Haemophilus influenzae and Staphylococcus aureus population shifts during social distancing as monitored by MALDI-TOF MS

The COVID-19 pandemic prompted widespread public health interventions, including lockdowns and social distancing measures, which influenced microbial transmission dynamics. This study evaluates the evolution of the hospital incidence and spectral diversity of Haemophilus influenzae and Staphylococcus aureus associated with these measures using MALDI-TOF mass spectrometry-based epidemiological surveillance. MALDI-TOF MS spectra analyses of routine clinical bacterial identifications were used as proxies for strain typing. Spectra from lockdown and reference periods were compared using unsupervised classification methods. A total of 251 main spectrum profiles of H. influenzae, 2079 main spectrum profiles of S. aureus for respiratory tract and blood samples, and 414 main spectrum profiles for skin samples of S. aureus were examined. The data were analyzed using hierarchical clustering and binary discriminant analysis. Spectral diversity of H. influenzae showed a transient shift, reverting to pre-lockdown patterns by 2021, whereas S. aureus exhibited a spectral shift that persisted post-lockdown. Clustering analyses revealed statistically significant grouping of lockdown strains, suggesting selection pressures due to containment measures. Social distancing measures were associated with modifications in bacterial population structures, with distinct post-lockdown recovery patterns. MALDI-TOF MS fingerprints proved to be a valuable tool for real-time epidemiological surveillance. This full-size experiment of social distancing highlights the complex interactions involving human behavior, bacterial ecology, and population dynamics and suggests different effects for different bacterial species.