Draft Genome Sequences of Four Yersinia enterocolitica Strains, Isolated from Wild Ungulate Carcasses

Macori, Guerrino; Romano, Angelo; Adriano, Daniela; Razzuoli, Elisabetta; Bianchi, Daniela Manila; Gallina, Silvia; Bellio, Alberto; Decastelli, Lucia

doi:10.1128/genomea.00192-17

Cited by 3 publications

(4 citation statements)

References 9 publications

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Section: Resultsmentioning

confidence: 99%

“…2, Table S1). Interestingly, while Y. enterocolitica can be found in aquatic environments, the two strains with putative T3SS2 gene clusters were isolated from wild ungulate carcasses and belong to the highly virulent biotype 1B [75]. Altogether, the taxonomic distribution of T3SS2 gene clusters in bacterial genomes indicates that this secretion system is not restricted to the family Vibrionaceae, suggesting that T3SS2 gene clusters can mobilize through HGT events among environmental bacteria.…”

Section: T3ss2 Gene Clusters Extend Beyond the Family Vibrionaceaementioning

confidence: 99%

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Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins

et al. 2023

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Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non- Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I–VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.

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Section: Resultsmentioning

confidence: 99%

Section: T3ss2 Gene Clusters Extend Beyond the Family Vibrionaceaementioning

confidence: 99%

Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins

et al. 2023

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“…2A and Table S1). Interestingly, while Yersinia enterocolitica can be found in aquatic environments, the 2 strains with putative T3SS2 gene clusters 12 were isolated from wild ungulate carcasses and belong to the highly virulent biotype 1B [73].…”

Section: T3ss2 Gene Clusters Extend Beyond the Vibrionaceae Familymentioning

confidence: 99%

TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins

Jerez

Plaza

Bravo

et al. 2022

Preprint

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Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, Type III Secretion System (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from eight bacterial genera and five bacterial families. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of T3SS2 effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of T3SS2 gene clusters that lack most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the Vibrionaceae family and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of all the bacteria that have acquired the Vibrio T3SS2 gene cluster.

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“…In the context of assessing serial bacterial genomes, the NGS has been a widely application to detect and to identify pathogens not only in clinical isolates, but also in food matrices as performed by Macori et al (15). These researches revealed the complete genomes of four Yersinia enterocolitica bacterial pathogens isolated at wild ungulate carcasses using the WGS approach in combination with phenotypic biochemical tests to determinate their virulence profile (high virulence or nonvirulent).…”

Section: Introductionmentioning

confidence: 99%

Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing

Almeida

Martinis

2019

Electron J Gen Med

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Next-Generation Sequencing (NGS) is becoming a reality in the clinical microbiology laboratory because it can speed diagnosis when compared to traditional culture based-methods and moreover, to aid in unravelling key virulence traits of important pathogens. Nonetheless, there are many limitations for its wide application in routine testing, as the requirement of high performance hardware and software to support bioinformatics analysis, as well as the expertise in different programming languages to perform the analyses. In this context, this review was drawn to synthesize some basic concepts involved in NGS for Whole-Genome Sequencing (WGS), based on two international straightforward efforts to standardize WGS data acquisition and processing in the clinical routine, the PulseNet International and the ENGAGE project, allied with other tools available for WGS analysis, beginning from the available sequencing platforms to the main user-friendly pipelines dedicated for the pathogen identification, including the use of properly databases to search for virulence factors, resistance genes and software resources for molecular typing of isolates.

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Draft Genome Sequences of Four Yersinia enterocolitica Strains, Isolated from Wild Ungulate Carcasses

Cited by 3 publications

References 9 publications

Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins

Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins

TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins

Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing

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