Genomic characterization and phylogenomic placement of AP66, an Acinetobacter pittii ST640 metagenome-assembled genome recovered from a human stool-derived mixed culture in Nigeria

Acinetobacter pittii , a member of the Acinetobacter calcoaceticus-baumannii complex, is increasingly recognized as an opportunistic pathogen with substantial genomic and ecological diversity. Although its genomic representation has expanded considerably, human-associated genomes from sub-Saharan Africa remain comparatively underrepresented. We characterized A. pittii AP66, a high-quality metagenome-assembled genome (MAG) recovered from a stool-derived mixed bacterial culture during diagnostic investigation for enteric pathogens in Nigeria. The AP66 genome comprised 3.79 Mb across 67 contigs and was estimated to be 100% complete, with 0% contamination and no detectable strain heterogeneity. GTDB-Tk independently classified AP66 as A. pittii , and multilocus sequence typing assigned it to ST640. Phylogenomic reconstruction based on 500 conserved single-copy protein families across 98 genomes identified A. pittii Ac-14 as the closest phylogenomic neighbour of AP66, with bootstrap support of 100. Pairwise ANI between AP66 and Ac-14 was 99.9238%, while similarly high identities were observed with the closely related ST640 genomes BS1 and ANC 3678. AP66 carried the intrinsic β-lactamase genes bla ADC-132 and bla OXA-273 together with resistance-associated efflux determinants and multiple virulence-associated homologues. Mobile-element analysis identified a 33,394-bp AB406 plasmid predicted to be non-mobilizable and lacking antimicrobial-resistance genes, seven insertion-sequence-associated sequences, two PHASTEST prophage regions including one intact region of approximately 51.4 kb, and 13 predicted genomic islands. Independent geNomad and VirSorter2 analyses further supported the presence of phage-associated regions. Two low-evidence CRISPR arrays were detected, but no confidently supported Cas-associated gene or complete CRISPR–Cas system was identified. KEGG reconstruction revealed complete modules for glycolysis, the tricarboxylic acid cycle, pentose phosphate pathway, glyoxylate cycle and methylcitrate cycle, together with pathways associated with aromatic-compound metabolism and stress responses. PathogenFinder2 classified AP66 as having human pathogenic capacity, with an ensemble mean score of 0.9893. AP66’s close phylogenomic relationship to ST640 genomes recovered from geographically and ecologically distinct sources suggests a potentially broad ecological distribution of the lineage. The combination of intrinsic resistance determinants, virulence-associated homologues, mobile genetic elements and metabolic diversity further illustrates the genomic versatility of A. pittii . However, these sequence-based findings do not establish phenotypic resistance, virulence or involvement of AP66 in the patient’s gastroenteritis.