Multi-Locus Sequence Typing of a Geographically and Temporally Diverse Sample of the Highly Clonal Human Pathogen Bartonella quintana

Bartonella quintana is a re-emerging pathogen and the causative agent of a variety of disease manifestations in humans including trench fever. Various typing methods have been developed for B. quintana, but these tend to be limited by poor resolution and, in the case of gel-based methods, a lack of portability. Multilocus sequence typing (MLST) has been used to study the molecular epidemiology of a large number of pathogens, including B. henselae, a close relative of B. quintana. We developed a MLST scheme for B. quintana based on the 7 MLST loci employed for B. henselae with two additional loci to cover underrepresented regions of the B. quintana chromosome. A total of 16 B. quintana isolates spanning over 60 years and three continents were characterized. Allelic variation was detected in five of the nine loci. Although only 8/4270 (0.002%) of the nucleotide sites examined were variable over all loci, these polymorphisms resolved the 16 isolates into seven sequence types (STs). We also demonstrate that MLST can be applied on uncultured isolates by direct PCR from cardiac valve tissue, and suggest this method presents a promising approach for epidemiological studies in this highly clonal organism. Phylogenetic and clustering analyses suggest that two of the seven STs form a distinct lineage within the population

The importance of cross-disciplinary research to combat antimicrobial resistance: introducing a new pop-up journal, X-AMR.

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The distribution of bacterial doubling times in the wild

Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the dou- bling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. How- ever, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild

Diversity and recombination in Wolbachia and Cardinium from Bryobia spider mites

Background Wolbachia and Cardinium are endosymbiotic bacteria infecting many arthropods and manipulating host reproduction. Although these bacteria are maternally transmitted, incongruencies between phylogenies of host and parasite suggest an additional role for occasional horizontal transmission. Consistent with this view is the strong evidence for recombination in Wolbachia, although it is less clear to what extent recombination drives diversification within single host species and genera. Furthermore, little is known concerning the population structures of other insect endosymbionts which co-infect with Wolbachia, such as Cardinium. Here, we explore Wolbachia and Cardinium strain diversity within nine spider mite species (Tetranychidae) from 38 populations, and quantify the contribution of recombination compared to point mutation in generating Wolbachia diversity. Results We found a high level of genetic diversity for Wolbachia, with 36 unique strains detected (64 investigated mite individuals). Sequence data from four Wolbachia genes suggest that new alleles are 7.5 to 11 times more likely to be generated by recombination than point mutation. Consistent with previous reports on more diverse host samples, our data did not reveal evidence for co-evolution of Wolbachia with its host. Cardinium was less frequently found in the mites, but also showed a high level of diversity, with eight unique strains detected in 15 individuals on the basis of only two genes. A lack of congruence among host and Cardinium phylogenies was observed. Conclusions We found a high rate of recombination for Wolbachia strains obtained from host species of the spider mite family Tetranychidae, comparable to rates found for horizontally transmitted bacteria. This suggests frequent horizontal transmission of Wolbachia and/or frequent horizontal transfer of single genes. Our findings strengthens earlier reports of recombination for Wolbachia, and shows that high recombination rates are also present on strains from a restrictive host range. Cardinium was found co-infecting several spider mite species, and phylogenetic comparisons suggest also horizontal transmission of Cardinium among host

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

International audienceThe dissection of natural selection and neutral processes remains a core problem for molecular evolutionary biologists. One of the longest-standing controversies con- cerns the causes of genome base compo- sition, notably the variation in the sum of G and C content (GC) between 17% and 75% in bacteria. Sueoka argued very early that GC content variation is driven by mutational biases and, as this bias affects non-synonymous sites, protein evolution might also be largely driven by neutral forces [1]. Later, Muto and Osawa showed that 4-fold degenerate positions in codons exhibit the largest range of GC content (GC4), whereas the non-degener- ate second codon positions (GC2) exhibit the narrowest (Figure 1) [2]. As the footprint of genomic GC variation is most evident in those sites under the least selective constraint for amino acid com- position, it has become accepted that GC content variation is primarily driven by neutral mutational effects and has little adaptive relevance [2]

Who Participates in an Internet-Based Research Program for Mothers of Infants? A Secondary Prevention Research Study Among Low-Income Families

Objective: The objective of this study was to evaluate the participation rates and factors associated with nonparticipation among mothers living in low-income households who were invited to join a parent-education and -support research program delivered via the Internet with professional support. Methods: Four hundred and seventy-seven mothers of infants were contacted via a variety of recruitment methods, including presentations at clinics/classes, direct mailings, print advertisement, and Internet posts. Research staff attempted to contact these mothers by phone, to assess their eligibility, and interest in participation. For those who were eligible but declined participation, we assessed reasons for declining and collected demographic information. Results: Seventy-four percent of those eligible agreed to participate in the program. Statistical tests comparing participants and decliners on demographic variables found no significant differences on mother’s age and marital status. There was a significant difference on baby’s age due to many decliners in the prenatal period. Mothers were an average age of 28 years and most were married (65.6%). Our sample of low-income participants was diverse with a large number of Latina mothers. Approximately half had a high-school diploma or less but 84% reported being moderately or very comfortable using a computer and half had a computer at home

Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 New Isolates Belonging to the Genus Salinivibrio

The draft genome sequences of 5 type strains of species of the halophilic genus Salinivibrio and 29 new isolates from different hypersaline habitats belonging to the genus Salinivibrio have been determined. The genomes have 3,123,148 to 3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading frames (ORFs).España, Ministerio de Ciencia e Innovación CGL2013-46941-