TY - JOUR
T1 - Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks
AU - Fitzpatrick, Margaret A.
AU - Ozer, Egon A.
AU - Hauser, Alan R.
N1 - Funding Information:
We thank Chao Qi and Michael Malczynski from the Northwestern Memorial Hospital Clinical Microbiology Laboratory for assisting with the identification and retrieval of Acinetobacter bloodstream isolates.Wealso thank Lisa Sadzewicz and Naomi Sengalamay at the University of Maryland Institute for Genome Sciences for assistance with the Illumina sequencing. M.A.F. participated in the study conception, design, and coordination, carried out the microbiological and molecular studies, performed data analysis, and helped draft the manuscript. E.A.O. participated in the study conception, design, and coordination, performed the bioinformatic analyses, aided in other data analyses, and helped draft the manuscript. A.R.H. participated in the study conception, design, and coordination and helped draft the manuscript. All authors read and approved the final manuscript. We declare no competing or conflicting interests. The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health, the American Cancer Society, or the Woman’s Board of Northwestern Memorial Hospital. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. HHS | National Institutes of Health (NIH) provided funding to Margaret A. Fitzpatrick, Egon A. Ozer, and Alan R. Hauser under grant numbers AI095207, AI053674, AI075191, AI099269, AI04831, and AI088286. American Cancer Society (ACS) provided funding to Egon A. Ozer under grant number MRSG-13-220-01-MPC. Funding was provided to Margaret A. Fitzpatrick through the Eleanor Wood Prince Grants Initiative, a project of the Woman’s Board of Northwestern Memorial Hospital.
Funding Information:
We thank Chao Qi and Michael Malczynski from the Northwestern Memorial Hospital Clinical Microbiology Laboratory for assisting with the identification and retrieval of Acinetobacter bloodstream isolates.Wealso thank Lisa Sadzewicz and Naomi Sengalamay at the University of Maryland Institute for Genome Sciences for assistance with the Illumina sequencing. M.A.F. participated in the study conception, design, and coordination, carried out the microbiological and molecular studies, performed data analysis, and helped draft the manuscript. E.A.O. participated in the study conception, design, and coordination, performed the bioinformatic analyses, aided in other data analyses, and helped draft the manuscript. A.R.H. participated in the study conception, design, and coordination and helped draft the manuscript. All authors read and approved the final manuscript. We declare no competing or conflicting interests. The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health, the American Cancer Society, or the Woman?s Board of Northwestern Memorial Hospital. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. HHS | National Institutes of Health (NIH) provided funding to Margaret A. Fitzpatrick, Egon A. Ozer, and Alan R. Hauser under grant numbers AI095207, AI053674, AI075191, AI099269, AI04831, and AI088286. American Cancer Society (ACS) provided funding to Egon A. Ozer under grant number MRSG-13-220-01-MPC. Funding was provided to Margaret A. Fitzpatrick through the Eleanor Wood Prince Grants Initiative, a project of the Woman?s Board of Northwestern Memorial Hospital.
Publisher Copyright:
© 2016, American Society for Microbiology. All Rights Reserved.
PY - 2016/3
Y1 - 2016/3
N2 - Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The bandbased techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.
AB - Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The bandbased techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.
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U2 - 10.1128/JCM.01818-15
DO - 10.1128/JCM.01818-15
M3 - Article
C2 - 26699703
AN - SCOPUS:84959511266
SN - 0095-1137
VL - 54
SP - 593
EP - 612
JO - Journal of clinical microbiology
JF - Journal of clinical microbiology
IS - 3
ER -