Phylogenetic groups, serogroups and virulence factors of uropathogenic Escherichia coli isolated from patients with urinary tract infection in Baghdad, Iraq

Comparative analysis of virulence gene profiles of Escherichia coli from human and non-human sources in Rivers State, Nigeria

Traditionally, the presence of virulence features has been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of the virulence potential of Escherichia coli isolates from various sources is essential to shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with E. coli from human and non-human sources in Rivers State, Nigeria. Two hundred samples from human (urine and faeces) and non-human (soil and poultry droppings) sources (50 each) were analysed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as E. coli using the Presto Mini gDNA Bacteria-Kit Quick protocol following the manufacturer's instructions. Isolate identities were confirmed using E. coli-specific 16S rRNA primers, and confirmed isolates were screened for the presence of six virulence genes [afimbriae binding adhesin (afa), type 1 fimbriae (fimH) and P-fimbrial usher protein (papC)], iron acquisition systems: aerobactin (aer), cytotoxic necrotizing factor I (cnf1) and alpha-hemolysin (hly). Results showed that all isolates harboured at least one of the tested virulence genes, with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-human isolates, though hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile being in general (33.3%). For non-human isolates, however, aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%). This study shows that the test E. coli from human and non-human sources do not carry distinct virulence gene profiles. Studies on a larger subset of isolates would however be necessary to determine if the virulence genes tested in this study really cannot be used to tell whether an isolate is from a human source or not in the South-South of Nigeria.

Antibiotic resistance and its correlation with biofilm formation and virulence genes in Klebsiella pneumoniae isolated from wounds

Klebsiella pneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over the world. In this study, we investigated the antibiotic resistance profile and the ability to produce extended-spectrum beta-lactamase (ESBL) among K. pneumoniae isolates, and then we investigated the relationship between these two factors with biofilm formation and the prevalence of different virulence genes. In this study, 130 isolates of K. pneumoniae isolated from wounds were investigated. The antibiotic resistance of the isolates was evaluated by the disk diffusion method. The microtiter plate method was used to measure biofilm formation. The prevalence of virulence genes was detected by multiplex PCR. Among the examined isolates, 85.3% showed multidrug resistance. 87.6% of the isolates were ESBL-positive. Imipenem, meropenem, and fosfomycin were the most effective drugs. The ability of the isolates to produce biofilm was strong (80%), moderate (12.3%), and weak (7.6%), respectively. fimH, mrKD, entB, and tolC virulence genes were observed in all isolates. High prevalence of antibiotic resistance (especially multidrug resistance), high prevalence of ESBL-producing isolates, the ability of all isolates to biofilm formation, and the presence of fimH, mrKD, entB, and tolC virulence genes in all isolates show the importance of these factors in the pathogenesis of K. pneumoniae isolates in Iraq.

Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli

Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.

Pathophysiologic Insights into the Transition from Asymptomatic Bacteriuria to Urinary Tract Infection

PURPOSE OF REVIEW

Asymptomatic bacteriuria (ASB) can be found in the general population but it is more common in catheterized patients. Some patients develop urinary tract infections (UTI) and others stay asymptomatic throughout time. The scientific community lacks a pathophysiologic explanation of why asymptomatic bacteriuria stays asymptomatic most of the time, and why and how it sometimes transitions to UTI. In an attempt to bridge this gap in knowledge, a summary of the current literature is conducted on the pathophysiologic differences between ASB and UTI, beyond their clinical differences.

RECENT FINDINGS

ASB and UTI cannot be differentiated just by their phylogroup or number of virulence factors. The difference may be in their metabolism gene expression. The literature lacks a pathophysiological explanation of the transition from ASB to UTI, and recent discoveries suggest that metabolic gene expression may hold the key.

Description of extraintestinal pathogenic Escherichia coli based on phylogenetic grouping, virulence factors, and antimicrobial susceptibility

Background and Objectives

Extraintestinal pathogenic Escherichia coli (ExPEC) is a recently recognized and highly diverse pathotype of E. coli. Its significance as a pathogen has increased due to the emergence of hypervirulent and multidrug-resistant (MDR) strains. The aim of this study was to characterize ExPEC isolates from humans based on their phylogenetic group, virulence factor profile, and antimicrobial susceptibility.

Materials and Methods

The isolates were collected from patients with extraintestinal infections caused by E. coli, including urinary tract infections, bacteremia, and surgical site infections. The E. coli phylogenetic groups were determined using multiplex PCR. Additionally, the isolates were evaluated for their biofilm-forming abilities, susceptibility to antimicrobial agents, and presence of virulence genes.

Results

In this study, the isolates were classified into four phylogenetic groups: A (48.3%), B2 (25.8%), D (19.35%), and B1 (6.45%). All isolates exhibited at least one of the ten analyzed virulence factors. However, there was no direct evidence linking a specific phylogenetic group to a particular virulence factor. Nevertheless, the presence of the fimH, fyuA, ompT, traT, and kpsMTII virulence genes was correlated with the production of strong biofilms, multidrug resistance (MDR), and the production of alpha hemolysin.

Conclusion

This study provides a description of the phylogenetic groups in ExPEC and their potential association with virulence factor profiles and antimicrobial susceptibility.