Unveiling the Virulent Genotype and Unusual Biochemical Behavior of Escherichia coli ST59.

Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of human and animal infections worldwide. The utilization of selective and differential media to facilitate the isolation and identification of E. coli from complex samples, such as water, food, sediment, and gut tissue, is common in epidemiological studies. During a surveillance study, we identified an E. coli strain isolated from human blood culture that displayed atypical light cream-colored colonies in chromogenic agar and was unable to produce ß-glucuronidase and ß-galactosidase in biochemical tests. Genomic analysis showed that the strain belongs to sequence type 59 (ST59) and phylogroup F. The evaluation in silico of 104 available sequenced lineages of ST59 complex showed that most of them belong to serotype O1:K1:H7, are ß-glucuronidase negative, and harbor a virulent genotype associated with the presence of important virulence markers such as pap, kpsE, chuA, fyuA, and yfcV. Most of them were isolated from extraintestinal human infections in diverse countries worldwide and could be clustered/subgrouped based on papAF allele analysis. Considering that all analyzed strains harbor a virulent genotype and most do not exhibit biochemical behavior typical of E. coli, we report that they could be misclassified or underestimated, especially in epidemiological studies where the screening criteria rely only on typical biochemical phenotypes, as happens when chromogenic media are used. IMPORTANCE The use of selective and differential media guides presumptive bacterial identification based on specific metabolic traits that are specific to each bacterial species. When a bacterial specimen displays an unusual phenotype in these media, this characteristic may lead to bacterial misidentification or a significant delay in its identification, putting a patient at risk depending on the infection type. In the present work, we describe a virulent E. coli sequence type (ST59) that does not produce beta-glucuronidase (GUS negative), production of which is the metabolic trait widely used for E. coli presumptive identification in diverse differential media. The recognition of this unusual metabolic trait may help in the proper identification of ST59 isolates, the identification of their reservoir, and the evaluation of the frequency of these pathogens in places where automatic identification methods are not available.

Characterization of antimicrobial resistance in chicken-source phylogroup F Escherichia coli: similar populations and resistance spectrums between E. coli recovered from chicken colibacillosis tissues and retail raw meats in Eastern China.

The extended-spectrum cephalosporin resistant E. coli from food animals transferring to community settings of humans causes a serious threat to public health. Unlike phylogroup B2 E. coli strains, the clinical significance of isolates in phylogroup F is not well revealed. Here, we report on a collection (n = 563) of phylogroup F E. coli isolates recovered from chicken colibacillosis tissues and retail raw chicken meat samples in Eastern China. There was an overlapped distribution of MLST types between chicken colibacillosis-origin and meat-source phylogroup F E. coli, including dominant STs (ST648, ST405, ST457, ST393, ST1158, etc). This study further investigated the presence of extended-spectrum ß-lactamase (ESBL/pAmpC) producers in these chicken-source phylogroup F E. coli strains. The prevalence of extended-spectrum cephalosporin resistant strains in phylogroup F E. coli from chicken colibacillosis and raw meat separately accounted for 66.1 and 71.2%. The resistance genotypes and plasmid replicon types of chicken-source phylogroup F E. coli isolates were characterized by multiplex PCR. Our results revealed ß-lactamase CTX-M, OXA, CMY and TEM genes were widespread in chicken-source phylogroup F E. coli, and blaCTX-M was the most predominant ESBL gene. Moreover, there was a high prevalence of non-lactamase resistance genes in these ß-lactam-resistant isolates. The replicons IncB/O/K/Z, IncI1, IncN, IncFIC, IncQ1, IncX4, IncY, and p0111, associated with antibiotic-resistant large plasmids, were widespread in chicken-source phylogroup F E. coli. There was no obvious difference for the populations, resistance spectrums, and resistance genotypes between phylogroup F E. coli from chicken colibacillosis tissues and retail meats. This detail assessment of the population and resistance genotype showed chicken-source phylogroup F E. coli might hold zoonotic risk and contribute the spread of multidrug-resistant E. coli to humans.

Chicken-source Escherichia coli within phylogroup F shares virulence genotypes and is closely related to extraintestinal pathogenic E. coli causing human infections.

ExPEC is an important pathogen that causes diverse infection in the human extraintestinal sites. Although avian-source phylogroup F Escherichia coli isolates hold a high level of virulence traits, few studies have systematically assessed the pathogenicity and zoonotic potential of E. coli isolates within phylogroup F. A total of 1,332 E. coli strains were recovered from chicken colibacillosis in China from 2012 to 2017. About 21.7% of chicken-source E. coli isolates were presented in phylogroup F. We characterized phylogroup F E. coli isolates both genotypically and phenotypically. There was a widespread prevalence of ExPEC virulence-related genes among chicken-source E. coli isolates within phylogroup F. ColV/BM plasmid-related genes (i.e. hlyF, mig-14p, ompTp, iutA and tsh) occurred in the nearly 65% of phylogroup F E. coli isolates. Population structure of chicken-source E. coli isolates within phylogroup F was revealed and contained several dominant STs (such as ST59, ST354, ST362, ST405, ST457 and ST648). Most chicken-source phylogroup F E. coli held the property to produce biofilm and exhibited strongly swimming and swarming motilities. Our result showed that the complement resistance of phylogroup F E. coli isolates was closely associated with its virulence genotype. Our research further demonstrated the zoonotic potential of chicken-source phylogroup F E. coli isolates. The phylogroup F E. coli isolates were able to cause multiple diseases in animal models of avian colibacillosis and human infections (sepsis, meningitis and UTI). The chicken-source phylogroup F isolates, especially dominant ST types, might be recognized as a high-risk food-borne pathogen. This was the first study to identify that chicken-source E. coli isolates within phylogroup F were associated with human ExPEC pathotypes and exhibited zoonotic potential.