269 research outputs found
Trends in fluoroquinolone resistance in Campylobacter
Members of the genus Campylobacter remain a leading cause of bacterial gastroenteritis worldwide. Infection is usually self-limiting but in severe cases may require antibiotic treatment. In a recent statement by the World Health Organization (WHO) Campylobacter was named as one of the 12 bacteria that pose the greatest threat to human health because they are resistant to antibiotics. In this mini review we describe recent trends in fluoroquinolone (FQ) (particularly ciprofloxacin) resistance in strains of members of the genus Campylobacter isolated from livestock and clinical samples from several countries. Using evidence from phenotyping surveys and putative resistance prediction from DNA sequence data, we discuss the acquisition and spread of FQ resistance and the role of horizontal gene transfer and describe trends in FQ-resistance in samples from livestock and clinical cases. This review emphasises that FQ resistance remains common among isolates of members of the genus Campylobacter from various sources
Genomic plasticity and rapid host switching can promote the evolution of generalism : a case study in the zoonotic pathogen Campylobacter
This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I02464X/1, the Medical Research Council (MRC) grants MR/M501608/1 and MR/L015080/1, and the Wellcome Trust grant 088786/C/09/Z. GM was supported by a NISCHR Health Research Fellowship (HF-14–13).Peer reviewedPublisher PD
Operationalising factors that explain the emergence of infectious diseases : A case study of the human campylobacteriosis epidemic
Peer reviewedPublisher PD
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A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0101-7) contains supplementary material, which is available to authorized users
MARVEL Analysis of the Measured High-Resolution Rovibronic Spectra of 90Zr16O
Zirconium oxide(ZrO) is an important astrophysical molecule that defines the
S-star classification class for cool giant stars. Accurate, empirical
rovibronic energy levels, with associated labels and uncertainties, are
reported for 9 low-lying electronic states of the diatomic 90Zr16O molecule.
These 8088 empirical energy levels are determined using the Marvel (Measured
Active Rotational-Vibrational Energy Levels) algorithm with 23 317 input
assigned transition frequencies, 22 549 of which were validated. A
temperature-dependent partition function is presented alongside updated
spectroscopic constants for the 9 low-lying electronic states
Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages
Acknowledgments The authors like to thank Brian Brooks and John Devenish (Canadian Food Inspection Agency) for providing strains and valuable suggestions.Peer reviewedPublisher PD
Molecular epidemiology and comparative genomics of <i>Campylobacter concisus</i> strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease
Abstract Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 individuals (26 IBD, 3 Gastroenteritis (GE), 12 Healthy controls (HC)). Whole genomes were sequenced and the dataset pan-genome examined, and genomic information was used for typing using multi-locus-sequence typing (MLST). C. concisus isolates clustered into two main groups/genomospecies (GS) with 71 distinct sequence types (STs) represented. Sampling site (p < 0.001), rather than disease phenotype (p = 1.00) was associated with particular GS. We identified 97 candidate genes associated with increase or decrease in prevalence during the anatomical descent from the oral cavity to mucosal biopsies to faeces. Genes related to cell wall/membrane biogenesis were more common in oral isolates, whereas genes involved in cell transport, metabolism and secretory pathways were more prevalent in enteric isolates. Furthermore, there was no correlation between individual genetic diversity and clinical phenotype. This study confirms the genetic heterogeneity of C. concisus and provides evidence that genomic variation is related to the source of isolation, but not clinical phenotype
Stress-resistance associated with multi-host transmission and enhanced biofilm formation at 42 °C among hyper-aerotolerant generalist Campylobacter jejuni
Characterisation of <i>Salmonella enterica</i> clones carrying <i>mcr</i>-1 plasmids in meat products and patients in Northern Thailand using long read sequencing
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