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 - 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
AN - SCOPUS:85140995003
SN - 2379-5077
VL - 7
JO - mSystems
JF - mSystems
IS - 5
ER -