Abstract
BackgroundFor the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infection has implemented since 2013 a system named MIDaS, based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results. The objective of this paper is to present the pipeline we use for processing MALDI-TOF spectra during epidemiological surveillance in order to disclose proteinic cues that may suggest the existence of epidemic processes in complement of incidence surveillance. It is illustrated by the analysis of an alarm observed for Streptococcus pneumoniae.MethodsThe MALDI-TOF spectra analysis process looks for the existence of clusters of spectra characterized by a double time and proteinic close proximity. This process relies on several specific methods aiming at contrasting and clustering the spectra, presenting graphically the results for an easy epidemiological interpretation, and for determining the discriminating spectra peaks with their possible identification using reference databases.ResultsThe use of this pipeline in the case of an alarm issued for Streptococcus pneumoniae has made it possible to reveal a cluster of spectra with close proteinic and temporal distances, characterized by the presence of three discriminant peaks (5228.8, 5917.8, and 8974.3 m/z) and the absence of peak 4996.9 m/z. A further investigation on UniProt KB showed that peak 5228.8 is possibly an OxaA protein and that the absent peak may be a transposase.ConclusionThis example shows this pipeline may support a quasi-real time identification and characterization of clusters that provide essential information on a potentially epidemic situation. It brings valuable information for epidemiological sensemaking and for deciding on the continuation of the epidemiological investigation, in particular the involving of additional costly resources to confirm or invalidate the alarm.Clinical trials registrationNCT03626987.
Highlights
For the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infec‐ tion has implemented since 2013 a system named Mediterranée Infection Data Warehousing and Surveillance (MIDaS), based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results
A previous study on Staphylococcus saprophyticus [14], allowed us to explore the capability of MALDI-TOF MS spectral clustering in epidemiology with the identification of a particular subspecies circulating in Marseille
We consider that a set of bacterial strains presenting a same phenotypic expression can be sufficiently similar for belonging to a sample of the same epidemic process, and, with respect to the limitations presented above, a possible epidemic clone
Summary
For the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infec‐ tion has implemented since 2013 a system named MIDaS, based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results. The objective of this paper is to present the pipeline we use for processing MALDI-TOF spectra during epidemiological surveillance in order to disclose proteinic cues that may sug‐ gest the existence of epidemic processes in complement of incidence surveillance It is illustrated by the analysis of an alarm observed for Streptococcus pneumoniae. Giraud‐Gatineau et al BMC Infect Dis (2021) 21:1109 This system is based on the systematic recording of routine results issued from clinical microbiology and virology laboratories, which are not done for surveillance purpose [3], including identification at species level and possibly phenotypic or genomic characters. MIDaS helps to contextualize the alarm, allowing an “in silico” investigation based on sample and patient characteristics
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