55 research outputs found
Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex
No full textCampylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation
Salmonella bongori provides insights into the evolution of the Salmonellae
No full textThe genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC
Genetic markers in s. Paratyphi c reveal primary adaptation to pigs
No full textSalmonella enterica with the identical antigenic formula 6,7:c:1,5 can be differentiated biochemically and by disease syndrome. One grouping, Salmonella Paratyphi C, is currently considered a typhoidal serovar, responsible for enteric fever in humans. The human-restricted typhoidal serovars (S. Typhi and Paratyphi A, B and C) typically display high levels of genome degradation and are cited as an example of convergent evolution for host adaptation in humans. However, S. Paratyphi C presents a different clinical picture to S. Typhi/Paratyphi A, in a patient group with predisposition, raising the possibility that its natural history is different, and that infection is invasive salmonellosis rather than enteric fever. Using whole genome sequencing and metabolic pathway analysis, we compared the genomes of 17 S. Paratyphi C strains to other members of the 6,7:c:1,5 group and to two typhoidal serovars: S. Typhi and Paratyphi A. The genome degradation observed in S. Paratyphi C was much lower than S. Typhi/Paratyphi A, but similar to the other 6,7:c:1,5 strains. Genomic and metabolic comparisons revealed little to no overlap between S. Paratyphi C and the other typhoidal serovars, arguing against convergent evolution and instead providing evidence of a primary adaptation to pigs in accordance with the 6,7:c:1.5 strains
Salmonella Typhi sense host neuroendocrine stress hormones and release the toxin haemolysin e
No full textSalmonella enterica serovar Typhi (S. typhi) causes typhoid fever. We show that exposure of S. typhi to neuroendocrine stress hormones results in haemolysis, which is associated with the release of haemolysin E in membrane vesicles. This effect is attributed to increased expression of the small RNA micA and RNA chaperone Hfq, with concomitant downregulation of outer membrane protein A. Deletion of micA or the two-component signal-transduction system, CpxAR, abolishes the phenotype. The hormone response is inhibited by the β 2-blocker propranolol. We provide mechanistic insights into the basis of neuroendocrine hormone-mediated haemolysis by S. typhi, increasing our understanding of inter-kingdom signalling. © 2011 European Molecular Biology Organization Embo
RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
No full textBACKGROUND: Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR. RESULTS: We found that 528 chromosomal genes were differentially expressed in response to anaerobic conditions; of these, 228 genes were also influenced by FNR. Genes that were up-regulated in anaerobic conditions are involved in carbon transport and metabolism (e.g. ptsG, manX, murQ, cysP, cra), DNA topology and regulation (e.g. ygiP, stpA, hns), host interactions (e.g. yciD, nmpC, slyB, gapA, shf, msbB) and survival within the gastrointestinal tract (e.g. shiA, ospI, adiY, cysP). Interestingly, there was a marked effect of available oxygen on genes involved in Type III secretion system (T3SS), which is required for host cell invasion and pathogenesis. These genes, located on the large Shigella virulence plasmid, were down regulated in anaerobiosis in an FNR-dependent manner. We also confirmed anaerobic induction of csrB and csrC small RNAs in an FNR-independent manner. CONCLUSIONS: Anaerobiosis promotes survival and adaption strategies of Shigella, while modulating virulence plasmid genes involved in T3SS-mediated host cell invasion. The influence of FNR on this process is more extensive than previously appreciated, although aside from the virulence plasmid, this transcriptional regulator does not govern expression of genes on other horizontally acquired sequences on the chromosome such as pathogenicity islands
Soft biometrics for surveillance: an overview
No full textBiometrics is the science of automatically recognizing people based on physical or behavioral characteristics such as face, fingerprint, iris, hand, voice, gait and signature. More recently, the use of soft biometric traits has been proposed to improve the performance of traditional biometric systems and allow identification based on human descriptions. Soft biometric traits include characteristics such as height, weight, body geometry, scars, marks and tattoos (SMT), gender, etc. These traits offer several advantages over traditional biometric techniques. Soft biometric traits can be typically described using human understandable labels and measurements, allowing for retrieval and recognition solely based on verbal descriptions. Unlike many primary biometric traits, soft biometrics can be obtained at a distance without subject cooperation and from low quality video footage, making them ideal for use in surveillance applications. This chapter will introduce the current state-of-the-art in the emerging field of soft biometric
Isolamento e indentificação de subsatâncias ativas de araucaria angustifolia (Bert.) O. Kuntze com potencial atividade antiviral
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências da Saúde. Programa de Pós-Graduação em Farmácia.Araucaria angustifolia é uma árvore de grande porte que ocorre na floresta ombrófila mista, um ecossistema único dentro do domínio da Mata Atlântica. É a única espécie da família Araucariaceae natural da região sul do Brasil. Atualmente está incluída na lista das espécies ameaçadas de extinção, devido a intensa exploração de sua madeira pelas indústrias madeireiras e de papel e celulose. O objetivo deste trabalho foi o isolamento e a identificação em Araucaria angustifolia substâncias potencialmente ativas, biomonitorado por ensaios de citotoxicidade e atividade antiviral para o vírus herpético tipo-1 (HSV-1), expressa pelo Índice de Seletividade (IS). Assim, partindo-se de um extrato hidroalcoólico das folhas (acículas) do material vegetal, seguido de partição com solventes de polaridade crescente, foi possível estabelecer a atividade antiviral para as frações acetato de etila (FAE, IS=9) e n-butaol (FBU, IS=11). Da FAE seguiu-se a subfração mais ativa SFAE-II (IS=7,13), e desta as subfrações SFAE-II-B, SFAE-II-C e SFAE-II-D (IS=7,13). Após purificação das subfrações, foi possível isolar as substâncias II-B [1] (bilobetina), II-C e II-D [2] (cupressuflavona), sendo que a substância II-C trata-se, provavelmente, de uma biflavona do tipo robustaflavona. Esta substância foi posteriormente acetilada, e os espectros de RMN estão sendo aguardados para a confirmação estrutural. Da FBU foram isolados esses mesmos biflavonóides, além de duas outras substâncias caracterizadas como taninos condensados (proantocianidinas), os quais parecem ter grande importância para a atividade antiviral das frações. A subfração mais ativa derivada da FBU foi a SFBU-I (IS=13,96), a qual deu origem a SFBU-I-4 (IS=51,71) e SFBU-I-5 (IS=57,56). Da SFBU-I-4 obteve-se a substância T4, e da SFBU-I-5 foi obtida a FR-1 (IS=38,16), a qual foi acetilada e purificada. Dessa forma, a Araucaria angustifolia mostra-se como uma fonte viável de obtenção de metabólitos secundários potencialmente ativos, devendo ser mais aprofundados os estudos de elucidação estrutural, assim como a pesquisa de outras atividades relacionadas a esses compostos. Assim, atribuindo-se à espécie outra importância, no caso a obtenção de substâncias ativas, que não a exploração de sua madeira, contribui-se para a sua preservação, uma vez que foram pesquisadas as partes aéreas da planta
Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
No full textStreptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex’s entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that upregulated
the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through
small alterations to the genotype
Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.
No full textBACKGROUND: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. genitalium relies on molecular tests targeting specific genes or regions of the genome and knowledge is limited by a general under-testing internationally. This is set against a background of drug resistance whereby M. genitalium has developed resistance to mainly all therapeutic antimicrobials. RESULTS: We sequenced 28 genomes of Mycoplasma genitalium from temporally (1980-2010) and geographically (Europe, Japan, Australia) diverse sources. All the strain showed essentially the same genomic content without any accessory regions found. However, we identified extensive recombination across their genomes with a total of 25 regions showing heightened levels of SNP density. These regions include the MgPar loci, associated with host interactions, as well as other genes that could also be involved in this role. Using these data, we generated a robust phylogeny which shows that there are two main clades with differing degrees of genomic variability. SNPs found in region V of 23S rRNA and parC were consistent with azithromycin/erythromycin and fluoroquinolone resistances, respectively, and with their phenotypic MIC data. CONCLUSIONS: The sequence data here generated is essential for designing rational approaches to type and track Mycoplasma genitalium as antibiotic resistance increases. It represents a first approach to its population genetics to better appreciate the role of this organism as a sexually transmitted pathogen
The secondary resistome of multidrug-resistant Klebsiella pneumoniae
No full textKlebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258). We constructed a high-density transposon mutant library of >430,000 unique Tn5 insertions and measured mutant depletion upon exposure to three clinically relevant antimicrobials (colistin, imipenem or ciprofloxacin) by Transposon Directed Insertion-site Sequencing (TraDIS). Using this high-throughput approach, we defined three sets of chromosomal non-essential genes essential for growth during exposure to colistin (n = 35), imipenem (n = 1) or ciprofloxacin (n = 1) in addition to known resistance determinants, collectively termed the “secondary resistome”. As proof of principle, we demonstrated that inactivation of a non-essential gene not previously found linked to colistin resistance (dedA) restored colistin susceptibility by reducing the minimum inhibitory concentration from 8 to 0.5 μg/ml, 4-fold below the susceptibility breakpoint (S ≤ 2 μg/ml). This finding suggests that the secondary resistome is a potential target for developing antimicrobial “helper” drugs that restore the efficacy of existing antimicrobials
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