Microbiologically confirmed infections and antibiotic-resistance in a national surveillance study of hospitalised patients who died with COVID-19, Italy 2020-2021

Antimicrob Resist Infect Control. 2022 May 21;11(1):74. doi: 10.1186/s13756-022-01113-y.

Abstract

Background: Patients hospitalised for COVID-19 may present with or acquire bacterial or fungal infections that can affect the course of the disease. The aim of this study was to describe the microbiological characteristics of laboratory-confirmed infections in hospitalised patients with severe COVID-19.

Methods: We reviewed the hospital charts of a sample of patients deceased with COVID-19 from the Italian National COVID-19 Surveillance, who had laboratory-confirmed bacterial or fungal bloodstream infections (BSI) or lower respiratory tract infections (LRTI), evaluating the pathogens responsible for the infections and their antimicrobial susceptibility.

Results: Among 157 patients with infections hospitalised from February 2020 to April 2021, 28 (17.8%) had co-infections (≤ 48 h from admission) and 138 (87.9%) had secondary infections (> 48 h). Most infections were bacterial; LRTI were more frequent than BSI. The most common co-infection was pneumococcal LRTI. In secondary infections, Enterococci were the most frequently recovered pathogens in BSI (21.7% of patients), followed by Enterobacterales, mainly K. pneumoniae, while LRTI were mostly associated with Gram-negative bacteria, firstly Enterobacterales (27.4% of patients, K. pneumoniae 15.3%), followed by A. baumannii (19.1%). Fungal infections, both BSI and LRTI, were mostly due to C. albicans. Antibiotic resistance rates were extremely high in Gram-negative bacteria, with almost all A. baumannii isolates resistant to carbapenems (95.5%), and K. pneumoniae and P. aeruginosa showing carbapenem resistance rates of 59.5% and 34.6%, respectively.

Conclusions: In hospitalised patients with severe COVID-19, secondary infections are considerably more common than co-infections, and are mostly due to Gram-negative bacterial pathogens showing a very high rate of antibiotic resistance.

Keywords: Antimicrobial resistance; Bacterial infections; Bloodstream infections; COVID-19; Co-infections; Fungal infections; Lower respiratory tract infections; Secondary infections.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents* / adverse effects
  • Anti-Bacterial Agents* / pharmacology
  • Anti-Bacterial Agents* / therapeutic use
  • Bacteremia* / complications
  • Bacteremia* / drug therapy
  • Bacteremia* / microbiology
  • COVID-19* / complications
  • Coinfection* / drug therapy
  • Coinfection* / epidemiology
  • Coinfection* / microbiology
  • Drug Resistance, Microbial*
  • Fungemia* / complications
  • Fungemia* / drug therapy
  • Fungemia* / microbiology
  • Hospitalization / statistics & numerical data
  • Humans
  • Italy / epidemiology
  • Population Surveillance
  • Respiratory Tract Infections / complications
  • Respiratory Tract Infections / drug therapy
  • Respiratory Tract Infections / microbiology
  • Respiratory Tract Infections / virology

Substances

  • Anti-Bacterial Agents