The challenges in the identification of Escherichia coli from environmental samples and their genetic characterization

Escherichia coli bacteria are an essential indicator in evaluations of environmental pollution, which is why they must be correctly identified. This study aimed to determine the applicability of various methods for identifying E. coli strains in environmental samples. Bacterial strains preliminary selected on mFc and Chromocult media as E. coli were identified using MALDI Biotyper techniques, based on the presence of genes characteristic of E. coli (uidA, uspA, yaiO), as well as by 16S rRNA gene sequencing. The virulence and antibiotic resistance genes pattern of bacterial strains were also analyzed to investigate the prevalence of factors that may indicate adaptation to unsupportive environmental conditions and could have any significance in further identification of E. coli. Of the strains that had been initially identified as E. coli with culture-based methods, 36-81% were classified as E. coli with the use of selected techniques. The value of Cohen's kappa revealed the highest degree of agreement between the results of 16S rRNA gene sequencing, the results obtained in the MALDI Biotyper system, and the results of the analysis based on the presence of the yaiO gene. The results of this study could help in the selection of more accurate and reliable methods which can be used in a preliminary screening and more precise identification of E. coli isolated from environmental samples.

Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River

Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.

Characterization of virulence determinants and phylogenetic background of multiple and extensively drug resistant Escherichia coli isolated from different clinical sources in Egypt

Abstract

Escherichia coli is a multifaceted microbe since some are commensals, normally inhabiting the gut of both humans and animals while others are pathogenic responsible for a wide range of intestinal and extra-intestinal infections. It is one of the leading causes of septicemia, neonatal meningitis, urinary tract infections (UTIs), cystitis, pyelonephritis, and traveler’s diarrhea. The present study aims to survey the distribution and unravel the association of phylotypes, virulence determinants, and antimicrobial resistance of E. coli isolated from different clinical sources in Mansoura hospitals, Egypt. One hundred and fifty E. coli isolates were collected from different clinical sources. Antimicrobial resistance profile, virulence determinants, and virulence encoding genes were detected. Moreover, phylogenetic and molecular typing using ERIC-PCR analysis was performed. Our results have revealed that phylogroup B2 (26.67%) with the greatest content in virulence traits was the most prevalent phylogenetic group. Different virulence profiles and varying incidence of virulence determinants were detected among tested isolates. High rates of resistance to different categories of antimicrobial agents, dramatic increase of MDR (92.67%), and emergence of XDR (4%) were detected. ERIC-PCR analysis revealed great diversity among tested isolates. There was no clustering of isolates according to resistance, virulence patterns, or phylotypes. Our research has demonstrated significant phylogenetic diversity of E. coli isolated from different clinical sources in Mansoura hospitals, Dakahlia governorate, Egypt. E. coli isolates are equipped with various virulence factors which contribute to their pathogenesis in human. The elevated rates of antimicrobial resistance and emergence of MDR and XDR mirror the trend detected globally in recent years.

Key points

• Clinical E. coli isolates exhibited substantial molecular and phylogenetic diversity.

• Elevated rates of antimicrobial resistance and emergence of XDR in pathogenic E. coli.

• B2 Phylogroup with the highest VS was the most prevalent among pathogenic E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11740-x.

Comparative Characteristics and Zoonotic Potential of Avian Pathogenic Escherichia coli (APEC) Isolates from Chicken and Duck in South Korea

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which is an economically important disease in the poultry industry worldwide. The present study investigated O-serogroups, phylogenetic groups, antimicrobial resistance, and the existence of virulence-associated genes (VAGs) and antimicrobial resistance genes in 125 APEC isolates between 2018 and 2019 in Korea. The phylogenetic group B2 isolates were confirmed for human-related sequence types (STs) through multi-locus sequence typing (MLST). O-serogroups O2 (12.5%) and O78 (10.3%) and phylogenetic group B1 (36.5%) and A (34.5%) were predominant in chicken and duck isolates, respectively. Out of 14 VAGs, iucD, iroN, hlyF, and iss were found significantly more in chicken isolates than duck isolates (p < 0.05). The resistance to ampicillin, ceftiofur, ceftriaxone, and gentamicin was higher in chicken isolates than duck isolates (p < 0.05). The multidrug resistance (MDR) rates of chicken and duck isolates were 77.1% and 65.5%, respectively. One isolate resistant to colistin (MIC 16 μg/mL) carried mcr-1. The B2-ST95 APEC isolates possessed more than 9 VAGs, and most of them were MDR (82.4%). This report is the first to compare the characteristics of APEC isolates from chickens and ducks in Korea and to demonstrate that B2-ST95 isolates circulating in Korea have zoonotic potential and pose a public health risk.