title: Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center.
abstract: Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistant Acinetobacter baumannii (MDRAB) at a large academic burn center. A reference genome from the index case was generated using de novo assembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first- and second-outbreak strains possessed a blaOXA-23-like group, while the third-outbreak strains harbored a blaOXA-40-like group. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.
authors.affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, North Carolina, USA kanamori@med.unc.edu.
authors.forename: Hajime
authors.initials: H
authors.lastname: Kanamori
authors.affiliation: University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
authors.forename: Christian M
authors.initials: CM
authors.lastname: Parobek
authors.affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, North Carolina, USA Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Weber
authors.affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
authors.forename: David
authors.initials: D
authors.lastname: van Duin
authors.affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, North Carolina, USA.
authors.forename: William A
authors.initials: WA
authors.lastname: Rutala
authors.affiliation: University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA North Carolina Jaycee Burn Center, University of North Carolina Health Care, Chapel Hill, North Carolina, USA.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Cairns
authors.affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
authors.forename: Jonathan J
authors.initials: JJ
authors.lastname: Juliano
mesh_terms: D000151:Acinetobacter Infections / Q000453:epidemiology* / Q000382:microbiology; D040981:Acinetobacter baumannii / Q000187:drug effects* / Q000235:genetics* / Q000472:pathogenicity; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001426:Bacterial Proteins / Q000235:genetics; D002053:Burn Units; D002056:Burns / Q000150:complications / Q000382:microbiology; D002648:Child; D024901:Drug Resistance, Multiple, Bacterial / Q000187:drug effects / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009657:North Carolina / Q000453:epidemiology; D012189:Retrospective Studies; D055815:Young Adult; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D001618:beta-Lactamases; C000599728:beta-lactamase OXA-23, Acinetobacter baumannii