Virulence Factors, Antimicrobial Resistance Genes and Protein Structure of Crohn's Disease-Derived E.Coli Strains Identified Using DNA Microarray and MALDI-TOF Analysis

ABSTRACT Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.

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A DNA microarray for identification of virulence and antimicrobial resistance genes in Salmonella serovars and Escherichia coli

Molecular and Cellular Probes ◽

10.1016/j.mcp.2004.11.008 ◽

2005 ◽

Vol 19 (3) ◽

pp. 195-201 ◽

Cited By ~ 55

Author(s):

Sheng Chen ◽

Shaohua Zhao ◽

Patrick F. McDermott ◽

Carl M. Schroeder ◽

David G. White ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Dna Microarray ◽

Resistance Genes ◽

Antimicrobial Resistance Genes ◽

Salmonella Serovars

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PathoFact: A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

10.1101/2020.03.24.006148 ◽

2020 ◽

Author(s):

Laura de Nies ◽

Sara Lopes ◽

Anna Heintz-Buschart ◽

Cedric Christian Laczny ◽

Patrick May ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Bacterial Toxins ◽

Metagenomic Data ◽

Genomic Context ◽

Pathogenic Potential ◽

Signature Genes ◽

Antimicrobial Resistance Genes ◽

Versatile Tool

AbstractBackgroundPathogenic microorganisms cause disease by invading, colonizing and damaging their host. Virulence factors including bacterial toxins contribute to their pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is therefore essential to identify virulence factors and antimicrobial resistance genes in metagenomic datasets. At present, there is a clear lack of computational approaches to simultaneously identifying these factors. Here we present PathoFact, a tool for the contextualized prediction of virulence factors and antimicrobial resistance genes in metagenomic data.ResultsPathoFact predicts virulence factors, bacterial toxins and antimicrobial resistance genes with high accuracy (0.92, 0.83 and 0.99) and specificity (0.96, 0.99 and 0.98), respectively. The performance of PathoFact was furthermore demonstrated on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins were predicted to play a role. With PathoFact, we identified virulence factors (including toxins) and antimicrobial resistance genes, and identified signature genes which differentiated between the disease and control groups.ConclusionPathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, toxins and antimicrobial resistance genes in metagenomic data. Additionally, PathoFact combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, each module (virulence factors, toxin and antimicrobial resistance genes) of PathoFact is also a standalone component, making it a flexible and versatile tool. PathoFact is freely available online at https://git-r3lab.uni.lu/laura.denies/PathoFact.

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Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.684400 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mohammed Elbediwi ◽

Yanting Tang ◽

Dawei Shi ◽

Hazem Ramadan ◽

Yaohui Xu ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Chick Embryo ◽

Virulence Factors ◽

Resistance Genes ◽

Salmonella Enterica ◽

Multidrug Resistant ◽

Henan Province ◽

Health Concern ◽

Antimicrobial Resistance Genes ◽

Genomic Characterization

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r < 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r > −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

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