Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890.

Thanwa Wongsuk,Siriphan Boonsilp,Anchalee Homkaew,Konrawee Thananon,Worrapoj Oonanant,Abdelazeem Mohamed Algammal

doi:10.1371/journal.pone.0264374

Thanwa Wongsuk, Siriphan Boonsilp + Show 4 more

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https://doi.org/10.1371/journal.pone.0264374

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Abstract

Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented extensively, complete knowledge on the antibiotic-resistant mechanisms and virulence factors responsible for pathogenesis has not been entirely elucidated. This study investigated the drug resistance pattern and characterized the genomic sequence by de novo assembly of PDR A. baumannii strain VJR422, which was isolated from a catheter-sputum specimen. The results showed that the VJR422 strain was resistant to any existing antibiotics. Based on de novo assembly, whole-genome sequences showed a total genome size of 3,924,675-bp. In silico and conventional MLST analysis of sequence type (ST) of this strain was new ST by Oxford MLST scheme and designated as ST1890. Moreover, we found 10,915 genes that could be classified into 45 categories by Gene Ontology (GO) analysis. There were 1,687 genes mapped to 34 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The statistics from Clusters of Orthologous Genes (COG) annotation identified 3,189 genes of the VJR422 strain. Regarding the existence of virulence factors, a total of 59 virulence factors were identified in the genome of the VJR422 strain by virulence factors of pathogenic bacteria databases (VFDB). The drug-resistant genes were investigated by searching in the Comprehensive Antibiotic Resistance Database (CARD). The strain harbored antibiotic-resistant genes responsible for aminoglycoside, β-lactam-ring-containing drugs, erythromycin, and streptogramin resistance. We also identified resistance-nodulation-cell division (RND) and the major facilitator superfamily (MFS) associated with the antibiotic efflux pump. Overall, this study focused on A. baumannii strain VJR422 at the genomic level data, i.e., GO, COG, and KEGG. The antibiotic-resistant genotype and phenotype as well as the presence of potential virulence associated factors were investigated.

Highlights

Acinetobacter baumannii is an opportunistic, gram-negative coccobacilli [1] commonly associated with hospital-acquired nosocomial infections that can cause bacteremia, pneumonia, meningitis, and urinary tract infections [2, 3]
A. baumannii strain VJR422 was isolated from the catheter-aspirated sputum of a patient who admitted to Vajira hospital
The sequence type of A. baumannii VJR422 was ST2 (2-2-2-2-2-2-2) based on the seven housekeeping genes in the Pasteur Multilocus Sequence Typing (MLST) scheme [61], which belong to international Clone II (IC-II) [62]

Summary

Introduction

Acinetobacter baumannii is an opportunistic, gram-negative coccobacilli [1] commonly associated with hospital-acquired nosocomial infections that can cause bacteremia, pneumonia, meningitis, and urinary tract infections [2, 3]. It is considered the most common organism in the intensive care unit (ICU) and has been recognized as an emerging cause of nosocomial outbreaks globally [3]. MDR-A. baumannii was suggested as being extensively drug-resistant (XDR), which refers to resistance to all antibiotics except colistin and tigecycline, and an XDRA. Pan drug-resistant (PDR) A. baumannii strains have been reported to resist colistin and tigecycline [24–27]. Some strains share genes related to adherence, invasion and survival, and form biofilms on the surface [31, 32]

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