Microbiologically confirmed infections and antibiotic-resistance in a national surveillance study of hospitalised patients who died with COVID-19, Italy 2020–2021
Authors: Floridia Marco , Giuliano Marina , Monaco Monica , Palmieri Luigi , Lo Noce Cinzia , Palamara Anna Teresa , Pantosti Annalisa , Brusaferro Silvio , Onder Graziano ,   The Italian National Institute of Health COVID-19 Mortality Group, Palmieri Luigi , Agazio Elvira , Barbariol Pierfrancesco , Bella Antonino , Benelli Eva , Bertinato Luigi , Bocci Matilde , Boros Stefano , Bressi Marco , Calcagnini Giovanni , Canevelli Marco , Censi Federica , Ciervo Alessandra , Colaizzo Elisa , Da Cas Roberto , Del Manso Martina , Di Benedetto Corrado , Donfrancesco Chiara , Fabiani Massimo , Facchiano Francesco , Floridia Marco , Galati Fabio , Giuliano Marina , Grisetti Tiziana , Guastadisegni Cecilia , Lega Ilaria , Lo Noce Cinzia , Maiozzi Pietro , Manno Valerio , Martini Margherita , Massari Marco , Urdiales Alberto Mateo , Mattei Eugenio , Meduri Claudia , Meli Paola , Menniti Ippolito Francesca , Minelli Giada , Onder Graziano , Petrone Daniele , Pezzotti Patrizio , Pricci Flavia , Punzo Ornella , Quarata Federica , Raparelli Valeria , Riccardo Flavia , Rocchetto Simone , Sacco Chiara , Salerno Paolo , Sarti Giulia , Serra Debora , Spila Alegiani Stefania , Spuri Matteo , Tallon Marco , Tamburo De Bella Manuela , Tiple Dorina , Toccaceli Blasi Marco , Trentin Federica , Unim Brigid , Vaianella Luana , Vanacore Nicola , Vescio Maria Fenicia , Villani Emanuele Rocco , Weimer Liliana Elena , Brusaferro Silvio 
Published: May 2022

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 byEnterobacterales, mainlyK. pneumoniae, while LRTI were mostly associated with Gram-negative bacteria, firstlyEnterobacterales(27.4% of patients,K. pneumoniae15.3%), followed byA. baumannii(19.1%). Fungal infections, both BSI and LRTI, were mostly due toC. albicans. Antibiotic resistance rates were extremely high in Gram-negative bacteria, with almost allA. baumanniiisolates resistant to carbapenems (95.5%), andK. pneumoniaeandP. aeruginosashowing 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.