Nigerian Stool Culture Yields Complete Genome of Opportunistic Pathogen Acinetobacter pittii

Researchers have assembled and characterized AP66, a high-quality metagenome-assembled genome of Acinetobacter pittii, recovered from a stool-derived mixed bacterial culture collected during diagnostic testing for enteric pathogens in Nigeria. The study, published as open-access research in BMC Genomic Data on 7 October 2026, addresses a notable gap: although genomic representation of A. pittii has expanded considerably, human-associated genomes from sub-Saharan Africa remain comparatively underrepresented.

A. pittii belongs to the Acinetobacter calcoaceticus-baumannii complex and is increasingly recognized as an opportunistic pathogen with substantial genomic and ecological diversity. The AP66 genome comprised 3.79 megabases across 67 contigs and was estimated to be 100% complete, with 0% contamination and no detectable strain heterogeneity. GTDB-Tk independently classified the genome as A. pittii, and multilocus sequence typing assigned it to sequence type 640 (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 average nucleotide identity between AP66 and Ac-14 was 99.9238%, and similarly high identities were observed with the closely related ST640 genomes BS1 and ANC 3678. Because these related genomes come from geographically and ecologically distinct sources, the authors suggest the lineage may have a potentially broad ecological distribution.

The genome carried the intrinsic β-lactamase genes blaADC-132 and blaOXA-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 kilobases, 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 metabolic modules for glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, the glyoxylate cycle and the 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. The authors are careful, however, to frame this as a sequence-based prediction: the study’s conclusions state explicitly that these findings do not establish phenotypic resistance, virulence, or any involvement of AP66 in the patient’s gastroenteritis. As a metagenome-assembled genome recovered from a mixed culture, AP66 represents an in silico reconstruction rather than a clinically characterized isolate.

The combination of intrinsic resistance determinants, virulence-associated homologues, mobile genetic elements and metabolic diversity, the researchers write, further illustrates the genomic versatility of A. pittii. The work adds a human-associated ST640 genome from Nigeria to the public record and offers a reference point for future phylogenomic comparisons across the Acinetobacter calcoaceticus-baumannii complex.

Subject of Research: Genomic characterization and phylogenomic placement of an Acinetobacter pittii ST640 metagenome-assembled genome from a human stool-derived mixed culture in Nigeria

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

Article References: Anunobi, O. O., Odiba, A. S., Gyebi, G. A., Chibuogwu, C. C., & Nwozor, N. C. (2026). Genomic characterization and phylogenomic placement of AP66, an Acinetobacter pittii ST640 metagenome-assembled genome recovered from a human stool-derived mixed culture in Nigeria. BMC Genomic Data. https://doi.org/10.1186/s12863-026-01492-w

Image Credits: AI Generated

DOI: 10.1186/s12863-026-01492-w

Keywords: Acinetobacter pittii, metagenome-assembled genome, ST640, Nigeria, antimicrobial resistance genes, prophage, phylogenomics, genomic islands, CRISPR, KEGG pathways, BMC Genomic Data, opportunistic pathogen