Antibiotic Consumption During the Coronavirus Disease 2019 Pandemic and Emergence of Carbapenemase-Producing <i>Klebsiella pneumoniae</i> Lineages Among Inpatients in a Chilean Hospital: A Time-Series Study and Phylogenomic Analysis
Journal
Clinical Infectious Diseases
ISSN
1058-4838
1537-6591
Date Issued
2023
Author(s)
Kasim Allel
José Conejeros
José R W Martínez
Maria Spencer-Sandino
Pamela Rojas
Cristian Orellana Chea
Patricia García
Olivia McGovern
Twisha S Patel
Cesar A Arias
Fernanda C Lessa
Eduardo A Undurraga
Type
Resource Types::text::journal::journal article
URL Institutional Repository
Abstract
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Background</jats:title>
<jats:p>The impact of coronavirus disease 2019 (COVID-19) on antimicrobial use (AU) and resistance has not been well evaluated in South America. These data are critical to inform national policies and clinical care.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Methods</jats:title>
<jats:p>At a tertiary hospital in Santiago, Chile, between 2018 and 2022, subdivided into pre- (3/2018–2/2020) and post–COVID-19 onset (3/2020–2/2022), we evaluated intravenous AU and frequency of carbapenem-resistant Enterobacterales (CRE). We grouped monthly AU (defined daily doses [DDD]/1000 patient-days) into broad-spectrum β-lactams, carbapenems, and colistin and used interrupted time-series analysis to compare AU during pre- and post-pandemic onset. We studied the frequency of carbapenemase-producing (CP) CRE and performed whole-genome sequencing analyses of all carbapenem-resistant (CR) Klebsiella pneumoniae (CRKpn) isolates collected during the study period.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>Compared with pre-pandemic, AU (DDD/1000 patient-days) significantly increased after the pandemic onset, from 78.1 to 142.5 (P < .001), 50.9 to 110.1 (P < .001), and 4.1 to 13.3 (P < .001) for broad-spectrum β-lactams, carbapenems, and colistin, respectively. The frequency of CP-CRE increased from 12.8% pre–COVID-19 to 51.9% after pandemic onset (P < .001). The most frequent CRE species in both periods was CRKpn (79.5% and 76.5%, respectively). The expansion of CP-CRE harboring blaNDM was particularly noticeable, increasing from 40% (n = 4/10) before to 73.6% (n = 39/53) after pandemic onset (P < .001). Our phylogenomic analyses revealed the emergence of two distinct genomic lineages of CP-CRKpn: ST45, harboring blaNDM, and ST1161, which carried blaKPC.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Conclusions</jats:title>
<jats:p>AU and the frequency of CP-CRE increased after COVID-19 onset. The increase in CP-CRKpn was driven by the emergence of novel genomic lineages. Our observations highlight the need to strengthen infection prevention and control and antimicrobial stewardship efforts.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Background</jats:title>
<jats:p>The impact of coronavirus disease 2019 (COVID-19) on antimicrobial use (AU) and resistance has not been well evaluated in South America. These data are critical to inform national policies and clinical care.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Methods</jats:title>
<jats:p>At a tertiary hospital in Santiago, Chile, between 2018 and 2022, subdivided into pre- (3/2018–2/2020) and post–COVID-19 onset (3/2020–2/2022), we evaluated intravenous AU and frequency of carbapenem-resistant Enterobacterales (CRE). We grouped monthly AU (defined daily doses [DDD]/1000 patient-days) into broad-spectrum β-lactams, carbapenems, and colistin and used interrupted time-series analysis to compare AU during pre- and post-pandemic onset. We studied the frequency of carbapenemase-producing (CP) CRE and performed whole-genome sequencing analyses of all carbapenem-resistant (CR) Klebsiella pneumoniae (CRKpn) isolates collected during the study period.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>Compared with pre-pandemic, AU (DDD/1000 patient-days) significantly increased after the pandemic onset, from 78.1 to 142.5 (P < .001), 50.9 to 110.1 (P < .001), and 4.1 to 13.3 (P < .001) for broad-spectrum β-lactams, carbapenems, and colistin, respectively. The frequency of CP-CRE increased from 12.8% pre–COVID-19 to 51.9% after pandemic onset (P < .001). The most frequent CRE species in both periods was CRKpn (79.5% and 76.5%, respectively). The expansion of CP-CRE harboring blaNDM was particularly noticeable, increasing from 40% (n = 4/10) before to 73.6% (n = 39/53) after pandemic onset (P < .001). Our phylogenomic analyses revealed the emergence of two distinct genomic lineages of CP-CRKpn: ST45, harboring blaNDM, and ST1161, which carried blaKPC.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Conclusions</jats:title>
<jats:p>AU and the frequency of CP-CRE increased after COVID-19 onset. The increase in CP-CRKpn was driven by the emergence of novel genomic lineages. Our observations highlight the need to strengthen infection prevention and control and antimicrobial stewardship efforts.</jats:p>
</jats:sec>
Cite this document
Allel, K., Peters, A., Conejeros, J., Martínez, J. R. W., Spencer-Sandino, M., Riquelme-Neira, R., Rivas, L., Rojas, P., Orellana Chea, C., García, P., Araos, R., McGovern, O., Patel, T. S., Arias, C. A., Lessa, F. C., Undurraga, E. A., & Munita, J. M. (2023). Antibiotic consumption during the coronavirus disease 2019 pandemic and emergence of carbapenemase-producing klebsiella pneumoniae lineages among inpatients in a chilean hospital: A time-series study and phylogenomic analysis. Clinical Infectious Diseases, 77(Supplement_1), S20-S28. https://doi.org/10.1093/cid/ciad151
Subjects
antibiotic consumption
;
antimicrobial resistance
;
carbapenemase-producing organisms
;
covid-19
;
klebsiella pneumoniae
;
anti-bacterial agents
;
anti-infective agents
;
bacterial proteins
;
beta-lactamases
;
beta-lactams
;
carbapenem-resistant enterobacteriaceae
;
carbapenems
;
chile
;
colistin
;
covid-19
;
hospitals
;
humans
;
inpatients
;
klebsiella pneumoniae
;
microbial sensitivity tests
;
pandemics
;
phylogeny
;
antibiotic agent
;
carbapenemase
;
cefepime
;
ceftazidime
;
colistin
;
ertapenem
;
imipenem
;
meropenem
;
piperacillin plus tazobactam
;
antiinfective agent
;
bacterial protein
;
beta lactam
;
beta lactamase
;
carbapenem derivative
;
carbapenemase
;
adult
;
antimicrobial stewardship
;
article
;
bacterial genome
;
bacterium isolate
;
carbapenem resistant klebsiella pneumoniae
;
carbapenemase producing enterobacteriaceae
;
chile
;
controlled study
;
coronavirus disease 2019
;
gene frequency
;
hospital patient
;
human
;
major clinical study
;
nonhuman
;
pandemic
;
phylogenomics
;
prospective study
;
tertiary care center
;
time series analysis
;
whole genome sequencing
;
carbapenem-resistant enterobacteriaceae
;
chile
;
coronavirus disease 2019
;
genetics
;
hospital
;
klebsiella pneumoniae
;
microbial sensitivity test
;
pandemic
;
phylogeny