Genomic and phylogenomic analyses reveal extensive diversity among soil-derived Acinetobacter baumannii isolates from Nigeria

Abstract

Abstract This study reports the genomic characterization of 24 representative Acinetobacter baumannii isolates recovered from soil across ecologically distinct sites in Nigeria’s Federal Capital Territory. From the 43 soil samples analyzed, 101 Acinetobacter spp. were recovered, predominantly A. baumannii (39/101; 38.61%). Analysis of the 24 A. baumannii isolates revealed extensive genetic diversity, including 20 distinct Pasteur and 19 Oxford sequence types (STs), of which 15 and 13, respectively, were novel. Additionally, we detected 20 capsular (KL) and seven outer core lipooligosaccharide (OCL) locus types. In silico prediction revealed that most isolates did not harbour clinically relevant antibiotic resistance genes and were unrelated to known international clonal complexes. However, one isolate (A23-4) belonged to the international clone 8 (IC8) lineage and harboured a class 1 integron-associated MDR cassette containing ant(3 ″ ) -Ia, dfrA1 , and sul2 , flanked by insertion sequences ISAIw4 , ISVsa3 , and IS1006 . Further analyses identified 4,975 pangenome gene clusters and a polyphyletic distribution of the A. baumannii isolates across multiple distinct evolutionary lineages. The studied soil samples harbour a highly diverse and largely antimicrobial-susceptible population of A. baumannii rich in novel lineages. However, the detection of a MDR ST10/IC8 clone highlights the value of genomic surveillance in identifying potentially high-risk strains within environmental reservoirs.