Draft genome sequence of a uropathogenic Escherichia coli isolate (ST38 O1:H15) from Pakistan, an emerging multidrug-resistant sequence type with a high virulence profile.

Sequence type 38 is considered a uropathogenic Escherichia coli/enteroaggregative E. coli hybrid associated with multidrug resistance and urinary tract infections. The draft genome sequence of UEC59 from a woman in Pakistan revealed a 5 324 938 bp genome with 5386 coding sequences (CDS), 86 transfer RNA genes and multiple antibiotic resistance genes (bla TEM-1, CMY-2, sul1, sul2, dfrA17, tetA, mphA) and mobile elements (int1, two transposons, 30 insertion sequence elements, one integrative conjugative element, four plasmids, five prophages), along with many virulence genes.

Urinary tract infections (UTI) are the second most common type of clinical infection globally. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTI. It exhibits multidrug resistance (MDR) and harbours virulence factors enabling colonization of the urinary tract [1]. In developing nations, horizontal gene transfer has enabled the spread of MDR and acquisition of novel virulence-factor portfolios, exacerbating the problems caused by UPEC. Sequence type (ST) 38 is considered a hybrid of enteroaggregative E. coli (EAEC) and UPEC, and is frequently associated with UTIs [2]. Genome sequencing of ST38 isolates from developing nations offers the opportunity to identify emerging UPEC strains that are a potential global threat to human health.

UEC59 is a UPEC from a 73-year-old woman in Pakistan. Antimicrobial susceptibility profiling performed according to Clinical and Laboratory Standards Institute guidelines demonstrated resistance to cephalosporins, fluoroquinolones, trimethoprim and ampicillin, characterizing it as an extended-spectrum β-lactamase–producing MDR strain [3]. Phenotypic profiling of virulence characteristics identified it as a haemolytic, adherent, biofilm-producing and serum-resistant strain. Invasion assays in the uroepithelial cell line ATCC HTB5637 showed that UEC59 is capable of invasion.

Genome sequencing of UEC59 was performed by MicrobesNG, Birmingham, on MiSeq and HiSeq 2500 platforms with sequence coverage of 30×. De novo assembly of the reads was performed by SPAdes 3.11 [4]. The quality of genome assemblies was assessed by QUAST [5], genomic features were determined with PATRIC [6] and insertion sequence (IS) and integrative conjugative elements (ICE) were sought with IS finder and ICEberg [7], [8]. A total of 146 contigs were obtained with a total genome size of 5 324 938 bp, a GC content of 50.55%, 5386 CDS and 86 transfer RNA genes. A yersiniabactin synthesis–associated ICE (similar to ICEEcoUMN026-1) of 65 732 bp was identified, as were a total of 30 IS elements (11 types).

UEC59 was identified as clonal type ST38 [9] and serotype O1:H15 [10]. Four plasmids were found [11]—IncFII, IncFIA, IncFIB and Col156—as were genes conferring resistance to extended-spectrum β-lactam drugs (blaTEM-1, CMY-2), sulfonamides (sul-1 and sul-2), trimethoprim (dfrA17), aminoglycosides (AadA5, APH(6)-Id, AAC(3)-IId), fluoroquinolone (mutation in parC, S80I), tetracycline (tet(A)), quaternary ammonium compounds (qacEΔ1) and macrolides (mph(A)). Moreover, an integron (int1) associated with dfrA17 and transposons (Tn2, Tn3) associated with tetA were identified. Virulence genes present include those for adhesins and invasins (fimH, papI, papGII, safC, kpsM), toxins (espC, ghoT) and a hypothetical enterotoxin (senB). The safC gene found in UEC59 is homologous to the aggregative adherence fimbria II usher protein AafC of EAEC, other than that no EAEC-specific gene such as aggR is encoded by UEC59. However, studies have reported the presence of EAEC transport regulator gene aggR as a key feature in evolution of ST38 UPEC strains (from the United Kingdom, Netherland and Germany) [12]. However, ST38 UPEC from Saudi Arabia and Brazil have shown only 27% (4/15) and 16 UPEC strains out of 225 carrying EAEC-specific genes such as aggR and aatA respectively [2], [13].

UEC59 also encodes iron-acquisition systems involved in the manufacture and utilization of the siderophores enterobactin, yersiniabactin and aerobactin; haeme (hemSRT-chuY-hmuUV) uptake; and ferrous iron (feoABC and efeUOB) utilization. There was a strong correlation between the various virulence factors identified phenotypically and those revealed from the genome sequence. The PHASTER tool [14] identified five intact (PHAGE_Entero_fiAA9, 36 kb; PHAGE_Entero_lambda, 48kb; PHAGE_Entero_lambda 28 kb; PHAGE_Vibrio_X29. 22 kb; PHAGE_Entero_BP, 17 kb) and three incomplete (PHAGE_Entero_N15, 8.5 kb; PHAGE_Salmon_118970, 213 kb; PHAGE_Salmon_118970, 27 kb) prophage regions. CRISPRCasfinder [15] confirmed two CRISPRs of more than ten direct repeats, but only one was associated with cas genes (CAS-TypeIE).

Nucleotide sequence accession numbers

This whole-genome draft shotgun sequence was deposited at GenBank under accession number QKMW00000000. The version described in this paper is version QKMW01000000.