1
|
Singh S, Ahmed AI, Almansoori S, Alameri S, Adlan A, Odivilas G, Chattaway MA, Salem SB, Brudecki G, Elamin W. A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges. Front Public Health 2024; 12:1445961. [PMID: 39139672 PMCID: PMC11319304 DOI: 10.3389/fpubh.2024.1445961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Introduction The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used to track water-borne or fecal-orally transmitted pathogens, providing a sensitive means of monitoring pathogens within a community. This technique offers a comprehensive, real-time, and cost-effective approach to disease surveillance, especially for diseases that are difficult to monitor through individual clinical screenings. Methods This narrative review examines the current state of knowledge on wastewater surveillance, emphasizing important findings and techniques used to detect potential pathogens from wastewater. It includes a review of literature on the detection methods, the pathogens of concern, and the challenges faced in the surveillance process. Results Wastewater surveillance has proven to be a powerful tool for early warning and timely intervention of infectious diseases. It can detect pathogens shed by asymptomatic and pre-symptomatic individuals, providing an accurate population-level view of disease transmission. The review highlights the applications of wastewater surveillance in tracking key pathogens of concern, such as gastrointestinal pathogens, respiratory pathogens, and viruses like SARS-CoV-2. Discussion The review discusses the benefits of wastewater surveillance in public health, particularly its role in enhancing existing systems for infectious disease surveillance. It also addresses the challenges faced, such as the need for improved detection methods and the management of antimicrobial resistance. The potential for wastewater surveillance to inform public health mitigation strategies and outbreak response protocols is emphasized. Conclusion Wastewater surveillance is a valuable tool in the fight against infectious diseases. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health.
Collapse
Affiliation(s)
- Surabhi Singh
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Amina Ismail Ahmed
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Sumayya Almansoori
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Shaikha Alameri
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Ashraf Adlan
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Giovanni Odivilas
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Marie Anne Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Laboratory, London, United Kingdom
| | - Samara Bin Salem
- Central Testing Laboratory, Abu Dhabi Quality and Conformity Council, Abu Dhabi, United Arab Emirates
| | - Grzegorz Brudecki
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Wael Elamin
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| |
Collapse
|
2
|
Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
Collapse
Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
| |
Collapse
|
3
|
Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis. WATER 2021. [DOI: 10.3390/w13243551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.
Collapse
|
4
|
Schwake DO, Alum A, Abbaszadegan M. Legionella Occurrence beyond Cooling Towers and Premise Plumbing. Microorganisms 2021; 9:microorganisms9122543. [PMID: 34946143 PMCID: PMC8706379 DOI: 10.3390/microorganisms9122543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Legionella is an environmental pathogen that is responsible for respiratory disease and is a common causative agent of water-related outbreaks. Due to their ability to survive in a broad range of environments, transmission of legionellosis is possible from a variety of sources. Unfortunately, a disproportionate amount of research that is devoted to studying the occurrence of Legionella in environmental reservoirs is aimed toward cooling towers and premise plumbing. As confirmed transmission of Legionella has been linked to many other sources, an over-emphasis on the most common sources may be detrimental to increasing understanding of the spread of legionellosis. This review aims to address this issue by cataloguing studies which have examined the occurrence of Legionella in less commonly investigated environments. By summarizing and discussing reports of Legionella in fresh water, ground water, saltwater, and distribution system drinking water, future environmental and public health researchers will have a resource to aid in investigating these pathogens in relevant sources.
Collapse
Affiliation(s)
- David Otto Schwake
- Department of Natural Sciences, Middle Georgia State University, 100 University Pkwy, Macon, GA 31206, USA;
| | - Absar Alum
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA;
| | - Morteza Abbaszadegan
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA;
- Correspondence: ; Tel.: +1-480-965-3868
| |
Collapse
|
5
|
An XL, Wang JY, Pu Q, Li H, Pan T, Li HQ, Pan FX, Su JQ. High-throughput diagnosis of human pathogens and fecal contamination in marine recreational water. ENVIRONMENTAL RESEARCH 2020; 190:109982. [PMID: 32745749 DOI: 10.1016/j.envres.2020.109982] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
Waterborne pathogens and their associated diseases are major threats to public health, and surveillance of pathogens and identification of the sources of pollution are imperative for preventing infections. However, simultaneously quantitative detection of multiple pathogens and pollution sources in water environments is the major challenge. In this study, we developed and validated a highly sensitive (mostly >80%) and highly specific (>99%) high-throughput quantitative PCR (HT-qPCR) approach, which could simultaneously quantify 68 marker genes of 33 human pathogens and 23 fecal markers of 10 hosts. The HT-qPCR approach was then successfully used to investigate pathogens and fecal pollution in marine recreational water samples of Xiamen, China. Totally, seven pathogenic marker genes were found in 13 beach bathing waters, which targeted Acanthamoeba spp., Clostridium perfringens, enteropathogenic Escherichia coli, Klebsiella pneumoniae, Vibrio cholera/V. parahaemolyticus and Legionella spp.. Fecal markers from human and dog were the most frequently detected, indicating human and dog feces were the main contamination in the recreational waters. Nanopore sequencing of full-length 16S rRNA gene revealed that 28 potential human pathogens were detected and electrical conductivity, salinity, oxidation-reduction potential and dissolved oxygen were significantly correlated with the variation in bacterial community. Our results demonstrated that HT-qPCR approach had the potential rapid quantification of microbial contamination, providing useful data for assessment of microbial pathogen associated health risk and development of management practices to protect human health.
Collapse
Affiliation(s)
- Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jia-Ying Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Pu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Ting Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan-Qin Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; College of the Environmental & Ecology, Xiamen University, 361102, China
| | - Fu-Xia Pan
- Jinan Environmental Research Institute, Jinan, 250100, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| |
Collapse
|
6
|
De Giglio O, Napoli C, Apollonio F, Brigida S, Marzella A, Diella G, Calia C, Scrascia M, Pacifico C, Pazzani C, Uricchio VF, Montagna MT. Occurrence of Legionella in groundwater used for sprinkler irrigation in Southern Italy. ENVIRONMENTAL RESEARCH 2019; 170:215-221. [PMID: 30594053 DOI: 10.1016/j.envres.2018.12.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Legionellae are opportunistic bacteria that cause various conditions after exposure to contaminated aerosols, ranging from a serious type of pneumonia to a mild case of an influenza-like illness. Despite the risks of exposure, little is known about the occurrence of Legionella in natural environments and, even though studies have shown that there is a potential risk of transmission via inhalation, it does not have to be detected in groundwater that is used for irrigation. The culture methods traditionally used to detect Legionella have several limits that can be partly solved by applying molecular techniques. Samples from 177 wells in Apulia, Southern Italy, were collected twice, in winter and in summer, and analyzed. When compared with the guidelines, 145 (81.9%) of the sampled wells were suitable for irrigation use. The culture-based method highlighted the presence of different species and serogroups of Legionella in 31 (21.2%) of the 145 wells that were shown to be suitable for irrigation use. A greater number of wells returned positive results for Legionella in summer than in winter (p = 0.023), and the median concentrations were mostly higher in summer (500 CFU/L) than in winter (300 CFU/L). The median temperature in the Legionella positive well waters was significantly higher than that in the negative ones, both in winter and in summer (p < 0.001). Using molecular techniques, Legionella non-pneumophila was found in 37 of the 114 wells earlier detected as suitable for irrigation use but negative for Legionella by the culture-based methods. The distribution of Legionella differ significantly in porous aquifers compared to the karst-fissured ones both with quantitative polymerase chain reaction (qPCR) (p = 0.0004) and viable cells by propidium monoazide (PMA-qPCR) (p = 0.0000). Legionella concentrations were weakly correlated with temperature of water both with qPCR (ρ = 0.47, p = 0.0033) and PMA-qPCR (ρ = 0.41, p = 0.0126). Our data suggest that water that aerosolizes when sprinkled on plants represents a potential source of Legionellosis, with a higher risk from exposure in summer. On a practical level, this finding is important for workers (farmers and gardeners) who are in contact with waters used for irrigation.
Collapse
Affiliation(s)
- Osvalda De Giglio
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | - Christian Napoli
- Department of Medical and Surgical sciences and translational Medicine, Sapienza University of Rome, Italy.
| | - Francesca Apollonio
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | - Silvia Brigida
- Water Research Institute, National Research Council, Bari, Italy.
| | - Angelo Marzella
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | - Giusy Diella
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | - Carla Calia
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | - Maria Scrascia
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.
| | - Claudia Pacifico
- Centre of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
| | - Carlo Pazzani
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.
| | | | - Maria Teresa Montagna
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| |
Collapse
|
7
|
Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, Fragiadakis GK, Holmes S, Gautam GP, Leach J, Sherchand JB, Bustamante CD, Sonnenburg JL. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol 2018; 16:e2005396. [PMID: 30439937 PMCID: PMC6237292 DOI: 10.1371/journal.pbio.2005396] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity's past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology.
Collapse
Affiliation(s)
- Aashish R. Jha
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
| | - Emily R. Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yoshina Gautam
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Katharine M. Ng
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | | | - Jeff Leach
- Human Food Project, Terlingua, Texas, United States of America
- Department of Twin Research and Genetic Epidemiology, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | | | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Center for Human Microbiome Studies, Stanford University, Stanford, California, United States of America
| |
Collapse
|
8
|
Shrestha RG, Tanaka Y, Malla B, Tandukar S, Bhandari D, Inoue D, Sei K, Sherchand JB, Haramoto E. Development of a Quantitative PCR Assay for Arcobacter spp. and its Application to Environmental Water Samples. Microbes Environ 2018; 33:309-316. [PMID: 30185726 PMCID: PMC6167121 DOI: 10.1264/jsme2.me18052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Arcobacter spp. are emerging pathogens associated with gastroenteritis in humans. The objective of this study was to develop a highly sensitive and broadly reactive quantitative PCR (qPCR) assay for Arcobacter spp. and to apply the developed assay to different water sources in the Kathmandu Valley, Nepal. Fifteen samples to be analyzed by next-generation sequencing were collected from 13 shallow dug wells, a deep tube well, and a river in the Kathmandu Valley in August 2015. Among the 86 potential pathogenic bacterial genera identified, Acinetobacter, Pseudomonas, Flavobacterium, and Arcobacter were detected with relatively high abundance in 15, 14, 12, and 8 samples, respectively. A primer pair was designed with maximal nucleotide homologies among Arcobacter spp. by comparing the sequences of 16S rRNA genes. These primers were highly specific to most of the known species of Arcobacter and quantified between 1.0×101 and 6.4×106 copies reaction−1 and sometimes detected as few as 3 copies reaction−1. The qPCR assay was used to quantify Arcobacter spp. in bacterial DNA in not only the above 15 water samples, but also in 33 other samples collected from 15 shallow dug wells, 6 shallow tube wells, 5 stone spouts, 4 deep tube wells, and 3 springs. Thirteen (27%) out of 48 samples tested were positive for Arcobacter spp., with concentrations of 5.3–9.1 log copies 100 mL−1. This qPCR assay represents a powerful new tool to assess the prevalence of Arcobacter spp. in environmental water samples.
Collapse
Affiliation(s)
- Rajani Ghaju Shrestha
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | - Yasuhiro Tanaka
- Department of Environmental Sciences, University of Yamanashi
| | - Bikash Malla
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | - Sarmila Tandukar
- Department of Natural, Biotic and Social Environment Engineering, University of Yamanashi
| | | | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University
| | - Kazunari Sei
- Department of Health Science, Kitasato University
| | | | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi
| |
Collapse
|
9
|
Haramoto E. Detection of Waterborne Protozoa, Viruses, and Bacteria in Groundwater and Other Water Samples in the Kathmandu Valley, Nepal. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1755-1315/120/1/012004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
10
|
Ghaju Shrestha R, Tanaka Y, Malla B, Bhandari D, Tandukar S, Inoue D, Sei K, Sherchand JB, Haramoto E. Next-generation sequencing identification of pathogenic bacterial genes and their relationship with fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 601-602:278-284. [PMID: 28558276 DOI: 10.1016/j.scitotenv.2017.05.105] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 06/07/2023]
Abstract
Bacteriological analysis of drinking water leads to detection of only conventional fecal indicator bacteria. This study aimed to explore and characterize bacterial diversity, to understand the extent of pathogenic bacterial contamination, and to examine the relationship between pathogenic bacteria and fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. Sixteen water samples were collected from shallow dug wells (n=12), a deep tube well (n=1), a spring (n=1), and rivers (n=2) in September 2014 for 16S rRNA gene next-generation sequencing. A total of 525 genera were identified, of which 81 genera were classified as possible pathogenic bacteria. Acinetobacter, Arcobacter, and Clostridium were detected with a relatively higher abundance (>0.1% of total bacterial genes) in 16, 13, and 5 of the 16 samples, respectively, and the highest abundance ratio of Acinetobacter (85.14%) was obtained in the deep tube well sample. Furthermore, the blaOXA23-like genes of Acinetobacter were detected using SYBR Green-based quantitative PCR in 13 (35%) of 37 water samples, including the 16 samples that were analyzed for next-generation sequencing, with concentrations ranging 5.3-7.5logcopies/100mL. There was no sufficient correlation found between fecal indicator bacteria, such as Escherichia coli and total coliforms, and potential pathogenic bacteria, as well as the blaOXA23-like gene of Acinetobacter. These results suggest the limitation of using conventional fecal indicator bacteria in evaluating the pathogenic bacteria contamination of different water sources in the Kathmandu Valley.
Collapse
Affiliation(s)
- Rajani Ghaju Shrestha
- Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Yasuhiro Tanaka
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Dinesh Bhandari
- Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Sarmila Tandukar
- Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan; Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Daisuke Inoue
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Division of Sustainable Energy and Environmental Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazunari Sei
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Jeevan B Sherchand
- Institute of Medicine, Tribhuvan University, Maharajgunj, Kathmandu, Nepal
| | - Eiji Haramoto
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| |
Collapse
|
11
|
Haramoto E, Kitajima M. Quantification and Genotyping of Aichi Virus 1 in Water Samples in the Kathmandu Valley, Nepal. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:350-353. [PMID: 28185207 DOI: 10.1007/s12560-017-9283-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/02/2017] [Indexed: 05/27/2023]
Abstract
Aichi virus 1 genomes were detected by quantitative PCR in groundwater from shallow dug (10/22) and tube wells (1/15), river water (14/14), and sewage (1/1), with the maximum concentration of 4.0 × 109 copies/l. Nucleotide sequencing analysis demonstrated the prevalence of genotype B in the virus positive samples.
Collapse
Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| |
Collapse
|
12
|
Deshmukh RA, Joshi K, Bhand S, Roy U. Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview. Microbiologyopen 2016; 5:901-922. [PMID: 27397728 PMCID: PMC5221461 DOI: 10.1002/mbo3.383] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022] Open
Abstract
Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.
Collapse
Affiliation(s)
- Rehan A Deshmukh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Kopal Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Sunil Bhand
- Biosensor Lab, Department of Chemistry, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| |
Collapse
|
13
|
Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL. Waterborne pathogens: detection methods and challenges. Pathogens 2015; 4:307-34. [PMID: 26011827 PMCID: PMC4493476 DOI: 10.3390/pathogens4020307] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.
Collapse
Affiliation(s)
- Flor Yazmín Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Abraham Loera-Muro
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Philippe Garneau
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Francisco Javier Avelar-González
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Josée Harel
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Alma Lilián Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| |
Collapse
|