Genome Sequences of Three Acinetobacter baumannii Strains Assigned to the Multilocus Sequence Typing Genotypes ST2, ST25, and ST78

Abstract

Acinetobacter baumannii is an emerging opportunistic Gram-negative pathogen responsible for hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant A. baumannii strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.

TEXT

Acinetobacter baumannii is an emerging opportunistic pathogen, causing a variety of nosocomial infections (13). Outbreaks of A. baumannii were caused by few genotypic clusters of strains that were initially named European clones I, II, and III and are now regarded as international (7, 10, 13) and referred to as ST1, ST2, and ST3, respectively, according to multilocus sequence typing (7). Epidemiological studies showed the prevalence of the international clone II lineage during the last few years (7, 8, 10, 13), as well as the occurrence of epidemics caused by multidrug-resistant strains belonging to novel genotypes ST25 and ST78 in several Mediterranean hospitals (8, 9).

The whole-genome sequences of six ST1 (1, 2, 15) and individual ST2, ST3, and ST77 A. baumannii strains were available to date (2, 11, 14, 15). Here, we announce the availability of three draft genome sequences for carbapenem-resistant A. baumannii ST2 strain 3990, ST78 strain 3909, and ST25 strain 4190, isolated during cross-transmission episodes that occurred at the Monaldi Hospital, Naples, Italy, during 2006, 2007, and 2009, respectively (8, 9).

The genomes were sequenced to at least 10-fold coverage using 454 FLX Titanium emPCR pyrosequencing (Roche) according to the manufacturer's recommendations. Draft genomes were assembled using Newbler and automatically annotated using the xBASE2 bacterial genome annotation service (4). The draft genome sequences of the ST2, ST25, and ST78 strains, respectively, consisted of 96, 396, and 236 contigs, comprised 4,015,011 bases, 4,032,291 bases, and 3,954,832 bases, and generated 3,806, 3,910, and 3,721 protein coding sequences by automated annotation against the A. baumannii AB0057 genome. Comparative analysis of the ST2, ST25, and ST78 genomes with the ACICU, AB0057, ABAYE, and ATCC17978 genomes using Mauve software (6) identified 3,068 homologous protein coding sequences at the same relative positions in the seven genomes. Sixty-three DNA segments, ranging in size from 3 to 126 kb, were present only in some of the seven genomes and were either missing or replaced by nonhomologous DNA sequences in others. Consistent with their close genetic relatedness, both the ST2 3990 and the ACICU strain carried a 15.4-kb region containing antimicrobial resistance genes inserted in the ATPase gene locus. At the corresponding chromosomal location, a 12.7-kb region flanked by transposases but devoid of resistance genes was identified in the ST78 but not in the ST25 strain.

Complete plasmid sequences for the ST2, ST25, and ST78 strains were obtained by comparing the DNA sequences of contigs with those determined by a primer-walking technique on purified plasmid preparations. Genome annotations were manually verified and corrected using the Artemis viewer (3). The ST2 3990 strain contained two plasmids, p1-ABST2 (63,320 bp) carrying a complete tra locus and p2-ABST2 (21,846 bp) carrying one copy of the carbapenem-hydrolyzing oxacillinase (CHDL) bla_OXA-58 gene, homologous to plasmids pACICU2 and pACICU1, respectively (11). The ST25 strain contained two distinct plasmids, p1-ABST25 (15,267 bp) and p2-ABST25 (8,970 bp), that both carried one copy of the CHDL bla_OXA-72 gene and were homologous to plasmids carrying the bla_OXA-24 gene (5, 12). The single plasmid p1-ABST78 (26,411 bp) identified in the ST78 strain contained one copy of the bla_OXA-58 gene and was homologous to plasmids p2-ABST2 and pACICU1 (11).

Nucleotide sequence accession numbers.

The draft genome sequences of strains 3990, 4190, and 3909 have been deposited at GenBank under accession numbers AEOY00000000, AEPA00000000, and AEOZ00000000, respectively.