The sixth pandemic of cholera and, presumably, the earlier pandemics were caused by the classical biotype of Vibrio cholerae O1, which was progressively replaced by the El Tor biotype representing the seventh cholera pandemic. Although the classical biotype of V. cholerae O1 is extinct, even in southern Bangladesh, the last of the niches where this biotype prevailed, we have identified new varieties of V. cholerae O1, of the El Tor biotype with attributes of the classical biotype, from hospitalized patients with acute diarrhea in Bangladesh. Twentyfour strains of V. cholerae O1 isolated between 1991 and 1994 from hospitalized patients with acute diarrhea in Matlab, a rural area of Bangladesh, were examined for the phenotypic and genotypic traits that distinguish the two biotypes of V. cholerae O1. Standard reference strains of V. cholerae O1 belonging to the classical and El Tor biotypes were used as controls in all of the tests. The phenotypic traits commonly used to distinguish between the El Tor and classical biotypes, including polymyxin B sensitivity, chicken cell agglutination, type of tcpA and rstR genes, and restriction patterns of conserved rRNA genes (ribotypes), differentiated the 24 strains of toxigenic V. cholerae O1 into three types designated the Matlab types. Although all of the strains belonged to ribotypes that have been previously found among El Tor vibrios, type I strains had more traits of the classical biotype while type II and III strains appeared to be more like the El Tor biotype but had some classical biotype properties. These results suggest that, although the classical and El Tor biotypes have different lineages, there are possible naturally occurring genetic hybrids between the classical and El Tor biotypes that can cause cholera and thus provide new insight into the epidemiology of cholera in Bangladesh. Furthermore, the existence of such novel strains may have implications for the development of a cholera vaccine.New epidemic strains of toxigenic Vibrio cholerae have appeared at least twice in recent human history (10). Strains of the classical biotype, which had probably been responsible for most of the epidemic disease in the 19th century and much of the 20th century, were largely replaced as the predominant cause of epidemic cholera by strains of the El Tor biotype in most of the regions where cholera is endemic, beginning in 1961. However, the classical biotype strains reemerged as a predominant epidemic strain in parts of Bangladesh in 1982 (8, 25) and coexisted with the El Tor strains, causing disease until 1993. A second new epidemic strain, carrying the O139 rather than the O1 antigen, emerged in southern Asia in 1992 (7, 24). The O139 and El Tor O1 strains continue to cause epidemics of cholera, and there are indications that the incidence of cholera due to the O139 serogroup is on the rise in parts of India and Bangladesh.The classical and El Tor biotypes of V. cholerae are closely related in their O-antigen biosynthetic genes (21, 31), although these two biotypes diffe...

To understand the evolutionary events and possible selection mechanisms involved in the emergence of pathogenic Vibrio cholerae, we analyzed diverse strains of V. cholerae isolated from environmental waters in Bangladesh by direct enrichment in the intestines of adult rabbits and by conventional laboratory culture. Strains isolated by conventional culture were mostly (99.2%) negative for the major virulence gene clusters encoding toxincoregulated pilus (TCP) and cholera toxin (CT) and were nonpathogenic in animal models. In contrast, all strains selected in rabbits were competent for colonizing infant mice, and 56.8% of these strains carried genes encoding TCP alone or both TCP and CT. Ribotypes of toxigenic O1 and O139 strains from the environment were similar to pandemic strains, whereas ribotypes of non-O1 non-O139 strains and TCP ؊ nontoxigenic O1 strains diverged widely from the seventh pandemic O1 and the O139 strains. Results of this study suggest that (i) the environmental V. cholerae population in a cholera-endemic area is highly heterogeneous, (ii) selection in the mammalian intestine can cause enrichment of environmental strains with virulence potential, (iii) pathogenicity of V. cholerae involves more virulence genes than currently appreciated, and (iv) most environmental V. cholerae strains are unlikely to attain a pandemic potential by acquisition of TCP and CT genes alone. Because most of the recorded cholera pandemics originated in the Ganges Delta region, this ecological setting presumably favors extensive genetic exchange among V. cholerae strains and thus promotes the rare, multiple-gene transfer events needed to assemble the critical combination of genes required for pandemic spread.

Bacterial chromosomes often carry integrated genetic elements (e.g., plasmids, transposons, prophages, and islands) whose precise function and contribution to the evolutionary fitness of the host bacterium are unknown. The CTXϕ prophage, which encodes cholera toxin in Vibrio cholerae1, is known to be adjacent to a chromosomally integrated element of unknown function termed the toxin-linked cryptic (TLC)2. Here we report characterization of a TLC-related element that corresponds to the genome of a satellite filamentous phage (TLC-Knϕ1) which uses the morphogenesis genes of another filamentous phage (fs2ϕ) to form infectious TLC-Knϕ1 phage particles. The TLC-Knϕ1 phage genome carries a sequence similar to the dif recombination sequence which functions in chromosome dimer resolution using XerC and XerD recombinases3. The dif sequence is also exploited by lysogenic filamentous phages (e.g., CTXϕ) for chromosomal integration of their genomes. Bacterial cells defective in the dimer resolution often show an aberrant filamentous cell morphology3,4. We found that acquisition and chromosomal integration of the TLC-Knϕ1 genome restored a perfect dif site and normal morphology to V. cholerae wild type and mutant strains that displayed dif -filamentation phenotypes. Furthermore, lysogeny of a dif -nontoxigenic V. cholerae with TLC-Knϕ1 promoted its subsequent toxigenic conversion through integration of CTXϕ into the restored dif site. These results reveal a remarkable level of cooperative interactions between multiple filamentous phages in the emergence of the bacterial pathogen that causes cholera.The TLC element of V. cholerae encodes the Cri replicase with homology to filamentous phage replication proteins and TlcR, a protein that displays sequence similarity to RstR, the Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms * Corresponding author: Mailing address: Shah M. Faruque, Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka-1212, Bangladesh., Phone: (+880 2) 8860523 through 8860532, Fax : (+880 2) 8812529, faruque@icddrb.org. Author contributions. F.H., M.K., and S.M.F. conducted the experiments, and performed analyses of bacterial strains and phages. S.M.F. and J.J.M. designed the studies, analyzed data and wrote the manuscript. Relevant nucleotide sequence data described in the article have been deposited at GenBank under accession numbers HM134797, HM134798, HM134799, and HM134800.Supplementary Information is linked to the online version of the paper at www.nature.com/nature. repressor controlling lysogeny of the filamentous CTXϕ and the target for anti-repression by the RstC product of satellite filamentous phage RS1ϕ1,2,5-9. For these reasons we hypothesized that the TLC element corresponds to the genome of a satellite filamentous phage that depended on another fi...

Sixty-six strains of Vibrio parahaemolyticus belonging to 14 serotypes were isolated from hospitalized patients in Dhaka, Bangladesh, from January 1998 to December 2000. Among these, 48 strains belonging to four serotypes had the pandemic genotype and possessed the tdh gene. A marker (open reading frame ORF8) for a filamentous phage previously thought to correspond to the pandemic genotype was found to have a poor correlation with the pandemic genotype

Bacillary dysentery caused by Shigella species is a public health problem in developing countries including Bangladesh. Although, shigellae-contaminated food and drinks are often the source of the epidemic's spread, the possible presence of the pathogen and transmission of it through environmental waters have not been adequately examined. We analyzed surface waters collected in Dhaka, Bangladesh, for the presence of shigellae by a combination of PCR assays followed by concentration and culturing of PCR-positive samples. Analysis of 128 water samples by PCR assays for Shigella-specific virulence genes including ipaBCD, ipaH, and stx1 identified 14 (10.9%) samples which were positive for one or more of these virulence genes. Concentration of the PCR-positive samples by filtration followed by culturing identified live Shigella species in 11 of the 14 PCR-positive samples. Analysis of rRNA gene restriction patterns (ribotype) showed that the environmental isolates shared ribotypes with a collection of clinical isolates, but in contrast to the clinical isolates, 10 of the 11 environmental isolates were either negative or carried deletions in the plasmid-encoded invasion-associated genes ipaB, ipaC, and ipaD. However, all environmental Shigella isolates were positive for the chromosomal multicopy invasion-associated gene ipaH and all Shigella dysenteriae type 1 isolates were positive for the stx1 gene in addition to ipaH. This study demonstrated the presence of Shigella in the aquatic environment and dispersion of different virulence genes among these isolates which appear to constitute an environmental reservoir of Shigella-specific virulence genes. Since critical virulence genes in Shigella are carried by plasmids or mobile genetic elements, the environmental gene pool may contribute to an optimum combination of genes, causing the emergence of virulent Shigella strains which is facilitated in particular by close contact of the population with surface waters in Bangladesh.

Cholera epidemics have long been known to spread through water contaminated with human fecal material containing the toxigenic bacterium Vibrio cholerae. However, detection of V. cholerae in water is complicated by the existence of a dormant state in which the organism remains viable, but resists cultivation on routine bacteriological media. Growth in the mammalian intestine has been reported to trigger "resuscitation" of such dormant cells, and these studies have prompted the search for resuscitation factors. Although some positive reports have emerged from these investigations, the precise molecular signals that activate dormant V. cholerae have remained elusive. Quorum-sensing autoinducers are small molecules that ordinarily regulate bacterial gene expression in response to cell density or interspecies bacterial interactions. We have found that isolation of pathogenic clones of V. cholerae from surface waters in Bangladesh is dramatically improved by using enrichment media containing autoinducers either expressed from cloned synthase genes or prepared by chemical synthesis. These results may contribute to averting future disasters by providing a strategy for early detection of V. cholerae in surface waters that have been contaminated with the stools of cholera patients or asymptomatic infected human carriers.biofilm formation | CVEC | transmissibility T he natural habitats of the species Vibrio cholerae are estuarine or fresh water aquatic environments (1-3). In cholera endemic areas such as Bangladesh, viable V. cholerae can be readily detected in water during seasonal cholera epidemics; however, as disease incidence decreases, the isolation of viable V. cholerae becomes dramatically more difficult perhaps in part due to the influence of lytic bacteriophages (4, 5). However, during the interepidemic period, the organism can also occasionally be found in a viable but dormant state, which has been alternately referred to as the viable but nonculturable (VBNC) cells (1), conditionally viable environmental cells (CVEC) (6), or active but nonculturable (ABNC) (7). Recently we have documented the existence of CVEC in surface waters of Bangladesh by using fluorescent antibody based microscopy, which revealed clumps of V. cholerae O1 cells in water, which were often negative for V. cholerae O1 by conventional culture. To detect possible presence of relatively small number of culturable cells in such water we also used enrichment and selection approaches that depend on antibiotic resistance profiles displayed by the strains that have caused the preceding cholera epidemic. This approach referred to as antibiotic selection technique (AST) (8) allowed enhanced detection of V. cholerae by suppressing growth of other environmental bacteria that would otherwise mask the small number of V. cholerae colonies.In our previous studies, CVEC were found to be organized as aggregates of cells embedded in extracellular material, presumably Vibrio extracellular polysaccharide (VPS) (6). The genes responsible for VPS production are c...

The factors that enhance the waterborne spread of bacterial epidemics and sustain the pathogens in nature are unclear. The epidemic diarrheal disease cholera caused by Vibrio cholerae spreads through water contaminated with the pathogen. However, the bacteria exist in water mostly as clumps of cells, which resist cultivation by standard techniques but revive into fully virulent form in the intestinal milieu. These conditionally viable environmental cells (CVEC), alternatively called viable but nonculturable cells, presumably play a crucial role in cholera epidemiology. However, the precise mechanism causing the transition of V. cholerae to the CVEC form and this form's significance in the biology of the pathogen are unknown. Here we show that this process involves biofilm formation that is dependent on quorum sensing, a regulatory response that is controlled by cell density. V. cholerae strains carrying mutations in genes required for quorum sensing and biofilm formation displayed altered CVEC formation in environmental water following intestinal infections. Analysis of naturally occurring V. cholerae CVEC showed that organisms that adopt this quiescent physiological state typically exist as clumps of cells that comprise a single clone closely related to isolates causing the most recent local cholera epidemic. These results support a model of cholera transmission in which in vivo-formed biofilms convert to CVEC upon the introduction of cholera stools into environmental water. Our data further suggest that a temporary loss of quorum sensing due to dilution of extracellular autoinducers confers a selective advantage to communities of V. cholerae by blocking quorum-mediated regulatory responses that would break down biofilms and thus interfere with CVEC formation.biofilm formation | conditionally viable environmental cells (CVEC) | quorum sensing | transmissibility of cholera B acterial gene regulation in response to cell density, known as "quorum sensing," is a regulatory response thought to occur in bacterial communities through the sensing of extracellular signal molecules called autoinducers that are produced by members of the community (1, 2). Quorum-sensing systems (Fig. S1) such as those described in Vibrio cholerae, the causative agent of the epidemic diarrheal disease cholera, have been shown to regulate certain phenotypes, including biofilm formation and virulence (1-4). As a waterborne pathogen, V. cholerae is known to transit between the host intestinal milieu and a hypotonic aquatic environment during spreading epidemics of cholera (5), and both biofilm formation and quorum sensing have been proposed to influence transmission of V. cholerae (2-4, 6). Although phage predation (7-9), along with other regulatory changes (10, 11) that have been proposed to occur in vivo and in vitro, might also influence transmissibility, the genetic mechanisms that promote survival of V. cholerae in the natural aquatic environments (and thus support waterborne disease) remain unknown.Although cholera is a waterborne disea...

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 CTX⌽ morphogenesis, and an RS2 region encoding regulation, replication, and integration functions. Integrated CTX⌽ 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 CTX⌽ 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-Km⌽). Analysis of V. cholerae strains for susceptibility to RS1-Km⌽ 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 CTX⌽ receptor toxin-coregulated pilus (TCP) were also more susceptible (>1,000-fold) to the phage compared to toxigenic El Tor or O139 strains. Like CTX⌽, the RS1⌽ genome also integrated into the host chromosomes by using the attRS sequence. However, only transductants of RS1-Km⌽ which also harbored the CTX⌽ genome produced a detectable level of extracellular RS1-Km⌽. This suggested that the core genes of CTX⌽ are also required for the morphogenesis of RS1⌽. 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 CTX⌽.Toxigenic Vibrio cholerae strains are lysogens of a filamentous bacteriophage designated CTX⌽ (20), which carries the ctxAB genes encoding cholera toxin (CT). CTX⌽ is unusual among filamentous phages because the phage genome encodes the functions necessary for a site-specific integration system and thus can integrate into the V. cholerae chromosome at a specific attachment site known as attRS, forming stable lysogens (7,9,20). A typical CTX⌽ genome has two regions, the core and the RS2. The 4.6-kb core region encodes CT as well as the functions that are required for the virion morphogenesis, whereas the 2.5-kb RS2 region encodes the regulation, replication, and integration functions of the CTX⌽ genome (21). In toxigenic V. cholerae, particularly in El Tor and O139 strains, the CTX⌽ genome is integra...