High magnitude of carbapenemase-producing Acinetobacter baumannii in sepsis patients at Ethiopian referral hospitals: a whole genome analysis

Abstract

Abstract Carbapenemase-producing Acinetobacter baumannii (CP-Ab) is a critical priority pathogen. Between October 2019 and September 2020, a multicentre study was conducted at four Ethiopian hospitals: Tikur Anbessa and Yekatit (central), Hawassa (southern), and Dessie (northern). A total of 1416 sepsis patients were enrolled, and blood cultures were performed. Acinetobacter isolates were confirmed using MALDI-TOF and tested for carbapenem susceptibility. All Acinetobacter isolates were subjected to whole-genome sequencing. Selected isolates underwent nanopore sequencing through Plasmidsaurus. Forty-five Acinetobacter isolates were identified, mostly A. baumannii ( n  = 38), with a few other species ( n  = 7). Among the 38 A. baumannii isolates, 18 carried bla NDM−1 and either bla OXA−23 or bla OXA−58 carbapenemase genes concurrently. bla OXA−58 and bla NDM−1 were co-located on plasmids of sizes 80 kb to 113 kb. bla OXA−66 ( n  = 13) and bla OXA−69 ( n  = 12) were frequently identified chromosomally encoded carbapenemase genes. Several STs of A. baumannii were identified, with ST2 ( n  = 14) and ST1 ( n  = 13) being frequent. One A. nosocomialis carried bla NDM−1 and bla OXA−58 simultaneously. Several other genes were identified that confer resistance to aminoglycosides ( n  = 37), phenicol ( n  = 19), trimethoprim ( n  = 16), macrolides ( n  = 25), quinolones ( n  = 10), tetracyclines ( n  = 22), sulphonamides ( n  = 36), and disinfectants ( n  = 23). The high prevalence of carbapenemase-producing A. baumannii and other Acinetobacter species underscores the need for nationwide antibiotic stewardship.