Complete Genome Sequence of Acinetobacter baumannii ATCC 19606^T, a Model Strain of Pathogenic Bacteria Causing Nosocomial Infection

Acinetobacter baumannii ATCC 19606^T, which is often used in genetic studies as a routine model microorganism, belongs to sequence type 52 (ST52), showing beta-lactam resistance. We present the complete 3.996-Mbp genome sequence (1 chromosome plus 2 plasmids), generated by combining long-read (MinION) and short-read (MiniSeq) sequencing data.

ABSTRACT

Acinetobacter baumannii ATCC 19606^T, which is often used in genetic studies as a routine model microorganism, belongs to sequence type 52 (ST52), showing beta-lactam resistance. We present the complete 3.996-Mbp genome sequence (1 chromosome plus 2 plasmids), generated by combining long-read (MinION) and short-read (MiniSeq) sequencing data.

ANNOUNCEMENT

Acinetobacter baumannii ATCC 19606^T, which was first reported in 1948 as an isolate from the urinary tract of a patient (1), was obtained from the American Type Culture Collection. A. baumannii is one of the leading causes of opportunistic nosocomial infections in immunocompromised hosts, and this human pathogen is responsible for a vast array of infections, of which ventilator-associated pneumonia and urinary tract and bloodstream infections are the most common. The mortality rate is serious and can reach up to 35% depending on the type of infection and the genetic background of the specific bacterial strain (2). A. baumannii is also known as one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) pathogens and tends to acquire resistance to various kinds of antibiotics relatively easily; therefore, this species is an emerging threat for humans (3). Here, we announce the complete genome sequence of A. baumannii ATCC 19606^T.

Strain ATCC 19606^T, which had been stored at −80°C, was streaked onto a Mueller-Hinton II agar (BD) plate and incubated at 37°C for about 16 h. Genomic DNA extraction was performed using the Genomic-tip 20/G kit (Qiagen). Whole-genome sequencing was performed using the MinION system (Oxford Nanopore Technologies [ONT]) and the MiniSeq system (Illumina) with a high-output reagent kit (300 cycles). The library for MinION sequencing was prepared using a rapid barcoding kit (SQK-RBK004), and the library for Illumina sequencing was prepared using the Nextera XT DNA library prep kit. In this study, default parameters were used for all software except where otherwise noted. Base calling of ONT reads was performed using Guppy v3.2.1. The MinION reads were filtered using Filtlong v0.2.0 (https://github.com/rrwick/Filtlong; lengths of ≥1,000 bp and quality scores of ≥10) to keep only the top 90% of reads, with a target output of 500 Mbp (N₅₀, 11,965 bp). These filtered reads were assembled de novo into three contigs using Canu v1.8 (4). The overlap region in the assembled contig was detected by a genome-scale sequence comparison using LAST (http://last.cbrc.jp) using the scaffold sequence for ATCC 19606 (GenBank accession number GCA_000737145) and was trimmed manually. Subsequently, long reads were mapped against the assembled genome with Racon v1.3.1.1 (5) twice to generate consensus sequences. These three contigs were combined with MiniSeq data (a total of 1,685,105 paired-end reads), which were quality filtered using Trimmomatic v0.30 (quality scores of ≥30) (6), to correct sequencing errors and to detect single nucleotide polymorphisms (SNPs) and indels using Pilon v1.20.1 (7) twice with binary alignment map (BAM) files generated from MinION and Illumina reads. Using Minimap 2 v2.17 (8), 99.7% of MiniSeq reads were mapped onto the final assembly, and the final genome coverage was 125×. The complete genome sequence was constructed as a total sequence of 3,995,851 bp, with a mean G+C content of 39.2%. A total of 3,884 coding DNA sequences (CDSs) and 6 sets of rRNA clusters were annotated using the DDBJ Fast Annotation and Submission Tool (DFAST) server (9). Using Pilon, the dnaA gene on the chromosome and rep-like gene on the plasmid were the first genes. The quality of the assembled genome sequence was evaluated using Benchmarking Universal Single-Copy Ortholog (BUSCO) v3 (10) with the Gammaproteobacteria odb9 data set. All 452 BUSCOs were located in the assembled genome. These six 16S rRNA genes shared 98.8% to 99.6% similarity with strain ATCC 19606^T (GenBank accession number Z93435). The genome sequence analyses were performed using ResFinder v3.2 (11) and MLST v2.0 (12) with default parameters. Strain ATCC 19606^T was classified by multilocus sequence typing as sequence type 52 (ST52), and the beta-lactam resistance genes bla_ADC-25 and bla_OXA-98 and the sulfonamide resistance gene sul2 were detected.

Our intention in publishing the complete genome sequence of strain ATCC 19606^T is to underpin studies of antimicrobial-resistant A. baumannii strains found in hospitals across the globe.

Data availability.

The complete genome sequence of A. baumannii strain ATCC 19606^T has been deposited in DDBJ/ENA/GenBank under accession numbers AP022836, AP022837, and AP022838. The raw sequence data are available in the Sequence Read Archive under accession numbers DRX202781 and DRX202782.