scholarly journals Viability and stability ofEscherichiacoliand enterococci populations in fecal samples upon freezing

2015 ◽  
Vol 61 (7) ◽  
pp. 495-501 ◽  
Author(s):  
N. Masters ◽  
M. Christie ◽  
H. Stratton ◽  
M. Katouli
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Host Species ◽  
Bacterial Species ◽  
Short Term ◽  
Fecal Samples ◽  
E Coli ◽  
Short Term Storage ◽  
Before And After ◽  
Term Storage

We studied the survival of Escherichia coli and enterococci populations in fecal samples of 7 host species after storage at –20 and –80 °C for 30 days. Composite fecal samples were collected from cows, chickens, horses, pigs, dogs, birds, and humans, and bacteria were enumerated before and after storage. Twenty-eight colonies of each bacterial species were typed before and after storage and the strains were assigned to different biochemical phenotypes (BPTs). A significant reduction in the number of E. coli was observed in all samples stored at –20 °C but in only 3 of those samples stored at –80 °C. However, the numbers of enterococci were similar in most stored samples (except cow and birds). The number and the distribution of E. coli and enterococci BPTs in fresh samples did not vary significantly from those stored at either temperature. Furthermore, the population structure of E. coli and enterococci did not change significantly after storage at –80 °C, this was always the case for those samples stored at –20 °C. We conclude that for those studies investigating E. coli or enterococci population structure, short-term storage (≤30 days) of fecal samples in a glycerol broth at –80 °C is a preferable option.

scholarly journals Genomic epidemiology and evolution of Escherichia coli in wild animals

2020 ◽  
Author(s):  
Robert Murphy ◽  
Martin Palm ◽  
Ville Mustonen ◽  
Jonas Warringer ◽  
Anne Farewell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Host Species ◽  
Bacterial Species ◽  
Clinical Importance ◽  
Wild Animal ◽  
Whole Genome ◽  
Wild Animals ◽  
E Coli ◽  
Wild Hosts

AbstractEscherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenic and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in non-human hosts and E. coli in humans is still scarce. In this study, we analysed the whole genome sequencing data of a collection of 119 commensal E. coli recovered from the guts of 68 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli colonizing wild animals and the phylogeny, taxonomy and ecological and physiological attributes of the host species, with distantly related E. coli often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic for Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harboured the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli in wild animal hosts often harboured known antibiotic resistance determinants, including against ciprofloxacin, aminoglycosides, tetracyclines and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that although the genome pools of E. coli colonizing wild animal and human gut are well separated, they share virulence and antibiotic resistance genes and E. coli underscoring that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections.ImportanceEscherichia coli is a clinically importance bacterial species implicated in human and livestock associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock and wild animals. Although wild animals are recognized to serve as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study we used the fine resolution of whole genome sequencing to provide novel insights into the evolution of E. coli genomes within a broad range of wild animal species (including mammals and birds), the co-evolution of E. coli strains with their hosts and the genetics of pathogenicity of E. coli strains in wild hosts. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and necessitate the inclusion of non-human hosts in the surveillance programs for E. coli infections.

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 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 Longitudinal Study of Antimicrobial Resistance among Escherichia coli Isolates from Integrated Multisite Cohorts of Humans and Swine

2008 ◽  
Vol 74 (12) ◽  
pp. 3672-3681 ◽  
Author(s):  
W. Q. Alali ◽  
H. M. Scott ◽  
R. B. Harvey ◽  
B. Norby ◽  
D. B. Lawhorn ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Longitudinal Study ◽  
Host Species ◽  
Food System ◽  
Temporal Trends ◽  
Multidrug Resistant ◽  
Fecal Samples ◽  
E Coli ◽  
Production Type ◽  
Swine Workers

ABSTRACT In a 3-year longitudinal study, we examined the relationship between the seasonal prevalence of antimicrobial-resistant (AR) Escherichia coli isolates from human wastewater and swine fecal samples and the following risk factors: the host species, the production type (swine), the vocation (human swine workers, non-swine workers, and slaughter plant workers), and the season, in a multisite, vertically integrated swine and human population representative of a closed agri-food system. Human and swine E. coli (n = 4,048 and 3,429, respectively) isolates from wastewater and fecal samples were tested for antimicrobial susceptibility, using the Sensititre broth microdilution system. There were significant (P < 0.05) differences among AR E. coli prevalence levels of (i) the host species, in which swine isolates were at higher risk for resistance to tetracycline, kanamycin, ceftiofur, gentamicin, streptomycin, chloramphenicol, sulfisoxazole, and ampicillin; (ii) the swine production group, in which purchased boars, nursery piglets, and breeding boars isolates had a higher risk of resistance to streptomycin and tetracycline; and iii) the vocation cohorts, in which swine worker cohort isolates exhibited lower sulfisoxazole and cefoxitin prevalence than the non-swine worker cohorts, while the slaughter plant worker cohort isolates exhibited elevated cefoxitin prevalence compared to that of non-swine workers. While a high variability was observed among seasonal samples over the 3-year period, no significant temporal trends were apparent. There were significant differences in the prevalence levels of multidrug-resistant isolates between host species, with swine at a higher risk of carrying multidrug-resistant strains than humans. Considering vocation, slaughter plant workers were at higher risk of exhibiting multidrug-resistant E. coli than non-swine workers.

Determining the Prevalence of Escherichia coli O157 in Cattle and Beef from the Feedlot to the Cooler

2006 ◽  
Vol 69 (12) ◽  
pp. 2824-2827 ◽  
Author(s):  
D. R. WOERNER ◽  
J. R. RANSOM ◽  
J. N. SOFOS ◽  
G. A. DEWELL ◽  
G. C. SMITH ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Risk Assessment ◽  
Fecal Sample ◽  
Mitigation Strategies ◽  
Escherichia Coli O157 ◽  
Fecal Samples ◽  
E Coli ◽  
Beef Carcasses ◽  
Before And After ◽  
Pathogen Prevalence

Prevalence of Escherichia coli O157 on cattle entering the slaughter floor may range from 10 to &gt;70%. This study was conducted to determine the effect of E. coli O157 prevalence in fecal pats collected from feedlot pen floors on subsequent E. coli O157 prevalence on carcasses at various points in the slaughter process. Fecal pats from the feedlot pen floor were collected within 3 days before slaughter. During cattle processing at the slaughter facility, additional samples were collected from the hide, from the colon, and from the carcasses before and after evisceration and after final decontamination. Of 15 lots (a group of cattle from the same pen from a feedlot) sampled, 87% had at least one positive fecal pat from the feedlot floor, 47% had a positive hide sample, 73% had a positive colon/fecal sample, and 47% had a positive carcass sample preevisceration; however, only 8% of lots had a positive carcass sample postevisceration or after final intervention. Of the total samples tested (n = 1,328), 24.7, 14.7, 27.6, 10.1, 1.4, and 0.3% of fecal pats from the feedlot floor, hide, colon, preevisceration, post-evisceration, and final intervention samples, respectively, were positive for E. coli O157. Pens with greater than 20% positive fecal pats from the feedlot floor had 25.5% hide, 51.4% colon, and 14.3, 2.9, and 0.7% carcass samples positive at preevisceration, at postevisceration, and after final intervention, respectively. However, fecal pats from feedlot floor samples that contained less than 20% positive fecal samples showed lower pathogen prevalence, with 5.0% hide, 7.5% colon, and 6.3, 0, and 0% carcass positive samples at preevisceration, postevisceration, and post–final intervention, respectively. Data from this study can be used as part of risk assessment processes in order to identify mitigation strategies to minimize prevalence of E. coli O157 on fresh beef carcasses.

Combinations of Intervention Treatments Resulting in 5-Log10-Unit Reductions in Numbers of Escherichia coli O157:H7 and Salmonella typhimurium DT104 Organisms in Apple Cider

1999 ◽  
Vol 65 (5) ◽  
pp. 1924-1929 ◽  
Author(s):  
Heidi E. Uljas ◽  
Steven C. Ingham
Keyword(s):  
Escherichia Coli ◽  
Organic Acids ◽  
Salmonella Typhimurium ◽  
Escherichia Coli O157 ◽  
Short Term ◽  
Apple Cider ◽  
E Coli ◽  
Unit Reduction ◽  
Pathogen Populations ◽  
Term Storage

ABSTRACT The U.S. Food and Drug Administration (FDA) recently mandated a warning statement on packaged fruit juices not treated to reduce target pathogen populations by 5 log10 units. This study describes combinations of intervention treatments that reduced concentrations of mixtures of Escherichia coli O157:H7 (strains ATCC 43895, C7927, and USDA-FSIS-380-94) or Salmonella typhimuriumDT104 (DT104b, U302, and DT104) by 5 log10 units in apple cider with a pH of 3.3, 3.7, and 4.1. Treatments used were short-term storage at 4, 25, or 35°C and/or freeze-thawing (48 h at −20°C; 4 h at 4°C) of cider with or without added organic acids (0.1% lactic acid, sorbic acid [SA], or propionic acid). Treatments more severe than those for S. typhimurium DT104 were always required to destroy E. coli O157:H7. In pH 3.3 apple cider, a 5-log10-unit reduction in E. coli O157:H7 cell numbers was achieved by freeze-thawing or 6-h 35°C treatments. In pH 3.7 cider the 5-log10-unit reduction followed freeze-thawing combined with either 6 h at 4°C, 2 h at 25°C, or 1 h at 35°C or 6 h at 35°C alone. A 5-log10-unit reduction occurred in pH 4.1 cider after the following treatments: 6 h at 35°C plus freeze-thawing, SA plus 12 h at 25°C plus freeze-thawing, SA plus 6 h at 35°C, and SA plus 4 h at 35°C plus freeze-thawing. Yeast and mold counts did not increase significantly (P < 0.05) during the 6-h storage at 35°C. Cider with no added organic acids treated with either 6 h at 35°C, freeze-thawing or their combination was always preferred by consumers over pasteurized cider (P < 0.05). The simple, inexpensive intervention treatments described in the present work could produce safe apple cider without pasteurization and would not require the FDA-mandated warning statement.

scholarly journals Impermanence of bacterial clones

2015 ◽  
Vol 112 (29) ◽  
pp. 8893-8900 ◽  
Author(s):  
Louis-Marie Bobay ◽  
Charles C. Traverse ◽  
Howard Ochman
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Homologous Recombination ◽  
Bacterial Species ◽  
Reproductive Mode ◽  
Unique Sequence ◽  
Gene Exchange ◽  
E Coli ◽  
Large Samples ◽  
Single Genome

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied inEscherichia colifor over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on theE. coligenome.

scholarly journals Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Robert Murphy ◽  
Martin Palm ◽  
Ville Mustonen ◽  
Jonas Warringer ◽  
Anne Farewell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Host Species ◽  
Bacterial Species ◽  
Clinical Importance ◽  
Wild Animal ◽  
Whole Genome ◽  
Wild Animals ◽  
Content Type ◽  
E Coli ◽  
Wild Hosts

ABSTRACT Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCE Escherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.

scholarly journals Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

2020 ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Gaëtan Thilliez ◽  
Nicholas Thomson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Host Species ◽  
The Gambia ◽  
Genomic Diversity ◽  
Whole Genome ◽  
E Coli ◽  
Sequence Types

AbstractIncreasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity, and antimicrobial resistance in Escherichia coli isolates from four species of non-human primate in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on eleven isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2—characterised by strains that cause human extraintestinal infections—and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and seven alleles respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes—indicating novel diversity specific to the primate niche. Our results are of public health importance, considering the increasing contact between humans and wild non-human primates.Impact statementLittle is known about the population structure, virulence potential and the burden of antimicrobial resistance among Escherichia coli from wild non-human primates, despite increased exposure to humans through the fragmentation of natural habitats. Previous studies, primarily involving captive animals, have highlighted the potential for bacterial exchange between non-human primates and humans living nearby, including strains associated with intestinal pathology. Using multiple-colony sampling and whole-genome sequencing, we investigated the strain distribution and population structure of E. coli from wild non-human primates from the Gambia. Our results indicate that these monkeys harbour strains that can cause extraintestinal infections in humans. We document the transmission of virulent E. coli strains between monkeys of the same species sharing a common habitat and evidence of recent interaction between strains from humans and wild non-human primates. Also, we present complete genome assemblies for five novel sequence types of E. coli.Author notesAll supporting data, code and protocols have been provided within the article or through supplementary data files. Nine supplementary figures and six supplementary files are available with the online version of this article.AbbreviationsExPEC, Extraintestinal pathogenic Escherichia coli; ST, Sequence type; AMR, Antimicrobial resistance; MLST, Multi-locus sequence typing; VFDB, Virulence factors database; SNP, single nucleotide polymorphism; SPRI, Solid phase reversible immobilisation.Data summaryThe raw sequences and polished assemblies from this study are available in the National Center for Biotechnology Information (NCBI) Short Read Archive, under the BioProject accession number PRJNA604701. The full list and characteristics of these strains and other reference strains used in the analyses are presented in Table 1 and Supplementary Files 1-4 (available with the online version of this article).

Sign in / Sign up

Export Citation Format

Share Document