Multilevel Genome Typing Describes Short- and Long-Term Vibrio cholerae Molecular Epidemiology

In 2017, the World Health Organization launched the “Ending Cholera” initiative to reduce cholera-related deaths by 90% by 2030. This strategy emphasized the importance of the speed and accessibility of newer technologies to contain outbreaks.

Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

Elucidation of global and local epidemiology of Salmonella Enteritidis through multilevel genome typing

Salmonella Enteritidis is a major foodborne pathogen that causes both local and international outbreaks with complex transmission pathways. Invasive infections which are associated with multidrug resistance are an increasing concern around the globe. However, the global epidemiological picture of S. Enteritidis remains unclear due to the lack of a fine scale typing scheme based on genomic sequencing data. Here, using the novel multilevel genome typing (MGT) approach, we have characterised the genomic epidemiology of S. Enteritidis in unpreceded detail. We examined 26,670 publicly available S. Enteritidis whole genome sequences from 86 countries over 101 years to reveal their spatial and temporal distributions. Using MGT4 and MGT5, we identified globally prevalent and regionally restricted STs. Source associated STs were identified, such as poultry associated MGT4-STs, which were common in human cases in the USA. Temporal trends were observed in the UK with MGT5-STs from 2014 to 2018, revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified MDR associated STs to facilitate tracking MDR spread. The majority of the global S. Enteritidis population fell within two predominant lineages with significant differences in geographic distribution, outbreak frequency, antimicrobial resistance and mutation rate. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens

Background Both long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection. Aim We aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels. Methods The system was applied to Salmonella enterica serovar Typhimurium. The MLST scheme used at each step (MGT level), defined a given MGT-level specific sequence type (ST). The list of STs generated from all of these increasing MGT levels, was named a genome type (GT). Using MGT, we typed 9,096 previously characterised isolates with publicly available data. Results Our approach could identify previously described S. Typhimurium populations, such as the DT104 multidrug resistance lineage (GT 19-2-11) and two invasive lineages of African isolates (GT 313-2-3 and 313-2-752). Further, we showed that MGT-derived clusters can accurately distinguish five outbreaks from each other and five background isolates. Conclusion MGT provides a universal and stable nomenclature at multiple resolutions for S. Typhimurium strains and could be implemented as an internationally standardised strain identification system. While established so far only for S. Typhimurium, the results here suggest that MGT could form the basis for typing systems in other similar microorganisms.

A critical re-evaluation of multilocus sequence typing (MLST) efforts inWolbachia

Wolbachia(Alphaproteobacteria, Rickettsiales) is the most common, and arguably one of the most important inherited symbionts. Molecular differentiation ofWolbachiastrains is routinely performed with a set of five multilocus sequence typing (MLST) markers. However, since its inception in 2006, the performance of MLST inWolbachiastrain typing has not been assessed objectively. Here, we evaluate the properties ofWolbachiaMLST markers and compare it to 252 other single copy loci present in the genome of mostWolbachiastrains. Specifically, we investigated how well MLST performs at strain differentiation, at reflecting genetic diversity of strains, and as phylogenetic marker. We find that MLST loci are outperformed by other loci at all tasks they are currently employed for, and thus that they do not reflect the properties of aWolbachiastrain very well. We argue that whole genome typing approaches should be used forWolbachiatyping in the future. Alternatively, if few-loci-approaches are necessary, we provide a characterization of 252 single copy loci for a number a criteria, which may assist in designing specific typing systems or phylogenetic studies.

Phylogenomic grouping of Listeria monocytogenes

The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.