Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections

Abstract

Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies.

Pathophysiology of Escherichia coli ventilator-associated pneumonia: implication of highly virulent extraintestinal pathogenic strains

“…This finding may explain clinical failure of antimicrobial treatment when the more susceptible strain has been picked for the antibiogram. We recently described the same phenomenon in other E. coli extraintestinal infections [43], and it has been reported for other microorganisms [44][45][46][47]. We, therefore, believe that several colonies of a single respiratory sample should be tested for antimicrobial susceptibility in case of GNB VAP.…”

UPEC strain characterization isolated from Mexican patients with recurrent urinary infections

“…Various epidemiological studies support the notion that specific subsets of genes are characteristic of each of the E. coli uropathogenic subtypes involved in the development of cystitis, pyelonephritis, and urosepsis [10,11,24,25]. There are reports showing that cystitis isolates differ specifically from prostatitis isolates due to the lower prevalence of hlyA and cnf1 [26,27,28] and that prostatitis isolates have significantly higher aggregate virulence factors scores than cystitis isolates. In the current study, these differences were found, but contrary to those former reports, the cystitis strains of our population presented higher frequency of hly, pap, sat and cnf1 than prostatitis isolates.…”

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

“…The central elements in gene regulation, e.g., the concentrations of sigma factors and alarmones such as ppGpp, vary greatly under the same environmental conditions across a species (98,304). The instability of such central elements of regulation is particularly evident within the lifetime of a clonal infection in a patient (177). Although variations are genotype specific, they do not always involve polymorphisms in the regulatory gene itself.…”