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