The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii

Daniel N Farrugia,Liam D H Elbourne,Melissa H Brown,Sasha G Tetu,Karl A Hassan,Anton Y Peleg,Bart A Eijkelkamp,Bhumika S Shah,Ian T Paulsen,Bridget C Mabbutt

doi:10.1371/journal.pone.0058628

Daniel N Farrugia, Liam D H Elbourne + Show 8 more

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https://doi.org/10.1371/journal.pone.0058628

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Abstract

Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable of resistance to multiple antimicrobials. Community-acquired A. baumannii in contrast, comprise a minor proportion of all A. baumannii infections and are highly susceptible to antimicrobial treatment. However, these infections also present acute clinical manifestations associated with high reported rates of mortality. We report the complete 3.70 Mbp genome of A. baumannii D1279779, previously isolated from the bacteraemic infection of an Indigenous Australian; this strain represents the first community-acquired A. baumannii to be sequenced. Comparative analysis of currently published A. baumannii genomes identified twenty-four accessory gene clusters present in D1279779. These accessory elements were predicted to encode a range of functions including polysaccharide biosynthesis, type I DNA restriction-modification, and the metabolism of novel carbonaceous and nitrogenous compounds. Conversely, twenty genomic regions present in previously sequenced A. baumannii strains were absent in D1279779, including gene clusters involved in the catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii antibiotic resistance island, known to bestow resistance to multiple antimicrobials in nosocomial strains. Phenomic analysis utilising the Biolog Phenotype Microarray system indicated that A. baumannii D1279779 can utilise a broader range of carbon and nitrogen sources than international clone I and clone II nosocomial isolates. However, D1279779 was more sensitive to antimicrobial compounds, particularly beta-lactams, tetracyclines and sulphonamides. The combined genomic and phenomic analyses have provided insight into the features distinguishing A. baumannii isolated from community-acquired and nosocomial infections.

Highlights

Acinetobacter baumannii is a significant nosocomial pathogen [1], known for its high intrinsic and laterally acquired resistance to antimicrobials [2,3] as well as its persistence on various abiotic surfaces [4,5,6]
A total of 3479 genes were annotated on the chromosome including 65 tRNAs, 6 rRNA operons and 3388 predicted protein coding sequences (CDS) (Table 1, Figure 1), which included 1019 annotated coding sequences 3388 (CDSs) (30%) predicted to encode hypothetical proteins
This MLSTbased analysis suggested that the nearest phylogenetic relatives of D1279779 were A. baumannii strains of the international clonal (IC) lineage II, though this strain did not fall within either the A. baumannii ICI or ICII lineages (Figure 2)

Summary

Introduction

Acinetobacter baumannii is a significant nosocomial pathogen [1], known for its high intrinsic and laterally acquired resistance to antimicrobials [2,3] as well as its persistence on various abiotic surfaces [4,5,6]. The complete genome sequences of ten A. baumannii strains have been determined to date: 1656-2 [7], AB0057 [8], AB307-0294 [8], ACICU [9], ATCC 17978 [10], AYE [11], MDR-TJ [12], MDR-ZJ06 [13], SDF [11] and TCDC-AB0715 [14]. Nine of these are nosocomial isolates, whereas A. baumannii SDF was isolated from a human body louse [11]. This organism is a public health issue outside of the hospital setting, in the form of community-acquired A. baumannii (CA-AB) infections

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