Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii

Abstract

The recent emergence of multidrug resistance (MDR) in Acinetobacter baumannii has raised concern in health care settings worldwide. In order to understand the repertoire of resistance determinants and their organization and origins, we compared the genome sequences of three MDR and three drug-susceptible A. baumannii isolates. The entire MDR phenotype can be explained by the acquisition of discrete resistance determinants distributed throughout the genome. A comparison of closely related MDR and drug-susceptible isolates suggests that drug efflux may be a less significant contributor to resistance to certain classes of antibiotics than inactivation enzymes are. A resistance island with a variable composition of resistance determinants interspersed with transposons, integrons, and other mobile genetic elements is a significant but not universal contributor to the MDR phenotype. Four hundred seventy-five genes are shared among all six clinical isolates but absent from the related environmental species Acinetobacter baylyi ADP1. These genes are enriched for transcription factors and transporters and suggest physiological features of A. baumannii that are related to adaptation for growth in association with humans.

FIG. 1.

Phylograms of A. baumannii isolates. The relationships of A. baumannii isolates were inferred based on the similarity of shared sequences that have most likely been retained in each genome from a common ancestor (A) and based on the extent of unique gene content in each isolate (B). (A) A maximum likelihood tree was constructed using dnaml from the PHYLIP package, based on the concatenated DNA sequences of 1,942 ORFs that were reciprocal best matches in each genome. Bar, 0.01 substitution per nucleotide. (B) A tree based on the shared content of accessory genes was constructed as described previously (44). Bar, 10% difference in gene content.

FIG. 2.

GO categories of core and A. baumannii-specific genes. GO categories were inferred for AB0057 genes by using the JCVI Annotation Engine. The percentage of genes in each GO category was determined for core A. baumannii genes (those present in all six clinical isolates), Acinetobacter core genes (A. baumannii core genes that are also present in ADP1), and pan-A. baumannii accessory genes (core genes absent from ADP1), using WEGO (58). Percentages indicate the fractions of gene groups annotated with each GO category. Stars indicate GO categories that are significantly underrepresented (open) or overrepresented (filled) among pan-A. baumannii accessory genes compared to core genes (P < 0.05).

FIG. 3.

RI composition. (A) Modules that comprise components of the RI in sequenced A. baumannii genomes are designated by the letters A to J. A bold bar indicates that the region is present in an isolate. (B) Representative genes present in each module are listed. (C) The presence of various RI components in additional A. baumannii isolates was tested by PCR. *, PCR results were inferred based on a BLAST search of each genome with primer sequences; ^a, these primer pairs flank the island location, so successful PCR amplification (+) indicates that the island, an insertion that is too long for PCR amplification, is absent. AB0057 was reported previously as AB057 (19). Abbreviations: AMP, ampicillin; CIP, ciprofloxacin; CAZ, ceftazidime; FEP, cefepime; AMK, amikacin; TOB, tobramycin; SAM, ampicillin-sulbactam; MEM, meropenem; IPM, imipenem. Hujer, data obtained from reference .