Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital

Abstract Background Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE). Objectives We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resist...

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Bibliographic Details
Published in:Journal of Antimicrobial Chemotherapy 2021-01, Vol.76 (2), p.380-384
Main Authors: Gomez-Simmonds, Angela, Annavajhala, Medini K, McConville, Thomas H, Dietz, Donald E, Shoucri, Sherif M, Laracy, Justin C, Rozenberg, Felix D, Nelson, Brian, Greendyke, William G, Furuya, E Yoko, Whittier, Susan, Uhlemann, Anne-Catrin
Format: Article
Language:English
Subjects:
Aged
Anti-Bacterial Agents - administration & dosage
Anti-Bacterial Agents - therapeutic use
Antiviral Agents - administration & dosage
Antiviral Agents - therapeutic use
Bacterial Proteins - genetics
beta-Lactamases - genetics
Carbapenem-Resistant Enterobacteriaceae - enzymology
Carbapenem-Resistant Enterobacteriaceae - genetics
Carbapenem-Resistant Enterobacteriaceae - isolation & purification
Cohort Studies
Comorbidity
COVID-19 - complications
COVID-19 - drug therapy
COVID-19 - epidemiology
COVID-19 - microbiology
Enterobacteriaceae Infections - complications
Enterobacteriaceae Infections - drug therapy
Enterobacteriaceae Infections - epidemiology
Enterobacteriaceae Infections - microbiology
Female
Hospitals
Humans
Male
Middle Aged
Nanopore Sequencing
New York City - epidemiology
Original Research
Phylogeny
Retrospective Studies
SARS-CoV-2
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Summary:Abstract Background Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE). Objectives We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19. Methods We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis. Results We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data. Conclusions While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.
ISSN:0305-7453
1460-2091
DOI:10.1093/jac/dkaa466