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Pandey P, Gaa ME, Huo J, Okada Y, Lee KY, Giat S, Li X, Zhang R, Pandey P. Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons. J Appl Microbiol 2024; 135:lxae103. [PMID: 38664008 DOI: 10.1093/jambio/lxae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/11/2024] [Accepted: 04/20/2024] [Indexed: 06/04/2024]
Abstract
AIM The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California. METHODS AND RESULTS To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator Escherichia coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157: H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157: H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, ∼11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. CONCLUSION These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.
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Affiliation(s)
- Prachi Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
| | - Megan Elise Gaa
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Jiang Huo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Yu Okada
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Katie Yen Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Sharon Giat
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Ruihong Zhang
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
| | - Pramod Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
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Zhang Q, Yang F, Gao J, Zhang W, Xu X. Development of multiplex TaqMan qPCR for simultaneous detection and differentiation of eight common swine viral and bacterial pathogens. Braz J Microbiol 2021; 53:359-368. [PMID: 34709596 DOI: 10.1007/s42770-021-00633-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 10/17/2021] [Indexed: 11/24/2022] Open
Abstract
It is laborious to diagnose the infections of classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), and Suid herpesvirus 1 (SuHV-1) because of the similar clinical symptoms in piglets. Staphylococcus aureus (S. aureus), Streptococcus suis (S. suis), Salmonella choleraesuis (S. choleraesuis, serotype: 6,7:c:1,5), and Escherichia coli (E. coli) are common secondary bacterial pathogens in viral infections. Furthermore, the mixed infection of these viral and bacterial pathogens is more and more common in practical swine breeding. Therefore, a TaqMan multiplex qPCR method for simultaneous detection and differentiation of their pathogen was established in this study by designing specific primers and probes for the E2 gene of CSFV, the ORF7 gene of PRRSV, the ORF1 gene of PCV2 and the gE gene of SuHV-1, the nuc gene of S. aureus, the ef-tu gene of S. suis, the ivnA gene of S. choleraesuis, and the 23S rRNA gene of E. coli, and its specificity, sensitivity, and reproducibility were subsequently tested. The results showed that TaqMan multiplex qPCR method showed a high specificity with no cross reaction between different viruses, and a good repeatability with its coefficient of variation lower than 5%. Besides, the sensitivity of this method was also at least 10 times higher compared with conventional PCR. Overall, this study provided a reliable multiplex TaqMan qPCR method for the diagnosis and differentiation of the mentioned pathogens in pigs, laying a certain technical basis for disease prevention and control.
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Affiliation(s)
- Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Feng Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Weimin Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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3
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Petri RM, Aditya S, Humer E, Zebeli Q. Effect of an intramammary lipopolysaccharide challenge on the hindgut microbial composition and fermentation of dairy cattle experiencing intermittent subacute ruminal acidosis. J Dairy Sci 2021; 104:5417-5431. [PMID: 33663865 DOI: 10.3168/jds.2020-19496] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022]
Abstract
Feeding grain-rich diets often results in subacute ruminal acidosis (SARA), a condition associated with ruminal dysbiosis and systemic inflammation. Yet, the effect of SARA on hindgut microbiota, and whether this condition is aggravated by exogenous immune stimuli, is less understood. Therefore, the aims of this study were to determine the effects of an intermittent high-grain SARA model on the hindgut microbial community, and to evaluate whether the effects of SARA on the fecal microbiome and fermentation were further affected by an intramammary lipopolysaccharide (LPS) challenge. A total of 18 early-lactating Simmental cows were divided into 3 groups (n = 6); 2 were fed a SARA-inducing feeding regimen (60% concentrate), 1 was fed a control (CON) diet (40% concentrate). On d 30, 1 SARA group (SARA-LPS) and the CON group (CON-LPS) were intramammarily challenged with a single dose of 50 µg of LPS from Escherichia coli O26:B6, whereas the remaining 6 SARA cows (SARA-PLA) received a placebo. Using a longitudinal randomized controlled design, with grouping according to parity and days in milk), statistical analysis was performed with baseline measurements used as a covariate in a mixed model procedure. The SARA-inducing feeding challenge resulted in decreased fecal pH and increased butyrate as a proportion of total short-chain fatty acids in the feces. On d 30, SARA-challenged cows had decreased fecal diversity as shown by the Shannon and Chao1 indices and a decrease in the relative abundance of Euryarchaeota and cellulolytic genera, and numerical increases in the relative abundance of several Firmicutes associated with starch and secondary fermentation. The LPS challenge did not affect the fecal pH and short-chain fatty acids, but increased the Chao1 richness index in an interaction with the SARA challenge, and affected the relative abundance of Verrucomicrobia (1.13%), Actinobacteria (0.19%), and Spirochaetes (0.002%), suggesting an effect on the microbial ecology of the hindgut during SARA conditions. In conclusion, the SARA-inducing feeding regimen promoted important microbial changes at d 30, including reduced diversity and evenness compared with CON, whereas the external LPS challenge led to changes in the microbial community without affecting fecal fermentation properties.
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Affiliation(s)
- R M Petri
- Agriculture and Agri-Food Canada, Research and Development Centre Sherbrooke, 2000 College Street, Sherbrooke, QC, Canada, J1M 1Z7.
| | - S Aditya
- Faculty of Veterinary Medicine, Brawijaya University, Jl. Mayjen Haryono No. 169, Malang 65145, East Java, Indonesia; Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - E Humer
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Q Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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Comparative Use of Quantitative PCR (qPCR), Droplet Digital PCR (ddPCR), and Recombinase Polymerase Amplification (RPA) in the Detection of Shiga Toxin-Producing E. coli (STEC) in Environmental Samples. WATER 2020. [DOI: 10.3390/w12123507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
E. coli O157:H7 is a foodborne pathogen that constitutes a global threat to human health. However, the quantification of this pathogen in food and environmental samples may be problematic at the low cell numbers commonly encountered in environmental samples. In this study, we used recombinase polymerase amplification (RPA) for the detection of E. coli O157:H7, real-time quantitative PCR (qPCR) for quantification, and droplet digital PCR (ddPCR) for absolute and accurate quantification of E. coli O157:H7 from spiked and environmental samples. Primer and probe sets were used for the detection of stx1 and stx2 using RPA. Genes encoding for stx1, stx2, eae, and rfbE were used to quantify E. coli O157:H7 in the water samples. Furthermore, duplex ddPCR assays were used to quantify the pathogens in these samples. Duplex assay set 1 used stx1 and rfbE genes, while assay set 2 used stx2 and eae genes. Droplet digital PCR was used for the absolute quantification of E. coli O15:H7 in comparison with qPCR for the spiked and environmental samples. The RPA results were compared to those from qPCR and ddPCR in order to assess the efficiency of the RPA compared with the PCR methods. The assays were further applied to the dairy lagoon effluent (DLE) and the high rate algae pond (HRAP) effluent, which were fed with diluted DLE. The RPA detected was <10 CFU/mL, while ddPCR showed quantification from 1 to 104 CFU/mL with a high reproducibility. In addition, quantification by qPCR was from 103 to 107 CFU/mL of the wastewater samples. Therefore, the RPA assay has potential as a point of care tool for the detection of E. coli O157:H7 from different environmental sources, followed by quantification of the target concentrations.
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You D, Chen F, Li J, Zeng X, Wang W, Guo Y, Yang F, Sun S, Wang L. Prospective case-control study of enterovirus detection differences in children's cerebrospinal fluid between multiplex PCR and real-time RT-PCR assay. J Clin Lab Anal 2020; 35:e23606. [PMID: 33146929 PMCID: PMC7891498 DOI: 10.1002/jcla.23606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Background Viral encephalitis is common in childhood. It is an acute brain parenchymal inflammation caused by a variety of viral infection, and enterovirus accounts for the majority. Due to atypical clinical manifestations, pathogenic testing is important for assisting clinical diagnosis. The purpose of this study was to evaluate the performance of the multiplex PCR assay compared with quantitative real‐time PCR for enterovirus detection. Methods A prospective case‐control study was performed involving 103 pediatric patients suspected for viral encephalitis and cerebrospinal fluid (CSF) samples were collected and tested for 9 pathogens using multiplex PCR assay during April to November in 2018. In parallel, an aliquot of samples was tested for enterovirus infection by real‐time PCR assay. Results There were 85.4% children were confirmed as viral encephalitis on discharge, the remaining ones were diagnosed as other CNS diseases, such as epilepsy. The specificity of the two methods was the same as that of the clinical diagnosis, but the sensitivity and consistency with clinical diagnosis of multiplex PCR were both higher than the real‐time PCR. Besides of enterovirus, multiplex PCR could also detect coinfection of enterovirus with Epstein‐Barr virus and mumps virus. Conclusion Results of multiplex PCR method are more consistent with the clinical diagnosis and are superior to real‐time PCR for detecting enterovirus in CSF.
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Affiliation(s)
- Dianping You
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Fang Chen
- Department of Neurology, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Jingjie Li
- Department of Neurology, Children's Hospital of Hebei Province, Shijiazhuang, China
| | | | | | - Yinghui Guo
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Fan Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Suzhen Sun
- Department of Neurology, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
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Remfry SE, Amachawadi RG, Shi X, Bai J, Woodworth JC, Tokach MD, Dritz SS, Goodband RD, DeRouchey JM, Nagaraja TG. Polymerase Chain Reaction-Based Prevalence of Serogroups of Escherichia coli Known to Carry Shiga Toxin Genes in Feces of Finisher Pigs. Foodborne Pathog Dis 2020; 17:782-791. [PMID: 32833570 DOI: 10.1089/fpd.2020.2814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens and seven serogroups, O26, O45, O103, O111, O121, O145, and O157, that account for the majority of the STEC-associated illness in humans. Similar to cattle, swine also harbor STEC and shed them in the feces and can be a source of human STEC infections. Information on the prevalence of STEC in swine feces is limited. Therefore, our objective was to utilize polymerase chain reaction (PCR) assays to determine prevalence of major virulence genes and serogroups of STEC. Fecal samples (n = 598), collected from finisher pigs within 3 weeks before marketing in 10 pig flows located in 8 states, were included in the study. Samples enriched in E. coli broth were subjected to a real-time PCR assay targeting three virulence genes, Shiga toxin 1 (stx1), Shiga toxin 2 (stx2), and intimin (eae), which encode for Shiga toxins 1 and 2, and intimin, respectively. A novel PCR assay was designed and validated to detect serogroups, O8, O20, O59, O86, O91, O100, O120, and O174, previously reported to be commonly present in swine feces. In addition, enriched fecal samples positive for Shiga toxin genes were subjected to a multiplex PCR assay targeting O26, O45, O103, O104, O111, O121, O145, and O157 serogroups implicated in human clinical infections. Of the 598 fecal samples tested by real-time PCR, 25.9%, 65.1%, and 67% were positive for stx1, stx2, and eae, respectively. The novel eight-plex PCR assay indicated the predominant prevalence of O8 (88.6%), O86 (35.5%), O174 (24.1%), O100 (20.2%), and O91 (15.6%) serogroups. Among the seven serogroups relevant to human infections, three serogroups, O121 (17.6%), O157 (14%), and O26 (11%) were predominant. PCR-based detection indicated high prevalence of Shiga toxin genes and serogroups that are known to carry Shiga toxin genes, including serogroups commonly prevalent in cattle feces and implicated in human infections and in edema disease in swine.
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Affiliation(s)
- Sarah E Remfry
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Xiaorong Shi
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jianfa Bai
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA.,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas, USA
| | - Jason C Woodworth
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Mike D Tokach
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Steve S Dritz
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Robert D Goodband
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Joel M DeRouchey
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes. J Clin Microbiol 2020; 58:JCM.01684-19. [PMID: 31896667 DOI: 10.1128/jcm.01684-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx 1 and stx 2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx 1 were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.
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Baker CA, De J, Bertoldi B, Dunn L, Chapin T, Jay-Russell M, Danyluk MD, Schneider KR. Prevalence and concentration of stx+ E. coli and E. coli O157 in bovine manure from Florida farms. PLoS One 2019; 14:e0217445. [PMID: 31125367 PMCID: PMC6534375 DOI: 10.1371/journal.pone.0217445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/10/2019] [Indexed: 12/25/2022] Open
Abstract
Fresh produce outbreaks due to Shiga toxin-producing Escherichia coli (STEC) continue to occur in the United States (US). Manure-amended soils can pose a public health risk when used for growing raw agricultural commodities. Knowing the prevalence and concentration of STEC in untreated biological soil amendments of animal origin (BSAAO) is important to help guide the most appropriate pre-harvest interval(s) following application to limit risks from these soil amendments. Bovine manure samples were collected from 12 farms in Florida, including samples from piles, lagoons, barns, and screened solids. Two methods were used to detect stx1/2 and rfbE genes in samples. A prevalence rate of 9% for stx1 and/or stx2 and 19% for rfbE was observed from the 518 bovine manure samples evaluated. A most probable number (MPN) assay was performed on stx+ samples when applicable. The geometric mean for stx+ samples (n = 20) was 3.37 MPN g-1 (0.53 log MPN g-1) with a maximum value of 6,800 MPN g-1 (3.83 log MPN g-1). This research was part of a larger nationwide geographical study on the prevalence and concentration of STEC in bovine manure to help guide regulations on feasible pre-harvest intervals for the application of untreated BSAAO.
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Affiliation(s)
- Christopher A. Baker
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, United States of America
| | - Jaysankar De
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, United States of America
| | - Bruna Bertoldi
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, United States of America
| | - Laurel Dunn
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - Travis Chapin
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - Michele Jay-Russell
- Western Center for Food Safety, University of California, Davis, California, United States of America
| | - Michelle D. Danyluk
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, United States of America
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - Keith R. Schneider
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Noll LW, Chall R, Shridhar PB, Liu X, Bai J, Delannoy S, Fach P, Nagaraja TG. Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces †. J Food Prot 2018; 81:1157-1164. [PMID: 29939793 DOI: 10.4315/0362-028x.jfp-18-049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbEO157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx1 and stx2) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbEO157, stx1, stx2, and eae genes and a culture method. Detection limits of the CRISPRO157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 103 and 2.3 × 100 CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPRO157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPRO157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbEO157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.
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Affiliation(s)
- Lance W Noll
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Rachel Chall
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Pragathi B Shridhar
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Xuming Liu
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Jianfa Bai
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Sabine Delannoy
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Patrick Fach
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - T G Nagaraja
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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Beauvais W, Gart EV, Bean M, Blanco A, Wilsey J, McWhinney K, Bryan L, Krath M, Yang CY, Manriquez Alvarez D, Paudyal S, Bryan K, Stewart S, Cook PW, Lahodny G, Baumgarten K, Gautam R, Nightingale K, Lawhon SD, Pinedo P, Ivanek R. The prevalence of Escherichia coli O157:H7 fecal shedding in feedlot pens is affected by the water-to-cattle ratio: A randomized controlled trial. PLoS One 2018; 13:e0192149. [PMID: 29414986 PMCID: PMC5802916 DOI: 10.1371/journal.pone.0192149] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/17/2018] [Indexed: 11/28/2022] Open
Abstract
Escherichia coli O157:H7 fecal shedding in feedlot cattle is common and is a public health concern due to the risk of foodborne transmission that can result in severe, or even fatal, disease in people. Despite a large body of research, few practical and cost-effective farm-level interventions have been identified. In this study, a randomized controlled trial was conducted to assess the effect of reducing the level of water in automatically refilling water-troughs on fecal shedding of E. coli O157:H7 in feedlot cattle. Pens in a feedlot in the Texas Panhandle were randomly allocated as control (total number: 17) or intervention (total number: 18) pens. Fecal samples (2,759 in total) were collected both at baseline and three weeks after the intervention, and tested for the presence of E. coli O157:H7 using immunomagnetic bead separation and selective culture. There was a strong statistical association between sampling date and the likelihood of a fecal sample testing positive for E. coli O157:H7. Pen was also a strong predictor of fecal prevalence. Despite accounting for this high level of clustering, a statistically significant association between reduced water levels in the trough and increased prevalence of E. coli O157:H7 in the feces was observed (Odds Ratio = 1.6; 95% Confidence Interval: 1.2–2.0; Likelihood Ratio Test: p = 0.02). This is the first time that such an association has been reported, and suggests that increasing water-trough levels may be effective in reducing shedding of E. coli O157:H7 in cattle feces, although further work would be needed to test this hypothesis. Controlling E. coli O157:H7 fecal shedding at the pre-harvest level may lead to a reduced burden of human foodborne illness attributed to this pathogen in beef.
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Affiliation(s)
- Wendy Beauvais
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Elena V. Gart
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Melissa Bean
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Anthony Blanco
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jennifer Wilsey
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kallie McWhinney
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Laura Bryan
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Mary Krath
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Ching-Yuan Yang
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Diego Manriquez Alvarez
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Sushil Paudyal
- West Texas A&M University, Canyon, Texas, United States of America
| | - Kelsey Bryan
- Texas A&M Agrilife Research, Amarillo, Texas, United States of America
| | - Samantha Stewart
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Peter W. Cook
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Glenn Lahodny
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karina Baumgarten
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Raju Gautam
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Kendra Nightingale
- Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Sara D. Lawhon
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Pablo Pinedo
- Texas A&M Agrilife Research, Amarillo, Texas, United States of America
| | - Renata Ivanek
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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11
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Shi X, Liu X, Wang Q, Das A, Ma G, Xu L, Sun Q, Peddireddi L, Jia W, Liu Y, Anderson G, Bai J, Shi J. A multiplex real-time PCR panel assay for simultaneous detection and differentiation of 12 common swine viruses. J Virol Methods 2016; 236:258-265. [PMID: 27506582 PMCID: PMC7119729 DOI: 10.1016/j.jviromet.2016.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
Abstract
A multiplex real-time PCR panel assay was developed for the detection of 12 major swine pathogens including VSV-IN, VSV-NJ, SVDV, CSFV, ASFV, FMDV, PCV2, PPV, PRV, PRRSV-NA, PRRSV-EU;. The panel assay was 100% specific against common swine pathogens;. Limits of detection of the assay were ranged 1–16 copies per reaction;. Detection sensitivity was not reduced by multiplexing three targets into one PCR reaction.
Mixed infection with different pathogens is common in swine production systems especially under intensive production conditions. Quick and accurate detection and differentiation of different pathogens are necessary for epidemiological surveillance, disease management and import and export controls. In this study, we developed and validated a panel of multiplex real-time PCR/RT-PCR assays composed of four subpanels, each detects three common swine pathogens. The panel detects 12 viruses or viral serotypes, namely, VSV-IN, VSV-NJ, SVDV, CSFV, ASFV, FMDV, PCV2, PPV, PRV, PRRSV-NA, PRRSV-EU and SIV. Correlation coefficients (R2) and PCR amplification efficiencies of all singular and triplex real-time PCR reactions are within the acceptable range. Comparison between singular and triplex real-time PCR assays of each subpanel indicates that there is no significant interference on assay sensitivities caused by multiplexing. Specificity tests on 226 target clinical samples or 4 viral strains and 91 non-target clinical samples revealed that the real-time PCR panel is 100% specific, and there is no cross amplification observed. The limit of detection of each triplex real-time PCR is less than 10 copies per reaction for DNA, and less than 16 copies per reaction for RNA viruses. The newly developed multiplex real-time PCR panel also detected different combinations of co-infections as confirmed by other means of detections.
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Affiliation(s)
- Xiju Shi
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China; Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Qin Wang
- China Institute of Veterinary Drug Control, Beijing, China
| | - Amaresh Das
- Foreign Animal Diseases Diagnostic Laboratory, NVSL, APHIS, USDA, Greenport, NY, United States
| | - Guiping Ma
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China
| | - Lu Xu
- China Institute of Veterinary Drug Control, Beijing, China
| | - Qing Sun
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Wei Jia
- Foreign Animal Diseases Diagnostic Laboratory, NVSL, APHIS, USDA, Greenport, NY, United States
| | - Yanhua Liu
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China
| | - Gary Anderson
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.
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12
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Luedtke BE, Bosilevac JM, Harhay DM, Arthur TM. Effect of Direct-Fed Microbial Dosage on the Fecal Concentrations of EnterohemorrhagicEscherichia coliin Feedlot Cattle. Foodborne Pathog Dis 2016; 13:190-5. [DOI: 10.1089/fpd.2015.2063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Brandon E. Luedtke
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Dayna M. Harhay
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Terrance M. Arthur
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
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13
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Shridhar PB, Noll LW, Shi X, An B, Cernicchiaro N, Renter DG, Nagaraja TG, Bai J. Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces. J Food Prot 2016; 79:66-74. [PMID: 26735031 DOI: 10.4315/0362-028x.jfp-15-319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.
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Affiliation(s)
- P B Shridhar
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - L W Noll
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - X Shi
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - B An
- Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66506, USA
| | - N Cernicchiaro
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - D G Renter
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506, USA.
| | - J Bai
- Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66506, USA.
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14
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Luedtke BE, Bosilevac JM. Comparison of methods for the enumeration of enterohemorrhagic Escherichia coli from veal hides and carcasses. Front Microbiol 2015; 6:1062. [PMID: 26483780 PMCID: PMC4586433 DOI: 10.3389/fmicb.2015.01062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/15/2015] [Indexed: 11/13/2022] Open
Abstract
The increased association of enterohemorrhagic Escherichia coli (EHEC) with veal calves has led the United States Department of Agriculture Food Safety and Inspection Service to report results of veal meat contaminated with the Top 7 serogroups separately from beef cattle. However, detection methods that can also provide concentration for determining the prevalence and abundance of EHEC associated with veal are lacking. Here we compared the ability of qPCR and a molecular based most probable number assay (MPN) to detect and enumerate EHEC from veal hides at the abattoir and the resulting pre-intervention carcasses. In addition, digital PCR (dPCR) was used to analyze select samples. The qPCR assay was able to enumerate total EHEC in 32% of the hide samples with a range of approximately 34 to 91,412 CFUs/100 cm2 (95% CI 4-113,460 CFUs/100 cm2). Using the MPN assay, total EHEC was enumerable in 48% of the hide samples and ranged from approximately 1 to greater than 17,022 CFUs/100 cm2 (95% CI 0.4–72,000 CFUs/100 cm2). The carcass samples had lower amounts of EHEC with a range of approximately 4–275 CFUs/100 cm2 (95% CI 3–953 CFUs/100 cm2) from 17% of samples with an enumerable amount of EHEC by qPCR. For the MPN assay, the carcass samples ranged from 0.1 to 1 CFUs/100 cm2 (95% CI 0.02–4 CFUs/100 cm2) from 29% of the samples. The correlation coefficient between the qPCR and MPN enumeration methods indicated a moderate relation (R2 = 0.39) for the hide samples while the carcass samples had no relation (R2 = 0.002), which was likely due to most samples having an amount of total EHEC below the reliable limit of quantification for qPCR. Interestingly, after enrichment, 81% of the hide samples and 94% of the carcass samples had a detectable amount of total EHEC by qPCR. From our analysis, the MPN assay provided a higher percentage of enumerable hide and carcass samples, however determining an appropriate dilution range and the limited throughput offer additional challenges.
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Affiliation(s)
- Brandon E Luedtke
- U. S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U. S. Meat Animal Research Center Clay Center, NE, USA
| | - Joseph M Bosilevac
- U. S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U. S. Meat Animal Research Center Clay Center, NE, USA
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15
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Noll LW, Shridhar PB, Shi X, An B, Cernicchiaro N, Renter DG, Nagaraja TG, Bai J. A Four-Plex Real-Time PCR Assay, Based on rfbE, stx1, stx2, and eae Genes, for the Detection and Quantification of Shiga Toxin-Producing Escherichia coli O157 in Cattle Feces. Foodborne Pathog Dis 2015; 12:787-94. [PMID: 26317538 DOI: 10.1089/fpd.2015.1951] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several real-time polymerase chain reaction (PCR) assays have been developed to detect and quantify Shiga toxin-producing Escherichia coli (STEC) O157:H7, but none have targeted the O-antigen specific gene (rfbEO157) in combination with the three major virulence genes, stx1, stx2, and eae. Our objectives were to develop and validate a four-plex, quantitative PCR (mqPCR) assay targeting rfbE(O157), stx1, stx2, and eae for the detection and quantification of STEC O157 in cattle feces, and compare the applicability of the assay to detect STEC O157 to a culture method and conventional PCR (cPCR) targeting the same four genes. Specificity of the mqPCR assay to differentially detect the four genes was confirmed with strains of O157 and non-O157 STEC with different profiles of target genes. In cattle feces spiked with pure cultures, detection limits were 2.8×10(4) and 2.8×10(0) colony-forming units/g before and after enrichment, respectively. Detection of STEC O157 in feedlot cattle fecal samples (n=278) was compared between mqPCR, cPCR, and a culture method. The mqPCR detected 48.9% (136/278) of samples as positive for E. coli O157. Of the 100 samples that were randomly picked from 136 mqPCR-positive samples, 35 and 48 tested positive by cPCR and culture method, respectively. Of the 100 samples randomly chosen from 142 mqPCR-negative samples, all were negative by cPCR, but 21 samples tested positive by the culture method. McNemar's chi-square tests indicated significant disagreement between the proportions of positive samples detected by the three methods. In conclusion, the mqPCR assay that targets four genes is a novel and more sensitive method than the cPCR or culture method to detect STEC O157 in cattle feces. However, the use of real-time PCR as a screening method to identify positive samples and then subjecting only positive samples to a culture method may underestimate the presence of STEC O157 in fecal samples.
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Affiliation(s)
- Lance W Noll
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Pragathi B Shridhar
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Xiaorong Shi
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Baoyan An
- 2 Department of Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
| | - Natalia Cernicchiaro
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - David G Renter
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Tiruvoor G Nagaraja
- 1 Department of Diagnostic Medicine/Pathobiology, Kansas State University , Manhattan, Kansas
| | - Jianfa Bai
- 2 Department of Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas
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16
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Further development of sample preparation and detection methods for O157 and the top 6 non-O157 STEC serogroups in cattle feces. J Microbiol Methods 2014; 105:22-30. [DOI: 10.1016/j.mimet.2014.06.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
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17
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Evaluation of real time PCR assays for the detection and enumeration of enterohemorrhagic Escherichia coli directly from cattle feces. J Microbiol Methods 2014; 105:72-9. [DOI: 10.1016/j.mimet.2014.07.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 01/29/2023]
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18
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Guy RA, Tremblay D, Beausoleil L, Harel J, Champagne MJ. Quantification of E. coli O157 and STEC in feces of farm animals using direct multiplex real time PCR (qPCR) and a modified most probable number assay comprised of immunomagnetic bead separation and qPCR detection. J Microbiol Methods 2014; 99:44-53. [DOI: 10.1016/j.mimet.2014.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/31/2014] [Accepted: 02/01/2014] [Indexed: 10/25/2022]
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19
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Verstraete K, Van Coillie E, Werbrouck H, Van Weyenberg S, Herman L, Del-Favero J, De Rijk P, De Zutter L, Joris MA, Heyndrickx M, De Reu K. A qPCR assay to detect and quantify Shiga toxin-producing E. coli (STEC) in cattle and on farms: a potential predictive tool for STEC culture-positive farms. Toxins (Basel) 2014; 6:1201-21. [PMID: 24681714 PMCID: PMC4014729 DOI: 10.3390/toxins6041201] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/03/2014] [Accepted: 03/11/2014] [Indexed: 11/16/2022] Open
Abstract
Shiga toxin-producing E. coli (STEC), of various serogroups harboring the intimin gene, form a serious threat to human health. They are asymptomatically carried by cattle. In this study, a quantitative real-time PCR (qPCR) method was developed as a molecular method to detect and quantify Shiga toxin genes stx1 and stx2 and the intimin gene eae. Subsequently, 59 fecal samples from six farms were tested using qPCR and a culture method as a reference. Three farms had contaminated animals as demonstrated by the culture method. Culture-positive farms showed moderate significantly higher stx prevalences than culture-negative farms (p = 0.05). This is the first study which showed preliminary results that qPCR can predict STEC farm contamination, with a specificity of 77% and a sensitivity of 83%, as compared with the culture method. Furthermore, the presence or quantity of stx genes in feces was not correlated to the isolation of STEC from the individual animal. Quantitative data thus did not add value to the results. Finally, the detection of both stx and eae genes within the same fecal sample or farm using qPCR was not correlated with the isolation of an eae-harboring STEC strain from the respective sample or farm using the culture method.
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Affiliation(s)
- Karen Verstraete
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Els Van Coillie
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Hadewig Werbrouck
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Stephanie Van Weyenberg
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Lieve Herman
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Jurgen Del-Favero
- Applied Molecular Genomics Group, Department of Molecular Genetics, Flemish Institute for Biotechnology (VIB), Universiteitsplein 1, Antwerpen 2610, Belgium.
| | - Peter De Rijk
- Applied Molecular Genomics Group, Department of Molecular Genetics, Flemish Institute for Biotechnology (VIB), Universiteitsplein 1, Antwerpen 2610, Belgium.
| | - Lieven De Zutter
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.
| | - Maria-Adelheid Joris
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium.
| | - Marc Heyndrickx
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
| | - Koen De Reu
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, Melle 9090, Belgium.
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20
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Jacob ME, Bai J, Renter DG, Rogers AT, Shi X, Nagaraja TG. Comparing real-time and conventional PCR to culture-based methods for detecting and quantifying Escherichia coli O157 in cattle feces. J Food Prot 2014; 77:314-9. [PMID: 24490927 DOI: 10.4315/0362-028x.jfp-13-304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Detection of Escherichia coli O157 in cattle feces has traditionally used culture-based methods; PCR-based methods have been suggested as an alternative. We aimed to determine if multiplex real-time (mq) or conventional PCR methods could reliably detect cattle naturally shedding high (≥10(4) CFU/g of feces) and low (∼10(2) CFU/g of feces) concentrations of E. coli O157. Feces were collected from pens of feedlot cattle and evaluated for E. coli O157 by culture methods. Samples were categorized as (i) high shedders, (ii) immunomagnetic separation (IMS) positive after enrichment, or (iii) culture negative. DNA was extracted pre- and postenrichment from 100 fecal samples from each category (high shedder, IMS positive, culture negative) and subjected to mqPCR and conventional PCR assays based on detecting three genes, rfbE, stx1, and stx2. In feces from cattle determined to be E. coli O157 high shedders by culture, 37% were positive by mqPCR prior to enrichment; 85% of samples were positive after enrichment. In IMS-positive samples, 4% were positive by mqPCR prior to enrichment, while 43% were positive after enrichment. In culture-negative feces, 7% were positive by mqPCR prior to enrichment, and 40% were positive after enrichment. The proportion of high shedder-positive and culture-positive (high shedder and IMS) samples were significantly different from mqPCR-positive samples before and after enrichment (P < 0.01). Similar results were observed for conventional PCR. Our data suggest that mqPCR and conventional PCR are most useful in identifying high shedder animals and may not be an appropriate substitute to culture-based methods for detection of E. coli O157 in cattle feces.
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Affiliation(s)
- M E Jacob
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, College of Veterinary Medicine, Raleigh, North Carolina 27607, USA.
| | - J Bai
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, 1800 Denison Avenue, Manhattan, Kansas 66506, USA
| | - D G Renter
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, 1800 Denison Avenue, Manhattan, Kansas 66506, USA
| | - A T Rogers
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, College of Veterinary Medicine, Raleigh, North Carolina 27607, USA
| | - X Shi
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, 1800 Denison Avenue, Manhattan, Kansas 66506, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, 1800 Denison Avenue, Manhattan, Kansas 66506, USA
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21
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The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows. BMC Vet Res 2012; 8:237. [PMID: 23217205 PMCID: PMC3582618 DOI: 10.1186/1746-6148-8-237] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 11/29/2012] [Indexed: 12/05/2022] Open
Abstract
Background Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with fatty acids during SARA. Four cannulated primiparous (60 to 90 day in milk) Holstein dairy cows were assigned to two diets in a 2 × 2 crossover experimental design. The diets contained (on a dry matter basis): 40% (control diet, COD) and 70% (SARA induction diet, SAID) concentrate feeds. Samples of ruminal fluid and feces were collected on day 12, 15, 17 and 21 of the treatment period, and the pH was measured in the ruminal and fecal samples; the fecal microbiota was determined by pyrosequencing analysis of the V1–V3 region of amplified 16S ribosomal RNA (16S rRNA). Results SAID decreased ruminal and fecal pH and increased the propionate, butyrate and total volatile fatty acid (TVFA) concentration in feces when compared with the COD. A barcoded DNA pyrosequencing method was used to generate 2116 16S operational taxonomic units (OTUs). A total of 11 phyla were observed, distributed amongst all cattle on both diets; however, only 5 phyla were observed in all animals regardless of dietary treatment, and considerable animal to animal variation was revealed. The average abundance and its range of the 5 phyla were as follows: Firmicutes (63.7%, 29.1–84.1%), Proteobacteria (18.3%, 3.4–46.9%), Actinobacteria (6.8%, 0.4–39.9%), Bacteroidetes (7.6%, 2.2–17.7%) and Tenericutes (1.6%, 0.3–3%). Feeding the SAID resulted in significant shifts in the structure of the fecal microbial community when compared with the traditional COD. Among the 2116 OTUs detected in the present study, 88 OTUs were affected significantly by diet; and the proportion of these OTUs was 20.6% and 17.4% among the total number of sequences, respectively. Among the OTUs affected, the predominant species, including OTU2140 (G: Turicibacter), OTU1695 (G: Stenotrophomonas) and OTU8143 (F: Lachnospiraceae), were increased, while the abundance of OTU1266 (S: Solibacillus silvestris) and OTU2022 (G: Lysinibacillus) was reduced in the SAID group compared with the COD. Further, our results indicated that the fecal volatile fatty acid (VFA) concentrations were significantly related to presence of some certain species of Bacteroidetes and Firmicutes in the feces. Conclusions This is, to our knowledge, the first study that has used barcoded DNA pyrosequencing to survey the fecal microbiome of dairy cattle during SARA. Our results suggest that particular bacteria and their metabolites in the feces appear to contribute to differences in host health between those given SAID and traditional COD feeding. A better understanding of these microbial populations will allow for improved nutrient management and increased animal growth performance.
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22
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Microbiological Surveillance of a Bovine Raw Milk Farm Through Multiplex Real-Time PCR. Foodborne Pathog Dis 2012; 9:406-11. [DOI: 10.1089/fpd.2011.1041] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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