Extraintestinal pathogenic E. coli (ExPEC) such as uropathogenic E. coli (UPEC) have acquired the ability to colonise anatomical sites distinct from the gastrointestinal tract. UPEC are the leading cause of community acquired urinary tract infections (UTI), costing approximately $24 million p.a. in Australia and $1.5 billion in the USA. After colonising the bladder a limited subset of infections ascend the urogenital tract and enter the bloodstream causing urosepsis, a condition that is life threatening in the absence of successful antibiotic intervention. UTI is generally treated with first-line antibiotics such as trimethoprim/sulfamethoxazole and nitrofurantoin. However, UPEC increasingly display resistance to these antibiotics.
This study describes the genomic analysis of two multidrug resistant E. coli strains, 2009-49 from a urine sample and 2009-52 from blood culture, obtained from the same patient over a period of 4 days. Antibiotic susceptibility testing, electronic multilocus sequence typing and phylotype analysis showed that both strains were ST58, phylotype A and resistant to ampicillin, trimethoprim, sulfafurazole, tetracycline, streptomycin, apramycin and kanamycin. Both strains carried identical complex resistance regions comprising Tn6029 (ampicillin, streptomycin, and sulfafurazole resistance). Tn6029 was found 24 bp into the 3´-CS of a class 1 integron (carrying the trimethoprim resistance gene dfrA5) in a hybrid Tn21/Tn1721 backbone in both strains. Bioinformatic analysis of the draft genomes revealed significant genetic identity. Several single nucleotide polymorphisms (SNPs) were identified, including one that caused an amino acid substitution in fimG. Notably, a 61,832 bp region comprising an IncI2 plasmid harbouring genes for a type IV secretion system was identified only in 2009-52.
Closed genome sequences are required to determine the full repertoire of SNPs and indels that constitute the unique features that differentiate these strains.