Abstract
The population structure of human isolates of Listeria monocytogenes in Emilia-Romagna, Italy, from 2012 to 2018 was investigated with the aim of evaluating the presence of genomic clusters indicative of possible outbreaks, the proportion of cluster-associated vs. sporadic isolates and different methods and metrics of genomic analysis for use in routine surveillance. In the 2012–2018 period the notification rate of confirmed invasive cases in Emilia-Romagna was 0.91 per 100,000 population per year, more than twice the average rate of EU countries. Out of the total 283 cases, 268 (about 95%) isolates were typed through whole genome sequencing (WGS) for cluster detection with methods based on core-genome multi-locus sequence typing and single nucleotide polymorphisms. Between 66 and 72% of listeriosis cases belonged to genomic clusters which included up to 27 cases and lasted up to 5 years. This proportion of cluster-associated cases is higher than previously estimated in other European studies. Rarefaction analysis, performed by reducing both the number of consecutive years of surveillance considered and the proportion of isolates included in the analysis, suggested that the observed high proportion of cluster-associated cases can be ascribed to the long surveillance duration (7 years) and the high notification and typing rates of this study. Our findings show that a long temporal perspective and high surveillance intensity, intended as both exhaustiveness of the system to report cases and high WGS-typing rate, are critical for sensitive detection of possible outbreaks within a WGS-based surveillance of listeriosis. Furthermore, the power and complexity of WGS interpretation emerged from the integration of genomic and epidemiological information in the investigation of few past outbreaks within the study, indicating that the use of multiple approaches, including the analysis of the accessory genome, is needed to accurately elucidate the population dynamics of Listeria monocytogenes.
Highlights
Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne disease mainly observed among elderly people, immunocompromised individuals, pregnant women, and newborn
Overall core-genome Multi-Locus Sequence Types (cgMLST)- and Single Nucleotide Polymorphisms (SNP)-based analyses show the presence of several clusters in the population, 38–39 depending on the detection method (Figure 2), with 7–11 of the clusters including more than 5 isolates, and the largest consisting of 26–27 isolates
The proportion of cases belonging to clusters ranges from 69 to 72% and it ranges from 66 to 71%—indicating that most cases of listeriosis in ER could be attributed to possible outbreaks—with 18–23 clusters lasting more than 1 year and 117–146 (43–54%) of isolates belong to multi-year clusters
Summary
Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne disease mainly observed among elderly people, immunocompromised individuals, pregnant women, and newborn. The confirmed identification of outbreaks and their sources of contamination is generally hampered by the long incubation of listeriosis and the common finding of L. monocytogenes in the food-chain and the environment This is only possible when laboratory surveillance is implemented and highresolution typing methods, able to pinpoint similar isolates in the population and in the sources of infection, are used. For this reason, whole genome sequencing (WGS), a highly discriminatory method, is being progressively introduced in routine surveillance of listeriosis and in food-safety monitoring [2]. The aims of the study were: (i) to assess the presence of clusters of isolates similar enough to represent possible outbreaks, considering that before WGS typing was introduced all notified cases had been classified as sporadic and no outbreaks had been reported in ER; (ii) to determine the structure of the population of L. monocytogenes, namely the proportion of isolates belonging to clusters vs. the proportion of sporadic isolates, as an indicator of the prevalent mode of infection (outbreak-associated vs. sporadic) and the duration and geographical extension of clusters; (iii) to create a background of genomes of L. monocytogenes from the Regional territory to allow for accurate assessment of genomic relationships among the incoming isolates in the new surveillance; and (iv) to evaluate methods and metrics of genomic analysis for their use in the surveillance
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
