Sunlight-induced propagation of the lysogenic phage encoding cholera toxin

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Baker‐Austin C, Hervio‐Heath D, Martinez‐Urtaza J, Caro ES, Strauch E, Thébault A, Guerra B, Messens W, Simon AC, Barcia‐Cruz R, Suffredini E. Public health aspects of Vibrio spp. related to the consumption of seafood in the EU

Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.

German coasts harbor non-O1/non-O139 Vibrio cholerae with clinical virulence gene profiles

Non-O1/non-O139 Vibrio cholerae (NOVC) are ubiquitous in aquatic ecosystems. In rare cases, they can cause intestinal and extra-intestinal infections in human. This ability is associated with various virulence factors. The presence of NOVC in German North Sea and Baltic Sea was observed in previous studies. However, data on virulence characteristics are still scarce. Therefore, this work aimed to investigating the virulence potential of NOVC isolated in these two regions. In total, 31 NOVC strains were collected and subjected to whole genome sequencing. In silico analysis of the pathogenic potential was performed based on the detection of genes involved in colonization and virulence. Phenotypic assays, including biofilm formation, mobility and human serum resistance assays were applied for validation. Associated toxin genes (hlyA, rtxA, chxA and stn), pathogenicity islands (Vibrio pathogenicity island 2 (VPI-II) and Vibrio seventh pathogenicity island 2 (VSP-II)) and secretion systems (Type II, III and VI secretion system) were observed. A maximum likelihood analysis from shared core genes revealed a close relationship between clinical NOVCs published in NCBI and environmental strains from this study. NOVC strains are more mobile at 37 °C than at 25 °C, and 68% of the NOVC strains could form strong biofilms at both temperatures. All tested strains were able to lyse erythrocytes from both human and sheep blood. Additionally, one strain could survive up to 60% and seven strains up to 40% human serum at 37 °C. Overall, the genetic virulence profile as well as the phenotypic virulence characteristics of the investigated NOVC from the German North Sea and Baltic Sea suggest potential human pathogenicity.

Cholera Dynamics and the Emergence of Pandemic Vibrio cholerae

Cholera is a severe diarrheal disease caused by the aquatic bacterium Vibrio cholerae. Interestingly, to date, only one major clade has emerged to cause pandemic disease in humans: the clade that encompasses the strains from the O1 and O139 serogroups. In this chapter, we provide a comprehensive perspective on the virulence factors and mobile genetic elements (MGEs) associated with the emergence of pandemic V. cholerae strains and highlight novel findings such as specific genomic background or interactions between MGEs that explain their confined distribution. Finally, we discuss pandemic cholera dynamics contextualizing them within the evolution of the bacterium.

Large Phenotypic and Genetic Diversity of Prophages Induced from the Fish Pathogen Vibrio anguillarum

Vibrio anguillarum is a marine pathogenic bacterium that causes vibriosis in fish and shellfish. Although prophage-like sequences have been predicted in V. anguillarum strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles that can infect and lysogenize other bacterial hosts. In this study, the genome sequences of 28 V. anguillarum strains revealed 55 different prophage-related elements. Chemical and spontaneous induction allowed a collection of 42 phage isolates, which were classified in seven different groups according to a multiplex PCR assay. One shared prophage sequence, p41 (group III), was present in 17 V. anguillarum strains, suggesting that this specific element is very dynamically exchanged among V. anguillarum populations. Interestingly, the host range of genetically identical phages was highly dependent on the strains used for proliferation, indicating that phenotypic properties of phages were partly regulated by the host. Finally, experimental evidence displayed that the induced phage ɸVa_90-11-287_p41 was able to lysogenize V. anguillarum strain Ba35, and subsequently spontaneously become released from the lysogenized cells, demonstrating an efficient transfer of the phage among V. anguillarum strains. Altogether, the results showed large genetic and functional diversity and broad distribution of prophages in V. anguillarum, and demonstrated the potential of prophages as drivers of evolution in V. anguillarum strains.

Environmental bacteriophages active on biofilms and planktonic forms of toxigenic Vibrio cholerae: Potential relevance in cholera epidemiology

In cholera-endemic areas, toxigenic Vibrio cholerae persist in the aquatic ecosystem mostly in a biofilm-associated state in which the bacteria remain embedded in an exopolysaccharide matrix. The biofilm-associated cells often enter into a dormant form referred to as conditionally viable environmental cells (CVEC), which resist cultivation on routine bacteriological media. However, these cells can naturally resuscitate into the active planktonic form through various mechanisms, multiply, and cause epidemics of cholera. This study was conducted to study possible effects of environmental bacteriophages on the prevalence and distribution of the pathogen between the biofilm associated state, and the planktonic form.

Pandemics, pathogenicity and changing molecular epidemiology of cholera in the era of global warming

Background

Vibrio cholerae, a Gram-negative, non-spore forming curved rod is found in diverse aquatic ecosystems around the planet. It is classified according to its major surface antigen into around 206 serogroups, of which O1 and O139 cause epidemic cholera. A recent spatial modelling technique estimated that around 2.86 million cholera cases occur globally every year, and of them approximately 95,000 die. About 1.3 billion people are currently at risk of infection from cholera. Meta-analysis and mathematical modelling have demonstrated that due to global warming the burden of vector-borne diseases like malaria, leishmaniasis, meningococcal meningitis, viral encephalitis, dengue and chikungunya will increase in the coming years in the tropics and beyond.

Cholera and climate

This review offers an overview of the interplay between global warming and the pathogenicity and epidemiology of V. cholerae. Several distinctive features of cholera survival (optimal thriving at 15% salinity, 30 °C water temperature, and pH 8.5) indicate a possible role of climate change in triggering the epidemic process. Genetic exchange (ctxAB, zot, ace, cep, and orfU) between strains and transduction process allows potential emergence of new toxigenic clones. These processes are probably controlled by precise environmental signals such as optimum temperature, sunlight and osmotic conditions. Environmental influences on phytoplankton growth and chitin remineralization will be discussed alongside the interplay of poor sanitary conditions, overcrowding, improper sewage disposal and global warming in promoting the growth and transmission of this deadly disease.

Conclusion

The development of an effective early warning system based on climate data could help to prevent and control future outbreaks. It may become possible to integrate real-time monitoring of oceanic regions, climate variability and epidemiological and demographic population dynamics to predict cholera outbreaks and support the design of cost-effective public health strategies.

Non-O1/non-O139 Vibrio cholerae septicaemia in a Saudi man: a case report

Background. The non-O1/non-O139 serogroups of Vibrio cholerae occur in diverse natural niches, and usually cause mild and self-limiting gastrointestinal illness. However, they have well-documented potential to cause invasive and extra-intestinal infections among immunocompromised patients. Furthermore, their ability to grow in low-salinity surface water, and the existence of asymptomatic human carriers, suggest novel acquisition routes for this unusual infection, even in people without obvious risk factors.

Case presentation. A 62-year-old man presented with epigastric pain, vomiting and fever. The patient had a history of diabetes and cholecystectomy, although our initial examination did not reveal any significant findings that might indicate V. cholerae infection. However, blood cultures subsequently revealed the presence of V. cholerae, which was positively identified using both conventional and modern non-conventional technologies. The identity of the V. cholerae isolate was confirmed using Vitek MS (matrix–assisted laser desorption ionization-time of flight MS) and the FilmArray system, in addition to its initial identification using the Vitek 2 system. The septicaemia was successfully treated using a 14 day course of ciprofloxacin.

Conclusion. The present case highlights the need to remain highly suspicious of non-O1/non-O139 V. cholerae infections in patients with known risk factors, as well as in healthy individuals with epidemiological exposure and compatible clinical symptoms. Special care should be taken to avoid false-positive results from confirmatory laboratory tests, as the organism can grow in fresh water, and the results should be verified using multiple methods.

Molecular Characterization of Vibrio cholerae Isolated From Clinical Samples in Kurdistan Province, Iran

Background:

Vibrio cholerae causes diarrhoeal disease that afflicts thousands of people annually. V. cholerae is classified on the basis of somatic antigens into serovars or serogroups and there are at least 200 known serogroup. Two serogroups, O1 and O139 have been associated with epidemic diseases. Virulence genes of these bacteria are OmpW, ctxA and tcpA.

Objectives:

Due to the importance of V. cholerae infection and developing molecular diagnostics of this organism in medical and microbiology sciences, this study aimed to describe molecular characterization of V. cholerae isolated from clinical samples using a molecular method.

Materials and Methods:

In this study, 48 samples were provided during summer 2013 (late August and early September) by reference laboratory. Samples were assessed using biochemical tests initially. The primer of OmpW, ctxA and tcpA genes was used in Polymerase Chain Reaction (PCR) protocols. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and Repetitive Extragenic Palindromic (REP)-PCR methods were used to subtype V. cholerae.

Results:

In this study, from a total of 48 clinical stool samples 39 (81.2 %) were positive for V. cholerae in biochemical tests and bacteria culture tests. The PCR results showed that of 39 positive isolates 35 (89.7%), 34 (87.1%) and 37 (94.8%) were positive for ctxA, tcpA and OmpW gene, respectively. Also, in the REP-PCR method with ERIC primer strains were divided into 10 groups. In the REP-PCR method with REP primer, strains were divided into 13 groups.

Conclusions:

Polymerase chain reaction has specificity and accuracy for identification of the organism and is able to differentiate biotypes. Enterobacterial repetitive intergenic consensus sequence is one of the informative and discriminative methods for the analysis of V. cholerae diversity. The REP-PCR is a less informative and discriminative method compared to other methods for the analysis of V. cholerae diversity.

Study of aminoglycoside resistance genes in enterococcus and salmonella strains isolated from ilam and milad hospitals, iran

Background:

Aminoglycosides are a group of antibiotics that have been widely used in the treatment of life-threatening infections of Gram-negative bacteria.

Objectives:

This study aimed to evaluate the frequency of aminoglycoside resistance genes in Enterococcus and Salmonella strains isolated from clinical samples by PCR.

Materials and Methods:

In this study, 140 and 79 isolates of Enterococcus and Salmonella were collected, respectively. After phenotypic biochemical confirmation, 117 and 77 isolates were identified as Enterococcus and Salmonella, respectively. After the biochemical identification of the isolates, antibiotic susceptibility for screening of resistance was done using the Kirby-Bauer method for gentamicin, amikacin, kanamycin, tobramycin and netilmycin. DNA was extracted from resistant strains and the presence of acc (3)-Ia, aac (3′)-Ib, acc (6)-IIa ,16SrRNA methylase genes (armA and rat) was detected by PCR amplification using special primers and positive controls.

Results:

Enterococcus isolates have the highest prevalence of resistance to both kanamycin and amikacin (68.4%), and Salmonella isolates have the highest prevalence of resistance against kanamycin (6.9%). Ninety-three and 26 isolates of Enterococcus and Salmonella at least were resistant against one of the aminoglycosides, respectively. Moreover, 72.04%, 66.7%, and 36.6% of the resistant strains of Enterococcus had the aac (3′)-Ia, aac (3′)-IIa, and acc (6′)-Ib genes, respectively. None of the Salmonella isolates have the studied aminoglycoside genes.

Conclusions:

Our results indicate that acetylation genes have an important role in aminoglycoside resistance of the Enterococcus isolates from clinical samples. Moreover, Salmonella strains indicate very low level of aminoglycoside resistance, and aminoglycoside resistance genes were not found in Salmonella isolates. These results indicate that other resistance mechanisms, including efflux pumps have an important role in aminoglycoside resistance of Salmonella.

Survival and proliferation of the lysogenic bacteriophage CTXΦ in Vibrio cholerae

The lysogenic phage CTXΦ of Vibrio cholerae can transfer the cholera toxin gene both horizontally (inter-strain) and vertically (cell proliferation). Due to its diversity in form and species, the complexity of regulatory mechanisms, and the important role of the infection mechanism in the production of new virulent strains of V. cholerae, the study of the lysogenic phage CTXΦ has attracted much attention. Based on the progress of current research, the genomic features and their arrangement, the host-dependent regulatory mechanisms of CTXΦ phage survival, proliferation and propagation were reviewed to further understand the phage's role in the evolutionary and epidemiological mechanisms of V. cholerae.

Persistence of infectious Shiga toxin-encoding bacteriophages after disinfection treatments

In Shiga toxin-producing Escherichia coli (STEC), induction of Shiga toxin-encoding bacteriophages (Stx phages) causes the release of free phages that can later be found in the environment. The ability of Stx phages to survive different inactivation conditions determines their prevalence in the environment, the risk of stx transduction, and the generation of new STEC strains. We evaluated the infectivity and genomes of two Stx phages (Φ534 and Φ557) under different conditions. Infectious Stx phages were stable at 4, 22, and 37°C and at pH 7 and 9 after 1 month of storage but were completely inactivated at pH 3. Infective Stx phages decreased moderately when treated with UV (2.2-log10 reduction for an estimated UV dose of 178.2 mJ/cm(2)) or after treatment at 60 and 68°C for 60 min (2.2- and 2.5-log10 reductions, respectively) and were highly inactivated (3 log10) by 10 ppm of chlorine in 1 min. Assays in a mesocosm showed lower inactivation of all microorganisms in winter than in summer. The number of Stx phage genomes did not decrease significantly in most cases, and STEC inactivation was higher than phage inactivation under all conditions. Moreover, Stx phages retained the ability to lysogenize E. coli after some of the treatments.

Amplified fragment length polymorphism of clinical and environmental Vibrio cholerae from a freshwater environment in a cholera-endemic area, India

Background

The region around Chandigarh in India has witnessed a resurgence of cholera. However, isolation of V. cholerae O1 from the environment is infrequent. Therefore, to study whether environmental nonO1-nonO139 isolates, which are native to the aquatic ecosystem, act as precursors for pathogenic O1 strains, their virulence potential and evolutionary relatedness was checked.

Methods

V. cholerae was isolated from clinical cases of cholera and from water and plankton samples collected from freshwater bodies and cholera-affected areas. PCR analysis for the ctxA, ctxB, tcpA, toxT and toxR genes and AFLP with six primer combinations was performed on 52 isolates (13 clinical, 34 environmental and 5 reference strains).

Results

All clinical and 3 environmental isolates belonged to serogroup O1 and remaining 31 environmental V. cholerae were nonO1-nonO139. Serogroup O1 isolates were ctxA, tcpA (ElTor), ctxB (Classical), toxR and toxT positive. NonO1-nonO139 isolates possessed toxR, but lacked ctxA and ctxB; only one isolate was positive for toxT and tcpA. Using AFLP, 2.08% of the V. cholerae genome was interrogated. Dendrogram analysis showed one large heterogeneous clade (n = 41), with two compact and distinct subclades (1a and 1b), and six small mono-phyletic groups. Although V. cholerae O1 isolates formed a distinct compact subclade, they were not clonal. A clinical O1 strain clustered with the nonO1-nonO139 isolates; one strain exhibited 70% similarity to the Classical control strain, and all O1 strains possessed an ElTor variant-specific fragment identified with primer ECMT. Few nonO1-nonO139 isolates from widely separated geographical locations intermingled together. Three environmental O1 isolates exhibited similar profiles to clinical O1 isolates.

Conclusion

In a unique study from freshwater environs of a cholera-endemic area in India over a narrow time frame, environmental V. cholerae population was found to be highly heterogeneous, diverse and devoid of major virulence genes. O1 and nonO1-nonO139 isolates showed distinct lineages. Clinical isolates were not clonal but were closely related, indicating accumulation of genetic differences over a short time span. Though, environment plays an important role in the spread of cholera, the possibility of an origin of pathogenic O1 strains from environmental nonO1-nonO139 strains seems to be remote in our region.

Detection of ctx gene positive non-O1/non-O139 V. cholerae in shrimp aquaculture environments

Water and post-larvae samples from black tiger (Penaeus monodon) shrimp hatcheries; pond water, pond sediment and shrimp from aquaculture farms were screened for the presence of V. cholerae. A V. cholerae-duplex PCR method was developed by utilizing V. cholerae species specific sodB primers and ctxAB genes specific primers. Incidence of V. cholerae was not observed in shrimp hatchery samples but was noticed in aquaculture samples. The incidence of V. cholerae was higher in pond water (7.6%) than in pond sediment (5.2%). Shrimp head (3.6%) portion had relatively higher incidence than shrimp muscle (1.6%). All the V. cholerae isolates (n = 42) belonged to non-O1/non-O139 serogroup, of which 7% of the V. cholerae isolates were potentially cholera-toxigenic (ctx positive). All the ctx positive V. cholerae (n = 3) were isolated from the pond water. Since, cholera toxin (CT) is the major contributing factor for cholera gravis, it is proposed that the mere presence of non-O1/non-O139 V. cholerae need not be the biohazard criterion in cultured black tiger shrimp but only the presence of ctx carrying non-O1/non-O139 V. cholerae may be considered as potential public health risk.

Genetic heterogeneity of non-O1 and non-O139 Vibrio cholerae isolates from shrimp aquaculture system: a comparison of RS-, REP- and ERIC-PCR fingerprinting approaches

AIMS

The genetic diversity of Vibrio cholerae isolated from black tiger shrimp (Penaeus monodon) aquaculture farms was determined using three PCR typing methods based on enterobacterial repetitive intergenic consensus (ERIC) sequences, ribosomal gene spacer (RS) sequence and repetitive extragenic palindromic (REP) sequences.

METHODS AND RESULTS

Non-O1 and non-O139 V. cholerae isolates were obtained from shrimp pond water, pond sediment, shrimp head and shrimp muscle. RS-PCR yielded fewer bands than REP-PCR and ERIC-PCR. Higher similarity was observed in RS-PCR (75-100%) than in REP-PCR (60-95%) and ERIC-PCR (40-95%).

CONCLUSIONS

A 100% similarity between V. cholerae isolates was only noticed in RS-PCR. The choleratoxigenic V. cholerae (non-O1 and non-O139) showed greater genetic similarity with ctx-negative V. cholerae than among ctx-positive V. cholerae.

SIGNIFICANCE AND IMPACT OF THE STUDY

The greater similarity of ctx-positive V. cholerae with ctx-negative V. cholerae isolates indicates that the ctx-positive strains (non-O1 and non-O139) might have originated from autochthonous V. cholerae in the aquatic niche.

Relationship of cholera incidence to El Niño and solar activity elucidated by time-series analysis

Using time-series analysis, we investigated the monthly cholera incidence in Dhaka, Bangladesh during an 18-year period for its relationship to the sea surface temperature (SST) linked to El Niño, and to the sunspot number. Dominant periodic modes identified for cholera incidence were 11·0, 4·8, 3·5, 2·9, 1·6, 1·0 and 0·5 years. The majority of these modes, e.g. the 11·0-, 4·8-, 3·5-, 1·6- and 1·0-year modes, were essentially consistent with those obtained for the SST data (dominant modes: 5·1, 3·7, 2·5, 2·1, 1·5, 1·0 years) and the sunspot number data (dominant modes: 22·1, 11·1, 7·3, 4·8, 3·1 years). We confirmed that the variations of cholera incidence were synchronous with SSTs, and were inversely correlated to the sunspot numbers. These results suggest that the cholera incidence in Bangladesh may have been influenced by the occurrence of El Niño and also by the periodic change of solar activity.

Phage diversity in a methanogenic digester

It has been shown that phages are present in natural and engineered ecosystems and influence the structure and performance of prokaryotic communities. However, little has been known about phages occurring in anaerobic ecosystems, including those in methanogenic digesters for waste treatment. This study investigated phages produced in an upflow anaerobic sludge blanket methanogenic digester treating brewery wastes. Phage-like particles (PLPs) in the influent and effluent of the digester were concentrated and purified by sequential filtration and quantified and characterized by transmission electron microscopy (TEM), fluorescence assay, and field inversion gel electrophoresis (FIGE). Results indicate that numbers of PLPs in the effluent of the digester exceeded 1 x 10(9) L-1 and at least 10 times greater than those in the influent, suggesting that substantial amounts of PLPs were produced in the digester. A production rate of the PLPs was estimated at least 5.2 x 10(7) PLPs day-1 L-1. TEM and FIGE showed that a variety of phages were produced in the digester, including those affiliated with Siphoviridae, Myoviridae, and Cystoviridae.

Prevalence of virulence genes (ctxA, stn, OmpW and tcpA) among non-O1 Vibrio cholerae isolated from fresh water environment

The virulence of a pathogen is reliant on the presence of a discrete set of genetic determinants and their expression in the host. The virulence of Vibrio spp. is regulated by the ctxAB and tcpA genes. These genes are alleged to be exclusively associated with clinical strains of O1 and O139 serogroups. In the present study, we examined the presence of virulence genes viz. stn, OmpW, ctxA and tcpA of classical and ElTor variants, in environmental strains of non-O1 Vibrio cholerae cultured seasonally from four sampling stations of the river Narmada at Jabalpur (MP), India. Unexpectedly, the PCR analysis of the strains revealed the presence of these genes among environmental V. cholerae. The strains harboring the tcpA gene also carried the ctxA gene. Sequencing of the tcpA gene and ctxA gene carried by an environmental strain showed approximately 97% homology with the previously sequenced genes submitted in the GenBank. We report here the prevalence of cholera toxin gene and the gene for toxin co-regulated pilus among non-O1 V. cholerae strains isolated from fresh water environment. This study supports the idea that cholera toxin has an environmental derivation and that the intricate aquatic environment can give rise to pathogenic Vibrio organisms.

Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages

The relationship among (i) the local incidence of cholera, (ii) the prevalence in the aquatic environment of Vibrio cholerae, and (iii) bacterial viruses that attack potentially virulent O1 and O139 serogroup strains of this organism (cholera phages) was studied in Dhaka, Bangladesh. Over nearly a 3-year period, we found that significantly more environmental water samples contained either a phage or a phage-susceptible V. cholerae strain than both (P < 0.00001). The number of cholera patients varied seasonally during this period and frequently coincided with the presence of pathogenic V. cholerae strains in water samples that otherwise lacked detectable cholera phages. Interepidemic periods were characterized by water samples containing cholera phages but no viable bacteria. Our data support the conclusion that cholera phages can influence cholera seasonality and may also play a role in emergence of new V. cholerae pandemic serogroups or clones.

Lipopolysaccharides of Vibrio cholerae

An account of our up to date knowledge of the genetics of biosynthesis of Vibrio cholerae lipopolysaccharide (LPS) is presented in this review. While not much information is available in the literature on the genetics of biosynthesis of lipid A of V. cholerae, the available information on the characteristics and proposed functions of the corepolysaccharide (core-PS) biosynthetic genes is discussed. The genetic organizations encoding the O-antigen polysaccharides (O-PS) of V. cholerae of serogroups O1 and O139, the disease causing ones, have been described along with the putative functions of the different constituent genes. The O-PS biosynthetic genes of some non-O1, non-O139 serogroups, particularly the serogroups O37 and O22, and their putative functions have also been discussed briefly. In view of the importance of the serogroup O139, the origination of the O139 strain and the possible donor of the corresponding O-PS gene cluster have been analyzed with a view to having knowledge of (i) the mode of evolution of different serogroups and (ii) the possible emergence of pathogenic strain(s) belonging to non-O1, non-O139 serogroups. The unsolved problems in this area of research and their probable impact on the production of an effective cholera vaccine have been outlined in conclusion.

Biosafety aspects of the recombinant live oral Vibrio cholerae vaccine strain CVD 103-HgR

The development of live attenuated vaccines, allowing for the safe and effective immunisation at mucosal surfaces, is a strategy of great interest for vaccinologists. The main advantage of this approach over conventional parenteral vaccines is the induction of strong mucosal immune responses, allowing targeting of the pathogen at the initial point of contact with the host. Further advantages include the ease of administration, high acceptance by vaccines, and relatively low production costs. Finally, well-characterised, safe and immunogenic vaccine strains are well suited as vectors for the mucosal delivery of foreign vaccine antigens and of DNA vaccines. However, such vaccines, when based on or containing genetically modified organisms (GMOs), are facing new and specific regulatory hurdles, particularly regarding the potential risks for humans and the environment. In this contribution we address selected aspects of the risk assessment of live attenuated bacterial vaccines covered in the course of the registration of vaccine strain CVD 103-HgR as a recombinant live oral vaccine against cholera.

Phage community dynamics in hot springs

In extreme thermal environments such as hot springs, phages are the only known microbial predators. Here we present the first study of prokaryotic and phage community dynamics in these environments. Phages were abundant in hot springs, reaching concentrations of a million viruses per milliliter. Hot spring phage particles were resistant to shifts to lower temperatures, possibly facilitating DNA transfer out of these extreme environments. The phages were actively produced, with a population turnover time of 1 to 2 days. Phage-mediated microbial mortality was significant, making phage lysis an important component of hot spring microbial food webs. Together, these results show that phages exert an important influence on microbial community structure and energy flow in extreme thermal environments.

Shigella dysenteriae type 1-specific bacteriophage from environmental waters in Bangladesh

Shigella dysenteriae type 1 is the causative agent of the most severe form of bacillary dysentery, which occurs as epidemics in many developing countries. We isolated a bacteriophage from surface water samples from Bangladesh that specifically lyses strains of S. dysenteriae type 1. This phage, designated SF-9, belongs to the Podoviridae family and has a 41-kb double-stranded DNA genome. Further screening of water samples for the prevalence of the phage revealed 9 of 71 (12.6%) water samples which were positive for the phage. These water samples were also positive in PCR assays for one or more S. dysenteriae type 1-specific genes, including ipaBCD and stx1, and live S. dysenteriae type 1 was isolated from three phage-positive samples. The results of this study suggest that phage SF-9 may have epidemiological applications in tracing the presence of S. dysenteriae type 1 in environmental waters.

Prevalence of cholera toxin genes (ctxA and zot) among non-O1/O139 Vibrio cholerae strains from Newport Bay, California

The examination of 137 non-O1/O139 Vibrio cholerae isolates from Newport Bay, California, indicated the presence of diverse genotypes and a temporal succession. Unexpectedly, the cholera toxin gene (ctxA) was found in 17% of the strains, of which one-third were also positive for the zot gene. This suggests that ctxA is prevalent in the region of nonepidemicity and is likely to have an environmental origin.

Comparative genomic analyses of the vibrio pathogenicity island and cholera toxin prophage regions in nonepidemic serogroup strains of Vibrio cholerae

Two major virulence factors are associated with epidemic strains (O1 and O139 serogroups) of Vibrio cholerae: cholera toxin encoded by the ctxAB genes and toxin-coregulated pilus encoded by the tcpA gene. The ctx genes reside in the genome of a filamentous phage (CTXphi), and the tcpA gene resides in a vibrio pathogenicity island (VPI) which has also been proposed to be a filamentous phage designated VPIphi. In order to determine the prevalence of horizontal transfer of VPI and CTXphi among nonepidemic (non-O1 and non-O139 serogroups) V. cholerae, 300 strains of both clinical and environmental origin were screened for the presence of tcpA and ctxAB. In this paper, we present the comparative genetic analyses of 11 nonepidemic serogroup strains which carry the VPI cluster. Seven of the 11 VPI(+) strains have also acquired the CTXphi. Multilocus sequence typing and restriction fragment length polymorphism analyses of the VPI and CTXphi prophage regions revealed that the non-O1 and non-O139 strains were genetically diverse and clustered in lineages distinct from that of the epidemic strains. The left end of the VPI in the non-O1 and non-O139 strains exhibited extensive DNA rearrangements. In addition, several CTXphi prophage types characterized by novel repressor (rstR) and ctxAB genes and VPIs with novel tcpA genes were found in these strains. These data suggest that the potentially pathogenic, nonepidemic, non-O1 and non-O139 strains identified in our study most likely evolved by sequential horizontal acquisition of the VPI and CTXphi independently rather than by exchange of O-antigen biosynthesis regions in an existing epidemic strain.

CTXphi-independent production of the RS1 satellite phage by Vibrio cholerae

The cholera toxin genes of Vibrio cholerae are encoded by the filamentous phage, CTXphi. Chromosomal CTXphi prophage DNA is often found flanked by copies of a related genetic element designated RS1, and RS1 DNA can be packaged into filamentous phage particles (designated RS1phi) by using the CTXphi morphogenesis genes. RS1phi is a satellite phage that further controls expression and dissemination of CTXphi. Here we describe a CTXphi-independent mechanism for production of RS1phi. A nontoxigenic environmental V. cholerae strain (55V71) was identified that supports production of RS1phi. However, newly infected CTX-negative strains did not produce RS1phi, indicating that additional 55V71 genes were involved in production of RS1phi. Analysis of nucleic acids from phage preparations of 55V71 revealed a 7.5-kb single-stranded DNA, whose corresponding replicative form was found in plasmid preparations. This DNA likely corresponds to the genome of a new filamentous phage, which we have designated KSF-1phi. The replicative form DNA of KSF-1phi was cloned into pUC18, and the resulting construct pKSF-1.1 supported the production of RS1phi particles by CTX-negative V. cholerae strains. RS1phi particles produced in this way infect recipient V. cholerae strains by a mechanism that is independent of the CTXphi receptor, the toxin-coregulated pilus. Thus, KSF-1phi is capable of facilitating the transfer of the RS1 element to strains that do not express toxin coregulated pilus. Given that RS1phi can enhance coproduction of CTXphi particles, KSF-1phi-mediated dissemination of RS1 may indirectly promote the spread of toxin genes among V. cholerae strains. This study also shows that filamentous phages can package diverse DNA elements and thus may play a role in horizontal transfer of more genes than previously appreciated.

Molecular ecology of toxigenic Vibrio cholerae

Toxigenic Vibrio cholerae is the etiological agent of cholera, an acute dehydrating diarrhea that occurs in epidemic form in many developing countries. Although V. cholerae is a human pathogen, aquatic ecosystems are major habitats of Vibrio species, which includes both pathogenic and nonpathogenic strains that vary in their virulence gene content. V. cholerae belonging to the 01 and 0139 serogroups is commonly known to carry a set of virulence genes necessary for pathogenesis in humans. Recent studies have indicated that virulence genes or their homologues are also dispersed among environmental strains of V. cholerae belonging to diverse serogroups, which appear to constitute an environmental reservoir of virulence genes. Although the definitive roles of the virulence-associated factors in the environment, and the environmental selection pressures for V. cholerae-carrying virulence genes or their homologues is not clear, the potential for origination of new epidemic strains from environmental progenitors seems real. It is likely that the aquatic environment harbors different virulence-associated genes scattered among environmental vibrios, which possess a lower virulence potential than the epidemic strains. The ecosystem comprising the aquatic environment, V. cholerae, genetic elements mediating gene transfer, and the mammalian host appears to support the clustering of critical virulence genes in a proper combination leading to the origination of new V. cholerae strains with epidemic potential.

Effects of global climate on infectious disease: the cholera model

Recently, the role of the environment and climate in disease dynamics has become a subject of increasing interest to microbiologists, clinicians, epidemiologists, and ecologists. Much of the interest has been stimulated by the growing problems of antibiotic resistance among pathogens, emergence and/or reemergence of infectious diseases worldwide, the potential of bioterrorism, and the debate concerning climate change. Cholera, caused by Vibrio cholerae, lends itself to analyses of the role of climate in infectious disease, coupled to population dynamics of pathogenic microorganisms, for several reasons. First, the disease has a historical context linking it to specific seasons and biogeographical zones. In addition, the population dynamics of V. cholerae in the environment are strongly controlled by environmental factors, such as water temperature, salinity, and the presence of copepods, which are, in turn, controlled by larger-scale climate variability. In this review, the association between plankton and V. cholerae that has been documented over the last 20 years is discussed in support of the hypothesis that cholera shares properties of a vector-borne disease. In addition, a model for environmental transmission of cholera to humans in the context of climate variability is presented. The cholera model provides a template for future research on climate-sensitive diseases, allowing definition of critical parameters and offering a means of developing more sophisticated methods for prediction of disease outbreaks.

Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh

Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence-PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease.

Stress, order and survival

Much of the sophisticated chemistry of life is accomplished by multicomponent complexes, which act as molecular machines. Intrinsic to their accuracy and efficiency is the energy that is supplied by hydrolysis of nucleoside triphosphates. Conditions that deplete energy sources should therefore cause decay and death. But studies on organisms that are exposed to prolonged stress indicate that this fate could be circumvented through the formation of highly ordered intracellular assemblies. In these thermodynamically stable structures, vital components are protected by a physical sequestration that is independent of energy consumption.

RS1 element of Vibrio cholerae can propagate horizontally as a filamentous phage exploiting the morphogenesis genes of CTXphi

In toxigenic Vibrio cholerae, cholera toxin is encoded by the CTX prophage, which consists of a core region carrying ctxAB genes and genes required for CTXPhi morphogenesis, and an RS2 region encoding regulation, replication, and integration functions. Integrated CTXPhi is often flanked by another genetic element known as RS1 which carries all open reading frames (ORFs) found in RS2 and an additional ORF designated rstC. We identified a single-stranded circularized form of the RS1 element, in addition to the CTXPhi genome, in nucleic acids extracted from phage preparations of 32 out of 83 (38.5%) RS1-positive toxigenic V. cholerae strains analyzed. Subsequently, the corresponding double-stranded replicative form (RF) of the RS1 element was isolated from a representative strain and marked with a kanamycin resistance (Km(r)) marker in an intergenic site to construct pRS1-Km. Restriction and PCR analysis of pRS1-Km and sequencing of a 300-bp region confirmed that this RF DNA was the excised RS1 element which formed a novel junction between ig1 and rstC. Introduction of pRS1-Km into a V. cholerae O1 classical biotype strain, O395, led to the production of extracellular Km(r) transducing particles, which carried a single-stranded form of pRS1-Km, thus resembling the genome of a filamentous phage (RS1-KmPhi). Analysis of V. cholerae strains for susceptibility to RS1-KmPhi showed that classical biotype strains were more susceptible to the phage compared to El Tor and O139 strains. Nontoxigenic (CTX(-)) O1 and O139 strains which carried genes encoding the CTXPhi receptor toxin-coregulated pilus (TCP) were also more susceptible (>1,000-fold) to the phage compared to toxigenic El Tor or O139 strains. Like CTXPhi, the RS1Phi genome also integrated into the host chromosomes by using the attRS sequence. However, only transductants of RS1-KmPhi which also harbored the CTXPhi genome produced a detectable level of extracellular RS1-KmPhi. This suggested that the core genes of CTXPhi are also required for the morphogenesis of RS1Phi. The results of this study showed for the first time that RS1 element, which encodes a site-specific recombination system in V. cholerae, can propagate horizontally as a filamentous phage, exploiting the morphogenesis genes of CTXPhi.

Recent developments in cholera

Cholera continues to be an important public health problem among many poorer communities in Africa, Asia and South America, despite the bacteriology and epidemiology of the disease having been described over a century ago. Molecular techniques have enabled current researchers to gain new insights into pathogenicity, into the relationships between environmental and clinical strains, and into new strategies for vaccine development. The description of non-culturable 'dormant' strains in the environment and the effect of environmental factors on toxin gene regulation provide valuable clues to the ecology of the disease. Disease management continues to be based on urgent and appropriate rehydration, and recent community studies emphasize the need for effective local health services to provide this if case fatality rates are to remain low. While antimicrobial agents may play a role in case management and prophylaxis, the increasing prevalence of antimicrobial resistance must be addressed. New vaccine candidates, based on a molecular understanding of pathogenicity, provide scope for improved strategies for disease prevention, though the appropriate public health context for their use has not been determined. This review summarizes activities in these fields of cholera research and considers the continuing global problem of the disease.

Characterization of VPI pathogenicity island and CTXphi prophage in environmental strains of Vibrio cholerae

Environmental isolates of Vibrio cholerae of eight randomly amplified polymorphic DNA (RAPD) fingerprint types from Calcutta, India, that were unusual in containing toxin-coregulated pilus or cholera toxin genes but not O1 or O139 antigens of epidemic strains were studied by PCR and sequencing to gain insights into V. cholerae evolution. We found that each isolate contained a variant form of the VPI pathogenicity island. Distinguishing features included (i) four new alleles of tcpF (which encodes secreted virulence protein; its exact function is unknown), 20 to 70% divergent (at the protein level) from each other and canonical tcpF; (ii) a new allele of toxT (virulence regulatory gene), 36% divergent (at the protein level) in its 5' half and nearly identical in its 3' half to canonical toxT; (iii) a new tcpA (pilin) gene; and (iv) four variant forms of a regulatory sequence upstream of toxT. Also found were transpositions of an IS903-related element and function-unknown genes to sites in VPI. Cholera toxin (ctx) genes were found in isolates of two RAPD types, in each case embedded in CTXphi-like prophages. Fragments that are inferred to contain only putative repressor, replication, and integration genes were present in two other RAPD types. New possible prophage repressor and replication genes were also identified. Our results show marked genetic diversity in the virulence-associated gene clusters found in some nonepidemic V. cholerae strains, suggest that some of these genes contribute to fitness in nature, and emphasize the potential importance of interstrain gene exchange in the evolution of this species.

Virulence of Pasteurella multocida recA mutants

In order to determine the role of the RecA protein in the virulence of Pasteurella multocida, a recA mutant was constructed and used in studies of virulence and competition in relation to wild-type strain. To achieve this, firstly, the recA gene was isolated and sequenced, showing an Escherichia coli-like SOS box and encoding a protein of 354 amino acids which has the closest identity with the Haemophilus influenzae RecA protein. Further, the recA mutant was constructed, by inactivating this gene by single recombination of a suicide plasmid containing an internal region of the P. multocida recA gene, and shown to be more sensitive to UV radiation than the parental strain. The P. multocida mutant was slightly attenuated in virulence, as indicated by the LD(50), the time of death of infected animals, and a failure to compete with the wild-type strain in mixed infections. Compared to the parent strain, the mutant had a similar growth rate but a longer lag phase. These data suggest that the diminished virulence of the recA mutant as well as its failure in competition were more a consequence of the long lag phase rather than a direct effect of the inactivation of the recA gene on genes involved in virulence.