Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Abstract

Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen. The Acinetobacter genus is comprised of 34 named species, many of which are found ubiquitously in the environment (1). The most clinically relevant species are members of what is known as the Acinetobacter calcoaceticus-baumannii (Acb) complex, which include A. baumannii, A. nosocomialis, A. pittii, and A. calcoaceticus (2). The organisms of the Acb complex are difficult to distinguish from each other using traditional culturing and molecular diagnostic methods employed in the current clinical microbiology laboratories (3). A. baumannii is the most frequently isolated Acinetobacter species in the health care setting (4), partly due to its ability to survive on abiotic surfaces for long periods of time (5), as well as its ability to rapidly develop antibiotic resistance (6). It is an important emerging nosocomial pathogen associated with common infections, multidrug resistance, and a high transmission rate within hospitals all over the world (7).Prior genomic studies of A. baumannii have mainly focused on multidrug-resistant strains and have identified key determinants associated with resistance (8-14). A genomic comparison of six clinical isolates of A. baumannii concluded that despite extensive genome-wide similarity, the resistance gene repertoire was highly variable, even in the genomically closely related isolates (10). In addition, anothe...

Antagonism and population dynamics of Acinetobacter baumannii from US military treatment centers

“…Our finding of extensive genetic diversity among clinical isolates, with a few dominant genetic clusters, is consistent with previous studies of hospital-associated A. baumannii (Wallace et al, 2016;Wright et al, 2014). By including the reference strains 19606, AYE and ACICU in this study, as well as previously published isolates (Table S1), we may infer that the major clades identified in this study correspond to Pasteur multi-locus sequence types (MLST) ST1 and ST2 (Wallace et al, 2016). Isolates with known ST in group A1 belong to ST1, and clade B appears to be equivalent to ST2.…”

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“…Our finding of extensive genetic diversity among clinical isolates, with a few 267 dominant genetic clusters, is consistent with previous studies of hospital-associated A. 268 baumannii (Wallace et al, 2016;Wright et al, 2014). By including the reference strains 19606, 269 AYE and ACICU in this study, as well as previously published isolates (Table S1), we may infer 270 that the major clades identified in this study correspond to Pasteur multi-locus sequence types 271 (MLST) ST1 and ST2 (Wallace et al, 2016).…”

“…268 baumannii (Wallace et al, 2016;Wright et al, 2014). By including the reference strains 19606, 269 AYE and ACICU in this study, as well as previously published isolates (Table S1), we may infer 270 that the major clades identified in this study correspond to Pasteur multi-locus sequence types 271 (MLST) ST1 and ST2 (Wallace et al, 2016). Isolates with known ST in group A1 belong to ST1, 272 and clade B appears to be equivalent to ST2.…”

Antibiotic Resistance Patterns and Prevalence of PER and VEB Resistance Genes among Clinical Isolates of ESBL-Producing Acinetobacter Baumannii

“…These bacteria are important opportunistic pathogens responsible for nosocomial infections. Acinetobacter baumannii is one of the main causes of hospital infections (1,2). Infections caused by this bacterium could be life threatening, particularly in patients who are hospitalized in the intensive care unit of hospitals such as patients with cystic fibrosis, neutropenia, immunodeficiency (3).…”

“…Thermal programs used for amplification of the PER gene was as follows: initial denaturation at 94 °C for 4 minutes, denaturation at 94 °C for 1 minute, annealing at 55 °C for 1 …”