1
|
Zhao L, Guzman HP, Xagoraraki I. Tracking Chlamydia and Syphilis in the Detroit Metro Area by Molecular Analysis of Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17606-17616. [PMID: 39344309 DOI: 10.1021/acs.est.4c05869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
This paper describes one of the first studies applying wastewater surveillance to monitor Chlamydia and Syphilis and back-estimate infections in the community, based on bacterial shedding and wastewater surveillance data. Molecular biology laboratory methods were optimized, and a workflow was designed to implement wastewater surveillance tracking Chlamydia and Syphilis in the Detroit metro area (DMA), one of the most populous metropolitan areas in the U.S. Untreated composite wastewater samples were collected weekly from the three main interceptors that service DMA, which collect wastewater and discharge it to the Great Lakes Water Authority Water Resource Recovery Facility. Additionally, untreated wastewater was also collected from street manholes in three neighborhood sewersheds in Wayne, Macomb, and Oakland counties. Centrifugation, DNA extraction, and ddPCR methods were optimized and performed, targeting Chlamydia trachomatis and Treponema pallidum, the causative agents of Chlamydia and Syphilis, respectively. The limit of blank and limit of detection methods were determined experimentally for both targets. Both targets were detected and monitored in wastewater between December 25th, 2023, and April 22nd, 2024. The magnitudes of C. trachomatis and T. pallidum concentrations observed in neighborhood sewersheds were higher as compared to the concentrations observed in the interceptors. Infections of Chlamydia and Syphilis were back-estimated through an optimized formula based on shedding dynamics and wastewater surveillance data, which indicated potentially underreported conditions relative to publicly available clinical data.
Collapse
Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
| | - Heidy Peidro Guzman
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, Michigan 48823, United States
| |
Collapse
|
2
|
Lobos AE, Brandt AM, Gallard-Góngora JF, Korde R, Brodrick E, Harwood VJ. Persistence of sewage-associated genetic markers in advanced and conventional treated recycled water: implications for microbial source tracking in surface waters. mBio 2024; 15:e0065524. [PMID: 38864636 PMCID: PMC11253620 DOI: 10.1128/mbio.00655-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Sewage contamination of environmental waters is increasingly assessed by measuring DNA from sewage-associated microorganisms in microbial source tracking (MST) approaches. However, DNA can persist through wastewater treatment and reach surface waters when treated sewage/recycled water is discharged, which may falsely indicate pollution from untreated sewage. Recycled water discharged from an advanced wastewater treatment (AWT) facility into a Florida stream elevated the sewage-associated HF183 marker 1,000-fold, with a minimal increase in cultured Escherichia coli. The persistence of sewage-associated microorganisms was compared by qPCR in untreated sewage and recycled water from conventional wastewater treatment (CWT) and AWT facilities. E. coli (EC23S857) and sewage-associated markers HF183, H8, and viral crAssphage CPQ_056 were always detected in untreated sewage (6.5-8.7 log10 GC/100 mL). Multivariate analysis found a significantly greater reduction of microbial variables via AWT vs CWT. Bacterial markers decayed ~4-5 log10 through CWT, but CPQ_056 was ~100-fold more persistent. In AWT facilities, the log10 reduction of all variables was ~5. In recycled water, bacterial marker concentrations were significantly correlated (P ≤ 0.0136; tau ≥ 0.44); however, CPQ_056 was not correlated with any marker, suggesting varying drivers of decay. Concentrations of cultured E. coli carrying the H8 marker (EcH8) in untreated sewage were 5.24-6.02 log10 CFU/100 mL, while no E. coli was isolated from recycled water. HF183 and culturable EcH8 were also correlated in contaminated surface waters (odds ratio β1 = 1.701). Culturable EcH8 has a strong potential to differentiate positive MST marker signals arising from treated (e.g., recycled water) and untreated sewage discharged into environmental waters. IMPORTANCE Genes in sewage-associated microorganisms are widely accepted indicators of sewage pollution in environmental waters. However, DNA persists through wastewater treatment and can reach surface waters when recycled water is discharged, potentially causing false-positive indications of sewage contamination. Previous studies have found that bacterial and viral sewage-associated genes persist through wastewater treatment; however, these studies did not compare different facilities or identify a solution to distinguish sewage from recycled water. In this study, we demonstrated the persistence of bacterial marker genes and the greater persistence of a viral marker gene (CPQ_056 of crAssphage) through varying wastewater treatment facilities. We also aim to provide a tool to confirm sewage contamination in surface waters with recycled water inputs. This work showed that the level of wastewater treatment affects the removal of microorganisms, particularly viruses, and expands our ability to identify sewage in surface waters.
Collapse
Affiliation(s)
- Aldo E. Lobos
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Amanda M. Brandt
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Javier F. Gallard-Góngora
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, USA
| | - Ruchi Korde
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Eleanor Brodrick
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
3
|
Renault T, Faury N, Morga B. Propidium monoazide PCR, a method to determine OsHV-1 undamaged capsids and to estimate virus Lethal Dose 50. Virus Res 2024; 340:199307. [PMID: 38160910 PMCID: PMC10800765 DOI: 10.1016/j.virusres.2023.199307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Ostreid herpes virus 1 (OsHV-1) has been classified within the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 is the etiological agent of a contagious viral disease of Pacific oysters, C. gigas, affecting also other bivalve species. Mortality rates reported associated with the viral infection vary considerably between sites and countries and depend on the age of affected stocks. A variant called μVar has been reported since 2008 in Europe and other variants in Australia and in New Zealand last decade. These variants are considered as the main causative agents of mass mortality events affecting C. gigas. Presently there is no established cell line that allows for the detection of infectious OsHV-1. In this context, a technique of propidium monoazide (PMA) PCR was developed in order to quantify "undamaged" capsids. This methodology is of interest to explore the virus infectivity. Being able to quantify viral particles getting an undamaged capsid (not only an amount of viral DNA) in tissue homogenates prepared from infected oysters or in seawater samples can assist in the definition of a Lethal Dose (LD) 50 and gain information in the experiments conducted to reproduce the viral infection. The main objectives of the present study were (i) the development/optimization of a PMA PCR technique for OsHV-1 detection using the best quantity of PMA and verifying its effectiveness through heat treatment, (ii) the definition of the percentage of undamaged capsids in four different tissue homogenates prepared from infected Pacific oysters and (iii) the approach of a LD50 during experimental viral infection assays on the basis of a number of undamaged capsids. Although the developped PMA PCR technique was unable to determine OsHV-1 infectivity in viral supensions, it could greatly improve interpretation of virus positive results obtained by qPCR. This technique is not intended to replace the quantification of viral DNA by qPCR, but it does make it possible to give a form of biological meaning to the detection of this DNA.
Collapse
Affiliation(s)
- Tristan Renault
- Département Ressources Biologiques et Environnement, Ifremer, Nantes, France.
| | - Nicole Faury
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
| | - Benjamin Morga
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
| |
Collapse
|
4
|
Reichelt B, Szott V, Stingl K, Roesler U, Friese A. Detection of Viable but Non-Culturable (VBNC)- Campylobacter in the Environment of Broiler Farms: Innovative Insights Delivered by Propidium Monoazide (PMA)-v-qPCR Analysis. Microorganisms 2023; 11:2492. [PMID: 37894150 PMCID: PMC10609165 DOI: 10.3390/microorganisms11102492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Campylobacteriosis cases in humans are of global concern, with high prevalence rates in the poultry reservoir considered the most important source of infection. Research findings show Campylobacters' ability to enter a viable but non-culturable (VBNC) state, remaining "viable" but unable to grow on culture media. We explored the persistence of VBNC states in specific environments, particularly at broiler farms, as this state may lead to an underestimation of the present Campylobacter prevalence. For VBNC detection, a propidium monoazide PMA-dye viability qPCR (v-qPCR) was used in combination with cultivation methods. We examined samples collected from broiler farm barns and their surroundings, as well as chicken manure from experimental pens. In addition, the tenacity of culturable and VBNC-Campylobacter was studied in vitro in soil and water. In a total of three visits, Campylobacter was not detected either culturally or by v-qPCR (no Campylobacter DNA) in the environment of the broiler farms. In four visits, however, VBNC-Campylobacter were detected both inside and outside the barns. The overall prevalence in environmental samples was 15.9% for VBNC-Campylobacter, 62.2% for Campylobacter DNA, and 1.2% for culturable C. jejuni. In the experimental pens, no cultivable C. jejuni was detected in chicken manure after 24 h. Strikingly, "VBNC-Campylobacter" persisted even after 72 h. "VBNC-Campylobacter" were confirmed in barn surroundings and naturally contaminated chicken manure. Laboratory studies revealed that VBNC-Campylobacter can remain intact in soil for up to 28 days and in water for at least 63 days, depending on environmental conditions.
Collapse
Affiliation(s)
- Benjamin Reichelt
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
| | - Vanessa Szott
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
| | - Anika Friese
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
| |
Collapse
|
5
|
Zhuang L, Gong J, Shen Q, Yang J, Song C, Liu Q, Zhao B, Zhang Y, Zhu M. Advances in detection methods for viable Salmonella spp.: current applications and challenges. ANAL SCI 2023; 39:1643-1660. [PMID: 37378821 DOI: 10.1007/s44211-023-00384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Salmonella is a common intestinal pathogen that can cause food poisoning and intestinal disease. The high prevalence of Salmonella necessitates efficient and sensitive methods for its identification, detection, and monitoring, especially of viable Salmonella. Conventional culture methods need to be more laborious and time-consuming. And they are relatively limited in their ability to detect Salmonella in the viable but non-culturable status if present in the sample to be tested. As a result, there is an increasing need for rapid and accurate techniques to detect viable Salmonella spp. This paper reviewed the status and progress of various methods reported in recent years that can be used to detect viable Salmonella, such as culture-based methods, molecular methods targeting RNAs and DNAs, phage-based methods, biosensors, and some techniques that have the potential for future application. This review can provide researchers with a reference for additional method options and help facilitate the development of rapid and accurate assays. In the future, viable Salmonella detection approaches will become more stable, sensitive, and fast and are expected to play a more significant role in food safety and public health.
Collapse
Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, 210096, People's Republic of China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Chunlei Song
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Qingxin Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Bin Zhao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, 210096, People's Republic of China.
| | - Mengling Zhu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China.
| |
Collapse
|
6
|
Hill ER, Chun CL, Hamilton K, Ishii S. High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers. ACS ES&T WATER 2023; 3:2647-2658. [PMID: 37593240 PMCID: PMC10428101 DOI: 10.1021/acsestwater.3c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
Contamination of water with bacterial, viral, and protozoan pathogens can cause human diseases. Both humans and nonhumans can release these pathogens through their feces. To identify the sources of fecal contamination in the water environment, microbial source tracking (MST) approaches have been developed; however, the relationship between MST markers and pathogens is still not well understood most likely due to the lack of comprehensive datasets of pathogens and MST marker concentrations. In this study, we developed a novel microfluidic quantitative PCR (MFQPCR) platform for the simultaneous quantification of 37 previously validated MST markers, two fecal indicator bacteria (FIB), 22 bacterial, 11 viral, and five protozoan pathogens, and three internal amplification/process controls in many samples. The MFQPCR chip was applied to analyze pathogen removal rates during the wastewater treatment processes. In addition, multiple host-specific MST markers, FIB, and pathogens were successfully quantified in human and avian-impacted surface waters. While the genes for pathogens were relatively infrequently detected, positive correlations were observed between some potential pathogens such as Clostridium perfringens and Mycobacterium spp., and human MST markers. The MFQPCR chips developed in this study, therefore, can provide useful information to monitor and improve water quality.
Collapse
Affiliation(s)
- Elizabeth R Hill
- Water Resource Science Graduate Program, University of Minnesota, 173 McNeal Hall, 1985 Buford Avenue, St. Paul, Minnesota 55108, United States
| | - Chan Lan Chun
- Water Resource Science Graduate Program, University of Minnesota, 173 McNeal Hall, 1985 Buford Avenue, St. Paul, Minnesota 55108, United States
- Natural Resources Research Institute, University of Minnesota, 5013 Miller Trunk Highway, Duluth, Minnesota 55811, United States
- Department of Civil Engineering, University of Minnesota, 221 Swenson Civil Engineering, 1405 University Drive, Duluth, Minnesota 55812, United States
| | - Kerry Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S. College Avenue, Tempe, Arizona 85281, United States
- Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler Street, Tempe, Arizona 85281, United States
| | - Satoshi Ishii
- Water Resource Science Graduate Program, University of Minnesota, 173 McNeal Hall, 1985 Buford Avenue, St. Paul, Minnesota 55108, United States
- BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Soil, Water, and Climate, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, Minnesota 55108, United States
| |
Collapse
|
7
|
Flores-Ramírez A, Ortega-Cuenca J, Cuetero-Martínez Y, de Los Cobos D, Noyola A. Viability and removal assessment of Escherichia coli and Salmonella spp. by real-time PCR with propidium monoazide in the hygienization of sewage sludge using three anaerobic processes. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:254-262. [PMID: 36907017 DOI: 10.1016/j.wasman.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Sewage sludge should be stabilized for its beneficial use and pathogens, among other factors, should comply with environmental regulations. Three sludge stabilization process were compared to assess their suitability for producing Class A biosolids: MAD-AT (mesophilic (37 °C) anaerobic digestion (MAD) followed by an alkaline treatment (AT)); TAD (thermophilic (55 °C) anaerobic digester); and TP-TAD (mild thermal (80 °C, 1 h) pretreatment (TP) followed by a TAD). E. coli and Salmonella spp. were determined, differentiating three possible states: total cells (qPCR), viable cells using the propidium monoazide method (PMA-qPCR), and culturable cells (MPN). Culture techniques followed by the confirmative biochemical tests identified the presence of Salmonella spp. in PS and MAD samples, while the molecular methods (qPCR and PMA-qPCR) showed negative results in all samples. The TP + TAD arrangement reduced the concentration of total and viable E. coli cells in a greater extent than the TAD process. However, an increase of culturable E. coli was observed in the corresponding TAD step, indicating that the mild thermal pretreatment induced the viable but non-culturable state in E. coli. In addition, the PMA technique did not discriminate viable from non-viable bacteria in complex matrices. The three processes produced Class A biosolids (fecal coliforms < 1000 MPN/gTS and Salmonella spp, < 3 MPN/gTS) maintaining compliance after a 72 h storage period. It appears that the TP step favors the viable but not culturable state in E. coli cells, a finding that should be considered when adopting mild thermal treatment in sludge stabilization process arrangements.
Collapse
Affiliation(s)
- A Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - J Ortega-Cuenca
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - Y Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - D de Los Cobos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - A Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México.
| |
Collapse
|
8
|
Kobayashi M, Zhang Q, Segawa T, Maeda M, Hirano R, Okabe S, Ishii S. Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese. WATER RESEARCH 2022; 217:118397. [PMID: 35421690 DOI: 10.1016/j.watres.2022.118397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.
Collapse
Affiliation(s)
- Mayumi Kobayashi
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
| | - Mitsuto Maeda
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Reiko Hirano
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Satoshi Ishii
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA.
| |
Collapse
|
9
|
Wang H, Wagnon R, Moreno D, Timilsina S, Jones J, Vallad G, Turechek WW. A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed. PLANT DISEASE 2022; 106:1474-1485. [PMID: 34894749 DOI: 10.1094/pdis-11-21-2509-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of Xanthomonas: X. euvesicatoria, X. gardneri, X. perforans, and X. vesicatoria. Contaminated or infected seed can be a major source of inoculum for this disease. The use of certified pathogen-free seed is one of the primary management practices to reduce the inoculum load in commercial production. Current seed testing protocols rely mainly on plating the seed extract and conventional PCR; however, the plating method cannot detect viable but nonculturable cells, and the conventional PCR assay has limited capability to differentiate DNA extracted from viable or dead bacterial cells. To improve the sensitivity and specificity of the tomato seed testing method for bacterial spot pathogens, a long-amplicon quantitative PCR (qPCR) assay coupled with propidium monoazide (PMA-qPCR) was developed to quantify selectively the four pathogenic Xanthomonas species in tomato seed. The optimized PMA-qPCR procedure was evaluated on pure bacterial suspensions, bacteria-spiked seed extracts, and seed extracts of inoculated and naturally infected seed. A crude DNA extraction protocol also was developed, and PMA-qPCR with crude bacterial DNA extracts resulted in accurate quantification of 104 to 108 CFU/ml of viable bacteria when mixed with dead cells at concentrations as high as 107 CFU/ml in the seed extracts. With DNA purified from concentrated seed extracts, the PMA-qPCR assay was able to detect DNA of the target pathogens in seed samples spiked with ≥75 CFU/ml (about 0.5 CFU/seed) of the viable pathogens. Latent class analysis of the inoculated and naturally infected seed samples showed that the PMA-qPCR assay had greater sensitivity than plating the seed extracts on the semiselective modified Tween Medium B and CKTM media for all four target species. Being much faster and more sensitive than dilution plating, the PMA-qPCR assay has potential to be used as a standalone tool or in combination with the plating method to improve tomato seed testing and advance the production of clean seed.
Collapse
Affiliation(s)
- Hehe Wang
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | - Rieanna Wagnon
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | - Daniela Moreno
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | | | | | - Gary Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | |
Collapse
|
10
|
Miłobedzka A, Ferreira C, Vaz-Moreira I, Calderón-Franco D, Gorecki A, Purkrtova S, Dziewit L, Singleton CM, Nielsen PH, Weissbrodt DG, Manaia CM. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127407. [PMID: 34629195 DOI: 10.1016/j.jhazmat.2021.127407] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 05/10/2023]
Abstract
Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.
Collapse
Affiliation(s)
- Aleksandra Miłobedzka
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; Institute of Evolutionary Biology, University of Warsaw, Warsaw, Poland.
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | | | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Caitlin M Singleton
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
| |
Collapse
|
11
|
Chern EC, Wymer L, Brenner K, Oshima K, Haugland RA. Persistence of fecal indicator bacteria and associated genetic markers from wastewater treatment plant effluents in freshwater microcosms. JOURNAL OF WATER AND HEALTH 2022; 20:205-215. [PMID: 35100168 PMCID: PMC9000909 DOI: 10.2166/wh.2021.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Limited information exists on the environmental persistence of genetic markers for fecal indicator bacteria (FIB) in treated wastewaters. Here, the decay rate constants of culturable cells and genetic markers for four diverse groups of FIBs, such as enterococci, Clostridium, Escherichia coli, and Bacteroides, were investigated in freshwater microcosms seeded with disinfected and non-disinfected secondary-treated wastewaters. Decay rate constants of genetic markers and culturable cells varied significantly among the different FIB groups. Water temperatures (winter vs. fall/spring/summer) significantly affected the decay of all genetic marker and cell types; however, genetic marker decay were not found to be significantly different in disinfected (chlorination/ultraviolet) and non-disinfected wastewater-seeded microcosms or, for example, lake- and river-receiving waters. No evidence was seen that decay rate constants of FIB genetic markers from treated wastewater were substantially different from those observed in similar, previously reported microcosm studies using raw sewage. Unexpected relationships between decay rate constants of genetic markers and culturable cells of Bacteroides were observed. Results suggest that decay rate constants of FIB genetic markers determined from other studies may be applicable to treated wastewaters. Results of this study should be informative for ongoing efforts to determine the persistence of FIB genetic markers relative to surviving pathogens after wastewater treatment.
Collapse
Affiliation(s)
- Eunice C Chern
- U.S. Environmental Protection Agency, Region 10 Laboratory, 7411 Beach Dr. E., Port Orchard, WA 98366, USA E-mail:
| | - Larry Wymer
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kristen Brenner
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| |
Collapse
|
12
|
A colorimetric lateral flow assay based on multiplex PCR for the rapid detection of viable Escherichia coli O157:H7 and Salmonella Typhimurium without enrichment. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
13
|
Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on Preterm Infant Skin. mSphere 2021; 6:e0053821. [PMID: 34523979 PMCID: PMC8550141 DOI: 10.1128/msphere.00538-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Preterm infants are at increased risk of infections caused by coagulase-negative staphylococci (CoNS) that colonize skin. Technical barriers in sequencing low-microbial-biomass skin swabs from preterm infants hinder attempts to gain a strain-level understanding of CoNS colonization dynamics within their developing skin microbiome. Here, the microbiome of five skin sites and available stool was studied from four preterm infants hospitalized over their first 2 months of life. We used propidium monoazide treatment of samples to enrich for the viable microbiome and metagenomic shotgun sequencing to resolve species and strains. The microbiome of different skin sites overlapped with each other, was dominated by the CoNS species Staphylococcus epidermidis and Staphylococcus capitis, and was distinct from stool. Species diversity on skin increased over time despite antibiotic exposure. Evidence of antagonism between the most common S. epidermidis strains, ST2 and ST59, included negative relationships for species correlation networks and in situ replication rates and that ST2 colonized skin earlier but was often replaced by ST59 over time. Experiments done with reference isolates showed that ST2 produced more biofilm than ST59 on plastic surfaces, which was reduced in mixed culture. We also discovered that a rare S. epidermidis strain, ST5, grew rapidly in stool in association with Stenotrophomonas maltophilia from a suspected episode of infection. Viability treatment of samples and moderate throughput shotgun sequencing provides strain-level information about CoNS colonization dynamics of preterm infant skin that ultimately might be exploited to prevent infections. IMPORTANCE The skin is a habitat for microbes that commonly infect preterm infants, but the use of sequencing for fine-scale study of the microbial communities of skin that develop in these infants has been limited by technical barriers. We treated skin swabs of preterm infants with a photoreactive dye that eliminates DNA from nonviable microbes and then sequenced the remaining DNA. We found that two strains of the most common species, Staphylococcus epidermidis, showed an antagonistic relationship on skin by cooccurring with different species, replicating fastest in different samples, and dominating skin sites at different times. Representatives of these strains also differed in their ability to stick to plastic surfaces—an important pathogenicity trait of this species. Our study shows the feasibility of gaining detailed information about strain colonization dynamics from this difficult-to-sequence body site of preterm infants, which might be used to guide novel approaches to prevent infections.
Collapse
|
14
|
Yin K, Ding X, Xu Z, Li Z, Wang X, Zhao H, Otis C, Li B, Liu C. Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 344:130242. [PMID: 34121812 PMCID: PMC8183101 DOI: 10.1016/j.snb.2021.130242] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.
Collapse
Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Zhiheng Xu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xingyu Wang
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154, USA
| | - Clifford Otis
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Baikun Li
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| |
Collapse
|
15
|
Survival of Escherichia coli and Listeria innocua on Lettuce after Irrigation with Contaminated Water in a Temperate Climate. Foods 2021; 10:foods10092072. [PMID: 34574181 PMCID: PMC8468451 DOI: 10.3390/foods10092072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 12/20/2022] Open
Abstract
Microbial disease outbreaks related to fresh produce consumption, including leafy green vegetables, have increased in recent years. Where contamination occurs, pathogen persistence may represent a risk for consumers' health. This study analysed the survival of E. coli and L. innocua on lettuce plants watered with contaminated irrigation water via a single irrigation event and within stored irrigation water. Separate lettuce plants (Lactuca sativa var. capitata) were irrigated with water spiked with Log10 7 cfu/mL of each of the two strains and survival assessed via direct enumeration, enrichment and qPCR. In parallel, individual 20 L water microcosms were spiked with Log10 7 cfu/mL of the individual strains and sampled at similar time points. Both strains were observed to survive on lettuce plants up to 28 days after inoculation. Direct quantification by culture methods showed a Log10 4 decrease in the concentration of E. coli 14 days after inoculation, and a Log10 3 decrease in the concentration of L. innocua 10 days after inoculation. E. coli was detected in water samples up to 7 days after inoculation and L. innocua was detected up to 28 days by direct enumeration. Both strains were recovered from enriched samples up to 28 days after inoculation. These results demonstrate that E. coli and L. innocua strains are able to persist on lettuce after a single contamination event up until the plants reach a harvestable state. Furthermore, the persistence of E. coli and L. innocua in water for up to 28 days after inoculation illustrates the potential for multiple plant contamination events from stored irrigation water, emphasising the importance of ensuring that irrigation water is of a high quality.
Collapse
|
16
|
Li X, Cheng Z, Dang C, Zhang M, Zheng Y. Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 7:100105. [PMID: 36160698 PMCID: PMC9488056 DOI: 10.1016/j.ese.2021.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 05/07/2023]
Abstract
Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.
Collapse
Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Corresponding author. School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055 China.
| |
Collapse
|
17
|
Lazou TP, Gelasakis AI, Chaintoutis SC, Iossifidou EG, Dovas CI. Method-Dependent Implications in Foodborne Pathogen Quantification: The Case of Campylobacter coli Survival on Meat as Comparatively Assessed by Colony Count and Viability PCR. Front Microbiol 2021; 12:604933. [PMID: 33732219 PMCID: PMC7956984 DOI: 10.3389/fmicb.2021.604933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/01/2021] [Indexed: 11/28/2022] Open
Abstract
The aim of the present study was to address method-dependent implications during the quantification of viable Campylobacter coli cells on meat over time. Traditional colony counting on selective and non-selective culture media along with an optimized viability real-time PCR utilizing propidium monoazide-quantitative PCR (PMA-qPCR), spheroplast formation and an internal sample process control (ISPC), were comparatively evaluated for monitoring the survival of C. coli on fresh lamb meat during refrigeration storage under normal atmospheric conditions. On day zero of three independent experiments, lamb meat pieces were artificially inoculated with C. coli and then stored under refrigeration for up to 8 days. Three meat samples were tested on different days and the mean counts were determined per quantification method. An overall reduction of the viable C. coli on lamb meat was observed regardless of the applied quantification scheme, but the rate of reduction followed a method-dependent pattern, the highest being observed for colony counting on modified charcoal cefoperazone deoxycholate agar (mCCDA). Univariate ANOVA indicated that the mean counts of viable C. coli using PMA-qPCR were significantly higher compared to Columbia blood agar (CBA) plating (0.32 log10 cell equivalents, p = 0.015) and significantly lower when mCCDA was compared to CBA plating (0.88 log10 CFU, p < 0.001), indicating that selective culture on mCCDA largely underestimated the number of culturable cells during the course of meat storage. PMA-qPCR outperformed the classical colony counting in terms of quantifying both the culturable and viable but non-culturable (VBNC) C. coli cells, which were generated over time on meat and are potentially infectious and equally important from a public health perspective as their culturable counterparts.
Collapse
Affiliation(s)
- Thomai P Lazou
- Laboratory of Hygiene of Foods of Animal Origin - Veterinary Public Health, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios I Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni G Iossifidou
- Laboratory of Hygiene of Foods of Animal Origin - Veterinary Public Health, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
18
|
Abstract
The development of viability quantitative PCR (v-qPCR) has allowed for a more accurate assessment of the viability of a microbial sample by limiting the amplification of DNA from dead cells. Although valuable, v-qPCR is not infallible. One of the most limiting factors for accurate live/dead distinction is the length of the qPCR amplicon used. However, no consensus or guidelines exist for selecting and designing amplicon lengths for optimal results. In this study, a wide range of incrementally increasing amplicon lengths (68 to 906 base pairs [bp]) was used on live and killed cells of nine bacterial species treated with a viability dye (propidium monoazide [PMA]). Increasing amplicon lengths up to approximately 200 bp resulted in increasing quantification cycle (Cq) differences between live and killed cells while maintaining a good qPCR efficiency. Longer amplicon lengths, up to approximately 400 bp, further increased the Cq difference but at the cost of qPCR efficiency. Above 400 bp, no valuable increase in Cq differences was observed. IMPORTANCE Viability quantitative PCR (v-qPCR) has evolved into a valuable, mainstream technique for determining the number of viable microorganisms in samples by qPCR. Amplicon length is known to be positively correlated with the ability to distinguish between live and dead bacteria but is negatively correlated with qPCR efficiency. This trade-off is often not taken into account and might have an impact on the accuracy of v-qPCR data. Currently, there is no consensus on the optimal amplicon length. This paper provides methods to determine the optimal amplicon length and suggests an amplicon length range for optimal v-qPCR, taking into consideration the trade-off between qPCR efficiency and live/dead distinction.
Collapse
|
19
|
Dufour A. A short history of methods used to measure bathing beach water quality. J Microbiol Methods 2021; 181:106134. [PMID: 33421445 PMCID: PMC7870561 DOI: 10.1016/j.mimet.2021.106134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
The enumeration of fecal indicators of bathing beach water to determine quality have been used since the mid-20th century. In the 1930s and as late the 1970s, the Most Probable Number procedure for estimating microbial densities in water was in general use. The most probable number procedure was replaced as a method of choice by the membrane filter procedure. The membrane filter had been developed in the early 1950s but did not find widespread use until the 1970s. Another development during the 1970s was the quanti -tray method, a proprietary multi-well tray, which was introduced as an innovative form of the Most Probable Number procedure. In 2005 molecular methods were introduced as a rapid 3-hourh procedure for measuring bathing beach water quality. Several variations of this approach are currently in use or in development.
Collapse
Affiliation(s)
- Al Dufour
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurements and Modeling, Cincinnati, OH, United States of America.
| |
Collapse
|
20
|
Lv X, Wang L, Zhang J, Zeng H, Chen X, Shi L, Cui H, He X, Zhao L. Rapid and sensitive detection of VBNC Escherichia coli O157: H7 in beef by PMAxx and real-time LAMP. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107292] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
21
|
Wang H, Turechek WW. Detection of Viable Xanthomonas fragariae Cells in Strawberry Using Propidium Monoazide and Long-Amplicon Quantitative PCR. PLANT DISEASE 2020; 104:1105-1112. [PMID: 32040389 DOI: 10.1094/pdis-10-19-2248-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas fragariae causes angular leaf spot in strawberry. The pathogen's association with its host tissue is thought to be a condition for its survival. Consequently, transmission of the pathogen to field production sites occurs almost exclusively through the movement of contaminated planting stock. The aim of this study was to develop a propidium monoazide (PMA)-quantitative PCR (qPCR) protocol for specific detection of viable X. fragariae cells. The qPCR procedure was developed for two different primer pairs: one producing a long amplicon (863 bp) and the other a short amplicon (61 bp). Both pairs were tested on mixtures of viable and heat-killed bacteria cells, bacteria-spiked strawberry petiole samples, and petioles collected from symptomatic, inoculated plants. The results showed that long-amplicon PMA-qPCR enabled specific and sensitive detection of X. fragariae with a detection limit of 103 CFU/ml, and it significantly improved PMA efficiency in differentiating viable from dead bacterial cells relative to short-amplicon PMA-qPCR. Based on the delta threshold cycle (Ct) values (i.e., the difference in Ct values between PMA-treated and nontreated samples), the long-amplicon PMA-qPCR was able to suppress the detection of dead X. fragariae cells 1.9- to 3.1-fold across all petiole samples tested. The quantification results from PMA-qPCR for mixtures of viable and dead cells were highly correlated with the predicted bacterial concentrations in a linear relationship (R2 = 0.981). This assay can be useful for identifying inoculum sources in the strawberry production cycle, which may lead to improved disease management strategies.
Collapse
Affiliation(s)
- Hehe Wang
- Department of Agricultural and Environmental Sciences, Clemson University, Blackville, SC
| | - William W Turechek
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL
| |
Collapse
|
22
|
Askar M, Sajid M, Nassif Y, Ashraf W, Scammell B, Bayston R. Propidium monoazide-polymerase chain reaction for detection of residual periprosthetic joint infection in two-stage revision. Mol Biol Rep 2019; 46:6463-6470. [PMID: 31587184 PMCID: PMC11358260 DOI: 10.1007/s11033-019-05092-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2019] [Indexed: 12/18/2022]
Abstract
False negative culture results in periprosthetic joint infection (PJI) are not uncommon particularly when patients have received long term antibiotics. Polymerase chain reaction (PCR) has a lower specificity partly due to detection of residual DNA from dead bacteria. Propidium monoazide (PMA) prevents DNA from dead bacteria from being amplified during the PCR. This study aimed to determine the role of PMA in PCR for diagnosis of PJI. Clinical samples were tested by PCR with and without prior treatment with PMA and compared to conventional microbiological culture. The PCR assay included genus-specific primers for staphylococci and enterococci and species-specific primers for Cutibacterium acnes. The validated conditions of PMA treatment used in this study were 20 μM concentration and 5 and 10 min of dark incubation and photo-activation respectively. 202 periprosthetic tissues and explanted prostheses from 60 episodes in 58 patients undergoing revision arthroplasties for either PJI or non-infective causes were tested, by culture, PCR, and PMA-PCR. 14 of the 60 episodes satisfied the Musculoskeletal Infection Society (MSIS) criteria for PJI and 46 did not. Sensitivity of culture, PCR, and PMA-PCR were 50%, 71%, and 79% respectively. Specificities were 98%, 72%, and 89% respectively. All figures were calculated for episodes rather than samples. PMA-PCR enhanced both the specificity and the sensitivity of PCR. It has the potential to detect residual bacterial viability prior to reimplantation in the two-stage revision for PJI.
Collapse
Affiliation(s)
- Mohamed Askar
- Department of Academic Orthopaedics, Queen's Medical Centre, University of Nottingham, C Floor, West Block, Derby Road, Nottingham, NG7 2UH, UK
| | - Mariam Sajid
- Department of Academic Orthopaedics, Queen's Medical Centre, University of Nottingham, C Floor, West Block, Derby Road, Nottingham, NG7 2UH, UK
| | - Yassar Nassif
- Trauma and Orthopaedic Department, University of Nottingham Hospitals, Nottingham, UK
| | - Waheed Ashraf
- Department of Academic Orthopaedics, Queen's Medical Centre, University of Nottingham, C Floor, West Block, Derby Road, Nottingham, NG7 2UH, UK
| | - Brigitte Scammell
- Department of Academic Orthopaedics, Queen's Medical Centre, University of Nottingham, C Floor, West Block, Derby Road, Nottingham, NG7 2UH, UK
- Trauma and Orthopaedic Department, University of Nottingham Hospitals, Nottingham, UK
| | - Roger Bayston
- Department of Academic Orthopaedics, Queen's Medical Centre, University of Nottingham, C Floor, West Block, Derby Road, Nottingham, NG7 2UH, UK.
| |
Collapse
|
23
|
A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. Sci Rep 2019; 9:15726. [PMID: 31673047 PMCID: PMC6823499 DOI: 10.1038/s41598-019-51997-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/10/2019] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.
Collapse
|
24
|
Acharya K, Khanal S, Pantha K, Amatya N, Davenport RJ, Werner D. A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. Sci Rep 2019. [PMID: 31673047 DOI: 10.1038/s41598-01951997-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.
Collapse
Affiliation(s)
- Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Santosh Khanal
- Department of Pharmacology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Kalyan Pantha
- Group for Rural Infrastructure Development, Wise use House, Jwagal, Lalitpur, Nepal
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, D-45141, Essen, Germany
| | - Niroj Amatya
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, D-45141, Essen, Germany
- Department of Medical Microbiology, Nobel College, Pokhara University, Kathmandu, Nepal
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
| |
Collapse
|
25
|
Ditommaso S, Giacomuzzi M, Memoli G, Cavallo R, Curtoni A, Avolio M, Silvestre C, Zotti CM. Reduction of turnaround time for non-tuberculous mycobacteria detection in heater-cooler units by propidium monoazide-real-time polymerase chain reaction. J Hosp Infect 2019; 104:365-373. [PMID: 31628958 DOI: 10.1016/j.jhin.2019.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Invasive non-tuberculous mycobacteria (NTM) infections are emerging worldwide in patients undergoing open-chest cardiac bypass surgery exposed to contaminated heater-cooler units (HCUs). Although this outbreak has been investigated by culturing bacteria isolated from HCU aerosol and water samples, these conventional methods have low-analytic sensitivity, high rates of sample contamination, and long turnaround time. AIM To develop a simple and effective method to detect NTM in HCUs by real-time polymerase chain reaction (PCR), with a short laboratory turnaround time and reliable culture results. METHODS A total of 281 water samples collected from various HCUs at seven Italian hospitals were simultaneously screened for NTM by a propidium monoazide (PMA)-PCR assay and by conventional culture testing. The results were analysed with culture testing as the reference method. FINDINGS (i) The agreement between culture testing and PMA-PCR was 85.0% with a cycle threshold (CT) cut-off value of <38 vs 80.0% with a CT of <43, with a moderate Cohen's κ-coefficient; (ii) the CT cut-off value of <42 was deemed more suitable for predicting positive specimens; (iii) given the low concentration of target DNA in water samples, the minimum volume to be tested was 1 L. CONCLUSION The use of PMA-PCR for fast detection of NTM from environmental samples is highly recommended in order to ascertain whether HCUs may represent a potential source of human exposure to NTM. This reliable and simple method reduces laboratory turnaround time compared to conventional methods (one to two days vs eight weeks, respectively), thereby improving control strategies and effective management of HCUs.
Collapse
Affiliation(s)
- S Ditommaso
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy.
| | - M Giacomuzzi
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - G Memoli
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - R Cavallo
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy; Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - A Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - M Avolio
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - C Silvestre
- AOU Città della salute e della Scienza, Turin, Italy
| | - C M Zotti
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| |
Collapse
|
26
|
Lazou TP, Iossifidou EG, Gelasakis AI, Chaintoutis SC, Dovas CI. Viability Quantitative PCR Utilizing Propidium Monoazide, Spheroplast Formation, and Campylobacter coli as a Bacterial Model. Appl Environ Microbiol 2019; 85:e01499-19. [PMID: 31420339 PMCID: PMC6805072 DOI: 10.1128/aem.01499-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/09/2019] [Indexed: 01/09/2023] Open
Abstract
A viability quantitative PCR (qPCR) utilizing propidium monoazide (PMA) is presented for rapid quantification of viable cells using the foodborne pathogen Campylobacter coli as a bacterial model. It includes optimized spheroplast formation via lysozyme and EDTA, induction of a mild osmotic shock for enhancing the selective penetration of PMA into dead cells, and exploitation of an internal sample process control (ISPC) involving cell inactivation to assess residual false-positive signals within each sample. Spheroplasting of bacteria in exponential phase did not permit PMA entrance into viable cells since a strong linear relationship was detected between simple qPCR and PMA-qPCR quantification, and no differences were observed regardless of whether spheroplasting was utilized. The PMA-qPCR signal suppression of dead cells was elevated using spheroplast formation. With regard to the ISPC, cell inactivation by hydrogen peroxide resulted in higher signal suppression during qPCR than heat inactivation did. Viability quantification of C. coli cells by optimized spheroplasting-PMA-qPCR with ISPC was successfully applied in an aging pure culture under aerobic conditions and artificially inoculated meat. The same method exhibited a high linear range of quantification (1.5 to 8.5 log10 viable cells ml-1), and results were highly correlated with culture-based enumeration. PMA-qPCR quantification of viable cells can be affected by their rigidity, age, culture media, and niches, but spheroplast formation along with osmotic shock and the use of a proper ISPC can address such variations. The developed methodology could detect cells in a viable-but-nonculturable state and might be utilized for the quantification of other Gram-negative bacteria.IMPORTANCE There is need for rapid and accurate methods to detect viable bacterial cells of foodborne pathogens. Conventional culture-based methods are time-consuming and unable to detect bacteria in a viable-but-nonculturable state. The high sensitivity and specificity of the quantitative PCR (qPCR) are negated by its inability to differentiate the DNAs from viable and dead cells. The combination of propidium monoazide (PMA), a DNA-intercalating dye, with qPCR assays is promising for detection of viable cells. Despite encouraging results, these assays still encounter various challenges, such as false-positive signals by dead cells and the lack of an internal control identifying these signals per sample. The significance of our research lies in enhancing the selective entrance of PMA into dead Campylobacter coli cells via spheroplasting and in developing an internal sample process control, thus delivering reliable results in pure cultures and meat samples, approaches that can be applicable to other Gram-negative pathogens.
Collapse
Affiliation(s)
- Thomai P Lazou
- Laboratory of Hygiene of Foods of Animal Origin-Veterinary Public Health, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni G Iossifidou
- Laboratory of Hygiene of Foods of Animal Origin-Veterinary Public Health, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios I Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
27
|
Kunadiya MB, Dunstan WD, White D, Hardy GESJ, Grigg AH, Burgess TI. A qPCR Assay for the Detection of Phytophthora cinnamomi Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples. PLANT DISEASE 2019; 103:2443-2450. [PMID: 31313641 DOI: 10.1094/pdis-09-18-1641-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.
Collapse
Affiliation(s)
- Manisha B Kunadiya
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - William D Dunstan
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Diane White
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Giles E St J Hardy
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Andrew H Grigg
- Alcoa of Australia Ltd., Huntly Mine, Pinjarra, WA 6208, Australia
| | - Treena I Burgess
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| |
Collapse
|
28
|
Betlem K, Kaur A, Hudson AD, Crapnell RD, Hurst G, Singla P, Zubko M, Tedesco S, Banks CE, Whitehead K, Peeters M. Heat-Transfer Method: A Thermal Analysis Technique for the Real-Time Monitoring of Staphylococcus aureus Growth in Buffered Solutions and Digestate Samples. ACS APPLIED BIO MATERIALS 2019; 2:3790-3798. [DOI: 10.1021/acsabm.9b00409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kai Betlem
- Division of Chemistry and Environmental Science, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Amanpreet Kaur
- Division of Chemistry and Environmental Science, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Alexander D. Hudson
- Division of Chemistry and Environmental Science, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Robert D. Crapnell
- Division of Chemistry and Environmental Science, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - George Hurst
- Division of Engineering, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Pankaj Singla
- Department of Chemistry, UGC-Centre for Advanced Studies-I, Guru Nanak Dev University, Amritsar 143005, India
| | - Mikhajlo Zubko
- Division of Biomedical Science, Faculty of Healthcare Science, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Silvia Tedesco
- Division of Engineering, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Craig E. Banks
- Division of Biomedical Science, Faculty of Healthcare Science, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Kathryn Whitehead
- Division of Biomedical Science, Faculty of Healthcare Science, Manchester Metropolitan University, John Dalton Building, M15GD Manchester, U.K
| | - Marloes Peeters
- Newcastle University, School of Engineering, Merz Court, Newcastle Upon Tyne NE1 7RU, United Kingdom
| |
Collapse
|
29
|
Dong L, Liu H, Meng L, Xing M, Lan T, Gu M, Zheng N, Wang C, Chen H, Wang J. Short communication: Quantitative PCR coupled with sodium dodecyl sulfate and propidium monoazide for detection of culturable Escherichia coli in milk. J Dairy Sci 2019; 102:6914-6919. [PMID: 31202653 DOI: 10.3168/jds.2018-15393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/22/2019] [Indexed: 11/19/2022]
Abstract
Escherichia coli has been frequently reported as a major foodborne bacterium contaminating raw milk or pasteurized milk. Therefore, the aim of this study was to explore a quantitative real-time PCR (qPCR) technique combined with sodium dodecyl sulfate (SDS) and propidium monoazide (PMA) to detect culturable E. coli in milk. An internal amplification control was also added into this reaction system as an indicator of false-negative results. The inclusivity and exclusivity of the primers were tested using DNA from 7 E. coli and 14 other bacterial strains. The concentrations of SDS and PMA were determined according to plate counts and quantitative cycle values of qPCR, respectively. A standard curve was established using series diluted E. coli DNA. The reliability and specificity of this method were further determined by the detection of E. coli in spiked milk. The results showed that the optimal concentrations of SDS and PMA were 100 µg/mL and 40 μM, respectively. A standard curve with a good linear relationship (coefficient of determination = 0.997; amplification efficiency = 100.5%) was obtained. Compared with conventional PCR and PMA-qPCR, the SDS-PMA-qPCR assay was more specific and sensitive in culturable E. coli detection. Therefore, we evaluated and improved the SDS-PMA-qPCR method for detecting culturable E. coli in milk.
Collapse
Affiliation(s)
- Lei Dong
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China; College of Food Science and Engineer, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Huimin Liu
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China; Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - Lu Meng
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Mengru Xing
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China; College of Food Science and Engineer, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Tu Lan
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China; Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - Mei Gu
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Nan Zheng
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Cheng Wang
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - He Chen
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - Jiaqi Wang
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Milk and Dairy Product Inspection Center of Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China.
| |
Collapse
|
30
|
Zhao Y, Chen H, Liu H, Cai J, Meng L, Dong L, Zheng N, Wang J, Wang C. Quantitative Polymerase Chain Reaction Coupled With Sodium Dodecyl Sulfate and Propidium Monoazide for Detection of Viable Streptococcus agalactiae in Milk. Front Microbiol 2019; 10:661. [PMID: 30984156 PMCID: PMC6450196 DOI: 10.3389/fmicb.2019.00661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Streptococcus agalactiae is an important pathogen causing bovine mastitis. The aim of this study was to develop a simple and specific method for direct detection of S. agalactiae from milk products. Propidium monoazide (PMA) and sodium dodecyl sulfate (SDS) were utilized to eliminate the interference of dead and injured cells in qPCR. Lysozyme (LYZ) was adopted to increase the extraction efficiency of target bacteria DNA in milk matrix. The specific primers were designed based on cfb gene of S. agalactiae for qPCR. The inclusivity and exclusivity of the assay were evaluated using 30 strains. The method was further determined by the detection of S. agalactiae in spiked milk. Results showed significant differences between the SDS–PMA–qPCR, PMA–qPCR and qPCR when a final concentration of 10 mg/ml (R2 = 0.9996, E = 95%) of LYZ was added in DNA extraction. Viable S. agalactiae was effectively detected when SDS and PMA concentrations were 20 μg/ml and 10 μM, respectively, and it was specific and more sensitive than qPCR and PMA–qPCR. Moreover, the SDS–PMA–qPCR assay coupled with LYZ was used to detect viable S. agalactiae in spiked milk, with a limit of detection of 3 × 103 cfu/ml. Therefore, the SDS–PMA–qPCR assay had excellent sensitivity and specificity for detection of viable S. agalactiae in milk.
Collapse
Affiliation(s)
- Yankun Zhao
- Institute of Quality Standard and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Urumqi, China.,Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Urumqi, China
| | - He Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Urumqi, China.,Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Urumqi, China
| | - Huimin Liu
- Institute of Quality Standard and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Urumqi, China.,Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Urumqi, China.,Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxing Cai
- Institute of Quality Standard and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Urumqi, China.,Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Urumqi, China
| | - Lu Meng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Dong
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Wang
- Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Urumqi, China.,Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Urumqi, China
| |
Collapse
|
31
|
Eramo A, Morales Medina WR, Fahrenfeld NL. Viability-based quantification of antibiotic resistance genes and human fecal markers in wastewater effluent and receiving waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:495-502. [PMID: 30522032 PMCID: PMC6526933 DOI: 10.1016/j.scitotenv.2018.11.325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Antibiotic resistance is a public health issue with links to environmental sources of antibiotic resistance genes (ARGs). ARGs from nonviable sources may pose a hazard given the potential for transformation whereas ARGs in viable sources may proliferate during host growth or conjugation. In this study, ARGs in the effluent from three municipal wastewater treatment plants (WWTPs) and the receiving surface waters were investigated using a viability-based qPCR technique (vPCR) with propidium monoazide (PMA). ARGs sul1, tet(G), and blaTEM, fecal indicator marker BacHum, and 16S rRNA gene copies/mL were found to be significantly lower in viable-cells than in total concentrations for WWTP effluent. Viable-cell and total gene copy concentrations were similar in downstream samples except for tet(G). Differences with respect to season in the prevalence of nonviable ARGs in surface water or WWTP effluent were not observed. The results of this study indicate that qPCR may overestimate viable-cell ARGs and fecal indicator genes in WWTP effluent but not necessarily in the surface water >1.8 km downstream.
Collapse
Affiliation(s)
- Alessia Eramo
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ 08854, United States
| | - William R Morales Medina
- Department of Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ 08854, United States
| | - Nicole L Fahrenfeld
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ 08854, United States.
| |
Collapse
|
32
|
Papanicolas LE, Wang Y, Choo JM, Gordon DL, Wesselingh SL, Rogers GB. Optimisation of a propidium monoazide based method to determine the viability of microbes in faecal slurries for transplantation. J Microbiol Methods 2018; 156:40-45. [PMID: 30529117 DOI: 10.1016/j.mimet.2018.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 02/02/2023]
Abstract
The efficacy of faecal microbiota transplantation (FMT) as a therapeutic intervention may depend on the viability of the microorganisms in faecal slurries (FS) prepared from donor stool. However, determining the viability of these organisms is challenging. Most microorganisms in stool are refractory to culture using standard techniques, and culture-independent PCR-based methods derive signal from both viable and non-viable cells. Propidium monoazide (PMA) treatment has been shown to be effective in preventing PCR amplification of DNA from non-viable bacteria in a range of contexts. However, this methodology can be sensitive to factors such as bacterial load and sample turbidity. We describe the optimisation of a PMA treatment methodology for FS that restricts quantitative PCR-based bacterial enumeration to viable cells. When applied to concentrated FS (10-25% stool content), PMA treatment at 100 μM concentration was ineffective in preventing DNA amplification from heat-killed cells. Efficacy was not significantly improved by doubling the PMA concentration. However, PMA treatment efficacy was improved markedly following 10-fold sample dilution, and was found to be optimal at 100-fold dilution. Substantial reductions in viable bacterial load could be observed following both freeze-thaw and heat-treatment of FS. This method successfully prevented DNA amplification of heat-killed Pseudomonas and Staphylococcus spiked into stool and could reliably determine the proportion of live bacteria and viable E. coli counts present in fresh and heat-treated stool. With appropriate sample dilution, PMA treatment excluded >97% of non-viable cells from amplification in all assays, without significantly affecting the amplification of DNA from viable cells. This method can be applied to optimise sample processing of FMT donor material, and to characterise bacterial viability within faecal samples more widely.
Collapse
Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
| | - Yanan Wang
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Jocelyn M Choo
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| |
Collapse
|
33
|
Yuan Y, Zheng G, Lin M, Mustapha A. Detection of viable Escherichia coli in environmental water using combined propidium monoazide staining and quantitative PCR. WATER RESEARCH 2018; 145:398-407. [PMID: 30173100 DOI: 10.1016/j.watres.2018.08.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/31/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The objectives of this study were to specifically detect viable Escherichia coli in environmental waters by targeting the ycjM gene in a propidium monoazide (PMA)-qPCR assay. PMA is a viability dye that can inhibit the amplification of DNA from dead cells, thus allowing for the detection and quantification of only viable cells. The ycjM primers were used to target E. coli that directly originated from the feces of warm blooded animals, and avoid false positive detection caused by "naturalized" E. coli that can exist in the environment. In this study, tap water and environmental waters were inoculated with E. coli isolated from animal feces. Following cell collection, samples were treated with PMA, followed by DNA isolation and qPCR detection. For pure cultures, 5 μM PMA with a 10-min light exposure was efficient at inhibiting the amplification of DNA from 105 CFU/mL dead E. coli cells, with a detection limit of 102 CFU/100 mL viable cells. For tap and environmental waters collected in the winter, a 10 μM PMA was required and as low as 103 CFU/100 mL viable cells could be detected in the presence of 105 CFU/100 mL dead cells. For water samples collected during the summer, 102 CFU/10 mL viable cells could be detected in the presence of 104 CFU/10 mL dead cells, after a 20 μM PMA treatment. No significant differences were found among the PMA-qPCR assay and two other standard culture-based methods for detection of viable E. coli in environmental water. In conclusion, with proper pretreatment of environmental water samples, this PMA-qPCR assay that targets the ycjM gene could quantify viable E. coli cells that directly come from the feces of warm-blooded animals, and therefore effectively and accurately indicate the quality of environmental water.
Collapse
Affiliation(s)
- Yuan Yuan
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Guolu Zheng
- Department of Agriculture and Environmental Sciences, Lincoln University of Missouri, USA
| | - Mengshi Lin
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Azlin Mustapha
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
34
|
Zimmer-Faust AG, Thulsiraj V, Lee CM, Whitener V, Rugh M, Mendoza-Espinosa L, Jay JA. Multi-tiered approach utilizing microbial source tracking and human associated-IMS/ATP for surveillance of human fecal contamination in Baja California, Mexico. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:475-484. [PMID: 29864661 DOI: 10.1016/j.scitotenv.2018.05.172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
As both the need for reuse of reclaimed wastewater and the burden placed on existing wastewater treatment plants increase, so does the need for methods that can reliably, rapidly and economically identify human-associated contamination. A survey of surface water quality was conducted in Baja California, Mexico where inadequate infrastructure or its inefficient operation leads to poor water quality. The HF183 and Bacteroides thetaiotaomicron (B. theta) human-associated gene markers were detected in 84% and 82% of samples collected during dry weather, illustrating evidence of widespread human fecal contamination. In addition, an inversely-coupled (Inv-IMS/ATP) viability-based assay for detection of B. theta was developed and applied for rapid detection and screening of human-associated fecal contamination. The Inv-IMS/ATP assay was able to effectively differentiate between surface waters impacted with human fecal contamination, and B. theta levels measured by Inv-IMS/ATP were highly correlated with HF183 and B. theta human marker measurements (r = 0.76; r = 0.82) in complex surface water samples. In areas with widespread human fecal contamination and limited access to more expensive methods, a multi-pronged approach utilizing a combination of methods including the Inv-IMS/ATP assay for rapid evaluation and screening of surface water quality alongside human-associated genetic markers may improve risk assessment and surveillance capabilities.
Collapse
Affiliation(s)
- Amity G Zimmer-Faust
- Western Ecology Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Currently at Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
| | - Vanessa Thulsiraj
- Biology Department, Mount Saint Mary's University, 12001 Chalon Road, Los Angeles, CA 90049, USA
| | - Christine M Lee
- Earth Science Division, American Association for the Advancement of Science, National Aeronautics and Space Administration Headquarters, WA, USA
| | - Victoria Whitener
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Megan Rugh
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | | | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
35
|
Acosta CP, Codony F, Fittipaldi M, Sierra-Torres CH, Morató J. Monitoring levels of viable Helicobacter pylori in surface water by qPCR in Northeast Spain. JOURNAL OF WATER AND HEALTH 2018; 16:839-845. [PMID: 30285964 DOI: 10.2166/wh.2018.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Helicobacter pylori infection is a risk factor for chronic active gastritis, peptic ulcers, gastric carcinoma and lymphoma. Although the infection may be acquired through different transmission routes, the presence and viability of H. pylori in water sources are not well known. Therefore, the aim of our study was to analyse the viability of H. pylori cells in urban surface waters collected at the Vallparadís public park in Terrassa, Barcelona, Spain. The water samples were analysed by viability quantitative polymerase chain reaction (qPCR) using propidium monoazide and specific primers for the H. pylori vacuolating cytotoxin (vacA gene). Viable H. pylori were found in 91.3% of the samples analysed, with an average concentration of 3.46 ± 1.06 log cell 100 mL-1. Our work proves a quick and simple procedure for evaluating viable H. pylori cells in environmental samples by qPCR. Furthermore, the results provide evidence that urban surface waters may contain considerable levels of viable H. pylori cells, thus indicating they are a potential source of infection, which represents a public health concern.
Collapse
Affiliation(s)
- Claudia Patricia Acosta
- Laboratorio de Genética Humana, Departamento de Ciencias Fisiológicas, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia and Unidad de Salud Ambiental, Fundación InnovaGen, Popayán, Colombia E-mail:
| | - Francesc Codony
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain; GenIUL R&D Laboratory, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa, Spain
| | - Mariana Fittipaldi
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain
| | - Carlos Hernán Sierra-Torres
- Laboratorio de Genética Humana, Departamento de Ciencias Fisiológicas, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia and Unidad de Salud Ambiental, Fundación InnovaGen, Popayán, Colombia E-mail:
| | - Jordi Morató
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain
| |
Collapse
|
36
|
Niu B, Hong B, Zhang Z, Mu L, Malakar PK, Liu H, Pan Y, Zhao Y. A Novel qPCR Method for Simultaneous Detection and Quantification of Viable Pathogenic and Non-pathogenic Vibrio parahaemolyticus ( tlh+ , tdh+ , and ureR + ). Front Microbiol 2018; 9:1747. [PMID: 30116230 PMCID: PMC6083054 DOI: 10.3389/fmicb.2018.01747] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
Pathogenic and non-pathogenic Vibrio parahaemolyticus strains were simultaneously detected and quantified using a novel viable multiplex real-time PCR (novel qPCR). We used a new PCR primer and probe, ureR, as a surrogate for detection of the toxin trh gene as the primer was better at identifying variant V. parahaemolyticus trh strains. The specificity of all primers and probes used in this study were validated on three standard strains of V. parahaemolyticus, 42 clinical strains, 12 wild strains, 4 strains of Vibrio spp., and 4 strains of other bacteria. Then, propidium monoazide (PMA) was applied to inhibit DNA of dead cell, and the results of PMA optimized treatments were 15 μM concentration, 5 min incubation periods, 15 min light exposure periods and 30 RPM rotational speed, which resulted in time and cost savings. Pathogenic and non-pathogenic strains were quantified using a two-reaction tube method where the tlh, tdh, and ureR genes were amplified. Additionally, standard curves with a 7-log dynamic range were generated for quantifying viable V. parahaemolyticus and the amplification efficiencies were 108.68, 105.17, and 115.61% for tlh+, tdh+, and ureR+. This novel qPCR accurately monitored V. parahaemolyticus contamination rates in shrimps (Penaeus vannamei) and clams (Ruditapes philippinarum) sampled from retail stores located in a major district in Shanghai. In conclusion, our assay can prioritize the detection and quantification of viable pathogenic V. parahaemolyticus and can prove to be a more effective tool for reducing infection risks from consumption of seafood in Shanghai.
Collapse
Affiliation(s)
- Ben Niu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Bin Hong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Lili Mu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China.,Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
| |
Collapse
|
37
|
Kanders L, Beier M, Nogueira R, Nehrenheim E. Sinks and sources of anammox bacteria in a wastewater treatment plant - screening with qPCR. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2018; 78:441-451. [PMID: 30101779 DOI: 10.2166/wst.2018.318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The deammonification process, which includes nitritation and anammox bacteria, is an energy-efficient nitrogen removal process. Starting up an anammox process in a wastewater treatment plant (WWTP) is still widely believed to require external seeding of anammox bacteria. To demonstrate the principle of a non-seeded anammox start-up, anammox bacteria in potential sources must be quantified. In this study, seven digesters, their substrates and reject water were sampled and quantitative polymerase chain reaction (qPCR) was used to quantify both total and viable anammox bacteria. The results show that mesophilic digesters fed with nitrifying sludge (with high sludge ages) can be classified as a reliable source of anammox bacteria. Sludge hygienization and dewatering of digestate reduce the amount of anammox bacteria by one to two orders of magnitude and can be considered as a sink. The sampled reject waters contained on average >4.0 × 104 copies mL-1 and the majority of these cells (>87%) were viable cells. Furthermore, plants with side-stream anammox treatment appear to have higher overall quantities of anammox bacteria than those without such treatment. The present study contributes to the development of sustainable strategies for both start-up of anammox reactors and the possibility of improving microbial management in WWTPs.
Collapse
Affiliation(s)
- Linda Kanders
- Purac AB, Box 1146, SE-221 05 Lund, Sweden E-mail: ; School of Business, Society and Engineering, Mälardalen University, Box 883, SE-721 23 Västerås, Sweden
| | - Maike Beier
- Institute for Sanitary Engineering and Waste Management (ISAH), Leibniz Universitaet Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management (ISAH), Leibniz Universitaet Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - Emma Nehrenheim
- School of Business, Society and Engineering, Mälardalen University, Box 883, SE-721 23 Västerås, Sweden
| |
Collapse
|
38
|
|
39
|
Eramo A, Medina WM, Fahrenfeld NL. Peracetic acid disinfection kinetics for combined sewer overflows: indicator organisms, antibiotic resistance genes, and microbial community. ENVIRONMENTAL SCIENCE : WATER RESEARCH & TECHNOLOGY 2017; 3:1061-1072. [PMID: 29333272 PMCID: PMC5761733 DOI: 10.1039/c7ew00184c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Combined sewer overflows (CSOs) degrade water quality and end-of-pipe treatment is one potential solution for retrofitting this outdated infrastructure. The goal of this research was to evaluate peracetic acid (PAA) as a disinfectant for CSOs using viability based molecular methods for antibiotic resistance genes (ARGs), indicator organism marker gene BacHum, and 16S rRNA genes. Simulated CSO effluent was prepared using 23-40% wastewater, representing the higher end of the range of wastewater concentrations reported in CSO effluent. PAA residual following disinfection was greatest for samples with the lowest initial COD. Treatment of simulated CSO effluent (23% wastewater) with 100 mg∙min/L PAA (5 mg/L PAA, 20 min) was needed to reduce viable cell sul1, tet(G), and BacHum (1.0±0.63-3.2±0.25-log) while 25 to 50 mg•min/L PAA (5 mg/L PAA, 5-10 min) was needed to reduce viable cell loads (0.62±0.56-1.6±0.08-log) in 40% wastewater from a different municipal treatment plant. Increasing contact time after the initial decrease in viable cell gene copies did not significantly improve treatment. A much greater applied Ct of 1200 mg∙min/L PAA (20 mg/L PAA, 60 min) was required for significant log reduction of 16S rRNA genes (3.29±0.13-log). No significant losses of mexB were observed during the study. Data were fitted to a Chick-Watson model and resulting inactivation constants for sul1 and tet(G) > BacHum > 16S rRNA. Amplicon sequencing of the 16S rRNA gene indicated the initial viable and total microbial communities were distinct and that treatment with PAA resulted in marked increases of the relative abundance of select phyla, particularly Clostridia which increased by 1-1.5 orders of magnitude. Results confirm that membrane disruption is a mechanism for PAA disinfection and further treatment is needed to reduce total ARGs in CSO effluent.
Collapse
Affiliation(s)
- Alessia Eramo
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, 96 Frelinghuysen Rd., Piscataway, New Jersey 08854, United States
| | - William Morales Medina
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, 96 Frelinghuysen Rd., Piscataway, New Jersey 08854, United States
| | - Nicole L. Fahrenfeld
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, 96 Frelinghuysen Rd., Piscataway, New Jersey 08854, United States
| |
Collapse
|
40
|
Li R, Tun HM, Jahan M, Zhang Z, Kumar A, Dilantha Fernando WG, Farenhorst A, Khafipour E. Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water. Sci Rep 2017; 7:5752. [PMID: 28720878 PMCID: PMC5515937 DOI: 10.1038/s41598-017-02516-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 12/22/2022] Open
Abstract
The limitation of 16S rRNA gene sequencing (DNA-based) for microbial community analyses in water is the inability to differentiate live (dormant cells as well as growing or non-growing metabolically active cells) and dead cells, which can lead to false positive results in the absence of live microbes. Propidium-monoazide (PMA) has been used to selectively remove DNA from dead cells during downstream sequencing process. In comparison, 16S rRNA sequencing (RNA-based) can target live microbial cells in water as both dormant and metabolically active cells produce rRNA. The objective of this study was to compare the efficiency and sensitivity of DNA-based, PMA-based and RNA-based 16S rRNA Illumina sequencing methodologies for live bacteria detection in water samples experimentally spiked with different combination of bacteria (2 gram-negative and 2 gram-positive/acid fast species either all live, all dead, or combinations of live and dead species) or obtained from different sources (First Nation community drinking water; city of Winnipeg tap water; water from Red River, Manitoba, Canada). The RNA-based method, while was superior for detection of live bacterial cells still identified a number of 16S rRNA targets in samples spiked with dead cells. In environmental water samples, the DNA- and PMA-based approaches perhaps overestimated the richness of microbial community compared to RNA-based method. Our results suggest that the RNA-based sequencing was superior to DNA- and PMA-based methods in detecting live bacterial cells in water.
Collapse
Affiliation(s)
- Ru Li
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of plant protection, Yunnan Agricultural University, Kunming, Yunnan province, 650201, China
| | - Hein Min Tun
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Pediatrics, University of Alberta, AB, Canada
| | - Musarrat Jahan
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Zhengxiao Zhang
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Ayush Kumar
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | | | - Annemieke Farenhorst
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| |
Collapse
|
41
|
Orta de Velásquez MT, Yáñez Noguez I, Casasola Rodríguez B, Román Román PI. Effects of ozone and chlorine disinfection on VBNC Helicobacter pylori by molecular techniques and FESEM images. ENVIRONMENTAL TECHNOLOGY 2017; 38:744-753. [PMID: 27432258 DOI: 10.1080/09593330.2016.1210680] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Helicobacter pylori is a pathogen bacteria associated with chronic gastritis, peptic ulceration, and gastric carcinoma. H. pylori has a spiral morphology, which under certain conditions of stress becomes a coccoid form. This type of morphology has been linked to a viable but non-culturable (VBNC) state, which is thought to allow its persistence in the environment. Membrane damage in VBNC H. pylori in water as a mechanism for inactivation using ozone (O3) and chlorine disinfection has not been reported in the literature. In this paper, disinfection assays with ozone and chlorine were conducted to evaluate their effects on VBNC H. pylori cells. The use of fluorescent dyes such as propidium monoazide (PMA) coupled with quantitative real-time polymerase chain reactions produced results necessary to assess the viability of the microorganism and demonstrate the effect of each disinfectant on the bacterial count. Applying ozone showed a 5-log bacterial reduction using a disinfectant concentration and exposure time (CT) of 4 mg min/L. Chlorine disinfection for the same 5-log reduction required a higher CT value. Field emission scanning electron microscope images of ozone-treated VBNC H. pylori also showed severe cell damage. The use of PMA revealed that chlorine produced physical damage in the membrane in addition to the known inhibiting effect on cell enzymatic processes. These findings are important for the detection and control of VBNC H. pylori cells in drinking water systems.
Collapse
Affiliation(s)
- María Teresa Orta de Velásquez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Isaura Yáñez Noguez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Beatriz Casasola Rodríguez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Priscila Ivette Román Román
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| |
Collapse
|
42
|
Development of Reverse Transcription Quantitative Real-Time PCR (RT-qPCR) Assays for Monitoring Saccharomycopsis fibuligera, Rhizopus oryzae, and Monascus purpureus During the Traditional Brewing of Hong Qu Glutinous Rice Wine. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-016-0565-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
43
|
Kibbee RJ, Örmeci B. Development of a sensitive and false-positive free PMA-qPCR viability assay to quantify VBNC Escherichia coli and evaluate disinfection performance in wastewater effluent. J Microbiol Methods 2017; 132:139-147. [DOI: 10.1016/j.mimet.2016.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 11/29/2022]
|
44
|
Janssen KJH, Hoebe CJPA, Dukers-Muijrers NHTM, Eppings L, Lucchesi M, Wolffs PFG. Viability-PCR Shows That NAAT Detects a High Proportion of DNA from Non-Viable Chlamydia trachomatis. PLoS One 2016; 11:e0165920. [PMID: 27812208 PMCID: PMC5094775 DOI: 10.1371/journal.pone.0165920] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022] Open
Abstract
Objectives According to the current guidelines for laboratory diagnosis of sexually transmitted infections (STIs), nucleic acid amplification tests (NAATs) are the preferred diagnostic method for Chlamydia trachomatis (CT) infections. However, NAATs amplify the available target DNA without discriminating between DNA originating from viable or non-viable CT. Assessing CT viability will provide more insights in the clinical and public health relevance of a CT positive test result. The aim of this study was to technically validate and implement viability-PCR (V-PCR) to asses CT viability. Methods Technical validation of V-PCR was performed by the assessment of predefined viability ratios of CT. Samples were subjected to V-PCR which consisted of propidium monoazide (PMA) treatment prior to DNA extraction followed by quantitative PCR (qPCR) targeting the ompA gene for the detection of CT DNA. Finally, V-PCR was applied to vaginal swabs of 50 CT positive patients, as indicated by routine NAAT, collected at our outpatient STD clinics before antimicrobial treatment. Results Technical validation of V-PCR showed that PMA treatment of heat-inactivated CT culture resulted in an almost complete loss of qPCR signal. PMA treated samples of the fresh viable CT culture showed no marked reduction of PCR signal, indicating that all DNA from viable CT could be detected. Applying V-PCR to clinical samples showed that in 36% of samples (18/50) less than 1% of CT DNA originated from viable bacteria. Conclusions V-PCR showed to be a fast and easy method to assess CT viability in clinical samples, without the need of traditional challenging cell culture methods. Furthermore, V-PCR results of clinical samples have indicated that a substantial amount of the amplified CT DNA originated from non-viable cells. Although results might be influenced by cell death during transport, this study suggests that there is a potential overestimation of quantitative CT positivity by currently used NAATs.
Collapse
Affiliation(s)
- Kevin J. H. Janssen
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Christian J. P. A. Hoebe
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Geleen, The Netherlands
| | - Nicole H. T. M. Dukers-Muijrers
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Geleen, The Netherlands
| | - Lisanne Eppings
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service (GGD South Limburg), Geleen, The Netherlands
| | - Mayk Lucchesi
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Petra F. G. Wolffs
- Department of Medical Microbiology, School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- * E-mail:
| |
Collapse
|
45
|
Suitability of different Escherichia coli enumeration techniques to assess the microbial quality of different irrigation water sources. Food Microbiol 2016; 58:29-35. [DOI: 10.1016/j.fm.2016.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
|
46
|
Gyawali P, Ahmed W, Sidhu JPS, Nery SV, Clements AC, Traub R, McCarthy JS, Llewellyn S, Jagals P, Toze S. Quantitative detection of viable helminth ova from raw wastewater, human feces, and environmental soil samples using novel PMA-qPCR methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:18639-18648. [PMID: 27306209 DOI: 10.1007/s11356-016-7039-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/05/2016] [Indexed: 06/06/2023]
Abstract
In this study, we have evaluated the efficacy of propidium monoazide quantitative polymerase chain reaction (PMA-qPCR) to differentiate between viable and non-viable Ancylostoma caninum ova. The newly developed method was validated using raw wastewater seeded with known numbers of A. caninum ova. Results of this study confirmed that PMA-qPCR has resulted in average of 88 % reduction (P < 0.05) in gene copy numbers for 50 % viable +50 % non-viable when compared with 100 % viable ova. A reduction of 100 % in gene copies was observed for 100 % non-viable ova when compared with 100 % viable ova. Similar reductions (79-80 %) in gene copies were observed for A. caninum ova-seeded raw wastewater samples (n = 18) collected from wastewater treatment plants (WWTPs) A and B. The newly developed PMA-qPCR method was applied to determine the viable ova of different helminths (A. caninum, A. duodenale, Necator americanus and Ascaris lumbricoides) in raw wastewater, human fecal and soil samples. None of the unseeded wastewater samples were positive for the above-mentioned helminths. N. americanus and A. lumbricoides ova were found in unseeded human fecal and soil samples. For the unseeded human fecal samples (1 g), an average gene copy concentration obtained from qPCR and PMA-qPCR was found to be similar (6.8 × 10(5) ± 6.4 × 10(5) and 6.3 × 10(5) ± 4.7 × 10(5)) indicating the presence of viable N. americanus ova. Among the 24 unseeded soil samples tested, only one was positive for A. lumbricoides. The mean gene copy concentration in the positively identified soil sample was 1.0 × 10(5) ± 1.5 × 10(4) (determined by qPCR) compared to 4.9 × 10(4) ± 3.7 × 10(3) (determined by PMA-qPCR). The newly developed PMA-qPCR methods were able to detect viable helminth ova from wastewater and soil samples and could be adapted for health risk assessment.
Collapse
Affiliation(s)
- P Gyawali
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, GPO Box 2583, Brisbane, QLD, 4102, Australia.
- School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia.
| | - W Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, GPO Box 2583, Brisbane, QLD, 4102, Australia
| | - J P S Sidhu
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, GPO Box 2583, Brisbane, QLD, 4102, Australia
- School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia
| | - S V Nery
- Research School of Population Health, College of Medicine, Biology and Environment, The Australian National University, Linnaeus Way, ACT, 2601, Australia
| | - A C Clements
- Research School of Population Health, College of Medicine, Biology and Environment, The Australian National University, Linnaeus Way, ACT, 2601, Australia
| | - R Traub
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - J S McCarthy
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
- School of Medicine, The University of Queensland, Herston, QLD, 4006, Australia
| | - S Llewellyn
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - P Jagals
- School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia
| | - S Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, GPO Box 2583, Brisbane, QLD, 4102, Australia
- School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia
| |
Collapse
|
47
|
Development of propidium monoazide combined with real-time quantitative PCR (PMA-qPCR) assays to quantify viable dominant microorganisms responsible for the traditional brewing of Hong Qu glutinous rice wine. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.01.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
48
|
Scaturro M, Fontana S, Dell’eva I, Helfer F, Marchio M, Stefanetti MV, Cavallaro M, Miglietta M, Montagna MT, De Giglio O, Cuna T, Chetti L, Sabattini MAB, Carlotti M, Viggiani M, Stenico A, Romanin E, Bonanni E, Ottaviano C, Franzin L, Avanzini C, Demarie V, Corbella M, Cambieri P, Marone P, Rota MC, Bella A, Ricci ML. A multicenter study of viable PCR using propidium monoazide to detect Legionella in water samples. Diagn Microbiol Infect Dis 2016; 85:283-288. [DOI: 10.1016/j.diagmicrobio.2016.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 11/26/2022]
|
49
|
Pinheiro ET, Neves VD, Reis CC, Longo PL, Mayer MPA. Evaluation of the Propidium Monoazide-quantitative Polymerase Chain Reaction Method for the Detection of Viable Enterococcus faecalis. J Endod 2016; 42:1089-92. [PMID: 27179593 DOI: 10.1016/j.joen.2016.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/17/2016] [Accepted: 04/03/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION One limitation of DNA-based molecular assays is their inability to distinguish between live and dead cells. A sample treatment with propidium monoazide (PMA) before DNA amplification has been proposed to overcome this problem. The aim of this in vitro study was to test different concentrations of PMA coupled with quantitative polymerase chain reaction (qPCR) for the detection of viable Enterococcus faecalis. METHODS Viable or heat-killed suspensions of E. faecalis (10⁶ colony-forming units/mL) were treated with PMA at 10, 50, and 100 μg/mL before DNA extraction. qPCR was performed using primers complementary for E. faecalis 16S ribosomal RNA sequence. PMA was also tested on bacteria suspensions containing different proportions of viable and dead cells. Bacterial suspensions without PMA treatment were used as positive controls. RESULTS The treatment of heat-killed suspensions with PMA at different concentrations significantly reduced the DNA amplification when compared with the group without treatment (P < .0001), indicating that DNA from dead cells was not used as templates. The greatest reduction in qPCR amplification of dead cell DNA was found when 100 μg/mL PMA was used (P < .005). In mixtures containing live/dead cells, PMA allowed selective detection of viable cells. CONCLUSIONS PMA was effective in inhibiting qPCR amplification from the DNA of dead cells, enabling in vitro detection and quantification of viable cells of E. faecalis.
Collapse
Affiliation(s)
- Ericka T Pinheiro
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil.
| | - Viviane D Neves
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Caroline C Reis
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Priscila L Longo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Márcia P A Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
50
|
Optimization and validation of a PMA qPCR method for Escherichia coli quantification in primary production. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|