Draft Genome Sequence of an Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strain.

Last year in 2013, we reported an outbreak due to indigo-pigmented Acinetobacter baumannii strains in a hospital from Buenos Aires, Argentina. Here, we present the draft genome sequence of one of the strains (A. baumannii A33405) involved in the outbreak. This isolate was categorized as extensively drug-resistant (XDR) and harbors different genetic elements associated with horizontal genetic transfer and multiple antibiotic resistances.

GENOME ANNOUNCEMENT

Acinetobacter baumannii has been recognized as one of the major causes of hospital-acquired infections (1, 2). Its ability to develop extreme drug resistance and survive for long periods on inanimate surfaces makes A. baumannii one of the most important enemies in intensive care units, being the cause of many outbreaks (1, 3). In the year 2013, we reported an outbreak due to indigo-pigmented A. baumannii strains, which are not common in clinical settings (4). Molecular studies revealed that all the isolates belonging to the clonal complex 113B (CC113B/CC79P) and were extensively drug resistant. They possessed the transposon Tn2006, class 2 integrons, AbaR-type islands, IS125, IS26, strA, strB, florR, and the small recombinase ISCR2 associated with the sul2 gene, preceded by ISAba1 (4). To date, there are no whole-genome sequences from indigo-pigmented A. baumannii strains available in GenBank/EMBL/DDBJ. Here, we report the draft genome sequence of an indigo-pigmented A. baumannii strain, A33405, which was isolated from a 65-year-old male patient from a coronary care unit (4).

Using pan-PCR as a molecular technique, this strain was classified as belonging to the CC113B/CC79P clonal complex, which was shown to be prevalent in clinical A. baumannii isolates from our country (5).

A draft sequence for A. baumannii A33405 was developed using Illumina MiSeq at the Argentinian Consortium of Genomic Technology (ACGT). A total of 1,615,755 high-quality paired-end reads were produced, with an average insertion size of 327 reads. De novo assembly was performed with the SPAdes assembler version 3.1.0 (6), using a preassembly approach with Velvet (7). Of the generated reads, 99.5% that showed an average length of 231 reads were mapped, resulting in a mean coverage of 31× (sequence depth). The assembled contigs sum 3,892,826 base pairs, with an N50 contig size of 91,003 (max length, 253,127), and have a G+C content of 39.07%. Open reading frames were predicted and annotated using the RAST server, which identified 3,741 possible open reading frames (ORFs) and 71 copies of rRNA operons (3). Using the tRNAscan-SE, a total of 62 tRNA genes were identified (8).

In order to confirm the result obtained by pan-PCR, in silico multilocus sequence typing (MLST) was carried out according to the scheme of Bartual et al. (9) by searching and comparing the internal regions of gltA, gyrB, gdhB, recA, cpn60, gpi, and rpoD (http://pubmlst.org/abaumannii/). The in silico MLST results using the concatenated allele sequences confirm the pan-PCR result, showing that A33405 belongs to sequence type 227 (ST227)/CC113.

The possibility of getting the complete genome sequence of strain A33405, which is not only the first whole-genome sequence of a CC113B/CC79P strain but also the first whole-genome sequence of an indigo-pigmented A. baumannii strain, is allowing us to get a more detailed analysis and study novel features in A. baumannii. Also, it will allow us to perform whole-genome sequence comparisons and phylogenetic analyses, thus expanding our understanding of this global pathogen and its characteristics in different parts of the world. The characterization of the resistance determinants and the virulence factors present in A. baumannii strain A33405 will be included in a future publication.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JPXZ00000000. The version described in this paper is version JPXZ01000000.