed SM, Colwell RR, Huq A. A comparative analysis of drinking water employing metagenomics. PLoS One 2020; 15:e0231210. [PMID: 32271799 PMCID: PMC7145143 DOI: 10.1371/journal.pone.0231210] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/18/2020] [Indexed: 12/13/2022] Open
Abstract
The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.
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Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, CA, United States of America
| | - Joseph A. Cotruvo
- Joseph Cotruvo and Associates LLC, Washington, DC, United States of America
| | - Shah M. Rashed
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
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Shi XJ, Liu G, Zhang M, Zhao J, Li H, Yang Z, Bai H, Liang P, Lu Y. Membrane-sensitive bacterial DNA extractions and absolute quantitation of recovery efficiencies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135125. [PMID: 31812430 DOI: 10.1016/j.scitotenv.2019.135125] [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: 09/04/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Absolute quantification of waterborne pathogens is mandatory for microbiological risk assessment (MRA). Determination of the DNA recovery efficiency is an essential step before the quantitative molecular measurements, which has been largely ignored. In this study, we compared the DNA recovery efficiency and quality of five extraction methods, including two modified phenol-chloroform-based extractions with mechanical shearing and three commercial kits for the extraction of DNA from indigenous mixed-bacteria culture of river water. All of the methods gave relatively satisfying results from the pelleted sample through centrifugation. However, the commercial kits provided surprisingly low DNA yields for membrane-filtered samples because of DNA trapping and/or absorption on the membrane. Integrating with enzymatic lysis, bath sonication, phenol extraction, and alcohol precipitation achieved highest DNA yields and an acceptable DNA integrity for quantitative PCR. A plasmid containing the human GADPH gene fragment was demonstrated to be a suitable spiking control for determining the absolute DNA recovery efficiency. The unexpectedly low efficiencies of commercial kit extractions imply the significant underestimation of pathogenic bacteria in previous studies, which should gain enough concern in the area of pathogen monitoring in the future.
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Affiliation(s)
- Xiao Jie Shi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Gang Liu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Mengyu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jinbo Zhao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Huijun Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zichao Yang
- Beijing North Canal Management Division, China
| | - Huiwen Bai
- Beijing North Canal Management Division, China
| | - Pu Liang
- Beijing North Canal Management Division, China
| | - Yun Lu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Diversity of Mycobacteriaceae from aquatic environment at the São Paulo Zoological Park Foundation in Brazil. PLoS One 2020; 15:e0227759. [PMID: 31935265 PMCID: PMC6959594 DOI: 10.1371/journal.pone.0227759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/28/2019] [Indexed: 12/22/2022] Open
Abstract
We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and eighty isolates were cultivated and identified by phenotypic characteristics (growth rate and pigmentation) and sequencing of hsp65, rpoB and 16S rRNA genes. The results revealed that almost 48% of the isolates could be identified at the species level; about 50% were classified at the genus level, and only less than 2% of the isolates showed an inconclusive identification. The isolates classified at the genus level and not identified were then evaluated by phylogenetic analyses using the same three concatenated target genes. The results allowed us to identify at the genus level some isolates that previously had inconclusive identification, and they also suggested the presence of putative candidate species within the sample, demonstrating that this zoological park is an important source of diversity.
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Thompson AF, English EL, Nock AM, Willsey GG, Eckstrom K, Cairns B, Bavelock M, Tighe SW, Foote A, Shulman H, Pericleous A, Gupta S, Kadouri DE, Wargo MJ. Characterizing species interactions that contribute to biofilm formation in a multispecies model of a potable water bacterial community. MICROBIOLOGY (READING, ENGLAND) 2020; 166:34-43. [PMID: 31585061 PMCID: PMC7137775 DOI: 10.1099/mic.0.000849] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022]
Abstract
Microbial biofilms are ubiquitous in drinking water systems, yet our understanding of drinking water biofilms lags behind our understanding of those in other environments. Here, a six-member model bacterial community was used to identify the interactions and individual contributions of each species to community biofilm formation. These bacteria were isolated from the International Space Station potable water system and include Cupriavidus metallidurans, Chryseobacterium gleum, Ralstonia insidiosa, Ralstonia pickettii, Methylorubrum (Methylobacterium) populi and Sphingomonas paucimobilis, but all six species are common members of terrestrial potable water systems. Using reconstituted assemblages, from pairs to all 6 members, community biofilm formation was observed to be robust to the absence of any single species and only removal of the C. gleum/S. paucimobilis pair, out of all 15 possible 2-species subtractions, led to loss of community biofilm formation. In conjunction with these findings, dual-species biofilm formation assays supported the view that the contribution of C. gleum to community biofilm formation was dependent on synergistic biofilm formation with either R. insidiosa or C. metallidurans. These data support a model of multiple, partially redundant species interactions to generate robustness in biofilm formation. A bacteriophage and multiple predatory bacteria were used to test the resilience of the community to the removal of individual members in situ, but the combination of precise and substantial depletion of a single target species was not achievable. We propose that this assemblage can be used as a tractable model to understand the molecular bases of the interactions described here and to decipher other functions of drinking water biofilms.
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Affiliation(s)
- Alex F. Thompson
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont Gradaute College, Burlington, VT 05405, USA
| | - Erika L. English
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | - Adam M. Nock
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- Present address: Host Parasite Interactions Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Graham G. Willsey
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- The Vermont Lung Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | - Brynn Cairns
- Department of Natural Sciences, Northern Vermont University, Johnson, VT 05656, USA
| | | | - Scott W. Tighe
- The Vermont Integrated Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Andrea Foote
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont Gradaute College, Burlington, VT 05405, USA
| | - Hannah Shulman
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
| | | | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103
| | - Daniel E. Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicin, Burlington, VT 05405, USA
- The Vermont Lung Center, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
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Ibekwe AM, Murinda SE. Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects. Microorganisms 2019; 7:microorganisms7120660. [PMID: 31817873 PMCID: PMC6955928 DOI: 10.3390/microorganisms7120660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.
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Affiliation(s)
- Abasiofiok Mark Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
- Correspondence: ; Tel.: +951-369-4828
| | - Shelton E. Murinda
- Animal and Veterinary Sciences Department, Center for Antimicrobial Research and Food Safety, California State Polytechnic University, Pomona, CA 91768, USA;
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32
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Nontuberculous Mycobacteria Infection: Source and Treatment. CURRENT PULMONOLOGY REPORTS 2019. [DOI: 10.1007/s13665-019-00237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Revisiting John Snow to Meet the Challenge of Nontuberculous Mycobacterial Lung Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214250. [PMID: 31683836 PMCID: PMC6862550 DOI: 10.3390/ijerph16214250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous components of the soil and surface water microbiome. Disparities by sex, age, and geography demonstrate that both host and environmental factors are key determinants of NTM disease in populations, which predominates in the form of chronic pulmonary disease. As the incidence of NTM pulmonary disease rises across the United States, it becomes increasingly evident that addressing this emerging human health issue requires a bold, multi-disciplinary research framework that incorporates host risk factors for NTM pulmonary disease alongside the determinants of NTM residence in the environment. Such a framework should include the assessment of environmental characteristics promoting NTM growth in soil and surface water, detailed evaluations of water distribution systems, direct sampling of water sources for NTM contamination and species diversity, and studies of host and bacterial factors involved in NTM pathogenesis. This comprehensive approach can identify intervention points to interrupt the transmission of pathogenic NTM species from the environment to the susceptible host and to reduce NTM pulmonary disease incidence.
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Waak MB, LaPara TM, Hallé C, Hozalski RM. Nontuberculous Mycobacteria in Two Drinking Water Distribution Systems and the Role of Residual Disinfection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8563-8573. [PMID: 31287948 DOI: 10.1021/acs.est.9b01945] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nontuberculous mycobacteria (NTM) are frequently found in chloraminated drinking water distribution systems (DWDSs) due to their chloramine tolerance. NTM were investigated in the water-main biofilms and drinking water of a chloraminated DWDS in the United States (initial chloramine residual = 3.8 ± 0.1 mg L-1) and a DWDS in Norway with minimal residual disinfectant (0.08 ± 0.01 mg L-1). Total mycobacteria and Mycobacterium avium complex (MAC) were quantified by qPCR targeting, respectively, atpE genes and the internal transcribed spacer region. Mycobacteria concentrations in drinking water did not differ between the two systems (P = 0.09; up to 6 × 104 copies L-1) but were higher in the biofilms from the chloraminated DWDS (P = 5 × 10-9; up to 5 × 106 copies cm-2). MAC were not detected in either system. Sequencing of mycobacterial hsp65 genes indicated that the chloraminated DWDS lacked diversity and consisted almost exclusively of M. gordonae. In contrast, there were various novel mycobacteria in the no-residual DWDS. Finally, Mycobacterium- and Methylobacterium-like 16S rRNA genes were often detected simultaneously, though without correlation as previously observed. We conclude that, though residual chloramine may increase mycobacterial biomass in a DWDS, it may also decrease mycobacterial diversity.
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Affiliation(s)
- Michael B Waak
- Department of Civil, Environmental, and Geo-Engineering , University of Minnesota , 500 Pillsbury Dr. SE , Minneapolis , Minnesota 55455 , United States
- Department of Civil and Environmental Engineering , Norwegian University of Science and Technology , S.P. Andersens veg 5 , 7491 Trondheim , Norway
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering , University of Minnesota , 500 Pillsbury Dr. SE , Minneapolis , Minnesota 55455 , United States
- BioTechnology Institute , University of Minnesota , 1479 Gortner Ave. , St. Paul , Minnesota 55108 , United States
| | - Cynthia Hallé
- Department of Civil and Environmental Engineering , Norwegian University of Science and Technology , S.P. Andersens veg 5 , 7491 Trondheim , Norway
| | - Raymond M Hozalski
- Department of Civil, Environmental, and Geo-Engineering , University of Minnesota , 500 Pillsbury Dr. SE , Minneapolis , Minnesota 55455 , United States
- BioTechnology Institute , University of Minnesota , 1479 Gortner Ave. , St. Paul , Minnesota 55108 , United States
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35
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Retrospective Analysis of Nontuberculous Mycobacterial Infection and Monochloramine Disinfection of Municipal Drinking Water in Michigan. mSphere 2019; 4:4/4/e00160-19. [PMID: 31270167 PMCID: PMC6609225 DOI: 10.1128/msphere.00160-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Infections by nontuberculous mycobacteria (NTM) result in significant morbidity, mortality, and health care costs. NTM are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in drinking water disinfected with chlorine. Our results suggest that municipal drinking water disinfection with monochloramine compared to chlorine is not associated with higher risk of NTM infection. This is important given that regulations that limit drinking water concentrations of disinfection by-products, which are formed primarily when chlorine disinfection is used, incentivize drinking water utilities to change from chlorine disinfection to monochloramine disinfection. Infections by nontuberculous mycobacteria (NTM) are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in that disinfected with chlorine. However, the relationships between water treatment practices and NTM infection are unclear. The objective of this study was to examine a possible relationship between residual disinfectant used for municipal drinking water treatment (monochloramine or chlorine) and NTM infection. We retrospectively reviewed NTM diagnostic tests performed at a single health care center during a 15-year period. Information on municipal water treatment practices, including disinfectant and primary source water type, was obtained for 140 cities. Based on a logistic regression model, municipal drinking water disinfection with monochloramine compared to chlorine was not associated with NTM infection (P = 0.24). An additional model variable examining water source showed that the likelihood of having an NTM infection was 1.46 times higher for patients residing in cities with drinking water derived from surface water than for those residing in cities with drinking water derived from groundwater (odds ratio [OR], 1.46; 95% confidence interval [CI], 1.03 to 2.08; P = 0.04). In an inverse propensity score weighted regression, monochloramine disinfection was also not associated with NTM infection. A moderate effect on NTM infection rates was observed in the weighted regression for municipal drinking water derived from surface water, though the results were not statistically significant (OR, 1.24; 95% CI, 0.92 to 1.69; P = 0.17). IMPORTANCE Infections by nontuberculous mycobacteria (NTM) result in significant morbidity, mortality, and health care costs. NTM are primarily acquired from environmental sources, including exposure to municipally treated drinking water. Higher levels of NTM have been reported in drinking water disinfected with monochloramine than in drinking water disinfected with chlorine. Our results suggest that municipal drinking water disinfection with monochloramine compared to chlorine is not associated with higher risk of NTM infection. This is important given that regulations that limit drinking water concentrations of disinfection by-products, which are formed primarily when chlorine disinfection is used, incentivize drinking water utilities to change from chlorine disinfection to monochloramine disinfection.
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mSphere of Influence: Engineering Microbes. mSphere 2019; 4:4/3/e00317-19. [PMID: 31243077 PMCID: PMC6595148 DOI: 10.1128/msphere.00317-19] [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] [Indexed: 11/28/2022] Open
Abstract
Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L. Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851–8859, 2012, https://doi.org/10.1021/es302042t) and “Differential resistance of drinking water bacterial populations to monochloramine disinfection” (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038–4047, 2014, https://doi.org/10.1021/es4055725) by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.
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Loret JF, Dumoutier N. Non-tuberculous mycobacteria in drinking water systems: A review of prevalence data and control means. Int J Hyg Environ Health 2019; 222:628-634. [DOI: 10.1016/j.ijheh.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/22/2018] [Accepted: 01/06/2019] [Indexed: 02/08/2023]
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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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Ishii S. Ecology of Pathogens and Antibiotic-resistant Bacteria in Environments: Challenges and Opportunities. Microbes Environ 2019; 34:1-4. [PMID: 30930405 PMCID: PMC6440737 DOI: 10.1264/jsme2.me3401rh] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota.,BioTechnology Institute, University of Minnesota
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Zhang H, Chang F, Shi P, Ye L, Zhou Q, Pan Y, Li A. Antibiotic Resistome Alteration by Different Disinfection Strategies in a Full-Scale Drinking Water Treatment Plant Deciphered by Metagenomic Assembly. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2141-2150. [PMID: 30673217 DOI: 10.1021/acs.est.8b05907] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Disinfection regimes are considered the most solid strategy to reduce microbial risks in drinking water, but their roles in shaping the antibiotic resistome are poorly understood. This study revealed the alteration of antibiotic resistance genes (ARGs) profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts during drinking water disinfection based on metagenomic assembly. We found the ozone/chlorine (O3/Cl2) coupled disinfection significantly increased the relative abundance of ARGs and MGE-carrying antibiotic resistance contigs (ARCs) through the enrichment of ARGs within the resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux families that are primarily carried by Pseudomonas, Acinetobacter, Mycobacterium, and Methylocystis, whereas the antimicrobial resin/chlorine coupled disinfection posed unremarkable changes to the ARG and MGE abundances. Moreover, the co-occurrence patterns of antibiotic efflux and beta-lactam ARGs and MGEs were widely identified, and ARCs carrying the recR and mexH genes were detected in all the samples, with the highest abundance of 2.25 × 10-2 copies per cell after O3/Cl2 disinfection. Sequence-independent binning analysis successfully retrieved two draft ARG-carrying genomes of Acidovorax sp. MR-S7 and Hydrogenophaga sp. IBVHS2, further revealing the host-ARG relationship during O3/Cl2 disinfection. Overall, this study provides novel insights into the antibiotic resistome alteration during drinking water disinfection.
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Affiliation(s)
- Huaicheng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Fangyu Chang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Qing Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Yang Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
| | - Aimin Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , 163 Xianlin Avenue , Nanjing 210023 , China
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Guo F, Zhang T, Li B, Wang Z, Ju F, Liang YT. Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants. Sci Rep 2019; 9:836. [PMID: 30696864 PMCID: PMC6351609 DOI: 10.1038/s41598-018-37332-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium often presents as an abundant bacterial genus in activated sludge in many wastewater treatment plants (WWTPs), but the species-level taxonomy and functions remain poorly understood. In this study, we profiled the mycobacterial communities in eleven WWTPs from five countries by pyrosequencing the rpoB amplicons and searching against a customized database of mycobacterial rpoB sequences. Results indicated that major mycobacterial species were related to M. brumae, M. crocinum, M. sphagni, etc., most of which belong to poorly characterized rapidly-growing group. A few opportunistic pathogenic species were detected, suggesting the potential risk of mycobacteria in WWTPs. Genomic analysis of four isolates from activated sludge indicated these genomes contained genes of degradations of alkane, aromatics, steroids and a variety of cytochrome P450 families. Additionally, a few key genes responsible for cholesterol degradation were detected in a full-scale activated sludge metatranscriptomic dataset reported previously and taxonomically assigned to mycobacteria. Evidence showed that all isolates can degrade cholesterol, a major composition of sewage. Relative abundance of mycobacteria in activated sludge was enriched by 4.7 folds after adding cholesterol into the influent for one week. Our results provided the insights into mycobacterial species and functions in WWTPs.
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Affiliation(s)
- Feng Guo
- School of Life Sciences, Xiamen University, Xiamen, China.
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Bing Li
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Zhiping Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Ju
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yi-Ting Liang
- School of Life Sciences, Xiamen University, Xiamen, China
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Dai D, Rhoads WJ, Edwards MA, Pruden A. Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation. Front Microbiol 2018; 9:2695. [PMID: 30542327 PMCID: PMC6277882 DOI: 10.3389/fmicb.2018.02695] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022] Open
Abstract
Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes.
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Affiliation(s)
| | | | | | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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