Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus

Although microorganisms make up the preponderance of the biodiversity on Earth, the ecological and evolutionary factors that structure microbial populations are not well understood. We investigated the genetic structure of a thermoacidophilic crenarchaeal species, Sulfolobus islandicus, using multilocus sequence analysis of six variable protein-coding loci on a set of 60 isolates from the Mutnovsky region of Kamchatka, Russia. We demonstrate significant incongruence among gene genealogies and a lack of association between alleles consistent with recombination rates greater than the rate of mutation. The observation of high relative rates of recombination suggests that the structure of this natural population does not fit the periodic selection model often used to describe populations of asexual microorganisms. We propose instead that frequent recombination among closely related individuals prevents periodic selection from purging diversity and provides a fundamental cohesive mechanism within this and perhaps other archaeal species.     

Covariability of Vibrio cholerae microdiversity and environmental parameters

Fine-scale diversity of natural bacterial assemblages has been attributed to neutral radiation because correspondence between bacterial phylogenetic signals in the natural environment and environmental parameters had not been detected. Evidence that such correspondence occurs is provided for Vibrio cholerae, establishing a critical role for environmental parameters in bacterial diversity.     

Virulence genes in environmental strains of Vibrio cholerae

The virulence of a pathogen is dependent on a discrete set of genetic determinants and their well-regulated expression. The ctxAB and tcpA genes are known to play a cardinal role in maintaining virulence in Vibrio cholerae, and these genes are believed to be exclusively associated with clinical strains of O1 and O139 serogroups. In this study, we examined the presence of five virulence genes, including ctxAB and tcpA, as well as toxR and toxT, which are involved in the regulation of virulence, in environmental strains of V. cholerae cultured from three different freshwater lakes and ponds in the eastern part of Calcutta, India. PCR analysis revealed the presence of these virulence genes or their homologues among diverse serotypes and ribotypes of environmental V. cholerae strains. Sequencing of a part of the tcpA gene carried by an environmental strain showed 97.7% homology to the tcpA gene of the classical biotype of V. cholerae O1. Strains carrying the tcpA gene expressed the toxin-coregulated pilus (TCP), demonstrated by both autoagglutination analysis and electron microscopy of the TCP pili. Strains carrying ctxAB genes also produced cholera toxin, determined by monosialoganglioside enzyme-linked immunosorbent assay and by passage in the ileal loops of rabbits. Thus, this study demonstrates the presence and expression of critical virulence genes or their homologues in diverse environmental strains of V. cholerae, which appear to constitute an environmental reservoir of virulence genes, thereby providing new insights into the ecology of V. cholerae.     

霍乱弧菌生物被膜发育与环境调控

生物被膜状态的霍乱弧菌具有极强的环境适应性和超高的感染性,生物被膜的发育调控研究对霍乱弧菌的宿主感染和环境适应非常重要。本文综述了近年来霍乱弧菌生物被膜研究结果,包括霍乱弧菌生物被膜的组成、发育和环境调控,尤其着重阐述了各种环境因子对霍乱弧菌生物被膜发育的影响,包括细菌自体信号分子、自然环境因子和宿主信号分子。     

Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae

Pathogenic Vibrio cholerae cycle between the nutrient-rich human intestinal tract and nutrient-poor aquatic environments and currently few bacterial factors are known that aid in the transition between these disparate environments. We hypothesized that the ability to store carbon as glycogen would facilitate both bacterial fitness in the aquatic environment and transmission of V. cholerae to new hosts. To investigate the role of glycogen in V. cholerae transmission, we constructed mutants that cannot store or degrade glycogen. Here, we provide the first report of glycogen metabolism in V. cholerae and demonstrate that glycogen prolongs survival in nutrient-poor environments that are known ecological niches of V. cholerae , including pond water and rice-water stool. Additionally, glycogen contributes to the pathogenesis of V. cholerae in a transmission model of cholera. A role for glycogen in the transmission of V. cholerae is further supported by the presence of glycogen granules in rice-water stool vibrios from cholera patients, indicating that glycogen is stored during human infection. Collectively, our findings indicate that glycogen metabolism is critical for V. cholerae to transition between host and aquatic environments.     

Self-Transfer and Genetic Recombination Mediated by P, the Sex Factor of Vibrio cholerae

Vibrio cholerae cells, infected with the sex factor P, produce discrete, plaque-like clearings when plated on lawns of P(-) cells. We investigated the nature of these clearings and conclude that they are probably sites of active mating. We developed a quantitative assay for P(+) cells and used it to study the kinetics of sex factor spread in broth cultures. Both established and newly infected donor populations were efficient sex factor donors, indicating that P is not self-repressed. We also investigated the kinetics of recombinant formation in broth matings. In 1-hr matings, we routinely found recombination frequencies of 10(-6) per donor cell. Kinetic studies of recombinant formation showed that the markers tested all appeared at early times. Thus P, the V. cholerae sex factor, seems to resemble F in its transfer properties.     

R plasmids in environmental Vibrio cholerae non-O1 strains

The occurrence of drug resistance and its plasmid-mediated transferability was investigated in 140 environmental strains of Vibrio cholerae non-O1 and 6 strains of Vibrio cholerae, both O1 and non-O1, of clinical origin. Of the 146 strains tested, 93% were resistant to at least one drug and 74% were resistant to two or more antibiotics. The O1 strains were susceptible to all antibiotics used. A total of 26 of 28 selected resistant wild strains carried R plasmids that were transferable by intraspecific and intergeneric matings. The most common transmissible R factor determined resistance to ampicillin, amoxicillin, and sulfanilamide (30%), followed by resistance to ampicillin and amoxicillin (13%) and resistance to ampicillin, amoxicillin, phosphomycin, and sulfanilamide (9%). Comparison of the three methods of plasmid analysis showed that the method of Birnboim and Doly (Nucleic Acids Res. 7:1513-1523, 1979) without EDTA and lysozyme was optimal for isolation of both large and small plasmids in environmental V. cholerae strains. Most strains harbored more than one plasmid, and the molecular sizes ranged from 1.1 to 74.8 megadaltons. The plasmids of high molecular size (around 74 megadaltons) were responsible for the resistance pattern transferred and were maintained with high stability in the hosts.     

Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates

Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.     

Interbacterial competition and anti-predatory behaviour of environmental Vibrio cholerae strains

Vibrio cholerae isolates responsible for cholera pandemics represent only a small portion of the diverse strains belonging to this species. Indeed, most V. cholerae are encountered in aquatic environments. To better understand the emergence of pandemic lineages, it is crucial to discern what differentiates pandemic strains from their environmental relatives. Here, we studied the interaction of environmental V. cholerae with eukaryotic predators or competing bacteria and tested the contributions of the haemolysin and the type VI secretion system (T6SS) to those interactions. Both of these molecular weapons are constitutively active in environmental isolates but subject to tight regulation in the pandemic clade. We showed that several environmental isolates resist amoebal grazing and that this anti-grazing defense relies on the strains' T6SS and its actincross-linking domain (ACD)-containing tip protein. Strains lacking the ACD were unable to defend themselves against grazing amoebae but maintained high levels of T6SS-dependent interbacterial killing. We explored the latter phenotype through whole-genome sequencing of 14 isolates, which unveiled a wide array of novel T6SS effector and (orphan) immunity proteins. By combining these in silico predictions with experimental validations, we showed that highly similar but non-identical immunity proteins were insufficient to provide cross-immunity among those wild strains.     

Genotypes associated with virulence in environmental isolates of Vibrio cholerae

Vibrio cholerae is an autochthonous inhabitant of riverine and estuarine environments and also is a facultative pathogen for humans. Genotyping can be useful in assessing the risk of contracting cholera, intestinal, or extraintestinal infections via drinking water and/or seafood. In this study, environmental isolates of V. cholerae were examined for the presence of ctxA, hlyA, ompU, stn/sto, tcpA, tcpI, toxR, and zot genes, using multiplex PCR. Based on tcpA and hlyA gene comparisons, the strains could be grouped into Classical and El Tor biotypes. The toxR, hlyA, and ompU genes were present in 100, 98.6, and 87.0% of the V. cholerae isolates, respectively. The CTX genetic element and toxin-coregulated pilus El Tor (tcpA ET) gene were present in all toxigenic V. cholerae O1 and V. cholerae O139 strains examined in this study. Three of four nontoxigenic V. cholerae O1 strains contained tcpA ET. Interestingly, among the isolates of V. cholerae non-O1/non-O139, two had tcpA Classical, nine contained tcpA El Tor, three showed homology with both biotype genes, and four carried the ctxA gene. The stn/sto genes were present in 28.2% of the non-O1/non-O139 strains, in 10.5% of the toxigenic V. cholerae O1, and in 14.3% of the O139 serogroups. Except for stn/sto genes, all of the other genes studied occurred with high frequency in toxigenic V. cholerae O1 and O139 strains. Based on results of this study, surveillance of non-O1/non-O139 V. cholerae in the aquatic environment, combined with genotype monitoring using ctxA, stn/sto, and tcpA ET genes, could be valuable in human health risk assessment.     

R plasmids in environmental Vibrio cholerae non-O1 strains.

The occurrence of drug resistance and its plasmid-mediated transferability was investigated in 140 environmental strains of Vibrio cholerae non-O1 and 6 strains of Vibrio cholerae, both O1 and non-O1, of clinical origin. Of the 146 strains tested, 93% were resistant to at least one drug and 74% were resistant to two or more antibiotics. The O1 strains were susceptible to all antibiotics used. A total of 26 of 28 selected resistant wild strains carried R plasmids that were transferable by intraspecific and intergeneric matings. The most common transmissible R factor determined resistance to ampicillin, amoxicillin, and sulfanilamide (30%), followed by resistance to ampicillin and amoxicillin (13%) and resistance to ampicillin, amoxicillin, phosphomycin, and sulfanilamide (9%). Comparison of the three methods of plasmid analysis showed that the method of Birnboim and Doly (Nucleic Acids Res. 7:1513-1523, 1979) without EDTA and lysozyme was optimal for isolation of both large and small plasmids in environmental V. cholerae strains. Most strains harbored more than one plasmid, and the molecular sizes ranged from 1.1 to 74.8 megadaltons. The plasmids of high molecular size (around 74 megadaltons) were responsible for the resistance pattern transferred and were maintained with high stability in the hosts.     

Antibiotic sensitivity of Vibrio cholerae 01 isolated from environmental objects]

The sensitivity of 252 Vibrio cholerae-O1 strains isolated from environmental objects to antibiotics of various groups was assayed by the method of serial dilutions on solid media. The biological characteristics of the isolates are presented. The Vibrio cholerae isolates with serological variation were the most frequent (36.6 per cent), so are the cultures detected by their sensitivity to the specific phages (87.5 per cent). It was found that changes in some biological properties of the strains did not coincide with the changes in the antibiotic sensitivity. The isolates were highly sensitive to tetracycline, chloramphenicol, gentamicin, erythromycin and rifampicin and less sensitive to novobiocin and the other aminoglycosides. The sensitivity to the beta-lactams was the lowest. The resistance determinants were detected in single strains (6.3 per cent), the kanamycin and novobiocin resistance determinants being detected in 15 out of the 16 strains tested. The study showed that the cultures of Vibrio cholerae-O1 isolated from the environmental objects generally preserved their sensitivity to the diverse group antibiotics.     

Expression of Vibrio cholerae virulence genes in response to environmental signals

Vibrio cholerae, the causative agent of Asiatic cholera, is a gram-negative motile bacterial species acquired via oral ingestion of contaminated food or water sources. The O1 serogroup of V. cholerae is responsible for pandemic cholera and is divided into two biotypes, classical and El Tor (Butterton and Calderwood, 1995; Mekalanos, 1985). The El Tor biotype is responsible for the current cholera pandemic. In the absence of disease, the vibrio life cycle consists of a free-swimming phase in marine and estuarine environments in association with zooplankton, crustaceans, insects, and water plants. Vibrios interact with various surfaces found in the environment to generate biofilms which may promote survival (Watnick etaL, 1999). Within the host the motile vibrios must evade the innate host defense mechanisms, penetrate the mucus layer covering the intestinal villi, adhere to and colonize the epithelial surface of the small intestine, assume a non-motile phase, replicate and cause disease by secreting numerous exoproteins at the site of infection (Oliver and Kaper, 1997). The voluminous diarrhea associated with cholera infection leads to the dissemination of the vibrios back into a watery environment and thus a continuation of the environmental phase of the life cycle. The host phase of the vibrio life cycle is only possible through the action of a group of virulence genes (ToxR-regulon) controlled by a complex and incompletely understood regulatory cascade. The ToxR regulon colonization and toxin genes are coordinately expressed in response to specific host signals that have yet to be completely defined (Skorupsky and Taylor 1997). Although little is known regarding the host signals that impact the ToxR regulatory cascade, it is clear that these intraintestinal signals play an important role in maximizing the ability of the vibrios to survive and multiply within the host. Key to understanding the complex events involved in the pathogenesis of V. cholerae will be elucidating the intraintestinal signaling molecules that trigger the expression of vibrio virulence genes. Understanding the molecular basis of this host-parasite interaction will provide important information with respect to how pathogenic bacteria establish infection and provide insights leading to novel methods for treating and/or preventing bacterial infections. This review will summarize what is known regarding host signaling and the complex ToxR regulatory system employed by V. cholerae to coordinate virulence gene expression within the host.     

Detection of an OmpA-like protein in Vibrio cholerae

Abstract Rhodopseudomonas marina/agilis was enriched from a natural microbial mat by using conditions that favor growth of anoxygenic photoheterotrophs able to fix N₂ rapidly. The isolated bacterium grows more readily on fructose or mannitol than on organic acid carbon sources, requires preformed biotin and thiamine as growth factors, and is extraordinarily motile; growth occurs up to a temperature of approx. 44°C. The photosynthetic pigments of R. marina/agilis are housed in intracytoplasmic lamellar membranes which show the in vivo absorbance characteristics of bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series. In common with other non-sulfur purple bacteria, R. marina/agilis can also grow as an aerobic heterotroph in darkness. Under these conditions, photopigment synthesis is severely repressed. R. marina/agilis requires 1–5% NaCl for optimal growth, and cells grown on N₂ showed nitrogenase activity of >1000 nmol acetylene reduced h/mg dry wt.     

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.     

Differentiation of environmental and clinical isolates of Vibrio mimicus from Vibrio cholerae by multilocus enzyme electrophoresis

In this study, we demonstrated that analyzed strains of Vibrio mimicus and Vibrio cholerae could be separated in two groups by using multilocus enzyme electrophoresis (MEE) data from 14 loci. We also showed that the combination of four enzymatic loci enables us to differentiate these two species. Our results showed that the ribosomal intergenic spacer regions PCR-mediated identification system failed, in some cases, to differentiate between V. mimicus and V. cholerae. On the other hand, MEE proved to be a powerful molecular tool for the discrimination of these two species even when atypical strains were analyzed.