The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage

The current circulating pandemic El Tor biotype of Vibrio cholerae has persisted for over sixty years and is characterized by its acquisition of two unique genomic islands called the Vibrio Seventh Pandemic Islands 1 and 2 (VSP-I and VSP-II). However, the functions of most of the genes on VSP-I and VSP-II are unknown and the advantages realized by El Tor through these two islands are not clear. Recent studies have broadly implicated these two mobile genetic elements with phage defense. Still, protection against phage infection through these islands has not been observed directly in any V. cholerae El Tor biotype. Here we report the isolation of a circulating phage from a cholera patient stool sample and demonstrate that propagation of this phage in its native host is inhibited by elements in both VSP-I and VSP-II, providing direct evidence for the role of these genomic islands in phage defense. Moreover, we show that these defense systems are regulated by quorum sensing and active only at certain cell densities. Finally, we have isolated a naturally occurring phage variant that is resistant to the defense conferred by the VSP islands, illustrating the countermeasures used by phages to evade these defense mechanisms. Together, this work demonstrates a functional role for the VSPs in V. cholerae and highlights the key regulatory and mechanistic insights that can be gained by studying anti-phage systems in their native contexts.

The current pandemic strain of Vibrio cholerae carries two unique genomic islands. How these two islands confer evolutionary advantage to the pathogen is unknown. We show here the identification of a circulating phage that is sensitive to the defense systems present on these two islands and demonstrate how phage variants can evade these defenses. Our studies provide the first direct evidence showing the importance of these genomic islands in defending against phage in their native environments; and in doing so provide novel insight into the mechanisms of these highly conserved defense elements.

Genomic diversities of ctxB, tcpA and rstR alleles of Vibrio cholerae O139 strains isolated from Odisha, India

The genome of Vibrio cholerae O139 strains has undergone cryptic changes since its first emergence in 1992 in South India. This study aimed to determine the presence of genotypic changes marked in ctxB, tcpA and rstR genes located within the CTX prophages among the strains of V. cholerae O139 isolated from 1999 to 2017 in Odisha. Antibiotic susceptibility test was conducted on 59 V. cholerae O139 strains. A conventional PCR assay was done for ctxB gene typing followed by sequencing along with identification of rstR and tcpA gene. Pulsed-field gel electrophoresis (PFGE) was carried out to reveal clonal variations among the V. cholerae O139 strains. Among V. cholerae O139 isolates more than 60% showed resistance to ampicillin, co-trimoxazole, furazolidone, streptomycin, neomycin and nalidixic acid. The ctxB sequencing and rstR allele-specific PCR assay revealed the presence of three genotypes 1, 3 and 4 with at least one copy of CTX Calc φ in addition to CTX ET and CTX Cl prophages in V. cholerae O139 isolates. PFGE analysis revealed 13 pulsotypes with two clades having 60% similarity among V. cholerae O139 strains. The circulating V. cholerae O139 strains in Odisha showed variation in genotypes with multiple clonal expansions over the years.

The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

Despite extensive studies on the curve-shaped bacterium Vibrio cholerae, the causative agent of the diarrheal disease cholera, its virulence-associated regulatory two-component signal transduction system VarS/VarA is not well understood. This pathway, which mainly signals through the downstream protein CsrA, is highly conserved among gamma-proteobacteria, indicating there is likely a broader function of this system beyond virulence regulation. In this study, we investigated the VarA-CsrA signaling pathway and discovered a previously unrecognized link to the shape of the bacterium. We observed that varA-deficient V. cholerae cells showed an abnormal spherical morphology during late-stage growth. Through peptidoglycan (PG) composition analyses, we discovered that these mutant bacteria contained an increased content of disaccharide dipeptides and reduced peptide crosslinks, consistent with the atypical cellular shape. The spherical shape correlated with the CsrA-dependent overproduction of aspartate ammonia lyase (AspA) in varA mutant cells, which likely depleted the cellular aspartate pool; therefore, the synthesis of the PG precursor amino acid meso-diaminopimelic acid was impaired. Importantly, this phenotype, and the overall cell rounding, could be prevented by means of cell wall recycling. Collectively, our data provide new insights into how V. cholerae use the VarA-CsrA signaling system to adjust its morphology upon unidentified external cues in its environment.

Responsible for the diarrheal disease cholera, the bacterium Vibrio cholerae tightly regulates its virulence program according to external stimuli. Here, we discovered that a sensing-response mechanism involved in the regulation of virulence also controls bacterial shape. We show that V. cholerae lacking this system lose their normal comma shape and become spherical due to an abnormal cell wall composition caused by metabolic changes that reduce available cell wall building blocks. Our study therefore sheds new light on how V. cholerae potentially modulates its morphology based on environmental changes.

The heptameric structure of the flagellar regulatory protein FlrC is indispensable for ATPase activity and disassembled by cyclic-di-GMP

The bacterial enhancer-binding protein (bEBP) FlrC, controls motility and colonization of Vibrio cholerae by regulating the transcription of class-III flagellar genes in σ54-dependent manner. However, the mechanism by which FlrC regulates transcription is not fully elucidated. Although, most bEBPs require nucleotides to stimulate the oligomerization necessary for function, our previous study showed that the central domain of FlrC (FlrCC) forms heptamer in a nucleotide-independent manner. Furthermore, heptameric FlrCC binds ATP in "cis-mediated" style without any contribution from sensor I motif 285REDXXYR291 of the trans protomer. This atypical ATP binding raises the question of whether heptamerization of FlrC is solely required for transcription regulation, or if it is also critical for ATPase activity. ATPase assays and size exclusion chromatography of the trans-variants FlrCC-Y290A and FlrCC-R291A showed destabilization of heptameric assembly with concomitant abrogation of ATPase activity. Crystal structures showed that in the cis-variant FlrCC-R349A drastic shift of Walker A encroached ATP-binding site, whereas the site remained occupied by ADP in FlrCC-Y290A. We postulated that FlrCC heptamerizes through concentration-dependent cooperativity for maximal ATPase activity and upon heptamerization, packing of trans-acting Tyr290 against cis-acting Arg349 compels Arg349 to maintain proper conformation of Walker A. Finally, a Trp quenching study revealed binding of cyclic-di-GMP with FlrCC Excess cyclic-di-GMP repressed ATPase activity of FlrCC through destabilization of heptameric assembly, especially at low concentration of protein. Systematic phylogenetic analysis allowed us to propose similar regulatory mechanisms for FlrCs of several Vibrio species and a set of monotrichous Gram-negative bacteria.

Vibrio cholerae strains with inactivated cqsS gene overproduce autoinducer-2 which enhances resuscitation of dormant environmental V. cholerae

BACKGROUND

Toxigenic Vibrio cholerae resides in aquatic reservoirs of cholera-endemic areas mostly in a dormant form known as conditionally viable environmental cells (CVEC) in which the bacteria remain embedded in an exopolysaccharide matrix, and fail to grow in routine bacteriological culture. The CVEC can be resuscitated by supplementing culture media with either of two autoinducers CAI-1 and AI-2, which are signal molecules controlling quorum sensing, a regulatory network of bacterial gene expression dependent on cell density. This study investigated possible existence of variant strains that overproduce AIs, sufficient to resuscitate CVEC in environmental waters.

METHODS

Environmental V. cholerae isolates and Tn insertion mutants of a V. cholerae strain C6706 were screened for production of AIs using bioluminescent reporter strains. Relevant mutations in environmental strains which overproduced AI-2 were characterized by nucleotide sequencing and genetic complementation studies. Effect of AIs produced in culture supernatants of relevant strains on reactivation of CVEC in water was determined by resuscitation assays.

RESULTS

Two of 54 environmental V. cholerae isolates were found to overproduce AI-2. Screening of a Tn-insertion library of V. cholerae strain C6706, identified a mutant which overproduced AI-2, and carried Tn insertion in the cqsS gene. Nucleotide sequencing also revealed mutations inactivating the cqsS gene in environmental isolates which overproduced AI-2, and this property was reversed when complemented with a wild type cqsS gene. Culture of river water samples supplemented with spent medium of these mutants resuscitated dormant V. cholerae cells in water.

SIGNIFICANCE

V. cholerae strains with inactivated cqsS gene may offer a convenient source of AI-2 in enhanced assays for monitoring bacteriological quality of water. The results also suggest a potential role of naturally occurring cqsS mutants in the environmental biology of V. cholerae. Furthermore, similar phenomenon may have relevance in the ecology of other waterborne bacterial pathogens beyond V. cholerae.

Hypermutation-induced in vivo oxidative stress resistance enhances Vibrio cholerae host adaptation

Bacterial pathogens are highly adaptable organisms, a quality that enables them to overcome changing hostile environments. For example, Vibrio cholerae, the causative agent of cholera, is able to colonize host small intestines and combat host-produced reactive oxygen species (ROS) during infection. To dissect the molecular mechanisms utilized by V. cholerae to overcome ROS in vivo, we performed a whole-genome transposon sequencing analysis (Tn-seq) by comparing gene requirements for colonization using adult mice with and without the treatment of the antioxidant, N-acetyl cysteine. We found that mutants of the methyl-directed mismatch repair (MMR) system, such as MutS, displayed significant colonization advantages in untreated, ROS-rich mice, but not in NAC-treated mice. Further analyses suggest that the accumulation of both catalase-overproducing mutants and rugose colony variants in NAC^- mice was the leading cause of mutS mutant enrichment caused by oxidative stress during infection. We also found that rugose variants could revert back to smooth colonies upon aerobic, in vitro culture. Additionally, the mutation rate of wildtype colonized in NAC^- mice was significantly higher than that in NAC⁺ mice. Taken together, these findings support a paradigm in which V. cholerae employs a temporal adaptive strategy to battle ROS during infection, resulting in enriched phenotypes. Moreover, ΔmutS passage and complementation can be used to model hypermuation in diverse pathogens to identify novel stress resistance mechanisms.

Cholera is a devastating diarrheal disease that is still endemic to many developing nations, with the worst outbreak in history having occurred recently in Yemen. Vibrio cholerae, the causative agent of cholera, transitions from aquatic reservoirs to the human gastrointestinal tract, where it expresses virulence factors to facilitate colonization of the small intestines and to combat host innate immune effectors, such as reactive oxygen species (ROS). We applied a genome-wide transposon screen (Tn-seq) and identified that deletion of mutS, which is part of DNA mismatch repair system, drastically increased colonization in ROS-rich mice. The deletion of mutS led to the accumulation of catalase-overproducing mutants and a high frequency rugose phenotype when exposed to ROS selective pressures in vivo. Additionally, ROS elevated mutation frequency in wildtype, both in vitro and in vivo. Our data imply that V. cholerae may modulate mutation frequency as a temporal adaptive strategy to overcome oxidative stress and to enhance infectivity.

Changing facades of Vibrio cholerae: An enigma in the epidemiology of cholera

Cholera, caused by the Gram-negative bacterium Vibrio cholerae, has ravaged humanity from time immemorial. Although the disease can be treated using antibiotics along with administration of oral rehydration salts and controlled by good sanitation, cholera is known to have produced mayhems in ancient times when little was known about the pathogen. By the 21st century, ample information about the pathogen, its epidemiology, genetics, treatment and control strategies was revealed. However, there is still fear of cholera outbreaks in developing countries, especially in the wake of natural calamities. Studies have proved that the bacterium is mutating and evolving, out-competing all our efforts to treat the disease with previously used antibiotics and control with existing vaccines. In this review, the major scientific insights of cholera research are discussed. Considering the important role of biofilm formation in the V. cholerae life cycle, the vast availability of next-generation sequencing data of the pathogen and multi-omic approach, the review thrusts on the identification of suitable biofilm-inhibiting targets and the discovery of anti-biofilm drugs from nature to control the disease.

Identification of a Small Molecule Activator for AphB, a LysR-Type Virulence Transcriptional Regulator in Vibrio cholerae

AphB is a LysR-type transcriptional regulator (LTTR) that cooperates with a second transcriptional activator, AphA, at the tcpPH promoter to initiate expression of the virulence cascade in Vibrio cholerae. Because it is not yet known whether AphB responds to a natural ligand in V. cholerae that influences its ability to activate transcription, we used a computational approach to identify small molecules that influence its activity. In silico docking was used to identify potential ligands for AphB, and saturation transfer difference nuclear magnetic resonance was subsequently employed to access the validity of promising targets. We identified a small molecule, BP-15, that specifically binds the C-terminal regulatory domain of AphB and increases its activity. Interestingly, molecular docking predicts that BP-15 does not bind in the putative primary effector-binding pocket located at the interface of RD-I and RD-II as in other LTTRs, but rather at the dimerization interface. The information gained in this study helps us to further understand the mechanism by which transcriptional activation by AphB is regulated by suggesting that AphB has a secondary ligand binding site, as observed in other LTTRs. This study also lays the groundwork for the future design of inhibitory molecules to block the V. cholerae virulence cascade, thereby preventing the devastating symptoms of cholera infection.

The nucleoid occlusion protein SlmA is a direct transcriptional activator of chitobiose utilization in Vibrio cholerae

Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors. In vitro, we find that SlmA binds directly to the chb operon promoter, and in vivo, we show that this interaction is required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator in V. cholerae in addition to its established role as a cell division licensing factor.

The cholera pathogen Vibrio cholerae is a natural resident of the aquatic environment and causes disease when ingested in the form of contaminated food or drinking water. In the aquatic environment, the shells of marine zooplankton, which are primarily composed of chitin, serve as an important food source for this pathogen. The genes required for the utilization of chitin are tightly regulated in V. cholerae, however, the exact mechanism underlying this regulation is currently unclear. Here, we uncover that a protein involved in regulating cell division is also important for regulating the genes involved in chitin utilization. This is a newly identified property for this cell division protein and the significance of a common regulator for these two disparate activities remains to be understood.

[The loop mediated isothermal amplification of DNA: principle of method and perspectives of application in molecular diagnostic of cholera: publications review]

The article considers characteristics of technology of reaction of loop mediated isothermal amplification of DNA (LAMP), issues of optimization of reaction and perspectives of its application as a quick highly-specific test in molecular diagnostics of infectious diseases and monitoring of contamination of environment objects with pathogens. The analysis of publications data concerning application of LAMP in diagnostics of cholera testifies high diagnostic value. The LAMP supports possibility of direct rapid detection of toxin-producing strains of Vibrio cholerae in clinical samples. This technique also provides identification of determinants of cholera vibrio in pure culture, samples from environment objects and food products. The research studies established exceeding of parameters of sensitivity and specificity of LAMP as compared with polymerase chain reaction that permits considering LAMP as a perspective technique for express-analysis of clinical material from patients with suspicion on cholera. The LAMP technique can be also used in screening studies of environment objects. The development of test-systems based on application of this technology is required.

[The application of MALDI-ToF mini-sequencing for detecting genetically altered versions of cholera agent]

The genetically altered modifications of V.cholerae eltor are characterized by occurrence of single-nucleotide polymorphisms in gene ctxB. To detect these modifications the technique is proposed based on mini-sequencing with MALDI-ToF by of products of reaction with selected probes adjacent to 115 and 203 positions of gene mentioned previously. The mass-spectrometry analysis of the results of reaction of mini-sequencing of strains of V.cholerae eltor isolated during epidemic complications at the territory of the Siberia and the Far East revealed mass-specters corresponding to values of molecular masses of probes (ctxB115, ctxB203) and those complementary completed to points of corresponding replacements (T/C) of didesoxinucleotides (ddTTP, ddCTP). For analyzed strains of V.cholerae eltor isolated in the 1970s, elongation is establishedfor both probes by didesoxinucleotide that testifies presence in their genome ctxB3 allele with thymine in 115 and 203 positions, distinctive for typical representatives of V.cholerae eltor. For V.cholerae eltor, isolated in 1990s, hybridization to points of replacement of didesoxicytosine and presence of ctxB1 allele with cytosine at analyzed positions, distinctive to vibrio of classic biovars. This allele is detected in genome of one of modifications of atypical genetically altered clones ofV.cholerae eltor. This technique, by its sensitivity and specificity, matches direct sequencing of gene ctxB of strains of V.cholerae eltor and proves promising for analysis of other valuable single-nucleotide polymorphisms.

[RETROSPECTIVE ANALYSIS OF BIOLOGICAL AND MOLECULAR-GENETIC PROPERTIES OF STRAINS - CAUSATIVE AGENTS OF CHOLERA - ISOLATED IN UKRAINE IN 1994 - 2011]

AIM

Retrospective analysis of biological and molecular-genetic properties of strains - cau- sative agents of cholera - isolated in the period of epidemics in Ukraine in 1994 - 2011.

MATERIALS AND METHODS

Phenotypic and molecular-genetic properties of 5 strains of cholera vibrios, biovar El Tor isolated from cholera patients and 4 strains from the environmental samples were studied using traditional bacteriological and genetic methods. Detection of DNA for toxigenicity genes and genes characteristic for El Tor and classic biovar were carried out by PCR method using rea- gent kits <<AmpliSens- Vibrio cholerae FRT>> and <<Vibrio cholerae ctxB-rstR-rstC genes, REF>> an experimental test system). Sequencing of genomes of 4 strains of causative agents of cholera was carried out in genetic analyzer Ion Torrent Personal Genome Machine.

RESULTS

Strains of cholera vibrios identified in Ukraine in 1994 and 2011 such as a typical toxigenic biovar El Tor (V cholerae Ο1, El Tor, Ogawa, Hly-, ctxA+, tcpA+) contain genes ofthe classic cholera vibrio in their genome and are genetically altered (hybrid) variants of cholera vibrio biovar El Tor producing enterotoxin CTI and having increased virulence, that was clinically manifested in predominance of severe forms of cholera in Mariupol of Donetsk region in 2011. Genome sequences ofthe 4 studied strains were deposited into the international database DDBJ/EMBL/GenBank.

CONCLUSION

The studied isolates were established to belong to a clade of strains associated with cholera outbreaks in Haiti and Asian continent, from where genetically altered strains of cholera vibrios biovar El Tor were introduced to Haiti in 2010, based on results of comparison of genomic sequences of the studied strains with genomes of V cholera strains from the international database GenBank.

MOLECULAR-GENETIC PROPERTIES OF VIBRIO CHOLERAE EL TOR STRAINS CIRCULATING IN AFRICA

The review contains some brief information on cholera epidemics in Africa. Based on the results of the whole genome sequencing of 30 clinical strains isolated in Africa in different periods of the 7th cholera pandemic (1985-2012), extensive genetic diversity has been revealed. It is demonstrated that at present cholera epidemics in Africa are caused by new variants of the agent, which emerged in South- Eastern Asia in consequence of not only new genes acquisition, but also genome alterations of pandemicity and pathogenicity islands. SNP analysis of 53 strains circulating at different times in the territory of the continent, as well as isolated in South-Eastern Asia, has been carried out. Phylogenetic relations between the majority of the African and Asian strains have been established. In addition, strains were shown to exist that are, apparently, endemic to the African region. Identified genetic diversity of the strains with varying virulence and drug resistance points out the necessity of continuous molecular monitoring of the cholera agent in Africa.

Mechanisms Underlying the Immune Response Generated by an Oral Vibrio cholerae Vaccine

Mechanistic details underlying the resulting protective immune response generated by mucosal vaccines remain largely unknown. We investigated the involvement of Toll-like receptor signaling in the induction of humoral immune responses following oral immunization with Dukoral, comparing wild type mice with TLR-2-, TLR-4-, MyD88- and Trif-deficient mice. Although all groups generated similar levels of IgG antibodies, the proliferation of CD4+ T-cells in response to V. cholerae was shown to be mediated via MyD88/TLR signaling, and independently of Trif signaling. The results demonstrate differential requirements for generation of immune responses. These results also suggest that TLR pathways may be modulators of the quality of immune response elicited by the Dukoral vaccine. Determining the critical signaling pathways involved in the induction of immune response to this vaccine would be beneficial, and could contribute to more precisely-designed versions of other oral vaccines in the future.

[The mass-spectrometric analysis of MALDI-TOF in identification and typing of strains of comma bacillus]

The data base “Protein profiles of mass-specters of representatives of species of Vibrio cholerae for program MALDI Biotyper” was used to implement typing of strains of comma bacillus isolated at the territory of the Russian Federation in 2010-2012. Also, analysis of degree of similarity and differences among constant ribosomal proteins was implemented. According the results of MALDI-TOF mass-spectrometry strains of V.cholerae were grouped in two distinct clusters. The first cluster included all epidemically dangerous strains isolated from people arrived in Moscow from India 2010-2012. The second cluster included atoxigenic vibrio with no relation to serogroups O1/O139 isolated from residents of Taganrog in 2011. The analysis of main specters of all collection permitted to identify taxon - specific components distinguishing strains of non-O1/non-O139 from strains of V.cholerae El Tor. Hence, the developed data base of proteom portraits of V.cholerae permits identifying, studying and to typing of agents of cholera and other representatives of V.cholerae species detecting their phylogenetic affinity that is ultimately useful for establishing origin of strains isolated from objects of environment and epidemiological decoding of episodes of disease.

ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization

The virulence regulator ToxR initiates and coordinates gene expression needed by Vibrio cholerae to colonize the small intestine and cause disease. Despite its prominence in V. cholerae virulence, our understanding of the direct ToxR regulon is limited to four genes: toxT, ompT, ompU and ctxA. Here, we determine ToxR’s genome-wide DNA-binding profile and demonstrate that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors and define pandemic lineages. We show that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS binding at shared binding locations. Importantly, we demonstrate that this regulatory interaction is the critical function of ToxR in V. cholerae colonization and biofilm formation. In the absence of H-NS, ToxR is no longer required for V. cholerae to colonize the infant mouse intestine or for robust biofilm formation. We further illustrate a dramatic difference in regulatory scope between ToxR and other prominent virulence regulators, despite similar predicted requirements for DNA binding. Our results suggest that factors in addition to primary DNA structure influence the ability of ToxR to recognize its target promoters.

The transcription factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express essential host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands that encode V. cholerae’s major virulence factors. Our results suggest that ToxR has gained regulatory control over important acquired elements that not only drive V. cholerae pathogenesis, but also define the major transitions of V. cholerae pandemic lineages. We demonstrate that ToxR shares more than a third of its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS for control of critical colonization functions. This regulatory interaction is the major role of ToxR in V. cholerae colonization, since deletion of hns abrogates the need for ToxR in V. cholerae host colonization. By comparing the genome-wide binding profiles of ToxR and other critical virulence regulators, we show that, despite similar predicted DNA binding requirements, ToxR is unique in its global control of progenitor-encoded and acquired genes. Our results suggest that factors in addition to primary DNA structure determine selection of ToxR binding sites.

[POSSIBILITIES OF APPLICATION OF MALDI-TOF MASS-SPECTROMETRY FOR STUDY OF CARBOHYDRATE-SPECIFIC RECEPTORS FOR DIAGNOSTIC BACTERIOPHAGE EL TOR]

AIM

Study mechanisms of interaction of diagnostic bacteriophage El Tor with sensitive strain Vibrio cholerae El Tor 18507 using direct protein profiling, identification of constant and variable proteins, taking part in interaction of the phage and cell, as well as carbohydrate-specific phage receptors.

MATERIALS AND METHODS

. A commercial preparation of cholera diagnostic bacteriophage El Tor, strain V. cholerae El Tor 18507 were used. Effect of carbohydrates on bacteriophage activity was determined in experiments with phage by a classic and modified by us method. Protein profiles of the studied objects were studied using MSP-analysis method.

RESULTS

Sucrose was shown to inhibit lytic activity of bacteriophage. Proteome profiles of El Tor bacteriophage and sensitive indicator strains were studied, identification of constant and variable proteins of the studied objects by MSP Peak-list program was carried out.

CONCLUSION

Analysis of changes of profiles of phage and microbial cell during interaction with sucrose gave a basis for assuming, that sucrose in the mixture of culture-phage enters interaction namely with phage protein receptors, blocking receptors specific for cholera vibrio, that subsequently manifests in a sharp decrease of phage activity against the sensitive strain.

Functional RelBE-Family Toxin-Antitoxin Pairs Affect Biofilm Maturation and Intestine Colonization in Vibrio cholerae

Toxin–antitoxin (TA) systems are small genetic elements that typically encode a stable toxin and its labile antitoxin. These cognate pairs are abundant in prokaryotes and have been shown to regulate various cellular functions. Vibrio cholerae, a human pathogen that is the causative agent of cholera, harbors at least thirteen TA loci. While functional HigBA, ParDE have been shown to stabilize plasmids and Phd/Doc to mediate cell death in V. cholerae, the function of seven RelBE-family TA systems is not understood. In this study we investigated the function of the RelBE TA systems in V. cholerae physiology and found that six of the seven relBE loci encoded functional toxins in E. coli. Deletion analyses of each relBE locus indicate that RelBE systems are involved in biofilm formation and reactive oxygen species (ROS) resistance. Interestingly, all seven relBE loci are induced under the standard virulence induction conditions and two of the relBE mutants displayed a colonization defect, which was not due to an effect on virulence gene expression. Although further studies are needed to characterize the mechanism of action, our study reveals that RelBE systems are important for V. cholerae physiology.

[EVALUATION OF FUNCTIONAL FEATURES AND STRESS RESISTANCE OF ISOGENIC TOXIGENIC AND NON-TOXIGENIC BIOVAR EL TOR VIBRIO CHOLERAE STRAINS]

AIM

Comparative evaluation of functional features of toxigenic biovar El Tor Vibrio cholerae strains and their spontaneous non-toxigenic mutants and study of their resistance to saline and oxidative stress.

MATERIALS AND METHODS

8 biovar El Tor V. cholerae strains were studied: 4 clinical strains isolated in 1970 from patients in Astrakhan and 4 spontaneous non-toxigenic mutants of these strains that have lost cholera toxin genes as a result of residence in river water at the temperature of 25°C. Protein composition was determined in polyacrylamide gel electrophoresis by Laemmli U.K. Stress resistance of the strains was studied by adding H2O2 to 20 mM concentration and NaCl to 3 mM concentration to the cultural suspension.

RESULTS

Loss of cholera toxin genes was shown to be accompanied by changes in the level of expression of 17 proteins including those that take part in energy metabolism, glucose transport, chemotaxis and purine bases. Moreover, non-toxigenic strains were established to be 5-15 times more resistant to saline and oxidative stress compared with toxigenic strains.

CONCLUSION

Non-toxigenic V. cholerae mutants adopt better to stress factors, therefore the loss of cholera toxin gene in water environment could be one of the methods of adaptation of pathogenic bacteria to changes in the environment.

[ISOLATION OF ANTIBIOTICS RESISTANCE GENES IN VIBRIO CHOLERAE O1 AND O139 SEROGROUP STRAINS]

AIM

Determination of sensitivity of V. cholerae O1 serogroup El Tor biovar and O139 serogroup strains to antibiotics and determination of the presence of antibiotics resistance genes in their genome.

MATERIALS AND METHODS

The studies were carried out in 75 V. cholerae O1 and O139 serogroup strains. Sensitivity of cultures to antibiotics was determined by disc-diffusion method. DNA isolation was carried out in the presence of 6M guanidine thiocyanate. PCR was carried out in multi-channel amplificator Tercyc.

RESULTS

A multiplex PCR was constructed, that includes 5 primer pairs for the detection of O1 and O139 serogroup resistance genes of vibrios to sulfame- thoxazolum, streptomycin B, trimethoprim, the presence of SXT element, an amplification program was developed. Using the developed PCR, V. cholerae O1 serogroup El Tor biovar strains with multiple drug resistance were established to be imported into Russia in 1993. The presence of SXT elements with genes of resistance to 4 antibiotics simultaneously was detected precisely in these strains, that belong to toxigenic genovariants of V. cholerae El Tor biovar. All the El Tor vibrio strains imported in the subsequent years were shown to stably preserve SXT element, this indicates its important role in biology of cholera vibrios. O139 serogroup strains with intact SXT element and having a deletion of the gene coding trimethoprim resistance were isolated.

CONCLUSION

The data obtained may be used to establish molecular-genetic mechanisms of emergence of antibiotics resistant strains of cholera vibrio, construction of novel gene diagnostic test-systems and carrying out passportization of strains that are stored in the State collection of pathogenic bacteria.

Biological characterization of v. Cholerae-specific bacteriophages isolated from water sources in Georgia

Vibrio cholerae, a widely spread bacterium in various marine, fresh, and brackish water environments, can cause a devastating diarrheal disease - cholera and also mild forms of gastroenteritis. Bacterial viruses are natural controllers of bacterial population density in water systems. The goal of this study was to isolate and characterize V. cholerae-specific bacteriophages occurring in the Georgian coastal zone of the Black Sea and inland water reservoirs in the eastern part of Georgia. During 2006-2009, 71 phages lytic to V. cholerae were collected from these aquatic environments. The phage isolation rate was varying from 8% to 15%, depending on the sampling season and site, and the abundance of host bacteria. The majority of phages specific to V. cholerae were collected from freshwater sources. The phage isolation showed seasonal character covering warm period -from April to September. Based on basic characteristics of primary phage isolates (lytic spectrum, virion morphology and DNA restriction profiles) 23 V. cholerae -specific phages were selected for series of consecutive screenings. Comparatively wide spectrum of lytic activity was revealed in case of 14 phages specific to V. cholerae O1, and one phage - VchBS3, active against non-O1 V. cholerae. Three phages active against V. cholerae non-O1 and six V. cholerae O1 -specific phages have been studied in detail for a number of biological features (stability in different solutions, temperature-, pH- and UV- sensitivity, influence of high ionic strength etc.), considered to be additional important characteristics for selection of phages with therapeutic potential.

[Improvement of laboratory diagnostics of cholera due to genetically altered (hybrid) variants of cholera Vibrio biovar El Tor]

AIM

Improvement of laboratory diagnostics of cholera taking into the account appearance of hybrid variants of cholera vibrio El Tor biovar in the 1990s.

MATERIALS AND METHODS

Phenotypic and molecular-genetic properties of typical toxigenic (151 strains) and hybrid (102 strains) variants of El Tor biovar cholera vibrios, isolated in the Caucuses in 1970-1990 and 1993-1998, respectively, were studied. Toxigenicity gene DNA fragments, inherent to El Tor biovars or classic, were detected by using a reagent kit "Genes of Vibrio cholerae variant ctxB-rstR-rstC, REF" developed by us.

RESULTS

Reagent kit "Genes of V. cholerae variant ctxB-rstR-rstC, REF" is proposed to be used for laboratory diagnostics of cholera during study of material from humans or environmental objects and for identification of V. cholerae 01 on genome level in PCR-analysis as a necessary addition to the classic scheme of bacteriological analysis.

CONCLUSION

Laboratory diagnostics of cholera due to genetically altered (hybrid) variants of cholera vibrio El Tor biovar is based on a complex study of material from humans and environmental objects by routine bacteriologic and PCR-analysis methods with the aim of detection of gene DNA fragments in the studied material, that determine biovar (classic or El Tor), identification of V. cholerae O1 strains with differentiation of El Tor vibrios into typical and altered, as well as determination of enterotoxin, produced by the specific cholera vibrio strain (by the presence ctxB(El) or ctxB(Cl) gene DNA fragment, coding biosynthesis of CT-2 or CT-1, respectively).

[Cholera Vibrio biofilm: production, characterization and role in reservation of causative agent in water environment]

AIM

Experimental production, characterization and evaluation of the role of cholera vibrio biofilm.

MATERIALS AND METHODS

33 strains of Vibrio cholerae eltor O1 and V. cholerae O139 of various epidemic significance and origin were studied in a series of experiments by bacteriologic, microscopic (light-optic, luminescent, scanning electron microscopy), molecular genetics, spectrophotometric and statistical methods.

RESULTS

Formation of a biofilm involving inter-cellular bonds, pili and extracellular material and variability of the microorganism (RO-phenotype and transition into uncultivable forms) was shown at various temperature and substrate conditions. A more pronounced ability to form biofilms was detected for strains isolated from environmental samples compared with isolated from clinical material regardless of their epidemic significance. Toxigenic strains of eltor biovar (from surface reservoirs during cholera outbreaks) have demonstrated the highest parameters of optical density compared with toxigenic clinical isolates and non-toxigenic O1 and O139 serogroup cultures. The presence of mbaA1 and mbaA2, vpsR, toxR, hapA genes is common for strains that form a biofilm.

CONCLUSION

The data obtained confirm the role of biofilm in reservation of cholera vibrio strains of various epidemic significance in saprophytic phase of microorganism existence.

[The application of mass spectrometry technique MALDI-TOF for inter-specific differentiation of closely-related vibrio]

The study was targeted to apply mass spectrometry analysis for inter-specific differentiation of collection strains of representatives of genus vibrio and identification of comma bacilli extracted from samples of boat ballast waters. The samples consisted of 207 museum strains of cultures and 347 microorganisms from samples of boat ballast waters. The identification of microorganisms was implemented using MALDI-TOF mass spectrometers. The application of MALDI biotyping made it possible to detect inaccuracies in specific and generic characteristics of collection strains V. alginolyticus, V. parahaemolyticus, Shewanella, V. mimicus and to enhance characteristic and quality of collections of microorganisms. The effective application of MALDI to monitor boat ballast waters is demonstrated. This technique allows detecting of complete vibrio landscape of pathogenic and non pathogenic genus. The possibility to detect strains of comma bacillus and cholera agents is demonstrated. The mode of orientation on V. albensis at the stage of selection of suspicious colonies is proposed.

Construction and evaluation of V. cholerae O139 mutant, VCUSM21P, as a safe live attenuated cholera vaccine

Cholera is a major infectious disease, affecting millions of lives annually. In endemic areas, implementation of vaccination strategy against cholera is vital. As the use of safer live vaccine that can induce protective immunity against Vibrio cholerae O139 infection is a promising approach for immunization, we have designed VCUSM21P, an oral cholera vaccine candidate, which has ctxA that encodes A subunit of ctx and mutated rtxA/C, ace and zot mutations. VCUSM21P was found not to disassemble the actin of HEp2 cells. It colonized the mice intestine approximately 1 log lower than that of the Wild Type (WT) strain obtained from Hospital Universiti Sains Malaysia. In the ileal loop assay, unlike WT challenge, 1×10⁶ and 1×10⁸ colony forming unit (CFU) of VCUSM21P was not reactogenic in non-immunized rabbits. Whereas, the reactogenicity caused by the WT in rabbits immunized with 1×10¹⁰ CFU of VCUSM21P was found to be reduced as evidenced by absence of fluid in loops administered with 1×10²–1×10⁷ CFU of WT. Oral immunization using 1×10¹⁰ CFU of VCUSM21P induced both IgA and IgG against Cholera Toxin (CT) and O139 lipopolysaccharides (LPS). The serum vibriocidal antibody titer had a peak rise of 2560 fold on week 4. Following Removable Intestinal Tie Adult Rabbit Diarrhoea (RITARD) experiment, the non-immunized rabbits were found not to be protected against lethal challenge with 1×10⁹ CFU WT, but 100% of immunized rabbits survived the challenge. In the past eleven years, V. cholerae O139 induced cholera has not been observed. However, attenuated VCUSM21P vaccine could be used for vaccination program against potentially fatal endemic or emerging cholera caused by V. cholerae O139.

[Retrospective macrorestrictive analysis of the Vibrio cholerae eltor strains isolated at epidemic complications in the Far East of Russia]

The retrospective study of the clonal structure of 24 Vibrio cholerae eltor strains isolated at epidemic complications in the Far East of Russia was carried out on the basis of the macrorestrictive analysis of the genome DNA using NotI and SfiI endonucleases. It was found that clonal (by amplification profiling data) toxigenic strains (n = 23) were characterized by variability of NotI/SfiI-generated restriction profiles. The V. cholerae eltor isolated in Yuzhno-Sakhalinsk outbreak were differentiated to four pulse-types with one dominating type detected in 76% of the strains. Individual restrictive NotI/SfiI-profile was characteristic for the isolates from Primorye Territory. A non-toxigenic strain formed a separate dendrogram line from the toxigenic strains on the basis of PFGE-pattern structure. Efficiency of macrorestriction analysis application for the profound characteristic of the V. cholerae population structure and ascertainment of molecular-epidemiological regularities of territorial distribution of the separate V. cholerae clones was shown.

Comparative phenotypic characterization of Vibrio cholerae isolates collected from aquatic environments of Georgia

Vibrio cholerae is ubiquitous in aquatic environment inhabiting marine, fresh and brackish waters. V. cholerae serotypes O1 and O139 cause the devastating diarrheal disease cholera, which is often fatal without proper treatment. Little is known regarding the abundance and diversity of clinically important nonhalophilic vibrios in the South Caucasus region, particularly in Georgia. Here we provide the data on the Georgian environmental strains of V. cholerae isolated in 2006-2009 years from the coastal waters of the Black Sea and inland water reservoirs near Tbilisi. In total, 846 V. cholerae strains were collected from the water samples, most of them (705 strains) obtained from fresh water lakes. Isolation pattern of V. cholerae showed obvious seasonality with the highest isolation rates in late summer - early autumn. Twenty-nine isolates of V. cholerae were attributed to the O1 serotype based on serological studies and PCR identification and were further grouped by biochemical properties into classical and El Tor biotypes as well as hybrids. The study of antibiotic susceptibility profiles for V. cholerae isolates showed that 95% were sensitive to tetracycline, 91% to doxycycline, and 91% to ciprofloxacin. Interestingly, the freshwater isolates appeared to be more resistant to antibiotics than the Black Sea isolates. Among Black Sea isolates of V. cholerae toxigenic strains of O1 serotype revealed higher antibiotic resistance compared to non- O1/non-O139 isolates. In addition, V. cholerae O1 and non- O1/non-O139 isolates differed by phage susceptibility profiles, with higher diversity within the population of environmental non-O1/non-O139 V. cholerae isolates.

Vibrio cholerae evades neutrophil extracellular traps by the activity of two extracellular nucleases

The Gram negative bacterium Vibrio cholerae is the causative agent of the secretory diarrheal disease cholera, which has traditionally been classified as a noninflammatory disease. However, several recent reports suggest that a V. cholerae infection induces an inflammatory response in the gastrointestinal tract indicated by recruitment of innate immune cells and increase of inflammatory cytokines. In this study, we describe a colonization defect of a double extracellular nuclease V. cholerae mutant in immunocompetent mice, which is not evident in neutropenic mice. Intrigued by this observation, we investigated the impact of neutrophils, as a central part of the innate immune system, on the pathogen V. cholerae in more detail. Our results demonstrate that V. cholerae induces formation of neutrophil extracellular traps (NETs) upon contact with neutrophils, while V. cholerae in return induces the two extracellular nucleases upon presence of NETs. We show that the V. cholerae wild type rapidly degrades the DNA component of the NETs by the combined activity of the two extracellular nucleases Dns and Xds. In contrast, NETs exhibit prolonged stability in presence of the double nuclease mutant. Finally, we demonstrate that Dns and Xds mediate evasion of V. cholerae from NETs and lower the susceptibility for extracellular killing in the presence of NETs. This report provides a first comprehensive characterization of the interplay between neutrophils and V. cholerae along with new evidence that the innate immune response impacts the colonization of V. cholerae in vivo. A limitation of this study is an inability for technical and physiological reasons to visualize intact NETs in the intestinal lumen of infected mice, but we can hypothesize that extracellular nuclease production by V. cholerae may enhance survival fitness of the pathogen through NET degradation.

Evidence for two different regulatory mechanisms linking replication and segregation of vibrio cholerae chromosome II

Understanding the mechanisms that coordinate replication initiation with subsequent segregation of chromosomes is an important biological problem. Here we report two replication-control mechanisms mediated by a chromosome segregation protein, ParB2, encoded by chromosome II of the model multichromosome bacterium, Vibrio cholerae. We find by the ChIP-chip assay that ParB2, a centromere binding protein, spreads beyond the centromere and covers a replication inhibitory site (a 39-mer). Unexpectedly, without nucleation at the centromere, ParB2 could also bind directly to a related 39-mer. The 39-mers are the strongest inhibitors of chromosome II replication and they mediate inhibition by binding the replication initiator protein. ParB2 thus appears to promote replication by out-competing initiator binding to the 39-mers using two mechanisms: spreading into one and direct binding to the other. We suggest that both these are novel mechanisms to coordinate replication initiation with segregation of chromosomes.

Replication and segregation are the two main processes that maintain chromosomes in growing cells. In eukaryotes, the two processes are restricted to distinct phases of the cell cycle. In bacteria, segregation follows replication initiation with a modest lag. Influences of one process on the other have been postulated. The act of replication has been suggested to provide a motive force in chromosome segregation. Moreover, segregation proteins (ParA) have been found to interact with and control the replication initiator, DnaA. Here we show that in V. cholerae chromosome II, which is believed to have originated from a plasmid, a centromere binding protein (ParB) could control replication by two distinct mechanisms: spreading from a centromeric site into the replication-control region, and direct binding to the primary replication-control site, which has limited homology to the centromeric site. These studies establish that Par proteins can influence replication by at least three mechanisms. Homologous Par proteins participate in plasmid segregation but they are not known to influence plasmid replication. The expanded role of Par proteins appears likely to have been warranted to coordinate chromosomal replication and segregation with the cell cycle, which appears less of an issue in plasmid maintenance.

John Snow's legacy: epidemiology without borders

This Review provides abstracts from a meeting held at the London School of Hygiene and Tropical Medicine, on April 11-12, 2013, to celebrate the legacy of John Snow. They describe conventional and unconventional applications of epidemiological methods to problems ranging from diarrhoeal disease, mental health, cancer, and accident care, to education, poverty, financial networks, crime, and violence. Common themes appear throughout, including recognition of the importance of Snow's example, the philosophical and practical implications of assessment of causality, and an emphasis on the evaluation of preventive, ameliorative, and curative interventions, in a wide variety of medical and societal examples. Almost all self-described epidemiologists nowadays work within the health arena, and this is the focus of most of the societies, journals, and courses that carry the name epidemiology. The range of applications evident in these contributions might encourage some of these institutions to consider broadening their remits. In so doing, they may contribute more directly to, and learn from, non-health-related areas that use the language and methods of epidemiology to address many important problems now facing the world.

Disulfide bond formation and ToxR activity in Vibrio cholerae

Virulence factor production in Vibrio cholerae is complex, with ToxRS being an important part of the regulatory cascade. Additionally, ToxR is the transcriptional regulator for the genes encoding the major outer membrane porins OmpU and OmpT. ToxR is a transmembrane protein and contains two cysteine residues in the periplasmic domain. This study addresses the influence of the thiol-disulfide oxidoreductase system DsbAB, ToxR cysteine residues and ToxR/ToxS interaction on ToxR activity. The results show that porin production correlates with ToxR intrachain disulfide bond formation, which depends on DsbAB. In contrast, formation of ToxR intrachain or interchain disulfide bonds is dispensable for virulence factor production and in vivo colonization. This study further reveals that in the absence of ToxS, ToxR interchain disulfide bond formation is facilitated, whereat cysteinyl dependent homo- and oligomerization of ToxR is suppressed if ToxS is coexpressed. In summary, new insights into gene regulation by ToxR are presented, demonstrating a mechanism by which ToxR activity is linked to a DsbAB dependent intrachain disulfide bond formation.

The Drosophila protein mustard tailors the innate immune response activated by the immune deficiency pathway

In this study, we describe a Drosophila melanogaster transposon insertion mutant with tolerance to Vibrio cholerae infection and markedly decreased transcription of diptericin as well as other genes regulated by the immune deficiency innate immunity signaling pathway. We present genetic evidence that this insertion affects a locus previously implicated in pupal eclosion. This genetic locus, which we have named mustard (mtd), contains a LysM domain, often involved in carbohydrate recognition, and a TLDc domain of unknown function. More than 20 Mtd isoforms containing one or both of these conserved domains are predicted. We establish that the mutant phenotype represents a gain of function and can be replicated by increased expression of a short, nuclearly localized Mtd isoform comprised almost entirely of the TLDc domain. We show that this Mtd isoform does not block Relish cleavage or translocation into the nucleus. Lastly, we present evidence suggesting that the eclosion defect previously attributed to the Mtd locus may be the result of the unopposed action of the NF-κB homolog, Relish. Mtd homologs have been implicated in resistance to oxidative stress. However, to our knowledge this is the first evidence that Mtd or its homologs alter the output of an innate immunity signaling cascade from within the nucleus.

[Point mutation of the Virbrio cholerae O139 cef (CHO cell elongating factor) gene alters the substrate specificity of its product]

Sequencing of the cef (CHO cell elongating factor) of Vibrio cholerae serogroup O139 revealed one nucleotide substitution (C for T in position 2015) in comparison with classical V. cholerae O1 and two substitutions (AC for GT in positions 2014-2015) in comparison with V. cholerae O1 E1 Tor. A comparative bioinformatic analysis showed that the substitution determines a threonine residue in position 672 of the Cefprotein, while the position is occupied by an isoleucine residue in the classical strains and a valine residue in the El Tor group. The last two amino acids are hydrophobic, while threonine is hydrophilic, having a polar R group. The non- synonymous substitution affects the predicted secondary and, probably, tertiary structures of the Cef-O139 protein and explained our previous finding that the protein fails to degrade tributyrin, while retaining the tweenase activity spectrum and all other characteristics. It cannot be excluded that the inability of Cef-O139 to cleave triglycerides, along with other genetic specifics, contribute to the fact that the O139 serogroup has been displaced from a dominating position in etiology of cholera by the El Tor genotype. The nucleotide sequence of the V. cholerae O139 cefgene and the deduced amino acid sequence of its product are reported for the first time and were deposited in GenBank under accession nos. JF499787 and AEC04822.1, respectively.

Genotypic and PFGE/MLVA analyses of Vibrio cholerae O1: geographical spread and temporal changes during the 2007-2010 cholera outbreaks in Thailand

BACKGROUND

Vibrio cholerae O1 El Tor dominated the seventh cholera pandemic which occurred in the 1960s. For two decades, variants of V. cholerae O1 El Tor that produce classical cholera toxin have emerged and spread globally, replacing the prototypic El Tor biotype. This study aims to characterize V. cholerae O1 isolates from outbreaks in Thailand with special reference to genotypic variations over time.

METHODS/FINDINGS

A total of 343 isolates of V. cholerae O1 from cholera outbreaks from 2007 to 2010 were investigated, and 99.4% were found to carry the classical cholera toxin B subunit (ctxB) and El Tor rstR genes. Pulsed-field gel electrophoresis (PFGE) differentiated the isolates into 10 distinct pulsotypes, clustered into two major groups, A and B, with an overall similarity of 88%. Ribotyping, multiple-locus variable-number tandem-repeat analysis (MLVA), and PCR to detect Vibrio seventh pandemic island II (VSP-II) related genes of randomly selected isolates from each pulsotype corresponded to the results obtained by PFGE. Epidemiological investigations revealed that MLVA type 2 was strongly associated with a cholera outbreak in northeastern Thailand in 2007, while MLVA type 7 dominated the outbreaks of the southern Gulf areas in 2009 and MLVA type 4 dominated the outbreaks of the central Gulf areas during 2009-2010. Only MLVA type 16 isolates were found in a Thai-Myanmar border area in 2010, whereas those of MLVA types 26, 39, and 41 predominated this border area in 2008. Type 39 then disappeared 1-2 years later as MLVA type 41 became prevalent. Type 41 was also found to infect an outbreak area.

CONCLUSIONS

MLVA provided a high-throughput genetic typing tool for understanding the in-depth epidemiology of cholera outbreaks. Our epidemiological surveys suggest that some clones of V. cholerae O1 with similar but distinctive genetic traits circulate in outbreak sites, while others disappear over time.

[Molecular-genetic analysis of the epidemical strains of the Vibrio cholerae El Tor isolated from the Siberian and maritime regions of Russia]

The detection of the biotype-specificity, pathogenicity determinants, and sequencing of the ctxB gene and the ctxAB promoter was carried out for analysis of the Vibrio cholerae El Tor strains genome structure. The strains (n = 90) were isolated during cholera epidemic outbreaks in Siberia and the Far East. All toxigenic Vibrio cholerae El Tor strains were divided into two groups: the first group included strains isolated during 1970s: they had the genotype ctxB3+rstREl+rstRCl-rstC+TLC+tbr4. All epidemic dangerous El Tor biotype strains isolated in 1990s belonged to the second group. The strains were characterized as atypical variants because of classical genotype (ctxB1) ctxB gene harboring. The second group fell into three genotypes according to the set of genetic markers (ctxB, rstR, rstC, TLC, tbr). It was suggested that the set of genetic determinants could be used as a marker for epidemiological analysis of spreading of atypical ET strains. The comparative analysis of genome structure enables to suggest possible ways of pathogen evolution.

A genome-wide approach to discovery of small RNAs involved in regulation of virulence in Vibrio cholerae

Small RNAs (sRNAs) are becoming increasingly recognized as important regulators in bacteria. To investigate the contribution of sRNA mediated regulation to virulence in Vibrio cholerae, we performed high throughput sequencing of cDNA generated from sRNA transcripts isolated from a strain ectopically expressing ToxT, the major transcriptional regulator within the virulence gene regulon. We compared this data set with ToxT binding sites determined by pulldown and deep sequencing to identify sRNA promoters directly controlled by ToxT. Analysis of the resulting transcripts with ToxT binding sites in cis revealed two sRNAs within the Vibrio Pathogenicity Island. When deletions of these sRNAs were made and the resulting strains were competed against the parental strain in the infant mouse model of V. cholerae colonization, one, TarB, displayed a variable colonization phenotype dependent on its physiological state at the time of inoculation. We identified a target of TarB as the mRNA for the secreted colonization factor, TcpF. We verified negative regulation of TcpF expression by TarB and, using point mutations that disrupted interaction between TarB and tpcF mRNA, showed that loss of this negative regulation was primarily responsible for the colonization phenotype observed in the TarB deletion mutant.

DNA damage and reactive nitrogen species are barriers to Vibrio cholerae colonization of the infant mouse intestine

Ingested Vibrio cholerae pass through the stomach and colonize the small intestines of its host. Here, we show that V. cholerae requires at least two types of DNA repair systems to efficiently compete for colonization of the infant mouse intestine. These results show that V. cholerae experiences increased DNA damage in the murine gastrointestinal tract. Agreeing with this, we show that passage through the murine gut increases the mutation frequency of V. cholerae compared to liquid culture passage. Our genetic analysis identifies known and novel defense enzymes required for detoxifying reactive nitrogen species (but not reactive oxygen species) that are also required for V. cholerae to efficiently colonize the infant mouse intestine, pointing to reactive nitrogen species as the potential cause of DNA damage. We demonstrate that potential reactive nitrogen species deleterious for V. cholerae are not generated by host inducible nitric oxide synthase (iNOS) activity and instead may be derived from acidified nitrite in the stomach. Agreeing with this hypothesis, we show that strains deficient in DNA repair or reactive nitrogen species defense that are defective in intestinal colonization have decreased growth or increased mutation frequency in acidified nitrite containing media. Moreover, we demonstrate that neutralizing stomach acid rescues the colonization defect of the DNA repair and reactive nitrogen species defense defective mutants suggesting a common defense pathway for these mutants.

Studies on intracellular bacterial pathogens have shown the need for maintaining genomic fidelity to promote colonization. Loss of DNA repair functions often leads to attenuation and rapid clearing of the invading pathogen. However, for some pathogens, an increased mutation rate has been shown to be beneficial for promoting host colonization, presumably by allowing the pathogen to rapidly adapt to adverse host conditions. We asked if the non-invasive pathogen V. cholerae experienced increased DNA damage during infection and if so, how the increased damage influenced host colonization and from where the source of the damage was derived. Our results demonstrate that V. cholerae experiences increased DNA damage during infection in the infant mouse model and that loss of ability to repair this damage results in attenuation of virulence. We specifically show that V. cholerae requires both base excision repair and mismatch repair for efficient intestinal colonization. Furthermore, we present evidence that the source of the DNA damage is derived from reactive nitrogen species (RNS) formed by acidified nitrite in the mouse gut and in doing so we identify a new RNS defense protein found in V. cholerae and several other pathogenic bacteria.

A bistable switch and anatomical site control Vibrio cholerae virulence gene expression in the intestine

A fundamental, but unanswered question in host-pathogen interactions is the timing, localization and population distribution of virulence gene expression during infection. Here, microarray and in situ single cell expression methods were used to study Vibrio cholerae growth and virulence gene expression during infection of the rabbit ligated ileal loop model of cholera. Genes encoding the toxin-coregulated pilus (TCP) and cholera toxin (CT) were powerfully expressed early in the infectious process in bacteria adjacent to epithelial surfaces. Increased growth was found to co-localize with virulence gene expression. Significant heterogeneity in the expression of tcpA, the repeating subunit of TCP, was observed late in the infectious process. The expression of tcpA, studied in single cells in a homogeneous medium, demonstrated unimodal induction of tcpA after addition of bicarbonate, a chemical inducer of virulence gene expression. Striking bifurcation of the population occurred during entry into stationary phase: one subpopulation continued to express tcpA, whereas the expression declined in the other subpopulation. ctxA, encoding the A subunit of CT, and toxT, encoding the proximal master regulator of virulence gene expression also exhibited the bifurcation phenotype. The bifurcation phenotype was found to be reversible, epigenetic and to persist after removal of bicarbonate, features consistent with bistable switches. The bistable switch requires the positive-feedback circuit controlling ToxT expression and formation of the CRP-cAMP complex during entry into stationary phase. Key features of this bistable switch also were demonstrated in vivo, where striking heterogeneity in tcpA expression was observed in luminal fluid in later stages of the infection. When this fluid was diluted into artificial seawater, bacterial aggregates continued to express tcpA for prolonged periods of time. The bistable control of virulence gene expression points to a mechanism that could generate a subpopulation of V. cholerae that continues to produce TCP and CT in the rice water stools of cholera patients.

Most pathogenic microorganisms infect in a stepwise manner: colonization of host surfaces is followed by invasion and injury of host tissues and, late in the infectious process, dissemination to other hosts occurs. During its residence in the host, the pathogen produces essential virulence determinants and often replicates rapidly, leading to a vast expansion of its biomass. Although this scenario is well established also for Vibrio cholerae, the cause of a potentially fatal diarrheal illness, it has not previously been possible to identify precisely when or where virulence determinants are produced in the intestine. We addressed this question by investigating the expression of virulence genes by individual V. cholerae during infection of the small intestine. Virulence genes were found to be powerfully expressed early in the infectious process by bacteria in close proximity to epithelial surfaces. Increased replication rates were also localized to epithelial surfaces. During later stages of the infection, the population of V. cholerae bifurcates into two fractions: one subpopulation continues to express virulence genes, whereas these genes are silenced in the other subpopulation. The genetic program controlling the continued production of virulence genes may mediate the persistence of a hyper-infectious subpopulation of bacteria in the stools of cholera patients.

Familial aggregation of Vibrio cholerae-associated infection in Matlab, Bangladesh

Vibrio cholerae is a major cause of diarrhoeal illness in endemic regions, such as Bangladesh. Understanding the factors that determine an individual's susceptibility to infection due to V. cholerae may lead to improved prevention and control strategies. Increasing evidence suggests that human genetic factors affect the severity of V. cholerae-associated infection. This study, therefore, sought to characterize the heritable component of susceptibility to infection due to V. cholerae using the Matlab Health and Demographic Surveillance System database of the International Centre for Diarrhoeal Disease Research, Bangladesh. In total, 144 pedigrees that included a cholera patient and 341 pedigrees without a cholera patient were evaluated during 1 January-31 December 1992. The odds of the sibling of a patient being admitted with cholera were 7.67 times the odds of the sibling of an unaffected individual being admitted with cholera [95% confidence interval (CI) 2.40-24.5, p < 0.001], after adjustment for gender, age, socioeconomic status, and hygiene practices. Although exposure to environmental reservoirs is essential in the epidemiology of cholera, household-specific factors, such as familial relatedness to an index case, may also be important determinants of risk of cholera. Further analysis of human genetic factors that contribute to susceptibility to cholera may be productive.

[Gene expression differences of toxigenic and nontoxigenic Vibrio cholerae strains in mannitol fermentation medium and Luria-Bertani broth]

OBJECTIVE

To analyze gene expression differences of toxigenic and nontoxigenic strains of El Tor Vibrio cholerae growing separately in mannitol fermentation medium and LB (Luria-Bertani) broth.

METHODS

Total RNA was extracted from the mannitol slow-fermenting strain N16961 (toxigenic) and the mannitol fast-fermenting strain 93097 (nontoxigenic) at 1 h of fermentation. The large scale gene expression profiles were detected and compared with high throughout microarray.

RESULTS

By comparing the strains growing in different cultures, we found 142 differentially expressed genes in N16961 and 418 genes in 93097. Most of these genes were grouped into six functional classes. They were mainly related to transport and binding, energy metabolism, protein biosynthesis, and protein fate.

CONCLUSION

The expression levels of genes in N16961 and 93097 were affected by culture conditions, which can serve as basis for further studying the mechanism of metabolism of mannitol.

A recalibrated molecular clock and independent origins for the cholera pandemic clones

Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6(th) (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7(th) pandemic clone, while the 6(th) pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared them with the published 7(th) pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6(th) and 7(th) pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000-50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.

[Genetically determined human susceptibility to selected infectious diseases]

As predictions show infectious diseases were, are and will be, responsible for a significant percentage (more than 12% in the year 2030) of deaths worldwide. Infectious diseases are, according to J.B.S. Haldane's theory, the major agent determining natural selection, as they lead to elimination of more susceptible people and only leave to survive these, who are more resistant. It has been revealed that susceptibility to pathogens varies among ethnic groups. Explanation of this phenomenon can be found in the human genome. Standard genetic analysis led to identification of several gene variants which modulate susceptibility to particular infectious disease as well as its progression. HLA genes encoding major histocompatibility complex are one of the most interesting ones as they are reported to influence the susceptibility to a wide range of pathogens. It is also proved that in several cases many other genes take part in modulation of clinical outcome of the diseases. Alleles conferring partial or total protection against disease development have already been identified. This review presents results of selected research concerning genetically determined susceptibility to malaria, cholera, leprosy and HIV.

Susceptibility to Vibrio cholerae infection in a cohort of household contacts of patients with cholera in Bangladesh

Background

Despite recent progress in understanding the molecular basis of Vibrio cholerae pathogenesis, there is relatively little knowledge of the factors that determine the variability in human susceptibility to V. cholerae infection.

Methods and Findings

We performed an observational study of a cohort of household contacts of cholera patients in Bangladesh, and compared the baseline characteristics of household members who went on to develop culture-positive V. cholerae infection with individuals who did not develop infection. Although the vibriocidal antibody is the only previously described immunologic marker associated with protection from V. cholerae infection, we found that levels of serum IgA specific to three V. cholerae antigens—the B subunit of cholera toxin, lipopolysaccharide, and TcpA, the major component of the toxin–co-regulated pilus—also predicted protection in household contacts of patients infected with V. cholerae O1, the current predominant cause of cholera. Circulating IgA antibodies to TcpA were also associated with protection from V. cholerae O139 infection. In contrast, there was no association between serum IgG antibodies specific to these three antigens and protection from infection with either serogroup. We also found evidence that host genetic characteristics and serum retinol levels modify susceptibility to V. cholerae infection.

Conclusions

Our observation that levels of serum IgA (but not serum IgG) directed at certain V. cholerae antigens are associated with protection from infection underscores the need to better understand anti–V. cholerae immunity at the mucosal surface. Furthermore, our data suggest that susceptibility to V. cholerae infection is determined by a combination of immunologic, nutritional, and genetic characteristics; additional factors that influence susceptibility to cholera remain unidentified.

Vibrio cholerae is the bacterium that causes cholera, a severe form of diarrhea that leads to rapid and potentially fatal dehydration when the infection is not treated promptly. Cholera remains an important cause of diarrhea globally, and V. cholerae continues to cause major epidemics in the most vulnerable populations. Although there have been recent discoveries about how the bacterium adapts to the human intestine and causes diarrhea, there is little understanding of why some people are protected from infection with V. cholerae. This article describes several factors that are associated with the risk of developing V. cholerae infection among people living in the same household with a patient with severe cholera who are at high risk of contracting the infection. One of the findings is that IgA antibodies, a type of antibody associated with immunity at mucosal surfaces such as the intestine, that target several components of the bacteria are associated with immunity to V. cholerae infection. This article also describes genetic and nutritional factors that additionally influence susceptibility to V. cholerae infection.

Differential expression of intestinal membrane transporters in cholera patients

Vibrio cholerae causes the cholera disease through secretion of cholera toxin (CT), resulting in severe diarrhoea by modulation of membrane transporters in the intestinal epithelium. Genes encoding membrane-spanning transporters identified as being differentially expressed during cholera disease in a microarray screening were studied by real-time PCR, immunohistochemistry and in a CaCo-2 cell model. Two amino acid transporters, SLC7A11 and SLC6A14, were upregulated in acute cholera patients compared to convalescence. Five other transporters were downregulated; aquaporin 10, SLC6A4, TRPM6, SLC23A1 and SLC30A4, which have specificity for water, serotonin (5-HT), magnesium, vitamin C and zinc, respectively. The majority of these changes appear to be attempts of the host to counteract the secretory response. Our results also support the concept that epithelial cells are involved in 5-HT signalling during acute cholera.

Molecular epidemiology and origin of cholera reemergence in Italy and Albania in the 1990s

In 1994 a cholera epidemic occurred in Italy and Albania after more than a decade of case absence. To investigate genotypic characteristics and the origin of the epidemic strains, 110 Vibrio cholerae O1 El Tor isolates from Italy and Albania were studied by randomly amplified polymorphic DNA analysis (RAPD), BglI ribotyping, and pulsed-field gel electrophoresis (PFGE) of genomic DNA. The Italian and Albanian strains were all ribotype 6 and their RAPD and PFGE patterns were identical as well. These findings indicated that the 1994 isolates belonged to the same clone and that the clone was part of the larger global spread of epidemic ribotype 6 strains, which started in southern Asia in 1990.

CFTR in cystic fibrosis and cholera: from membrane transport to clinical practice

We have used a brief analysis of transport via cystic fibrosis (CF) transmembrane conductance regulators (CFTRs) in various organ systems to highlight the importance of basic membrane transport processes across epithelial cells for first-year medical students in physiology. Because CFTRs are involved in transport both physiologically and pathologically in various systems, we have used this clinical correlation to analyze how a defective gene leading to defective transport proteins can be directly involved in the symptoms of cholera and CF. This article is a "Staying Current" approach to transport via CFTRs including numerous helpful references with further information for a teaching faculty member. The article follows our normal presentation which begins with a discussion of the involvement of CFTR transport in the intestine and how cholera affects intestinal transport, extends to CFTR transport in various organ systems in CF, and concludes with the logic behind many of the treatments that improve CF. Student learning objectives are included to assist in assessment of student understanding of the basic concepts.

Second-generation recombination-based in vivo expression technology for large-scale screening for Vibrio cholerae genes induced during infection of the mouse small intestine

We have constructed an improved recombination-based in vivo expression technology (RIVET) and used it as a screening method to identify Vibrio cholerae genes that are transcriptionally induced during infection of infant mice. The improvements include the introduction of modified substrate cassettes for resolvase that can be positively and negatively selected for, allowing selection of resolved strains from intestinal homogenates, and three different tnpR alleles that cover a range of translation initiation efficiencies, allowing identification of infection-induced genes that have low-to-moderate basal levels of transcription during growth in vitro. A transcriptional fusion library of 8,734 isolates of a V. cholerae El Tor strain that remain unresolved when the vibrios are grown in vitro was passed through infant mice, and 40 infection-induced genes were identified. Nine of these genes were inactivated by in-frame deletions, and their roles in growth in vitro and fitness during infection were measured by competition assays. Four mutant strains were attenuated >10-fold in vivo compared with the parental strain, demonstrating that infection-induced genes are enriched in genes essential for virulence.

Construction and Characterization of a thyA Mutant Derived From Cholera Vaccine Candidate IEM101

A naturally cholera toxin gene negative Vibrio cholerae (O1, El Tor, Ogawa) strain, named IEM101, was isolated in China. The human volunteer tests showed that this strain was safe, able to colonize the intestinal mucosa, and able to induce a strong immune response. Also other studies indicated that it was an efficient live vector to deliver heterologous antigens. In this article, a thymidylate synthase gene (thyA)-defined mutant was constructed using homologous recombination. Except for the morphological changes in minimal medium and slightly reduced colonization capacity, mutant strain IEM101-T maintained most of the desirable features as the wild-type strain IEM101 in terms of growth rate and immunogenicity. However, the mutant was more biosafe than its parent strain. In conclusion, IEM101-T may be a promising strain to develop live vaccine candidate of cholera or an attractive vaccine vector to deliver heterologous antigens in vivo.

Use of in vivo-induced antigen technology (IVIAT) to identify genes uniquely expressed during human infection with Vibrio cholerae

In vivo-induced antigen technology is a method to identify proteins expressed by pathogenic bacteria during human infection. Sera from 10 patients convalescing from cholera infection in Bangladesh were pooled, adsorbed against in vitro-grown El Tor Vibrio cholerae O1, and used to probe a genomic expression library in Escherichia coli constructed from El Tor V. cholerae O1 strain N16961. We identified 38 positive clones in the screen, encoding pili (PilA and TcpA), cell membrane proteins (PilQ, MshO, MshP, and CapK), methyl-accepting chemotaxis proteins, chemotaxis and motility proteins (CheA and CheR), a quorum-sensing protein (LuxP), and four hypothetical proteins. Analysis of immune responses to purified PilA and TcpA in individual patients demonstrated that the majority seroconverted to these proteins, confirming results with pooled sera. These results suggest that PilA and its outer membrane secretin, PilQ, are expressed during human infection and may be involved in colonization of the gastrointestinal tract. These results also demonstrate substantial immune responses to TcpA in patients infected with El Tor V. cholerae O1. In vivo-induced antigen technology provides a simple method for identifying microbial proteins expressed during human infection, but not during in vitro growth.