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

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 blaNDM−1 and either blaOXA−23 or blaOXA−58 carbapenemase genes concurrently. blaOXA−58 and blaNDM−1 were co-located on plasmids of sizes 80 kb to 113 kb. blaOXA−66 (n = 13) and blaOXA−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 blaNDM−1 and blaOXA−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.