SHORT COMMUNICATION NEW MICROBIOLOGICA, 43, 4, 186-190, 2020, ISSN 1121-7138 Tracking over time the developing gut microbiota in newborns admitted to a neonatal intensive care unit during an outbreak caused by ESBL-producing Klebsiella pneumoniae Simona Panelli 1 , Marta Corbella 2 , Alessandra Gazzola 2,3 , Antonio Piralla 2 , Alessia Girello 2 , Simone Rampelli 4 , Marco Candela 4 , Patrizia Cambieri 2 1 Centro di Ricerca Pediatrica “Romeo ed Enrica Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milano, Milano, Italy; 2 U.O.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 3 U.O.C. Malattie Infettive, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 4 Unit of Holobiont Microbiome and Microbiome Engineering, Department of Pharmacy and Biotechnology, University of Bologna, Italy Hospital-acquired infections (HAIs) constitute a major health concern worldwide, with great social and econom- ic costs. A hospital is per se a perfectly suited setting for the development of HAIs, often sustained by multi-drug resistant (MDR) bacteria. Within a hospital, the neonatal intensive care unit (NICU) stands out as a unique envi- ronment. It contains a heterogeneous cohort of patients, with underdeveloped immune systems and nascent micro- biota communities, who often spend several months in the same room and are exposed to invasive medical de- vices and a variety of clinical treatments. These patients are often preterm neonates, known to exhibit peculiar colonization routes and bacterial strains (Stewart et al., 2017). Antibiotic therapies that interfere with physiolog- ical microbial colonization routes are frequently admin- istered, promoting the growth of bacterial taxa originat- ing from the hospital environment (Groer et al., 2014; Brooks et al., 2017). Not rarely, these strains, such as the Gram-positive Enterococcus spp. and Staphylococcus au- Corresponding author: Simona Panelli E-mail: simona.panelli1@unimi.it ©2020 by EDIMES - Edizioni Internazionali Srl. All rights reserved reus, and the Gram-negative Klebsiella pneumoniae (the most commonly reported causative agent), Acinetobacter spp., Pseudomonas aeruginosa, Serratia marcescens (Hu et al., 2015) are also implicated in nosocomial infections. These strains often display a burden of antibiotic resist- ance genes thought to provide competitive advantages for survival in the highly cleaned room environment; among resistance mechanisms, extended spectrum beta-lactama- se (ESBL) enzymes are the most commonly retrieved (La Rosa et al., 2014; Johnson and Quach, 2017). Another rel- evant feature of the colonization trajectories of neonates in NICUs is so-called “personalization,” i.e., extreme in- ter-individual variability (Wandro et al., 2018). Finally, the microbiota composition does not appear to be univocally linked to health outcomes (e.g., necrotizing enterocolitis and late-onset sepsis), but appears to partially reflect no- socomial “variables” such as antibiotic usage (Hartz et al., 2015; Wandro et al., 2018). This study describes the evolution of gut bacterial coloni- zation in newborns admitted to an NICU in Fondazione IRCCS Policlinico San Matteo, a 900-bed tertiary-care teaching hospital in Pavia (Lombardy region, northern It- aly), during an outbreak caused by ESBL K. pneumoniae (ESBL-Kp). The outbreak event involved 97 patients from January to September 2013 and was previously described in detail (Corbella et al., 2018). For the microbiota char- acterization, 14 neonates admitted to the NICU immedi- ately after birth (August-September 2013) were analysed. Key words: Infant gut microbiota; Neonatal Intensive Care Unit (NICU); preterm neonates; nosocomial outbreaks; extended spectrum beta-lactamase (ESBL) producing Klebsiella pneumoniae (ESBL-Kp). SUMMARY The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Kleb- siella pneumoniae and compared colonized and non-colonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Entero- bacteriaceae, with marked interindividual variability. This picture was retrieved independently of coloniza- tion status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evo- lution of microbiota patterns according to individual conditions, also in non-colonized patients. Received April 08, 2020 Accepted October 10, 2020