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

Kasim Allel, Anne Peters, Jose Conejeros, Jose R.W. Martínez, Maria Spencer-Sandino, Roberto Riquelme-Neira, Lina Rivas, Pamela Rojas, Cristian Orellana Chea, Patricia García, Rafael Araos, Olivia Mcgovern, Twisha S. Patel, Cesar A. Arias, Fernanda C. Lessa, Eduardo A. Undurraga, Jose M. Munita

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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 < .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.

Original languageEnglish (US)
Pages (from-to)S20-S28
JournalClinical Infectious Diseases
Volume77
Issue numberSuppl 1
DOIs
StatePublished - Jul 5 2023

Keywords

  • Antibiotic consumption
  • Antimicrobial resistance
  • COVID-19
  • Carbapenemase-producing organisms
  • Klebsiella pneumoniae
  • Carbapenems/pharmacology
  • Pandemics
  • Colistin
  • Humans
  • Chile/epidemiology
  • Klebsiella pneumoniae/genetics
  • Phylogeny
  • beta-Lactams
  • Anti-Bacterial Agents/pharmacology
  • Anti-Infective Agents
  • Microbial Sensitivity Tests
  • Inpatients
  • Carbapenem-Resistant Enterobacteriaceae
  • COVID-19/epidemiology
  • Bacterial Proteins/genetics
  • Hospitals
  • beta-Lactamases/genetics

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

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