Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen

The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research

The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries.

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Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues, and is exposed to new selective pressures, thus potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation, however a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2,590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single-nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures

O uso de substâncias inibidoras da brotação de tubérculos de batatinha Use op sprouting inhibiting substances on potato tubers

A conservação de tubérculos de batatinha para o consumo vem preocupando os pesquisadores em diferentes países, por se tratar de um produto fácilmente perecível. Além dos trabalhos sôbre frigorificação, já bem conhecidos, iniciou-se o emprêgo de substâncias químicas inibidoras da brotação e que impedem as podridões causadas por Fusarium. Dentre essas drogas sobressairam-se o éster metílico do ácido alfanaftaleno acético e o tetracloronitrobenzeno. Os resultados alcançados, embora contraditórios em alguns pontos, vieram demonstrar a viabilidade do seu uso, principalmente em países onde o inverno é rigoroso. Das experiências e observações feitas no Instituto Agronômico de Campinas a partir de 1946, chegou-se à conclusão que as referidas drogas somente trouxeram bons resultados quando os tubérculos tratados foram conservados a baixa temperatura (4°C). Por outro lado, as batatinhas armazenadas a essa temperatura tornaram-se adocicadas e de má aceitação pelos consumidores, devido à formação de açúcares. Mantendo-se as temperaturas entre 18 e 26°C não houve, na maioria dos casos, influência nítida das drogas sôbre a redução da brotação, constatando--se, ao contrário, um aumento na porcentagem de tubérculos deteriorados devido à podridão mole causada por bactérias.<br>Storage of Irish potato tubers under 3 to 5° C, with air moisture remaining between 70 and 90%, affords good results in preventing sprouting of the tubers. As this treatment enables sugar formation in the tubers, the latter should not be used for consumption due to their unpalatability. At temperatures above 8°C sprouting occurs with loss of weight and other disadvantages. In the experiments herein reported two hormonlike substances were used to prevent sprouting under different temperatures. The chemical used were the methyl ester of alphanaphtaleneacetic acid (MENA) and 2, 3, 5, 6 tetrachloronitrobenzene (TCNB) mixed with talc. Under room temperatures practically little or no influence was shown by the treatments. However, under 8°C with an air moisture of 85%, MENA gave satisfactory results when tubers were stored during a period of 6 to 8 months. The results obtained were not alike for all varieties tested. It has also been found that some varieties show an increase in the percentage of soft rot in tubers receiving the hormonlike substances, mainly at room temperatures (20 to 25° C)

Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages

A hallmark of Listeria (L.) monocytogenes pathogenesis is bacterial escape from maturing entry vacuoles, which is required for rapid bacterial replication in the host cell cytoplasm and cell-to-cell spread. The bacterial transcriptional activator PrfA controls expression of key virulence factors that enable exploitation of this intracellular niche. The transcriptional activity of PrfA within infected host cells is controlled by allosteric coactivation. Inhibitory occupation of the coactivator site has been shown to impair PrfA functions, but consequences of PrfA inhibition for L. monocytogenes infection and pathogenesis are unknown. Here we report the crystal structure of PrfA with a small molecule inhibitor occupying the coactivator site at 2.0 Å resolution. Using molecular imaging and infection studies in macrophages, we demonstrate that PrfA inhibition prevents the vacuolar escape of L. monocytogenes and enables extensive bacterial replication inside spacious vacuoles. In contrast to previously described spacious Listeria-containing vacuoles, which have been implicated in supporting chronic infection, PrfA inhibition facilitated progressive clearance of intracellular L. monocytogenes from spacious vacuoles through lysosomal degradation. Thus, inhibitory occupation of the PrfA coactivator site facilitates formation of a transient intravacuolar L. monocytogenes replication niche that licenses macrophages to effectively eliminate intracellular bacteria. Our findings encourage further exploration of PrfA as a potential target for antimicrobials and highlight that intra-vacuolar residence of L. monocytogenes in macrophages is not inevitably tied to bacterial persistence.Originally included in thesis in manuscript form. </p