Phylogeny, Sequence-typing and virulence profile of uropathogenic E. coli (UPEC) strains from Pakistan

Abstract Background Escherichia coli lineage ST131 predominates across various spectra of extra-intestinal infections, including urinary tract infection (UTI). The distinctive resistance profile, diverse armamentarium of virulence factors and rapid global dissemination of ST131 E. coli makes it an intriguing pathogen. However, not much is known about the prevalence and genetic attributes of ST131 lineage in Pakistan. Methods We estimated the prevalence and genetic attributes of E. coli ST131 isolates causing UTI among 155 randomly selected samples. Samples were analyzed by phylogenetic grouping, O-typing, fumC/fimH typing. Isolates were further tested for ESBL and virulence factors using PCR. Results Overall, 59% of the UPEC isolates belonged to the phylogenetic group B2, followed by D=28%, B1= 8% and A= 5%. Among 18 different Sequence-types, ST131 was the dominant lineage (n=71; 46%) out of which 72% of the isolates were assigned to phylogenetic group B2 while 61% adhered to serogroup O25b. FumC/fimH typing confirmed 49% of the ST131 as H30 sub-types. In this study, significant numbers of the identified ST131 isolates were MDR and 42% showed ESBL phenotypes, out of which 57% carried blaCTX-M-15. Moreover, different virulence factors were detected in following percentages: fimH,155 (100%), iutA 86 (55%), feoB 76 (49%), papC 75 (48%), papGII 70 (45%), kpsMTII 40 (26%), papEF 37 (24%), fyuA 37 (24%), usp 22 (14%), papA 20 (13%), sfa/foc 20 (13%), hlyA 18 (12%), afa 15 (10%), cdtB 11 (7%), papGI 6 (4%), papGIII 6 (4%), kpsMTIII 4 (3%) and bmaE2 (1%). Conclusion Conclusively, this study provides important insights into the genetic and virulence attributes of pandemic MDR ST131 strains involved in UTIs. It also highlights high prevalence of ST131-O25b-H30 UPEC isolates in local population, which was previously unreported from this part of globe. Keywords: ST131, VF genes, ESBL, UPEC, MDR