Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.
Highlights
Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important pathogen in healthcare-associated infections and leads to high mortality, especially in intensive care units [1]
We provide a comparative analysis of the single nucleotide variant (SNV) approach, where single nucleotide differences compared to a reference genome are identified and compared among isolates, and the multilocus sequence typing (MLST) approach, where variations in loci of genes are compared among isolates
This study investigated 11 A. baumannii isolates collected in 2015 and 2016 at Seoul National University Bundang Hospital; 9 of the isolates were obtained from the intensive care unit (ICU) and Ward A during a hospital outbreak in 2016, and 2 of the isolates were from patients with CRAB from 2015 in the same institution (Table 1)
Summary
Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important pathogen in healthcare-associated infections and leads to high mortality, especially in intensive care units [1]. The emergence of multidrug-resistant A. baumannii is a challenge in the treatment of patients and infection control since it has the ability to survive on the surface of plastics and can spread in the hospital environment [3]. A well-validated workflow of rapid screening, antimicrobial resistance (AMR) analysis, and accurate strain typing is required for managing antimicrobial resistant strains in healthcare-associated infections [6]. Typing clinical isolates by suitable methods allows health professionals to distinguish outbreak isolates from sporadic or endemic isolates and design rational pathogen control methods such as isolation, cleaning, and/or removal of sources of infection [7]
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