TY - JOUR
T1 - Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow
AU - the Antibacterial Resistance Leadership Group
AU - Fida, Madiha
AU - Cunningham, Scott A.
AU - Murphy, Matthew P.
AU - Bonomo, Robert A.
AU - Hujer, Kristine M.
AU - Hujer, Andrea M.
AU - Kreiswirth, Barry N.
AU - Chia, Nicholas
AU - Jeraldo, Patricio R.
AU - Nelson, Heidi
AU - Zinsmaster, Nicole M.
AU - Toraskar, Nikhil
AU - Chang, Weizhong
AU - Patel, Robin
N1 - Funding Information:
We thank the Mayo Clinic Center for Individualized Medicine Microbiome Program for supporting this study. We thank Dag Harmsen for his thoughtful review of this manuscript. Dr. Patel is supported, in part, by UM1 AI104681. We thank the ARLG for providing isolates used in this study. We thank OpGen for providing the genotypic AST prediction data. This study was also supported in part by funds the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH) to R.A.B. under Award Numbers R01AI100560, R01AI063517, and R01AI072219, and the Cleveland Department of Veterans Affairs Award Number 1I01BX001974 to R.A.B. from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development, and the Geriatric Research Education and Clinical Center VISN 10. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or the Department of Veterans Affairs.
Funding Information:
We thank the Mayo Clinic Center for Individualized Medicine Microbiome Program for supporting this study. We thank Dag Harmsen for his thoughtful review of this manuscript. Dr. Patel is supported, in part, by UM1 AI104681. We thank the ARLG for providing isolates used in this study. We thank OpGen for providing the genotypic AST prediction data. This study was also supported in part by funds the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH) to R.A.B. under Award Numbers R01AI100560 , R01AI063517 , and R01AI072219 , and the Cleveland Department of Veterans Affairs Award Number 1I01BX001974 to R.A.B. from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development, and the Geriatric Research Education and Clinical Center VISN 10. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or the Department of Veterans Affairs.
Publisher Copyright:
© 2020 Elsevier Inc.
PY - 2020/5
Y1 - 2020/5
N2 - Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
AB - Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
KW - Core genome multilocus sequence typing
KW - Klebsiella pneumoniae
KW - Pulse field gel electrophoresis
KW - Whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85080069439&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85080069439&partnerID=8YFLogxK
U2 - 10.1016/j.diagmicrobio.2020.114996
DO - 10.1016/j.diagmicrobio.2020.114996
M3 - Article
C2 - 32098688
AN - SCOPUS:85080069439
VL - 97
JO - Diagnostic Microbiology and Infectious Disease
JF - Diagnostic Microbiology and Infectious Disease
SN - 0732-8893
IS - 1
M1 - 114996
ER -