Dataset Information

Frequency of Diarrheagenic Virulence Genes and Characteristics in Escherichia coli Isolates from Pigs with Diarrhea in China.

ABSTRACT: Intestinal pathogenic Escherichia coli (InPEC) is a leading cause of postweaning diarrhea (PWD) in pigs. Here, a total of 455 E. coli strains were isolated from small intestinal content or feces from pigs with PWD in 56 large-scale (>500 sows; 10,000 animals per year) swine farms between 2014 and 2016. The frequency of occurrence of selected virulence factors for InPEC pathotypes was detected in 455 isolates by real-time PCR. Sequence types (STs), pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility profiles of 171 E. coli isolates from 56 swine farms were further determined. The heat-labile enterotoxin (LT) was the most common (61.76%), followed by heat-stable enterotoxin (STb) (33.19%), stx2e (21.54%), STa (15.00%), eae (8.98%), cnf2 (5.71%), stx2 (5.71%), F18 (3.25%), and F4 (2.25%) with rates varying by geographic area and year of isolation. Notably, hybrids of E. coli isolates were potentially more virulent, as some InPEC hybrids (virotype F18:LT:eae:stx2e) can rapidly cause cell death in vitro. Genotypic analysis revealed that the most prominent genotype was ST10 (12.87%). The PFGE patterns were heterogeneous but were not ST or virotype related. A total of 94.15% of isolates were multidrug-resistant, with average resistance rates ranging from 90.05% for nalidixic acid to 2.34% for meropenem. Our investigation contributes to establishing the etiology of diarrhea and developing intervention strategies against E. coli-associated diarrheal disease in the future.

SUBMITTER: Yang GY

PROVIDER: S-EPMC6780709 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Frequency of Diarrheagenic Virulence Genes and Characteristics in Escherichia coli Isolates from Pigs with Diarrhea in China.

Yang Gui-Yan GY Guo Liang L Su Jin-Hui JH Zhu Yao-Hong YH Jiao Lian-Guo LG Wang Jiu-Feng JF

Microorganisms 20190902 9

Intestinal pathogenic Escherichia coli (InPEC) is a leading cause of postweaning diarrhea (PWD) in pigs. Here, a total of 455 E. coli strains were isolated from small intestinal content or feces from pigs with PWD in 56 large-scale (>500 sows; 10,000 animals per year) swine farms between 2014 and 2016. The frequency of occurrence of selected virulence factors for InPEC pathotypes was detected in 455 isolates by real-time PCR. Sequence types (STs), pulsed-field gel electrophoresis ( ...[more]

PMID: 31480723

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Project description:Diarrhea is the leading infectious cause of childhood morbidity and mortality. Among bacterial agents, diarrheagenic Escherichia coli (DEC) is the major causal agent of childhood diarrhea in developing countries, particularly in children under the age of 5 years. Here, we performed a hospital-based prospective study to explore the pathotype distribution, epidemiological characteristics and antibiotic resistance patterns of DEC from <?5-year-old diarrheal children.Between August 2015 and September 2016, 684 stool samples were collected from children (<?5 years old) with acute diarrhea. All samples were cultured and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and biochemical tests. PCR was used for subtyping, and enteropathogenic E. coli (EPEC) isolates were identified simultaneously with serology. Furthermore, antimicrobial sensitivity tests and sequencing of antibiotic resistance-related genes were conducted.DEC strains were identified in 7.9% of the 684 stool samples. Among them, the most commonly detected pathotype was EPEC (50.0% of DEC), of which 77.8% were classified as atypical EPEC (aEPEC). Age and seasonal distribution revealed that DEC tended to infect younger children and to occur in summer/autumn periods. Multidrug-resistant DEC isolates were 66.7%; resistance rates to ampicillin, co-trimoxazole, cefazolin, cefuroxime, cefotaxime, and ciprofloxacin were ??50%. Among 5 carbapenem-resistant DEC, 60.0% were positive for carbapenemase genes (2 blaNDM-1 and 1 blaKPC-2). Among 30 cephalosporin-resistant DEC, 93.3% were positive for extended-spectrum ?-lactamase (ESBL) genes, with blaTEM-1 and blaCTX-M-55 being the most common types. However, no gyrA or gyrB genes were detected in 16 quinolone-resistant isolates. Notably, aEPEC, which has not received much attention before, also exhibited high rates of drug resistance (81.0%, 66.7%, and 14.3% for ampicillin, co-trimoxazole , and carbapenem resistance, respectively).EPEC was the most frequent DEC pathotype in acute diarrheal children, with aEPEC emerging as a dominant diarrheal agent in central China. Most DEC strains were multidrug-resistant, making even ciprofloxacin unsuitable for empiric treatment against DEC infection. Among carbapenem-resistant DEC strains, those harboring blaNDM-1 and blaKPC-2 were the main causal agents. blaTEM-1 and blaCTX-M-55 were the major genetic determinants associated with high levels of cephalosporin resistance.

Project description:This study aimed to characterize in silico enterotoxigenic Escherichia coli F4- and F18-positive isolates (n = 90) causing swine postweaning diarrhea, including pathogenic potential, phylogenetic relationship, antimicrobial and biocide resistance, prophage content, and metal tolerance rates. F4 strains belonged mostly to the O149 and O6 serogroups and ST100 and ST48 sequence types (STs). F18 strains were mainly assigned to the O8 and O147 serogroups and ST10, ST23, and ST42. The highest rates of antimicrobial resistance were found against streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and ampicillin. No resistance was found toward ciprofloxacin, cefotaxime, ceftiofur, and colistin. Genes conferring tolerance to copper (showing the highest diversity), cadmium, silver, and zinc were predicted in all genomes. Enterotoxin genes (ltcA, 100% F4, 62% F18; astA, 100% F4, 38.1% F18; sta, 18.8% F4, 38.1% F18; stb, 100% F4, 76.2% F18) and fimbria-encoding genes typed as F4ac and F18ac were detected in all strains, in addition to up to 16 other virulence genes in individual strains. Phage analysis predicted between 7 and 20 different prophage regions in each strain. A highly diverse variety of plasmids was found; IncFII, IncFIB, and IncFIC were prevalent among F4 isolates, while IncI1 and IncX1 were dominant among F18 strains. Interestingly, F4 isolates from the early 1990s belonged to the same clonal group detected for most of the F4 strains from 2018 to 2019 (ONT:H10-A-ST100-CH27-0). The small number of single-nucleotide polymorphism differences between the oldest and recent F4 ST100 isolates suggests a relatively stable genome. Overall, the isolates analyzed in this study showed remarkably different genetic traits depending on the fimbria type.IMPORTANCE Diarrhea in the postweaning period due to enterotoxigenic E. coli (ETEC) is an economically relevant disease in pig production worldwide. In Denmark, prevention is mainly achieved by zinc oxide administration (to be discontinued by 2022). In addition, a breeding program has been implemented that aims to reduce the prevalence of this illness. Treatment with antimicrobials contributes to the problem of antimicrobial resistance (AMR) development. As a novelty, this study aims to deeply understand the genetic population structure and variation among diarrhea-associated isolates by whole-genome sequencing characterization. ST100-F4ac is the dominant clonal group circulating in Danish herds and showed high similarity to ETEC ST100 isolates from China, the United States, and Spain. High rates of AMR and high diversity of virulence genes were detected. The characterization of diarrhea-related ETEC is important for understanding the disease epidemiology and pathogenesis and for implementation of new strategies aiming to reduce the impact of the disease in pig production.

Dataset Information

Frequency of Diarrheagenic Virulence Genes and Characteristics in Escherichia coli Isolates from Pigs with Diarrhea in China.

Publications

Frequency of Diarrheagenic Virulence Genes and Characteristics in <i>Escherichia coli</i> Isolates from Pigs with Diarrhea in China.

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