Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain

Abstract

We report the complete genome sequence of Acinetobacter baumannii strain AbH12O-A2, isolated during a large outbreak in Spain. The genome has 3,875,775 bp and 3,526 coding sequences, with 39.4% G+C content. The availability of this genome will facilitate the study of the pathogenicity of the Acinetobacter species.

GENOME ANNOUNCEMENT

Acinetobacter baumannii is a major cause of hospital-acquired infections. Its success in the hospital environment lies in its genetic versatility and its ability to persist in extreme conditions. During 2006–2008, 377 patients were colonized/infected with multiresistant A. baumannii strains in a hospital in Madrid, Spain. This was one of the most important nosocomial outbreak produced by A. baumannii known to date (1, 2). The clones isolated during the outbreak harbored different plasmids, all containing a bla_OXA-24 gene mobilized through a Xer recombination mechanism. Two mutations found to modify the gene expression of virulence factors provided an advantage to strain AbH12O-A2, whose genome sequence is described here. Previous studies have described the molecular mechanisms involved in the spread and epidemiology of this strain (1–6).

The total genomic DNA isolated from strain AbH12O-A2 was sheared into smaller fragments with the Covaris S/E210 system. Specific adapters were ligated to DNA fragments, and libraries containing inserts of 500 bp were purified and selectively enriched by PCR. After quality and quantity controls, 90 nucleotide fragments were paired-end sequenced in an HiSeq2000 system, with the TruSeq PE cluster kit version 3, cBot-HS, and TruSeq SBS kit-HS version 3 (Illumina Inc.). Once the gaps were identified, pairs of primers were designed and specific regions were amplified. Products were sequenced by BigDye Terminator version 3.1 chemistry in an ABI Seq Instrument (Applied Biosystems). After quality control of the raw data, clean data were aligned to Acinetobacter baumannii ATCC 17978, as a reference sequence. Assembly of the short reads into the genome sequence was performed using the SOAPdenovo version 1.05 program (http://soap.genomics.org.cn/soapdenovo.html). Key parameter K setting at 47 is determined by optimal assembly according to the paired-end and overlap relationship via mapping reads to contigs.

The A. baumannii AbH12O-A2 complete genome consists of 3,875,775 bp with a G+C content of 39.4% and contains 3,526 coding sequences, 72 tRNA genes, and 6 rRNA clusters. A. baumannii ACICU (score 518), A. baumannii AB900 (score 500), and A. baumannii AYE (score 483) were the closest neighbors to strain AbH12O-A2. Moreover, 56 genes associated with resistance to antibiotics and toxic compounds were found. The ResFinder bioinformatic application (7) was used to identify genes coding for antibiotic resistance. The following resistance genes were detected in the genome: aac(3)-lla, strA, and strB conferring resistance to aminoglycosides; bla_OXA-65, bla_ADC-25, and bla_TEM-1B conferring resistance to β-lactams; and sul2 conferring resistance to sulfonamides. Comparison of the AbH12O-A₂ genome with other completed genomes of A. baumannii by use of Mauve version 2.3.1 (8) revealed a resistance island (3,612,846–3,637,461 bp) flanked by two sequences of ISAba1 in opposite directions. PHAST (9) analysis revealed four putative intact phages integrated in the genome, two of which are similar to Acinetobacter phage Bphi-B1251 and another two that have not previously been identified in A. baumannii: one is similar to Enterobacteria phage mEp235 and the other is similar to Haemophilus phage SuMu.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in GenBank under accession number CP009534.