Genomic heterogeneity of Multidrug Resistance E.coli recovered from diarrheagenic children under five years from Mukuru Informal Settlement, Nairobi, Kenya

Abstract

Introduction High genomic plasticity within E. coli enables it to acquire and accumulate genetic material through horizontal gene transfer like mobile genetic elements. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes( ARGs), plasmid replicons, MLST, and cgMLST of multidrug-resistant E.coli recovered from diarrheagenic children under five years from Mukuru Informal Settlement, Nairobi Kenya. Methods A total of 39 MDR strains had their DNA extracted, and Whole Genome Sequencing was done using the Illumina HiSeq 2500 platform. Twenty-six E.coliassemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology (TDU) and EnteroBase. Results The isolates fell into 4 main phylogroups, where 10/26(38.5%) belonged to the B2 phylogroup, 4/26 ( 15.4%) belonged to D, 3/26( 11.5%) belonged to A, 1/26( 3.8%) belonged to B1, while 8/26 ( 30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and Sequence Type(ST) 131. A total of 40 diverse virulence genes were detected among the isolates. 13 different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46 and ST 1722. Only two isolates ( 2/26, 7.7%) from the Municipal City Council ( MCC) clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107) in particular, followed by the Col family. Of 26 isolates, 15 had at least one nonsynonymous mutation in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC(p.S57T), and parE(p.I529L),associated with resistance to fluoroquinolones. Conclusion The study highlighted the first E.coli ST46 to harbor the NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.