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Länsivaara A, Lehto KM, Hyder R, Janhonen ES, Lipponen A, Heikinheimo A, Pitkänen T, Oikarinen S. Comparison of Different Reverse Transcriptase-Polymerase Chain Reaction-Based Methods for Wastewater Surveillance of SARS-CoV-2: Exploratory Study. JMIR Public Health Surveill 2024; 10:e53175. [PMID: 39158943 DOI: 10.2196/53175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/09/2024] [Accepted: 05/30/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND Many countries have applied the wastewater surveillance of the COVID-19 pandemic to their national public health monitoring measures. The most used methods for detecting SARS-CoV-2 in wastewater are quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) and reverse transcriptase-droplet digital polymerase chain reaction (RT-ddPCR). Previous comparison studies have produced conflicting results, thus more research on the subject is required. OBJECTIVE This study aims to compare RT-qPCR and RT-ddPCR for detecting SARS-CoV-2 in wastewater. It also aimed to investigate the effect of changes in the analytical pipeline, including the RNA extraction kit, RT-PCR kit, and target gene assay, on the results. Another aim was to find a detection method for low-resource settings. METHODS We compared 2 RT-qPCR kits, TaqMan RT-qPCR and QuantiTect RT-qPCR, and RT-ddPCR based on sensitivity, positivity rates, variability, and correlation of SARS-CoV-2 gene copy numbers in wastewater to the incidence of COVID-19. Furthermore, we compared 2 RNA extraction methods, column- and magnetic-bead-based. In addition, we assessed 2 target gene assays for RT-qPCR, N1 and N2, and 2 target gene assays for ddPCR N1 and E. Reverse transcription strand invasion-based amplification (RT-SIBA) was used to detect SARS-CoV-2 from wastewater qualitatively. RESULTS Our results indicated that the most sensitive method to detect SARS-CoV-2 in wastewater was RT-ddPCR. It had the highest positivity rate (26/30), and its limit of detection was the lowest (0.06 gene copies/µL). However, we obtained the best correlation between COVID-19 incidence and SARS-CoV-2 gene copy number in wastewater using TaqMan RT-qPCR (correlation coefficient [CC]=0.697, P<.001). We found a significant difference in sensitivity between the TaqMan RT-qPCR kit and the QuantiTect RT-qPCR kit, the first having a significantly lower limit of detection and a higher positivity rate than the latter. Furthermore, the N1 target gene assay was the most sensitive for both RT-qPCR kits, while no significant difference was found between the gene targets using RT-ddPCR. In addition, the use of different RNA extraction kits affected the result when the TaqMan RT-qPCR kit was used. RT-SIBA was able to detect SARS-CoV-2 RNA in wastewater. CONCLUSIONS As our study, as well as most of the previous studies, has shown RT-ddPCR to be more sensitive than RT-qPCR, its use in the wastewater surveillance of SARS-CoV-2 should be considered, especially if the amount of SARS-CoV-2 circulating in the population was low. All the analysis steps must be optimized for wastewater surveillance as our study showed that all the analysis steps including the compatibility of the RNA extraction, the RT-PCR kit, and the target gene assay influence the results. In addition, our study showed that RT-SIBA could be used to detect SARS-CoV-2 in wastewater if a qualitative result is sufficient.
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Affiliation(s)
- Annika Länsivaara
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rafiqul Hyder
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Anssi Lipponen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority - Ruokavirasto, Seinäjoki, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Badilla-Aguilar A, Hallack DMC, Ginn O, Snyder E, Bolster D, Tank JL, Bibby K. Streambed immobilization controls the transport of antibiotic resistance genes in flowing water. WATER RESEARCH 2024; 259:121833. [PMID: 38865913 DOI: 10.1016/j.watres.2024.121833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024]
Abstract
Antibiotic resistance is a serious global health issue, resulting in at least 1.2 million deaths in 2019. The environment is a potentially important reservoir of antibiotic resistance; however, the fate of Antibiotic Resistance Genes (ARGs) in the environment remains poorly characterized. One important environmental source of ARGs is manure used as a soil amendment. ARGs from manure may then enter nearby flowing waterbodies, where the factors governing their downstream transport remain unknown. To address this, we conducted experiments by spiking cattle manure in an artificial stream to estimate removal rates (k; m-1) for three ARGs (mefA, tetQ, and tetW) and a ruminant fecal marker (bacR). We then used a Stochastic Mobile-Immobile Model (SMIM) to separate the overall removal into two components, rs, and rh, corresponding to immobilizations in the surface (i.e., water column) and subsurface (i.e., streambed), respectively. Finally, we applied the SMIM across four model streams to predict the downstream travel distance of ARGs and bacR. Our results showed measurable removal for all targets in all experimental replicates (n = 3) and no differences were found in the removal rates among replicates for any target (ANCOVA; p > 0.05). We found that the removal of bacR was significantly lower than tetW (p < 0.05) and slightly lower than mefA (p = 0.088), while tetQ removal was slightly different from tetW's (p = 0.072). We also found that rh values were orders of magnitude larger than rs for ARGs and bacR (t-test; p < 0.05). These findings suggest that ARGs and bacR are being removed from the water column through immobilization reactions occurring in the streambed. Additionally, we predicted that the 90 % removal (or D90) of targets occurs within the first 500 m in all model streams except in a slow-flow pastoral stream, which required 1400 m of downstream transport for 90 % removal. Our findings and model stand out as promising tools to predict the fate of ARGs in streams and will contribute to improving and managing agricultural practices that employ animal manure.
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Affiliation(s)
- A Badilla-Aguilar
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - D M C Hallack
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - O Ginn
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556 USA; School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA
| | - E Snyder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - D Bolster
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - J L Tank
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - K Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN 46556, USA.
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Kahler AM, Hofstetter J, Arrowood M, Peterson A, Jacobson D, Barratt J, da Silva ALBR, Rodrigues C, Mattioli MC. Sources and Prevalence of Cyclospora cayetanensis in Southeastern U.S. Growing Environments. J Food Prot 2024; 87:100309. [PMID: 38815808 DOI: 10.1016/j.jfp.2024.100309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Recent cyclosporiasis outbreaks associated with fresh produce grown in the United States highlight the need to better understand Cyclospora cayetanensis prevalence in U.S. agricultural environments. In this study, C. cayetanensis occurrence was assessed in municipal wastewater sludge, on-farm portable toilets, irrigation pond water, and spent packing house dump tank water in a Southeastern Georgia growing region over two years. Detection of the C. cayetanensis 18S rRNA qPCR gene target in pond samples was 0%, 28%, and 42% (N = 217) depending on the detection definition used, and ≤1% in dump tank samples (N = 46). However, no qPCR detections were confirmed by sequencing, suggesting false detection occurred due to cross-reactions. C. cayetanensis qPCR detections were confirmed in 9% of wastewater sludge samples (N = 76). The human-specific fecal markers HF183 and crAssphage were detected in 33% and 6% of pond samples, respectively, and 4% and 0% of dump tank samples, respectively. Despite community Cyclospora shedding and evidence of human fecal contamination in irrigation water, there was no correlation between C. cayetanensis and HF183 qPCR detections, further supporting that 18S gene target qPCR amplifications were due to cross-reactions. When evaluating C. cayetanensis qPCR environmental detection data, the impact of assay specificity and detection criteria should be considered. Moreover, additional sequence-based testing may be needed to appropriately interpret Cyclospora qPCR environmental data.
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Affiliation(s)
- Amy M Kahler
- Centers for Disease Control and Prevention (CDC), Division of Foodborne, Waterborne, and Environmental Diseases, Atlanta, GA 30329, USA
| | - Jessica Hofstetter
- Chenega Enterprise Systems & Solutions, LLC, Chesapeake, VA 23320, USA; Auburn University, Department of Horticulture, Auburn, AL 36849, USA
| | - Michael Arrowood
- Centers for Disease Control and Prevention (CDC), Division of Foodborne, Waterborne, and Environmental Diseases, Atlanta, GA 30329, USA
| | - Anna Peterson
- Centers for Disease Control and Prevention (CDC), Division of Parasitic Diseases and Malaria, Atlanta, GA 30329, USA
| | - David Jacobson
- Centers for Disease Control and Prevention (CDC), Division of Parasitic Diseases and Malaria, Atlanta, GA 30329, USA
| | - Joel Barratt
- Centers for Disease Control and Prevention (CDC), Division of Parasitic Diseases and Malaria, Atlanta, GA 30329, USA
| | | | - Camila Rodrigues
- Auburn University, Department of Horticulture, Auburn, AL 36849, USA
| | - Mia C Mattioli
- Centers for Disease Control and Prevention (CDC), Division of Foodborne, Waterborne, and Environmental Diseases, Atlanta, GA 30329, USA.
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Walsh JF, Scher DP, de Lambert JR, Anderson AC. Risk factors for Cryptosporidium contamination in Minnesota public supply wells. JOURNAL OF WATER AND HEALTH 2024; 22:612-626. [PMID: 38557575 DOI: 10.2166/wh.2024.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/23/2024] [Indexed: 04/04/2024]
Abstract
In a recent monitoring study of Minnesota's public supply wells, Cryptosporidium was commonly detected with 40% of the wells having at least one detection. Risk factors for Cryptosporidium occurrence in drinking water supply wells, beyond surface water influence, remain poorly understood. To address this gap, physical and chemical factors were assessed as potential predictors of Cryptosporidium occurrence in 135 public supply wells in Minnesota. Univariable analysis, regression techniques, and classification trees were used to analyze the data. Many variables were identified as significant risk factors in univariable analysis and several remained significant throughout the succeeding analysis techniques. These factors fell into general categories of well use and construction, aquifer characteristics, and connectedness to the land surface, well capture zones, and land use therein, existence of potential contaminant sources within 200-feet of the well, and variability in the chemical and isotopic parameters measured during the study. These risk categories, and the specific variables and threshold values we have identified, can help guide future research on factors influencing Cryptosporidium contamination of wells and can be used by environmental health programs to develop risk-based sampling plans and design interventions that reduce associated health risks.
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Affiliation(s)
- James F Walsh
- Minnesota Department of Health (retired), Saint Paul, MN 55164-0975, USA
| | - Deanna P Scher
- Minnesota Department of Health, Saint Paul, MN 55164-0975, USA E-mail:
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He P, Zhou W, Wei H, Yu J. Fast and Ultrasensitive Detection of Monkeypox by a Pyrococcus furiosus Argonaute System Coupled with a Short Amplification. Viruses 2024; 16:382. [PMID: 38543748 PMCID: PMC10975468 DOI: 10.3390/v16030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/17/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Monkeypox virus (MPXV), the pathogen responsible for the infectious disease monkeypox, causes lesions on the skin, lymphadenopathy, and fever. It has posed a global public health threat since May 2022. Highly sensitive and specific detection of MPXV is crucial for preventing the spread of the disease. Pyrococcus furiosus Argonaute (PfAgo) is an artificial DNA-guided restriction cleavage enzyme programmable with 5'-phosphorylated ssDNA sequences, which can be developed to specifically detect nucleic acids of pathogens. Here, a PfAgo-based system was established for the detection of MPXV-specific DNA targeting the F3L gene. A short amplicon of 79 bp could be obtained through a fast PCR procedure, which was completed within 45 min. Two 5'-phosphorylation guide DNAs were designed to guide PfAgo to cleave the amplicon to obtain an 18 bp 5'-phosphorylation sequence specific to MPXV, not to other orthopoxviruses (cowpox, variola, and vaccinia viruses). The 18 bp sequence guided PfAgo to cleave a designed probe specific to MPXV to emit fluorescence. With optimized conditions for the PfAgo-MPXV system, it could be completed in 60 min for the detection of the extracted MPXV DNA with the limit of detection (LOD) of 1.1 copies/reaction and did not depend on expensive instruments. Successful application of the PfAgo-MPXV system in sensitively detecting MPXV in simulated throat swabs, skin swabs, sera, and wastewater demonstrated the system's good performance. The PfAgo platform, with high sensitivity and specificity established here, has the potential to prevent the spread of MPXV.
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Affiliation(s)
- Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Zhao B, Fujita T, Nihei Y, Yu Z, Chen X, Tanaka H, Ihara M. Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166420. [PMID: 37611711 DOI: 10.1016/j.scitotenv.2023.166420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in regions of low prevalence, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Here, we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to December 2022 during the third, fourth, fifth, sixth, seventh, and eighth waves of the COVID-19 outbreak in Japan. Viral RNA was below the limit of detection in all samples during the third and fourth waves. However, by counting the number of positive replicates in qPCR of each sample, we found that the positive ratio to all replicates in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during the third, fourth, and fifth waves. Time-step analysis indicated that, for 2 days either side of symptom onset, COVID-19 patients excreted in their feces large amounts of virus that wastewater surveillance could detect. We also demonstrated that the viral genome copy number in wastewater, as estimated from the positive ratio of SARSA-CoV-2 RNA, was correlated with the number of clinically confirmed cases. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.
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Affiliation(s)
- Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Tomonori Fujita
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Yoshiaki Nihei
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Water Agency Inc., 3-25 Higashi-Goken-cho, Shinjuku-ku, Tokyo 162-0813, Japan
| | - Zaizhi Yu
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Xiaohan Chen
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe-Otsu, Nankoku city, Kochi 783-8502, Japan.
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Rao G, Capone D, Zhu K, Knoble A, Linden Y, Clark R, Lai A, Kim J, Huang CH, Bivins A, Brown J. Simultaneous detection and quantification of multiple pathogen targets in wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.23.23291792. [PMID: 37425908 PMCID: PMC10327253 DOI: 10.1101/2023.06.23.23291792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
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Affiliation(s)
- Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Kevin Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abigail Knoble
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ryan Clark
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ching-Hua Huang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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8
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Ginn O, Tank JL, Badilla-Aguilar A, Snyder E, Brandão-Dias PFP, Thrift E, Bolster D, Bibby K. Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37290054 DOI: 10.1021/acs.est.3c02374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antibiotic resistance (AR) determinants are enriched in animal manures, a significant portion of which is land-applied as a soil amendment or as fertilizer, leading to potential AR runoff and microbial pollution in adjacent surface waters. To effectively inform AR monitoring and mitigation efforts, a thorough understanding and description of the persistence and transport of manure-derived AR in flowing waters are needed. We used experimental recirculating mesocosms to assess water-column removal rates of antibiotic resistance genes (ARGs) originating from a cow manure slurry collected from a dairy farm. We quantified the effect of three benthic (i.e., bottom) substrate variations and particle sizes of manure slurry on water column removal rates. Overall, we observed variation in ARG behavior across substrate treatments and particle sizes. For ARGs associated with small particles, removal rates were higher in mesocosms with a substrate. tetW was typically removed at the highest rates across particle size and treatment, followed by ermB and blaTEM. Our data suggests that both substrate character and particle size exert control on the fate and transport of ARGs in surface waters, laying the foundation for future research in this area to establish a predictive framework for AR persistence and fate in flowing waters.
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Affiliation(s)
- Olivia Ginn
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andrei Badilla-Aguilar
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elise Snyder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | | | - Emma Thrift
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Diogo Bolster
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Capone D, Bivins A, Brown J. Producing ratio measures of effect with quantitative microbial risk assessment. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023. [PMID: 35689350 DOI: 10.17605/osf.io/jwzy9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.
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Affiliation(s)
- Drew Capone
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Capone D, Bivins A, Brown J. Producing ratio measures of effect with quantitative microbial risk assessment. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023; 43:917-927. [PMID: 35689350 PMCID: PMC9734285 DOI: 10.1111/risa.13972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/06/2023]
Abstract
Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.
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Affiliation(s)
- Drew Capone
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aaron Bivins
- Louisiana State University, Baton Rouge, Louisiana, USA
| | - Joe Brown
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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11
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Alegbeleye O, Sant'Ana AS. Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance. ENVIRONMENTAL RESEARCH 2023; 220:114771. [PMID: 36586712 DOI: 10.1016/j.envres.2022.114771] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.
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Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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12
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Capone D, Adriano Z, Cumming O, Irish SR, Knee J, Nala R, Brown J. Urban Onsite Sanitation Upgrades and Synanthropic Flies in Maputo, Mozambique: Effects on Enteric Pathogen Infection Risks. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:549-560. [PMID: 36516327 PMCID: PMC9835884 DOI: 10.1021/acs.est.2c06864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Synanthropic filth flies transport enteric pathogens from feces to food, which upon consumption poses an infection risk. We evaluated the effect of an onsite sanitation intervention─including fly control measures─in Maputo, Mozambique, on the risk of infection from consuming fly-contaminated food. After enumerating flies at intervention and control sites, we cultured fecal indicator bacteria, quantified gene copies for 22 enteric pathogens via reverse transcription quantitative polymerase chain reaction (RT-qPCR), and developed quantitative microbial risk assessment (QMRA) models to estimate annual risks of infection attributable to fly-contaminated foods. We found that the intervention reduced fly counts at latrine entrances by 69% (aRR = 0.31, [0.13, 0.75]) but not at food preparation areas (aRR = 0.92, [0.33, 2.6]). Half of (23/46) of individual flies were positive for culturable Escherichia coli, and we detected ≥1 pathogen gene from 45% (79/176) of flies, including enteropathogenic E. coli (37/176), adenovirus (25/176), Giardia spp. (13/176), and Trichuris trichiura (12/176). We detected ≥1 pathogen gene from half the flies caught in control (54%, 30/56) and intervention compounds (50%, 17/34) at baseline, which decreased 12 months post-intervention to 43% (23/53) at control compounds and 27% (9/33) for intervention compounds. These data indicate flies as a potentially important mechanical vector for enteric pathogen transmission in this setting. The intervention may have reduced the risk of fly-mediated enteric infection for some pathogens, but infrequent detection resulted in wide confidence intervals; we observed no apparent difference in infection risk between groups in a pooled estimate of all pathogens assessed (aRR = 0.84, [0.61, 1.2]). The infection risks posed by flies suggest that the design of sanitation systems and service delivery should include fly control measures to prevent enteric pathogen transmission.
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Affiliation(s)
- Drew Capone
- Department
of Environmental and Occupational Health, School of Public Health, Indiana University, 2719 E 10th St, Bloomington, Indiana47401, United States
| | - Zaida Adriano
- WE
Consult ltd, 177 Rua
Tomas Ribeiro, Maputo1102, Mozambique
| | - Oliver Cumming
- Department
of Disease Control, London School of Hygiene
and Tropical Medicine, LondonWC1E 7HT, United
Kingdom
| | - Seth R. Irish
- Epidemiology
and Public Health Department, Swiss Tropical
and Public Health Institute, Kreuzstrasse 2, Allschwil4123, Switzerland
| | - Jackie Knee
- Department
of Disease Control, London School of Hygiene
and Tropical Medicine, LondonWC1E 7HT, United
Kingdom
| | - Rassul Nala
- Ministério
da Saúde, Instituto Nacional de Saúde
Maputo, Maputo1102, Mozambique
| | - Joe Brown
- Department
of Environmental Sciences and Engineering, Gillings School of Public
Health, University of North Carolina at
Chapel Hill, Chapel
Hill, North Carolina27599, United States
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13
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Direct and Rapid Identification of Vibrio Cholerae Serogroup and Toxigenicity by a Novel Multiplex Real-Time Assay. Pathogens 2022; 11:pathogens11080865. [PMID: 36014986 PMCID: PMC9416260 DOI: 10.3390/pathogens11080865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/27/2022] Open
Abstract
Molecular diagnostic assays for cholera detection have superior sensitivity to conventional assays and are now being accepted as the new standard method, especially the real-time PCR/RT-PCR. However, limited throughput capacity and long detection duration prevent them from detecting more specimens and more targets in one turnaround time simultaneously. In this study, we utilized nucleic acid extraction-free, direct RT-PCR and high-speed amplification to develop a novel multiplex assay, a quadplex direct one-tube real-time RT-PCR assay, for rapid detection of the serogroup and cholera toxin toxigenicity of Vibrio cholerae targeting the epsM, ctxA, rfb-O1, and rfb-O139 genes. Performance of the multiplex assay was evaluated by comparison with the monoplex real-time PCR assay according to the China Cholera Prevention Manual. Detection data from clinical specimens showed that the new assay had good diagnostic sensitivities for epsM (100%, n = 301), ctxA (100%, n = 125), rfb-O1 (100%, n = 85), and rfb-O139 (97.87%, n = 49). Analysis of the analytical sensitivities with serial dilutions of positive standards showed that the detection limits of the new assay for Vibrio cholerae epsM,ctxA,rfb-O1, and rfb-O139 were up to 200, 590, 115, and 1052 copies per mL lower than the monoplex real-time PCR (910, 345, and 1616 copies/mL respectively, for ctxA,rfb-O1, and rfb-O139). The results indicate that the multiplex assay is a rapid, sensitive, specific, and easy-to-use detection tool for Vibrio cholerae, especially suitable for rapid identification and screening detection of mass specimens.
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14
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Mota TF, Brodskyn CI, Morello LG, Marchini FK, Krieger MA, de Cássia Pontello Rampazzo R, Fraga DBM. Multiplex qPCR assay to determine Leishmania infantum load in Lutzomyia longipalpis sandfly samples. MEDICAL AND VETERINARY ENTOMOLOGY 2022; 36:176-184. [PMID: 35089617 DOI: 10.1111/mve.12564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The study aimed to develop a multiplex qPCR to detect Leishmania infantum load in different sandfly sample settings using Leishmania kDNA and sandfly vacuolar ATPase (VATP) subunit C as internal control gene. The amplification of Lutzomyia longipalpis VATP gene was evaluated together with Leishmania infantum kDNA in a multiplex reaction. The concentration of VATP gene oligonucleotides was adjusted until no statistically significant difference was observed between all multiplex standard curves and singleplex curves, that is, only kDNA amplification. Limit of detection (LoD) was measured using a probit model and a cut-off defined by receiver operating characteristic analysis. Limit of quantification (LoQ) was assessed by a linear model using the coefficient of variation threshold of 25%. After assuring VATP gene amplification, its primer-probe concentrations were best at 100 nM/10 nM, respectively. The cut-off Cq value for L. infantum kDNA was defined as 35.46 with 100% of sensitivity and specificity. A total of 95% LoD was determined to be of 0.162 parasites while LoQ was 5.858. Our VATP/kDNA multiplex qPCR assay shows that it can be used to evaluate both DNA integrity and determine L. infantum load in L. longipalpis even for low yielded samples, that is, individual midguts.
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Affiliation(s)
- Tiago Feitosa Mota
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
| | - Claudia Ida Brodskyn
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
| | - Luis Gustavo Morello
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, Curitiba, Brazil
| | - Fabricio Klerynton Marchini
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, Curitiba, Brazil
| | - Marco Aurelio Krieger
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, Curitiba, Brazil
| | | | - Deborah Bittencourt Mothé Fraga
- Laboratório de Interação Parasito-Hospedeiro e Epidemiologia (LaIPHE), Instituto Gonçalo Moniz (IGM), FIOCRUZ-BA, Rua Waldemar Falcão, Salvador, Brazil
- Departamento de Medicina Veterinária Preventiva e Produção Animal, Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
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15
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Fast and Sensitive Multiplex Real-Time Quantitative PCR to Detect Cutibacterium Periprosthetic Joint Infections. J Mol Diagn 2022; 24:666-673. [PMID: 35364323 DOI: 10.1016/j.jmoldx.2022.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Diagnosis of Cutibacterium periprosthetic joint infections (PJIs) is challenging due to a long cultivation time of up to 14 days. Faster culture-independent diagnosis would improve patient care with early and accurate treatment. Specific primers and probes were designed for Cutibacterium acnes, Cutibacterium avidum, and Cutibacterium granulosum and evaluated in a multiplex TaqMan real-time quantitative PCR (qPCR) format on 57 skin swabs and 20 culture-negative cerebrospinal fluid samples. The multiplex qPCR was tested in a PJI cohort of 41 sonication fluid samples from removed implants infected with different pathogens. All five culture-positive Cutibacterium PJIs were detected with the corresponding Cutibacterium-specific probe (100% positive percent agreement). The multiplex qPCR additionally detected C. avidum in two PJI sonication fluid samples that were diagnosed as Staphylococcus species infections according to culture (95% negative percent agreement). The new multiplex qPCR can provide a Cutibacterium PJI diagnosis within 1 day, allowing early and accurate antibiotic treatment. A prospective diagnostic trial in PJI with a high number of Cutibacterium species infections (shoulder PJI) is needed for further evaluation.
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16
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Verbyla ME, Symonds EM, Simpson SL. Evaluation of process limit of detection and quantification variation of SARS-CoV-2 RT-qPCR and RT-dPCR assays for wastewater surveillance. WATER RESEARCH 2022; 213:118132. [PMID: 35152136 PMCID: PMC8812148 DOI: 10.1016/j.watres.2022.118132] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/29/2022] [Indexed: 05/21/2023]
Abstract
Effective wastewater surveillance of SARS-CoV-2 RNA requires the rigorous characterization of the limit of detection resulting from the entire sampling process - the process limit of detection (PLOD). Yet to date, no studies have gone beyond quantifying the assay limit of detection (ALOD) for RT-qPCR or RT-dPCR assays. While the ALOD is the lowest number of gene copies (GC) associated with a 95% probability of detection in a single PCR reaction, the PLOD represents the sensitivity of the method after considering the efficiency of all processing steps (e.g., sample handling, concentration, nucleic acid extraction, and PCR assays) to determine the number of GC in the wastewater sample matrix with a specific probability of detection. The primary objective of this study was to estimate the PLOD resulting from the combination of primary concentration and extraction with six SARS-CoV-2 assays: five RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab (CCDC N and CCDC ORF1ab), and E_Sarbeco RT-qPCR, and one RT-dPCR assay (US CDC N1 RT-dPCR) using two models (exponential survival and cumulative Gaussian). An adsorption extraction (AE) concentration method (i.e., virus adsorption on membrane and the RNA extraction from the membrane) was used to concentrate gamma-irradiated SARS-CoV-2 seeded into 36 wastewater samples. Overall, the US CDC N1 RT-dPCR and RT-qPCR assays had the lowest ALODs (< 10 GC/reaction) and PLODs (<3,954 GC/50 mL; 95% probability of detection) regardless of the seeding level and model used. Nevertheless, consistent amplification and detection rates decreased when seeding levels were < 2.32 × 103 GC/50 mL even for US CDC N1 RT-qPCR and RT-dPCR assays. Consequently, when SARS-CoV-2 RNA concentrations are expected to be low, it may be necessary to improve the positive detection rates of wastewater surveillance by analyzing additional field and RT-PCR replicates. To the best of our knowledge, this is the first study to assess the SARS-CoV-2 PLOD for wastewater and provides important insights on the analytical limitations for trace detection of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Erin M Symonds
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
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17
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Ginn O, Rocha-Melogno L, Bivins A, Lowry S, Cardelino M, Nichols D, Tripathi SN, Soria F, Andrade M, Bergin M, Deshusses MA, Brown J. Detection and Quantification of Enteric Pathogens in Aerosols Near Open Wastewater Canals in Cities with Poor Sanitation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14758-14771. [PMID: 34669386 DOI: 10.1021/acs.est.1c05060] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Urban sanitation infrastructure is inadequate in many low-income countries, leading to the presence of highly concentrated, uncontained fecal waste streams in densely populated areas. Combined with mechanisms of aerosolization, airborne transport of enteric microbes and their genetic material is possible in such settings but remains poorly characterized. We detected and quantified enteric pathogen-associated gene targets in aerosol samples near open wastewater canals (OWCs) or impacted (receiving sewage or wastewater) surface waters and control sites in La Paz, Bolivia; Kanpur, India; and Atlanta, USA, via multiplex reverse-transcription qPCR (37 targets) and ddPCR (13 targets). We detected a wide range of enteric targets, some not previously reported in extramural urban aerosols, with more frequent detections of all enteric targets at higher densities in La Paz and Kanpur near OWCs. We report density estimates ranging up to 4.7 × 102 gc per mair3 across all targets including heat-stable enterotoxigenic Escherichia coli, Campylobacter jejuni, enteroinvasive E. coli/Shigella spp., Salmonella spp., norovirus, and Cryptosporidium spp. Estimated 25, 76, and 0% of samples containing positive pathogen detects were accompanied by culturable E. coli in La Paz, Kanpur, and Atlanta, respectively, suggesting potential for viability of enteric microbes at the point of sampling. Airborne transmission of enteric pathogens merits further investigation in cities with poor sanitation.
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Affiliation(s)
- Olivia Ginn
- Department of Civil and Environmental Engineering and Earth Science, University of Notre Dame, Notre Dame, Indiana 46656, United States
| | - Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, and Duke Global Health Institute, Duke University, Durham, North Carolina 27708, United States
- ICF, 2635 Meridian Parkway Suite 200, Durham, North Carolina 27713, United States
| | - Aaron Bivins
- Department of Civil and Environmental Engineering and Earth Science, University of Notre Dame, Notre Dame, Indiana 46656, United States
| | - Sarah Lowry
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Maria Cardelino
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dennis Nichols
- Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Sachchida Nand Tripathi
- Department of Civil Engineering & Centre for Environmental Science and Engineering, Indian Institute of Technology - Kalyanpur, Kanpur 208016, Uttar Pradesh, India
| | - Freddy Soria
- Centro de Investigación en Agua, Energía y Sostenibilidad, Universidad Católica Boliviana "San Pablo", La Paz 4807, Bolivia
| | - Marcos Andrade
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andres, La Paz 1995, Bolivia
- Department of Atmospheric and Oceanic Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Mike Bergin
- Department of Civil and Environmental Engineering, and Duke Global Health Institute, Duke University, Durham, North Carolina 27708, United States
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, and Duke Global Health Institute, Duke University, Durham, North Carolina 27708, United States
| | - Joe Brown
- Deparment of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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18
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Bueno I, Beaudoin A, Arnold WA, Kim T, Frankson LE, LaPara TM, Kanankege K, Wammer KH, Singer RS. Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States. Sci Rep 2021; 11:18747. [PMID: 34548591 PMCID: PMC8455696 DOI: 10.1038/s41598-021-98300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Abstract
The environment plays a key role in the spread and persistence of antimicrobial resistance (AMR). Antimicrobials and antimicrobial resistance genes (ARG) are released into the environment from sources such as wastewater treatment plants, and animal farms. This study describes an approach guided by spatial mapping to quantify and predict antimicrobials and ARG in Minnesota’s waterbodies in water and sediment at two spatial scales: macro, throughout the state, and micro, in specific waterbodies. At the macroscale, the highest concentrations across all antimicrobial classes were found near populated areas. Kernel interpolation provided an approximation of antimicrobial concentrations and ARG abundance at unsampled locations. However, there was high uncertainty in these predictions, due in part to low study power and large distances between sites. At the microscale, wastewater treatment plants had an effect on ARG abundance (sul1 and sul2 in water; blaSHV, intl1, mexB, and sul2 in sediment), but not on antimicrobial concentrations. Results from sediment reflected a long-term history, while water reflected a more transient record of antimicrobials and ARG. This study highlights the value of using spatial analyses, different spatial scales, and sampling matrices, to design an environmental monitoring approach to advance our understanding of AMR persistence and dissemination.
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Affiliation(s)
- Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.
| | - Amanda Beaudoin
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.,Minnesota Department of Health, P.O. Box 64975, St. Paul, MN, 55164-0975, USA
| | - William A Arnold
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA.,Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Lara E Frankson
- Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Kaushi Kanankege
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, 1354 Eckles Ave., St. Paul, MN, 55108, USA
| | - Kristine H Wammer
- College of Arts & Sciences, University of St. Thomas, 2115 Summit Ave., St. Paul, MN, 55105, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA
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19
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Borchardt MA, Boehm AB, Salit M, Spencer SK, Wigginton KR, Noble RT. The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10210-10223. [PMID: 34286966 DOI: 10.1021/acs.est.1c01767] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
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Affiliation(s)
- Mark A Borchardt
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, California 94305, United States
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Susan K Spencer
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rachel T Noble
- Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States
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20
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Bivins A, Lowry S, Wankhede S, Hajare R, Murphy HM, Borchardt M, Labhasetwar P, Brown J. Microbial water quality improvement associated with transitioning from intermittent to continuous water supply in Nagpur, India. WATER RESEARCH 2021; 201:117301. [PMID: 34139512 DOI: 10.1016/j.watres.2021.117301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/12/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Nearly half a billion people living in Indian cities receive their drinking water from an intermittent water supply (IWS), which can be associated with degraded water quality and risk of waterborne disease. The municipal water supply in Nagpur, India is transitioning from intermittent to continuous supply in phases. We conducted cross-sectional sampling to compare microbial water quality under IWS and continuous water supply (CWS) in Nagpur. In 2015 and 2017, we collected 146 grab samples and 90 large-volume dead-end ultrafiltration (DEUF) samples (total volume: 6,925 liters). In addition to measuring traditional water quality parameters, we also assayed DEUF samples by droplet digital PCR (ddPCR) for waterborne pathogen gene targets. At household taps served by IWS, we detected targets from enterotoxigenic E. coli, Shigella spp./enteroinvasive E. coli, norovirus GI and GII, adenovirus A-F, Cryptosporidium spp., and Giardia duodenalis. We observed a significant increase in the proportion of grab samples positive for culturable E. coli (p = 0.0007) and DEUF concentrates positive for waterborne pathogen gene targets (p = 0.0098) at household taps served by IWS compared to those served by CWS. IWS continues to be associated with fecal contamination, and, in this study, with increased prevalence of molecular evidence of waterborne pathogens. These findings add mounting evidence that, despite the presence of piped on premise infrastructure, IWS is less likely to meet the requirements for safely-managed drinking water as defined by the Sustainable Development Goals. Importantly, these findings demonstrate the transition from IWS to CWS in Nagpur is yielding meaningful improvements in microbial water quality.
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Affiliation(s)
- Aaron Bivins
- Environmental Change Initiative, University of Notre Dame, 721 Flanner Hall, Notre Dame, IN 46556, USA; Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Sarah Lowry
- School of Civil & Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA
| | - Sonal Wankhede
- Director's Research Cell, Council of Scientific and Industrial Research, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India
| | - Rajashree Hajare
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Heather M Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mark Borchardt
- Agricultural Research Service, U.S. Dept of Agriculture, 2615 Yellowstone Drive, Marshfield, WI 54449, USA
| | - Pawan Labhasetwar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill NC 27599-7431, USA..
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21
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de Lambert JR, Walsh JF, Scher DP, Firnstahl AD, Borchardt MA. Microbial pathogens and contaminants of emerging concern in groundwater at an urban subsurface stormwater infiltration site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145738. [PMID: 33631564 DOI: 10.1016/j.scitotenv.2021.145738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/29/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Urban stormwater may contain a variety of pollutants, including viruses and other pathogens, and contaminants of emerging concern (pharmaceuticals, artificial sweeteners, and personal care products). In vulnerable geologic settings, the potential exists for these contaminants to reach underlying aquifers and contaminate drinking water wells. Viruses and other pathogens, as well as other contaminants of emerging concern, were measured in stormwater and groundwater at an urban site containing a stormwater cistern and related subsurface infiltration gallery, three shallow lysimeter wells, and a monitoring well. Five of 12 microbial targets were detected more than once across the eight rounds of sampling and at multiple sampling points, with human-specific Bacteroides detected most frequently. The microbial and chemical contaminants present in urban stormwater were much lower in the water table monitoring well than the vadose zone lysimeters. There may be numerous causes for these reductions, but they are most likely related to transit across fine-grained sediments that separate the water table from the vadose zone at this location. Precipitation amount prior to sample collection was significantly associated with microbial load. A significant relation between microbial load and chloride-bromide ratio was also observed. The reduction in number and concentrations of contaminants found in the monitoring well indicates that although geologically sensitive aquifers receiving urban stormwater effluent in the subsurface may be prone to contamination, those with a protective cap of fine-grained sediments are less vulnerable. These results can inform stormwater infiltration guidance relative to drinking water wells, with an emphasis on restricting infiltration near water supply wells finished in geologically sensitive aquifers to reduce public health risks.
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Affiliation(s)
- Jane R de Lambert
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN 55164, United States.
| | - James F Walsh
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN 55164, United States
| | - Deanna P Scher
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN 55164, United States
| | - Aaron D Firnstahl
- U.S. Geological Survey Upper Midwest Water Science Center, 2615 Yellowstone Drive, Marshfield, WI 54449, United States
| | - Mark A Borchardt
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Drive, Marshfield, WI 54449, United States
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22
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Ginn O, Berendes D, Wood A, Bivins A, Rocha-Melogno L, Deshusses MA, Tripathi SN, Bergin MH, Brown J. Open Waste Canals as Potential Sources of Antimicrobial Resistance Genes in Aerosols in Urban Kanpur, India. Am J Trop Med Hyg 2021; 104:1761-1767. [PMID: 33684068 PMCID: PMC8103454 DOI: 10.4269/ajtmh.20-1222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/05/2021] [Indexed: 11/07/2022] Open
Abstract
Understanding the movement of antimicrobial resistance genes (ARGs) in the environment is critical to managing their spread. To assess potential ARG transport through the air via urban bioaerosols in cities with poor sanitation, we quantified ARGs and a mobile integron (MI) in ambient air over periods spanning rainy and dry seasons in Kanpur, India (n = 53), where open wastewater canals (OWCs) are prevalent. Gene targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and a class 1 mobile integron (intI1). Over half of air samples located near, and up to 1 km from OWCs with fecal contamination (n = 45) in Kanpur had detectable targets above the experimentally determined limits of detection (LOD): most commonly intI1 and tetA (56% and 51% of samples, respectively), followed by blaTEM (8.9%) and qnrB (0%). ARG and MI densities in these positive air samples ranged from 6.9 × 101 to 5.2 × 103 gene copies/m3 air. Most (7/8) control samples collected 1 km away from OWCs were negative for any targets. In comparing experimental samples with control samples, we found that intI1 and tetA densities in air are significantly higher (P = 0.04 and P = 0.01, respectively, alpha = 0.05) near laboratory-confirmed fecal contaminated waters than at the control site. These data suggest increased densities of ARGs and MIs in bioaerosols in urban environments with inadequate sanitation. In such settings, aerosols may play a role in the spread of AR.
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Affiliation(s)
- Olivia Ginn
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - David Berendes
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Anna Wood
- Department of Civil and Environmental Engineering and Earth Science, University of Notre Dame, Notre Dame, Indiana
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Marc A. Deshusses
- Department of Civil and Environmental Engineering, Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Sachchida N. Tripathi
- Department of Civil Engineering, Centre for Environmental Science and Engineering, Indian Institute of Technology, Kanpur, India
| | - Michael H. Bergin
- Department of Civil and Environmental Engineering, Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Joe Brown
- Deparment of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina,Address correspondence to Joe Brown, Department of Environmental Sciences and Engineering, University of North Carolina, 135 Dauer Dr., Chapel Hill, NC 27599. E-mail:
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23
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Ginn O, Nichols D, Rocha-Melogno L, Bivins A, Berendes D, Soria F, Andrade M, Deshusses MA, Bergin M, Brown J. Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia. ENVIRONMENTAL RESEARCH 2021; 194:110730. [PMID: 33444611 PMCID: PMC10906805 DOI: 10.1016/j.envres.2021.110730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistance poses a major global health threat. Understanding emergence and dissemination of antibiotic resistance in environmental media is critical to the design of control strategies. Because antibiotic resistance genes (ARGs) may be aerosolized from contaminated point sources and disseminated more widely in localized environments, we assessed ARGs in aerosols in urban La Paz, Bolivia, where wastewater flows in engineered surface water channels through the densely populated urban core. We quantified key ARGs and a mobile integron (MI) via ddPCR and E. coli spp. as a fecal indicator by culture over two years during both the rainy and dry seasons in sites near wastewater flows. ARG targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and an MI (intI1) represented the potential for mobility of genetic material. Most air samples (82%) had detectable targets above the experimentally determined LOD: most commonly blaTEM and intI1 (68% and 47% respectively) followed by tetA and qnrB (17% and 11% respectively). ARG and MI densities in positive air samples ranged from 1.3 × 101 to 6.6 × 104 gene copies/m3 air. Additionally, we detected culturable E. coli in the air (52% of samples <1 km from impacted surface waters) with an average density of 11 CFU/m3 in positive samples. We observed decreasing density of blaTEM with increasing distance up to 150 m from impacted surface waters. To our knowledge this is the first study conducting absolute quantification and a spatial analysis of ARGs and MIs in ambient urban air of a city with contaminated surface waters. Environments in close proximity to urban wastewater flows in this setting may experience locally elevated concentrations of ARGs, a possible concern for the emergence and dissemination of antimicrobial resistance in cities with poor sanitation.
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Affiliation(s)
- Olivia Ginn
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, United States.
| | - Dennis Nichols
- Rollins School of Public Health, Emory University, Atlanta, GA, United States.
| | - Lucas Rocha-Melogno
- Department of Civil and Environmental Engineering, And Duke Global Health Institute, Duke University, Durham, NC, 27708, United States.
| | - Aaron Bivins
- Department of Civil and Environmental Engineering and Earth Science, University of Notre Dame, Notre Dame, IN, 46656, United States.
| | - David Berendes
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.
| | - Freddy Soria
- Centro de Investigación en Agua, Energía y Sostenibilidad, Universidad Católica Boliviana "San Pablo", La Paz, Bolivia.
| | - Marcos Andrade
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andres, La Paz, Bolivia; Department of Atmospheric and Oceanic Sciences, University of Maryland, College Park, MD, USA.
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, And Duke Global Health Institute, Duke University, Durham, NC, 27708, United States.
| | - Mike Bergin
- Department of Civil and Environmental Engineering, And Duke Global Health Institute, Duke University, Durham, NC, 27708, United States.
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, United States; Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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24
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Capone D, Bivins A, Knee J, Cumming O, Nalá R, Brown J. Quantitative Microbial Risk Assessment of Pediatric Infections Attributable to Ingestion of Fecally Contaminated Domestic Soils in Low-Income Urban Maputo, Mozambique. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1941-1952. [PMID: 33472364 PMCID: PMC7860170 DOI: 10.1021/acs.est.0c06972] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 05/03/2023]
Abstract
Rigorous studies of water, sanitation, and hygiene interventions in low- and middle-income countries (LMICs) suggest that children are exposed to enteric pathogens via multiple interacting pathways, including soil ingestion. In 30 compounds (household clusters) in low-income urban Maputo, Mozambique, we cultured Escherichia coli and quantified gene targets from soils (E. coli: ybbW, Shigella/enteroinvasive E. coli (EIEC): ipaH, Giardia duodenalis: β-giardin) using droplet digital PCR at three compound locations (latrine entrance, solid waste area, dishwashing area). We found that 88% of samples were positive for culturable E. coli (mean = 3.2 log10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log10), and 41% for β-giardin (mean = 2.1 log10). Performing stochastic quantitative microbial risk assessment using soil ingestion parameters from an LMIC setting for children 12-23 months old, we estimated that the median annual infection risk by G. duodenalis was 7100-fold (71% annual infection risk) and by Shigella/EIEC was 4000-fold (40% annual infection risk) greater than the EPA's standard for drinking water. Compounds in Maputo, and similar settings, require contact and source control strategies to reduce the ingestion of contaminated soil and achieve acceptable levels of risk.
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Affiliation(s)
- Drew Capone
- Civil
and Environmental Engineering, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Department
of Environmental Sciences and Engineering, Gillings School of Public
Health, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aaron Bivins
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jackie Knee
- Department
of Disease Control, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Oliver Cumming
- Department
of Disease Control, London School of Hygiene
and Tropical Medicine, London WC1E 7HT, U.K.
| | - Rassul Nalá
- Ministério
da Saúde, Instituto Nacional de Saúde Maputo, Maputo 1100, Mozambique
| | - Joe Brown
- Civil
and Environmental Engineering, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Department
of Environmental Sciences and Engineering, Gillings School of Public
Health, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
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25
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Hozalski RM, LaPara TM, Zhao X, Kim T, Waak MB, Burch T, McCarty M. Flushing of Stagnant Premise Water Systems after the COVID-19 Shutdown Can Reduce Infection Risk by Legionella and Mycobacterium spp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15914-15924. [PMID: 33232602 DOI: 10.1021/acs.est.0c06357] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There is concern about potential exposure to opportunistic pathogens when reopening buildings closed due to the COVID-19 pandemic. In this study, water samples were collected before, during, and after flushing showers in five unoccupied (i.e., for ∼2 months) university buildings with quantification of opportunists via a cultivation-based assay (Legionella pneumophila only) and quantitative PCR. L. pneumophila were not detected by either method; Legionella spp., nontuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC), however, were widespread. Using quantitative microbial risk assessment (QMRA), the estimated risks of illness from exposure to L. pneumophila and MAC via showering were generally low (i.e., less than a 10-7 daily risk threshold), with the exception of systemic infection risk from MAC exposure in some buildings. Flushing rapidly restored the total chlorine (as chloramine) residual and decreased bacterial gene targets to building inlet concentrations within 30 min. During the postflush stagnation period, the residual chlorine dissipated within a few days and bacteria rebounded, approaching preflush concentrations after 6-7 days. These results suggest that flushing can quickly improve water quality in unoccupied buildings, but the improvement may only last a few days.
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Affiliation(s)
- Raymond M Hozalski
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Xiaotian Zhao
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis 55455, Minnesota, United States
| | - Michael B Waak
- Norwegian University of Science and Technology, Trondheim 7031, Norway
- Department of Infrastructure, SINTEF Community, Trondheim 7031, Norway
| | - Tucker Burch
- Agricultural Research Service, U.S. Department of Agriculture, Marshfield, Wisconsin 54449, United States
| | - Michael McCarty
- School of Public Health, University of Minnesota, Minneapolis 55455, Minnesota, United States
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26
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Brunner JL. Pooled samples and eDNA-based detection can facilitate the "clean trade" of aquatic animals. Sci Rep 2020; 10:10280. [PMID: 32581260 PMCID: PMC7314758 DOI: 10.1038/s41598-020-66280-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
The regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved—hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DNA (eDNA)—the genetic material shed into an organism’s environment—collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDNA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts.
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Affiliation(s)
- Jesse L Brunner
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.
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27
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Stokdyk JP, Spencer SK, Walsh JF, de Lambert JR, Firnstahl AD, Anderson AC, Rezania LIW, Borchardt MA. Cryptosporidium Incidence and Surface Water Influence of Groundwater Supplying Public Water Systems in Minnesota, USA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3391-3398. [PMID: 30895775 DOI: 10.1021/acs.est.8b05446] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Regulations for public water systems (PWS) in the U.S. consider Cryptosporidium a microbial contaminant of surface water supplies. Groundwater is assumed free of Cryptosporidium unless surface water is entering supply wells. We determined the incidence of Cryptosporidium in PWS wells varying in surface water influence. Community and noncommunity PWS wells ( n = 145) were sampled ( n = 964) and analyzed for Cryptosporidium by qPCR and immunofluorescence assay (IFA). Surface water influence was assessed by stable isotopes and the expert judgment of hydrogeologists using site-specific data. Fifty-eight wells (40%) and 107 samples (11%) were Cryptosporidium-positive by qPCR, and of these samples 67 were positive by IFA. Cryptosporidium concentrations measured by qPCR and IFA were significantly correlated ( p < 0.001). Cryptosporidium incidence was not associated with surface water influence as assessed by stable isotopes or expert judgment. We successfully sequenced 45 of the 107 positive samples to identify species, including C. parvum (41), C. andersoni (2), and C. hominis (2), and the predominant subtype was C. parvum IIa A17G2R1. Assuming USA regulations for surface water-supplied PWS were applicable to the study wells, wells positive for Cryptosporidium by IFA would likely be required to add treatment. Cryptosporidium is not uncommon in groundwater, even when surface water influence is absent.
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Affiliation(s)
- Joel P Stokdyk
- USGS Upper Midwest Water Science Center, 2615 Yellowstone Drive , Marshfield , Wisconsin 54449 , United States
| | - Susan K Spencer
- USDA-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Drive , Marshfield , Wisconsin 54449 , United States
| | - James F Walsh
- Minnesota Department of Health , 625 Robert St. N , St. Paul , Minnesota 55164 , United States
| | - Jane R de Lambert
- Minnesota Department of Health , 625 Robert St. N , St. Paul , Minnesota 55164 , United States
| | - Aaron D Firnstahl
- USGS Upper Midwest Water Science Center, 2615 Yellowstone Drive , Marshfield , Wisconsin 54449 , United States
| | - Anita C Anderson
- Minnesota Department of Health , 625 Robert St. N , St. Paul , Minnesota 55164 , United States
| | - Lih-In W Rezania
- Minnesota Department of Health , 625 Robert St. N , St. Paul , Minnesota 55164 , United States
| | - Mark A Borchardt
- USDA-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Drive , Marshfield , Wisconsin 54449 , United States
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28
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Arseneau JR, Gautreau C, Boston L, Goguen ML, Laflamme M. Accelerated ISAV replication detection by cell culture methods combined with time-monitoring RT-qPCR. JOURNAL OF FISH DISEASES 2019; 42:257-267. [PMID: 30488967 DOI: 10.1111/jfd.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Infectious salmon anaemia (ISA) is a viral disease that affects farmed Atlantic salmon (Salmo salar L.), often leading to mass mortalities. A quick detection of the ISA virus (ISAV) is crucial for decision-making and can prevent the occurrence of future outbreaks. Screening done by Canada's National Aquatic Animal Health Laboratory System (NAAHLS) uses quantitative reverse transcription PCR (RT-qPCR) followed by sequencing of PCR amplicons. As neither technique provides information regarding the infectivity of the virus, suspected virulent strains are subsequently tested using viral isolation. However, this stepwise process can require significant time to deliver results. To speed up this delivery, we have improved on these pre-existing techniques by combining the use of cell culture with RT-qPCR to detect replicative virus in as little as 5 days. Preliminary assays enabled the establishment of a minimal shift in Ct values over time, which is representative of viral replication in cultured cells. Subsequent blind panel analyses allowed the establishment of the optimal sampling days, as well as diagnostic sensitivity (DSe) and specificity (DSp) estimates. This method could be adopted not only by laboratories conducting diagnostic analyses for ISAV, but also for other slow-replicating viral agents that replicate through a budding mechanism.
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Affiliation(s)
- Jean-René Arseneau
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada
| | - Chantal Gautreau
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada
| | - Linda Boston
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada
| | - Michel L Goguen
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada
| | - Mark Laflamme
- Fisheries and Oceans Canada, Gulf Fisheries Centre, Moncton, New Brunswick, Canada
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29
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Diéguez L, Winter M, Molan S, Monis P, King B, Thierry B. Disposable microfluidic micromixers for effective capture of Cryptosporidium parvum oocysts from water samples. J Biol Eng 2018; 12:4. [PMID: 29599821 PMCID: PMC5870503 DOI: 10.1186/s13036-018-0095-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/14/2018] [Indexed: 01/08/2023] Open
Abstract
Background Protecting drinking water supplies from pathogens such as Cryptosporidium parvum is a major concern for water utilities worldwide. The sensitivity and specificity of current detection methods are largely determined by the effectiveness of the concentration and separation methods used. The purpose of this study is to develop micromixers able to specifically isolate and concentrate Cryptosporidium, while allowing in situ analysis. Results In this study, disposable microfluidic micromixers were fabricated to effectively isolate Cryptosporidium parvum oocysts from water samples, while allowing direct observation and enabling quantification of oocysts captured in the device using high quality immunofluorescence microscopy. In parallel, quantitative analysis of the capture yield was carried out by analyzing the waste from the microfluidics outlet with an Imaging Flow Cytometer. At the optimal flow rate, capture efficiencies up to 96% were achieved in spiked samples. Conclusions Scaled microfluidic isolation and detection of Cryptosporidium parvum will provide a faster and more efficient detection method for Cryptosporidium compared to other available laboratory-scale technologies.
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Affiliation(s)
- L Diéguez
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia.,2International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - M Winter
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
| | - S Molan
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
| | - P Monis
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia.,3South Australian Water Corporation, Adelaide, SA Australia
| | - B King
- 3South Australian Water Corporation, Adelaide, SA Australia
| | - B Thierry
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
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