Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

Lee, Isaiah Paolo A.; Andam, Cheryl P.

doi:10.1038/s41598-022-04995-5

Cited by 8 publications

(5 citation statements)

References 86 publications

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“…The smc gene encodes the condensin protein SMC and is not essential in S. pneumoniae —albeit it is important for timely localization of the division site (van Raaphorst et al 2017 ). A similar role for smc has recently been demonstrated in S. agalactiae (Lee and Andam 2022 ).…”

Section: Resultssupporting

confidence: 76%

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Two putative glutamate decarboxylases of Streptococcus pneumoniae as possible antigens for the production of anti-GAD65 antibodies leading to type 1 diabetes mellitus

Garcı́a

2023

Int Microbiol

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Type 1 diabetes mellitus (T1DM) has been increasing in prevalence in the last decades and has become a global burden. Autoantibodies against human glutamate decarboxylase (GAD65) are among the first to be detected at the onset of T1DM. Diverse viruses have been proposed to be involved in the triggering of T1DM because of molecular mimicry, i.e., similarity between parts of some viral proteins and one or more epitopes of GAD65. However, the possibility that bacterial proteins might also be responsible for GAD65 mimicry has been seldom investigated. To date, many genomes of Streptococcus pneumoniae (the pneumococcus), a prominent human pathogen particularly prevalent among children and the elderly, have been sequenced. A dataset of more than 9000 pneumococcal genomes was mined and two different (albeit related) genes (gadA and gadB), presumably encoding two glutamate decarboxylases similar to GAD65, were found. The various gadASpn alleles were present only in serotype 3 pneumococci belonging to the global lineage GPSC83, although some homologs have also been discovered in two subspecies of Streptococcus constellatus (pharyngis and viborgensis), an isolate of the group B streptococci, and several strains of Lactobacillus delbrueckii. Besides, gadBSpn alleles are present in > 10% of the isolates in our dataset and represent 16 GPSCs with 123 sequence types and 20 different serotypes. Sequence analyses indicated that gadA- and gadB-like genes have been mobilized among different bacteria either by prophage(s) or by integrative and conjugative element(s), respectively. Substantial similarities appear to exist between the putative pneumococcal glutamate decarboxylases and well-known epitopes of GAD65. In this sense, the use of broader pneumococcal conjugate vaccines such as PCV20 would prevent the majority of serotypes expressing those genes that might potentially contribute to T1DM. These results deserve upcoming studies on the possible involvement of S. pneumoniae in the etiopathogenesis and clinical onset of T1DM.

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Section: Resultssupporting

confidence: 76%

“…pyogenes , and S. suis , respectively. Likewise, a noticeable number of genes appear to correspond to phage-associated cargo genes in the same species (Lee and Andam 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Two putative glutamate decarboxylases of Streptococcus pneumoniae as possible antigens for the production of anti-GAD65 antibodies leading to type 1 diabetes mellitus

Garcı́a

2023

Int Microbiol

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“…Together this suggests that the island was acquired once by a common ancestor of all pathogenic lineages. As homologous recombination is common in S. suis (23), the inheritance of this island is unlikely to have been entirely vertical, but our observations suggest that it has followed similar patterns to core genes (Figure 2c).…”

Section: Consistent Genomic Changes Reveal Evolutionary Constraints O...mentioning

confidence: 74%

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

Murray

Hossain

Miller

et al. 2023

Preprint

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The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species this can affect the health of humans as well as livestock. Here we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realised.

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“…Natural transformation within the genus Vibrio may play a large part in the frequent homologous recombination occurring between the Vibrio species. Streptococcus species have been extensively studied for their ability to engage in natural transformation, and their genetic diversity and adaptivity could be the result of the frequent introgression that we observed between species within this genus 63,64 .…”

Section: Discussionmentioning

confidence: 88%

“…Streptococcus species have been extensively studied for their ability to engage in natural transformation, and their genetic diversity and adaptivity could be the result of the frequent introgression that we observed between species within this genus 63,64 .…”

Section: Discussionmentioning

confidence: 90%

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Diop,

Bobay

2024

Preprint

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Most bacteria engage in gene flow and that this may act as a force maintaining species cohesiveness like it does in sexual organisms. However, introgression (gene flow between the genomic backbone of distinct species) has been reported in bacteria and is associated with fuzzy species borders in some lineages, but its prevalence and impact on the delimitation of bacterial species has not been systematically characterized. Here, we quantified the patterns of introgression across 50 major bacterial lineages. Our results reveal that bacteria present various levels of introgression, with an average of 2% of introgressed core genes and up to 12% in Campylobacter. Furthermore, our results show that some species are more prone to introgression than others within the same genus and introgression is most frequent between highly related species. We found evidence that the various levels of introgression across lineages are likely related to ecological proximity between species. Introgression can occasionally lead to fuzzy species borders, although many of these cases are likely instances of ongoing speciation. Overall, our results indicate that introgression has substantially shaped the evolution and the diversification of bacteria, but this process does not substantially blur species borders.

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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

Cited by 8 publications

References 86 publications

Two putative glutamate decarboxylases of Streptococcus pneumoniae as possible antigens for the production of anti-GAD65 antibodies leading to type 1 diabetes mellitus

Two putative glutamate decarboxylases of Streptococcus pneumoniae as possible antigens for the production of anti-GAD65 antibodies leading to type 1 diabetes mellitus

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

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