Temporal trends in gonococcal population genetics in a high prevalence urban community

Pérez‐Losada, Marcos; Crandall, Keith A.; Zenilman, Jonathan M.; Viscidi, Raphael P.

doi:10.1016/j.meegid.2006.11.003

Cited by 37 publications

(42 citation statements)

References 32 publications

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“…However, the discriminatory ability of the present MLST schemes, examining seven housekeeping loci, is suboptimal for several epidemiological questions involving more microepidemiological analysis (71,(129)(130)(131)163; M. Unemo, unpublished data). An MLST typing scheme which seems to provide a higher discrimination has been developed based on the seven housekeeping genes abcZ, adk, fumC, gdh, glnA, gnd, and pyrD (184).…”

Section: Dna-based Typing Methodsmentioning

confidence: 99%

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

2011

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SUMMARY Gonorrhea, which may become untreatable due to multiple resistance to available antibiotics, remains a public health problem worldwide. Precise methods for typing Neisseria gonorrhoeae , together with epidemiological information, are crucial for an enhanced understanding regarding issues involving epidemiology, test of cure and contact tracing, identifying core groups and risk behaviors, and recommending effective antimicrobial treatment, control, and preventive measures. This review evaluates methods for typing N. gonorrhoeae isolates and recommends various methods for different situations. Phenotypic typing methods, as well as some now-outdated DNA-based methods, have limited usefulness in differentiating between strains of N. gonorrhoeae. Genotypic methods based on DNA sequencing are preferred, and the selection of the appropriate genotypic method should be guided by its performance characteristics and whether short-term epidemiology (microepidemiology) or long-term and/or global epidemiology (macroepidemiology) matters are being investigated. Currently, for microepidemiological questions, the best methods for fast, objective, portable, highly discriminatory, reproducible, typeable, and high-throughput characterization are N. gonorrhoeae multiantigen sequence typing (NG-MAST) or full- or extended-length porB gene sequencing. However, pulsed-field gel electrophoresis (PFGE) and Opa typing can be valuable in specific situations, i.e., extreme microepidemiology, despite their limitations. For macroepidemiological studies and phylogenetic studies, DNA sequencing of chromosomal housekeeping genes, such as multilocus sequence typing (MLST), provides a more nuanced understanding.

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Section: Dna-based Typing Methodsmentioning

confidence: 99%

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

2011

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“…However, this mutation rate estimate is quite low compared with, for example, some laboratory estimates for E. coli (Lenski et al 1998) and Pseudomonas (Buckling et al 2007). A number of studies have estimated lineage divergence using a more rapid rate of molecular evolution (Falush et al 2001;Perez-Losada et al 2007;Feng et al 2008;Wilson et al 2009;Sheppard et al 2010a). One calibration of divergence in C. jejuni was based on the rate of nucleotide substitution in a longitudinal 3-year study of molecular variation in MLST data from a confined geographic location (Wilson et al 2009).…”

Section: The Timescale Of Campylobacter Evolutionmentioning

confidence: 99%

The Evolution ofCampylobacter jejuniandCampylobacter coli

Sheppard

Maiden

2015

Cold Spring Harb Perspect Biol

137

127

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The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.

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“…This approach has multiple applications such as phylogeny [18], molecular structure analysis [42], and molecular epidemiology. In molecular epidemiology, MLST can be used to study the evolution of antibiotic resistant strains [17], the temporal trends in strain expansion [29], or the distribution of strains of various lineages within a population [20].…”

Section: Epidemiological Analysismentioning

confidence: 99%

Genotyping ofMycoplasma mycoidessubsp.mycoidesSC by multilocus sequence analysis allows molecular epidemiology of contagious bovine pleuropneumonia

et al. 2008

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-Mycoplasma mycoides subsp. mycoides SC (MmmSC) is the etiological agent of contagious bovine pleuropneumonia (CBPP). Although eradicated in most developed countries, the disease reappeared in Europe in the 1990s. This reappearance may have been caused either by importation from sub-Saharan Africa, where CBPP is still endemic, or by the reemergence of virulent strains in Europe, as suggested by earlier studies. A multilocus sequence analysis scheme has been developed to address this issue and, most importantly, to be able to monitor new epidemics. The alignment of the full genome sequence of the reference strain PG1 and the partial genome sequence of a pathogenic strain allowed the identification of polymorphic sites. Nineteen initial loci were selected within housekeeping genes, genes of unknown function and non coding sequences. The suitability of these loci for genotyping MmmSC strains was first tested on six strains of diverse geographic origin. The analyses showed that the published PG1 sequence contained a number of specific polymorphisms that were therefore of no use for molecular typing. Among the eight informative polymorphic loci finally selected, only one (ftsY) was positioned within a housekeeping gene. Three main groups and 31 different allelic profiles were identified among 51 strains and strain variants examined. Cluster analysis confirmed that European strains from the 1990s did not originate from Africa. It also showed a genetic link between a European strain isolated in 1967 and those found in southern Africa and Australia. This was in agreement with historical data showing that CBPP was introduced in these regions during colonisation in the 19th century.Mycoplasma mycoides / contagious bovine pleuropneumonia / multilocus sequence analysis / molecular epidemiology

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Temporal trends in gonococcal population genetics in a high prevalence urban community

Cited by 37 publications

References 32 publications

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

The Evolution ofCampylobacter jejuniandCampylobacter coli

Genotyping ofMycoplasma mycoidessubsp.mycoidesSC by multilocus sequence analysis allows molecular epidemiology of contagious bovine pleuropneumonia

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