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Sunday, July 7, 2019

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen.

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent…

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Sunday, July 7, 2019

Distinct Salmonella enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further…

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Sunday, July 7, 2019

Salmonella degrades the host glycocalyx leading to altered infection and glycan remodeling.

Complex glycans cover the gut epithelial surface to protect the cell from the environment. Invasive pathogens must breach the glycan layer before initiating infection. While glycan degradation is crucial for infection, this process is inadequately understood. Salmonella contains 47 glycosyl hydrolases (GHs) that may degrade the glycan. We hypothesized that keystone genes from the entire GH complement of Salmonella are required to degrade glycans to change infection. This study determined that GHs recognize the terminal monosaccharides (N-acetylneuraminic acid (Neu5Ac), galactose, mannose, and fucose) and significantly (p?

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Sunday, July 7, 2019

Genome sequence of highly virulent Pseudomonas aeruginosa strain VA-134, isolated from a burn patient.

Infection with Pseudomonas aeruginosa leads to impairment of healing and many deaths in severe burn patients. The phenotypic diversity of P. aeruginosa strains makes it difficult to define a therapeutic strategy. Here we report the genome sequence of a highly virulent strain of P. aeruginosa, VA-134, isolated from a burn patient. Copyright © 2016 Miller et al.

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Sunday, July 7, 2019

Comparative genomics analysis of Streptococcus tigurinus strains identifies genetic elements specifically and uniquely present in highly virulent strains.

Streptococcus tigurinus is responsible for severe invasive infections such as infective endocarditis, spondylodiscitis and meningitis. As described, S. tigurinus isolates AZ_3aT and AZ_14 were highly virulent (HV phenotype) in an experimental model of infective endocarditis and showed enhanced adherence and invasion of human endothelial cells when compared to low virulent S. tigurinus isolate AZ_8 (LV phenotype). Here, we sought whether genetic determinants could explain the higher virulence of AZ_3aT and AZ_14 isolates. Several genetic determinants specific to the HV strains were identified through extensive comparative genomics amongst which some were thought to be highly relevant for the observed HV phenotype.…

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Sunday, July 7, 2019

Effector diversification contributes to Xanthomonas oryzae pv. oryzae phenotypic adaptation in a semi-isolated environment.

Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races.…

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Sunday, July 7, 2019

Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.

Carbapenem-resistant Enterobacteriaceae (CRE) are a pressing public health issue due to limited therapeutic options to treat such infections. CREs have been predominantly isolated from humans and environmental samples and they are rarely reported among companion animals. In this study we report on the isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from a companion animal. Carbapenemase-producing S. enterica Typhimurium carrying blaIMP-4 was identified from a systemically unwell (index) cat and three additional cats at an animal shelter. All isolates were identical and belonged to ST19. Genome sequencing revealed the acquisition of a multidrug-resistant IncHI2 plasmid (pIMP4-SEM1) that…

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Sunday, July 7, 2019

Complete circular genome sequence of successful ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (OC8) in Russia: one-megabase genomic inversion, IS256’s spread, and evolution of Russia ST8-IV.

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaß split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all…

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Sunday, July 7, 2019

Genomic recombination leading to decreased virulence of group B Streptococcus in a mouse model of adult invasive disease.

Adult invasive disease caused by Group B Streptococcus (GBS) is increasing worldwide. Whole-genome sequencing (WGS) now permits rapid identification of recombination events, a phenomenon that occurs frequently in GBS. Using WGS, we described that strain NGBS375, a capsular serotype V GBS isolate of sequence type (ST)297, has an ST1 genomic background but has acquired approximately 300 kbp of genetic material likely from an ST17 strain. Here, we examined the virulence of this strain in an in vivo model of GBS adult invasive infection. The mosaic ST297 strain showed intermediate virulence, causing significantly less systemic infection and reduced mortality than a…

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Sunday, July 7, 2019

Genomic insights into Campylobacter jejuni virulence and population genetics

Campylobacter jejuni has long been recognized as a main food-borne pathogen in many parts of the world. Natural reservoirs include a wide variety of domestic and wild birds and mammals, whose intestines offer a suitable biological niche for the survival and dissemination of the organism. Understanding the genetic basis of the biology and pathogenicity of C. jejuni is vital to prevent and control Campylobacter-associated infections. The recent progress in sequencing techniques has allowed for a rapid increase in our knowledge of the molecular biology and the genetic structures of Campylobacter. Single-molecule realtime (SMRT) sequencing, which goes beyond four-base sequencing, revealed…

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Sunday, July 7, 2019

Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense.

Mycobacterium avium complex (MAC) contains clinically important nontuberculous mycobacteria worldwide and is the second largest medical complex in the Mycobacterium genus after the Mycobacterium tuberculosis complex. MAC comprises several species that are closely phylogenetically related but diverse regarding their host preference, course of disease, virulence and immune response. In this study we provided immunologic and virulence-related insights into the M. colombiense genome as a model of an opportunistic pathogen in the MAC. By using bioinformatic tools we found that M. colombiense has deletions in the genes involved in p-HBA/PDIM/PGL, PLC, SL-1 and HspX production, and loss of the ESX-1 locus. This information…

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Sunday, July 7, 2019

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes.

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence.A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to…

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Sunday, July 7, 2019

Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.

Enterococcus faecalis, the type strain of the genus Enterococcus, is not only a commensal bacterium in the gastrointestinal tract in vertebrates and invertebrates, but also causes serious disease as an opportunistic pathogen. To date, genome sequences have been published for over four hundred E. faecalis strains; however, pathogenicity of these microbes remains complicated. To increase our knowledge of E. faecalis virulence factors, we isolated strain CBA7120 from the feces of an 81-year-old female from the Republic of Korea and performed a comparative genomic analysis.The genome sequence of E. faecalis CBA7120 is 3,134,087 bp in length, with a G + C content of 37.35 mol%,…

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Sunday, July 7, 2019

Identification of a virulence determinant that is conserved in the Jawetz and Heyl biotypes of [Pasteurella] pneumotropica.

[Pasteurella] pneumotropica is a ubiquitous bacterium frequently isolated from laboratory rodents. Although this bacterium causes various diseases in immunosuppressed animals, little is known about major virulence factors and their roles in pathogenicity. To identify virulence factors, we sequenced the genome of [P.] pneumotropica biotype Heyl strain ATCC 12555, and compared the resulting non-contiguous draft genome sequence with the genome of biotype Jawetz strain ATCC 35149. Among a large number of genes encoding virulence-associated factors in both strains, four genes encoding for YadA-like proteins, which are known virulence factors that function in host cell adherence and invasion in many pathogens. In…

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