Use of the Accessory Genome for Characterization and Typing of Acinetobacter baumannii

Abstract

Outbreak strains of Acinetobacter baumannii are highly clonal, and cross-infection investigations can be difficult. We sought targets based on AbaR resistance islands and on other genes found in some, but not all, sequenced isolates of A. baumannii among a set of clinical isolates (n ‫؍‬ 70) that included multiple representatives of a number of pulsed-field gel electrophoresis (PFGE)-defined types. These included representatives that varied in their profiles at two variable-number tandem repeat (VNTR) loci, which can provide discrimination within a PFGE cluster. Detection, or not, of each element sought provided some degree of discrimination among the set, with the presence or absence of genes coding for a phage terminase (ACICU_02185), a sialic acid synthase (ACICU_00080), a polysaccharide biosynthesis protein (AB57_0094), aphA1, bla TEM , and integron-associated orfX (Kyoto Encyclopedia of Genes and Genomes [KEGG] no. K03830) proving the most helpful in discriminating between closely related isolates in our panel. The results support VNTR data in describing distinct populations of highly similar isolates. Such analysis, in combination with other typing methods, can inform epidemiological investigations and provide additional characterization of isolates. Most genotypes carrying bla OXA-23-like were PCR positive for a yeeA-bla OXA-23 fragment found in an AbaR4-type island, suggesting that this is widespread.

AbaR4-Type Resistance Island Including the bla OXA-23 Gene in Acinetobacter nosocomialis Isolates

“…They were PCR positive for the AbaR-comM junction, confirming the presence of an AbaRtype resistance island. The structure of the AbaR-type resistance islands was determined by several PCR procedures and sequencing using previously published primers (9,10). Both showed the AbaR4 type, although their subtypes were also identified (see Fig.…”

Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data

“…In general, PCR-based typing assays, such as those designed for Streptococcus pneumoniae (13), Neisseria meningitidis (14), and Acinetobacter baumannii (15), are desirable because of their inherent advantages of low cost and high speed. The expense comprises the cost of standard PCR reagents, and the turnaround time consists of only the few hours needed to prepare DNA and run the PCR.…”

“…Several groups are attempting to take advantage of existing genome sequence data to design sequence-and PCR-based typing assays. In the last year, PCR-based typing assays have been published for organisms such as Streptococcus pneumoniae (13), Neisseria meningitidis (14), and Acinetobacter baumannii (15).…”

Are we closing in on an "elusive enemy"? The current status of our battle withAcinetobacter baumannii

“…Using VNTR analysis, in combination with other typing methods, can inform epidemiological investigations and provide additional characterization of isolates. 59 Where do we stand with A. baumannii? Because of the "complex" nature of A. baumannii (Table 1), we conclude that the success of A. baumannii as a pathogen is largely driven by the contemporary dynamics of selective pressure driven by broad spectrum antibiotics.…”