Evolution towards small colony variants of pandemic multidrug resistant ST131 Escherichia coli isolates from a 10-year bone infection

Abstract

ABSTRACTBackgroundChronic wounds are usually challenging to treat due to underlying medical conditions of the individual and as they readily become infected by microorganisms due to the failure of mechanical and physiological first line innate immune responses. We report here the characterization of host adaptation of five E. coli genomes including three E. coli ST131 genomes that occurred concomitantly with Enterococcus faecalis from a 10-year chronic wound infection after a foot fracture during the 2004 tsunami.MethodsThe five E. coli strains were characterized by various microbiological and genomic approaches. Microbiological methods were antimicrobial resistance, growth in different media and biofilm formation. Genomic methods were determination of the genome sequence by PacBio RSII and Illumina sequencing. Phylogenetic analyses and genome alterations such as single nucleotide polymorphisms, deletion and rearrangements that led to pseudogenes and chromosomal inversions were documented. Relevant selected metabolic and physiological pathways were analyzed for integrity.FindingStrains of two initially present sequence types, including the highly antimicrobial resistant ST405 clone, were subsequently replaced by isolates of the ubiquitous ST131 clone. The three E. coli ST131 strains showed a heavily host-adapted genome with a high number of pseudogenes and a large chromosomal inversion compared to ST131 reference strains. Furthermore, two of three E. coli ST131 isolates were small colony variants with its genetic basis in multiple genome alterations including pseudogenes and deletions in the pathway for heme biosynthesis. Pseudogene analysis indicated also the three ST131 strains to be mutator strains. Although enhanced capability of biofilm formation of the ST131 isolates was indicated by the agar plate assay, the a liquid culture biofilm assay did not display pronounced biofilm formation suggesting unconventional modes of biofilm formation.InterpretationST131 clone members, which originally appeared as commensal strains can cause urinary tract and blood stream infections and are ubiquitously found in the environment including waste water and in animals. ST131 strains have presumably been already acquired from the environment on occurrence of the initial foot fracture and can persist in wounds showing an outmost genome plasticity and adaptability which might causing the chronic infection. Although co-infection with E. faecalis might have supported chronicity, these findings indicate that in individuals with underlying metabolic diseases wound infection by ST131 E. coli isolates can be a health risk.FundingThis work was partially funded by ALF.