Population genetics of pathogenic bacteria

Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping

Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1) species-level identification and (2) variant mapping at different levels of genotypic resolution for population-based tracking and surveillance, in addition to predicting traits such as antimicrobial resistance (AMR). Multi-locus sequence typing (MLST) aids this process by identifying sequence types (ST) based on seven ubiquitous genome-scattered loci. In this paper, we selected one assembly-dependent and one assembly-free method for ST mapping and applied them with the default settings and ST schemes they are distributed with, and systematically assessed their accuracy and scalability across a wide array of phylogenetically divergent Public Health-relevant bacterial pathogens with available MLST databases. Our data show that the optimal k-mer length for stringMLST is species-specific and that genome-intrinsic and -extrinsic features can affect the performance and accuracy of the program. Although suitable parameters could be identified for most organisms, there were instances where this program may not be directly deployable in its current format. Next, we integrated stringMLST into our freely available and scalable hierarchical-based population genomics platform, ProkEvo, and further demonstrated how the implementation facilitates automated, reproducible bacterial population analysis.

Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens

The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.

Candida species biotypes and polyclonality of potentially virulent Candida albicans isolated from oral cavity of patients with orofacial clefts

OBJECTIVES

This study evaluated the incidence of Candida species, and the genetic diversity and virulence of C. albicans of the oral cavity from patients with cleft lip and palate (CLP).

MATERIALS AND METHODS

Oral samples were investigated by microbiological and species-specific PCR methods. The genetic diversity of C. albicans was established using isoenzyme markers, Nei's statistics, and clustering analysis. Hydrolytic enzymes (SAPs and PLs) were analyzed in vitro.

RESULTS

Oral colonization by Candida species was observed in 29 patients with CLP (65.9%), and C. albicans was highly prevalent. SAP and PL activities were observed in 100% and 51.9% of isolates, respectively. High genetic diversity and patterns of monoclonal and polyclonal oral colonization by C. albicans were observed among patients with CLP. Two major polymorphic taxa (A and B) and other minor polymorphic taxa (C to J) were identified. Only one of the 16 clusters (taxon A) harbored strains from patients with and without CLP, whereas other clusters harbored strains exclusively from CLP patients.

CONCLUSIONS

The anatomical conditions of the oral cavity of patients with CLP contribute to the high incidence of Candida species (C. albicans, C. krusei, C. tropicalis, and/or Candida spp.). Data suggest high genetic diversity of potentially virulent C. albicans strains in the oral cavity of CLP patients.

CLINICAL RELEVANCE

Microbiological niches in orofacial clefts can contribute to the emergence of a relative clinical genotypic identity of C. albicans. However, orofacial rehabilitation centers can contribute to the direct and indirect sources of transmission and propagation of Candida species.

Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli

Escherichia coli is a versatile bacterial species that includes both harmless commensal strains and pathogenic strains found in the gastrointestinal tract in humans and warm-blooded animals. The growing amount of DNA sequence information generated in the era of "genomics" has helped to increase our understanding of the factors and mechanisms involved in the diversification of this bacterial species. The pathogenic side of E. coli that is afforded through horizontal transfers of genes encoding virulence factors enables this bacterium to become a highly diverse and adapted pathogen that is responsible for intestinal or extraintestinal diseases in humans and animals. Many of the accessory genes acquired by horizontal transfers form syntenic blocks and are recognized as genomic islands (GIs). These genomic regions contribute to the rapid evolution, diversification and adaptation of E. coli variants because they are frequently subject to rearrangements, excision and transfer, as well as to further acquisition of additional DNA. Here, we review a subgroup of GIs from E. coli termed pathogenicity islands (PAIs), a concept defined in the late 1980s by Jörg Hacker and colleagues in Werner Goebel's group at the University of Würzburg, Würzburg, Germany. As with other GIs, the PAIs comprise large genomic regions that differ from the rest of the genome by their G + C content, by their typical insertion within transfer RNA genes, and by their harboring of direct repeats (at their ends), integrase determinants, or other mobility loci. The hallmark of PAIs is their contribution to the emergence of virulent bacteria and to the development of intestinal and extraintestinal diseases. This review summarizes the current knowledge on the structure and functional features of PAIs, on PAI-encoded E. coli pathogenicity factors and on the role of PAIs in host-pathogen interactions.

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.

Epidemiologic and Clinical Utility of Typing Systems for Differentiating Among Strains of Methicillin-Resistant Staphylococcus aureus

Typing systems for differentiating among strains of methicillin-resistant Staphylococcus aureus (MRSA) can be valuable tools for the epidemiologist and the clinician. Specific criteria for evaluating such systems are typeability, reproducibility, and discriminatory power. An ideal typing system also would be rapid, inexpensive, technically simple, and readily available. Systems based on the detection of phenotypic variations include antimicrobial susceptibility testing, bacteriophage typing, multilocus enzyme electrophoresis, and electrophoretic methods such as protein eletrophoresis and immunoblotting. Systems that directly detect genotypic variations include plasmid profile analysis, restriction enzyme analysis of plasmid DNA, restriction enzyme analysis of chromosomal DNA, Southern blot analysis of specific restriction fragment length polymorphisms, and pulse field gel electrophoresis. in general, the more widely available typing systems based on phenotypic assays and plasmid analysis have limitations in typeability and/or discriminatory power.The chromosomal DNA-based techniques, although promising, are unproven approaches still under active investigation.

Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes

For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects.

The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.

Impermanence of bacterial clones

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.

Extended-spectrum β-lactamase-producing Escherichia coli isolated from poultry: a review of current problems, illustrated with some laboratory findings

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been documented in humans as well as in food-producing birds, including chickens, and for unknown reasons the prevalence has increased significantly during the last decade. With E. coli as a major opportunistic pathogen in chickens and with a potential for zoonotic transfer to human beings, ESBL-producing E. coli represents a major risk both to poultry production and to human health. This review presents some of the current problems with ESBL-producing E. coli in relation to poultry production, with a focus on chickens. To illustrate issues in relation to screening and typing, two case studies are included where one collection of ESBL-producing E. coli isolates was obtained from asymptomatic carrier chickens while the other was obtained from lesions in chickens. Pulsed-field gel electrophoresis and multi-locus sequence typing revealed a highly heterogeneous population of ESBL-producing E. coli. All isolates harboured between one and three large plasmids (>100 kb). Among isolates associated with asymptomatic chickens, the ESBL types SHV and TEM dominated, while CTX-M-1 dominated in disease-associated isolates. The isolates from diseased birds were occasionally of sequence types often associated with human infections, such as ST131. With improved tools to trace and screen for ESBL-producing E. coli at farm level, strategies can be selected that aim to reduce or eliminate the presence of ESBL-producing E. coli in poultry and poultry products meant for human consumption.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity.

DOI:http://dx.doi.org/10.7554/eLife.00093.001

Malaria is an infectious disease that is estimated to kill more than half a million people every year, mostly young children in Africa. It is spread by mosquitos that are infected with Plasmodium parasites that attack red blood cells in the human body. Plasmodium falciparum, the species that is responsible for most of these deaths, causes malaria by entering red blood cells and releasing antigens that travel to the surface of the cells, where they change the adhesion properties. This causes the infected red blood cells to accumulate in small blood vessels, surface capillaries or the brain, which can have severe consequences for the person infected.

P. falciparum is particularly dangerous because of its ability to vary the antigens displayed on the cell surface: this process, known as antigenic variation, helps to maintain infections for extended periods of time by allowing the antigens to stay one step ahead of the immune system (a process known as immune escape). The origins of antigenic variation lie in the fact that each P. falciparum genome has a repertoire of between 50 and 60 var genes that code for the variability of a major antigen that is responsible for immune escape in malaria. Molecular sequencing has shown that local parasite populations contain thousands of different types of var genes: hence, meiotic recombination in the mosquito can create a vast number of combinations of var repertoires.

Artzy-Randrup et al. have developed a computational model of this highly diverse and complex system to address the following question: is a local pathogen population composed of largely random and ephemeral repertoires of these genes, or is it structured into independently circulating strains? Their model goes beyond previous models by including interactions within the local host population that arise as a result of indirect competition between different strains of the pathogen for available hosts: this competition is influenced by the history of infection and, therefore, by the patterns of immunity within the host population. Previous models included within-host processes but not these higher, local population-level interactions.

The model simulates the dynamics of all the unique combinations of var genes in a population of hosts, and shows that even with high rates of reproduction, the parasite population self-organizes into a limited number of coexisting strains: the distinct var repertoires of these strains only weakly overlap, suggesting that the immune response of the host population has been partitioned into distinct niches. By investigating genetic variation at both antigenic sites and regions of the genome that do not code for antigens, Artzy-Randrup et al. suggest that immune selection—the selection imposed on var repertoires by the build up of specific immunity at the population level—plays a central role in structuring parasite diversity.

The new model should lead to a better understanding of the epidemiology of Plasmodium and other pathogens that work in similar ways, including Trypanosoma brucei (sleeping sickness), Borellia burgdorferi (Lyme disease) and Giardia lamblia (gastroenteritis), and help with global efforts to eliminate malaria and other diseases.

DOI:http://dx.doi.org/10.7554/eLife.00093.002

The 2011 Garrod Lecture: From penicillin-binding proteins to molecular epidemiology

In this review, based on my Garrod Lecture to the British Society for Antimicrobial Chemotherapy, I have given a brief outline of my career over the past 40 years, starting with research in the 1970s into the properties and functions of penicillin-binding proteins (PBPs), leading to the identification of the high molecular mass PBPs as the physiological targets of penicillin, and subsequent studies showing the emergence of low-affinity PBPs in penicillin-resistant clinical isolates by inter-species recombination and the generation of mosaic PBP genes. The studies of clinical isolates of gonococci, meningococci and pneumococci with PBP-mediated resistance to penicillin led to new interests in molecular epidemiology and the population and evolutionary biology of bacterial pathogens. The development (with colleagues) of multilocus sequence typing provided a method for the unambiguous characterization of bacterial strains that has proved to be very widely used, but the recent remarkable (and ongoing) developments in DNA sequencing technologies have provided the prospect of being able routinely to use whole genome sequences to characterize pathogen isolates. These developments will soon have major implications for diagnostic microbiology, outbreak investigations and our ability to follow the spread of strains of community-acquired and nosocomial pathogens at local, national and international levels. However, there are major barriers to be overcome, particularly with respect to how the avalanche of genome sequence data will be stored so that its transformative potential for molecular epidemiology and international public health are fully realized.

Population structure of Pseudomonas aeruginosa from five Mediterranean countries: evidence for frequent recombination and epidemic occurrence of CC235

Several studies in recent years have provided evidence that Pseudomonas aeruginosa has a non-clonal population structure punctuated by highly successful epidemic clones or clonal complexes. The role of recombination in the diversification of P. aeruginosa clones has been suggested, but not yet demonstrated using multi-locus sequence typing (MLST). Isolates of P. aeruginosa from five Mediterranean countries (n = 141) were subjected to pulsed-field gel electrophoresis (PFGE), serotyping and PCR targeting the virulence genes exoS and exoU. The occurrence of multi-resistance (≥3 antipseudomonal drugs) was analyzed with disk diffusion according to EUCAST. MLST was performed on a subset of strains (n = 110) most of them had a distinct PFGE variant. MLST data were analyzed with Bionumerics 6.0, using minimal spanning tree (MST) as well as eBURST. Measurement of clonality was assessed by the standardized index of association (I_A^S). Evidence of recombination was estimated by ClonalFrame as well as SplitsTree4.0. The MST analysis connected 70 sequence types, among which ST235 was by far the most common. ST235 was very frequently associated with the O11 serotype, and frequently displayed multi-resistance and the virulence genotype exoS⁻/exoU⁺. ClonalFrame linked several groups previously identified by eBURST and MST, and provided insight to the evolutionary events occurring in the population; the recombination/mutation ratio was found to be 8.4. A Neighbor-Net analysis based on the concatenated sequences revealed a complex network, providing evidence of frequent recombination. The index of association when all the strains were considered indicated a freely recombining population. P. aeruginosa isolates from the Mediterranean countries display an epidemic population structure, particularly dominated by ST235-O11, which has earlier also been coupled to the spread of ß-lactamases in many countries.

Multilocus enzyme electrophoresis for parasites and other pathogens

In this chapter, I expose the main properties and theoretical background of a somewhat out-of-fashion technique, multilocus enzyme electrophoresis (MLEE). I show that the remarkable properties of this marker-clear Mendelian inheritance, codominance, strong phylogenetic signal-are still valid, although of course more modern markers now are able to yield far more refined results. MLEE can still be used in many circumstances when a cheap and reliable marker is required. I summarize what have been the main contributions of MLEE to the study of parasites and other pathogens.

Source identification of airborne Escherichia coli of swine house surroundings using ERIC-PCR and REP-PCR

Evidence is mounting that microorganisms originating from livestock impact the air quality of the animal houses themselves and the public in the surrounding neighborhoods. The aim of this study was to develop efficient bacterial source tracking capabilities to identify sources of Escherichia coli aerosol pollution caused by pigs. Airborne E. coli were isolated from indoor air, upwind air (10 and 50 m away) and downwind air samples (10, 50, 100, 200 and 400 m away) for five swine houses using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli strains from pig fecal samples were also collected simultaneously. The enterobacterial repetitive intergenic consensus polymerize chain reaction (ERIC-PCR) and the repetitive extragenic palindromic (REP-PCR) approaches were used to study the genetic variability and to determine the strain relationships among E. coli isolated from different sites in each swine house. Results showed that 35.1% (20/57) of the bacterial DNA fingerprints from the fecal isolates matched with the corresponding strains isolated from indoor and downwind air samples (similarity > or = 90%). E. coli strains from the indoor and downwind air samples were closely related to the E. coli strains isolated from feces, while those isolated from upwind air samples (swine house C) had low similarity (61-69%). Our results suggest that some strains isolated from downwind and indoor air originated in the swine feces. Effective hygienic measures should be taken in animal farms to prevent or minimize the downwind spread of microorganism aerosol.

Molecular genetic basis of ribotyping

Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.

Multilocus sequence typing of bacteria

Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.

Virulence factor gene profiles of Escherichia coli isolates from clinically healthy pigs

Nonpathogenic, intestinal Escherichia coli (commensal E. coli) supports the physiological intestinal balance of the host, whereas pathogenic E. coli with typical virulence factor gene profiles can cause severe outbreaks of diarrhea. In many reports, E. coli isolates from diarrheic animals were classified as putative pathogens. Here we describe a broad variety of virulence gene-positive E. coli isolates from swine with no clinical signs of intestinal disease. The isolation of E. coli from 34 pigs from the same population and the testing of 331 isolates for genes encoding heat-stable enterotoxins I and II, heat-labile enterotoxin I, Shiga toxin 2e, and F4, F5, F6, F18, and F41 fimbriae revealed that 68.6% of the isolates were positive for at least one virulence gene, with a total of 24 different virulence factor gene profiles, implying high rates of horizontal gene transfer in this E. coli population. Additionally, we traced the occurrence of hemolytic E. coli over a period of 1 year in this same pig population. Hemolytic isolates were differentiated into seven clones; only three were found to harbor virulence genes. Hemolytic E. coli isolates without virulence genes or with only the fedA gene were found to be nontypeable by slide agglutination tests with OK antisera intended for screening live cultures against common pathogenic E. coli serogroups. The results appear to indicate that virulence gene-carrying E. coli strains are a normal part of intestinal bacterial populations and that high numbers of E. coli cells harboring virulence genes and/or with hemolytic activity do not necessarily correlate with disease.

Prophagic DNA fragments in Streptococcus agalactiae strains and association with neonatal meningitis

We identified-by randomly amplified polymorphic DNA (RAPD) analysis at the population level followed by DNA differential display, cloning, and sequencing-three prophage DNA fragments (F5, F7, and F10) in Streptococcus agalactiae that displayed significant sequence similarity to the DNA of S. agalactiae and Streptococcus pyogenes. The F5 sequence aligned with a prophagic gene encoding the large subunit of a terminase, F7 aligned with a phage-associated cell wall hydrolase and a phage-associated lysin, and F10 aligned with a transcriptional regulator (ArpU family) and a phage-associated endonuclease. We first determined the prevalence of F5, F7, and F10 by PCR in a collection of 109 strains isolated in the 1980s and divided into two populations: one with a high risk of causing meningitis (HR group) and the other with a lower risk of causing meningitis (LR group). These fragments were significantly more prevalent in the HR group than in the LR group (P < 0.001). Our findings suggest that lysogeny has increased the ability of some S. agalactiae strains to invade the neonatal brain endothelium. We then determined the prevalence of F5, F7, and F10 by PCR in a collection of 40 strains recently isolated from neonatal meningitis cases for comparison with the cerebrospinal fluid (CSF) strains isolated in the 1980s. The prevalence of the three prophage DNA fragments was similar in these two populations isolated 15 years apart. We suggest that the prophage DNA fragments identified have remained stable in many CSF S. agalactiae strains, possibly due to their importance in virulence or fitness.

Increase in probing depth is correlated with a higher number of Prevotella intermedia genotypes

BACKGROUND

The aims of this study were to determine the genotypic diversity of Prevotella intermedia in subgingival plaque samples by using two techniques, arbitrarily primed polymerase chain reaction (AP-PCR) and heteroduplex analysis, and to assess the relationship of this diversity with increase in probing depth.

METHODS

The subgingival plaque samples were obtained from 12 patients using paper points inserted into periodontal pockets (diseased sites) and healthy gingival sulci (healthy sites) of the same subjects. After isolation and identification, AP-PCR was performed for genotypic characterization of P. intermedia (80 isolates). The clinical samples with a positive result for P. intermedia were amplified by 16S rRNA-based PCR method, and the amplicons were subjected to heteroduplex analysis.

RESULTS

The agreement between the two methods was very high; the AP-PCR and heteroduplex analysis showed that subjects harbored between one and five distinct genotypes of P. intermedia, with a positive association between numbers of genotypes by AP-PCR (P = 0.0042) or heteroduplex (P = 0.0099) and increase in probing depth. No matching of P. intermedia genotypes was observed between healthy and diseased sites of the same individual. Interindividual analyses demonstrated absence of identical clones and indicated a high level of genetic diversity in the species.

CONCLUSION

A clear relationship was observed between a higher number of genotypes and increase in probing depth; these results suggest that environmental challenges in the periodontal pockets may modulate the microbiota by selecting genotypes best able to exploit the environment.

Transmission of periodontal bacteria and models of infection

BACKGROUND

Bacteria play an essential role in the aetiology of periodontitis. Most bacterial species isolated from subgingival plaque are indigenous to the oral cavity. Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis are detected infrequently in periodontal health, which makes these species prime candidates to study person-to-person transmission. The aim of the present study was to review the literature on transmission of these periodontal bacterial species.

METHOD

We review the literature on bacterial typing techniques and summarize the information on clonal distribution of A. actinomycetemcomitans and P. gingivalis in family units based on different typing techniques in order to establish the likelihood for person-to-person transmission of these periodontal pathogens.

RESULTS

Vertical transmission of A. actinomycetemcomitans is estimated to be between 30% and 60%, whereas vertical transmission of P. gingivalis has rarely been observed. Horizontal transmission between spouses ranges between 14% and 60% for A. actinomycetemcomitans and between 30% and 75% for P. gingivalis. There is some evidence to show that cohabitation with a periodontitis patient influences the periodontal status of the spouse; however, substantially more information is needed to prove this hypothesis.

CONCLUSIONS

Transmission of putative periodontal pathogens between family members has been shown. The clinical consequences of these events have been poorly documented. Based on the current knowledge, screening for and prevention of transmission of specific virulent clones of A. actinomycetemcomitans may be feasible and effective in preventing some forms of periodontal disease. P. gingivalis is usually recovered from diseased adult subjects, and transmission of this pathogens seems largely restricted to adult individuals. Horizontal transmission of P. gingivalis may therefore be controlled by periodontal treatment involving elimination or significant suppression of the pathogen in diseased individuals and by a high standard of oral hygiene.

Towards a population genetics of microorganisms: The clonal theory of parasitic protozoa

Over the past 15 years, molecular investigations, including the study of isozymes and DNA markers, have provided much information on the genetic variation, population structure, breeding system and other population characteristics of parasitic protozoa. For some parasitic protozoa, but not for others, the evidence indicates that their reproduction is prevailingly clonal. In this article, Michel Tibayrenc and Francisco Ayala propose that the issue of whether the predominant mode of reproduction of a given micro-organism is clonal or sexual can only be settled by population genetics information, and they summarize evidence favoring a clonal population structure for a number of parasitic protozoa.

Multilocus enzyme electrophoresis typing of Candida albicans populations isolated from healthy children according to socioeconomic background

The aim of this research was to evaluate the genetic diversity within and between C. albicans populations isolated from the oral cavity of healthy Brazilian children classified into five socioeconomic categories (A to E). Multilocus Enzyme Electrophoresis (MLEE) analysis was the method used to assess genetic diversity. High genetic diversity was observed in all populations that showed predominance of some C. albicans subtypes (Electrophoretic Types - ETs). However, no correlation was observed between a specific ET and a specific population of children. Clustering analysis showed one or more highly related ET clusters, suggesting the existence of indirect and direct propagation routes of C. albicans among healthy children. Microevolutionary changes were observed in some C. albicans populations isolated from children with the same or very similar socioeconomic condition. Furthermore, low transition of C. albicans subtypes can be occurring among certain populations of children coming from high and medium/high, or high and medium/low, or medium/high and medium/low socioeconomic categories, which can also be explained by their own socioeconomic and cultural characteristics.

Molecular genetic methods in diagnosis and direct characterization of acute bacterial central nervous system infections

Acute bacterial infection of the central nervous system requires rapid and adequate management. Etiological diagnosis is hence crucial. Moreover, the epidemic threat of certain bacteria necessitates a reliable characterization of the involved bacterial strains to follow the spread of epidemic strains. Conventional identification and characterization of etiological agents are basically based on culture and identification of bacterial markers most frequently by serological assays. Molecular identification and characterization of bacteria have been employed. They provide more reliable analysis of bacterial isolates. Molecular methods for non-culture diagnosis of bacterial infections have recently been developed. In many cases, the molecular assays have decreased the identification time of positive cultures and rescued detection of pathogens in culture-negative clinical samples.

Molecular epidemiology of avian pathogenic Escherichia coli (APEC) isolated from colisepticemia in poultry

The molecular biology and epidemiology of 150 avian pathogenic Escherichia coli strains (APEC) isolated from septicemic poultry in Germany was investigated by serotyping, pulsed field gel electrophoresis (PFGE), and polymerase chain reaction (PCR). Only 49.6% of the isolates could be grouped to serogroups O1, O2, and O78. Macrorestriction analyses data revealed two large clonal groups (clusters I and II) among the APEC strains with a similarity of 60.9% to each other. An association between restriction pattern and serogroup or origin of the strains was only present in a few subgroups of each clusters I and II, but was not evident. In contrast, our data revealed distinct combinations of virulence-associated genes in that 51.2% of the O2-strains harboured a combination of the genes fyuA, irp2, iucD, tsh, vat, fimC, and colV and 36.4% of the O78-strains possessed the same gene combination with exception of vat. With 34 different gene combinations the non-O1, -O2, -O78 isolates revealed a higher variability in their virulence gene pattern than O1-, O2-, and O78-strains with 6, 13, and 9 patterns, respectively. Our data indicate only a limited association between the virulence gene pattern and the serogroup of APEC strains and question the sensitivity of O-typing for APEC identification without the application of further diagnostic tools. Although a limited number of APEC clones exist, horizontal gene transfer seems to be common in these pathogens. These findings strengthen further research on the population structure of APEC and may be the reason for the lack of clear definition of this common E. coli pathotype.

eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data

The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

The clonal theory of parasitic protozoa: 12 years on

The question of population structure in parasitic protozoa has recently gained a renewed topicality with significant contributions on medically important pathogens, such as Plasmodium falciparum, Toxoplasma gondii and Cryptosporidium parvum. The proposals that initiated this debate are reviewed here and the subsequent developments of the clonal theory, in light of recent contributions, are examined.

Redefining bacterial populations: a post-genomic reformation

Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host pathogen relationships.

Evolutionary genetics and molecular diagnosis of Leishmania species

An extensive study has been performed on various natural populations of Leishmania from the 'Old' and 'New Worlds' using multilocus enzyme electrophoresis and random amplification of polymorphic deoxyribonucleic acid. The data are interpreted in evolutionary genetic terms in order to give a firm basis to studies dealing with the relevant medical properties of pathogens. We confirm that Leishmania undergoes clonal evolution with occasional phenomena of hybridization. This suggests that the microorganism genotypes are stable in space and time and consequently have epidemiological and medical relevance. It is crucial to have a clear definition of the taxa to be identified. In the case of Leishmania, there is at present no firm consensus on the species concept. We propose that any new species of Leishmania should correspond to a 'discrete typing unit' that exhibits specific medical and/or epidemiological characters. Based on this approach, the species status of L. peruviana can be supported. On the contrary, L. panamensis cannot be clearly distinguished from L. guyanensis. Our studies on the genetic diversity of Leishmania show that a given stock is not representative of the genus, the subgenera, or any species. We suggest that the genetic polymorphism of Leishmania has a strong impact on the parasite's biomedical properties.

Functional genomics of pathogenic bacteria

Microbial diseases remain the commonest cause of global mortality and morbidity. Automated-DNA sequencing has revolutionized the investigation of pathogenic microbes by making the immense fund of information contained in their genomes available at reasonable cost. The challenge is how this information can be used to increase current understanding of the biology of commensal and virulence behaviour of pathogens with particular emphasis on in vivo function and novel approaches to prevention. One example of the application of whole-genome-sequence information is afforded by investigations of the pathogenic role of Haemophilus influenzae lipopolysaccharide and its candidacy as a vaccine.

Comparative genetic characterization of Listeria monocytogenes isolates from human and animal listeriosis cases

Listeria monocytogenes isolates from human sporadic and epidemic cases (n=119) and from animal cases (n=76) were characterized by automated ribotyping and PCR-restriction fragment length polymorphism (PCR-RFLP) typing of the virulence genes actA and hly. This combination of typing methods differentiated 39 distinctive strains, each reflecting a unique combination of ribotypes, hly and actA alleles. Simpson's index of discrimination indicated a high discriminatory ability of ribotyping for both animal (0.867) and human isolates (0.857), which was further increased by the addition of hly and actA typing (0.916 and 0.904, respectively). Ribotype and hly allele data were further used to group isolates into three genetically distinct lineages. Each lineage is composed of several ribotype fragment subsets, each of which contains multiple ribotypes characterized by common ribotype fragments. To determine whether certain clones of L. monocytogenes show indications for unique pathogenic potential or host specificity, frequency distributions for five genetic characteristics (i.e. lineage, ribotype, ribotype fragment subset and hly and actA allele) were calculated for isolates from animal cases, human epidemic cases and human sporadic cases. Lineage III isolates were found less frequently in human cases (1 of 119 isolates) than in animal cases (8 of 76 isolates; P=0.003). These results suggest the possibility of host specificity for non-primate mammals among lineage III strains. In addition, lineage I strains were found more frequently among human cases than among animal cases (P<0.001). Among the eight hly alleles observed, hly allele 1 was more common among human isolates as compared to animal isolates (P=0.002). We also identified one ribotype (DUP-1030) which was significantly more common among animal isolates (P=0.005) and one ribotype (DUP-1038; lineage I) which was significantly more common among human epidemic isolates as compared to human sporadic isolates (P<0.001). These findings confirm the presence of clonal groups of L. monocytogenes, which appear to be characterized by unique virulence or host specificity patterns. This study also establishes baseline data describing the genetic diversity of human and animal L. monocytogenes isolates which can be utilized in future surveillance programmes to track the emergence of new strains.

Resistance rather than virulence selects for the clonal spread of methicillin-resistant Staphylococcus aureus: implications for MRSA transmission

The population structure of methicillin-resistant Staphylococcus aureus (MRSA) is predominantly clonal, which may be related to the fitness of the genetic background of the methicillin-susceptible S. aureus (MSSA) into which the mecA chromosomal resistant determinant has inserted. To test this idea, we assessed whether the genotypes of New York MRSA are present in MSSA populations by using a combination of protein A gene sequence typing (spa typing) and pulsed-field gel electrophoresis (PFGE). Although about 16% of colonizing MSSA isolated from community subjects were related to MRSA, only one of the five predominant New York MRSA clonal types was found among the MSSA isolates. Similarly, among nosocomial MSSA, only four MRSA homologues were observed, two of which may have arisen through deletion of the mec element. Thus, MRSA clonal types represent a limited spectrum of the diversity seen in community and hospital S. aureus populations. The data are best explained by antibiotic selection pressure, as opposed to increased transmissibility or virulence, being responsible for the clonal dissemination of the resistance phenotype in MRSA genetic backgrounds, an in turn, the limited spread of these strains outside of the hospital environment.

Clonal population structure of Pseudomonas stutzeri, a species with exceptional genetic diversity

Genetic diversity and genetic relationships among 42 Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, this P. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (I(A)) for the P. stutzeri strains analyzed was 1.10. The I(A) values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.

Toward an integrated genetic epidemiology of parasitic protozoa and other pathogens

Due to the increase of human migrations, the appearance of emerging and reemerging endemies, growing antibiotic resistance, and climatic changes, infectious diseases most probably constitute the major challenge for medicine in the next century. The advent of molecular methods of pathogen characterization has considerably improved our knowledge of the epidemiology of these diseases. However, the use of concepts of evolutionary genetics for interpreting "molecular epidemiology" data remains limited, although the application of such methods would broaden considerably the scope of this field of research, and allow epidemiologic and taxonomic approaches to be ascertained on a much firmer basis. In turn, pathogens, hosts, and vectors provide fascinating models for basic research. The artificial character of the border between "basic" and "applied" research is especially apparent with regard to the "integrated genetic epidemiology of infectious diseases" concept. The goal of this chapter is to evaluate the respective impact, on the transmission and pathogenicity of infectious diseases, of the host's, the pathogen's, and the vector's (for vector-borne diseases) genetic diversity, and the interactions between these three parameters (coevolution phenomena).

Intrafamilial Transmission of Black-pigmented, Putative Periodontal Pathogens

Porphyromonas gingivalis and Prevotella intermedia are black-pigmented, putative periodontopathogenic bacteria considered to cause some forms of periodontal disease. Porphyromonas gingivalis and P. intermedia can be transmitted between humans and produce periodontal disease in susceptible hosts. In this article, studies using molecular typing methods for determining the transmission of black-pigmented, putative periodontopathogens between family members are reviewed. As individuals living close to each other are more prone to transmit bacteria, the studies on transmission of periodontopathogens have been performed on family members. It has been shown that black-pigmented bacteria are not only transferred between spouses but also between parents and child. Since only a limited number of studies have been done, longitudinal and controlled studies should be carried out to elucidate further the transmittance potential of these bacteria.

Enzyme polymorphism in Pseudomonas aeruginosa strains recovered from cystic fibrosis patients in France

Each of 314 strains of Pseudomonas aeruginosa recovered from 87 French cystic fibrosis (CF) patients was typed by multilocus enzyme electrophoresis to investigate the genetic diversity, the relatedness and the molecular epidemiology of strains isolated from cases of chronic pulmonary colonization. Comparison of allele profiles at 18 enzyme loci identified 17 electrophoretic types (ETs). Of the 314 isolates, 290 (92%) were either ET1 (n = 127) or ET2 (n = 163), which differed only at the shikimate dehydrogenase (SKD) locus. The mean genetic diversity (H) was 0.138. These results suggest that there is cross-colonization between patients and/or that two predominant groups of strains are able to colonize French CF patients. Sequential isolates collected from 18 patients during a period of 12-28 months were analysed to assess genomic variability and its relationship to clinical outcome. Six patients were colonized by a stable strain. For the others, double infections or changes in colonization over time were observed. No relationships were detected between the clinical outcome and the persistence of stable isolates, the emergence of transient superinfecting variants, the presence of multiple ETs or the shift of ET during the monitoring.

Oral ecology and person-to-person transmission of Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis

The ecological characteristics of the oral cavity are dissimilar for A. actinomycetemcomitans and for P. gingivalis, as judged by differences in their colonization preferences and patterns, associations with periodontal disease parameters, relationships with the subgingival microbiota and the type of periodontitis and their clonal persistence in the oral cavity. These features also suggest that as a periodontal pathogen, A. actinomycetemcomitans is different from P. gingivalis. Probably in most infected individuals, low levels of A. actinomycetemcomitans can persist for years in equilibrium with the host and the resident oral microbiota. However, it is well established that A. actinomycetemcomitans can cause disease in some individuals or in some circumstances when the regulatory mechanisms are unable to maintain homeostasis in the ecosystem. Elevated A. actinomycetemcomitans proportions of the biota can be regarded as a sign of ecological imbalance, leading to increased risk of periodontal destruction. There is also evidence showing elevated pathogenic potential of certain A. actinomycetemcomitans clones. Although A. actinomycetemcomitans seems to be relatively rarely transmitted between cohabiting adults, transmission can occur to periodontally healthy children of A. actinomycetemcomitans-positive parents. Parents and children may share factors that promote successful oral colonization of A. actinomycetemcomitans, or the window of opportunity is in childhood. Therefore, to prevent parent-child transmission of A. actinomycetemcomitans, bacterium-positive parents of young children are optimal targets for enhanced information and treatment. In selected populations, screening for specific clones of A. actinomycetemcomitans has been employed in prevention of peridontitis. Future research aiming at finding the reasons which cause the changes in the oral homeostasis to allow the growth of A. actinomycetemcomitans may give insight into novel prevention strategies for A. actinomycetemcomitans-associated periodontitis. Compared with A. actinomycetemcomitans, P. gingivalis shows a different pattern of coexistence with the host. In periodontal health or in children, P. gingivalis is absent or only rarely detected. When present, P. gingivalis is commonly recovered in high numbers from dentitions exhibiting inflamed periodontitis and poor oral hygiene. Contrary to A. actinomycetemcomitans, the data on the vertical transmission of P. gingivalis are limited. The major infection route of P. gingivalis seems to be between adults, indicating that P. gingivalis commonly colonizes in an established oral microbiota. These characteristics suggest that the degree of tolerance between P. gingivalis and the host is inferior to that between A. actinomycetemcomitans and the host. It appears that the association of P. gingivalis with disease is a rule rather than an accidental incident. On these grounds, it seems that the host-P. gingivalis relationship approaches antibiosis. Since P. gingivalis infection is related to a typical periodontal eco-pathology, the susceptibility to person-to-person transmission of this pathogen may be controlled by periodontal treatment and emphasizing the significance of high standard oral hygiene.

Free recombination within Helicobacter pylori

Sequences of three gene fragments (flaA, flaB, and vacA) from Helicobacter pylori strains isolated from patients in Germany, Canada, and South Africa were analyzed for diversity and for linkage equilibrium by using the Homoplasy Test and compatibility matrices. Horizontal genetic exchange in H. pylori is so frequent that different loci and polymorphisms within each locus are all at linkage equilibrium. These results indicate that H. pylori is panmictic. Comparisons with sequences from Escherichia coli, Neisseria meningitidis, and Drosophila melanogaster showed that recombination in H. pylori was much more frequent than in other species. In contrast, when multiple family members infected with H. pylori were investigated, some strains were indistinguishable at all three loci. Thus, H. pylori is clonal over short time periods after natural transmission.

Epidemiological markers in Neisseria meningitidis: an estimate of the performance of genotyping vs phenotyping

In order to estimate the performance of genotypic vs phenotypic characterization of Neisseria meningitidis, 2 methods, DNA fingerprinting and multilocus enzyme electrophoresis (MEE), were assessed as regards applicability, reproducibility and discriminating capacity. 50 serogroup B and 52 serogroup C Neisseria meningitidis strains from 96 patients with meningococcal disease and 22 serogroup C strains from healthy carriers were investigated. Both methods were 100% applicable to meningococcal strains and results of DNA fingerprinting as well as of MEE were reproducible. The number of types defined by DNA fingerprinting and MEE as compared to that defined by phenotypic characteristics (serogroup, serotype, serosubtype and sulphonamide resistance) was as follows: for serogroup B strains from patients, 11 and 12 vs 8; for serogroup C strains from patients, 10 and 15 vs 8; and for serogroup C carrier strains, 12 and 19 genotypes vs 10 phenotypes were defined. By use of both DNA fingerprinting and MEE the number of genotypes defined for the 3 groups of strains was 14, 17 and 19, respectively. DNA fingerprinting and MEE showed a discriminating capacity superior to that of phenotyping, and as applied in the study MEE was superior to DNA fingerprinting. Clusters of invasive strains were reliably identified by phenotyping alone, whereas determination of identity of carrier strains and an invasive strain required genotyping.

Variable serum immunoglobulin G immune response to genetically distinct Eikenella corrodens strains coexisting in the human oral cavity

This study examined the variable serum immunoglobulin G (IgG) levels to genetically distinct autologous Eikenella corrodens strains by enzyme-linked immunosorbent assay (ELISA). Twenty subjects, including 10 adult periodontitis patients, 5 juvenile periodontitis patients and 5 periodontally healthy subjects were examined. Each subject was colonized by 2-8 genetically distinct E. corrodens strains. The serum IgG levels to autologous E. corrodens within individuals were significantly different in 7 adult periodontitis patients, 4 juvenile periodontitis patients and a periodontally healthy subject. Poor correlation was found in diseased subjects between serum IgG levels to autologous strains and to reference strains ATCC 23834 or FDC 373. Four adult periodontitis patients and two juvenile periodontitis patients exhibited significant serum IgG levels to autologous E. corrodens strains (two standard deviations above the mean for periodontally healthy subjects); two of these six diseased subjects exhibited low serum IgG levels to reference strains and would have been classified as low immune responders if only reference strains had been used in ELISA. This study showed the importance of using autologous E. corrodens strains in the assessment of serum IgG immune responses to this organism.

Clonal analysis by ribotyping of Fusobacterium nucleatum isolates obtained from healthy young adults with optimal plaque control

Fusobacterium nucleatum is a Gram-negative anaerobic rod implicated in the pathogenesis of periodontal disease. However, this organism has also been frequently identified in high numbers in healthy adults. These observations suggest that the species may comprise different clonal types, some of which may participate in disease. The purpose of the present investigation was to use restriction endonuclease analysis (REA) and ribotyping to characterize F. nucleatum clonal types isolated from healthy young adults with optimal plaque control and investigate the stability of some of these clonal types. A group comprising 11 dental students and 11 dental outpatients with optimal plaque control was sampled. Clonal stability was investigated by sampling the dental student group at baseline and at 16 months. One hundred and thirty-two clinical isolates of F. nucleatum were successfully recovered from 15/22 individuals. For the positive subjects, 29 different clonal types were identified by REA and ribotyping, each subject and site being colonized by 1-4 clonal types. For the dental students, 9 and 15 different clonal types were identified at baseline and 16 months, respectively. None of the students harboured identical clonal types at both sampling times. Our results show that ribotyping is a useful technique for monitoring the distributions of F. nucleatum clonal types and indicate that healthy individuals with optimal plaque control can be colonized by more than one F. nucleatum clonal type and that these clonal types appear to be unstable.

Microevolution during epidemic spread of Neisseria meningitidis

Similar to many other naturally transformable bacteria, Neisseria meningitidis has yielded many examples where horizontal genetic exchange has resulted in genetic variation of individual strains. Epidemic strains are purified of genetic variants due to bottlenecks during the spread from country to country, resulting in clonal descent. Occasionally, clonal replacement also occurs during epidemic spread. These processes occur rapidly in serogroup A meningococci; such that after their descent from a common ancestor, clonally related bacteria have diversified at numerous loci within the last decades.

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Genetic epidemiology of parasitic protozoa and other infectious agents: the need for an integrated approach

This paper emphasises the relevance of the concepts and methods of evolutionary genetics for studying the epidemiology of parasitic protozoa and other pathogenic agents. Population genetics and phylogenetic analysis both contribute to identifying the relevant evolutionary and epidemiologically discrete units of research (Discrete typing units = DTUs), that can be equated to distinct phylogenetic lines. It is necessary (i) to establish that a given species represents a reliable DTU; (ii) to see whether a given species is further structured into lower DTUs that correspond to either clonal lineages or to cryptic species, and could exhibit distinct biomedical properties (virulence, resistance to drugs, etc). DTUs at the species and subspecies level can be conveniently identified by specific genetic markers or sets of genetic markers ("tags") for epidemiological follow-up. For any kind of pathogen (protozoa, fungi, bacteria, viruses), DTUs represent the relevant units of research, not only for epidemiology, but also, for other applied researches (clinical study, pathogenicity, vaccine and drug design, immunology, etc). The development of an "integrated genetic epidemiology of infectious diseases", that would explore the respective role of, and the interactions between, the genetic diversity (and its biological consequences) of the pathogen, the host and the vector (in the case of vector-borne diseases) is called for.