Draft genome sequence of Acinetobacter junii strain ABJ_A23_1 isolated from soil in Gwagwalada, Nigeria

TL;DR

This paper presents the draft genome sequence of a soil-isolated Acinetobacter junii strain from Nigeria.

Contribution

The study provides a new draft genome sequence of Acinetobacter junii strain ABJ_A23_1 from Nigeria.

Findings

The genome is 3,200,723 bp with 38.48% GC content.

It contains 3,075 genes, including 2,975 protein-coding sequences and 73 RNA genes.

An integrative conjugative element was identified in the genome.

Abstract

We report the draft genome sequence of Acinetobacter junii strain ABJ_A23_1 isolated from soil in Gwagwalada, Nigeria. The genome has a total size of 3,200,723 bp, 38.48% GC content, and 3,075 genes, including 2,975 protein-coding sequences, 73 RNA genes, and an integrative conjugative element.

Tables

TABLE 1. Assembly and genome annotation metrics for A. junii ABJ_A23_1

Metric	Value
Completeness	100
Contamination	0.09
Genome size (bp)	3,200,723
GC content (%)	38.48
Number of contigs	126
Contig N50 (bp)	62,941
Contig N90 (bp)	21,165
L 50	13
Total genes	3,075
CDSs (total)	3,002
Total coding genes	2,975
Total RNA	73
rRNA	5
tRNA	64
Repeat regions	1

Full text

ANNOUNCEMENT

The genus Acinetobacter comprises gram-negative, non-fermentative bacteria widely distributed in various environments (1, 2). Acinetobacter junii is a species within this genus that has been less studied compared to its clinically significant relatives in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (3). However, A. junii has emerged as an ecologically diverse, One Health pathogen that has been implicated in clinical infections (4, 5). In this study, we report the draft genome sequence of A. junii strain ABJ_A23_1 isolated from soil collected in Gwagwalada, Nigeria.

Acinetobacter junii strain ABJ_A23_1 was isolated from a stream sediment sample collected in Passo, Gwagwalada, Nigeria (8°58′51″N, 7°03′04″E; altitude, 177.64 m) in August 2024. The sample was pre-enriched in mineral salt medium supplemented with 0.2% sodium acetate for 5 h at 37°C and subsequently plated on CHROMagar Acinetobacter and incubated overnight at 37°C (6). Bright red colonies with morphology typical of Acinetobacter species were selected for further characterization. Genomic DNA was extracted from one of the colonies using the MasterPure DNA Purification Kit (Epicentre) and quantified using the Invitrogen Qubit Assay. Sequencing of the genome on the Illumina MiSeq platform generated 13,398,908 paired-end reads (2 × 150 bp). The genome sequence was de novo assembled using the SPAdes version 4.0 algorithm in shovill version 1.1.0 (7, 8). The completeness, contamination, and genomic metrics were assessed using checkm2 version 1.0.2 and QUAST version 5.2.0 (9, 10). The genome functional annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (11). The taxonomic position of the strain was confirmed through average nucleotide identity (ANI) analysis against the type strain of A. junii (12). Subsequently, antibiotic resistance genes were identified using ResFinder and the Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (13, 14). A web-based tool, ICEfinder version 3.0, was used to detect integrative and conjugative elements (ICEs) in the assembled genome (15).

The assembly resulted in 126 contigs with an N50 of 62,941 bp. The completeness of the genome of A. junii ABJ_A23_1 was estimated at 100%, with a contamination level of 0.09%. The draft genome has a total size of 3,200,723 bp, with a GC content of 38.48%. The average gene length is 311 bp. The NCBI PGAP annotation of the genome of A. junii ABJ_A23_1 identified a total of 3,075 genes, including 2,975 protein-coding genes and 73 RNA genes (64 tRNAs and 4 non-coding RNAs). A CRISPR array and an additional 27 pseudogenes were predicted (Table 1). ANI analysis revealed a 97.42% identity between the genome of strain ABJ_A23_1 (ASM4490305v1) and A. junii NCTC10307^T^ (46338_C01). This ANI value exceeds the species delineation threshold of 95%, confirming A. junii ABJ_A23_1 as a member of the A. junii species. While antibiotic resistance gene (ARG) prediction using ResFinder did not detect any ARG, including blaOXA genes, which are intrinsic to the genomes of many Acinetobacter species, CARD Resistance Gene Identifier analysis predicted the presence of a small multidrug resistance antibiotic efflux pump (qacG) conferring resistance to disinfecting agents and antiseptics. ICEberg version 3.0 analysis detected a 143,064 bp putative ICE with a type IV secretion system spanning between positions 2,229,798 and 2,372,861 bp.