Bacterial diversity screening in endangered pelicans reveals high prevalence of methicillin-susceptible Staphylococcus aureus

In 2022, an avian influenza outbreak caused a massive mortality of Dalmatian pelicans (Pelecanus crispus, hereafter DP) in their world's largest breeding colony located at Mikri Prespa Lake (Greece), while great white pelicans (Pelecanus onocrotalus, hereafter GWP) were not affected. The aim of this study was to describe bacterial diversity and antimicrobial resistance carriage from choanal clefts of DPs and GWPs, to elucidate differences between the two species of pelicans and age groups. Fifty-two choanal swab samples were collected from 31 nestlings (N) (20 DP/11 GWP) late in the 2022 breeding season, and 21 adults (A) DPs (DP-A) in early 2023. Samples were seeded in general and chromogenic selective media. Isolates were identified by MALDI-TOF mass spectrometry and antimicrobial susceptibility was evaluated by disk diffusion method for staphylococci/mammaliicocci, enterococci and Enterobacterales. A total of 248 non-repetitive isolates (46A/202N) were recovered, representing 39 bacterial species from 18 genera. A very high prevalence of S. aureus (80.8 % of samples tested) was detected in both age groups (85.7 %A/77.4 %N), with nestlings also showing greater staphylococcal/mammaliicoccal diversity. Most isolates recovered were susceptible to all the antibiotics tested, and none S. aureus was methicillin-resistant. Nevertheless, one multi-drug resistant (MDR) CTX-M-15-producing E. coli-ST69 isolate was found in one DP-A. This study revealed a high rate of antimicrobial susceptibility and staphylococcal/mammaliicoccal diversity in choanal samples of pelicans, with the occasional detection of MDR isolates of concern, like the extended-spectrum beta-lactamase-producing E. coli strain.