Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces†

2016 ◽  
Vol 79 (1) ◽  
pp. 66-74 ◽  
Author(s):  
P. B. SHRIDHAR ◽  
L. W. NOLL ◽  
X. SHI ◽  
B. AN ◽  
N. CERNICCHIARO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Quantitative Pcr ◽  
Foodborne Pathogens ◽  
Virulence Genes ◽  
Target Genes ◽  
Culture Methods ◽  
Fecal Samples ◽  
E Coli ◽  
Cattle Feces ◽  
Before And After

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.

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

A Comparison of the Survival in Feces and Water of Escherichia coli O157:H7 Grown under Laboratory Conditions or Obtained from Cattle Feces

2006 ◽  
Vol 69 (1) ◽  
pp. 6-11 ◽  
Author(s):  
L. SCOTT ◽  
P. McGEE ◽  
J. J. SHERIDAN ◽  
B. EARLEY ◽  
N. LEONARD
Keyword(s):  
Escherichia Coli ◽  
Foodborne Pathogen ◽  
Hemorrhagic Colitis ◽  
Contaminated Water ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Cattle Feces ◽  
Oral Inoculation ◽  
Before And After ◽  
Uremic Syndrome

Escherichia coli O157:H7 is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic uremic syndrome. Cattle feces and fecally contaminated water are important in the transmission of this organism on the farm. In this study, the survival of E. coli O157:H7 in feces and water was compared following passage through the animal digestive tract or preparation in the laboratory. Feces were collected from steers before and after oral inoculation with a marked strain of E. coli O157:H7. Fecal samples collected before cattle inoculation were subsequently inoculated with the marked strain of E. coli O157:H7 prepared in the laboratory. Subsamples were taken from both animal and laboratory-inoculated feces to inoculate 5-liter volumes of water. E. coli O157:H7 in feces survived up to 97 days, and survival was not affected by the method used to prepare the inoculating strain. E. coli O157:H7 survived up to 109 days in water, and the bacteria collected from inoculated cattle were detected up to 10 weeks longer than the laboratory-prepared culture. This study suggests that pathogen survival in low-nutrient conditions may be enhanced by passage through the gastrointestinal tract.

Comparing Real-Time and Conventional PCR to Culture-Based Methods for Detecting and Quantifying Escherichia coli O157 in Cattle Feces

2014 ◽  
Vol 77 (2) ◽  
pp. 314-319 ◽  
Author(s):  
M. E. JACOB ◽  
J. BAI ◽  
D. G. RENTER ◽  
A. T. ROGERS ◽  
X. SHI ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Positive Culture ◽  
Feedlot Cattle ◽  
Escherichia Coli O157 ◽  
Conventional Pcr ◽  
Culture Methods ◽  
E Coli ◽  
Cattle Feces ◽  
Culture Negative

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 (≥104 CFU/g of feces) and low (~102 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.

scholarly journals Antimicrobial Resistance of Escherichia coli and Salmonella isolated from Raw Retail Broiler Chicken Carcasses in Zambia

2020 ◽  
Author(s):  
Elizabeth Muligisa Muonga ◽  
Geoffrey Mainda ◽  
Mercy Mukuma ◽  
Geoffrey Kwenda ◽  
Bernard Hang'ombe ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Foodborne Pathogens ◽  
Broiler Chicken ◽  
Target Genes ◽  
Health Concern ◽  
Public Health Concern ◽  
E Coli ◽  
Genes Encoding

Abstract BackgroundAntimicrobial resistance (AMR) of foodborne pathogens is of public health concern, especially in developing countries such as Zambia. This study was undertaken to determine the antimicrobial resistance profiles of Escherichia coli ( E. coli ) and Salmonella isolated from raw retail broiler chicken carcasses purchased from open and supermarkets in Zambia.ResultsA total of 189 E. coli and five Salmonella isolates were isolated. Identification and confirmation of the isolates were done using Analytical Profile Index (API 20E) (Biomerieux ® ) and 16S rRNA sequencing. Antimicrobial susceptibility tests (AST) were performed using the Kirby Bauer disk diffusion technique using a panel of 10 antibiotics. Multiplex PCR was used to determine the presence of three target genes encoding for resistance: tet A, Sul 1 and bla CTX-M . WHONET 2018 software was used to analyse AST results. The E. coli isolates were mostly resistant to tetracycline (79.4%), ampicillin (51.9%), and trimethoprim/sulfamethoxazole (49.7%). Two of the five Salmonella isolates were resistant to at least one antibiotic. Forty- seven (45.2%) of the 104 isolates that were screened for the presence of the resistant genes possessed at least one of the targeted resistance genes.ConclusionThis study has demonstrated the presence of AMR E. coli and Salmonella on raw retail broiler chicken carcasses from open and supermarkets, which is of public health concern.

Risk of Escherichia coli O157:H7, Non-O157 Shiga Toxin–Producing Escherichia coli, and Campylobacter spp. in Food Animals and Their Products in Qatar

2015 ◽  
Vol 78 (10) ◽  
pp. 1812-1818 ◽  
Author(s):  
HUSSNI O. MOHAMMED ◽  
KORANA STIPETIC ◽  
AHMED SALEM ◽  
PATRICK McDONOUGH ◽  
YUNG FU CHANG ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Cross Sectional Study ◽  
Campylobacter Coli ◽  
Escherichia Coli O157 ◽  
Cross Sectional ◽  
Fecal Samples ◽  
E Coli ◽  
Cattle Feces ◽  
Campylobacter Spp

Escherichia coli O157:H7, non-O157 E. coli, and Campylobacter spp. are among the top-ranked pathogens that threaten the safety of food supply systems around the world. The associated risks and predisposing factors were investigated in a dynamic animal population using a repeat-cross-sectional study design. Animal and environmental samples were collected from dairy and camel farms, chicken processing plants, and abattoirs and analyzed for the presence of these pathogens using a combination of bacterial enrichment and real-time PCR tests without culture confirmation. Data on putative risk factors were also collected and analyzed. E. coli O157:H7 was detected by PCR at higher levels in sheep and camel feces than in cattle feces (odds ratios [OR], 6.8 and 21.1, respectively). Although the genes indicating E. coli O157:H7 were detected at a relatively higher rate (4.3%) in fecal samples from dairy cattle, they were less common in milk and udder swabs from the same animals (1 and 2%, respectively). Among the food adulterants, E. coli O103 was more common in cattle fecal samples, whereas O26 was more common in sheep feces and O45 in camel feces compared with cattle (OR, 2.6 and 3.1, respectively). The occurrence of E. coli in the targeted populations differed by the type of sample and season of the year. Campylobacter jejuni and Campylobacter coli were more common in sheep and camel feces than in cattle feces. Most of the survey and surveillance of E. coli focused on serogroup O157 as a potential foodborne hazard; however, based on the PCR results, non-O157 Shiga toxin–producing E. coli serotypes appeared to be more common, and efforts should be made to include them in food safety programs.

scholarly journals Longitudinal Emergence and Distribution of Escherichia coli O157 Genotypes in a Beef Feedlot

2006 ◽  
Vol 72 (12) ◽  
pp. 7614-7619 ◽  
Author(s):  
Michael W. Sanderson ◽  
Jan M. Sargeant ◽  
Xiarong Shi ◽  
T. G. Nagaraja ◽  
Ludek Zurek ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Feedlot Cattle ◽  
Longitudinal Distribution ◽  
Single Strain ◽  
Fecal Samples ◽  
E Coli ◽  
Before And After ◽  
Water Tanks ◽  
Feed Samples ◽  
Bird Feces

ABSTRACT The purpose of this study was to describe the prevalence and longitudinal distribution of Escherichia coli O157 in feedlot cattle and the feedlot environment. Pen floors, water tanks, other cattle in the feedlot, feed, and bird feces were sampled for 2 weeks prior to entry of the study cattle. Twelve pens of study cattle were sampled twice weekly. At each sample time cattle feces, water from tanks in each pen, bunk feed, feed components, bird feces, and houseflies were collected. Bunk feed samples were collected before and after cattle had access to the feed. Overall, 28% of cattle fecal samples, 3.9% of bird fecal samples, 25% of water samples, 3.4% of housefly samples, 1.25% of bunk feed before calf access, and 3.25% of bunk feed samples after cattle had access to the feed were positive for E. coli O157. Genetic analysis of E. coli O157 isolates was done using pulsed-field gel electrophoresis (PFGE). PFGE types identified in sampling of the feedlot prior to calf entry were different than the majority of types identified following calf entry. A single strain type predominated in the samples collected after entry of the cattle. It was first identified 5 days after entry of the first pen of cattle and was subsequently identified in all pens. Data support that the incoming cattle introduced a new strain that became the predominant strain in the feedlot.

scholarly journals Diversity, Frequency, and Persistence of Escherichia coli O157 Strains from Range Cattle Environments

2003 ◽  
Vol 69 (1) ◽  
pp. 542-547 ◽  
Author(s):  
David G. Renter ◽  
Jan M. Sargeant ◽  
Richard D. Oberst ◽  
Mansour Samadpour
Keyword(s):  
Escherichia Coli ◽  
Water Source ◽  
Water Sources ◽  
Latex Agglutination ◽  
Positive Sample ◽  
Fecal Samples ◽  
E Coli ◽  
Cattle Feces ◽  
Production Environments ◽  
Shiga Toxin Genes

ABSTRACT Genetic diversity, isolation frequency, and persistence were determined for Escherichia coli O157 strains from range cattle production environments. Over the 11-month study, analysis of 9,122 cattle fecal samples, 4,083 water source samples, and 521 wildlife fecal samples resulted in 263 isolates from 107 samples presumptively considered E. coli O157 as determined by culture and latex agglutination. Most isolates (90.1%) were confirmed to be E. coli O157 by PCR detection of intimin and Shiga toxin genes. Pulsed-field gel electrophoresis (PFGE) of XbaI-digested preparations revealed 79 unique patterns (XbaI-PFGE subtypes) from 235 typeable isolates confirmed to be E. coli O157. By analyzing up to three isolates per positive sample, we detected an average of 1.80 XbaI-PFGE subtypes per sample. Most XbaI-PFGE subtypes (54 subtypes) were identified only once, yet the seven most frequently isolated subtypes represented over one-half of the E. coli O157 isolates (124 of 235 isolates). Recurring XbaI-PFGE subtypes were recovered from samples on up to 10 sampling occasions and up to 10 months apart. Seven XbaI-PFGE subtypes were isolated from both cattle feces and water sources, and one of these also was isolated from the feces of a wild opossum (Didelphis sp.). The number of XbaI-PFGE subtypes, the variable frequency and persistence of subtypes, and the presence of identical subtypes in cattle feces, free-flowing water sources, and wildlife feces indicate that the complex molecular epidemiology of E. coli O157 previously described for confined cattle operations is also evident in extensively managed range cattle environments.

scholarly journals Chromogenic Agar Medium for Detection and Isolation of Escherichia coli Serogroups O26, O45, O103, O111, O121, and O145 from Fresh Beef and Cattle Feces†

2013 ◽  
Vol 76 (2) ◽  
pp. 192-199 ◽  
Author(s):  
NORASAK KALCHAYANAND ◽  
TERRANCE M. ARTHUR ◽  
JOSEPH M. BOSILEVAC ◽  
JAMES E. WELLS ◽  
TOMMY L. WHEELER
Keyword(s):  
Escherichia Coli ◽  
Foodborne Pathogens ◽  
Agar Medium ◽  
Immunomagnetic Separation ◽  
Feedlot Cattle ◽  
E Coli ◽  
Cattle Feces ◽  
Selective Agents ◽  
Chromogenic Agar ◽  
Single Agar

Non-O157 Shiga toxin–producing Escherichia coli (STEC) strains are clinically important foodborne pathogens. Unlike E. coli O157:H7, these foodborne pathogens have no unique biochemical characteristics to readily distinguish them from other E. coli strains growing on plating media. In this study, a chromogenic agar medium was developed in order to differentiate among non-O157 STEC strains of serogroups O26, O45, O103, O111, O121, and O145 on a single agar medium. The ability of this chromogenic agar medium to select and distinguish among these pathogens is based on a combination of utilization of carbohydrates, β-galactosidase activity, and resistance to selective agents. The agar medium in combination with immunomagnetic separation was evaluated and successfully allowed for the detection and isolation of these six serogroups from artificially contaminated fresh beef. The agar medium in combination with immunomagnetic separation also allowed successful detection and isolation of naturally occurring non-O157 STEC strains present in cattle feces. Thirty-five strains of the top six non-O157 STEC serogroups were isolated from 1,897 fecal samples collected from 271 feedlot cattle. This chromogenic agar medium could help significantly in routine screening for the top six non-O157 STEC serogroups from beef cattle and other food.

Development of Methods for the Recovery of Escherichia coli O157:H7 and Salmonella from Beef Carcass Sponge Samples and Bovine Fecal and Hide Samples†

2002 ◽  
Vol 65 (10) ◽  
pp. 1527-1534 ◽  
Author(s):  
GENEVIEVE A. BARKOCY-GALLAGHER ◽  
ELAINE D. BERRY ◽  
MILDRED RIVERA-BETANCOURT ◽  
TERRANCE M. ARTHUR ◽  
XIANGWU NOU ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Immunomagnetic Separation ◽  
Research Unit ◽  
Optimal Recovery ◽  
Escherichia Coli O157 ◽  
Culture Methods ◽  
Potassium Tellurite ◽  
Fecal Samples ◽  
E Coli ◽  
Pure Cultures

Culture methods were developed for the concurrent recovery of Escherichia coli O157:H7 and Salmonella from bovine carcass, hide, and fecal samples. Several enrichment conditions were tested for the overall growth of pure cultures; tryptic soy broth for 2 h at 25°C and then for 6 h at 42°C was the protocol selected for use. Immunomagnetic separation (IMS) was incorporated for sensitivity and selectivity, along with a post-IMS enrichment for the recovery of Salmonella as recommended by the manufacturer. Selective agars for plating after IMS were chosen on the basis of ease of target colony identification. Sorbitol MacConkey agar supplemented with cefixime and potassium tellurite and Rainbow agar supplemented with novobiocin and potassium tellurite were chosen for the recovery of E. coli O157:H7. Brilliant green agar with sulfadiazine and Hektoen enteric agar supplemented with novobiocin were selected for the recovery of Salmonella. The resulting methods were evaluated along with standard or previously used methods for the recovery of E. coli O157:H7 and Salmonella from bovine hide and fecal samples and carcass sponge samples. The Meats Research Unit (MRU) methods performed at least as well as the established methods, except that a secondary enrichment in tetrathionate (TT) broth prior to IMS was required for the optimal recovery of Salmonella from feces. Thus, the MRU and MRU-TT methods are effective in the recovery of both E. coli O157: H7 and Salmonella from a single bovine carcass, hide, or fecal sample.

Limitations of Immunomagnetic Separation for Detection of the Top Seven Serogroups of Shiga Toxin–Producing Escherichia coli

2017 ◽  
Vol 80 (4) ◽  
pp. 598-603 ◽  
Author(s):  
J. Hallewell ◽  
T. Alexander ◽  
T. Reuter ◽  
K. Stanford
Keyword(s):  
Escherichia Coli ◽  
Quantitative Pcr ◽  
Foodborne Pathogens ◽  
Shiga Toxin ◽  
Immunomagnetic Separation ◽  
Detection Methods ◽  
Conventional Pcr ◽  
E Coli ◽  
Pure Cultures

ABSTRACT Shiga toxin–producing Escherichia coli (STEC) strains are foodborne pathogens that negatively impact human health and compromise food safety. Serogroup O157 is the most frequently isolated and studied STEC serogroup, but six others (O26, O45, O103, O111, O121, and O145) have also been identified as significant sources of human disease and collectively have been referred to as the “top six” pathogenic serogroups. Because detection methods for non-O157 serogroups are not yet refined, the objective of this study was to compare the effectiveness of immunomagnetic separation (IMS) for recovery of serogroup O157 isolates with that for each of the top six E. coli serogroups in pure and mixed cultures of STEC at 103 to 107 CFU/mL. After serogroup-specific IMS, DNA was extracted from cultured isolates to analyze the specificity of each IMS assay using conventional and quantitative PCR. In pure cultures, DNA copy number obtained after IMS was lower for O111 and O157 (P < 0.01) than for other serogroups. Based on quantitative PCR (qPCR) analyses, specificity was reduced for all IMS assays when STEC isolates were mixed at 7 log CFU/mL, although the O157 IMS assays recovered only O157 over a wider range of concentrations than did assays for non-O157 serogroups. At the lowest dilution tested, conventional PCR was specific for all serogroups except O121 and O145. For these two serogroups, no dilution tested recovered only O121 or O145 when evaluated with conventional PCR. Refinements to IMS assays, development of selective media, and determination of optimal enrichment times to reduce background microflora or competition among serogroups would be especially beneficial for recovery of O111, O121, and O145 serogroups to improve STEC detection and isolation.

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