Genomic epidemiology of Escherichia coli isolates from a tertiary referral center in Lilongwe, Malawi

• DOI: 10.1099/mgen.0.000490
• Publication Date: 2020-12-09T18:07:30Z
• Authors: Gerald Tegha; Emily J. Ciccone; Robert Krysiak; James Kaphatika; Tarsizio Chikaonda; Isaac Ndhlovu; David van Duin; Irving Hoffman; Jonathan J. Juliano; Jeremy Wang
• Keywords: Molecular Epidemiology

Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little known about the genetics of resistant bacteria region. In Malawi, there growing concern increasing rates antimicrobial to most empirically used antimicrobials. The highly drug Escherichia coli sequence type (ST) 131, which associated with extended spectrum β-lactamase blaCTX-M-15, has been prevalence globally. Previous data from isolates collected between 2006 and 2013 southern Malawi have revealed presence ST131 blaCTX-M-15 gene country. We performed whole genome sequencing (WGS) 58 clinical E. at Kamuzu Central Hospital, tertiary care centre central 2012 2018. Oxford Nanopore Technologies (ONT) sequencing, was Malawi. show that observed more often (14.9% 32.8%) occurring higher frequency (21.3% 44.8%). Phylogenetics indicates are related geographic regions confirms contained single group. All AMR genes, were widely distributed across types. also identified an increased number ST410 isolates, this study tend carry plasmid-located copy than occurs ST131. This expanding nature wide distribution highlight feasibility conducting longitudinal genomic epidemiology studies important done on site using nanopore platform requires minimal infrastructure.