Diversity of Acinetobacter baumannii in four French military hospitals, as assessed by multiple locus variable number of tandem repeats analysis

Abstract

Background: Infections by A. calcoaceticus-A. baumannii (ACB) complex isolates represent a serious threat for wounded and burn patients. Three international multidrug-resistant (MDR) clones (EU clone I-III) are responsible for a large proportion of nosocomial infections with A. baumannii but other emerging strains with high epidemic potential also occur.

Methodology/principal findings: We automatized a Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) protocol and used it to investigate the genetic diversity of 136 ACB isolates from four military hospitals and one childrens hospital. Acinetobacter sp other than baumannii isolates represented 22.6% (31/137) with a majority being A. pittii. The genotyping protocol designed for A.baumannii was also efficient to cluster A. pittii isolates. Fifty-five percent of A. baumannii isolates belonged to the two international clones I and II, and we identified new clones which members were found in the different hospitals. Analysis of two CRISPR-cas systems helped define two clonal complexes and provided phylogenetic information to help trace back their emergence.

Conclusions/significance: The increasing occurrence of A. baumannii infections in the hospital calls for measures to rapidly characterize the isolates and identify emerging clones. The automatized MLVA protocol can be the instrument for such surveys. In addition, the investigation of CRISPR/cas systems may give important keys to understand the evolution of some highly successful clonal complexes.

Figure 1. Genetic diversity of 59 A. baumannii isolates.

A 40% cut-off value was used to define MLVA clusters, shown with different colors when containing 5 isolates or more. On the side are indicated the year of isolation, the source, the antibiotics resistance status and the existence of a CRISPR -cas system.

Figure 2. Genetic diversity of 56 A. baumannii isolates.

The legend is that of Figure 1.

Figure 3. Polymorphism of the AYE CRISPR locus in A. baumannii.

A) Schematic representation of the CRISPR locus in three sequenced genomes and at the growing end of isolates A28, P054 and P065. Arrows show the position of primers used to amplify a portion of the locus. Specific spacers are shown with grey boxes. B) Sequence of the growing end of strain AB307 and isolate A28. The sequence flanking the last DR is in italics.