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Marius M, Fernandez C. Non-Microbiological Mycobacterial Detection Techniques for Quality Control of Biological Products: A Comprehensive Review. Microorganisms 2024; 12:788. [PMID: 38674732 PMCID: PMC11052345 DOI: 10.3390/microorganisms12040788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients' health. For this reason, the European Pharmacopoeia mandates the specific testing of biological products for mycobacteria, a critical regulatory requirement aimed at ensuring the safety of these products before they are released to the market. The current pharmacopeial reference, i.e., microbial culture method, cannot ensure an exhaustive detection of mycobacteria due to their growth characteristics. Additionally, the method is time consuming and requires a continuous supply of culture media, posing logistical challenges. Thus, to overcome these issues, pharmaceutical industries need to consider alternative non-microbiological techniques to detect these fastidious, slow-growing contaminating agents. This review provides an overview of alternative methods, which could be applied within a quality control environment for biological products and underlines their advantages and limitations. Nucleic acid amplification techniques or direct measurement of mycobacteria stand out as the most suitable alternatives for mycobacterial testing in biological products.
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Affiliation(s)
- Marine Marius
- Sanofi, 1541 Ave. Marcel Mérieux, 69280 Marcy l’Etoile, France;
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2
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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Aoki M, Takemura Y, Kawakami S, Yoochatchaval W, Tran P. T, Tomioka N, Ebie Y, Syutsubo K. Quantitative detection and reduction of potentially pathogenic bacterial groups of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex, and Mycobacterium in wastewater treatment facilities. PLoS One 2023; 18:e0291742. [PMID: 37768925 PMCID: PMC10538766 DOI: 10.1371/journal.pone.0291742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Water quality parameters influence the abundance of pathogenic bacteria. The genera Aeromonas, Arcobacter, Klebsiella, and Mycobacterium are among the representative pathogenic bacteria identified in wastewater. However, information on the correlations between water quality and the abundance of these bacteria, as well as their reduction rate in existing wastewater treatment facilities (WTFs), is lacking. Hence, this study aimed to determine the abundance and reduction rates of these bacterial groups in WTFs. Sixty-eight samples (34 influent and 34 non-disinfected, treated, effluent samples) were collected from nine WTFs in Japan and Thailand. 16S rRNA gene amplicon sequencing analysis revealed the presence of Aeromonas, Arcobacter, and Mycobacterium in all influent wastewater and treated effluent samples. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify the abundance of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex (KpSC), and Mycobacterium. The geometric mean abundances of Aeromonas, Arcobacter, KpSC, and Mycobacterium in the influent wastewater were 1.2 × 104-2.4 × 105, 1.0 × 105-4.5 × 106, 3.6 × 102-4.3 × 104, and 6.9 × 103-5.5 × 104 cells mL-1, respectively, and their average log reduction values were 0.77-2.57, 1.00-3.06, 1.35-3.11, and -0.67-1.57, respectively. Spearman's rank correlation coefficients indicated significant positive or negative correlations between the abundances of the potentially pathogenic bacterial groups and Escherichia coli as well as water quality parameters, namely, chemical/biochemical oxygen demand, total nitrogen, nitrate-nitrogen, nitrite-nitrogen, ammonium-nitrogen, suspended solids, volatile suspended solids, and oxidation-reduction potential. This study provides valuable information on the development and appropriate management of WTFs to produce safe, hygienic water.
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Affiliation(s)
- Masataka Aoki
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Yasuyuki Takemura
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Shuji Kawakami
- Department of Civil Engineering, National Institute of Technology (KOSEN), Nagaoka College, Nagaoka, Niigata, Japan
| | - Wilasinee Yoochatchaval
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok, Thailand
| | - Thao Tran P.
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Noriko Tomioka
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Yoshitaka Ebie
- Material Cycles Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Kazuaki Syutsubo
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
- Research Center of Water Environment Technology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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4
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Marshall JE, Gebert MJ, Lipner EM, Salfinger M, Falkinham Iii JO, Prevots DR, Mercaldo RA. Methods of isolation and identification of nontuberculous mycobacteria from environmental samples: A scoping review. Tuberculosis (Edinb) 2023; 138:102291. [PMID: 36521261 DOI: 10.1016/j.tube.2022.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous in the environment. Some species of NTM are pathogenic and cause lung disease in susceptible persons. Epidemiologic studies of environmental NTM infection risk rely on both culture-dependent and culture-independent techniques for NTM isolation and identification. In this review, we summarized current methods used to isolate and identify NTM from the environment. We searched PubMed, Embase, Scopus, Web of Science: Core Collection, and Global Health (CAB Direct) for peer-reviewed studies from the last 12 years. We identified 1685 unique citations and 110 studies met our inclusion and exclusion criteria. Approximately half (55%) of the studies identified in this review used a combination of culture-independent and culture-dependent methods. The most common environmental substrate analyzed was water (n = 90). Identification of current, common methods for the isolation and identification of NTM from environmental samples may contribute to the development of standard methodological practices in the future. The choice of isolation method is based on the research question, environment, and species. A summary of common methods may contribute to the development of standard practices for isolation and identification of NTM from environmental samples, which may lead to more robust and comparable results.
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Affiliation(s)
- Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Matthew J Gebert
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Max Salfinger
- College of Public Health & Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | | | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
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Mapili K, Rhoads WJ, Coughter M, Pieper KJ, Edwards MA, Pruden A. Occurrence of opportunistic pathogens in private wells after major flooding events: A four state molecular survey. Sci Total Environ 2022; 826:153901. [PMID: 35182640 DOI: 10.1016/j.scitotenv.2022.153901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Private wells can become contaminated with waterborne pathogens during flooding events; however, testing efforts focus almost exclusively on fecal indicator bacteria. Opportunistic pathogens (OPs), which are the leading cause of identified waterborne disease in the United States, are understudied in private wells. We conducted a quantitative polymerase chain reaction survey of Legionella spp., L. pneumophila, Mycobacterium spp., M. avium, Naegleria fowleri, and shiga toxin-producing Escherichia coli gene markers and total coliform and E. coli in drinking water supplied by private wells following the Louisiana Floods (2016), Hurricane Harvey (2017), Hurricane Irma (2017), and Hurricane Florence (2018). Self-reported well characteristics and recovery status were collected via questionnaires. Of the 211 water samples collected, 40.3% and 5.2% were positive for total coliform and E. coli, which were slightly elevated positivity rates compared to prior work in coastal aquifers. DNA markers for Legionella and Mycobacterium were detected in 54.5% and 36.5% of samples, with L. pneumophila and M. avium detected in 15.6% and 17.1%, which was a similar positivity rate relative to municipal system surveys. Total bacterial 16S rRNA gene copies were positively associated with Legionella and Mycobacterium, indicating that conditions that favor occurrence of general bacteria can also favor OPs. N. fowleri DNA was detected in 6.6% of samples and was the only OP that was more prevalent in submerged wells compared to non-submerged wells. Self-reported well characteristics were not associated with OP occurrence. This study exposes the value of routine baseline monitoring and timely sampling after flooding events in order to effectively assess well water contamination risks.
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Affiliation(s)
- Kris Mapili
- Virginia Tech, Civil and Environmental Engineering, 418 Durham Hall, Blacksburg, VA 24061, United States of America
| | - William J Rhoads
- Virginia Tech, Civil and Environmental Engineering, 418 Durham Hall, Blacksburg, VA 24061, United States of America; Eawag - Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Überlandstrasse 133, 8600 Dübendorf, Switzerland.
| | - Mary Coughter
- Virginia Tech, Civil and Environmental Engineering, 418 Durham Hall, Blacksburg, VA 24061, United States of America
| | - Kelsey J Pieper
- Northeastern University, Civil and Environmental Engineering, 360 Huntington Ave., Boston, MA 02115, United States of America.
| | - Marc A Edwards
- Virginia Tech, Civil and Environmental Engineering, 418 Durham Hall, Blacksburg, VA 24061, United States of America
| | - Amy Pruden
- Virginia Tech, Civil and Environmental Engineering, 418 Durham Hall, Blacksburg, VA 24061, United States of America
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Sevillano M, Vosloo S, Cotto I, Dai Z, Jiang T, Santiago Santana JM, Padilla IY, Rosario-Pabon Z, Velez Vega C, Cordero JF, Alshawabkeh A, Gu A, Pinto AJ. Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria. Water Res X 2021; 13:100123. [PMID: 34704006 PMCID: PMC8524244 DOI: 10.1016/j.wroa.2021.100123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
Loss of basic utilities, such as drinking water and electricity distribution, were sustained for months in the aftermath of Hurricane Maria's (HM) landfall in Puerto Rico (PR) in September 2017. The goal of this study was to assess if there was deterioration in biological quality of drinking water due to these disruptions. This study characterized the microbial composition of drinking water following HM across nine drinking water systems (DWSs) in PR and utilized an extended temporal sampling campaign to determine if changes in the drinking water microbiome were indicative of HM associated disturbance followed by recovery. In addition to monitoring water chemistry, the samples were subjected to culture independent targeted and non-targeted microbial analysis including quantitative PCR (qPCR) and genome-resolved metagenomics. The qPCR results showed that residual disinfectant was the major driver of bacterial concentrations in tap water with marked decrease in concentrations from early to late sampling timepoints. While Mycobacterium avium and Pseudomonas aeruginosa were not detected in any sampling locations and timepoints, genetic material from Leptospira and Legionella pneumophila were transiently detected in a few sampling locations. The majority of metagenome assembled genomes (MAGs) recovered from these samples were not associated with pathogens and were consistent with bacterial community members routinely detected in DWSs. Further, whole metagenome-level comparisons between drinking water samples collected in this study with samples from other full-scale DWS indicated no significant deviation from expected community membership of the drinking water microbiome. Overall, our results suggest that disruptions due to HM did not result in significant and sustained deterioration of biological quality of drinking water at our study sites.
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Affiliation(s)
- Maria Sevillano
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Solize Vosloo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Irmarie Cotto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Jiang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Jose M. Santiago Santana
- Department of Natural Sciences, University of Puerto Rico, Carolina, PR, United States of America
| | - Ingrid Y. Padilla
- Department of Civil Engineering and Surveying, University of Puerto Rico, Mayagüez, PR, United States of America
| | - Zaira Rosario-Pabon
- University of Puerto Rico—Medical Sciences Campus, San Juan, PR, United States of America
| | - Carmen Velez Vega
- University of Puerto Rico—Medical Sciences Campus, San Juan, PR, United States of America
| | - José F. Cordero
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Akram Alshawabkeh
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - April Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
| | - Ameet J. Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
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Pavlik I, Ulmann V, Modra H, Gersl M, Rantova B, Zukal J, Zukalova K, Konecny O, Kana V, Kubalek P, Babak V, Weston RT. Nontuberculous Mycobacteria Prevalence in Bats' Guano from Caves and Attics of Buildings Studied by Culture and qPCR Examinations. Microorganisms 2021; 9:microorganisms9112236. [PMID: 34835362 PMCID: PMC8620717 DOI: 10.3390/microorganisms9112236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
A total of 281 guano samples were collected from caves (N = 181) in eight European countries (Bulgaria, Czech Republic, France, Hungary, Italy, Romania, Slovakia and Slovenia) and attics in the Czech R. (N = 100). The correlation of detection of mycobacteria between Ziehl–Neelsen (ZN) microscopy and culture examination and qPCR was strong. ZN microscopy was positive in guano from caves (58.6%) more than double than positivity in guano from attics (21.0%; p < 0.01). From 89 mycobacterial isolates (73 isolates from cave guano and 16 isolates from attics’ guano), 68 (76.4%) isolates of 19 sp., ssp. and complex were identified as members of three Groups (M. fortuitum, M.chelonae, and M. mucogenicum) and four complexes (M. avium, M. terrae, M.vaccae, and M.smegmatis). A total of 20 isolates (22.5%) belonged to risk group 1 (environmental saprophytes), 48 isolates (53.9%) belonged to risk group 2 (potential pathogens), and none of the isolates belonged to risk group 3 (obligatory pathogens). When comparing bat guano collected from caves and attics, differences (p < 0.01; Mann–Whitney test) were observed for the electrical conductivity, total carbon, total organic, and total inorganic carbon. No difference (p > 0.05; Mann–Whitney test) was found for pH and oxidation-reduction potential parameters.
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Affiliation(s)
- Ivo Pavlik
- Faculty of Regional Development and International Studies, Mendel University in Brno, Tr. Generala Piky 7, 613 00 Brno, Czech Republic; (H.M.); (O.K.)
- Correspondence: ; Tel.: +420-773-491-836
| | - Vit Ulmann
- Public Health Institute Ostrava, Partyzanske Nam. 7, 702 00 Ostrava, Czech Republic;
| | - Helena Modra
- Faculty of Regional Development and International Studies, Mendel University in Brno, Tr. Generala Piky 7, 613 00 Brno, Czech Republic; (H.M.); (O.K.)
| | - Milan Gersl
- Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1/1665, 613 00 Brno, Czech Republic; (M.G.); (B.R.)
| | - Barbora Rantova
- Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1/1665, 613 00 Brno, Czech Republic; (M.G.); (B.R.)
| | - Jan Zukal
- Institute of Vertebrate Biology of the Czech Academy of Sciences, v.v.i., Kvetna 8, 603 65 Brno, Czech Republic;
| | - Katerina Zukalova
- Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackeho Tr. 1946/1, 612 42 Brno, Czech Republic;
| | - Ondrej Konecny
- Faculty of Regional Development and International Studies, Mendel University in Brno, Tr. Generala Piky 7, 613 00 Brno, Czech Republic; (H.M.); (O.K.)
| | - Vlastislav Kana
- Museum Blanenska, Zamek 1/1, 678 01 Blansko, Czech Republic;
| | - Pavel Kubalek
- Central Bohemian Archaeological Heritage Institute, Nad Olsinami 448/3, 100 00 Prague, Czech Republic;
| | - Vladimir Babak
- Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic;
| | - Ross Tim Weston
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia;
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Ghosh S, Zhu NJ, Milligan E, Falkinham JO, Pruden A, Edwards MA. Mapping the Terrain for Pathogen Persistence and Proliferation in Non-potable Reuse Distribution Systems: Interactive Effects of Biofiltration, Disinfection, and Water Age. Environ Sci Technol 2021; 55:12561-12573. [PMID: 34448580 DOI: 10.1021/acs.est.1c02121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Diverse pathogens can potentially persist and proliferate in reclaimed water distribution systems (RWDSs). The goal of this study was to evaluate interactive effects of reclaimed water treatments and water age on persistence and proliferation of multiple fecal (e.g., Klebsiella, Enterobacter) and non-fecal (e.g., Legionella, mycobacteria) gene markers in RWDSs. Six laboratory-scale RWDSs were operated in parallel receiving the influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. After 3 years of operation, the RWDSs were subject to sacrificial sampling and shotgun metagenomic sequencing. We developed an in-house metagenome-derived pathogen quantification pipeline, validated by quantitative polymerase chain reaction and mock community analysis, to estimate changes in abundance of ∼30 genera containing waterborne pathogens. Microbial community composition in the RWDS bulk water, biofilm, and sediments was clearly shaped by BAC filtration, disinfectant conditions, and water age. Key commonalities were noted in the ecological niches occupied by fecal pathogen markers in the RWDSs, while non-fecal pathogen markers were more varied in their distribution. BAC-filtration + chlorine was found to most effectively control the widest range of target genera. However, filtration alone or chlorine secondary disinfection alone resulted in proliferation of some of these genera containing waterborne pathogens.
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Affiliation(s)
- Sudeshna Ghosh
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ni Joyce Zhu
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Erin Milligan
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marc A Edwards
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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Keenum I, Medina MC, Garner E, Pieper KJ, Blair MF, Milligan E, Pruden A, Ramirez-Toro G, Rhoads WJ. Source-to-Tap Assessment of Microbiological Water Quality in Small Rural Drinking Water Systems in Puerto Rico Six Months After Hurricane Maria. Environ Sci Technol 2021; 55:3775-3785. [PMID: 33645970 DOI: 10.1021/acs.est.0c08814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Maria made a landfall in Puerto Rico on September 20, 2017 as a category 4 hurricane, causing severe flooding, widespread electricity outages, damage to infrastructure, and interruptions in water and wastewater treatment. Small rural community water systems face unique challenges in providing drinking water, which intensify after natural disasters. The purpose of this study was to evaluate the functionality of six very small rural public water systems and one large regulated system in Puerto Rico six months after Maria and survey a broad sweep of fecal, zoonotic, and opportunistic pathogens from the source to tap. Samples were collected from surface and groundwater sources, after water treatment and after distribution to households. Genes indicative of pathogenic Leptospira spp. were detected by polymerase chain reaction (PCR) in all systems reliant on surface water sources. Salmonella spp. was detected in surface and groundwater sources and some distribution system water both by culture and PCR. Legionella spp. and Mycobacteria spp. gene numbers measured by quantitative PCR were similar to nonoutbreak conditions in the continental U.S. Amplicon sequencing provided a nontarget screen for other potential pathogens of concern. This study aids in improving future preparedness, assessment, and recovery operations for small rural water systems after natural disasters.
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Affiliation(s)
- Ishi Keenum
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Melitza Crespo Medina
- Center for Environmental Education, Conservation and Research, Inter American University, San Germán, Puerto Rico 00683, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Kelsey J Pieper
- Department of Civil & Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Matthew Forrest Blair
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Erin Milligan
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Graciela Ramirez-Toro
- Center for Environmental Education, Conservation and Research, Inter American University, San Germán, Puerto Rico 00683, United States
| | - William J Rhoads
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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10
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Bakker A, Siegel JA, Mendell MJ, Prussin AJ, Marr LC, Peccia J. Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors. Indoor Air 2020; 30:326-334. [PMID: 31845419 DOI: 10.1111/ina.12632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.
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Affiliation(s)
- Alexa Bakker
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jeffrey A Siegel
- Department of Civil & Mineral Engineering, The University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada
| | - Mark J Mendell
- California Department of Public Health, Environmental Health Laboratory Branch, Richmond, CA, USA
| | - Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
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11
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Perrin Y, Bouchon D, Héchard Y, Moulin L. Spatio-temporal survey of opportunistic premise plumbing pathogens in the Paris drinking water distribution system. Int J Hyg Environ Health 2019; 222:687-694. [PMID: 31085113 DOI: 10.1016/j.ijheh.2019.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/07/2019] [Accepted: 04/19/2019] [Indexed: 11/26/2022]
Abstract
Opportunistic premise plumbing pathogens present in drinking water are linked to a significant number of infections for health compromised patients. However, their monitoring is not required in current water potability standards and they have been poorly studied in a full-scale network. In this study, we quantified, by qPCR, three opportunistic pathogens, Mycobacterium spp., Legionella pneumophila, Pseudomonas aeruginosa throughout the Paris drinking water network over a one-year sampling campaign. While Mycobacteria spp. seemed ubiquitous whatever the distribution system and the time of the year, the occurrence of L. pneumophila and P. aeruginosa showed seasonal variations. Unlike L. pneumophila and P. aeruginosa, the concentration (copies number/L) of Mycobacterium spp. varied between sampling sites. The variation in microbial numbers did not demonstrate any correlations with temperature, pH, chlorine, conductivity, orthophosphate or nitrate levels. In conclusion, Mycobacterium spp. are common inhabitants of the Paris network while L. pneumophila and P. aeruginosa presence fluctuate over space and time. Such qPCR approach would help to better understand the behaviour of opportunistic premise plumbing pathogens.
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Affiliation(s)
- Yoann Perrin
- Laboratoire Ecologie et Biologie des Interactions, Equipes « Microbiologie de l'Eau » et « Ecologie, Evolution, Symbiose », Université de Poitiers, UMR CNRS 7267, F8 86073, Poitiers, France; Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, Equipes « Microbiologie de l'Eau » et « Ecologie, Evolution, Symbiose », Université de Poitiers, UMR CNRS 7267, F8 86073, Poitiers, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipes « Microbiologie de l'Eau » et « Ecologie, Evolution, Symbiose », Université de Poitiers, UMR CNRS 7267, F8 86073, Poitiers, France.
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, F-94200, Ivry sur Seine, France.
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12
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Seth-Smith HMB, Imkamp F, Tagini F, Cuénod A, Hömke R, Jahn K, Tschacher A, Grendelmeier P, Bättig V, Erb S, Reinhard M, Rütimann G, Borrell S, Gagneux S, Casanova C, Droz S, Osthoff M, Tamm M, Nübel U, Greub G, Keller PM, Egli A. Discovery and Characterization of Mycobacterium basiliense sp. nov., a Nontuberculous Mycobacterium Isolated From Human Lungs. Front Microbiol 2019; 9:3184. [PMID: 30671031 PMCID: PMC6331445 DOI: 10.3389/fmicb.2018.03184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 12/22/2022] Open
Abstract
Bacteria belonging to the genus Mycobacterium are predominantly responsible for pulmonary diseases; most notably Mycobacterium tuberculosis causes granulomatous pulmonary infections. Here we describe a novel slow growing mycobacterial species isolated from respiratory samples from five patients, four with underlying pulmonary disease. The isolates were characterized by biochemical and molecular techniques, including whole genome sequencing. Biochemical characteristics generally match those of M. marinum and M. ulcerans; however, the most striking difference of the new species is its ability to grow at 37°C. The new species was found to grow in human macrophages, but not amoebae, suggesting a pathogenic rather than an environmental lifestyle. Phylogenetic analysis reveals a deep-rooting relationship to M. marinum and M. ulcerans. A complete genome sequence was obtained through combining short and long-read sequencing, providing a genome of 5.6 Mb. The genome appears to be highly intact, syntenic with that of M. marinum, with very few insertion sequences. A vast array of virulence factors includes 283 PE/PPE surface-associated proteins, making up 10% of the coding capacity, and 22 non-ribosomal peptide synthase clusters. A comparison of six clinical isolates from the five patients shows that they differ by up to two single nucleotide polymorphisms, suggesting a common source of infection. Our findings are in accordance with the recognition of a new taxonomic entity. We propose the name M. basiliense, as all isolates were found in patients from the Basel area of Switzerland.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Florian Tagini
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Rico Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,National Center for Mycobacteria, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Kathleen Jahn
- Division of Pneumology, University Hospital Basel, Basel, Switzerland
| | - Anne Tschacher
- Division of Pneumology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Peter Grendelmeier
- Division of Pneumology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Veronika Bättig
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefan Erb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sara Droz
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Michael Osthoff
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Michael Tamm
- Division of Pneumology, University Hospital Basel, Basel, Switzerland
| | - Ulrich Nübel
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,National Center for Mycobacteria, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Adrian Egli
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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13
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Garner E, McLain J, Bowers J, Engelthaler DM, Edwards MA, Pruden A. Microbial Ecology and Water Chemistry Impact Regrowth of Opportunistic Pathogens in Full-Scale Reclaimed Water Distribution Systems. Environ Sci Technol 2018; 52:9056-9068. [PMID: 30040385 DOI: 10.1021/acs.est.8b02818] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Need for global water security has spurred growing interest in wastewater reuse to offset demand for municipal water. While reclaimed (i.e., nonpotable) microbial water quality regulations target fecal indicator bacteria, opportunistic pathogens (OPs), which are subject to regrowth in distribution systems and spread via aerosol inhalation and other noningestion routes, may be more relevant. This study compares the occurrences of five OP gene markers ( Acanthamoeba spp., Legionella spp., Mycobacterium spp., Naegleria fowleri, Pseudomonas aeruginosa) in reclaimed versus potable water distribution systems and characterizes factors potentially contributing to their regrowth. Samples were collected over four sampling events at the point of compliance for water exiting treatment plants and at five points of use at four U.S. utilities bearing both reclaimed and potable water distribution systems. Reclaimed water systems harbored unique water chemistry (e.g., elevated nutrients), microbial community composition, and OP occurrence patterns compared to potable systems examined here and reported in the literature. Legionella spp. genes, Mycobacterium spp. genes, and total bacteria, represented by 16S rRNA genes, were more abundant in reclaimed than potable water distribution system samples ( p ≤ 0.0001). This work suggests that further consideration should be given to managing reclaimed water distribution systems with respect to nonpotable exposures to OPs.
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Affiliation(s)
- Emily Garner
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Jean McLain
- Water Resources Research Center , University of Arizona , Tucson , Arizona 85719 , United States
| | - Jolene Bowers
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - David M Engelthaler
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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14
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Roguet A, Therial C, Catherine A, Bressy A, Varrault G, Bouhdamane L, Tran V, Lemaire BJ, Vincon-Leite B, Saad M, Moulin L, Lucas FS. Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes. Microb Ecol 2018; 75:834-846. [PMID: 29063147 DOI: 10.1007/s00248-017-1088-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 103 to 1.9 × 108 genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.
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Affiliation(s)
- Adélaïde Roguet
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France.
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
| | - Claire Therial
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005, Paris, France
| | - Adèle Bressy
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Gilles Varrault
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Lila Bouhdamane
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Viet Tran
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Bruno J Lemaire
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | | | - Mohamed Saad
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Laurent Moulin
- Eau de Paris, Direction Recherche et Développement Qualité de l'Eau (DRDQE), 33 avenue Jean Jaurès, FR 94200, Ivry-sur-Seine, France
| | - Françoise S Lucas
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
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15
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Li Q, Yu S, Li L, Liu G, Gu Z, Liu M, Liu Z, Ye Y, Xia Q, Ren L. Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety. Front Microbiol 2017; 8:2465. [PMID: 29312177 PMCID: PMC5733044 DOI: 10.3389/fmicb.2017.02465] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 11/27/2017] [Indexed: 12/02/2022] Open
Abstract
Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Shuili Yu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Lei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Guicai Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Zhengyang Gu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Minmin Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Zhiyuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Yubing Ye
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Qing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Liumo Ren
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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16
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Wang H, Bédard E, Prévost M, Camper AK, Hill VR, Pruden A. Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review. Water Res 2017; 117:68-86. [PMID: 28390237 PMCID: PMC5693313 DOI: 10.1016/j.watres.2017.03.046] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 05/06/2023]
Abstract
Opportunistic premise (i.e., building) plumbing pathogens (OPPPs, e.g., Legionella pneumophila, Mycobacterium avium complex, Pseudomonas aeruginosa, Acanthamoeba, and Naegleria fowleri) are a significant and growing source of disease. Because OPPPs establish and grow as part of the native drinking water microbiota, they do not correspond to fecal indicators, presenting a major challenge to standard drinking water monitoring practices. Further, different OPPPs present distinct requirements for sampling, preservation, and analysis, creating an impediment to their parallel detection. The aim of this critical review is to evaluate the state of the science of monitoring OPPPs and identify a path forward for their parallel detection and quantification in a manner commensurate with the need for reliable data that is informative to risk assessment and mitigation. Water and biofilm sampling procedures, as well as factors influencing sample representativeness and detection sensitivity, are critically evaluated with respect to the five representative bacterial and amoebal OPPPs noted above. Available culturing and molecular approaches are discussed in terms of their advantages, limitations, and applicability. Knowledge gaps and research needs towards standardized approaches are identified.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Anne K Camper
- Center for Biofilm Engineering and Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA
| | - Vincent R Hill
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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17
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Scoleri GP, Choo JM, Leong LE, Goddard TR, Shephard L, Burr LD, Bastian I, Thomson RM, Rogers GB. Culture-Independent Detection of Nontuberculous Mycobacteria in Clinical Respiratory Samples. J Clin Microbiol 2016; 54:2395-8. [PMID: 27413194 DOI: 10.1128/JCM.01410-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/20/2022] Open
Abstract
Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory samples is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical samples that is specific, sensitive, and robust.
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18
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Lee ES, Lee MH, Kim BS. Evaluation of propidium monoazide-quantitative PCR to detect viable Mycobacterium fortuitum after chlorine, ozone, and ultraviolet disinfection. Int J Food Microbiol 2015; 210:143-8. [DOI: 10.1016/j.ijfoodmicro.2015.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 06/16/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
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19
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Chern EC, King D, Haugland R, Pfaller S. Evaluation of quantitative polymerase chain reaction assays targeting Mycobacterium avium, M. intracellulare, and M. avium subspecies paratuberculosis in drinking water biofilms. J Water Health 2015; 13:131-9. [PMID: 25719473 DOI: 10.2166/wh.2014.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mycobacterium avium (MA), Mycobacterium intracellulare (MI), and Mycobacterium avium subsp. paratuberculosis (MAP) are difficult to culture due to their slow growing nature. A quantitative polymerase chain reaction (qPCR) method for the rapid detection of MA, MI, and MAP can be used to provide data supporting drinking water biofilms as potential sources of human exposure. The aim of this study was to characterize two qPCR assays targeting partial 16S rRNA gene sequences of MA and MI and use these assays, along with two previously reported MAP qPCR assays (IS900 and Target 251), to investigate Mycobacterium occurrence in kitchen faucet biofilms. MA and MI qPCR assays demonstrated 100% specificity and sensitivity when evaluated against 18 non-MA complex, 76 MA, and 17 MI isolates. Both assays detected approximately 1,000 cells from a diluted cell stock inoculated on a sampling swab 100% of the time. DNA analysis by qPCR indicated that 35.3, 56.9 and 11.8% of the 51 kitchen faucet biofilm samples collected contained MA, MI, and MAP, respectively. This study introduces novel qPCR assays designed to specifically detect MA and MI in biofilm. Results support the use of qPCR as an alternative to culture for detection and enumeration of MA, MI, and MAP in microbiologically complex samples.
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Affiliation(s)
- Eunice C Chern
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Dawn King
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Richard Haugland
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Stacy Pfaller
- National Exposure Research Laboratory, US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
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20
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Ichijo T, Izumi Y, Nakamoto S, Yamaguchi N, Nasu M. Distribution and respiratory activity of mycobacteria in household water system of healthy volunteers in Japan. PLoS One 2014; 9:e110554. [PMID: 25350137 PMCID: PMC4211706 DOI: 10.1371/journal.pone.0110554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 09/24/2014] [Indexed: 11/29/2022] Open
Abstract
The primary infectious source of nontuberculous mycobacteria (NTM), which are known as opportunistic pathogens, appears to be environmental exposure, and it is important to reduce the frequency of exposure from environmental sources for preventing NTM infections. In order to achieve this, the distribution and respiratory activity of NTM in the environments must be clarified. In this study, we determined the abundance of mycobacteria and respiratory active mycobacteria in the household water system of healthy volunteers using quantitative PCR and a fluorescent staining method, because household water has been considered as one of the possible infectious sources. We chose healthy volunteer households in order to lessen the effect of possible residential contamination from an infected patient. We evaluated whether each sampling site (bathroom drain, kitchen drain, bath heater pipe and showerhead) have the potential to be the sources of NTM infections. Our results indicated that drains in the bathroom and kitchen sink are the niche for Mycobacterium spp. and M. avium cells were only detected in the bathtub inlet. Both physicochemical and biologic selective pressures may affect the preferred habitat of Mycobacterium spp. Regional differences also appear to exist as demonstrated by the presence (US) or absence (Japan) of Mycobacterium spp. on showerheads. Understanding of the country specific human activities and water usage will help to elucidate the infectious source and route of nontuberculous mycobacterial disease.
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Affiliation(s)
- Tomoaki Ichijo
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Research Institute for Humanity and Nature, Kyoto, Japan
| | - Yoko Izumi
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Sayuri Nakamoto
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Nobuyasu Yamaguchi
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- * E-mail:
| | - Masao Nasu
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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21
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Radomski N, Roguet A, Lucas FS, Veyrier FJ, Cambau E, Accrombessi H, Moilleron R, Behr MA, Moulin L. atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples. BMC Microbiol 2013; 13:277. [PMID: 24299240 PMCID: PMC4219376 DOI: 10.1186/1471-2180-13-277] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background The environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets. Results Among the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples. Conclusions The results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.
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Affiliation(s)
- Nicolas Radomski
- Laboratoire Eau Environnement Systèmes Urbains (Leesu) UMR MA 102-AgroParisTech, Université Paris-Est, 6-8 avenue Blaise Pascal Cité, Descartes, FR 77455, Champs sur Marne, France.
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Räsänen NH, Rintala H, Miettinen IT, Torvinen E. Comparison of culture and qPCR methods in detection of mycobacteria from drinking waters. Can J Microbiol 2013; 59:280-6. [DOI: 10.1139/cjm-2012-0695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Environmental mycobacteria are common bacteria in man-made water systems and may cause infections and hypersensitivity pneumonitis via exposure to water. We compared a generally used cultivation method and a quantitative polymerase chain reaction (qPCR) method to detect mycobacteria in 3 types of drinking waters: surface water, ozone-treated surface water, and groundwater. There was a correlation between the numbers of mycobacteria obtained by cultivation and qPCR methods, but the ratio of the counts obtained by the 2 methods varied among the types of water. The qPCR counts in the drinking waters produced from surface or groundwater were 5 to 34 times higher than culturable counts. In ozone-treated surface waters, both methods gave similar counts. The ozone-treated drinking waters had the highest concentration of assimilable organic carbon, which may explain the good culturability. In warm tap waters, qPCR gave 43 times higher counts than cultivation, but both qPCR counts and culturable counts were lower than those in the drinking waters collected from the same sites. The TaqMan qPCR method is a rapid and sensitive tool for total quantitation of mycobacteria in different types of clean waters. The raw water source and treatments affect both culturability and total numbers of mycobacteria in drinking waters.
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Affiliation(s)
- Noora H.J. Räsänen
- Department of Environmental Science, University of Eastern Finland, P.O. Box 1627, FI-70211, Finland
- Department of Biology, University of Eastern Finland, P.O. Box 111, FI-80101, Finland
| | - Helena Rintala
- Environmental Microbiology Unit, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ilkka T. Miettinen
- Water and Health Unit, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Eila Torvinen
- Department of Environmental Science, University of Eastern Finland, P.O. Box 1627, FI-70211, Finland
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Wang H, Edwards M, Falkinham JO 3rd, Pruden A. Molecular survey of the occurrence of Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa, and amoeba hosts in two chloraminated drinking water distribution systems. Appl Environ Microbiol 2012; 78:6285-94. [PMID: 22752174 DOI: 10.1128/AEM.01492-12] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spread of opportunistic pathogens via public water systems is of growing concern. The purpose of this study was to identify patterns of occurrence among three opportunistic pathogens (Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa) relative to biotic and abiotic factors in two representative chloraminated drinking water distribution systems using culture-independent methods. Generally, a high occurrence of Legionella (≥69.0%) and mycobacteria (100%), lower occurrence of L. pneumophila (≤20%) and M. avium (≤33.3%), and rare detection of Pseudomonas aeruginosa (≤13.3%) were observed in both systems according to quantitative PCR. Also, Hartmanella vermiformis was more prevalent than Acanthamoeba, both of which are known hosts for opportunistic pathogen amplification, the latter itself containing pathogenic members. Three-minute flushing served to distinguish distribution system water from plumbing in buildings (i.e., premise plumbing water) and resulted in reduced numbers of copies of Legionella, mycobacteria, H. vermiformis, and 16S rRNA genes (P < 0.05) while yielding distinct terminal restriction fragment polymorphism (T-RFLP) profiles of 16S rRNA genes. Within certain subgroups of samples, some positive correlations, including correlations of numbers of mycobacteria and total bacteria (16S rRNA genes), H. vermiformis and total bacteria, mycobacteria and H. vermiformis, and Legionella and H. vermiformis, were noted, emphasizing potential microbial ecological relationships. Overall, the results provide insight into factors that may aid in controlling opportunistic pathogen proliferation in real-world water systems.
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Radomski N, Betelli L, Moilleron R, Haenn S, Moulin L, Cambau E, Rocher V, Gonçalves A, Lucas FS. Mycobacterium behavior in wastewater treatment plant, a bacterial model distinct from Escherichia coli and Enterococci. Environ Sci Technol 2011; 45:5380-6. [PMID: 21591688 DOI: 10.1021/es104084c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Mycobacteria are waterborne emerging pathogens causing infections in human. Mycobacteria have been previously isolated from wastewater and sludge, but their densities were not estimated due to cultural biases. In order to evaluate the impact of wastewater treatment processes on mycobacteria removal, we used a real time PCR method. First we compared six DNA extraction methods and second we used the more efficient DNA extraction procedure (i.e., enzymatic lysis combined with hexadecyltrimethylammonium bromide-NaCl procedure) in order to quantify Mycobacterium. With the aim to identify parameters that could serve as indicator of mycobacterial behavior, mycobacterial densities were measured in parallel to those of Escherichia coli and enterococci, and to concentrations of chemical parameters usually monitored in wastewater. Mycobacterium reached 5.5 × 10⁵ ± 3.9 × 10⁵ copies/L in the influent, but was not detected in the effluent after decantation and biofiltration. Most mycobacteria (98.6 ± 2.7%, i.e. 2.4 ± 0.7 log₁₀) were removed by the physical-chemical decantation, and the remaining mycobacteria were removed by biofiltration. In contrast, enterococci and E. coli were lightly removed by decantation step and mainly removed by biofiltration. Our results showed that Mycobacterium corresponds to a hydrophobic behavior linked to insoluble compound removal, whereas enterococci and E. coli refer to hydrophilic behaviors linked to soluble compound removals.
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Affiliation(s)
- Nicolas Radomski
- Laboratoire Eau Environnement Systèmes Urbains UMR MA 102 AgroParisTech, Université Paris-Est, FR 77455 Champs sur Marne.
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