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

Kasim Allel; Anne Peters; José Conejeros; José R W Martínez; Maria Spencer-Sandino; Roberto Riquelme-Neira; RIVAS JIMENEZ, LINA MARIA; Pamela Rojas; Cristian Orellana Chea; Patricia García; ARAOS BRALIC, RAFAEL IGNACIO; Olivia McGovern; Twisha S Patel; Cesar A Arias; Fernanda C Lessa; Eduardo A Undurraga; MUNITA SEPULVEDA, JOSE MANUEL

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

Anne Peters

Facultad de Medicina Clínica Alemana Universidad del Desarrollo

José Conejeros

José R W Martínez

Maria Spencer-Sandino

Roberto Riquelme-Neira

Facultad de Medicina Clínica Alemana Universidad del Desarrollo

RIVAS JIMENEZ, LINA MARIA

Facultad de Medicina Clínica Alemana Universidad del Desarrollo

Pamela Rojas

Cristian Orellana Chea

Patricia García

ARAOS BRALIC, RAFAEL IGNACIO

Facultad de Medicina Clínica Alemana Universidad del Desarrollo

Olivia McGovern

Twisha S Patel

Cesar A Arias

Fernanda C Lessa

Eduardo A Undurraga

MUNITA SEPULVEDA, JOSE MANUEL

Facultad de Medicina Clínica Alemana Universidad del Desarrollo

Type

Resource Types::text::journal::journal article

DOI

10.1093/cid/ciad151

URL

https://investigadores.udd.cl/handle/123456789/8347

Abstract

Abstract 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 &lt; .001), 50.9 to 110.1 (P &lt; .001), and 4.1 to 13.3 (P &lt; .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 &lt; .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 &lt; .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.