1
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Yip SWY, Griffith JF, Tong CSL, Cheung KK, Tsoi C, Hung EHY. Ultrasound accuracy for brachial plexus pathology. Clin Radiol 2024:S0009-9260(24)00149-1. [PMID: 38644074 DOI: 10.1016/j.crad.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 04/23/2024]
Abstract
AIM To determine (a) the accuracy of ultrasound in detecting brachial plexus pathology and (b) outline the advantages and limitations of ultrasound compared to MRI for imaging the brachial plexus. MATERIAL AND METHODS cases with clinically suspected brachial plexus pathology were evaluated first by ultrasound, followed by MRI. Patients with prior brachial plexus imaging were excluded. The final diagnosis was based on a combination of ultrasound, MRI, clinical follow-up, and surgical findings. The accuracy of the ultrasound was assessed by comparing the ultrasound and the final diagnoses. The mean clinical follow-up time following ultrasound was 1.8 ± 1.4 years. RESULTS Ninety-two (64%) of the 143 cases had normal brachial plexus ultrasound and MRI examinations. Fifty-one (36%) of 143 cases had brachial plexus pathology on MRI, comprising post-radiation fibrosis (n=25, 49%), nerve sheath tumor (n=11, 21%), traumatic injury (n=7, 14%), inflammatory polyneuropathy (n=4, 8%), malignant infiltration (n=2, 4%), desmoid fibromatosis (n=1,2%), and neuralgic amyotrophy (n=1, 2%). Overall diagnostic accuracy of ultrasound for brachial plexus pathology was 98% (140/143), with three discordant cases (neuralgic amyotrophy n=1, inflammatory neuropathy n=1, postradiation fibrosis n=1) regarded as normal on ultrasound assessment. Sensitivity, specificity, and positive and negative predictive value of ultrasound for identifying brachial plexus pathology were 94%, 100%, 100%, and 97%, respectively. CONCLUSION Ultrasound identifies brachial plexus pathology with high accuracy and specificity, showing comparable diagnostic efficacy to MRI. Ultrasound can serve as an effective first-line imaging investigation for suspected brachial plexus pathology.
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Affiliation(s)
- S W Y Yip
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong.
| | - J F Griffith
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong.
| | - C S L Tong
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong.
| | - K K Cheung
- Department of Radiology, North District Hospital, 9 Po Kin Road, Sheung Shui, Hong Kong.
| | - C Tsoi
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong.
| | - E H Y Hung
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong.
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2
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Zimmer-Faust AG, Griffith JF, Steele JA, Santos B, Cao Y, Asato L, Chiem T, Choi S, Diaz A, Guzman J, Laak D, Padilla M, Quach-Cu J, Ruiz V, Woo M, Weisberg SB. Relationship between coliphage and Enterococcus at southern California beaches and implications for beach water quality management. Water Res 2023; 230:119383. [PMID: 36630853 DOI: 10.1016/j.watres.2022.119383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Coliphage have been suggested as an alternative to fecal indicator bacteria for assessing recreational beach water quality, but it is unclear how frequently and at what types of beaches coliphage produces a different management outcome. Here we conducted side-by-side sampling of male-specific and somatic coliphage by the new EPA dead-end hollow fiber ultrafiltration (D-HFUF-SAL) method and Enterococcus at southern California beaches over two years. When samples were combined for all beach sites, somatic and male-specific coliphage both correlated with Enterococcus. When examined categorically, Enterococcus would have resulted in approximately two times the number of health advisories as somatic coliphage and four times that of male-specific coliphage,using recently proposed thresholds of 60 PFU/100 mL for somatic and 30 PFU/100 mL for male-specific coliphage. Overall, only 12% of total exceedances would have been for coliphage alone. Somatic coliphage exceedances that occurred in the absence of an Enterococcus exceedance were limited to a single site during south swell events, when this beach is known to be affected by nearby minimally treated sewage. Thus, somatic coliphage provided additional valuable health protection information, but may be more appropriate as a supplement to FIB measurements rather than as replacement because: (a) EPA-approved PCR methods for Enterococcus allow a more rapid response, (b) coliphage is more challenging owing to its greater sampling volume and laboratory time requirements, and (c) Enterococcus' long data history has yielded predictive management models that would need to be recreated for coliphage.
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Affiliation(s)
- Amity G Zimmer-Faust
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd., Costa Mesa, CA 92626, United States.
| | - John F Griffith
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd., Costa Mesa, CA 92626, United States
| | - Joshua A Steele
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd., Costa Mesa, CA 92626, United States
| | - Bryan Santos
- City of San Diego, Environmental Monitoring and Technical Services, United States
| | - Yiping Cao
- Orange County Sanitation District, United States
| | - Laralyn Asato
- City of San Diego, Environmental Monitoring and Technical Services, United States
| | - Tania Chiem
- Orange County Public Health Laboratory, United States
| | - Samuel Choi
- Orange County Sanitation District, United States
| | - Arturo Diaz
- Orange County Sanitation District, United States
| | - Joe Guzman
- Orange County Public Health Laboratory, United States
| | - David Laak
- Ventura County Public Works Agency, United States
| | | | | | - Victor Ruiz
- Los Angeles City Sanitation Department, United States
| | - Mary Woo
- California State University Channel Islands, Ventura, CA, United States
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd., Costa Mesa, CA 92626, United States
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3
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Rothman JA, Saghir A, Chung SA, Boyajian N, Dinh T, Kim J, Oval J, Sharavanan V, York C, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. Water Res 2023; 229:119421. [PMID: 36455460 DOI: 10.1016/j.watres.2022.119421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.
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Affiliation(s)
- Jason A Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America.
| | - Andrew Saghir
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Seung-Ah Chung
- Genomics High-Throughput Facility, Department of Biological Chemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Nicholas Boyajian
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Thao Dinh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Jinwoo Kim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Jordan Oval
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Vivek Sharavanan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Courtney York
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America
| | - Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States of America
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States of America.
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4
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Rothman JA, Saghir A, Chung SA, Boyajian N, Dinh T, Kim J, Oval J, Sharavanan V, York C, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. bioRxiv 2022:2022.08.02.502560. [PMID: 35982656 PMCID: PMC9387120 DOI: 10.1101/2022.08.02.502560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Andrew Saghir
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Seung-Ah Chung
- Genomics High-Throughput Facility, Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Nicholas Boyajian
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Thao Dinh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Jinwoo Kim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Jordan Oval
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Vivek Sharavanan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Courtney York
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
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5
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Tsai CSC, Lee RKL, Tam KKW, Yung PSH, Griffith JF. Focal Bone Lesions Following Ultrasound Diathermy: Case Series. Hong Kong Journal of Radiology 2022. [DOI: 10.12809/hkjr2217230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- CSC Tsai
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - RKL Lee
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - KKW Tam
- Orthopaedics, Asia Medical Specialists
| | - PSH Yung
- Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - JF Griffith
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
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6
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Kim S, Kennedy LC, Wolfe MK, Criddle CS, Duong DH, Topol A, White BJ, Kantor RS, Nelson KL, Steele JA, Langlois K, Griffith JF, Zimmer-Faust AG, McLellan SL, Schussman MK, Ammerman M, Wigginton KR, Bakker KM, Boehm AB. SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environ Sci (Camb) 2022. [PMID: 35433013 DOI: 10.1101/2021.11.10.21266138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.
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Affiliation(s)
- Sooyeol Kim
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Lauren C Kennedy
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Marlene K Wolfe
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
- Rollins School of Public Health, Emory University Atlanta GA 30329 USA
| | - Craig S Criddle
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | | | - Aaron Topol
- Verily Life Sciences South San Francisco CA 94080 USA
| | | | - Rose S Kantor
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Kara L Nelson
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - Kylie Langlois
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - John F Griffith
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | | | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Melissa K Schussman
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Michelle Ammerman
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Kevin M Bakker
- Department of Epidemiology, University of Michigan Ann Arbor MI 48109 USA
| | - Alexandria B Boehm
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
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7
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Kim S, Kennedy LC, Wolfe MK, Criddle CS, Duong DH, Topol A, White BJ, Kantor RS, Nelson KL, Steele JA, Langlois K, Griffith JF, Zimmer-Faust AG, McLellan SL, Schussman MK, Ammerman M, Wigginton KR, Bakker KM, Boehm AB. SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environ Sci (Camb) 2022; 8:757-770. [PMID: 35433013 PMCID: PMC8969789 DOI: 10.1039/d1ew00826a] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 05/21/2023]
Abstract
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.
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Affiliation(s)
- Sooyeol Kim
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Lauren C Kennedy
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | - Marlene K Wolfe
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
- Rollins School of Public Health, Emory University Atlanta GA 30329 USA
| | - Craig S Criddle
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
| | | | - Aaron Topol
- Verily Life Sciences South San Francisco CA 94080 USA
| | | | - Rose S Kantor
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Kara L Nelson
- Dept of Civil and Environmental Engineering, University of California Berkeley CA 94720 USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - Kylie Langlois
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | - John F Griffith
- Southern California Coastal Water Research Project Costa Mesa CA 92626 USA
| | | | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Melissa K Schussman
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee WI 53204 USA
| | - Michelle Ammerman
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan Ann Arbor MI 48109 USA
| | - Kevin M Bakker
- Department of Epidemiology, University of Michigan Ann Arbor MI 48109 USA
| | - Alexandria B Boehm
- Dept of Civil and Environmental Engineering, Stanford University Stanford CA 94305 USA
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8
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Sci Total Environ 2022. [PMID: 34818780 DOI: 10.20944/preprints202104.0481.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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9
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Sci Total Environ 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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10
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Rothman JA, Loveless TB, Kapcia J, Adams ED, Steele JA, Zimmer-Faust AG, Langlois K, Wanless D, Griffith M, Mao L, Chokry J, Griffith JF, Whiteson KL. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants. Appl Environ Microbiol 2021; 87:e0144821. [PMID: 34550753 PMCID: PMC8579973 DOI: 10.1128/aem.01448-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Theresa B. Loveless
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Joseph Kapcia
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Eric D. Adams
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - David Wanless
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Lucy Mao
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jeffrey Chokry
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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11
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Ng AWH, Griffith JF, Ng ISH. MRI of carpal tunnel syndrome: before and after carpal tunnel release. Clin Radiol 2021; 76:940.e29-940.e35. [PMID: 34474748 DOI: 10.1016/j.crad.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Carpal tunnel syndrome (CTS) is the most common peripheral nerve entrapment syndrome. Magnetic resonance imaging (MRI) is increasingly used to diagnose CTS, exclude secondary causes of CTS, and investigate patients with persistent symptoms after carpal tunnel release. Median nerve compression may also be either subclinical in the early stages or present with atypical symptoms. Radiologists are therefore not infrequently the first to alert clinicians as to the possibly of subclinical or atypical CTS. This review shows the normal and abnormal appearances of the carpal tunnel before and after CTR.
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Affiliation(s)
- A W H Ng
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong.
| | - J F Griffith
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - I S H Ng
- Cardiff Sixth Form College, Cardiff, UK
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12
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McClary-Gutierrez JS, Mattioli MC, Marcenac P, Silverman AI, Boehm AB, Bibby K, Balliet M, de Los Reyes FL, Gerrity D, Griffith JF, Holden PA, Katehis D, Kester G, LaCross N, Lipp EK, Meiman J, Noble RT, Brossard D, McLellan SL. SARS-CoV-2 Wastewater Surveillance for Public Health Action. Emerg Infect Dis 2021. [PMID: 34424162 DOI: 10.20944/preprints202104.0167.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has garnered extensive public attention during the coronavirus disease pandemic as a proposed complement to existing disease surveillance systems. Over the past year, methods for detection and quantification of SARS-CoV-2 viral RNA in untreated sewage have advanced, and concentrations in wastewater have been shown to correlate with trends in reported cases. Despite the promise of wastewater surveillance, for these measurements to translate into useful public health tools, bridging the communication and knowledge gaps between researchers and public health responders is needed. We describe the key uses, barriers, and applicability of SARS-CoV-2 wastewater surveillance for supporting public health decisions and actions, including establishing ethics consideration for monitoring. Although wastewater surveillance to assess community infections is not a new idea, the coronavirus disease pandemic might be the initiating event to make this emerging public health tool a sustainable nationwide surveillance system, provided that these barriers are addressed.
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13
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McClary-Gutierrez JS, Mattioli MC, Marcenac P, Silverman AI, Boehm AB, Bibby K, Balliet M, de Los Reyes FL, Gerrity D, Griffith JF, Holden PA, Katehis D, Kester G, LaCross N, Lipp EK, Meiman J, Noble RT, Brossard D, McLellan SL. SARS-CoV-2 Wastewater Surveillance for Public Health Action. Emerg Infect Dis 2021; 27:1-8. [PMID: 34424162 PMCID: PMC8386792 DOI: 10.3201/eid2709.210753] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has garnered extensive public attention during the coronavirus disease pandemic as a proposed complement to existing disease surveillance systems. Over the past year, methods for detection and quantification of SARS-CoV-2 viral RNA in untreated sewage have advanced, and concentrations in wastewater have been shown to correlate with trends in reported cases. Despite the promise of wastewater surveillance, for these measurements to translate into useful public health tools, bridging the communication and knowledge gaps between researchers and public health responders is needed. We describe the key uses, barriers, and applicability of SARS-CoV-2 wastewater surveillance for supporting public health decisions and actions, including establishing ethics consideration for monitoring. Although wastewater surveillance to assess community infections is not a new idea, the coronavirus disease pandemic might be the initiating event to make this emerging public health tool a sustainable nationwide surveillance system, provided that these barriers are addressed.
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14
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Zimmer-Faust AG, Steele JA, Xiong X, Staley C, Griffith M, Sadowsky MJ, Diaz M, Griffith JF. A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border. Front Microbiol 2021; 12:674214. [PMID: 34421839 PMCID: PMC8377738 DOI: 10.3389/fmicb.2021.674214] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB), Enterococcus by culture-based methods, and human-associated genetic marker (HF183) and Enterococcus by droplet digital polymerase chain reaction (ddPCR). In addition, 16S rRNA gene sequence analysis was performed and the SourceTracker algorithm was used to characterize the bacterial community of the wastewater treatment plume and its contribution to beach waters. Sampling dates were chosen based on ocean conditions associated with northern currents. Evidence of a gradient in human fecal pollution that extended north from the wastewater discharge across the United States/Mexico border from the point source was observed using human-associated genetic markers and microbial community analysis. The spatial extent of fecal contamination observed was largely dependent on swell and ocean conditions. These findings demonstrate the utility of a combination of molecular tools for understanding and tracking specific pollutant sources in dynamic coastal water environments.
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Affiliation(s)
- Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Xianyi Xiong
- BioTechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Margarita Diaz
- Proyecto Fronterizo de Educación Ambiental, A.C., Tijuana, Mexico
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
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15
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Zimmer-Faust AG, Steele JA, Griffith JF, Schiff K. The challenges of microbial source tracking at urban beaches for Quantitative Microbial Risk Assessment (QMRA). Mar Pollut Bull 2020; 160:111546. [PMID: 32898736 DOI: 10.1016/j.marpolbul.2020.111546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Urban beaches are frequently impacted from multiple sources of fecal contamination. This along with high beach usage underscores the importance of appropriate management that protects swimmer health. The USEPA has enabled the use of QMRA as a tool for quantifying swimmer health risk and setting site-specific water quality objectives. This study illustrates the challenges associated with human and non-human source identification and how these challenges influence the decision of whether QMRA at typical urban beaches for water quality management is appropriate. In this study, a similar and correlated spatial relationship with elevated Enterococcus and avian-specific markers was observed, suggesting shorebirds as a primary source of FIB. However, human-associated markers were also detected frequently but at low concentrations. Ultimately, a QMRA was not conducted because pathogen loading from potential human sources could not be confidently quantified, having consequences for health risk in receiving waters where recreational contact occurs.
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Affiliation(s)
- Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626, United States of America.
| | - Joshua A Steele
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626, United States of America
| | - John F Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626, United States of America
| | - Ken Schiff
- Southern California Coastal Water Research Project, 3535 Harbor Blvd, Suite 110, Costa Mesa, CA 92626, United States of America
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16
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Rothman JA, Loveless TB, Griffith ML, Steele JA, Griffith JF, Whiteson KL. Metagenomics of Wastewater Influent from Southern California Wastewater Treatment Facilities in the Era of COVID-19. Microbiol Resour Announc 2020; 9:e00907-20. [PMID: 33033132 PMCID: PMC7545286 DOI: 10.1128/mra.00907-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/18/2020] [Indexed: 12/02/2022] Open
Abstract
Sequencing wastewater may be useful for detecting pathogens and assaying microbial water quality. We concentrated, extracted, and sequenced nucleic acids from 17 composite influent wastewater samples spanning seven southern California wastewater treatment facilities in May 2020. Bacteria were the most proportionally abundant taxonomic group present, followed by viruses and archaea.
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Affiliation(s)
- Jason A Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Theresa B Loveless
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Madison L Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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17
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Wu D, Griffith JF, Lam SHM, Wong P, Yue J, Shi L, Li EK, Cheng IT, Li TK, Hung VW, Qin L, Tam LS. Comparison of bone structure and microstructure in the metacarpal heads between patients with psoriatic arthritis and healthy controls: an HR-pQCT study. Osteoporos Int 2020; 31:941-950. [PMID: 31938819 DOI: 10.1007/s00198-020-05298-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/10/2020] [Indexed: 01/01/2023]
Abstract
UNLABELLED Human cadaveric study has indicated that the metacarpal head (MCH) is intracapsular in location. We hypothesized that exposure to the intra-articular inflammatory milieu in psoriatic arthritis (PsA) will lead to bone loss in the MCH. INTRODUCTION To compare the bone structure and microstructure in the MCH between patients with PsA and healthy controls by high-resolution peripheral quantitative CT (HR-pQCT), and to ascertain factors associated with bone loss in PsA patients. METHODS Sixty-two PsA patients without joint destruction and 62 age-, gender-, and body mass index-matched healthy subjects underwent HR-pQCT imaging of the second and third MCH (MCH 2&3). The number and volume of bone erosion and enthesiophytes, as well as volumetric bone mineral density (vBMD) and microstructure at the MCH 2&3, were recorded. Correlation analysis and multivariable linear regression models were used to determine the association of demographic and disease-specific variables with compromised bone structure and microstructure in PsA. RESULTS At the MCH 2&3, bone erosion (p = 0.003) and enthesiophyte (p = 0.000) volumes in PsA patients were significantly larger than healthy controls. In PsA patients, older age was associated with a larger erosion and enthesiophyte volume. Concerning the mean vBMD and microstructure at the MCH 2&3, PsA patients had significantly lower mean vBMD (average vBMD - 6.9%, trabecular vBMD - 8.8%, peri-trabecular vBMD - 7.7%, meta-trabecular vBMD - 9.8%), trabecular bone volume fraction (- 8.8%), and trabecular thickness (- 8.1%) compared with control subjects. Multivariable regression analysis revealed that older age and a higher C-reactive protein level were associated with trabecular bone loss. CONCLUSIONS PsA patients had a higher burden of bone damages (erosions and enthesiophytes) and trabecular bone loss compared with healthy control at the MCH. Inflammation contributed to the deterioration in trabecular microstructure in these patients.
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Affiliation(s)
- D Wu
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - J F Griffith
- Department of Imaging and Interventional Radiology, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - S H M Lam
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - P Wong
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - J Yue
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - L Shi
- Research Centre for Medical Image Computing, Department of Imaging and Interventional Radiology, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - E K Li
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - I T Cheng
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - T K Li
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - V W Hung
- Bone Quality and Health Centre of the Department of Orthopedics & Traumatology, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - L Qin
- Bone Quality and Health Centre of the Department of Orthopedics & Traumatology, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - L-S Tam
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
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18
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Catalan L, Xiao F, Griffith JF. Reporting of Osteoporotic Vertebral Fracture Detected Opportunistically on Thoraco-abdominal Computed Tomography. Hong Kong Journal of Radiology 2019. [DOI: 10.12809/hkjr1916919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- L Catalan
- Augustana College, Rock Island, Illinois, United States
| | - F Xiao
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - JF Griffith
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
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19
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Wáng YXJ, Che-Nordin N, Deng M, Griffith JF, Leung JCS, Kwok AWL, Leung PC, Kwok TCY. Elderly males with or without existing osteoporotic vertebral fracture have much lower future vertebral fracture risk than elderly females: the MrOS (Hong Kong) year-4 follow-up spine radiograph study. Osteoporos Int 2019; 30:2505-2514. [PMID: 31478068 DOI: 10.1007/s00198-019-05136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
Abstract
UNLABELLED MrOS (Hong Kong)'s year-4 follow-up shows, for subjects at baseline without vertebral deformity (VD) and endplate or/and cortex fracture (ECF), the VD progression/new VD rate during follow-up in males was half of our paired MsOS (Hong Kong) study's results. For those with VD or ECF, the VD progression/new VD was less than one sixth of females' rate. INTRODUCTION This study documents MrOS (Hong Kong)'s year-4 follow-up, and the results are compared with the MsOS (Hong Kong) study. Of elderly females with Genant's grade-0, -1, -2, and -3 VD, at year-4 follow-up, 4.6%, 8%, 10.6%, and 28.9% had at least one VD progression or incident VD, respectively. METHODS Spine radiographs of 1500 Chinese males with baseline (mean age 71.7 years, range 65-91 years) and year-4 follow-up were evaluated according to Genant's VD criteria and ECF (non-existent, ECF0; or existent, ECF1). Grade-2 VDs were divided into mild (VD2m, 25-34% height loss) and severe (VD2s, 34-40% height loss) subgroups. Study subjects were graded into eight categories: VD0/ECF0, VD1/ECF0, VD2m/ECF0, VD0/ECF1, VD1/ECF1, VD2m/ECF1, VD2s/ECF1, and VD3/ECF1. With an existing VD, a further height loss of ≥ 15% was a VD progression. A new VD incident was a change from grade-0 to grade-2/3, or to grade-1 with ≥ 10% height loss. RESULTS Of subjects with Genant's grade-0, 2.05% (25/1219) developed at least one VD progression or/and new VD, while of subjects with Genant's grade-1, -2, and -3 VD, only 2% (3/149), 3.1% (3/96), and 2.8% (1/36) developed at least one VD progression/new VD, respectively. Among the three ECF0 groups, there was a significant difference in new ECF incidence, with VD0/ECF0 being the lowest and VD2m/ECF0 being the highest. CONCLUSION VD progression/new VD is much less common in elderly men than in elderly women. Vertebrae with VD had a higher risk of developing ECF.
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Affiliation(s)
- Y X J Wáng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China.
| | - N Che-Nordin
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - M Deng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - J F Griffith
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - J C S Leung
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - A W L Kwok
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - P C Leung
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
| | - T C Y Kwok
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, SAR, China
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20
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Gomez-Alvarez V, Ashbolt NJ, Griffith JF, Santo Domingo J, Lu J. Whole-Genome Sequencing of Four Campylobacter Strains Isolated from Gull Excreta Collected from Hobie Beach (Oxnard, CA, USA). Microbiol Resour Announc 2019; 8:e00560-19. [PMID: 31395635 PMCID: PMC6687922 DOI: 10.1128/mra.00560-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Campylobacter spp. are commensal organisms in avian species and are one of the leading causes of bacterial foodborne human diarrheal disease worldwide. We report the draft genome sequences of Campylobacter volucris, C. lari, and C. jejuni strains isolated from California gull (Larus californicus) excreta collected from a California beach.
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Affiliation(s)
- Vicente Gomez-Alvarez
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jorge Santo Domingo
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Jingrang Lu
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
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21
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Wáng YXJ, Che-Nordin N, Deng M, Leung JCS, Kwok AWL, He LC, Griffith JF, Kwok TCY, Leung PC. Osteoporotic vertebral deformity with endplate/cortex fracture is associated with higher further vertebral fracture risk: the Ms. OS (Hong Kong) study results. Osteoporos Int 2019; 30:897-905. [PMID: 30666373 DOI: 10.1007/s00198-019-04856-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/13/2019] [Indexed: 12/12/2022]
Abstract
UNLABELLED Compared with vertebrae without deformity, vertebrae with mild/moderate deformity have a higher risk of endplate or/and cortex fracture (ecf). Compared with subjects without ecf, subjects with ecf are at a higher risk of short-term (4-year period) deformity progression and new incident deformity. INTRODUCTION The progression and incidence of osteoporotic vertebral deformity/fracture (VD/VF) in elderly Chinese females remain not well documented. METHODS Spine radiographs of 1533 Chinese females with baseline and year-4 follow-up (mean age 75.7 years) were evaluated according to Genant's VD criteria and endplate/cortex fracture (non-existent: ecf0 or existent: ecf1). Grade-2 VDs were divided into mild (vd2m, 25-34% height loss) and severe (vd2s, 34-40% height loss) subgroups. According to their VD/VF, subjects were graded into seven categories: vd0/ecf0, vd1/ecf0, vd2m/ecf0, vd1/ecf1, vd2m/ecf1, vd2s/ecf1, and vd3/ecf1. With an existing VD, a further height loss of ≥ 15% was a VD progression. A new incident VD was a change from grade-0 to grade-2/3 or to grade-1 with ≥ 10% height loss. RESULTS Of subjects with Genant's grades 0, - 1, - 2, and - 3 VD, at follow-up, 4.6%, 8%, 10.6%, and 28.9% had at least one VD progression or new incident VD respectively. Among the three ecf0 groups, there was no difference in VD progression or new VD; while there was a significant difference in new ecf incidence, with vd0/ecf0 being lowest and vd2m/ecf0 being highest. Vd1/ecf0 and vd2m/ecf0 vertebrae had a higher risk of turning to ecf1 than vd0/ecf0 vertebrae. If vd1/ecf0 and vd2m/ecf0 subjects were combined together (range 20-34% height loss) to compare with vd1/ecf1 and vd2m/ecf1 subjects, the latter had significantly higher VD progression and new VD rates. CONCLUSION Vertebrae with grade-1/2 VDs had a higher risk of developing ECF. Subjects with pre-existing ECFs had a higher risk of worsening or new vertebral deformities.
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Affiliation(s)
- Y X J Wáng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - N Che-Nordin
- Department of Imaging and Interventional Radiology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - M Deng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - J C S Leung
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - A W L Kwok
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - L C He
- Department of Radiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - J F Griffith
- Department of Imaging and Interventional Radiology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - T C Y Kwok
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - P C Leung
- JC Centre for Osteoporosis Care and Control, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China
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22
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Steele JA, Blackwood AD, Griffith JF, Noble RT, Schiff KC. Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California. Water Res 2018; 136:137-149. [PMID: 29501758 DOI: 10.1016/j.watres.2018.01.056] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 05/08/2023]
Abstract
Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater discharge sample. Higher concentrations of avian source markers were noted in the stormwater discharge located immediately downstream of a large bird sanctuary along with increased Campylobacter concentrations and notably different Campylobacter species composition than the watershed that had no bird sanctuary. This study is one of the few to directly measure an array of important bacterial and viral pathogens in stormwater discharges to recreational beaches, and provides context for stormwater-based management of beaches during high risk wet-weather periods. Furthermore, the combination of culture-based and digital PCR-derived data is demonstrated to be valuable for assessing hydrographic relationships, considering delivery mechanisms, and providing foundational exposure information for risk assessment.
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Affiliation(s)
- Joshua A Steele
- Southern California Coastal Water Research Project, 3535 Harbor Blvd. Ste 110, Costa Mesa, CA 92626, USA.
| | - A Denene Blackwood
- UNC Institute of Marine Science, 3431 Arendell Street, Morehead City, NC 28557, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd. Ste 110, Costa Mesa, CA 92626, USA
| | - Rachel T Noble
- UNC Institute of Marine Science, 3431 Arendell Street, Morehead City, NC 28557, USA
| | - Kenneth C Schiff
- Southern California Coastal Water Research Project, 3535 Harbor Blvd. Ste 110, Costa Mesa, CA 92626, USA
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23
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Cao Y, Sivaganesan M, Kelty CA, Wang D, Boehm AB, Griffith JF, Weisberg SB, Shanks OC. A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method. Water Res 2018; 128:148-156. [PMID: 29101858 PMCID: PMC7228037 DOI: 10.1016/j.watres.2017.10.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/25/2017] [Accepted: 10/31/2017] [Indexed: 05/05/2023]
Abstract
Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Dan Wang
- Department of Civil and Environmental Engineering, Stanford University, Stanford CA 94305, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford CA 94305, USA
| | - John F Griffith
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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24
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Abstract
qPCR has become increasingly popular for microbial water quality testing because it is faster, more specific, and more flexible than culture-based methods. However, qPCR method limitations such as quantification bias introduced by reliance on standards and susceptibility to PCR inhibitors are major obstacles for implementation in water testing. This is because water testing requires accurate quantification of rare targets and because environmental waters often contain PCR inhibitors. Digital PCR offers the opportunity to maintain qPCR's advantages over culture-based methods while ameliorating two of qPCR's major limitations: the necessity to run standard curves and high susceptibility to inhibition. Here we describe a complete method for simultaneous testing for a general microbial water quality indicator (Enterococcus spp.) and a human-associated fecal marker in environmental waters. The complete method includes water sampling and filtration to capture bacteria, DNA extraction from bacteria captured on the filter, and droplet digital PCR to quantify the genetic markers from bacteria indicative of general and human-associated fecal contamination.
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Affiliation(s)
- Yiping Cao
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
- Source Molecular Corporation, Miami, FL, USA.
| | - Meredith R Raith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
| | - John F Griffith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
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25
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Arnold BF, Schiff KC, Ercumen A, Benjamin-Chung J, Steele JA, Griffith JF, Steinberg SJ, Smith P, McGee CD, Wilson R, Nelsen C, Weisberg SB, Colford JM. Acute Illness Among Surfers After Exposure to Seawater in Dry- and Wet-Weather Conditions. Am J Epidemiol 2017; 186:866-875. [PMID: 28498895 PMCID: PMC5860265 DOI: 10.1093/aje/kwx019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/23/2017] [Indexed: 11/17/2022] Open
Abstract
Rainstorms increase levels of fecal indicator bacteria in urban coastal waters, but it is unknown whether exposure to seawater after rainstorms increases rates of acute illness. Our objective was to provide the first estimates of rates of acute illness after seawater exposure during both dry- and wet-weather periods and to determine the relationship between levels of indicator bacteria and illness among surfers, a population with a high potential for exposure after rain. We enrolled 654 surfers in San Diego, California, and followed them longitudinally during the 2013–2014 and 2014–2015 winters (33,377 days of observation, 10,081 surf sessions). We measured daily surf activities and illness symptoms (gastrointestinal illness, sinus infections, ear infections, infected wounds). Compared with no exposure, exposure to seawater during dry weather increased incidence rates of all outcomes (e.g., for earache or infection, adjusted incidence rate ratio (IRR) = 1.86, 95% confidence interval (CI): 1.27, 2.71; for infected wounds, IRR = 3.04, 95% CI: 1.54, 5.98); exposure during wet weather further increased rates (e.g., for earache or infection, IRR = 3.28, 95% CI: 1.95, 5.51; for infected wounds, IRR = 4.96, 95% CI: 2.18, 11.29). Fecal indicator bacteria measured in seawater (Enterococcus species, fecal coliforms, total coliforms) were strongly associated with incident illness only during wet weather. Urban coastal seawater exposure increases the incidence rates of many acute illnesses among surfers, with higher incidence rates after rainstorms.
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Affiliation(s)
- Benjamin F. Arnold
- Correspondence to Dr. Benjamin F. Arnold, Division of Epidemiology, School of Public Health, University of California, Berkeley, 101 Haviland Hall, MC #7358, Berkeley, CA 94720-7358 (e-mail: )
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Soller JA, Schoen M, Steele JA, Griffith JF, Schiff KC. Incidence of gastrointestinal illness following wet weather recreational exposures: Harmonization of quantitative microbial risk assessment with an epidemiologic investigation of surfers. Water Res 2017; 121:280-289. [PMID: 28558279 DOI: 10.1016/j.watres.2017.05.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 05/26/2023]
Abstract
We modeled the risk of gastrointestinal (GI) illness associated with recreational exposures to marine water following storm events in San Diego County, California. We estimated GI illness risks via quantitative microbial risk assessment (QMRA) techniques by consolidating site specific pathogen monitoring data of stormwater, site specific dilution estimates, literature-based water ingestion data, and literature based pathogen dose-response and morbidity information. Our water quality results indicated that human sources of contamination contribute viral and bacterial pathogens to streams draining an urban watershed during wet weather that then enter the ocean and affect nearshore water quality. We evaluated a series of approaches to account for uncertainty in the norovirus dose-response model selection and compared our model results to those from a concurrently conducted epidemiological study that provided empirical estimates for illness risk following ocean exposure. The preferred norovirus dose-response approach yielded median risk estimates for water recreation-associated illness (15 GI illnesses per 1000 recreation events) that closely matched the reported epidemiological results (12 excess GI illnesses per 1000 wet weather recreation events). The results are consistent with norovirus, or other pathogens associated with norovirus, as an important cause of gastrointestinal illness among surfers in this setting. This study demonstrates the applicability of QMRA for recreational water risk estimation, even under wet weather conditions and describes a process that might be useful in developing site-specific water quality criteria in this and other locations.
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Affiliation(s)
- Jeffrey A Soller
- Soller Environmental, LLC, 3022 King St., Berkeley, CA 94703, USA.
| | - Mary Schoen
- Soller Environmental, LLC, 3022 King St., Berkeley, CA 94703, USA
| | - Joshua A Steele
- Southern California Coastal Water Research Project, 3535 Harbor Blvd #110, Costa Mesa, CA 92626, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd #110, Costa Mesa, CA 92626, USA
| | - Kenneth C Schiff
- Southern California Coastal Water Research Project, 3535 Harbor Blvd #110, Costa Mesa, CA 92626, USA
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Zimmer-Faust AG, Thulsiraj V, Marambio-Jones C, Cao Y, Griffith JF, Holden PA, Jay JA. Effect of freshwater sediment characteristics on the persistence of fecal indicator bacteria and genetic markers within a Southern California watershed. Water Res 2017; 119:1-11. [PMID: 28433878 DOI: 10.1016/j.watres.2017.04.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
In this study, the aging of culturable FIB and DNA representing genetic markers for Enterococcus spp. (ENT1A), general Bacteroides (GB3), and human-associated Bacteroides (HF183) in freshwater sediments was evaluated. Freshwater sediment was collected from four different sites within the upper and lower reach of the Topanga Creek Watershed and two additional comparator sites within the Santa Monica Bay, for a total of six sites. Untreated (ambient) and oven-dried (reduced microbiota) sediment was inoculated with 5% sewage and artificial freshwater. Microcosms were held for a 21-day period and sampled on day 0, 1, 3, 5, 7, 12, and 21. There were substantial differences in decay among the sediments tested, and decay rates were related to sediment characteristics. In the ambient sediments, smaller particle size and higher levels of organic matter and nutrients (nitrogen and phosphorus) were associated with increased persistence of the GB3 marker and culturable Escherichia coli (cEC) and enterococci (cENT). The HF183 marker exhibited decay rates of -0.50 to -0.96 day-1, which was 2-5 times faster in certain ambient sediments than decay of culturable FIB and the ENT1A and GB3 markers. The ENT1A and GB3 markers decayed at rates of between -0.07 and -0.28 and -0.10 to -0.44 day-1, and cEC and cENT decayed at rates of between -0.22 and -0.81 and -0.03 and -0.40 day-1, respectively. In the oven-dried sediments, increased persistence of all indicators and potential for limited growth of culturable FIB and the GB3 and ENT1A markers was observed. A simplified two-box model using the HF183 marker and cENT decay rates generated from the microcosm experiments was applied to two reaches within the Topanga Canyon watershed in order to provide context for the variability in decay rates observed. The model predicted lower ambient concentrations of enterococci in sediment in the upper (90 MPN g-1) versus lower Topanga watershed (530 MPN g-1) and low ambient levels of the HF183 marker (below the LLOQ) in sediments in both lower and upper watersheds. It is important to consider the variability in the persistence of genetic markers and FIB when evaluating indicators of fecal contamination in sediments, even within one watershed.
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Affiliation(s)
- Amity G Zimmer-Faust
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, United States
| | - Vanessa Thulsiraj
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, United States
| | - Catalina Marambio-Jones
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, United States
| | - Yiping Cao
- Southern California Coastal Water Research Project, 3535 Harbor Blvd Ste 110, Costa Mesa, CA 92626, United States
| | - John F Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd Ste 110, Costa Mesa, CA 92626, United States
| | - Patricia A Holden
- Earth Research Institute and Bren School of Environmental Science & Management, University of California, Santa Barbara, CA 93106, United States
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, United States.
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Arnold BF, Benjamin-Chung J, Schiff KC, Griffith JF, Weisberg SB, Colford JM. Arnold et al. Respond. Am J Public Health 2016; 107:e10-e11. [PMID: 27925809 DOI: 10.2105/ajph.2016.303505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Benjamin F Arnold
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
| | - Jade Benjamin-Chung
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
| | - Kenneth C Schiff
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
| | - John F Griffith
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
| | - Stephen B Weisberg
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
| | - John M Colford
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa
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Wu J, Cao Y, Young B, Yuen Y, Jiang S, Melendez D, Griffith JF, Stewart JR. Decay of Coliphages in Sewage-Contaminated Freshwater: Uncertainty and Seasonal Effects. Environ Sci Technol 2016; 50:11593-11601. [PMID: 27709921 DOI: 10.1021/acs.est.6b03916] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the fate of enteric viruses in water is vital for protection of water quality. However, the decay of enteric viruses is not well characterized, and its uncertainty has not been examined yet. In this study, the decay of coliphages, an indicator for enteric viruses, was investigated in situ under both sunlit and shaded conditions as well as in summer and winter. The decay rates of coliphages and their uncertainties were analyzed using a Bayesian approach. The results from the summer experiments revealed that the decay rates of somatic coliphages were significantly higher in sunlight (1.29 ± 0.06 day-1) than in shade (0.96 ± 0.04 day-1), but the decay rates of male-specific (F+) coliphages were not significantly different between sunlight (1.09 ± 0.09 day-1) and shaded treatments (1.11 ± 0.08 day-1). The decay rates of both F+ coliphages (0.25 ± 0.02 day-1) and somatic coliphages (0.12 ± 0.01 day-1) in winter were considerably lower than those in summer. Temperature and chlorophyll a (chla) concentration varied significantly (p < 0.001) between the two seasons, suggesting that these parameters might be important contributors to the seasonal variation of coliphage decay. Additionally, the Bayesian approach provided full distributions of decay rates and reduced the uncertainty, offering useful information for comparing decay rates under different conditions.
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Affiliation(s)
- Jianyong Wu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Yiping Cao
- Southern California Coastal Water Research Project Authority , Costa Mesa, California 92626, United States
| | - Brianna Young
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Yvonne Yuen
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Sharon Jiang
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Daira Melendez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - John F Griffith
- Southern California Coastal Water Research Project Authority , Costa Mesa, California 92626, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Arnold BF, Wade TJ, Benjamin-Chung J, Schiff KC, Griffith JF, Dufour AP, Weisberg SB, Colford JM. Acute Gastroenteritis and Recreational Water: Highest Burden Among Young US Children. Am J Public Health 2016; 106:1690-7. [PMID: 27459461 DOI: 10.2105/ajph.2016.303279] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES To provide summary estimates of gastroenteritis risks and illness burden associated with recreational water exposure and determine whether children have higher risks and burden. METHODS We combined individual participant data from 13 prospective cohorts at marine and freshwater beaches throughout the United States (n = 84 411). We measured incident outcomes within 10 days of exposure: diarrhea, gastrointestinal illness, missed daily activity (work, school, vacation), and medical visits. We estimated the relationship between outcomes and 2 exposures: body immersion swimming and Enterococcus spp. fecal indicator bacteria levels in the water. We also estimated the population-attributable risk associated with these exposures. RESULTS Water exposure accounted for 21% of diarrhea episodes and 9% of missed daily activities but was unassociated with gastroenteritis leading to medical consultation. Children aged 0 to 4 and 5 to 10 years had the most water exposure, exhibited stronger associations between levels of water quality and illness, and accounted for the largest attributable illness burden. CONCLUSIONS The higher gastroenteritis risk and associated burden in young children presents important new information to inform future recreational water quality guidelines designed to protect public health.
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Affiliation(s)
- Benjamin F Arnold
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - Timothy J Wade
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - Jade Benjamin-Chung
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - Kenneth C Schiff
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - John F Griffith
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - Alfred P Dufour
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - Stephen B Weisberg
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
| | - John M Colford
- Benjamin F. Arnold, Jade Benjamin-Chung, and John M. Colford Jr are with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Timothy J. Wade is with the US Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC. Kenneth C. Schiff, John F. Griffith, and Stephen B. Weisberg are with the Southern California Coastal Water Research Project, Costa Mesa, CA. Alfred P. Dufour is with the US EPA, National Exposure Research Laboratory, Cincinnati, OH
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Maraccini PA, Mattioli MCM, Sassoubre LM, Cao Y, Griffith JF, Ervin JS, Van De Werfhorst LC, Boehm AB. Solar Inactivation of Enterococci and Escherichia coli in Natural Waters: Effects of Water Absorbance and Depth. Environ Sci Technol 2016; 50:5068-5076. [PMID: 27119980 DOI: 10.1021/acs.est.6b00505] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The decay of sewage-sourced Escherichia coli and enterococci was measured at multiple depths in a freshwater marsh, a brackish water lagoon, and a marine site, all located in California. The marine site had very clear water, while the waters from the marsh and lagoon contained colored dissolved organic matter that not only blocked light but also produced reactive oxygen species. First order decay rate constants of both enterococci and E. coli were between 1 and 2 d(-1) under low light conditions and as high as 6 d(-1) under high light conditions. First order decay rate constants were well correlated to the daily average UVB light intensity corrected for light screening incorporating water absorbance and depth, suggesting endogenous photoinactivation is a major pathway for bacterial decay. Additional laboratory experiments demonstrated the presence of colored dissolved organic matter in marsh water enhanced photoinactivation of a laboratory strain of Enterococcus faecalis, but depressed photoinactivation of sewage-sourced enterococci and E. coli after correcting for UVB light screening, suggesting that although the exogenous indirect photoinactivation mechanism may be active against Ent. faecalis, it is not for the sewage-source organisms. A simple linear regression model based on UVB light intensity appears to be a useful tool for predicting inactivation rate constants in natural waters of any depth and absorbance.
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Affiliation(s)
- Peter A Maraccini
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
- Engineering Research Center (ERC) for Re-inventing the Nation's Urban Water Infrastructure (ReNUWIt)
| | - Mia Catharine M Mattioli
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Lauren M Sassoubre
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Yiping Cao
- Southern California Coastal Water Research Project, 3535 Harbor Blvd Suite 110, Costa Mesa, California 92626, United States
| | - John F Griffith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd Suite 110, Costa Mesa, California 92626, United States
| | - Jared S Ervin
- Earth Research Institute and Bren School of Environmental Science & Management, University of California , Santa Barbara, California 93106, United States
| | - Laurie C Van De Werfhorst
- Earth Research Institute and Bren School of Environmental Science & Management, University of California , Santa Barbara, California 93106, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
- Engineering Research Center (ERC) for Re-inventing the Nation's Urban Water Infrastructure (ReNUWIt)
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Griffith JF, Weisberg SB, Arnold BF, Cao Y, Schiff KC, Colford JM. Epidemiologic evaluation of multiple alternate microbial water quality monitoring indicators at three California beaches. Water Res 2016; 94:371-381. [PMID: 27040577 DOI: 10.1016/j.watres.2016.02.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Advances in molecular methods provide new opportunities for directly measuring pathogens or host-associated markers of fecal pollution instead of relying on fecal indicator bacteria (FIB) alone for beach water quality monitoring. Adoption of new indicators depends on identifying relationships between either the presence or concentration of the indicators and illness among swimmers. Here we present results from three epidemiologic studies in which a broad range of bacterial and viral indicators of fecal contamination were measured simultaneously by either culture or molecular methods along with Enterococcus to assess whether they provide better health risk prediction than current microbial indicators of recreational water quality. METHODS We conducted prospective cohort studies at three California beaches -- Avalon Bay (Avalon), Doheny State Beach (Doheny), Surfrider State Beach (Malibu) -- during the summers of 2007, 2008 and 2009. The studies enrolled 10,785 swimmers across the beaches and recorded each swimmer's water exposure. Water and sand samples were collected several times per day at multiple locations at each beach and analyzed for up to 41 target indicators using 67 different methodologies. Interviewers contacted participants by phone 10-14 days later and recorded symptoms of gastrointestinal illness occurring after their beach visit. Regression models were used to evaluate the association between water quality indicators and gastrointestinal illness among swimmers at each beach. RESULTS F+ coliphage (measured using EPA Method 1602) exhibited a stronger association with GI illness than did EPA Method 1600 at the two beaches where it was measured, while a molecular method, F+ RNA Coliphage Genotype II, was the only indicator significantly associated with GI illness at Malibu. MRSA, a known pathogen, had the strongest association with GI illness of any microbe measured at Avalon. There were two methods targeting human-associated fecal anaerobic bacteria that were more strongly associated with GI illness than EPA Method 1600, but only at Avalon. No indicator combinations consistently had a higher odds ratio than EPA Method 1600, but one composite indicator, based on the number of pathogens detected at a beach, was significantly associated with gastrointestinal illness at both Avalon and Doheny when freshwater flow was high. DISCUSSION While EPA Method1600 performed adequately at two beaches based on its consistency of association with gastrointestinal illness and the precision of its estimated associations, F+ coliphage measured by EPA Method 1602 had a stronger association with GI illness under high risk conditions at the two beaches where it was measured. One indicator, F+ Coliphage Genotype II was the only indicator significantly associated with GI illness at Malibu. Several indicators, particularly those targeting human associated bacteria, exhibited relationships with GI illness that were equal to or greater than that of EPA Method 1600 at Avalon, which has a focused human fecal source. Our results suggest that site-specific conditions at each beach determine which indicator or indicators best predict GI illness.
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Affiliation(s)
- John F Griffith
- Department of Microbiology, Southern California Coastal Water Research Project, 3535 Harbor Blvd. Suite 110, Costa Mesa, CA 92626, USA.
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - Benjamin F Arnold
- Division of Epidemiology, School of Public Health, University of California, Berkeley, USA
| | - Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - Kenneth C Schiff
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - John M Colford
- Division of Epidemiology, School of Public Health, University of California, Berkeley, USA
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Cao Y, Raith MR, Griffith JF. A Duplex Digital PCR Assay for Simultaneous Quantification of the Enterococcus spp. and the Human Fecal-associated HF183 Marker in Waters. J Vis Exp 2016. [PMID: 27023488 DOI: 10.3791/53611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This manuscript describes a duplex digital PCR assay (EntHF183 dPCR) for simultaneous quantification of Enterococcus spp. and the human fecal-associated HF183 marker. The EntHF183 duplex dPCR (referred as EntHF183 dPCR hereon) assay uses the same primer and probe sequences as its published individual quantitative PCR (qPCR) counterparts. Likewise, the same water filtration and DNA extraction procedures as performed prior to qPCR are followed prior to running dPCR. However, the duplex dPCR assay has several advantages over the qPCR assays. Most important, the dPCR assay eliminates the need for running a standard curve and hence, the associated bias and variability, by direct quantification of its targets. In addition, while duplexing (i.e., simultaneous quantification) Enterococcus and HF183 in qPCR often leads to severe underestimation of the less abundant target in a sample, dPCR provides consistent quantification of both targets, whether quantified individually or simultaneously in the same reaction. The dPCR assay is also able to tolerate PCR inhibitor concentrations that are one to two orders of magnitude higher than those tolerated by qPCR. These advantages make the EntHF183 dPCR assay particularly attractive because it simultaneously provides accurate and repeatable information on both general and human-associated fecal contamination in environmental waters without the need to run two separate qPCR assays. Despite its advantages over qPCR, the upper quantification limit of the dPCR assay with currently available instrumentation is approximately four orders of magnitude lower than that achievable by qPCR. Consequently, dilution is needed for measurement of high concentrations of target organisms such as those typically observed following sewage spills.
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Affiliation(s)
- Yiping Cao
- Department of Microbiology, Southern California Costal Water Research Project Authority;
| | - Meredith R Raith
- Department of Microbiology, Southern California Costal Water Research Project Authority
| | - John F Griffith
- Department of Microbiology, Southern California Costal Water Research Project Authority;
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Abstract
Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - John F Griffith
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA.
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Zhu TY, Griffith JF, Qin L, Hung VWY, Fong TN, Au SK, Tang XL, Kun EW, Kwok AW, Leung PC, Li EK, Tam LS. Cortical thinning and progressive cortical porosity in female patients with systemic lupus erythematosus on long-term glucocorticoids: a 2-year case-control study. Osteoporos Int 2015; 26:1759-71. [PMID: 25736166 DOI: 10.1007/s00198-015-3077-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
UNLABELLED In this study, we characterized longitudinal changes of volumetric bone mineral density and cortical and trabecular microstructure at the distal radius using HR-pQCT in female systemic lupus erythematosus (SLE) patients on long-term glucocorticoids. Cortical thinning and increased cortical porosity are the major features of longitudinal microstructural deterioration in SLE patients. INTRODUCTION The study aims to characterize longitudinal changes of volumetric bone mineral density (vBMD) and bone microstructure at distal radius in female systemic lupus erythematosus (SLE) patients on long-term glucocorticoids. METHODS This 2-year case-control study consisted of 166 premenopausal subjects (75 SLE patients and 91 controls) and 79 postmenopausal subjects (44 SLE patients and 35 controls). We obtained areal BMD (aBMD) by dual-energy X-ray absorptiometry at multiple skeletal sites and indices of vBMD and microstructure at distal radius by high-resolution peripheral quantitative computed tomography (HR-pQCT) at baseline, 12 and 24 months. RESULTS In either premenopausal or postmenopausal subjects, changes in aBMD did not differ between patients and controls except that decrease in aBMD at total hip at 24 months in premenopausal patients was significantly higher. In premenopausal subjects, decrease in cortical area (-0.51 vs. -0.06 %, p = 0.039) and thickness (-0.63 vs. 0.02 %, p = 0.031) and increase in cortical porosity (21.7 vs. 7.16 %, p = 0.030) over study period were significantly larger in patients after adjustment of age and body mass index. Decreased in trabecular vBMD was significantly less (-0.63 vs. -2.32 %, p = 0.001) with trabecular microstructure better maintained in patients. In postmenopausal subjects, decrease in cortical vBMD (-2.66 vs. -1.56 %, p = 0.039) and increase in cortical porosity (41.6 vs. 16.3 %, p = 0.021) were significantly higher in patients, and there was no group-wise difference in change of trabecular microstructure. CONCLUSION Longitudinal microstructural deterioration in SLE is characterized by cortical thinning and increased cortical porosity. Cortical bone is an important source of bone loss in SLE patients on glucocorticoids.
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Affiliation(s)
- T Y Zhu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Bone Quality and Health Center, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - J F Griffith
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - L Qin
- Bone Quality and Health Center, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - V W Y Hung
- Bone Quality and Health Center, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - T-N Fong
- Bone Quality and Health Center, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - S-K Au
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - X-L Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - E W Kun
- Department of Medicine and Geriatrics, Tai Po Hospital, Tai Po, Hong Kong SAR, China
| | - A W Kwok
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - P-C Leung
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - E K Li
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - L-S Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, 9/F Clinical Sciences Building, 30-32 Ngan Shing Street, Shatin, N.T, Hong Kong SAR, China.
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Cao Y, Raith MR, Griffith JF. Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment. Water Res 2015; 70:337-49. [PMID: 25543243 DOI: 10.1016/j.watres.2014.12.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/25/2014] [Accepted: 12/07/2014] [Indexed: 05/18/2023]
Abstract
Despite wide application to beach water monitoring and microbial source identification, results produced by quantitative PCR (qPCR) methods are subject to bias introduced by reliance on quantitative standards. Digital PCR technology provides direct, standards-free quantification and may potentially alleviate or greatly reduce other qPCR limitations such as difficulty in multiplexing and susceptibility to PCR inhibition. This study examined the efficacy of employing a duplex droplet digital PCR (ddPCR) assay that simultaneously quantifies Enterococcus spp. and the human fecal-associated HF183 marker for water quality assessment. Duplex ddPCR performance was evaluated side-by-side with qPCR and simplex ddPCR using reference material and 131 fecal and water samples. Results for fecal and water samples were highly correlated between ddPCR and simplex qPCR (coefficients > 0.93, p < 0.001). Duplexing Enterococcus and HF183 in qPCR led to competition and resulted in non-detection or underestimation of the target with low concentration relative to the other, while results produced by simplex and duplex ddPCR were consistent and often indistinguishable from one another. ddPCR showed greater tolerance for inhibition, with no discernable effect on quantification at inhibitor concentrations one to two orders of magnitude higher than that tolerated by qPCR. Overall, ddPCR also exhibited improved precision, higher run-to-run repeatability, similar diagnostic sensitivity and specificity on the HF183 marker, but a lower upper limit of quantification than qPCR. Digital PCR has the potential to become a reliable and economical alternative to qPCR for recreational water monitoring and fecal source identification. Findings from this study may also be of interest to other aspects of water research such as detection of pathogens and antibiotic resistance genes.
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Affiliation(s)
- Yiping Cao
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
| | - Meredith R Raith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
| | - John F Griffith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
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Zhu TY, Griffith JF, Qin L, Hung VWY, Fong TN, Au SK, Kwok AW, Leung PC, Li EK, Tam LS. Density, structure, and strength of the distal radius in patients with psoriatic arthritis: the role of inflammation and cardiovascular risk factors. Osteoporos Int 2015; 26:261-72. [PMID: 25160570 DOI: 10.1007/s00198-014-2858-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/13/2014] [Indexed: 01/21/2023]
Abstract
UNLABELLED We investigated the densitometric and microstructural features of the distal radius in psoriatic arthritis (PsA) patients using high-resolution peripheral quantitative computed tomography. PsA patients have unique bone microstructural deficits, manifested as lower cortical bone density and higher cortical porosity, which are associated with a propensity to bone fragility. INTRODUCTION The aim of this study was to investigate the densitometric, geometric, microstructural, and biomechanical features of the distal radius in psoriatic arthritis (PsA) patients. METHODS This study cohort consisted of 53 PsA patients (24 males and 29 females), with an average age of 53.1 years and 53 gender- and age-matched controls. Areal bone mineral density (aBMD) of the hip, lumbar spine, and ultradistal radius was measured by dual-energy X-ray absorptiometry. High-resolution peripheral quantitative computed tomography (HR-pQCT) was performed at the distal radius to obtain measures of volumetric BMD (vBMD), microstructure, and derived biomechanical indices. RESULTS There were no significant between-group differences in aBMD at the femoral neck, total hip, and ultradistal radius, while aBMD at the lumbar spine was significantly higher in patients. The only indices indicating compromised bone quality in PsA patients were related to cortical bone quality. Cortical vBMD were -3.8% significantly lower, while cortical pore volume, porosity index, and pore diameter were 108, 79.5, and 8.6%, respectively, significantly higher in patients. Cortical stress was marginally lower (-1.3%, p = 0.077) in patients with stress significantly more unevenly distributed (4.9%, p = 0.035). Endocortical perimeter and cortical pore volume were significantly higher in patients with vertebral fracture. Deficits in cortical bone quality were associated with indices of disease activity/severity and were more prominent in patients with type 2 diabetes mellitus or hypertension. CONCLUSIONS There is an intertwined relationship between chronic inflammation, cardiovascular risk factors, and bone loss in PsA. PsA patients seem to have unique bone microstructural deficits which are associated with a propensity to bone fragility.
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Affiliation(s)
- T Y Zhu
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, 9/F Clinical Sciences Building, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, N.T., Hong Kong, SAR, China
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Yau VM, Schiff KC, Arnold BF, Griffith JF, Gruber JS, Wright CC, Wade TJ, Burns S, Hayes JM, McGee C, Gold M, Cao Y, Boehm AB, Weisberg SB, Colford JM. Effect of submarine groundwater discharge on bacterial indicators and swimmer health at Avalon Beach, CA, USA. Water Res 2014; 59:23-36. [PMID: 24776951 DOI: 10.1016/j.watres.2014.03.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/21/2014] [Accepted: 03/18/2014] [Indexed: 05/20/2023]
Abstract
Use of fecal indicator bacteria (FIB) for monitoring beach water quality is based on their co-occurrence with human pathogens, a relationship that can be dramatically altered by fate and transport processes after leaving the human intestine. We conducted a prospective cohort study at Avalon Beach, California (USA), where the indicator relationship is potentially affected by the discharge of sewage-contaminated groundwater and by solar radiation levels at this shallow, relatively quiescent beach. The goals of this study were to determine: 1) if swimmers exposed to marine water were at higher risk of illness than non-swimmers; 2) if FIB measured in marine water were associated with swimmer illness, and; 3) if the associations between FIB and swimmer health were modified by either submarine groundwater discharge or solar radiation levels. There were 7317 individuals recruited during the summers of 2007-08, 6165 (84%) of whom completed follow-up within two weeks of the beach visit. A total of 703 water quality samples were collected across multiple sites and time periods during recruitment days and analyzed for FIB using both culture-based and molecular methods. Adjusted odds ratios (AOR) indicated that swimmers who swallowed water were more likely to experience Gastrointestinal Illness (GI Illness) within three days of their beach visit than non-swimmers, and that this risk was significantly elevated when either submarine groundwater discharge was high (AOR [95% CI]:2.18 [1.22-3.89]) or solar radiation was low (2.45 [1.25-4.79]). The risk of GI Illness was not significantly elevated for swimmers who swallowed water when groundwater discharge was low or solar radiation was high. Associations between GI Illness incidence and FIB levels (Enterococcus EPA Method 1600) among swimmers who swallowed water were not significant when we did not account for groundwater discharge, but were strongly associated when groundwater discharge was high (1.85 [1.06, 3.23]) compared to when it was low (0.77 [0.42, 1.42]; test of interaction: P = 0.03). These results demonstrate the need to account for local environmental conditions when monitoring for, and making decisions about, public health at recreational beaches. The views expressed in this article are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency.
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Affiliation(s)
- Vincent M Yau
- School of Public Health, University of California, Berkeley and Kaiser Permanente Division of Research, United States
| | - Kenneth C Schiff
- Southern California Coastal Water Research Project, United States
| | - Benjamin F Arnold
- School of Public Health, University of California, Berkeley, United States
| | - John F Griffith
- Southern California Coastal Water Research Project, United States
| | - Joshua S Gruber
- School of Public Health, University of California, Berkeley, United States
| | - Catherine C Wright
- School of Public Health, University of California, Berkeley, United States
| | - Timothy J Wade
- United States Environmental Protection Agency, National Environmental Health Effects Research Laboratory, Chapel Hill, United States
| | - Susan Burns
- University of California, Berkeley, Survey Research Center, United States
| | - Jacqueline M Hayes
- University of California, Berkeley, Survey Research Center, United States
| | | | - Mark Gold
- Institute of Environment and Sustainability, University of California, Los Angeles, United States
| | - Yiping Cao
- Southern California Coastal Water Research Project, United States
| | - Alexandria B Boehm
- Environmental and Water Studies, Dept. Civil & Environmental Engineering, Stanford University, Stanford, CA 94305, United States
| | | | - John M Colford
- School of Public Health, University of California, Berkeley, United States.
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Riedel TE, Zimmer-Faust AG, Thulsiraj V, Madi T, Hanley KT, Ebentier DL, Byappanahalli M, Layton B, Raith M, Boehm AB, Griffith JF, Holden PA, Shanks OC, Weisberg SB, Jay JA. Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. J Environ Manage 2014; 136:112-20. [PMID: 24583609 DOI: 10.1016/j.jenvman.2014.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 05/04/2023]
Abstract
Some molecular methods for tracking fecal pollution in environmental waters have both PCR and quantitative PCR (qPCR) assays available for use. To assist managers in deciding whether to implement newer qPCR techniques in routine monitoring programs, we compared detection limits (LODs) and costs of PCR and qPCR assays with identical targets that are relevant to beach water quality assessment. For human-associated assays targeting Bacteroidales HF183 genetic marker, qPCR LODs were 70 times lower and there was no effect of target matrix (artificial freshwater, environmental creek water, and environmental marine water) on PCR or qPCR LODs. The PCR startup and annual costs were the lowest, while the per reaction cost was 62% lower than the Taqman based qPCR and 180% higher than the SYBR based qPCR. For gull-associated assays, there was no significant difference between PCR and qPCR LODs, target matrix did not effect PCR or qPCR LODs, and PCR startup, annual, and per reaction costs were lower. Upgrading to qPCR involves greater startup and annual costs, but this increase may be justified in the case of the human-associated assays with lower detection limits and reduced cost per sample.
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Affiliation(s)
- Timothy E Riedel
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
| | - Amity G Zimmer-Faust
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA; Institute of the Environment and Sustainability, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Vanessa Thulsiraj
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Tania Madi
- Source Molecular Corporation, Miami, FL 33155, USA
| | - Kaitlyn T Hanley
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Darcy L Ebentier
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Muruleedhara Byappanahalli
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Porter, IN 46304, USA
| | - Blythe Layton
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Meredith Raith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Alexandria B Boehm
- Environmental and Water Studies, Department of Civil and Environmental, Engineering, Stanford University, Stanford, CA 94305, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, and Earth Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
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Zhu TY, Griffith JF, Au SK, Tang XL, Kwok AW, Leung PC, Li EK, Tam LS. Incidence of and risk factors for non-vertebral and vertebral fracture in female Chinese patients with systemic lupus erythematosus: a five-year cohort study. Lupus 2014; 23:854-61. [DOI: 10.1177/0961203314528555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/26/2014] [Indexed: 11/15/2022]
Abstract
Objective The objective of this paper is to investigate the incidence of both non-vertebral and vertebral fracture in female patients with systemic lupus erythematosus (SLE) and to identify risk factors for incident fracture. Methods In a five-year prospective study of 127 female Chinese SLE patients with an average age of 46.9 years (SD: 10.1 years), information on potential risk factors, including demographics, clinical data and bone mineral density (BMD) at lumbar spine and hip by dual-energy X-ray absorptiometry was collected at baseline. At follow-up, participants reported incident non-vertebral fracture during the study period. Semi-quantitative analysis was used to determine incident vertebral fracture on lateral thoracic and lumbar radiographs, defined as any vertebral body graded normal at baseline and at least mildly deformed (20%–25% reduction or more in any vertebral height) at follow-up. Results Nine incident non-vertebral fractures occurred in eight patients during the study period. Six patients had one or more incident vertebral fractures. The incidence of non-vertebral and vertebral fracture was 1.26 and 0.94 per 100 patient-years, respectively. In multivariate logistic analyses, independent variables associated with incident non-vertebral fracture were duration of glucocorticoid use and prevalent lumbar spine osteoporosis, while risk factors associated with incident vertebral fracture were higher organ damage and prevalent lumbar spine osteoporosis. Conclusions The incidence of fracture in SLE patients is lower than the prevalence reported in cross-sectional studies. Lumbar spine BMD appears to have a stronger relationship with incident fracture than hip BMD. This warrants further investigation regarding the optimal site of BMD measurement when predicting fracture risk in SLE patients.
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Affiliation(s)
- TY Zhu
- Department of Medicine and Therapeutics
| | - JF Griffith
- Department of Imaging and Interventional Radiology
| | - S-K Au
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - X-L Tang
- Department of Medicine and Therapeutics
| | - AW Kwok
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - P-C Leung
- The Jockey Club Centre for Osteoporosis Care and Control, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - EK Li
- Department of Medicine and Therapeutics
| | - L-S Tam
- Department of Medicine and Therapeutics
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Abstract
SUMMARY This study used the "functional muscle-bone unit" concept to investigate muscle-bone interaction of the lumbar spine in subjects of varying bone mineral density. It was found that unit bone mass corresponded to a relatively more muscle mass in subjects with reduced bone mineral density, indicating a relatively higher mechanical load from muscles exerted on trabecular bone. INTRODUCTION Bone is an architecturally adaptive tissue which responds to mechanical loading. This study is proposed to use "functional muscle-bone unit" to reflect this muscle-bone interaction at spine in subjects with different bone mineral density. METHODS The study was carried out in young normal subjects (21 females; age, 29 ± 3) and elderly subjects (155 females; age, 73 ± 3.9) with varying bone mineral density. Cross-sectional area of paravertebral muscle groups was measured in MR images to indicate the muscle mass, while the bone mineral content by dual X-ray absorptiometry was used to represent the bone mass. The functional muscle-bone unit was calculated as the ratio between the bone mass to muscle mass. RESULTS It showed that with aging, the muscle mass decreased with the bone mass losing. However, more pronounced reduction was found in bone mass than in muscle mass in the subjects with lower bone mineral density. CONCLUSIONS Muscle-bone interaction was changed in elderly, especially in those with osteoporosis. Unit bone mass corresponded to a higher muscle mass in subjects with reduced bone mineral density than those normal subjects. This may be contributory to the occurrence of nontraumatic vertebral fractures in elderly subjects with reduced bone mineral density.
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Affiliation(s)
- H T Ma
- Department of Electronic and Information Engineering, Harbin Institute of Technology Shenzhen Graduate School, Rm 205C, C Building, HIT Campus, University Town, Xili, Nanshan, Shenzhen, China, 518055,
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Love DC, Rodriguez RA, Gibbons CD, Griffith JF, Yu Q, Stewart JR, Sobsey MD. Human viruses and viral indicators in marine water at two recreational beaches in Southern California, USA. J Water Health 2014; 12:136-150. [PMID: 24642440 DOI: 10.2166/wh.2013.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Waterborne enteric viruses may pose disease risks to bather health but occurrence of these viruses has been difficult to characterize at recreational beaches. The aim of this study was to evaluate water for human virus occurrence at two Southern California recreational beaches with a history of beach closures. Human enteric viruses (adenovirus and norovirus) and viral indicators (F+ and somatic coliphages) were measured in water samples over a 4-month period from Avalon Beach, Catalina Island (n = 324) and Doheny Beach, Orange County (n = 112). Human viruses were concentrated from 40 L samples and detected by nested reverse transcriptase polymerase chain reaction (PCR). Detection frequencies at Doheny Beach were 25.5% (adenovirus) and 22.3% (norovirus), and at Avalon Beach were 9.3% (adenovirus) and 0.7% (norovirus). Positive associations between adenoviruses and fecal coliforms were observed at Doheny (p = 0.02) and Avalon (p = 0.01) Beaches. Human viruses were present at both beaches at higher frequencies than previously detected in the region, suggesting that the virus detection methods presented here may better measure potential health risks to bathers. These virus recovery, concentration, and molecular detection methods are advancing practices so that analysis of enteric viruses can become more effective and routine for recreational water quality monitoring.
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Affiliation(s)
- David C Love
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA E-mail:
| | - Roberto A Rodriguez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA E-mail: ; Current address: Environmental and Occupational Health Sciences, School of Public Health-El Paso Regional Campus, University of Texas-Health Science Center at Houston, El Paso, TX 79902, USA
| | - Christopher D Gibbons
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA E-mail:
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Qilu Yu
- Division of Geriatric Medicine and Gerontology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - 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, 27599, USA E-mail:
| | - Mark D Sobsey
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA E-mail:
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Layton BA, Cao Y, Ebentier DL, Hanley K, Ballesté E, Brandão J, Byappanahalli M, Converse R, Farnleitner AH, Gentry-Shields J, Gidley ML, Gourmelon M, Lee CS, Lee J, Lozach S, Madi T, Meijer WG, Noble R, Peed L, Reischer GH, Rodrigues R, Rose JB, Schriewer A, Sinigalliano C, Srinivasan S, Stewart J, Van De Werfhorst LC, Wang D, Whitman R, Wuertz S, Jay J, Holden PA, Boehm AB, Shanks O, Griffith JF. Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study. Water Res 2013; 47:6897-908. [PMID: 23992621 DOI: 10.1016/j.watres.2013.05.060] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 05/24/2023]
Abstract
A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman(®) was found to be the most effective marker of human fecal contamination in this California-based study.
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Affiliation(s)
- Blythe A Layton
- Southern California Coastal Water Research Project, 3535 Harbor Blvd Ste 110, Costa Mesa, CA 92626, United States
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Harwood VJ, Boehm AB, Sassoubre LM, Vijayavel K, Stewart JR, Fong TT, Caprais MP, Converse RR, Diston D, Ebdon J, Fuhrman JA, Gourmelon M, Gentry-Shields J, Griffith JF, Kashian DR, Noble RT, Taylor H, Wicki M. Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study. Water Res 2013; 47:6929-43. [PMID: 23886543 DOI: 10.1016/j.watres.2013.04.064] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 03/04/2013] [Accepted: 04/03/2013] [Indexed: 05/26/2023]
Abstract
An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10-50 gene copies or plaques × 50 ml(-1)) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40-70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent.
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Affiliation(s)
- Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA.
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45
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Stewart JR, Boehm AB, Dubinsky EA, Fong TT, Goodwin KD, Griffith JF, Noble RT, Shanks OC, Vijayavel K, Weisberg SB. Recommendations following a multi-laboratory comparison of microbial source tracking methods. Water Res 2013; 47:6829-6838. [PMID: 23891204 DOI: 10.1016/j.watres.2013.04.063] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/07/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions.
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Affiliation(s)
- Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, 1301 Michael Hooker Research Center, 135 Dauer Drive, Campus Box #7431, Chapel Hill, NC 27599, USA.
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46
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Ebentier DL, Hanley KT, Cao Y, Badgley BD, Boehm AB, Ervin JS, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Kelty CA, Lozach S, McGee C, Peed LA, Raith M, Ryu H, Sadowsky MJ, Scott EA, Santo Domingo J, Schriewer A, Sinigalliano CD, Shanks OC, Van De Werfhorst LC, Wang D, Wuertz S, Jay JA. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Res 2013; 47:6839-6848. [PMID: 23911226 DOI: 10.1016/j.watres.2013.01.060] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/17/2013] [Accepted: 01/20/2013] [Indexed: 06/02/2023]
Abstract
Many PCR-based methods for microbial source tracking (MST) have been developed and validated within individual research laboratories. Inter-laboratory validation of these methods, however, has been minimal, and the effects of protocol standardization regimes have not been thoroughly evaluated. Knowledge of factors influencing PCR in different laboratories is vital to future technology transfer for use of MST methods as a tool for water quality management. In this study, a blinded set of 64 filters (containing 32 duplicate samples generated from 12 composite fecal sources) were analyzed by three to five core laboratories with a suite of PCR-based methods utilizing standardized reagents and protocols. Repeatability (intra-laboratory variability) and reproducibility (inter-laboratory variability) of observed results were assessed. When standardized methodologies were used, intra- and inter-laboratory %CVs were generally low (median %CV 0.1-3.3% and 1.9-7.1%, respectively) and comparable to those observed in similar inter-laboratory validation studies performed on other methods of quantifying fecal indicator bacteria (FIB) in environmental samples. ANOVA of %CV values found three human-associated methods (BsteriF1, BacHum, and HF183Taqman) to be similarly reproducible (p > 0.05) and significantly more reproducible (p < 0.05) than HumM2. This was attributed to the increased variability associated with low target concentrations detected by HumM2 (approximately 1-2 log10copies/filter lower) compared to other human-associated methods. Cow-associated methods (BacCow and CowM2) were similarly reproducible (p > 0.05). When using standardized protocols, variance component analysis indicated sample type (fecal source and concentration) to be the major contributor to total variability with that from replicate filters and inter-laboratory analysis to be within the same order of magnitude but larger than inherent intra-laboratory variability. However, when reagents and protocols were not standardized, inter-laboratory %CV generally increased with a corresponding decline in reproducibility. Overall, these findings verify the repeatability and reproducibility of these MST methods and highlight the need for standardization of protocols and consumables prior to implementation of larger scale MST studies involving multiple laboratories.
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Affiliation(s)
- Darcy L Ebentier
- Department of Civil and Environmental Engineering, University of California Los Angeles, 5732 Boelter Hall, Los Angeles, CA 90095, USA
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47
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Raith MR, Kelty CA, Griffith JF, Schriewer A, Wuertz S, Mieszkin S, Gourmelon M, Reischer GH, Farnleitner AH, Ervin JS, Holden PA, Ebentier DL, Jay JA, Wang D, Boehm AB, Aw TG, Rose JB, Balleste E, Meijer WG, Sivaganesan M, Shanks OC. Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Res 2013; 47:6921-6928. [PMID: 23871256 DOI: 10.1016/j.watres.2013.03.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/27/2013] [Accepted: 03/31/2013] [Indexed: 06/02/2023]
Abstract
The State of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusion of cow-associated methods a logical choice. Because the performance of these methods has been shown to change based on geography and/or local animal feeding practices, laboratory comparisons are needed to determine which assays are best suited for implementation. We describe the performance characterization of two end-point PCR assays (CF128 and CF193) and five real-time quantitative PCR (qPCR) assays (Rum2Bac, BacR, BacCow, CowM2, and CowM3) reported to be associated with either ruminant or cattle feces. Each assay was tested against a blinded set of 38 reference challenge filters (19 duplicate samples) containing fecal pollution from 12 different sources suspected to impact water quality. The abundance of each host-associated genetic marker was measured for qPCR-based assays in both target and non-target animals and compared to quantities of total DNA mass, wet mass of fecal material, as well as Bacteroidales, and enterococci determined by 16S rRNA qPCR and culture-based approaches (enterococci only). Ruminant- and cow-associated genetic markers were detected in all filters containing a cattle fecal source. However, some assays cross-reacted with non-target pollution sources. A large amount of variability was evident across laboratories when protocols were not fixed suggesting that protocol standardization will be necessary for widespread implementation. Finally, performance metrics indicate that the cattle-associated CowM2 qPCR method combined with either the BacR or Rum2Bac ruminant-associated methods are most suitable for implementation.
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Affiliation(s)
- Meredith R Raith
- Southern California Coastal Water Research Project, 3535 Harbor Blvd STE 110, Costa Mesa, CA 92626, USA
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48
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Cao Y, Van De Werfhorst LC, Scott EA, Raith MR, Holden PA, Griffith JF. Bacteroidales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal bacteria TRFLP. Water Res 2013; 47:6944-6955. [PMID: 23880219 DOI: 10.1016/j.watres.2013.03.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 03/04/2013] [Accepted: 03/17/2013] [Indexed: 06/02/2023]
Abstract
Terminal restriction fragment length polymorphism (TRFLP) is an attractive community analysis method for microbial source tracking (MST) because it is accessible, relatively inexpensive, and can discern multiple fecal sources simultaneously. A new Bacteroidales TRFLP (Bac-TRFLP) method was developed and its source identification performance was evaluated by itself, in comparison to, and in combination with an existing universal bacterial TRFLP method in two laboratories. Sixty-four blind samples from 12 fecal sources (sewage, septage, human, dog, horse, cow, deer, pig, chicken, goose, pigeon, and gull) were used for evaluation. Bac- and Univ-TRFLP exhibited similarly high overall correct identification (>88% and >89%, respectively), excellent specificity regardless of fecal sources, variable sensitivity depending on the source, and stable performance across two laboratories. Compared to Univ-TRFLP, Bac-TRFLP had better sensitivity and specificity with horse, cow, and pig fecal sources but was not suited for certain avian sources such as goose, gull, and pigeon. Combining the general and more targeted TRFLP methods (Univ&Bac-TRFLP) achieved higher overall correct identification (>92%), higher sensitivity and specificity metrics, and higher reproducibility between laboratories. Our results suggest that the Bac-TRFLP and Univ&Bac-TRFLP methods are promising additions to the MST toolbox and warrant further evaluation and utilization in field MST applications.
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MESH Headings
- Animals
- Bacteroidetes/classification
- Bacteroidetes/genetics
- Bacteroidetes/isolation & purification
- Bacteroidetes/metabolism
- Birds/microbiology
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Environmental Monitoring/methods
- Feces/microbiology
- Humans
- Mammals/microbiology
- Polymerase Chain Reaction/methods
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sensitivity and Specificity
- Wastewater/microbiology
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA
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49
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Schriewer A, Goodwin KD, Sinigalliano CD, Cox AM, Wanless D, Bartkowiak J, Ebentier DL, Hanley KT, Ervin J, Deering LA, Shanks OC, Peed LA, Meijer WG, Griffith JF, SantoDomingo J, Jay JA, Holden PA, Wuertz S. Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study. Water Res 2013; 47:6909-6920. [PMID: 23916711 DOI: 10.1016/j.watres.2013.03.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 03/18/2013] [Accepted: 03/24/2013] [Indexed: 06/02/2023]
Abstract
The contribution of fecal pollution from dogs in urbanized areas can be significant and is an often underestimated problem. Microbial source tracking methods (MST) utilizing quantitative PCR of dog-associated gene sequences encoding 16S rRNA of Bacteroidales are a useful tool to estimate these contributions. However, data about the performance of available assays are scarce. The results of a multi-laboratory study testing two assays for the determination of dog-associated Bacteroidales (DogBact and BacCan-UCD) on 64 single and mixed fecal source samples created from pooled fecal samples collected in California are presented here. Standardization of qPCR data treatment lowered inter-laboratory variability of sensitivity and specificity results. Both assays exhibited 100% sensitivity. Normalization methods are presented that eliminated random and confirmed non-target responses. The combination of standardized qPCR data treatment, use of normalization via a non-target specific Bacteroidales assay (GenBac3), and application of threshold criteria improved the calculated specificity significantly for both assays. Such measures would reasonably improve MST data interpretation not only for canine-associated assays, but for all qPCR assays used in identifying and monitoring fecal pollution in the environment.
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Affiliation(s)
- Alexander Schriewer
- Department of Civil and Environmental Engineering, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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50
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Boehm AB, Van De Werfhorst LC, Griffith JF, Holden PA, Jay JA, Shanks OC, Wang D, Weisberg SB. Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study. Water Res 2013. [PMID: 23880218 DOI: 10.1016/j/waters.2012.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 41 MST methodologies by analyzing data generated in 27 laboratories. MST methodologies that targeted human, cow, ruminant, dog, gull, pig, horse, and sheep were tested against sewage, septage, human, cow, dog, deer, pig, chicken, pigeon, gull, horse, and goose fecal samples. Each laboratory received 64 blind samples containing a single source (singletons) or two sources (doubletons), as well as diluted singleton samples to assess method sensitivity. Laboratories utilized their own protocols when performing the methods and data were deposited in a central database before samples were unblinded. Between one and seven laboratories tested each method. The most sensitive and specific assays, based on an analysis of presence/absence of each marker in target and non-target fecal samples, were HF183 endpoint and HF183SYBR (human), CF193 and Rum2Bac (ruminant), CowM2 and CowM3 (cow), BacCan (dog), Gull2SYBR and LeeSeaGull (gull), PF163 and pigmtDNA (pig), HoF597 (horse), PhyloChip (pig, horse, chicken, deer), Universal 16S TRFLP (deer), and Bacteroidales 16S TRFLP (pig, horse, chicken, deer); all had sensitivity and specificity higher than 80% in all or the majority of laboratories. When the abundance of MST markers in target and non-target fecal samples was examined, some assays that performed well in the binary analysis were found to not be sensitive enough as median concentrations fell below a minimum abundance criterion (set at 50 copies per colony forming units of enterococci) in target fecal samples. Similarly, some assays that cross-reacted with non-target fecal sources in the binary analysis were found to perform well in a quantitative analysis because the cross-reaction occurred at very low levels. Based on a quantitative analysis, the best performing methods were HF183Taqman and BacH (human), Rum2Bac and BacR (ruminant), LeeSeaGull (gull), and Pig2Bac (pig); no cow or dog-specific assay met the quantitative specificity and sensitivity criteria. Some of the best performing assays in the study were run by just one laboratory so further testing of assay portability is needed. While this study evaluated the marker performance in defined samples, further field testing as well as development of frameworks for fecal source allocation and risk assessment are needed.
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Affiliation(s)
- Alexandria B Boehm
- Environmental and Water Studies, Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.
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