TY - JOUR
T1 - Systematic Analysis of Mobile Genetic Elements Mediating b-Lactamase Gene Amplification in Noncarbapenemase- Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections
AU - Shropshire, W. C.
AU - Konovalova, A.
AU - McDaneld, P.
AU - Gohel, M.
AU - Strope, B.
AU - Sahasrabhojane, P.
AU - Tran, C. N.
AU - Greenberg, D.
AU - Kim, J.
AU - Zhan, X.
AU - Aitken, S.
AU - Bhatti, M.
AU - Savidge, T. C.
AU - Treangen, T. J.
AU - Hanson, B. M.
AU - Arias, C. A.
AU - Shelburne, S. A.
N1 - Funding Information:
Illumina short-read sequencing was done through the MDACC Advanced Technology Core (ATGC) using core grant CA016672 (ATGC) with the Illumina NovaSeq6000 (NIH 1S10OD024977-01). Support for this study was provided by the National Institute of Allergy and Infectious Diseases (NIAID) R21AI151536 and P01AI152999 for S.A.S. NIAID K24AI121296, R01AI134637, R01AI148342, and P01AI152999 supported C.A.A. B.M.H. was supported by the NIAID K01AI148593. The research in the A.K. laboratory is supported by NIGMS 1R01GM133904-01 and the Welch Foundation Research Grant AU-1998-20190330.
Funding Information:
Editor Zackery Bulman, University of Illinois at Chicago Copyright © 2022 Shropshire et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to S. A. Shelburne, sshelburne@mdanderson.org. The authors declare a conflict of interest. CAA reports grants from NIH, Merck, MeMed Diagnostics and Entasis Therapeutics. In addition, CAA receives royalties from UpToDate and editor's stipend from American Society for Microbiology. Received 31 May 2022 Accepted 26 July 2022 Published 29 August 2022
Publisher Copyright:
© 2022 Shropshire et al.
PY - 2022/9
Y1 - 2022/9
N2 - Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non- CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem- resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/ copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum b-lactamase (ESBL) genes (Wilcoxon Test; P-value , 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated b-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes.
AB - Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non- CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem- resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/ copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum b-lactamase (ESBL) genes (Wilcoxon Test; P-value , 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated b-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes.
KW - carbapenem resistance
KW - extended spectrum beta lactamase
KW - mobile genetic elements
KW - multi-drug resistance
KW - osmoporin gene regulation
KW - oxford nanopore technologies
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U2 - 10.1128/msystems.00476-22
DO - 10.1128/msystems.00476-22
M3 - Article
C2 - 36036505
AN - SCOPUS:85140995003
SN - 2379-5077
VL - 7
JO - mSystems
JF - mSystems
IS - 5
ER -