Carried Meningococci in the Czech Republic: a Diverse Recombining Population

Jolley, Keith A.; Kalmusová, J.; Feil, Edward J.; Gupta, Sunetra; Musílek, Martin; Kriz, Paula; Maiden, Martin C. J.

doi:10.1128/jcm.40.9.3549-3550.2002

Cited by 108 publications

(105 citation statements)

References 30 publications

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“…These analyses yielded comparable mean ρvalues within each species, indicating that LDhat estimates of this parameter are not strongly affected by sample size (see other examples by Jolley et al, 2000;Maggi-Solcà et al, 2001;Feil et al, 2003;Viscidi and Demma, 2003). However, many MLST data sets represent biased samples that are concentrated on disease isolates and confirmation of our results with more population-based samples is desirable.…”

Section: Species Comparisonsmentioning

confidence: 53%

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Pérez‐Losada

Browne

Madsen

et al. 2006

Infection, Genetics and Evolution

145

107

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The inference of population recombination (ρ), population mutation (Θ), and adaptive selection is of great interest in microbial population genetics. These parameters can be efficiently estimated using explicit statistical frameworks (evolutionary models) that describe their effect on gene sequences. Within this framework, we estimated ρand Θ using a coalescent approach, and adaptive (or destabilizing) selection under heterogeneous codon-based and amino acid property models in microbial sequences from MLST databases. We analyzed a total of 91 different housekeeping gene regions (loci) corresponding to one fungal and sixteen bacterial pathogens. Our results show that these three population parameters vary extensively across species and loci, but they do not seem to be correlated. For the most part, estimated recombination rates among species agree well with previous studies. Over all taxa, the ρ/Θ ratio suggests that each factor contributes similarly to the emergence of variant alleles. Comparisons of Θ estimated under finite-and infinite-site models indicate that recurrent mutation (i.e., multiple mutations at some sites) can increase Θ by up to 39%. Significant evidence of molecular adaptation was detected in 28 loci from 13 pathogens. Three of these loci showed concordant patterns of adaptive selection in two to four different species.

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Section: Species Comparisonsmentioning

confidence: 53%

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Pérez‐Losada

Browne

Madsen

et al. 2006

Infection, Genetics and Evolution

145

107

View full text Add to dashboard Cite

show abstract

“…Epidemic outbreaks of varying scale, up to global pandemics, require intricate genetic typing to identify case clusters. MLST is the most powerful and, simultaneously, the most portable approach to keep track of the epidemic spread and has identified clones with apparent increased virulence (14,15). It can now be considered the gold standard for genotyping N. meningitidis.…”

Section: Resultsmentioning

confidence: 99%

Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing

Honisch

Chen

Mortimer³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…To fit the predictions of the model to empirical data requires representative samples of the natural population. Here we use four samples from cross-sectional studies of carriage within a local area (9)(10)(11)(12) in which isolates were characterized by using multilocus sequence typing (MLST), a technique in which DNA sequences are obtained for seven housekeeping loci and the different sequences at each locus are assigned as different alleles (13). The samples are described in more detail in Table 3, which is published as supporting information on the PNAS web site.…”

Section: Methodsmentioning

confidence: 99%

Neutral microepidemic evolution of bacterial pathogens

Fraser

Hanage

Spratt

2005

Proc. Natl. Acad. Sci. U.S.A.

139

138

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Understanding bacterial population genetics is vital for interpreting the response of bacterial populations to selection pressures such as antibiotic treatment or vaccines targeted at only a subset of strains. The evolution of transmissible bacteria occurs by mutation and localized recombination and is influenced by epidemiological as well as molecular processes. We demonstrate that the observed population genetic structure of three important human pathogens, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus, can be explained by using a simple evolutionary model that is based on neutral mutational drift, modulated by recombination, and which incorporates the impact of epidemic transmission in local populations. The predictions of this neutral ''microepidemic'' model are found to closely fit observed genetic relatedness distributions of bacteria sampled from their natural population, and it provides estimates of the relative rate of recombination that agree well with empirical estimates. The analysis suggests the emergence of neutral bacterial population structure from overlapping microepidemics within clustered host populations and provides insight into the nature and size distribution of these clusters. These findings challenge the assumption that strains of bacterial pathogens differ markedly in relative fitness. infinite-alleles model ͉ multilocus sequence typing ͉ recombination I t is now accepted that bacteria do not conform to the clonal model of evolution (1). The importance of recombination has become increasingly clear in recent years, both as a fundamental process in strain diversification (2) and as a mechanism by which strains acquire virulence factors or resistance determinants (3). Homologous recombination in bacteria involves the replacement of a small segment of the bacterial chromosome (a few kilobases) with the corresponding region from another isolate (2). The frequency of these localized recombinational events may be extremely rare, resulting in species that are highly clonal [e.g., Mycobacterium species (4, 5)], or extremely frequent, resulting in species that are almost completely nonclonal [e.g., Helicobacter pylori (6)]. Consequently, theoretical approaches developed for exclusively sexual or asexual organisms are inappropriate, and, at present, there is no general theory reconciling these variable properties of bacteria. The problem is further complicated by serious sampling biases arising as a result of overrepresentation of disease isolates or antibiotic-resistant isolates in clinical strain collections (1). This problem is especially acute for some species, including Streptococcus pneumoniae, Staphylococcus aureus, and Neisseria meningitidis, which we focus on here and which are ''accidental'' pathogens in that healthy carriage is common, with disease a rare outcome. Finally, the host population structure will influence transmission and needs to be accounted for when considering bacterial population structure: Spread of directly transmitted bacteria within a ...

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Carried Meningococci in the Czech Republic: a Diverse Recombining Population

Cited by 108 publications

References 30 publications

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing

Neutral microepidemic evolution of bacterial pathogens

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