Association between lockdown and changes in subspecies diversity with a focus on Haemophilus influenzae and Staphylococcus aureus

Background: The social distancing measures implemented to curb SARS-CoV-2 transmission provided a unique opportunity to study the association between reduced human interaction and epidemiological changes related to human bacterial pathogens. While studies have indicated a decrease in respiratory infections during lockdowns, further description is needed regarding the changes in the incidence of bacterial populations. This study investigates the changes in strain richness of community infections with two bacterial species, Haemophilus influenzae and Staphylococcus aureus during the waning related to France’s social distancing measures, especially lockdown. Methods: MALDI-TOF MS spectra analyses of routine clinical bacterial identifications were used as proxies for genomic analyses. 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. Data were analyzed using hierarchical clustering, binary discriminant analysis, and statistical tests for significance. Results: The strain mix of both bacteria during the lockdown was deeply altered, but with different further evolutions. H. influenzae exhibited a shift in spectra composition, with a subsequent return towards pre-lockdown diversity observed in 2021. In contrast, S. aureus exhibited a persistent change in spectra composition, with a gradual return to pre-lockdown patterns one year later. Conclusions: Hindering inter-human transmission, as was done during the lockdown measures, was associated with significant alterations in bacterial species compositions, with differential impacts observed for H. influenzae and S. aureus . This study provides data on the putative relationship between genetic diversity and transmission dynamics during a public health crisis. Describing the dynamics of bacterial populations during lockdowns could contribute providing information for the implementation of future strategies for infectious disease control and surveillance. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Yes ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Not Applicable The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The surveillance system is in conformance with the Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation), declared on the RGPD/AP-HM register with number 2019-73 (“Epidemiological monitoring of potentially pathogenic microorganisms”). The study SpectraSurv was approved by the Commission Nationale Informatique et Libertés (decision DR-2018-177). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Not Applicable I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Not Applicable I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Not Applicable The data underlying the results presented in the study are available from the corresponding author (herve.chaudet@univ-amu.fr)