TY - JOUR
T1 - Antibiotic Consumption During the Coronavirus Disease 2019 Pandemic and Emergence of Carbapenemase-Producing Klebsiella pneumoniae Lineages Among Inpatients in a Chilean Hospital
T2 - A Time-Series Study and Phylogenomic Analysis
AU - Allel, Kasim
AU - Peters, Anne
AU - Conejeros, Jose
AU - Martínez, Jose R.W.
AU - Spencer-Sandino, Maria
AU - Riquelme-Neira, Roberto
AU - Rivas, Lina
AU - Rojas, Pamela
AU - Orellana Chea, Cristian
AU - García, Patricia
AU - Araos, Rafael
AU - Mcgovern, Olivia
AU - Patel, Twisha S.
AU - Arias, Cesar A.
AU - Lessa, Fernanda C.
AU - Undurraga, Eduardo A.
AU - Munita, Jose M.
N1 - Funding Information:
Financial support. This research was partially supported by the Agencia Nacional de Investigación y Desarrollo (ANID) Beca de Doctorado en el Extranjero Becas Chile, Chile (grant number 73200098; to K. A.); Agencia Nacional de Investigación y Desarrollo ANID/ Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias (FONDAP) Centro Nacional deInvestigación para la Gestión Integrada de Desastres Naturales (CIGIDEN) (grant number 1522A0005; to E. A. U.); Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT; grant number 1211933; to P. G., E. A. U., J. M. M); FONDECYT (grant number 1211947; to J. M. M.); and Canadian Institute for Advanced Research (CIFAR), under the Humans and Microbiome Programme to E. A. U.
Funding Information:
Potential conflicts of interest. R. A. reports funding from the US Centers for Disease Control and Prevention, the China Center for Disease Control, and the Chile Ministry of Science (ANID). They report receiving consulting fees for COVID-19 vaccines from AstraZeneca, Pfizer, and Sinovac; attending the Tecnofarma meeting on COVID-19 vaccines; and holding a leadership position with the COVID-19 external advisory group to the Chile Ministry of Health.
Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Infectious Diseases Society of America.
PY - 2023/7/5
Y1 - 2023/7/5
N2 - BACKGROUND: 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.METHODS: 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.RESULTS: 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.CONCLUSIONS: 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.
AB - BACKGROUND: 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.METHODS: 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.RESULTS: 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.CONCLUSIONS: 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.
KW - Antibiotic consumption
KW - Antimicrobial resistance
KW - COVID-19
KW - Carbapenemase-producing organisms
KW - Klebsiella pneumoniae
KW - Carbapenems/pharmacology
KW - Pandemics
KW - Colistin
KW - Humans
KW - Chile/epidemiology
KW - Klebsiella pneumoniae/genetics
KW - Phylogeny
KW - beta-Lactams
KW - Anti-Bacterial Agents/pharmacology
KW - Anti-Infective Agents
KW - Microbial Sensitivity Tests
KW - Inpatients
KW - Carbapenem-Resistant Enterobacteriaceae
KW - COVID-19/epidemiology
KW - Bacterial Proteins/genetics
KW - Hospitals
KW - beta-Lactamases/genetics
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U2 - 10.1093/cid/ciad151
DO - 10.1093/cid/ciad151
M3 - Article
C2 - 37406053
AN - SCOPUS:85163940906
SN - 1058-4838
VL - 77
SP - S20-S28
JO - Clinical Infectious Diseases
JF - Clinical Infectious Diseases
IS - Suppl 1
ER -