Characterisation of an early South African multiply antibiotic-resistant global clone 1 Acinetobacter baumannii isolate

Abstract

The aim of this study was to characterise an early clinical multiply antibiotic resistant Acinetobacter baumannii global clone 1 (GC1) isolate from Africa. The draft genome sequence was determined using short-read (Illumina MiSeq) sequence data and compared to other early GC1 isolates. Resistance genes and other features were identified using various bioinformatics tools. Plasmids were visualised. LUH6050, recovered in South Africa between January 1997 and January 1999, is ST1IP:ST231Ox:KL1:OCL1. Several antibiotic resistance genes (aacC1, aadA2, aphA1, catA1, sul1, and tetA(A)) reside in AbaR32. LUH6050 also includes the plasmid pRAY*, carrying the aadB gentamicin and tobramycin resistance gene, and a 29.9 kb plasmid, pLUH6050-3, carrying the msrE-mphE (macrolide resistance) and dfrA44 (trimethoprim resistance) genes and a small cryptic Rep_1 plasmid. Plasmid pLUH6050-3, a cointegrate of pA1-1 (R3-T1; RepAci1) with an R3-T33 type plasmid encoding a different Rep_3 family Rep, carries 15 pdif sites and 13 dif modules, including those that carry the mrsE-mphE and dfrA44 genes and three that include toxin-antitoxin gene pairs. The closest relative of pLUH6050-3 found in GenBank was from an unrelated 2013 Tanzanian A. baumannii isolate. The chromosome has an AbaR0-type region in comM and includes no ISAba1 copies. Similar features were found in most other sequenced lineage 1 GC1 isolates recovered prior to 2000. LUH6050 represents an early form of the GC1 lineage 1, supplementing limited information about early isolates and isolates from Africa. These data contribute to the understanding of the emergence, evolution, and dissemination of the A. baumannii GC1 clonal complex.