Antecedentes Locales

The cost of sequencing itself is not a limiting factor anymore (Joensen et al., 2014). In silico typing methods are fairly easy to set up and subsequently run for each isolate. However, careful evaluation and validation is needed when new typing methods are applied in the surveillance of pathogenic bacteria.

There are plenty of easy-to-use tools available for non-bioinformatician users. One of these is Ridom SeqSphere+ (Ridom GmbH, Münster, Germany), which was used in this thesis. However, only a limited set of in silico typing methods are currently available, and customized methods need to be set up for STEC and many other bacteria. Automatic on-line tools for in silico typing of enteric pathogens using WGS data are available. SeroTypeFinder detects E. coli O- and H-antigens (Joensen et al., 2015). VirulenceFinder detects a large set of virulence genes among enteric pathogens (Joensen et al., 2014). ResFinder detects antimicrobial resistance genes (Zankari et al., 2012).

Extraction of the O:H-serotyping result from the sequence data was tested in this study. The results were partly inconsistent with results of the traditional phenotypic methods. Antisera agglutination relies on the bacterial phenotype, which may sometimes give a different result compared to the genotype if the genes are silent. In Public Health England, STEC non-O157 serotyping using WGS data gave concordant results for 96% of the isolates when compared to O- and H- agglutination data (Chattaway et al., 2016). In addition, nearly all previously H non- typeable isolates were typed using WGS data.

In this study, stx1 and stx2 gene subtypes extracted from the sequence data were

consistent with the results obtained by PCR. In Public Health England, STEC non- O157 stx subtyping using WGS data gave concordant results in 92% of isolates when compared to stx subtyping PCR results (Chattaway et al., 2016). This inconsistency was probably due to non-specific primer binding during PCR amplification.

In Public Health England, WGS has already been validated as a tool for STEC O157 and non-O157 surveillance (Dallman et al., 2015, Chattaway et al., 2016). At the Bacterial Infections Unit, THL, Finland, the validation is currently being performed.

7 CONCLUSIONS

In this thesis, new knowledge on variety of the virulence genes and hybrid virulence of STEC and other DEC strains was obtained:

- Retail meats in Burkina Faso are a reservoir of various DEC, especially STEC strains. The presence of these pathogens can be due to contamination during meat processing at slaughterhouses or due to the retailers' poor handling of meat. The lack of a cold chain may worsen the situation. If the meat is not properly cooked or food-preparation hygiene is compromised, human infections may occur.

- _{In Burkina Faso, STEC strains belonging to diverse serotypes and with} various virulence profiles were found to be present in raw meats. Based on the pheno- and genotypic characteristics of the isolated STEC strains, they may potentially be a serious health risk to people in Burkina Faso.

- STEC/ETEC hybrid strains are present in both Finland and Burkina Faso, in two climatically and socioeconomically distant countries. In Finland, STEC/ETEC hybrid strains have infected humans. In addition, they are carried by food production animals. In Burkina Faso, STEC/ETEC hybrids are present in raw meat products.

- STEC- and ETEC-associated virulence genes co-exist in strains originating from different phylogenetic lineages, suggesting their independent emergence. In addition, the STEC/ETEC hybrid strains possess a combination of several additional virulence genes and adhesins, some of which have been associated with ETEC, EAEC/STEC, and EAEC strains.

- The multiple virulence factors, especially the ability to produce several cytotoxins and to adhere to intestinal epithelial cells, may increase the virulence of hybrid E. coli for humans. This may result in more severe disease in a patient and an increased spreading potential.

- _{Hybrid E. coli strains should be considered as emerging pathogens, which} may have serious consequences for public health. They challenge the traditional diagnostics of E. coli infections.

- _{WGS is becoming a common priority method for obtaining detailed typing} information in the service of patient care and surveillance. Using WGS, it is possible to replace the phenotype-based and gene-based typing methods in STEC typing.

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