1
|
Heijnen L, de Vries HJ, van Pelt G, Stroobach E, Atsma A, Vranken J, De Maeyer K, Vissers L, Medema G. Qualitative detection of E. coli in distributed drinking water using real-time reverse transcription PCR targeting 16S rRNA: Validation and practical experiences. WATER RESEARCH 2024; 259:121843. [PMID: 38824794 DOI: 10.1016/j.watres.2024.121843] [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: 02/20/2024] [Revised: 05/17/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024]
Abstract
Escherichia coli (E. coli) plays a central role as an indicator for fecal contamination to predict the possible presence of microbial pathogens in drinking water. Current detection methods for E. coli are based on time-consuming culture-based techniques. There is a strong need for methods to detect fecal contamination rapidly in distributed drinking water to prevent outbreaks of waterborne disease and support water utilities to efficiently manage their operations like actions to repair or maintain distribution pipes, to minimize impact on consumers. This study describes the validation and application of a qualitative real time reverse transcription PCR (RT-PCR) method targeting 16S ribosomal RNA (rRNA) for rapid detection of E. coli in distributed drinking water. The RT-PCR assay targets 16S rRNA, a highly abundant RNA in viable cells, enabling robust detection at the required sensitivity of 1 CFU/100 ml. The validation was performed by comparing the RT-PCR method with the culture-based chromogenic reference method (CCA) using the protocol and criteria described in ISO 16,140-2:2016. The validation demonstrated that this RT-PCR method can be used to specifically detect E. coli in a broad range of drinking water samples with at least the same limit of detection as the culture method (Relative Limit Of Detection = 0.75, range 0.43-1.43). The inclusivity study showed that the RT-PCR method was able to detect a broad range of E. coli strains derived from different sources and geographic areas, including pathogenic serotype O157 strains that are not detected with the culture method. The exclusivity study determined that other bacterial genera are not detected with this RT-PCR. However, Escherichia fergusonii was detected and, based on "in silico" analysis, it is expected that also E. albertii and E. marmotae and Shigella species will be detectable using this RT-PCR. An interlaboratory study confirmed that the RT-PCR and culture method have comparable sensitivities when tested by different participants at different laboratories. The application of RT-PCR to confirm the hygienic quality of distributed drinking water after actions to repair or maintain distribution pipes was compared with the culture method on 8076 routine samples, analyzed by the drinking water laboratories in the Netherlands. This comparison study showed a 96.4 % agreement between RT-PCR and culture. In 3.3 % of the samples E. coli was detected with RT-PCR and not with the culture method and in 0.1 % of the samples E. coli was only detected by culture confirming either a higher sensitivity for RT-PCR or the detection of RNA from uncultivable cells. Finally, the application of RT-PCR was highlighted during a contamination event in Belgium where we demonstrate the potency of RT-PCR as a tool to rapidly monitor the spread of microbial contamination and to monitor the effect of measures to remove the contamination This is the first fully validated rapid nucleic based method for detection of E. coli in distributed drinking water. These results demonstrate that this RT-PCR method can be used as a rapid alternative to the culture method to monitor E. coli in distributed drinking water. However, it should be emphasized that nucleic acid based detection methods rely on highly different detection principles (detection of captured nucleic acids present in a sample) than culture base methods (presence of cells cultivable on a selective medium) resulting in occasional different analysis results. Varying treatment and disinfection steps (UV, chlorine, monochloramine, Ozone) or environmental factors (decay) can influence the results and cause differences between RT-PCR and culture methods.
Collapse
Affiliation(s)
- Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands.
| | | | | | | | - Adrie Atsma
- Vitens Water Expertise Center, Leeuwarden, the Netherlands
| | | | | | - Liesbeth Vissers
- AQZ (Aqualab Zuid), Werkendam, the Netherlands; Brabant Water, 's-Hertogenbosch, the Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands; Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
2
|
Paar J, Willis JR, Sette L, Wood SA, Bogomolni A, Dulac M, Sivaganesan M, Shanks OC. Occurrence of recreational water quality monitoring general fecal indicator bacteria and fecal source identification genetic markers in gray seal scat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173220. [PMID: 38761521 DOI: 10.1016/j.scitotenv.2024.173220] [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: 12/08/2023] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
The number of gray seals (Halichoerus grypus) observed along the United States Northwest Atlantic region has been increasing for decades. These colonial animals often haul-out on beaches seasonally in numbers ranging from a few individuals to several thousands. While these larger aggregations are an important part of gray seal behavior, there is public concern that haul-outs could lead to large amounts of fecal waste in recreational areas, potentially resulting in beach closures. Yet, data to confirm whether these animals contribute to beach closures is lacking and minimal information is available on the occurrence of key water quality monitoring genetic markers in gray seal scat. This study evaluates the concentration of E. coli (EC23S857), enterococci (Entero1a), and fecal Bacteroidetes (GenBac3) as well as six fecal source identification genetic markers (HF183/BacR287, HumM2, CPQ_056, Rum2Bac, DG3, and GFD) measured by qPCR in 48 wild gray seal scat samples collected from two haul-out areas in Cape Cod (Massachusetts, U.S.A.). Findings indicate that FIB genetic markers are shed in gray seal scat at significantly different concentrations with the Entero1a genetic marker exhibiting the lowest average concentration (-0.73 log10 estimated mean copies per nanogram of DNA). In addition, systematic testing of scat samples demonstrated that qPCR assays targeting host-associated genetic markers indicative of human, ruminant, and canine fecal pollution sources remain highly specific in waters frequented by gray seals (>97 % specificity).
Collapse
Affiliation(s)
- Jack Paar
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Lisa Sette
- Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Stephanie A Wood
- University of Massachusetts, Boston, Biology Department, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Andrea Bogomolni
- Massachusetts Maritime Academy, Marine Science, Safety and Environmental Protection, 101 Academy Drive, Buzzards Bay, MA 02532, USA
| | - Monique Dulac
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA.
| |
Collapse
|
3
|
Lobos AE, Brandt AM, Gallard-Góngora JF, Korde R, Brodrick E, Harwood VJ. Persistence of sewage-associated genetic markers in advanced and conventional treated recycled water: implications for microbial source tracking in surface waters. mBio 2024:e0065524. [PMID: 38864636 DOI: 10.1128/mbio.00655-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Sewage contamination of environmental waters is increasingly assessed by measuring DNA from sewage-associated microorganisms in microbial source tracking (MST) approaches. However, DNA can persist through wastewater treatment and reach surface waters when treated sewage/recycled water is discharged, which may falsely indicate pollution from untreated sewage. Recycled water discharged from an advanced wastewater treatment (AWT) facility into a Florida stream elevated the sewage-associated HF183 marker 1,000-fold, with a minimal increase in cultured Escherichia coli. The persistence of sewage-associated microorganisms was compared by qPCR in untreated sewage and recycled water from conventional wastewater treatment (CWT) and AWT facilities. E. coli (EC23S857) and sewage-associated markers HF183, H8, and viral crAssphage CPQ_056 were always detected in untreated sewage (6.5-8.7 log10 GC/100 mL). Multivariate analysis found a significantly greater reduction of microbial variables via AWT vs CWT. Bacterial markers decayed ~4-5 log10 through CWT, but CPQ_056 was ~100-fold more persistent. In AWT facilities, the log10 reduction of all variables was ~5. In recycled water, bacterial marker concentrations were significantly correlated (P ≤ 0.0136; tau ≥ 0.44); however, CPQ_056 was not correlated with any marker, suggesting varying drivers of decay. Concentrations of cultured E. coli carrying the H8 marker (EcH8) in untreated sewage were 5.24-6.02 log10 CFU/100 mL, while no E. coli was isolated from recycled water. HF183 and culturable EcH8 were also correlated in contaminated surface waters (odds ratio β1 = 1.701). Culturable EcH8 has a strong potential to differentiate positive MST marker signals arising from treated (e.g., recycled water) and untreated sewage discharged into environmental waters. IMPORTANCE Genes in sewage-associated microorganisms are widely accepted indicators of sewage pollution in environmental waters. However, DNA persists through wastewater treatment and can reach surface waters when recycled water is discharged, potentially causing false-positive indications of sewage contamination. Previous studies have found that bacterial and viral sewage-associated genes persist through wastewater treatment; however, these studies did not compare different facilities or identify a solution to distinguish sewage from recycled water. In this study, we demonstrated the persistence of bacterial marker genes and the greater persistence of a viral marker gene (CPQ_056 of crAssphage) through varying wastewater treatment facilities. We also aim to provide a tool to confirm sewage contamination in surface waters with recycled water inputs. This work showed that the level of wastewater treatment affects the removal of microorganisms, particularly viruses, and expands our ability to identify sewage in surface waters.
Collapse
Affiliation(s)
- Aldo E Lobos
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Amanda M Brandt
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Javier F Gallard-Góngora
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, USA
| | - Ruchi Korde
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Eleanor Brodrick
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
4
|
Saleem F, Li E, Tran KL, Rudra B, Edge TA, Schellhorn HE, Gupta RS. Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality. Microbiologyopen 2024; 13:e1410. [PMID: 38682792 PMCID: PMC11057252 DOI: 10.1002/mbo3.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/19/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24 h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developed quantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.
Collapse
Affiliation(s)
- Faizan Saleem
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Enze Li
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Kevin L. Tran
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
| | - Thomas A. Edge
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | | | - Radhey S. Gupta
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
| |
Collapse
|
5
|
Calarco J, Pruden A, Harwood VJ. Comparison of methods proposed for monitoring cefotaxime-resistant Escherichia coli in the water environment. Appl Environ Microbiol 2024; 90:e0212823. [PMID: 38572968 PMCID: PMC11107173 DOI: 10.1128/aem.02128-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Escherichia coli is a promising subject for globally coordinated surveillance of antimicrobial resistance (AMR) in water environments due to its clinical relevance and widespread use as an indicator of fecal contamination. Cefotaxime-resistant E. coli was recently evaluated favorably for this purpose by the World Health Organization TriCycle Protocol, which specifies tryptone bile x-glucuronide (TBX) medium and incubation at 35°C. We assessed comparability with the U.S. Environmental Protection Agency-approved method for E. coli quantification, which uses membrane-thermotolerant E. coli (mTEC) agar and incubation at 44.5°C, in terms of recovery of E. coli and cefotaxime-resistant E. coli from wastewater influent and surface waters. Total E. coli concentrations in wastewater influent were 106-108 CFU/100 mL, while cefotaxime-resistant E. coli were ~100-fold lower. Total E. coli in surface waters were ~102 CFU/100 mL, and cefotaxime-resistant isolates were near the limit of detection (0.4 CFU/100 mL). Total and putative cefotaxime-resistant E. coli concentrations did not differ significantly between media or by incubation method; however, colonies isolated on mTEC were more frequently confirmed to species (97.1%) compared to those from TBX (92.5%). Incubation in a water bath at 44.5°C significantly decreased non-specific background growth and improved confirmation frequency on both media (97.4%) compared to incubation at 35°C (92.3%). This study helps to advance globally coordinated AMR in water environments and suggests that the TriCycle Protocol is adaptable to other standard methods that may be required in different locales, while also offering a means to improve specificity by decreasing the frequency of false-positive identification of cefotaxime-resistant E. coli by modifying incubation conditions.IMPORTANCEAs antibiotic-resistant bacteria in water environments are increasingly recognized as contributors to the global antibiotic resistance crisis, the need for a monitoring subject that captures antibiotic resistance trends on a global scale increases. The World Health Organization TriCycle Protocol proposes the use of cefotaxime-resistant Escherichia coli isolated on tryptone bile x-glucuronide agar. The U.S. Environmental Protection Agency (USEPA) criteria for safe recreational waters also use E. coli as an indicator but specify the use of mTEC agar at a higher incubation temperature (44.5°C vs 35°C). We assessed the comparability of these methods for isolating total and cefotaxime-resistant E. coli, finding overall good agreement and performance, but significantly higher specificity toward E. coli selection with the use of the USEPA incubation protocol and mTEC agar. This study is the first to directly compare these methods and provides evidence that the methods may be used interchangeably for global surveillance of antibiotic resistance in the environment.
Collapse
Affiliation(s)
- Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
6
|
Abuawad A, Ashhab Y, Offenhäusser A, Krause HJ. DNA Sensor for the Detection of Brucella spp. Based on Magnetic Nanoparticle Markers. Int J Mol Sci 2023; 24:17272. [PMID: 38139102 PMCID: PMC10744106 DOI: 10.3390/ijms242417272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Due to the limitations of conventional Brucella detection methods, including safety concerns, long incubation times, and limited specificity, the development of a rapid, selective, and accurate technique for the early detection of Brucella in livestock animals is crucial to prevent the spread of the associated disease. In the present study, we introduce a magnetic nanoparticle marker-based biosensor using frequency mixing magnetic detection for point-of-care testing and quantification of Brucella DNA. Superparamagnetic nanoparticles were used as magnetically measured markers to selectively detect the target DNA hybridized with its complementary capture probes immobilized on a porous polyethylene filter. Experimental conditions like density and length of the probes, hybridization time and temperature, and magnetic binding specificity, sensitivity, and detection limit were investigated and optimized. Our sensor demonstrated a relatively fast detection time of approximately 10 min, with a detection limit of 55 copies (0.09 fM) when tested using DNA amplified from Brucella genetic material. In addition, the detection specificity was examined using gDNA from Brucella and other zoonotic bacteria that may coexist in the same niche, confirming the method's selectivity for Brucella DNA. Our proposed biosensor has the potential to be used for the early detection of Brucella bacteria in the field and can contribute to disease control measures.
Collapse
Affiliation(s)
- Abdalhalim Abuawad
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (A.A.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Yaqoub Ashhab
- Palestine–Korea Biotechnology Center, Palestine Polytechnic University, Hebron P720, Palestine
| | - Andreas Offenhäusser
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (A.A.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Hans-Joachim Krause
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (A.A.)
| |
Collapse
|
7
|
Wang Y. Algorithms for the Uniqueness of the Longest Common Subsequence. J Bioinform Comput Biol 2023; 21:2350027. [PMID: 38212873 DOI: 10.1142/s0219720023500270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works only consider how to find one longest common subsequence. In this paper, we consider how to determine the uniqueness of the longest common subsequence. If there are multiple longest common subsequences, we also determine which number appears in all/some/none of the longest common subsequences. We focus on four scenarios: (1) linear sequences without duplicated numbers; (2) circular sequences without duplicated numbers; (3) linear sequences with duplicated numbers; (4) circular sequences with duplicated numbers. We develop corresponding algorithms and apply them to gene sequencing data.
Collapse
Affiliation(s)
- Yue Wang
- Department of Computational Medicine, University of California, Los Angeles, California, USA
- Irving Institute for Cancer Dynamics and Department of Statistics, Columbia University, New York, New York, USA
| |
Collapse
|
8
|
Flores ME, Jafarzadeh A, Moghadam SV, Vadde KK, Dhar DA, Nunu RR, Kapoor V. Occurrence and removal of fecal bacteria and microbial source tracking markers in a stormwater detention basin overlying the Edwards Aquifer recharge zone in Texas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:103836-103850. [PMID: 37691063 DOI: 10.1007/s11356-023-29636-w] [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: 04/19/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
The Edwards Aquifer is the primary water resource for over 2 million people in Texas and faces challenges including fecal contamination of water recharging the aquifer, while effectiveness of best management practices (BMPs) such as detention basins in mitigating fecal pollution remains poorly understood. For this study, the inlet and outlet of a detention basin overlying the aquifer's recharge zone were sampled following storm events using automated samplers. Microbial source tracking and culture-based methods were used to determine the occurrence and removal of fecal genetic markers and fecal coliform bacteria in collected water samples. Markers included E. coli (EC23S857), Enterococcus (Entero1), human (HF183), canine (BacCan), and bird (GFD). Fecal coliforms, EC23S857, and Entero1 were detected following each storm event. GFD was the most frequent host-associated marker detected (91% of samples), followed by BacCan (46%), and HF183 (17%). Wilcoxon signed rank tests indicated significantly lower outlet concentrations for fecal coliforms, EC23S857, and Entero1, but not for HF183, GFD, and BacCan. Higher GFD and BacCan outlet concentrations may be due to factors independent of basin design, such as the non-point source nature of bird fecal contamination and domestic dog care practices in neighborhoods contributing to the basin. Mann-Whitney tests showed marker concentrations were not significantly higher during instances of fecal coliform water quality criterion exceedance, except for E. coli, and that fecal coliform concentrations were not significantly different based on marker detection. Overall, results suggest that the detention basin is effective in attenuating fecal contamination associated with fecal coliforms and the general markers, but not for host-associated markers. Consequently, management efforts should focus on mitigating dog and bird-associated fecal pollution in the study region.
Collapse
Affiliation(s)
- Mauricio Eduardo Flores
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
- Southwest Research Institute, 6220 Culebra Rd, San Antonio, TX, 78238, USA
| | - Arash Jafarzadeh
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Sina Vedadi Moghadam
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Kiran Kumar Vadde
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Dipti Anik Dhar
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Rebecca R Nunu
- Southwest Research Institute, 6220 Culebra Rd, San Antonio, TX, 78238, USA
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA.
| |
Collapse
|
9
|
Nilghaz A, Lee SM, Su H, Yuan D, Tian J, Guijt RM, Wang X. Development of a pumpless acoustofluidic device for rapid food pathogen detection. Anal Chim Acta 2023; 1275:341581. [PMID: 37524466 DOI: 10.1016/j.aca.2023.341581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
Mixing, homogenization, separation, and filtration are crucial processes in miniaturized analytical systems employed for in-vitro biological, environmental, and food analysis. However, in microfluidic systems achieving homogenization becomes more challenging due to the laminar flow conditions, which lack the turbulent flows typically used for mixing in traditional analytical systems. Here, we introduce an acoustofluidic platform that leverages an acoustic transducer to generate microvortex streaming, enabling effective homogenizing of food samples. To reduce reliance on external equipment, tubing, and pump, which is desirable for Point-of-Need testing, our pumpless platform employs a hydrophilic yarn capable of continuous wicking for sample perfusion. Following the homogenization process, the platform incorporates an array of micropillars for filtering out large particles from the samples. Additionally, the porous structure of the yarn provides a secondary screening mechanism. The resulting system is compact, and reliable, and was successfully applied to the detection of Escherichia coli (E. coli) in two different types of berries using quantitative polymerase chain reaction (qPCR). The platform demonstrated a detection limit of 5 CFU g-1, showcasing its effectiveness in rapid and sensitive pathogen detection.
Collapse
Affiliation(s)
- Azadeh Nilghaz
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic, 3216, Australia; Drug Delivery, Disposition, And Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
| | - Soo Min Lee
- Australian Centre for Regional and Rural Futures, Deakin University, Waurn Ponds, Vic, 3216, Australia
| | - Hongli Su
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic, 3216, Australia
| | - Dan Yuan
- Drug Delivery, Disposition, And Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; Australian Centre for Regional and Rural Futures, Deakin University, Waurn Ponds, Vic, 3216, Australia; School of Mechanical & Mining Engineering, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Junfei Tian
- State Key Laboratory of Pulp & Paper Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Rosanne M Guijt
- Drug Delivery, Disposition, And Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Xungai Wang
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic, 3216, Australia; JC STEM Lab of Sustainable Fibers and Textiles, School of Fashion and Textiles, The Hong Kong Polytechnic University, Hung Hom, Kowloon, 999077, Hong Kong.
| |
Collapse
|
10
|
Yang Y, Deng Y, Shi X, Liu L, Yin X, Zhao W, Li S, Yang C, Zhang T. QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. WATER RESEARCH 2023; 235:119858. [PMID: 36931186 DOI: 10.1016/j.watres.2023.119858] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.
Collapse
Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
| |
Collapse
|
11
|
Zwirzitz B, Oladeinde A, Johnson J, Zock G, Milfort MC, Fuller AL, Ghareeb AFA, Foutz JC, Teran JA, Woyda R, Abdo Z, Looft T, Lawrence JP, Cudnik D, Aggrey SE. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Front Physiol 2023; 14:1083192. [PMID: 36935743 PMCID: PMC10018173 DOI: 10.3389/fphys.2023.1083192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).
Collapse
Affiliation(s)
- Benjamin Zwirzitz
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | | | - Jasmine Johnson
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Marie C. Milfort
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | | | - Ahmed F. A. Ghareeb
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - James C. Foutz
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Jose Alexis Teran
- College of Engineering, University of Georgia, Athens, GA, United States
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, IA, United States
| | | | - Denice Cudnik
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, United States
| | - Samuel E. Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| |
Collapse
|
12
|
Zhang Y, Li K, Wu Y, Liu Y, Wu R, Zhong Y, Xiao S, Mao H, Li G, Wang Y, Li W. Distribution and correlation between antibiotic resistance genes and host-associated markers before and after swine fever in the longjiang watershed. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120101. [PMID: 36064059 DOI: 10.1016/j.envpol.2022.120101] [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: 05/24/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) are abundantly shed in feces. Thus, it is crucial to identify their host sources so that ARG pollution can be effectively mitigated and aquatic ecosystems can be properly conserved. Here, spatiotemporal variations and sources of ARGs in the Longjiang watershed of South China were investigated by linking them with microbial source tracker (MST) indicators. The most frequently detected ARGs (>90%) were sulI, sulII, blaTEM, tetW, ermF, and the mobile element intI1. Spatial distribution analyses showed that tributaries contributed significantly more sulI, sulII, and ermF contamination to the Longjiang watershed than the main channel. MST indicator analysis revealed that the Longjiang watershed was contaminated mainly by human fecal pollution. Livestock- and poultry-associated fecal pollution significantly declined after the swine fever outbreak. The occurrence of most ARGs is largely explained by human fecal pollution. In contrast, pig fecal pollution might account for the prevalence of tetO. Moreover, combined human-pig fecal pollution contributed to the observed blaNDM-1 distribution in the Longjiang watershed. Subsequent analysis of the characteristics of MST markers disclosed that the relatively lower specificities of BacHum and Rum-2-Bac may lead to inaccurate results of tracking ARG pollution source. The present study determined spatiotemporal variations and ARG origins in the Longjiang watershed by combining MST markers. It also underscored the necessity of using multiple MST markers simultaneously to identify and characterize ARG pollution sources accurately.
Collapse
Affiliation(s)
- Yang Zhang
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Kaiming Li
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Yongjie Wu
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Yi Liu
- Zhaoqing Municipal Ecology and Environment Bureau, Zhaoqing, 526060, PR China
| | - Renren Wu
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China; Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, PR China.
| | - Yi Zhong
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Shijie Xiao
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, PR China
| | - Han Mao
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Guodong Li
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Yishu Wang
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| | - Wenjing Li
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
| |
Collapse
|
13
|
McNair JN, Lane MJ, Hart JJ, Porter AM, Briggs S, Southwell B, Sivy T, Szlag DC, Scull BT, Pike S, Dreelin E, Vernier C, Carter B, Sharp J, Nowlin P, Rediske RR. Validity assessment of Michigan's proposed qPCR threshold value for rapid water-quality monitoring of E. coli contamination. WATER RESEARCH 2022; 226:119235. [PMID: 36257159 DOI: 10.1016/j.watres.2022.119235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/01/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Michigan's water-quality standards specify that E. coli concentrations at bathing beaches must not exceed 300 E. coli per 100 mL, as determined by the geometric mean of culture-based concentrations in three or more representative samples from a given beach on a given day. Culture-based analysis requires 18-24 h to complete, so results are not available on the day of sampling. This one-day delay is problematic because results cannot be used to prevent recreation at beaches that are unsafe on the sampling day, nor do they reliably indicate whether recreation should be prevented the next day, due to high between-day variability in E. coli concentrations demonstrated by previous studies. By contrast, qPCR-based E. coli concentrations can be obtained in 3-4 h, making same-day beach notification decisions possible. Michigan has proposed a qPCR threshold value (qTV) for E. coli of 1.863 log10 gene copies per reaction as a potential equivalent value to the state standard, based on statistical analysis of a set of state-wide training data from 2016 to 2018. The main purpose of the present study is to assess the validity of the proposed qTV by determining whether the implied qPCR-based beach notification decisions agree well with culture-based decisions on two sets of test data from 2016-2018 (6,564 samples) and 2019-2020 (3,205 samples), and whether performance of the proposed qTV is similar on the test and training data. The results show that performance of Michigan's proposed qTV on both sets of test data was consistently good (e.g., 95% agreement with culture-based beach notification decisions during 2019-2020) and was as good as or better than its performance on the training data set. The false-negative rate for the proposed qTV was 25-29%, meaning that beach notification decisions based on the qTV would be expected to permit recreation on the day of sampling in 25-29% of cases where the beach exceeds the state standard for FIB contamination. This false-negative rate is higher than one would hope to see but is well below the corresponding error rate for culture-based decisions, which permit recreation at beaches that exceed the state standard on the day of sampling in 100% of cases because of the one-day delay in obtaining results. The key advantage of qPCR-based analysis is that it permits a large percentage (71-75%) of unsafe beaches to be identified in time to prevent recreation on the day of sampling.
Collapse
Affiliation(s)
- James N McNair
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA.
| | - Molly J Lane
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA
| | - John J Hart
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA
| | - Alexis M Porter
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy, 525W. Allegan St., Lansing, MI 48909, USA
| | - Benjamin Southwell
- Lake Superior State University, 650W Easterday Ave., Sault Ste Marie, MI 49783, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI 48710, USA
| | - David C Szlag
- Oakland University, Department of Chemistry, 146 Library Dr., Rochester, MI 48309, USA
| | - Brian T Scull
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA
| | - Schuyler Pike
- Ferris State University, Shimadzu Core Laboratory, 820 Campus Dr., Big Rapids, MI 49307, USA
| | - Erin Dreelin
- Michigan State University, Department of Fisheries and Wildlife, 420 Wilson Rd, East Lansing, MI 48824, USA
| | - Chris Vernier
- Assurance Water Laboratory, Central Michigan District Health Department, 103N Bowery Ave, Gladwin, MI 48624, USA
| | - Bonnie Carter
- Oakland County Health Division Laboratory, 1200N. Telegraph, Pontiac, MI, 48341, USA
| | - Josh Sharp
- Biology Department, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, MI 49855, USA
| | - Penny Nowlin
- Northern Michigan Regional Lab, Health Department of Northwest Michigan, 95 Livingston Blvd, Gaylord, MI 49735, USA
| | - Richard R Rediske
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr., Muskegon, MI 49441, USA
| |
Collapse
|
14
|
Sivaganesan M, Willis JR, Karim M, Babatola A, Catoe D, Boehm AB, Wilder M, Green H, Lobos A, Harwood VJ, Hertel S, Klepikow R, Howard MF, Laksanalamai P, Roundtree A, Mattioli M, Eytcheson S, Molina M, Lane M, Rediske R, Ronan A, D'Souza N, Rose JB, Shrestha A, Hoar C, Silverman AI, Faulkner W, Wickman K, Kralj JG, Servetas SL, Hunter ME, Jackson SA, Shanks OC. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. WATER RESEARCH 2022; 225:119162. [PMID: 36191524 PMCID: PMC9932931 DOI: 10.1016/j.watres.2022.119162] [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: 06/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mohammad Karim
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - Akin Babatola
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - David Catoe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Maxwell Wilder
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Hyatt Green
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Aldo Lobos
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Stephanie Hertel
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Regina Klepikow
- U.S. Environmental Protection Agency, Region 7 Laboratory, Kansas City, KS, USA
| | | | | | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie Eytcheson
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Molly Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Richard Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Amanda Ronan
- U.S. Environmental Protection Agency, Region 2 Laboratory, Edison, NJ, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | | | | | - Jason G Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| |
Collapse
|
15
|
Sources and Drivers of ARGs in Urban Streams in Atlanta, Georgia, USA. Microorganisms 2022; 10:microorganisms10091804. [PMID: 36144405 PMCID: PMC9503305 DOI: 10.3390/microorganisms10091804] [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: 07/12/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The spread of antibiotic resistance genes (ARGs) in the aquatic environment is an emerging concern in the interest of protecting public health. Stemming the environmental dissemination of ARGs will require a better understanding of the sources and drivers of ARGs in the water environment. In this study, we used direct measurement of sewage-associated molecular markers, the class 1 integron gene, standard water quality parameters, and watershed characteristics to evaluate the sources and drivers of ARGs in an urban watershed impacted by a gradient of human activities. Quantitative polymerase chain reaction (qPCR) was used to quantify the abundance of the sewage-associated HF183, the E. coli fecal indicator, class 1 integron gene (int1), and the ARGs sulI, sulII, tetW, tetM, ampC, and blaSHV in stream water samples collected from the Proctor Creek watershed in Atlanta, Georgia. Our findings show that ARGs were widely distributed, with detection frequencies of 96% (sulI and sulII), 82% (tetW and tetM), and 49% (ampC and blaSHV). All the ARGs were positively and significantly correlated (r > 0.5) with the HF183 and E. coli markers. Non-linear machine learning models developed using generalized boosting show that more than 70% of the variation in ARG loads in the watershed could be explained by fecal source loading, with other factors such as class 1 integron, which is associated with acquired antibiotic resistance, and environmental factors contributing < 30% to ARG variation. These results suggest that input from fecal sources is a more critical driver of ARG dissemination than environmental stressors or horizontal gene transfer in aquatic environments highly impacted by anthropogenic pollution. Finally, our results provide local watershed managers and stakeholders with information to mitigate the burden of ARGs and fecal bacteria in urban streams.
Collapse
|
16
|
Cyterski M, Shanks OC, Wanjugi P, McMinn B, Korajkic A, Oshima K, Haugland R. Bacterial and viral fecal indicator predictive modeling at three Great Lakes recreational beach sites. WATER RESEARCH 2022; 223:118970. [PMID: 35985141 PMCID: PMC9724166 DOI: 10.1016/j.watres.2022.118970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Coliphage are viruses that infect Escherichia coli (E. coli) and may indicate the presence of enteric viral pathogens in recreational waters. There is an increasing interest in using these viruses for water quality monitoring and forecasting; however, the ability to use statistical models to predict the concentrations of coliphage, as often done for cultured fecal indicator bacteria (FIB) such as enterococci and E. coli, has not been widely assessed. The same can be said for FIB genetic markers measured using quantitative polymerase chain reaction (qPCR) methods. Here we institute least-angle regression (LARS) modeling of previously published concentrations of cultured FIB (E. coli, enterococci) and coliphage (F+, somatic), along with newly reported genetic concentrations measured via qPCR for E. coli, enterococci, and general Bacteroidales. We develop site-specific models from measures taken at three beach sites on the Great Lakes (Grant Park, South Milwaukee, WI; Edgewater Beach, Cleveland, OH; Washington Park, Michigan City, IN) to investigate the efficacy of a statistical predictive modeling approach. Microbial indicator concentrations were measured in composite water samples collected five days per week over a beach season (∼15 weeks). Model predictive performance (cross-validated standardized root mean squared error of prediction [SRMSEP] and R2PRED) were examined for seven microbial indicators (using log10 concentrations) and water/beach parameters collected concurrently with water samples. Highest predictive performance was seen for qPCR-based enterococci and Bacteroidales models, with F+ coliphage consistently yielding poor performing models. Influential covariates varied by microbial indicator and site. Antecedent rainfall, bird abundance, wave height, and wind speed/direction were most influential across all models. Findings suggest that some fecal indicators may be more suitable for water quality forecasting than others at Great Lakes beaches.
Collapse
Affiliation(s)
- Mike Cyterski
- U.S. Environmental Protection Agency, Office of Research and Development, Athens, GA, 30605, United States.
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States
| | - Pauline Wanjugi
- New York State Department of Health, Center for Environmental Health, Bureau of Water Supply Protection, New York City Watershed Section, Albany, NY 12201, United States
| | - Brian McMinn
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States
| | - Asja Korajkic
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States
| | - Rich Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States
| |
Collapse
|
17
|
Tang MLY, Lau SCK. Strategy to Evaluate Changes in Bacterial Community Profiles and Bacterial Pathogen Load Reduction After Sewage Disinfection. Front Microbiol 2022; 13:919207. [PMID: 35898906 PMCID: PMC9309643 DOI: 10.3389/fmicb.2022.919207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022] Open
Abstract
Sewage effluent discharge is a major source of pathogenic contamination to the environment. The disinfection process is critical for the elimination of pathogens in sewage. In this study, we examined the impact of chlorine disinfection on the total, viable, and culturable populations of indicator bacteria, pathogens, and bacterial communities in two contrasting types of effluents (primarily treated saline and secondarily treated freshwater). Effluents collected bimonthly over 1 year were examined using cultivation, quantitative PCR (qPCR), and 16S rRNA gene amplicon sequencing coupled with or without propidium monoazide (PMA) treatment. The results showed that each type of effluent was characterized by a specific set of representative genera before disinfection. Salinity appeared to be the major abiotic factor associated with the differences in bacterial community compositions. The pathogen analysis pipeline revealed over 20 viable clinically important pathogenic species in the effluents. Although the bacterial communities differed markedly between the two types of effluents before disinfection, the species of pathogens persisting after disinfection were similar, many of them were members of Enterobacter and Vibrio. The relative abundances of all pathogens identified in the amplicon sequences were multiplied by the 16S rRNA gene copy numbers of total bacteria detected by PMA-qPCR to estimate their concentrations. Pathogens remained viable after disinfection reached 8 log10 16S rRNA copies ml−1 effluent. Meanwhile, around 80 % of the populations of three indicator bacteria including Escherichia coli, Enterococcus, and Bacteroidales were viable after disinfection, but over 99 % of the viable E. coli and Enterococcus were in the non-culturable state. We estimated the total pathogen load by adding the concentrations of all viable pathogens and examined their correlations with indicator bacteria of different types, physiological states, and effluents. The results showed that the PMA-qPCR measurement of E. coli is a reliable proxy of bacterial pathogen loads in both types of effluents. The utility of viable indicator bacteria as a biological index to assess the overall bacteriological hazards in effluents is discussed.
Collapse
|
18
|
A Mobile Laboratory Enables Fecal Pollution Source Tracking in Catchments Using Onsite qPCR Assays. WATER 2022. [DOI: 10.3390/w14081224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Onsite molecular diagnostics can revolutionize fecal pollution source tracking. We aimed to validate a method for onsite qPCR assays with a miniature speaker-sized Q qPCR instrument and other portable equipment items. We showed that marker genes for total bacteria (16S) and E. coli (rodA) in 100 mL of river water measured with this method agreed within ±0.3 log10 units with results obtained when using conventional laboratory equipment items. We then deployed the portable method in a mobile laboratory (‘lab in a van’) and quantified HF183 marker genes for human host associated Bacteroides in river water within 3 h of sampling. We also used the mobile laboratory to investigate urban river water and effluents from two storm drains and a retention pond and collected comprehensive microbial and physicochemical water quality data. We found significantly higher HF183 gene levels in the older storm drain compared to the river water (6.03 ± 0.04 vs. 4.23 ± 0.03 log10 gene copies per 100 mL), and a principal component analysis revealed that storm drain effluent retention in a pond beneficially altered water characteristics, making them more like those of the receiving river. In conclusion, onsite qPCR assays can be performed with portable equipment items to quickly test water.
Collapse
|
19
|
Willis JR, Sivaganesan M, Haugland RA, Kralj J, Servetas S, Hunter ME, Jackson SA, Shanks OC. Performance of NIST SRM® 2917 with 13 recreational water quality monitoring qPCR assays. WATER RESEARCH 2022; 212:118114. [PMID: 35091220 PMCID: PMC10786215 DOI: 10.1016/j.watres.2022.118114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Fecal pollution remains a significant challenge for recreational water quality management worldwide. In response, there is a growing interest in the use of real-time quantitative PCR (qPCR) methods to achieve same-day notification of recreational water quality and associated public health risk as well as to characterize fecal pollution sources for targeted mitigation. However, successful widespread implementation of these technologies requires the development of and access to a high-quality standard control material. Here, we report a single laboratory qPCR performance assessment of the National Institute of Standards and Technology Standard Reference Material 2917 (NIST SRM® 2917), a linearized plasmid DNA construct that functions with 13 recreational water quality qPCR assays. Performance experiments indicate the generation of standard curves with amplification efficiencies ranging from 0.95 ± 0.006 to 0.99 ± 0.008 and coefficient of determination values (R2) ≥ 0.980. Regardless of qPCR assay, variability in repeated measurements at each dilution level were very low (quantification threshold standard deviations ≤ 0.657) and exhibited a heteroscedastic trend characteristic of qPCR standard curves. The influence of a yeast carrier tRNA added to the standard control material buffer was also investigated. Findings demonstrated that NIST SRM® 2917 functions with all qPCR methods and suggests that the future use of this control material by scientists and water quality managers should help reduce variability in concentration estimates and make results more consistent between laboratories.
Collapse
Affiliation(s)
- Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jason Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| |
Collapse
|
20
|
Jarquín-Díaz VH, Balard A, Ferreira SCM, Mittné V, Murata JM, Heitlinger E. DNA-based quantification and counting of transmission stages provides different but complementary parasite load estimates: an example from rodent coccidia (Eimeria). Parasit Vectors 2022; 15:45. [PMID: 35120561 PMCID: PMC8815199 DOI: 10.1186/s13071-021-05119-0] [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: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Counting parasite transmission stages in faeces is the classical measurement to quantify “parasite load”. DNA-based quantifications of parasite intensities from faecal samples are relatively novel and often validated against such counts. When microscopic and molecular quantifications do not correlate, it is unclear whether oocyst counts or DNA-based intensity better reflects biologically meaningful concepts. Here, we investigate this issue using the example of Eimeria ferrisi (Coccidia), an intracellular parasite of house mice (Mus musculus). Methods We performed an infection experiment of house mice with E. ferrisi, in which the intensity of infection correlates with increased health impact on the host, measured as temporary weight loss during infection. We recorded the number of parasite transmissive stages (oocysts) per gram of faeces (OPG) and, as a DNA-based measurement, the number of Eimeria genome copies per gram of faeces for 10 days post-infection (dpi). We assessed weight loss relative to the day of experimental infection as a proxy of host health and evaluated whether DNA or oocyst counts are better predictors of host health. Results Absolute quantification of Eimeria DNA and oocyst counts showed similar but slightly diverging temporal patterns during 10 dpi. We detected Eimeria DNA earlier than the first appearance of oocysts in faeces. Additionally, Eimeria OPGs within each dpi did not explain parasite DNA intensity. Early dpi were characterized by high DNA intensity with low oocyst counts, while late infections showed the opposite pattern. The intensity of Eimeria DNA was consistently a stronger predictor of either maximal weight loss (1 value per animal during the infection course) or weight loss on each day during the experiment when controlling for between-dpi and between-individual variance. Conclusions Eimeria ferrisi oocyst counts correlate weakly with parasite intensity assessed through DNA quantification. DNA is likely partially derived from life-cycle stages other than transmissive oocysts. DNA-based intensities predict health outcomes of infection for the host more robustly than counts of transmissive stages. We conclude that DNA-based quantifications should not necessarily require validation against counts of transmissive stages. Instead, DNA-based load estimates should be evaluated as complementary sources of information with potential specific biological relevance for each host-parasite system. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-05119-0.
Collapse
Affiliation(s)
- Víctor Hugo Jarquín-Díaz
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany. .,Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW), im Forschungsverbund Berlin e.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany. .,Experimental and Clinical Research Center, jointly operated by Charité-Universitätsmedizin Berlin and the Max Delbrück Center for Molecular Medicine, Charité Campus Berlin Buch, Lindenberger Weg 80, 13125, Berlin, Germany.
| | - Alice Balard
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.,Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW), im Forschungsverbund Berlin e.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Susana Carolina Martins Ferreira
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.,Division of Computational Systems Biology, University of Vienna, Althanstr. 14, 1090, Wien, Austria
| | - Vivian Mittné
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany
| | - Julia Mari Murata
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany
| | - Emanuel Heitlinger
- Institute for Biology, Department of Molecular Parasitology, Humboldt University Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.,Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW), im Forschungsverbund Berlin e.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| |
Collapse
|
21
|
Chern EC, Wymer L, Brenner K, Oshima K, Haugland RA. Persistence of fecal indicator bacteria and associated genetic markers from wastewater treatment plant effluents in freshwater microcosms. JOURNAL OF WATER AND HEALTH 2022; 20:205-215. [PMID: 35100168 PMCID: PMC9000909 DOI: 10.2166/wh.2021.152] [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] [Indexed: 06/14/2023]
Abstract
Limited information exists on the environmental persistence of genetic markers for fecal indicator bacteria (FIB) in treated wastewaters. Here, the decay rate constants of culturable cells and genetic markers for four diverse groups of FIBs, such as enterococci, Clostridium, Escherichia coli, and Bacteroides, were investigated in freshwater microcosms seeded with disinfected and non-disinfected secondary-treated wastewaters. Decay rate constants of genetic markers and culturable cells varied significantly among the different FIB groups. Water temperatures (winter vs. fall/spring/summer) significantly affected the decay of all genetic marker and cell types; however, genetic marker decay were not found to be significantly different in disinfected (chlorination/ultraviolet) and non-disinfected wastewater-seeded microcosms or, for example, lake- and river-receiving waters. No evidence was seen that decay rate constants of FIB genetic markers from treated wastewater were substantially different from those observed in similar, previously reported microcosm studies using raw sewage. Unexpected relationships between decay rate constants of genetic markers and culturable cells of Bacteroides were observed. Results suggest that decay rate constants of FIB genetic markers determined from other studies may be applicable to treated wastewaters. Results of this study should be informative for ongoing efforts to determine the persistence of FIB genetic markers relative to surviving pathogens after wastewater treatment.
Collapse
Affiliation(s)
- Eunice C Chern
- U.S. Environmental Protection Agency, Region 10 Laboratory, 7411 Beach Dr. E., Port Orchard, WA 98366, USA E-mail:
| | - Larry Wymer
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kristen Brenner
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| |
Collapse
|
22
|
Zegarra Ruiz DF, Kim DV, Norwood K, Saldana-Morales FB, Kim M, Ng C, Callaghan R, Uddin M, Chang LC, Longman RS, Diehl GE. Microbiota manipulation to increase macrophage IL-10 improves colitis and limits colitis-associated colorectal cancer. Gut Microbes 2022; 14:2119054. [PMID: 36062329 PMCID: PMC9450902 DOI: 10.1080/19490976.2022.2119054] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic life-long inflammatory disease affecting almost 2 million Americans. Although new biologic therapies have been developed, the standard medical treatment fails to selectively control the dysregulated immune pathways involved in chronic colonic inflammation. Further, IBD patients with uncontrolled colonic inflammation are at a higher risk for developing colorectal cancer (CRC). Intestinal microbes can impact many immune functions, and here we asked if they could be used to improve intestinal inflammation. By utilizing an intestinal adherent E. coli that we find increases IL-10 producing macrophages, we were able to limit intestinal inflammation and restrict tumor formation. Macrophage IL-10 along with IL-10 signaling to the intestinal epithelium were required for protection in both inflammation and tumor development. Our work highlights that administration of immune modulating microbes can improve intestinal outcomes by altering tissue inflammation.
Collapse
Affiliation(s)
| | - Dasom V. Kim
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Kendra Norwood
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fatima B. Saldana-Morales
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Neuroscience Program, Baylor College of Medicine, Houston, TX, USA
| | - Myunghoo Kim
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Charles Ng
- Department of Pathology, Joan & Sanford I. Weill Medical College of Cornell University, New York, NY, USA
| | - Ryann Callaghan
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Maisha Uddin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lin-Chun Chang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Randy S. Longman
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
| | - Gretchen E. Diehl
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| |
Collapse
|
23
|
Appel M, Longwell SA, Morri M, Neff N, Herschlag D, Fordyce PM. uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry. ACS OMEGA 2021; 6:30542-30554. [PMID: 34805683 PMCID: PMC8600632 DOI: 10.1021/acsomega.1c04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
New high-throughput biochemistry techniques complement selection-based approaches and provide quantitative kinetic and thermodynamic data for thousands of protein variants in parallel. With these advances, library generation rather than data collection has become rate-limiting. Unlike pooled selection approaches, high-throughput biochemistry requires mutant libraries in which individual sequences are rationally designed, efficiently recovered, sequence-validated, and separated from one another, but current strategies are unable to produce these libraries at the needed scale and specificity at reasonable cost. Here, we present a scalable, rapid, and inexpensive approach for creating User-designed Physically Isolated Clonal-Mutant (uPIC-M) libraries that utilizes recent advances in oligo synthesis, high-throughput sample preparation, and next-generation sequencing. To demonstrate uPIC-M, we created a scanning mutant library of SpAP, a 541 amino acid alkaline phosphatase, and recovered 94% of desired mutants in a single iteration. uPIC-M uses commonly available equipment and freely downloadable custom software and can produce a 5000 mutant library at 1/3 the cost and 1/5 the time of traditional techniques.
Collapse
Affiliation(s)
- Mason
J. Appel
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Scott A. Longwell
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Maurizio Morri
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
| | - Norma Neff
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
| | - Daniel Herschlag
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Polly M. Fordyce
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94110, United States
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
24
|
Nooij S, Ducarmon QR, Laros JFJ, Zwittink RD, Norman JM, Smits WK, Verspaget HW, Keller JJ, Terveer EM, Kuijper EJ. Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients. Gastroenterology 2021; 161:1218-1228.e5. [PMID: 34126062 DOI: 10.1053/j.gastro.2021.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/18/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+E coli is influenced by pks status of the donor feces. METHODS In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+E coli and compared the presence of pks in patients before and after treatment and to their respective donors. RESULTS The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+E coli in pks+ patients was correlated to pks in the donor (P = .004). CONCLUSIONS We conclude that FMT contributes to pks+E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+E coli is unlikely.
Collapse
Affiliation(s)
- Sam Nooij
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Quinten R Ducarmon
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen F J Laros
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Romy D Zwittink
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Wiep Klaas Smits
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology, Leiden University Medical Center, Leiden, the Netherlands; Department of Biobanking, Leiden University Medical Center, Leiden, the Netherlands
| | - Josbert J Keller
- Department of Gastroenterology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gastroenterology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Elisabeth M Terveer
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ed J Kuijper
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Netherlands Donor Feces Bank, Leiden, the Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | |
Collapse
|
25
|
Tropea E, Hynds P, McDermott K, Brown RS, Majury A. Environmental adaptation of E. coli within private groundwater sources in southeastern Ontario: Implications for groundwater quality monitoring and human health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117263. [PMID: 33940229 DOI: 10.1016/j.envpol.2021.117263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/19/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Groundwater quality monitoring typically employs testing for the presence of E. coli as a fecal indicator of recent ingress of human or animal fecal material. The efficacy of fecal indicator organisms is based on the primary criteria that the organism does not reproduce in the aquatic environment. However, recent studies have reported that E. coli may proliferate (i.e., has adapted to) in the external environment, including soil and surface water. To date, the presence of environmentally-adapted E. coli in groundwater has not been examined. The current study employed Clermont phylotyping and the presence of six accessory genes to identify the likely presence of adapted E. coli in private groundwater sources. E. coli isolates (n = 325) from 76 contaminated private water wells located in a southeastern Ontario watershed were compared with geographically analogous human and animal fecal E. coli isolates (n = 234). Cryptic clades III-V, a well-described environmentally-adapted Escherichia population, were identified in three separate groundwater wells, one of which exclusively comprised this adapted population. Dimensionality reduction (via Principal Component Analysis) was used to develop an "E. coli adaptation model", comprising three distinct components (groundwater, animal feces, human feces) and suggests adaptation occurs frequently in the groundwater environment. Model findings indicate that 23/76 (30.3%) wells had an entirely adapted community. Accordingly, the use of E. coli as a FIO returned a false positive result in these instances, while an additional 23/76 (30.3%) wells exhibited some evidence of adaptation (i.e., not all isolates were adapted) representing an over-estimate of the magnitude (concentration) of contamination. Study findings highlight the need to further characterize environmentally-adapted E. coli in the groundwater environment and the potential implications with respect to water quality policy, legislation and determinants of human health risk both regionally and internationally.
Collapse
Affiliation(s)
- Erica Tropea
- School of Environmental Studies, Queen's University, Kingston, Ontario, Canada; Public Health Ontario, Kingston, Ontario, Canada
| | - Paul Hynds
- Technological University Dublin, Dublin, Ireland.
| | | | - R Stephen Brown
- School of Environmental Studies, Queen's University, Kingston, Ontario, Canada
| | - Anna Majury
- School of Environmental Studies, Queen's University, Kingston, Ontario, Canada; Public Health Ontario, Kingston, Ontario, Canada
| |
Collapse
|
26
|
Holcomb DA, Knee J, Capone D, Sumner T, Adriano Z, Nalá R, Cumming O, Brown J, Stewart JR. Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11667-11679. [PMID: 34382777 PMCID: PMC8429117 DOI: 10.1021/acs.est.1c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.
Collapse
Affiliation(s)
- David A. Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Drew Capone
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| |
Collapse
|
27
|
Zhou Z, Hu S, Zhang R, Ma Y, Du K, Sun M, Zhang H, Jiang X, Tu H, Wang X, Chen P. A simple and novel biomarker panel for serofluid dish rapid quality and safety assessment based on gray relational analysis. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
28
|
Ahmed W, Gyawali P, Hamilton KA, Joshi S, Aster D, Donner E, Simpson SL, Symonds EM. Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow. Front Microbiol 2021; 12:632850. [PMID: 34177821 PMCID: PMC8226142 DOI: 10.3389/fmicb.2021.632850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022] Open
Abstract
Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except blaVIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.
Collapse
Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd. (ESR), Porirua, New Zealand
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, United States.,Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Sayalee Joshi
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, United States.,Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - David Aster
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA, Australia
| | | | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
| |
Collapse
|
29
|
Zegarra-Ruiz DF, Kim DV, Norwood K, Kim M, Wu WJH, Saldana-Morales FB, Hill AA, Majumdar S, Orozco S, Bell R, Round JL, Longman RS, Egawa T, Bettini ML, Diehl GE. Thymic development of gut-microbiota-specific T cells. Nature 2021; 594:413-417. [PMID: 33981034 PMCID: PMC8323488 DOI: 10.1038/s41586-021-03531-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023]
Abstract
Humans and their microbiota have coevolved a mutually beneficial relationship in which the human host provides a hospitable environment for the microorganisms and the microbiota provides many advantages for the host, including nutritional benefits and protection from pathogen infection1. Maintaining this relationship requires a careful immune balance to contain commensal microorganisms within the lumen while limiting inflammatory anti-commensal responses1,2. Antigen-specific recognition of intestinal microorganisms by T cells has previously been described3,4. Although the local environment shapes the differentiation of effector cells3-5 it is unclear how microbiota-specific T cells are educated in the thymus. Here we show that intestinal colonization in early life leads to the trafficking of microbial antigens from the intestine to the thymus by intestinal dendritic cells, which then induce the expansion of microbiota-specific T cells. Once in the periphery, microbiota-specific T cells have pathogenic potential or can protect against related pathogens. In this way, the developing microbiota shapes and expands the thymic and peripheral T cell repertoire, allowing for enhanced recognition of intestinal microorganisms and pathogens.
Collapse
Affiliation(s)
| | - Dasom V Kim
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Kendra Norwood
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Myunghoo Kim
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Animal Science, Pusan National University, Pusan, South Korea
| | - Wan-Jung H Wu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Baylor College of Medicine, Houston, TX, USA
| | - Fatima B Saldana-Morales
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Neuroscience Program, Baylor College of Medicine, Houston, TX, USA
| | - Andrea A Hill
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Shubhabrata Majumdar
- Immunology Program, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephanie Orozco
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rickesha Bell
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - June L Round
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Randy S Longman
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
| | - Takeshi Egawa
- Department of Pathology, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Matthew L Bettini
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Gretchen E Diehl
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
30
|
Wang Q, McDermott TR, Walk ST. A Single Microbiome Gene Alters Murine Susceptibility to Acute Arsenic Exposure. Toxicol Sci 2021; 181:105-114. [PMID: 33560341 PMCID: PMC8599829 DOI: 10.1093/toxsci/kfab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Environmental toxicant exposure contributes to morbidity and mortality of many human diseases. With respect to arsenic, microbially driven chemical transformations dictate its toxicity and mobility in virtually every environment yet studied, so a general hypothesis is that the human gut microbiome determines disease outcome following exposure. However, the complex nature of the gut microbiome and the myriad of potential interactions with human cells/tissues make it challenging to quantify the influence of specific arsenic-active functions-a requisite step in developing effective disease prevention and/or clinical intervention strategies. To control both mammalian and microbial function during toxicant exposure, we genetically defined the gut microbiome of mice using only Escherichia coli strain, AW3110 (▵arsRBC), or the same strain carrying a single genome copy of the Fucus vesiculosus metallothionein gene (AW3110::fmt); a cysteine-rich peptide that complexes with arsenite, facilitating bioaccumulation and reducing its toxic effects. AW3110::fmt bioaccumulated significantly more arsenic and gnotobiotic mice colonized by this strain excreted significantly more arsenic in stool and accumulated significantly less arsenic in organs. Moreover, AW3110::fmt gnotobiotic mice were protected from acute toxicity exposure (20 ppm AsIII) relative to controls. This study demonstrates-in a highly controlled fashion-that a single microbiome function (arsenic bioaccumulation) encoded by a single gene in a single human gut microbiome bacterium significantly alters mammalian host arsenic exposure. The experimental model described herein allows for a highly controlled and directed assessment of microbiome functions, and is useful to quantify the influence of specific microbiome-arsenic interactions that help mitigate human disease.
Collapse
Affiliation(s)
- Qian Wang
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| |
Collapse
|
31
|
Large-scale comparison of E. coli levels determined by culture and a qPCR method (EPA Draft Method C) in Michigan towards the implementation of rapid, multi-site beach testing. J Microbiol Methods 2021; 184:106186. [PMID: 33766609 DOI: 10.1016/j.mimet.2021.106186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 11/20/2022]
Abstract
Fecal pollution remains a challenge for water quality managers at Great Lakes and inland recreational beaches. The fecal indicator of choice at these beaches is typically Escherichia coli (E. coli), determined by culture-based methods that require over 18 h to obtain results. Researchers at the United States Environmental Protection Agency (EPA) have developed a rapid E. coli qPCR methodology (EPA Draft Method C) that can provide same-day results for improving public health protection with demonstrated sensitivity, specificity, and data acceptance criteria. However, limited information is currently available to compare the occurrence of E. coli determined by cultivation and by EPA Draft Method C (Method C). This study provides a large-scale data collection effort to compare the occurrence of E. coli determined by these alternative methods at more than 100 Michigan recreational beach and other sites using the complete set of quantitative data pairings and selected subsets of the data and sites meeting various eligibility requirements. Simple linear regression analyses of composite (pooled) data indicated a correlation between results of the E. coli monitoring approaches for each of the multi-site datasets as evidenced by Pearson R-squared values ranging from 0.452 to 0.641. Theoretical Method C threshold values, expressed as mean log10 target gene copies per reaction, that corresponded to an established E. coli culture method water quality standard of 300 MPN or CFU /100 mL varied only from 1.817 to 1.908 for the different datasets using this model. Different modeling and derivation approaches that incorporated within and between-site variability in the estimates also gave Method C threshold values in this range but only when relatively well-correlated datasets were used to minimize the error. A hypothetical exercise to evaluate the frequency of water impairments based on theoretical qPCR thresholds corresponding to the E. coli water quality standard for culture methods suggested that the methods may provide the same beach notification outcomes over 90% of the time with Method C results differing from culture method results that indicated acceptable and unacceptable water quality at overall rates of 1.9% and 6.6%, respectively. Results from this study provide useful information about the relationships between E. coli determined by culture and qPCR methods across many diverse freshwater sites and should facilitate efforts to implement qPCR-based E. coli detection for rapid recreational water quality monitoring on a large scale in the State of Michigan.
Collapse
|
32
|
Brumfield KD, Cotruvo JA, Shanks OC, Sivaganesan M, Hey J, Hasan NA, Huq A, Colwell RR, Leddy MB. Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed. FRONTIERS IN WATER 2021; 3:626849. [PMID: 34263162 PMCID: PMC8274573 DOI: 10.3389/frwa.2021.626849] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Microbial contamination of recreation waters is a major concern globally, with pollutants originating from many sources, including human and other animal wastes often introduced during storm events. Fecal contamination is traditionally monitored by employing culture methods targeting fecal indicator bacteria (FIB), namely E. coli and enterococci, which provides only limited information of a few microbial taxa and no information on their sources. Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution. Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and application of employing a multi-assay approach for examining microbial content of ambient source waters. Cultivated E. coli and enterococci enumeration confirmed presence of fecal contamination in all samples exceeding local single sample recreational water quality thresholds (E. coli, 410 MPN/100 mL; enterococci, 107 MPN/100 mL) following a rainfall. Test results obtained with qPCR showed concentrations of E. coli, enterococci, and human-associated genetic markers increased after rainfall by 1.52-, 1.26-, and 1.11-fold log10 copies per 100 mL, respectively. Taxonomic analysis of the surface water microbiome and detection of antibiotic resistance genes, general FIB, and human-associated microorganisms were also employed. Results showed that fecal contamination from multiple sources (human, avian, dog, and ruminant), as well as FIB, enteric microorganisms, and antibiotic resistance genes increased demonstrably after a storm event. In summary, the addition of qPCR and WMS to traditional surrogate techniques may provide enhanced characterization and improved understanding of microbial pollution sources in ambient waters.
Collapse
Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | | | - Orin C. Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Jessica Hey
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
- CosmosID Inc., Rockville, MD, United States
- Correspondence: Rita R. Colwell , Menu B. Leddy
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, CA, United States
- Correspondence: Rita R. Colwell , Menu B. Leddy
| |
Collapse
|
33
|
Shahraki AH, Chaganti SR, Heath DD. Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario. MICROBIAL ECOLOGY 2021; 81:1-13. [PMID: 32621209 DOI: 10.1007/s00248-020-01539-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.
Collapse
Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
- Cooperative Institute for Great Lakes Research, School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
| |
Collapse
|
34
|
Thibodeaux RJ, Brady JA, Maryak CCK, Swiger SL, Jones BW. Short communication: Screening stable flies and house flies as potential vectors of digital dermatitis in dairy cattle. J Dairy Sci 2020; 104:977-980. [PMID: 33189292 DOI: 10.3168/jds.2020-18550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/04/2020] [Indexed: 11/19/2022]
Abstract
Digital dermatitis is a bacterial infection that causes lesions above the heel bulbs on cattle hooves, and several bacterial species from the genus Treponema are suspected to be causative agents of this polymicrobial condition. Transmission of the bacteria to healthy cows is understudied, particularly with regard to potential insect vectors. Therefore, the objective of this research was to determine if flies captured from a dairy farm known to have digital dermatitis are contaminated with Treponema bacteria. The DNA-based assays did not detect any Treponema phagedenis from stable flies and house flies collected at a dairy experiencing an outbreak of digital dermatitis. Other potential means of bacterial transmission are discussed.
Collapse
Affiliation(s)
- R J Thibodeaux
- Department of Animal Science and Veterinary Technology, Tarleton State University, Stephenville, TX 76402
| | - J A Brady
- Texas A&M AgriLife Research, Stephenville 76401
| | | | - S L Swiger
- Texas A&M AgriLife Extension, Stephenville 76401
| | - B W Jones
- Department of Animal Science and Veterinary Technology, Tarleton State University, Stephenville, TX 76402; Texas A&M AgriLife Research, Stephenville 76401.
| |
Collapse
|
35
|
Bunce JT, Robson A, Graham DW. Seasonal influences on the use of genetic markers as performance indicators for small wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139928. [PMID: 32540662 DOI: 10.1016/j.scitotenv.2020.139928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
The development of microbial source tracking methods has resulted in an array of genetic faecal markers for assessing human health risks posed from surface water pollution. However, their use as performance metrics at wastewater treatment plants (WWTPs) has not been explored extensively. Here we compared three Bacteroides (HF183, HumM2, AllBac) and two E. coli (H8, RodA) genetic markers for summer and winter performance monitoring at twelve small rural (<250 PE) and three larger WWTPs in NE England. Small WWTPs are of interest because they are poorly understood and their impact on surface water quality may be underestimated. Overall, genetic marker data showed significant differences in treatment performance at smaller versus larger WWTPs. For example, effluent abundances of HF183 and HumM2 were significantly higher in smaller systems (p = 0.003 for HumM2; p = 0.02 for HF183). Genetic markers also showed significant differences in performance between seasons (p < 0.01, n = 120), with human-specific markers (i.e., HF183, HumM2, H8) being generally better for summer WWTP monitoring. In contrast, Bacteroides markers were much more suitable for winter monitoring, possibly because the E. coli markers are less sensitive to differences in temperature and sunlight conditions. Overall, Bacteroides markers best described WWTP treatment performance across all samples, although seasonal differences suggest caution is needed when markers are used for performance monitoring. Genetic markers definitely provide rapid and new information about WWTP performance, but more spatially diverse studies are needed to refine their use for routine WWTP monitoring.
Collapse
Affiliation(s)
- Joshua T Bunce
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Aidan Robson
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
36
|
Lane MJ, Rediske RR, McNair JN, Briggs S, Rhodes G, Dreelin E, Sivy T, Flood M, Scull B, Szlag D, Southwell B, Isaacs NM, Pike S. A comparison of E. coli concentration estimates quantified by the EPA and a Michigan laboratory network using EPA Draft Method C. J Microbiol Methods 2020; 179:106086. [PMID: 33058947 DOI: 10.1016/j.mimet.2020.106086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 01/15/2023]
Abstract
We evaluated data from 10 laboratories that analyzed water samples from 82 recreational water sites across the state of Michigan between 2016 and 2018. Water sample replicates were analyzed by experienced U.S. Environmental Protection Agency (EPA) analysts and Michigan laboratories personnel, many of whom were newly trained, using EPA Draft Method C-a rapid quantitative polymerase chain reaction (qPCR) technique that provides same day Escherichia coli (E. coli) concentration results. Beach management decisions (i.e. remain open or issue an advisory or closure) based on E. coli concentration estimates obtained by Michigan labs and by the EPA were compared; the beach management decision agreed in 94% of the samples analyzed. We used the Wilcoxon one-sample signed rank test and nonparametric quantile regression to assess (1) the degree of agreement between E. coli concentrations quantified by Michigan labs versus the EPA and (2) Michigan lab E. coli measurement precision, relative to EPA results, in different years and water body types. The median quantile regression curve for Michigan labs versus EPA approximated the 1:1 line of perfect agreement more closely as years progressed. Similarly, Michigan lab E. coli estimates precision also demonstrated yearly improvements. No meaningful difference was observed in the degree of association between Michigan lab and EPA E. coli concentration estimates for inland lake and Great Lakes samples (median regression curve average slopes 0.93 and 0.95, respectively). Overall, our study shows that properly trained laboratory personnel can perform Draft Method C to a degree comparable with experienced EPA analysts. This allows health departments that oversee recreational water quality monitoring to be confident in qPCR results generated by the local laboratories responsible for analyzing the water samples.
Collapse
Affiliation(s)
- Molly J Lane
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - Richard R Rediske
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - James N McNair
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA.
| | - Geoff Rhodes
- Michigan Department of Environment, Great Lakes and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA.
| | - Erin Dreelin
- Michigan State University, Department of Fisheries and Wildlife, Natural Resource Building, 420 Wilson Rd, Room 13, East Lansing, MI 48824, USA.
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI 48710, USA.
| | - Matthew Flood
- Michigan State University, Department of Fisheries and Wildlife, Natural Resource Building, 420 Wilson Rd, Room 13, East Lansing, MI 48824, USA.
| | - Brian Scull
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - David Szlag
- Oakland University, Department of Chemistry, 146 Library Dr., Rochester, MI 48309, USA.
| | - Benjamin Southwell
- Lake Superior State University, 650 W Easterday Ave., Sault Ste Marie, MI 49783, USA.
| | - Natasha M Isaacs
- U.S. Geological Survey (USGS), Upper Midwest Water Science Center, 5840 Enterprise Dr., Lansing, MI 48911, USA.
| | - Schuyler Pike
- Ferris State University, Shimadzu Core Laboratory for Academic and Research Excellence, 820 Campus Dr., Big Rapids, MI 49307, USA.
| |
Collapse
|
37
|
Hinojosa J, Green J, Estrada F, Herrera J, Mata T, Phan D, Pasha ABMT, Matta A, Johnson D, Kapoor V. Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer. WATER RESEARCH 2020; 184:116211. [PMID: 32721766 DOI: 10.1016/j.watres.2020.116211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The Edwards Aquifer serves as a primary source of drinking water to more than 2 million people in south-central Texas, and as a karst aquifer, is vulnerable to human and animal fecal contamination which poses a serious risk to human and environmental health. A one-year study (Jan 2018 - Feb 2019) was conducted to determine the primary sources of fecal pollution along the Balcones and Leon Creek within the Edwards Aquifer recharge and contributing zones using general (E. coli, enterococci, and universal Bacteriodales) and host-associated (human-, dog-, cow- and chicken/duck-associated Bacteriodales) microbial source tracking (MST) assays. Additionally, sites were classified based on surrounding land use as a potential source predictor and marker levels were correlated with rain events and water quality parameters. Levels for the three general indicators were highest and exhibited similar trends across the sampling sites, suggesting that the sole use of these markers is not sufficient for specific fecal source identification. Among the host-associated markers, highest concentrations were observed for the dog marker (BacCan) in the Leon Creek area and the cow marker (BacCow) in the Balcones Creek area. Additionally, Chicken/Duck-Bac, BacCan and BacCow all exhibited higher concentrations during the spring season and the end of fall/early winter. Relatively lower concentrations were observed for the human-associated markers (HF183 and BacHum), however, levels were higher in the Leon Creek area and highest following rainfall events. Additionally, relatively higher levels in HF183 and BacHum were observed at sites having greater human population and septic tank density and may be attributed to leaks or breaks in these infrastructures. This study is the first to examine and compare fecal contamination at rural and urban areas in the recharge and contributing zones of the Edwards Aquifer using a molecular MST approach targeting Bacteroidales 16S rRNA gene-based assays. The Bacteroidales marker assays, when combined with land use and weather information, can allow for a better understanding of the sources and fluxes of fecal contamination, which can help devise effective mitigation measures to protect water quality.
Collapse
Affiliation(s)
- Jessica Hinojosa
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jemima Green
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Fabiola Estrada
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jonathan Herrera
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Troy Mata
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Duc Phan
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - A B M Tanvir Pasha
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Akanksha Matta
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Drew Johnson
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Vikram Kapoor
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| |
Collapse
|
38
|
Gyawali P, Hamilton K, Joshi S, Aster D, Ahmed W. Identification of reliable marker genes for the detection of canine fecal contamination in sub-tropical Australia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137246. [PMID: 32105941 DOI: 10.1016/j.scitotenv.2020.137246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
Animal fecal contamination in aquatic environments is a major source of zoonotic diseases in humans. While concerns are focused on livestock, companion animals such as dogs can also be a source of a wide range of zoonotic pathogens. Therefore, detection of dog or canine fecal contamination in aquatic environments is important for mitigating risks. In this study, host-sensitivity and specificity of four canine fecal-associated marker genes were evaluated by analyzing 30 canine and 240 non-canine fecal samples. The application of these markers was also tested in water from an urban river under dry weather conditions. The host sensitivity values of the Bacteroides BacCan-UCD, DogBact, DF113 and DF418 were 1.00, 0.90, 0.83, and 0.90, respectively. The host specificity value of the BacCan-UCD, DogBact, DF113 and DF418 were 0.87, 0.98, 0.83, and 0.41, respectively. The mean concentrations of DF418 were highest (7.82 ± 1.13 log10 gene copies (GC)/g of feces) followed by BacCan-UCD (7.61 ± 1.06 log10 GC/g) and DogBact (7.15 ± 0.92 log10 GC/g). The mean concentration of DF113 (5.80 ± 1.25 log10 GC/g) was 1.5 to 2.5 orders of magnitude lower than the other marker genes. The DogBact marker gene was not detected in any other animal feces other than a small number of untreated sewage samples. The BacCan-UCD marker gene cross-reacted with cat, chicken, and pig fecal samples, while the DF113 marker gene cross-reacted with cat, chicken, cattle fecal and untreated sewage samples. The DF418 marker gene was detected in all sewage and animal feces and deemed not suitable for canine fecal contamination tracking in sub-tropical Australia. Canine fecal contamination was infrequently detected in environmental water samples. Based on the results obtained in this study, we recommend that at least two canine feces-associated marker genes should be used in field studies.
Collapse
Affiliation(s)
- Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | - Kerry Hamilton
- The School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA; The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAlister Ave, Tempe, AZ 85281, USA
| | - Sayalee Joshi
- The School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA; The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAlister Ave, Tempe, AZ 85281, USA
| | - David Aster
- Department of Agriculture and Fisheries, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| |
Collapse
|
39
|
Holcomb DA, Knee J, Sumner T, Adriano Z, de Bruijn E, Nalá R, Cumming O, Brown J, Stewart JR. Human fecal contamination of water, soil, and surfaces in households sharing poor-quality sanitation facilities in Maputo, Mozambique. Int J Hyg Environ Health 2020; 226:113496. [PMID: 32135507 PMCID: PMC7174141 DOI: 10.1016/j.ijheh.2020.113496] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/09/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Identifying the origin of fecal contamination can support more effective interventions to interrupt enteric pathogen transmission. Microbial source tracking (MST) assays may help to identify environmental routes of pathogen transmission although these assays have performed poorly in highly contaminated domestic settings, highlighting the importance of both diagnostic validation and understanding the context-specific ecological, physical, and sociodemographic factors driving the spread of fecal contamination. We assessed fecal contamination of compounds (clusters of 2-10 households that share sanitation facilities) in low-income neighborhoods of urban Maputo, Mozambique, using a set of MST assays that were validated with animal stool and latrine sludge from study compounds. We sampled five environmental compartments involved in fecal microbe transmission and exposure: compound water source, household stored water and food preparation surfaces, and soil from the entrance to the compound latrine and the entrances to each household. Each sample was analyzed by culture for the general fecal indicator Escherichia coli (cEC) and by real-time PCR for the E. coli molecular marker EC23S857, human-associated markers HF183/BacR287 and Mnif, and GFD, an avian-associated marker. We collected 366 samples from 94 households in 58 compounds. At least one microbial target (indicator organism or marker gene) was detected in 96% of samples (353/366), with both E. coli targets present in the majority of samples (78%). Human targets were frequently detected in soils (59%) and occasionally in stored water (17%) but seldom in source water or on food surfaces. The avian target GFD was rarely detected in any sample type but was most common in soils (4%). To identify risk factors of fecal contamination, we estimated associations with sociodemographic, meteorological, and physical sample characteristics for each microbial target and sample type combination using Bayesian censored regression for target concentration responses and Bayesian logistic regression for target detection status. Associations with risk factors were generally weak and often differed in direction between different targets and sample types, though relationships were somewhat more consistent for physical sample characteristics. Wet soils were associated with elevated concentrations of cEC and EC23S857 and odds of detecting HF183. Water storage container characteristics that expose the contents to potential contact with hands and other objects were weakly associated with human target detection. Our results describe a setting impacted by pervasive domestic fecal contamination, including from human sources, that was largely disconnected from the observed variation in socioeconomic and sanitary conditions. This pattern suggests that in such highly contaminated settings, transformational changes to the community environment may be required before meaningful impacts on fecal contamination can be realized.
Collapse
Affiliation(s)
- David A Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Zaida Adriano
- We Consult, Maputo, Mozambique; Departamento de Geografia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
| |
Collapse
|
40
|
Viral and Bacterial Fecal Indicators in Untreated Wastewater across the Contiguous United States Exhibit Geospatial Trends. Appl Environ Microbiol 2020; 86:AEM.02967-19. [PMID: 32060019 DOI: 10.1128/aem.02967-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United States are sparse. We report geospatial trends of cultivated bacteriophage (somatic, F+, and total coliphages and GB-124 phage), as well as genetic markers targeting polyomavirus, enterococci, E. coli, Bacteroidetes, and human-associated Bacteroides spp. (HF183/BacR287 and HumM2) in 49 primary influent sewage samples collected from facilities across the contiguous United States. Samples were selected from rural and urban facilities spanning broad latitude, longitude, elevation, and air temperature gradients by using a geographic information system stratified random site selection procedure. Most indicators in sewage demonstrated a remarkable similarity in concentration regardless of location. However, some exhibited predictable shifts in concentration based on either facility elevation or local air temperature. Geospatial patterns identified in this study, or the absence of such patterns, may have several impacts on the direction of future water quality management research, as well as the selection of alternative metrics to estimate sewage pollution on a national scale.IMPORTANCE This study provides multiple insights to consider for the application of bacterial and viral indicators in sewage to surface water quality monitoring across the contiguous United States, ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirmed that crAssphage genetic markers occur at a higher average concentration than key human-associated Bacteroides spp. on a national scale. Geospatial testing also suggested that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial trends in untreated sewage represents an important step toward the validation of these newer methods for future water quality monitoring applications. In addition, the large paired-measurement data set reported here affords the opportunity to conduct a range of secondary analyses, such as the generation of new or updated quantitative microbial risk assessment models used to estimate public health risk.
Collapse
|
41
|
Gryp T, Huys GR, Joossens M, Van Biesen W, Glorieux G, Vaneechoutte M. Isolation and Quantification of Uremic Toxin Precursor-Generating Gut Bacteria in Chronic Kidney Disease Patients. Int J Mol Sci 2020; 21:E1986. [PMID: 32183306 PMCID: PMC7139965 DOI: 10.3390/ijms21061986] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/22/2022] Open
Abstract
In chronic kidney disease (CKD), impaired kidney function results in accumulation of uremic toxins, which exert deleterious biological effects and contribute to inflammation and cardiovascular morbidity and mortality. Protein-bound uremic toxins (PBUTs), such as p-cresyl sulfate, indoxyl sulfate and indole-3-acetic acid, originate from phenolic and indolic compounds, which are end products of gut bacterial metabolization of aromatic amino acids (AAA). This study investigates gut microbial composition at different CKD stages by isolating, identifying and quantifying PBUT precursor-generating bacteria. Fecal DNA extracts from 14 controls and 138 CKD patients were used to quantify total bacterial number and 11 bacterial taxa with qPCR. Moreover, isolated bacteria from CKD 1 and CKD 5 fecal samples were cultured in broth medium supplemented with AAA under aerobic and anaerobic conditions, and classified as PBUT precursor-generators based on their generation capacity of phenolic and indolic compounds, measured with U(H)PLC. In total, 148 different fecal bacterial species were isolated, of which 92 were PBUT precursor-generators. These bacterial species can be a potential target for reducing PBUT plasma levels in CKD. qPCR indicated lower abundance of short chain fatty acid-generating bacteria, Bifidobacterium spp. and Streptococcus spp., and higher Enterobacteriaceae and E. coli with impaired kidney function, confirming an altered gut microbial composition in CKD.
Collapse
Affiliation(s)
- Tessa Gryp
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (W.V.B.); (G.G.)
- Department of Diagnostic Sciences, Laboratory Bacteriology Research, Ghent University, 9000 Ghent, Belgium;
- Department of Microbiology, Immunology and Transplantation, Molecular Microbiology—Microbiome Research Lab, KU Leuven, 3000 Leuven, Belgium (M.J.)
| | - Geert R.B. Huys
- Department of Microbiology, Immunology and Transplantation, Molecular Microbiology—Microbiome Research Lab, KU Leuven, 3000 Leuven, Belgium (M.J.)
| | - Marie Joossens
- Department of Microbiology, Immunology and Transplantation, Molecular Microbiology—Microbiome Research Lab, KU Leuven, 3000 Leuven, Belgium (M.J.)
| | - Wim Van Biesen
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (W.V.B.); (G.G.)
| | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (W.V.B.); (G.G.)
| | - Mario Vaneechoutte
- Department of Diagnostic Sciences, Laboratory Bacteriology Research, Ghent University, 9000 Ghent, Belgium;
| |
Collapse
|
42
|
Lane MJ, McNair JN, Rediske RR, Briggs S, Sivaganesan M, Haugland R. Simplified Analysis of Measurement Data from A Rapid E. coli qPCR Method (EPA Draft Method C) Using A Standardized Excel Workbook. WATER 2020; 12:1-775. [PMID: 32461809 PMCID: PMC7252523 DOI: 10.3390/w12030775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Draft method C is a standardized method for quantifying E. coli densities in recreational waters using quantitative polymerase chain reaction (qPCR). The method includes a Microsoft Excel workbook that automatically screens for poor-quality data using a set of previously proposed acceptance criteria, generates weighted linear regression (WLR) composite standard curves, and calculates E. coli target gene copies in test samples. We compared standard curve parameter values and test sample results calculated with the WLR model to those from a Bayesian master standard curve (MSC) model using data from a previous multi-lab study. The two models' mean intercept and slope estimates from twenty labs' standard curves were within each other's 95% credible or confidence intervals for all labs. E. coli gene copy estimates of six water samples analyzed by eight labs were highly overlapping among labs when quantified with the WLR and MSC models. Finally, we compared multiple labs' 2016-2018 composite curves, comprised of data from individual curves where acceptance criteria were not used, to their corresponding composite curves with passing acceptance criteria. Composite curves developed from passing individual curves had intercept and slope 95% confidence intervals that were often narrower than without screening and an analysis of covariance test was passed more often. The Excel workbook WLR calculation and acceptance criteria will help laboratories implement draft method C for recreational water analysis in an efficient, cost-effective, and reliable manner.
Collapse
Affiliation(s)
- Molly J. Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - James N. McNair
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - Richard R. Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
- Correspondence:
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA
| | - Mano Sivaganesan
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
| | - Richard Haugland
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
| |
Collapse
|
43
|
Schoepp NG, Liaw EJ, Winnett A, Savela ES, Garner OB, Ismagilov RF. Differential DNA accessibility to polymerase enables 30-minute phenotypic β-lactam antibiotic susceptibility testing of carbapenem-resistant Enterobacteriaceae. PLoS Biol 2020; 18:e3000652. [PMID: 32191697 PMCID: PMC7081982 DOI: 10.1371/journal.pbio.3000652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
The rise in carbapenem-resistant Enterobacteriaceae (CRE) infections has created a global health emergency, underlining the critical need to develop faster diagnostics to treat swiftly and correctly. Although rapid pathogen-identification (ID) tests are being developed, gold-standard antibiotic susceptibility testing (AST) remains unacceptably slow (1-2 d), and innovative approaches for rapid phenotypic ASTs for CREs are urgently needed. Motivated by this need, in this manuscript we tested the hypothesis that upon treatment with β-lactam antibiotics, susceptible Enterobacteriaceae isolates would become sufficiently permeabilized, making some of their DNA accessible to added polymerase and primers. Further, we hypothesized that this accessible DNA would be detectable directly by isothermal amplification methods that do not fully lyse bacterial cells. We build on these results to develop the polymerase-accessibility AST (pol-aAST), a new phenotypic approach for β-lactams, the major antibiotic class for gram-negative infections. We test isolates of the 3 causative pathogens of CRE infections using ceftriaxone (CRO), ertapenem (ETP), and meropenem (MEM) and demonstrate agreement with gold-standard AST. Importantly, pol-aAST correctly categorized resistant isolates that are undetectable by current genotypic methods (negative for β-lactamase genes or lacking predictive genotypes). We also test contrived and clinical urine samples. We show that the pol-aAST can be performed in 30 min sample-to-answer using contrived urine samples and has the potential to be performed directly on clinical urine specimens.
Collapse
Affiliation(s)
- Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Eric J. Liaw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Alexander Winnett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Emily S. Savela
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Omai B. Garner
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, United States of America
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| |
Collapse
|
44
|
Gryp T, Glorieux G, Joossens M, Vaneechoutte M. Comparison of five assays for DNA extraction from bacterial cells in human faecal samples. J Appl Microbiol 2020; 129:378-388. [PMID: 32034968 PMCID: PMC7384110 DOI: 10.1111/jam.14608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/30/2022]
Abstract
Aim To determine the most effective DNA extraction method for bacteria in faecal samples. Materials and Results This study assessed five commercial methods, that is, NucliSens easyMag, QIAamp DNA Stool Mini kit, PureLink Microbiome DNA purification kit, QIAamp PowerFecal DNA kit and RNeasy PowerMicrobiome kit, of which the latter has been optimized for DNA extraction. The DNA quantity and quality were determined using Nanodrop, Qubit and qPCR. The PowerMicrobiome kit recovered the highest DNA concentration, whereby this kit also recovered the highest gene copy number of Gram positives, Gram negatives and total bacteria. Furthermore, the PowerMicrobiome kit in combination with mechanical pre‐treatment (bead beating) and with combined enzymatic and mechanical pre‐treatment (proteinase K+mutanolysin+bead beating) was more effective than without pre‐treatment. Conclusion From the five DNA extraction methods that were compared, the PowerMicrobiome kit, preceded by bead beating, which is standard included, was found to be the most effective DNA extraction method for bacteria in faecal samples. Significance and Impact of the Study The quantity and quality of DNA extracted from human faecal samples is a first important step to optimize molecular methods. Here we have shown that the PowerMicrobiome kit is an effective DNA extraction method for bacterial cells in faecal samples for downstream qPCR purpose.
Collapse
Affiliation(s)
- T Gryp
- Department of Diagnostic Sciences, Laboratory Bacteriology Research, Ghent University, Ghent, Belgium.,Nephrology Section, Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Microbiology, Immunology and Transplantation, Molecular Microbiology - Microbiome Research Lab, KU Leuven, Leuven, Belgium
| | - G Glorieux
- Nephrology Section, Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
| | - M Joossens
- Department of Microbiology, Immunology and Transplantation, Molecular Microbiology - Microbiome Research Lab, KU Leuven, Leuven, Belgium
| | - M Vaneechoutte
- Department of Diagnostic Sciences, Laboratory Bacteriology Research, Ghent University, Ghent, Belgium
| |
Collapse
|
45
|
Tanvir Pasha ABM, Hinojosa J, Phan D, Lopez A, Kapoor V. Detection of human fecal pollution in environmental waters using human mitochondrial DNA and correlation with general and human-associated fecal genetic markers. JOURNAL OF WATER AND HEALTH 2020; 18:8-18. [PMID: 32129182 DOI: 10.2166/wh.2019.197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human mitochondrial DNA (mtDNA) genetic markers are abundant in sewage and highly human-specific, suggesting a great potential for the environmental application as human fecal pollution indicators. Limited data are available on the occurrence and co-occurrence of human mtDNA with fecal bacterial markers in surface waters, and how the abundance of these markers is influenced by rain events. A 1-year sampling study was conducted in a suburban watershed impacted by human sewage contamination to evaluate the performance of a human mtDNA-based marker along with the bacterial genetic markers for human-associated Bacteroidales (BacHum and HF183) and Escherichia coli. Additionally, the human mtDNA-based assay was correlated with rain events and other markers. The mtDNA marker was detected in 92% of samples (n = 140) with a mean concentration of 2.96 log10 copies/100 ml throughout the study period. Human mtDNA was detected with greater abundance than human-associated Bacteroidales that could be attributed to differences in the decay of these markers in the environment. The abundance of all markers was positively correlated with rain events, and human mtDNA abundance was significantly correlated with various bacterial markers. In general, these results should support future risk assessment for impacted watersheds, particularly those affected by human fecal pollution, by evaluating the performance of these markers during rain events.
Collapse
Affiliation(s)
- A B M Tanvir Pasha
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA E-mail:
| | - Jessica Hinojosa
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA E-mail:
| | - Duc Phan
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA E-mail:
| | - Adrianne Lopez
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA E-mail:
| | - Vikram Kapoor
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA E-mail:
| |
Collapse
|
46
|
Occurrence of Bacterial Markers and Antibiotic Resistance Genes in Sub-Saharan Rivers Receiving Animal Farm Wastewaters. Sci Rep 2019; 9:14847. [PMID: 31619758 PMCID: PMC6795877 DOI: 10.1038/s41598-019-51421-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/01/2019] [Indexed: 01/03/2023] Open
Abstract
Antibiotic resistant bacteria and genes which confer resistance to antibiotics from human/animal sources are currently considered a serious environmental and a public health concern. This problem is still little investigated in aquatic environment of developing countries according to the different climatic conditions. In this research, the total bacterial load, the abundance of relevant bacteria (Escherichia coli (E. coli), Enterococcus (Ent), and Pseudomonas), and antibiotic resistance genes (ARGs: blaOXA-48, blaCTX-M, sul1, sul2, sul3, and tet(B)) were quantified using Quantitative Polymerase Chain Reaction (qPCR) in sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo. Human and pig host-specific markers were exploited to examine the sources of contamination. The total bacterial load correlated with relevant bacteria and genes blaOXA-48, sul3, and tet(B) (P value < 0.01). E. coli strongly correlated with 16s rDNA, Enterococcus, Pseudomonas spp., blaOXA-48, sul3, and tet(B) (P value < 0.01) and with blaCTX-M, sul1, and sul2 at a lower magnitude (P value < 0.05). The most abundant and most commonly detected ARGs were sul1, and sul2. Our findings confirmed at least two sources of contamination originating from pigs and anthropogenic activities and that animal farm wastewaters didn’t exclusively contribute to antibiotic resistance profile. Moreover, our analysis sheds the light on developing countries where less than adequate infrastructure or lack of it adds to the complexity of antibiotic resistance proliferation with potential risks to the human exposure and aquatic living organisms. This research presents useful tools for the evaluation of emerging microbial contaminants in aquatic ecosystems which can be applied in the similar environment.
Collapse
|
47
|
Nappier SP, Ichida A, Jaglo K, Haugland R, Jones KR. Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:732-740. [PMID: 30939326 PMCID: PMC6555561 DOI: 10.1016/j.scitotenv.2019.03.242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/13/2019] [Accepted: 03/15/2019] [Indexed: 05/31/2023]
Abstract
The United States Environmental Protection Agency's (EPA)1 2012 Recreational Water Quality Criteria included an Enterococcus spp. quantitative polymerase chain reaction (qPCR) method as a supplemental indicator-method. In 2012, performance of qPCR for beach monitoring remained limited, specifically with addressing interference. A systematic literature search of peer-reviewed publications was conducted to identify where Enterococcus spp. and E. coli qPCR methods have been applied in ambient waters. In the present study, we evaluated interference rates, contributing factors resulting in increased interference in these methods, and method improvements that reduced interference. Information on qPCR methods of interest and interference controls were reported in 16 papers for Enterococcus spp. and 13 papers for E. coli. Of the Enterococcus spp. qPCR methods assessed in this effort, the lowest frequencies of interference were reported in samples using Method 1609. Low frequencies of sample interference were also reported EPA's modified E. coli qPCR method, which incorporates the same reagents and interference controls as Method 1609. The literature indicates that more work is needed to demonstrate the utility of E. coli qPCR for widespread beach monitoring purposes, whereas more broad use of Method 1609 for Enterococcus spp. is appropriate when the required and suggested controls are employed.
Collapse
Affiliation(s)
- Sharon P Nappier
- U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, 1200 Pennsylvania Avenue, NW, Washington, DC 20460, USA.
| | | | | | - Rich Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, USA
| | | |
Collapse
|
48
|
Aw TG, Sivaganesan M, Briggs S, Dreelin E, Aslan A, Dorevitch S, Shrestha A, Isaacs N, Kinzelman J, Kleinheinz G, Noble R, Rediske R, Scull B, Rosenberg S, Weberman B, Sivy T, Southwell B, Siefring S, Oshima K, Haugland R. Evaluation of multiple laboratory performance and variability in analysis of recreational freshwaters by a rapid Escherichia coli qPCR method (Draft Method C). WATER RESEARCH 2019; 156:465-474. [PMID: 30953844 PMCID: PMC9994418 DOI: 10.1016/j.watres.2019.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 06/01/2023]
Abstract
There is interest in the application of rapid quantitative polymerase chain reaction (qPCR) methods for recreational freshwater quality monitoring of the fecal indicator bacteria Escherichia coli (E. coli). In this study we determined the performance of 21 laboratories in meeting proposed, standardized data quality acceptance (QA) criteria and the variability of target gene copy estimates from these laboratories in analyses of 18 shared surface water samples by a draft qPCR method developed by the U.S. Environmental Protection Agency (EPA) for E. coli. The participating laboratories ranged from academic and government laboratories with more extensive qPCR experience to "new" water quality and public health laboratories with relatively little previous experience in most cases. Failures to meet QA criteria for the method were observed in 24% of the total 376 test sample analyses. Of these failures, 39% came from two of the "new" laboratories. Likely factors contributing to QA failures included deviations in recommended procedures for the storage and preparation of reference and control materials. A master standard curve calibration model was also found to give lower overall variability in log10 target gene copy estimates than the delta-delta Ct (ΔΔCt) calibration model used in previous EPA qPCR methods. However, differences between the mean estimates from the two models were not significant and variability between laboratories was the greatest contributor to overall method variability in either case. Study findings demonstrate the technical feasibility of multiple laboratories implementing this or other qPCR water quality monitoring methods with similar data quality acceptance criteria but suggest that additional practice and/or assistance may be valuable, even for some more generally experienced qPCR laboratories. Special attention should be placed on providing and following explicit guidance on the preparation, storage and handling of reference and control materials.
Collapse
Affiliation(s)
- Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Shannon Briggs
- Water Resources Division, Michigan Department of Environmental Quality, P. O. Box 30458, 525 West Allegan Street, Lansing, MI, 48909, USA
| | - Erin Dreelin
- Center for Water Sciences, Michigan State University, 1405 South Harrison Road, East Lansing, MI, 48823, USA
| | - Asli Aslan
- Georgia Southern University, Department of Environmental Health Sciences, 501 Forest Drive, Statesboro, GA, 30458, USA
| | - Samuel Dorevitch
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Abhilasha Shrestha
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Natasha Isaacs
- U.S. Geological Survey, Upper Midwest Water Science Center, 6520 Mercantile Way, Ste 5, Lansing, MI, 48911, USA
| | - Julie Kinzelman
- City of Racine Public Health Department, 730 Washington Ave, Racine, WI, 53403, USA
| | - Greg Kleinheinz
- University of Wisconsin-Oshkosh, Environmental Research Laboratory, 800 Algoma Boulevard, Oshkosh, WI, 54901, USA
| | - Rachel Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC, 28557, USA
| | - Rick Rediske
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Brian Scull
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Susan Rosenberg
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Barbara Weberman
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI, 48710, USA
| | - Ben Southwell
- Lake Superior State University, Environmental Analysis Laboratory, 650 W. Easterday Ave, Sault Ste Marie, MI, 49783, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA.
| |
Collapse
|
49
|
Sivaganesan M, Aw TG, Briggs S, Dreelin E, Aslan A, Dorevitch S, Shrestha A, Isaacs N, Kinzelman J, Kleinheinz G, Noble R, Rediske R, Scull B, Rosenberg S, Weberman B, Sivy T, Southwell B, Siefring S, Oshima K, Haugland R. Standardized data quality acceptance criteria for a rapid Escherichia coli qPCR method (Draft Method C) for water quality monitoring at recreational beaches. WATER RESEARCH 2019; 156:456-464. [PMID: 30952079 PMCID: PMC9943056 DOI: 10.1016/j.watres.2019.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 05/31/2023]
Abstract
There is growing interest in the application of rapid quantitative polymerase chain reaction (qPCR) and other PCR-based methods for recreational water quality monitoring and management programs. This interest has strengthened given the publication of U.S. Environmental Protection Agency (EPA)-validated qPCR methods for enterococci fecal indicator bacteria (FIB) and has extended to similar methods for Escherichia coli (E. coli) FIB. Implementation of qPCR-based methods in monitoring programs can be facilitated by confidence in the quality of the data produced by these methods. Data quality can be determined through the establishment of a series of specifications that should reflect good laboratory practice. Ideally, these specifications will also account for the typical variability of data coming from multiple users of the method. This study developed proposed standardized data quality acceptance criteria that were established for important calibration model parameters and/or controls from a new qPCR method for E. coli (EPA Draft Method C) based upon data that was generated by 21 laboratories. Each laboratory followed a standardized protocol utilizing the same prescribed reagents and reference and control materials. After removal of outliers, statistical modeling based on a hierarchical Bayesian method was used to establish metrics for assay standard curve slope, intercept and lower limit of quantification that included between-laboratory, replicate testing within laboratory, and random error variability. A nested analysis of variance (ANOVA) was used to establish metrics for calibrator/positive control, negative control, and replicate sample analysis data. These data acceptance criteria should help those who may evaluate the technical quality of future findings from the method, as well as those who might use the method in the future. Furthermore, these benchmarks and the approaches described for determining them may be helpful to method users seeking to establish comparable laboratory-specific criteria if changes in the reference and/or control materials must be made.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Shannon Briggs
- Water Resources Division, Michigan Department of Environmental Quality, P. O. Box 30458, 525 West Allegan Street, Lansing, MI, 48909, USA
| | - Erin Dreelin
- Center for Water Sciences, Michigan State University, 1405 South Harrison Road, East Lansing, MI, 48823, USA
| | - Asli Aslan
- Georgia Southern University, Department of Environmental Health Sciences, 501 Forest Drive, Statesboro, GA, 30458, USA
| | - Samuel Dorevitch
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Abhilasha Shrestha
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Natasha Isaacs
- U.S. Geological Survey, Upper Midwest Water Science Center, 6520 Mercantile Way, Ste 5, Lansing, MI, 48911, USA
| | - Julie Kinzelman
- City of Racine Public Health Department, 730 Washington Ave, Racine, WI, 53403, USA
| | - Greg Kleinheinz
- University of Wisconsin-Oshkosh, Environmental Research Laboratory, 800 Algoma Boulevard, Oshkosh, WI, 54901, USA
| | - Rachel Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC, 28557, USA
| | - Rick Rediske
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Brian Scull
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Susan Rosenberg
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Barbara Weberman
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI, 48710, USA
| | - Ben Southwell
- Lake Superior State University, Environmental Analysis Laboratory, 650 W. Easterday Ave, Sault Ste Marie, MI, 49783, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA.
| |
Collapse
|
50
|
Shrestha A, Dorevitch S. Evaluation of rapid qPCR method for quantification of E. coli at non-point source impacted Lake Michigan beaches. WATER RESEARCH 2019; 156:395-403. [PMID: 30933697 DOI: 10.1016/j.watres.2019.03.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/06/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Most Great Lakes communities rely on culture-based E. coli methods for monitoring fecal indicator bacteria (FIB) at recreational beaches. These cultivation methods require 18 or more hours to generate results. As a consequence, public notifications about beach action value (BAV) exceedance are based on prior-day water quality. Rapid qPCR monitoring of bacteria in beach water solves the 24-h delay problem, though the USEPA-approved qPCR method targets enterococci bacteria, while Great Lakes communities are familiar with E. coli monitoring. For an E. coli qPCR method to be useful for water quality management, it is important to systematically characterize method performance, and establish BAVs for public notification purposes. In this study, we 1) evaluated a draft USEPA E. coli qPCR method, 2) compared E. coli qPCR measurements with two established FIB (E. coli culture and enterococci qPCR) results, and explored potential strategies to establish E. coli qPCR BAV criteria in the absence of an epidemiological study. Based on analyses of 288 water samples collected from eight of Chicago's Lake Michigan beaches, the E. coli qPCR method demonstrates acceptable performance characteristics. The method is prone to low level DNA contamination, possibly originating from assay reagents derived from E. coli bacteria. Both E. coli and enterococci BAVs were exceeded in approximately 18% of the samples. E. coli qPCR values were correlated with both E. coli culture (r = 0.83; p < 0.0001) and enterococci qPCR (r = 0.67; p < 0.0001) values. The approach recommended by the USEPA in its Technical Support Material (TSM) was used to generate candidate E. coli qPCR BAVs, as was receiver operating characteristic (ROC) analysis. Potential BAV thresholds differed substantially, ranging from 200.9 calibrator cell equivalents (CCE)/100 mL (ROC analysis, enterococci qPCR BAV as the reference) to 1000 CCE/100 mL (TSM analysis, enterococci qPCR BAV as the reference). Because we found that different approaches to establishing potential BAVs generate quite different values, guidance from USEPA about approaches to defining comparable BAVs would be useful.
Collapse
Affiliation(s)
- Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, USA.
| | - Samuel Dorevitch
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, USA
| |
Collapse
|