Draft genome sequence of Acinetobacter baumannii Ab10, a clinical isolate from Hospital University Sains Malaysia (HUSM), Malaysia

TL;DR

This paper presents the genome sequence of a drug-resistant Acinetobacter baumannii strain isolated in Malaysia.

Contribution

The novel contribution is the genome sequence of strain Ab10, revealing multiple antibiotic resistance genes.

Findings

The genome of Acinetobacter baumannii Ab10 is 3.89 Mbp in size.

The strain carries antibiotic resistance genes including blaOXA-23, ant(3'')-Ila, blaADC-32, and blaOXA-699.

Abstract

Acinetobacter baumannii strain Ab10 retrieved in Malaysia in 2017 represents a pathogen carrying multiple antibiotic-resistant genes (blaOXA-23, ant(3”)-Ila, blaADC-32, and blaOXA-699). We introduce the 3.89 Mbp genome sequence from short-read sequencing (Illumina’s NovaSeq6000).

Full text

ANNOUNCEMENT

An Acinetobacter baumannii strain Ab10 was recovered from the peripheral blood of a Malay female pediatric patient (1 year 5 months) in June 2017 at Hospital Universiti Sains Malaysia (HUSM) Kubang Kerian, Kelantan, Malaysia. The patient presented with high-grade fever associated with vesicular rash secondary to Varicella zoster infection with toxic shock syndrome and was ventilated for 8 days. Blood cultures were performed using BD BACTEC FX Blood Culture System, and species identification was done using standard culture procedure and Vitek 2 Identification System (BioMérieux). Isolates were grown in tryptic soy broth at 37°C overnight and stored in 15% glycerol. The sample was retrieved from storage (−80°C) and grown in blood agar at 37°C for 18 hours. The sample collection was in compliance with the Universiti Sains Malaysia Human Ethical Committee (JEPeM, USM) (approval code USM/JEPeM/18010015).

Whole-cell DNA was processed from a culture grown on Mueller Hinton Agar for 18 hours at 37°C. Gram stain was used to check general cell morphology. The DNA was sent to a third-party company (GeneSeq) for whole-genome sequencing. DNA extraction was performed using the WizPrep gDNA mini kit (WizBio, South Korea) per the manufacturer’s instructions. Illumina library preparation was done using the Covaris UltraSonicator (Covaris, Woburn, USA) and processed using the NEB Ultra II Library Preparation kit (NEB, Ipswich, USA). The library was quantified using the Qubit fluorometer (Invitrogen, Waltham, USA) and TapeStation (Agilent, Santa Clara, USA), followed by concentration adjustment and sequencing on a NovaSeq6000 (150 bp read length, paired-end). A total of 10,148,656 reads were acquired and quality-controlled using Galaxy’s FastQC v.0.74+galaxy0 (1). The raw reads were adapter-trimmed and quality-trimmed with fastp v.0.23 (2) and assembled using Unicycler v.0.4.8, retaining only contigs of 500 bp or longer (3). Genome assembly statistics were obtained using QUAST v.5.2.0, reporting 144 contigs with the largest contig at 227,605 bp. The strain exhibited a total genome length of 3,890,005 bp at 196× coverage, with a 39.1% GC content, and an N50 of 76,135 (4). Genome completeness was evaluated using BUSCO5 v.5.3 with a complete single-copy gene value of 95.2% (5).

The NCBI PGAP annotation v.6.3 (JAPDKJ000000000) identified 3,849 genes, 3,651 protein-coding genes, and 71 RNAs. The nearest neighbor organism was determined to be A. baumannii ATCC 17978 according to RAST v.2.0 (6–8) and ANI Calculator with an OrthoANIu value of 97.6% (9, 10). Multilocus Sequence Typing (MLST) analysis revealed Ab10 to be of sequence type 1904 (Pasteur scheme) and unknown sequence type (Oxford scheme) (11). Gene analysis using Abricate v.1.0.1 (https://github.com/tseemann/abricate) (12) suggested potential resistance to carbapenem, spectinomycin, streptomycin, cephalosporin, and beta-lactam (13–15). In addition, one integrated prophage genome of 41.6 kbp (bases 2943-44619 region position) was detected using the PHASTER (upgrade 6) (16, 17). Insertion sequences ISAba26, ISAba63, ISAba22, ISAba1, and ISAba19 were detected using ISfinder (https://www-is.biotoul.fr/) (18). Default parameters were used for all software unless otherwise noted.