Molecular epidemiology of Escherichia coli bacteremia in liver transplant recipients

No association between resistance mutations, empiric antibiotic, and mortality in ceftriaxone-resistant Escherichia coli and Klebsiella pneumoniae bacteremia

The objective of this study was to correlate resistance mutations of extended spectrum beta-lactamases (ESBL) and AmpC beta-lactamases and virulence factors (VF) with 30-day mortality in patients treated with either piperacillin-tazobactam or carbapenems. A post-hoc analysis on 123 patients with ceftriaxone-resistant Escherichia coli and Klebsiella pneumoniae bacteremia treated empirically with piperacillin-tazobactam and carbapenems was performed. Beta-lactamase resistance mutations and VF were identified by whole genome sequencing (WGS). The primary endpoint was 30-day mortality. Multivariate analyses were performed using logistic regression. WGS showed diverse multilocus sequence types (MLST) in 43 K. pneumoniae strains, while ST131 predominated in E. coli strains (57/80). CTX-M was most commonly detected (76/80 [95%] of E. coli; 39/43 [91%] of K pneumoniae.), followed by OXA (53/80 [66%] of E. coli; 34/43 [79%] of K. pneumoniae). A significant correlation was found between the number of genes encoding third-generation cephalosporin-resistant beta-lactamases and 30-day mortality (p = 0.045). The positive association was not significant after controlling for empiric carbapenem, Pitt score 3 and K. pneumoniae (OR 2.43, P = 0.073). None of the VF was associated with 30-day mortality. No association was found between 30-day mortality and any ESBL and AmpC beta-lactamases or VF when piperacillin-tazobactam or carbapenems were given. No significant association between 30-day mortality and active empiric therapy was found.

[Molecular epidemiology and kinetics of early Escherichia coli urinary tract infections in kidney transplant recipients]

BACKGROUND

Escherichia coli strains causing Urinary Tract Infections (UTI) have a fecal origin.

METHODS

A fecal sample was collected before Kidney Transplantation (KT) and concomitantly with urine at each of the 15 E. coli UTIs which occurred in 11 KT recipients. Unique E. coli strains were identified among 25 isolates per feces and 5 isolates per urinary sample by random amplification of polymorphic DNA. Phylogenetic group (which is correlated to virulence in the E. coli species) was determined for each E. coli strain by a PCR based method.

RESULTS

Forty-three unique fecal strains and 14 unique urinary strains were identified among 650 fecal isolates and 75 urinary isolates. Urinary strains frequently (55% of the cases) belonged to a phylogroup usually not linked to virulence. They were detected in the feces collected concomitantly in 60% of the cases. Urinary strains belonging to a phylogroup usually linked to virulence were more frequently dominant in the feces (100%) than urinary strains belonging to a non-pathogenic phylogroup (42%; P<0.05). Vesical catheter was a facilitating factor only for urinary strains belonging to non-pathogenic phylogroups. Thirty-three percent of the fecal strains were persisting in two consecutive fecal samples and 62% were detected for the first time at the UTI. Numerous pathway lead to UTIs: from a unique, virulent and persisting strain to a non-virulent recently acquired strain facilitated by a vesical catheter.

CONCLUSION

Our work shows the diversity of host-microbial interactions which precede extra-intestinal virulence.

Population Phylogenomics of Extraintestinal Pathogenic Escherichia coli

The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.

Molecular characterization of bacteremic Escherichia coli isolates in Romania

The increasing prevalence of invasive infections caused by antibiotic resistant Escherichia coli strains in Romanian patients, already mentioned in the European reports, requires better knowledge of their specific traits. Thus, a set of 38 E. coli blood isolates, collected between 2010 and 2012 at one of the local hospitals participating into the European Antimicrobial Resistance Surveillance Network, was investigated retrospectively with respect to the phylogenetic origin, extraintestinal virulence-associated markers (i.e. fimH, papC, papG alleles, sfa/foc, afa/dra, hly, cnf1, sat, iucC, fyuA, ibeA), and beta-lactamase encoding genes (i.e. bla CTX-M, bla TEM, and bla SHV alleles). The isolates with extended-spectrum beta-lactamase (ESBL) phenotypes were further characterized using PCR-based replicon typing and multilocus sequencing typing. For ST131 members, pulsed-field gel electrophoresis (PFGE) and PCR-based detection of fimH30 allele were performed. Overall, the isolates were more likely members of the major phylogenetic group A (53 %) and to a lesser extent of groups B2 (29 %), D (10 %), and B1 (8 %). All but three of the virulence markers sought (i.e. papGI, hly, cnf1) were detected with prevalence ranging from 3 % (i.e. ibeA, papGIII) to 87 % (fimH). As expected, the most complex genotypes (four to seven virulence markers) defined the isolates derived from phylogenetic groups B2 and D. ESBL producers were bla CTX-M-15-positive, mostly of phylogroup A (67 %), harboured IncF multireplicon plasmids, and belonged to six sequence types (i.e. ST10, ST131, ST167, ST410, ST540, ST1275). Members of ST10 clonal complex (i.e. ST10, ST167) were the most common. The ST131 isolates belonged to H30 subclone and displayed 74 % similarity at PFGE analysis.

Molecular screening of virulence genes in extraintestinal pathogenic Escherichia coli isolated from human blood culture in Brazil

Extraintestinal pathogenic Escherichia coli (ExPEC) is one of the main etiological agents of bloodstream infections caused by Gram-negative bacilli. In the present study, 20 E. coli isolates from human hemocultures were characterized to identify genetic features associated with virulence (pathogenicity islands markers, phylogenetic group, virulence genes, plasmid profiles, and conjugative plasmids) and these results were compared with commensal isolates. The most prevalent pathogenicity island, in strains from hemoculture, were PAI IV536, described by many researchers as a stable island in enterobacteria. Among virulence genes, iutA gene was found more frequently and this gene enconding the aerobactin siderophore receptor. According to the phylogenetic classification, group B2 was the most commonly found. Additionally, through plasmid analysis, 14 isolates showed plasmids and 3 of these were shown to be conjugative. Although in stool samples of healthy people the presence of commensal strains is common, human intestinal tract may serve as a reservoir for ExPEC.

A subset of two adherence systems, acute pro-inflammatory pap genes and invasion coding dra, fim, or sfa, increases the risk of Escherichia coli translocation to the bloodstream

An analysis of the phylogenetic distribution and virulence genes of Escherichia coli isolates which predispose this bacteria to translocate from the urinary tract to the bloodstream is presented. One-dimensional analysis indicated that the occurrence of P fimbriae and α-hemolysin coding genes is more frequent among the E. coli which cause bacteremia. However, a two-dimensional analysis revealed that a combination of genes coding two adherence factors, namely, P + Dr, P + S, S + Dr, S + fim, and hemolysin + one adherence factor, were associated with bacteremia and, therefore, with the risk of translocation to the vascular system. The frequent and previously unrecognized co-existence of pro-inflammatory P fimbriae with the invasion promoting Dr adhesin in the same E. coli isolate may represent high-risk and potentially lethal pathogens.

Host stress and virulence expression in intestinal pathogens: development of therapeutic strategies using mice and C. elegans

The intestinal tract of a host exposed to extreme physiologic stress and modern medical intervention represents a relatively unexplored yet important area of infection research, given the frequency with which this site becomes colonized by highly pathogenic microorganisms that cause subsequent sepsis. Our laboratory has focused on the host tissue derived environmental cues that are released into the intestinal tract during extreme physiologic stress that induce the expression of virulence in colonizing pathogens with the goal of developing novel gut directed therapies that maintain host pathogen neutrality through the course of host stress. Here we demonstrate that maintenance of phosphate sufficiency/ abundance within the intestinal microenvironment may be considered as a universal strategy to prevent virulence activation across a broad range of pathogens that colonize the gut and cause sepsis, given that phosphate depletion occurs following stress and is a universal cue that activates the virulence of a wide variety of organisms. Using small animal models (Caenorhabditis elegans and mice) to create local phosphate depletion at sites of colonization of Pseudomonas aeruginosa, a common cause of lethal gut-derived sepsis, we demonstrate the importance of maintaining phosphate sufficiency to suppress the expression of a lethal phenotype during extreme physiologic stress. The molecular details and potential therapeutic implications are reviewed.