WO1995018633A1

WO1995018633A1 - Soft agar penetration-defective mutants

Info

Publication number: WO1995018633A1
Application number: PCT/US1995/000174
Authority: WO
Inventors: John Mekalanos; Claudette L. Gardel; Andrew Camilli; David Beattie
Original assignee: President And Fellows Of Harvard College; Virus Research Institute
Priority date: 1994-01-06
Filing date: 1995-01-03
Publication date: 1995-07-13
Also published as: ZA9582B

Abstract

V. cholerae vaccine strains which have a soft agar penetration-defective phenotype and methods for making such strains are described. Also described are methods for identifying new genes involve in V. cholerae motility and the cloning, identification, and sequencing of V. cholerae motB and fliC genes.

Description

SOFT AGAR PENETRATION-DEFECTIVE MUTANTS
Background of the Invention
The field of invention is Vibrio cholerae vaccines. After more than 100 years of research on cholerae, there remains a need for an effective cholerae vaccine. There have been six pandemics of this disease caused by strains of V. cholerae belonging to the "Classical"biotype. The etiological agents of the current (seventh) pandemic belong to the"E1 Tor" biotype. Recently the seventh pandemic has extended to a new locale, that of South America. Beginning in January of 1991, an epidemic of cholerae resulted in greater than 250,000 cases and over 2,000 deaths in Peru, Ecuador,
Columbia, and Chile. In November of 1992, an antigenically distinct, non-01 form of V. cholerae emerged in India and Bangladesh and within eight months caused an estimated 500,000 cases and 6,000 deaths.

The pandemic potential of this new strain, designated serogroup 0139 synonym"Bengal", seems assured and is a new cause of concern throughout the developing world.

These recent experiences underline the need for effective cholera vaccines against disease due to 01 serogroup E1
Tor biotype of V. cholerae and Bengal 0139 serogroup of
V. cholerae.

The major issues which must be overcome to produce effective cholerae vaccines are safety, stability and a high degree of antigenicity. Because natural infection by and recovery from cholerae induces immunity lasting at least 3 years, much effort has been made to produce live, attenuated cholerae vaccines that, when administered orally, would mimic the disease in its immunization properties, but would not cause adverse symptoms or reactions in the immunized individual (i. e., vaccines which display low reactogenicity). Vaccines of this type involve deletion mutations that inactivate the gene encoding the A subunit of cholerae toxin, a protein which is responsible for most of the diarrhea seen in this disease. See, for example, Mekalanos, U. S. Patent Nos.

5,098,998 and 4,882,278, and Kaper et al., U. S. Patent
No. 4,935,364, hereby incorporated by reference. While both oral, killed whole cell vaccines and several live, attenuated cholerae vaccines have been developed, the most promising of these provide little protection against the E1 Tor biotype of V. cholerae and probably no protection against the 0139 serotype.

V. cholerae only causes disease when colonization of the small bowel occurs. This colonization is also required for the induction of a localized immune response, an important aspect of development of effective vaccines. It is thought that interaction and uptake of bacteria by Peyers patches is the essential step in the localized immune response pathway. Thus, colonization of the intestine can be divided into two distinct steps: 1) interaction with Peyers patches and subsequent immune responses; and 2) interaction with enterocytes and subsequent disease processes (reactogenicity). Although the factors affecting colonization are not well understood, they are believed to include the TcpA pili and motility.

Summary of the Invention
The invention features nontoxigenic genetically stable mutant strains of V. cholerae which are useful as a live, oral vaccines for inducing immunological protection against cholerae. The mutant strains are genetically engineered mutants which lack DNA encoding a functional ctxA subunit and which also have genetic defects causing them to be soft agar penetrationdefective. We have found that such mutants have extremely low reactogenicity in both clinical and laboratory tests, yet elicit a strong immune response.

As a result, the soft agar penetration-defective strains have the necessary and desirable characteristics of a human vaccine to V. cholerae.

By parental strain is meant any strain from which the mutant strain descends. Any number of mutations may be added to the parental strain prior to or subsequent to the introduction of the soft agar penetration-defective mutation.

By soft agar penetration-defective strain is meant a strain lacking the ability to penetrate a media of high viscosity as measured in vitro by swarming on and within agar media which is between 0.25 and 0.45% agar. Mutants which fail to penetrate soft agar are those which will not spread beyond a diameter of 2mM, most preferably imM, when stabbed or plated by dilution onto soft agar and incubated overnight at 30 . Soft agar penetrationdefective mutants may be filamentous, motility defective (Mot-), lacking flagella (Fla-), and/or show a decreased ability to bind HEp-2 cells (HEp-2-). The most preferable strains are Mot-Fla+ HEp-2-, or filamentous.

Filamentous strains are defined as those which appear elongated by microscopic examination, i. e. 25% or more cells appear to be greater than 15 nM in length under conditions of stationary phase growth. Preferably, 25% or more of cells appear greater than 15nM under conditions of logarithmic growth.

Mot-Fla+ strains are defined as those strains which have complete flagellum when inspected by electron microscopy, yet remain soft agar penetration-defective and show decreased or non-existent swimming behavior relative to the parent strain when observed in liquid medium. Useful Mot-Fla+ strains include strains which have disruptions of the motB gene described below or V. cholerae homolog of the motA gene from E. coli. Most involve deletion mutations that inactivate the gene encoding the A subunit of cholerae toxin, a protein which is responsible for most of the diarrhea seen in this disease. See, for example, Mekalanos, U. S. Patent Nos.

Summary of the Invention
The invention features nontoxigenic genetically stable mutant strains of V. cholerae which are useful as a live, oral vaccines for inducing immunological protection against cholerae. The mutant strains are genetically engineered mutants which lack DNA encoding a functional ctxA subunit and which also have genetic defects causing them to be soft agar penetrationdefective. We have found that such mutants have extremely low reactogenicity in both clinical and
TABLE 1. Flagellar and motility gene products of S.
typhimurium and E. coli and their known or
suspected functions
Gene product Function/location
Regulatory nroteins
FlhC, FlhD Master regulators of the flagellar
regulon
acting on class 2 operons.

Transcription initiation (a)
factors?
FliA Transcription initiation (a) factor for
class 3a and 3b operons.

FlgM Anti-FliA (anti-a) factor. Also known as
RflB. Active only when flagellar
assembly has not proceeded through
completion of the hook.

FliS, FliT, FliD? Repressor of class 3a and 3b operons (RflA
activity).

FljA Repressor of fliC operon.

Hin Site-specific recombinase, affecting fljB
promoter.

Proteins involved in the assembly process
FlhA, FliH, FliI Export of flagellar proteins? FlhA is
homolog of various virulence
factors. FliI is homolog of
the catalytic subunit on the
FoFl ATPase.

FlgA Assembly of basal-body periplasmic
P ring.

FlgD Initiation of hook assembly.

FliK Control of hook length.

FliB Methylation of lysine residues on the
filament protein, flagellin;
function of this modification
unknown.

Flagella structural components
FliG, FliM, FliN Components of flagellar switch, enabling
rotation and determining its
direction (CCW vs CW). FliM is also
implicated as a signalling protein.

MotA, MotB Enable motor rotation. No effect on
switching.

FliF Basal-body MS (Membrane and
Supramembrane)
ring and collar.

FliE Basal-body component, possibly at
(MS-ring)-rod junction.

FlgB, FlgC, FlgF Cell-proximal portion of basal-body rod.

FlgG Cell-distal portion of basal-body rod.

FlgI Basal-body periplasmic P ring.

FlgH Basal-body outer-membrane L
(Lipopolysaccharide layer) ring.

FlgE Hook.

FlgK, FlgL Hook-filament junction.

FliC, FljB Filament (flagellin protein). FljB (found in
S. typhimurium only) is an
alternative, serotypically
distinct, flagellin.

FliD Filament cap, enabling filament assembly.

Flaaellar proteins of unknown function
FlgJ, FlhB, FlhE, FliJ, FliL, FliO, FliP, FliQ, FliR.

Strains which are HEp-2-are defined as those strains which show a 5-fold or greater decrease in binding to HEp-2 cells relative to the non-soft agar penetration-defective mutant parent strain in the assay provided below.

By a ctxA subunit is meant the A subunit of the
V. cholerae toxin which is responsible, when functional, for many of the symptoms of cholerae (e. g., nausea, diarrhea etc.). Most preferably, the strains include deletion of the entire so-called"core genetic element", which includes not only the ctxA/B, but also a region known as icf (encoding Intestinal Colonization Factor, probably equivalent CEP"core encoded pilin") and zot, described in greater detail below. In preferred embodiments the strain is also att-.

The method by which the vaccine strains of the invention are made includes introducing a mutation causing a soft agar penetration-defective phenotype into a V. cholerae strain containing a mutation in the ctxA sequences. The V. cholerae soft agar penetrationdefective mutation preferably shows a reversion frequency of less than 1 X 10-9 mutant cells. Soft agar penetration-defective mutations may be isolated as spontaneous mutants or by genetic engineering of genes identified by transposon mutagenesis or by homology to genes previously identified in another enteric bacteria such as E. coli, S. typhimurium, species Bacillus,
V. parahaemolyticus, species Helicobacter, C. crescentus,
P. mirabilif, and B. Pertussis. Preferably, the gene identified by homology is one of the Fla, Mot or Che genes in Table 1, above. Most preferably the gene is either MotB or FliC.

The disruptions may be spontaneous mutation or may be genetically engineered deletions or insertions.

Preferably, the disruption is a deletion.

FliF Basal-body MS (Membrane and
Supramembrane)
ring and collar.

FliE Basal-body component, possibly at
(MS-ring)-rod junction.

FlgB, FlgC, FlgF Cell-proximal portion of basal-body rod.

FlgG Cell-distal portion of basal-body rod.

FlgI Basal-body periplasmic P ring.

FlgH Basal-body outer-membrane L
(Lipopolysaccharide layer) ring.

FlgE Hook.

FlgR, FlgL Hook-filament junction.

FliD Filament cap, enabling filament assembly.

Flaoellar proteins of unknown function
FlgJ, FlhB, FlhE, FliJ, FliL, FliO, FliP, FliQ, FliR.

Bah-2, Bah-3, Bengal-2, or Bengal-3, or the genetic equivalents thereof.

By genetic equivalent is meant any strain having the same combination of ctxA/B, attRSI, recA, and icf mutations as are present in the stated strains.

Because the Mot-sot agar penetration-defective strains show increased constitutive expression of toxin,
Tcp pili and hemolysin proteins, the strains may also be used in the manufacture of killed vaccine substrates.

In preferred embodiments, the invention includes a vaccine comprising at least two different strains of V. cholerae which are nontoxigenic genetically stable mutants which lack DNA encoding a functional ctxA subunit and are also soft agar penetration-defective. One of the two strains is preferably derived from an El Tor 01 strain and the other one is derived from a Bengal strain.

More preferably, one of the serotypes in the El Tor 01 component of the vaccine is an Ogawa serotype or an Inaba serotype. Most preferably, the vaccine includes Peru-15 and Bengal-15 as Peru-14 and Bengal-15.

Most preferably, the live or killed oral vaccine comprises at least two vaccine strains chosen from the soft agar penetration-defective derivatives of Bah-3,
Peru-3, Bang-3 and Bengal-3. Most preferably, the live vaccine includes Peru-15 and either Bengal-15 or strains bearing genetically engineered deletions of the genes conferring the soft agar penetration-defective phenotypes present in these strains. The preferable killed vaccine contains one strain of each of the serotypes Ogawa and
Inaba and one strain of the Bengal serotype. The most preferable killed vaccine contains Peru-15, Bah-15 and
Bengal-15 or strains bearing genetically engineered deletions of the genes conferring the soft agar penetration-defective phenotypes present in these strains.

Depending upon the relevant local epidemiology, the vaccine strains may be administered together in a single dose, or, more preferably, separately 7-28 days apart. Where only one of the serotypes presents a threat of disease, it may be preferable to-'minister a vaccine regimen comprising only one strain.

Strains such as those described above are useful as cholerae vaccines and are improved in their genetic properties compared with previous vaccines.

In another aspect, the invention provides substantially pure DNA encoding motB and fliC. By motB and fliC DNA is meant by the DNA sequence comprising the sequences in Figures 4 and 5, respectively, and fragments, deletions, disruptions, and homologous sequences thereof.

Substantially pure DNA is DNA that is not immediately contiguous with both of the coding sequences with which it is immediately contiguous (i. e., one at the 5'end and one at the 3'end) in the naturally-occurring genome of the organism from which the DNA of the invention is derived. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e. g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other
DNA sequences. It also includes a recombinant DNA which is part of a hybrid gene encoding additional polypeptide sequence.

Homologous refers to the sequence similarity between two polypeptide molecules or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same base or amino acid monomeric subunit, e. g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences. For example, 6 of 10, of the positions in two sequences are matched or homologous then the two sequences are 60% homologous. By way of example, the DNA sequences ATGCC and TATGGC share 50% homology.

Generally, homologous sequences exhibit at least 70%, more preferably 80%, and most preferably 95% homology with a segment of more than 60 nucleotides, or preferably more than 120 nucleotides or most perferably, the entire sequence of the naturally occurring motB or fliC gene.

Other features and advantages of the invention will be apparent from the following description of preferred embodiments thereof, and from the claims.

Detailed Description
The drawings will first be briefly described.

The Drawinqs
Fig. 1 is a photograph showing soft agar penetration-defective and soft agar penetrating strains in a soft agar penetration assay. A14456, left, is a wild-type V. cholerae serotype 0139 strain; A14456 Sm, middle, is a streptomycin resistant isolate of A14456; and VR1-16, right, is a derivative of A14456 which has an attRSl deletion.

Fig. 2 is a schematic diagram of the method used to isolate soft agar penetration-defective mutants using transposon mutagenesis.

Fig. 3 depicts the general characteristics of spontaneously isolated hypermotile, wild-type and nonmotile mutants.

Fig. 4 is the sequence of V. cholerae motB.

Fig. 5 is the sequence of V. cholerae fliC gene.

The invention features attenuated strains of V. cholerae that can be used as live oral vaccines to protect individuals against cholerae and potentially other diseases. We have discovered that V. cholerae strains which are soft agar penetrationdefective have surprisingly low reactogenicity when compared with soft agar penetrating strains.

Nonetheless, these strains have strong immunogenicity.

We believe these vaccines may interact strongly with
Peyers patch tissue without interacting strongly with entrocyte epithelium. When combined with disruptions of the ctxA gene, the soft agar penetration-defective mutations result in strains which are excellent vaccines for the prevention of cholerae in humans.

Without wishing to bind ourselves to a specific theory, we believe that the low reactogenicity of these strains stems from their inability to penetrate the mucosa of the intestine. The mucous layer of the intestine is thought to be viscous and mutants defective in penetration of soft agar might be deficient in penetration of this mucous. Although defective in penetration through mucous, these mutants may still present antigen to the Peyer patches, which are not covered by a thick mucous gel. Localization to the Peyer patches is important for an effective vaccine because the patches include antigen-sampling cells specific for IgA antibody production. As a result, penetration defective mutants are predicted to generally have low reactogenicity, yet be highly antigenic.

We have constructed both filamentous and non-motile mutant vaccines which demonstrate these features (see Examples 1-6, below). Mot-Fla+ mutants are one class of mutants defective in penetration of soft agar, however, other types of mutants, such as filamentous and Fla-mutants, also result in a soft agar penetration-defective phenotype (i. e., a non-swarming phenotype) and may be useful for vaccines.

Although decreased mucosal penetration is likely to be the primary reason for the success of the soft agar penetration-defective vaccines, we have also found that
Mot-strains display increased constitutive expression of toxin, Tcp pili and hemolysin genes. This increased expression may account for the enhanced immunogenicity of these strains. Paradoxically, the increased production of the Tcp pili does not cause increased reactogenicity; it may be that Tcp pilus-mediated adherence to the mucosa in these strains is of a nature which is either less disruptive to gut physiology or is dependent on a step which first requires motility to deliver the organisms to
Tcp host receptors.

I. Methods of constructing soft agar penetrationdefective vaccines
Parental V. cholerae strains.

Provided below in Table 2 is a list of strains which may be used to isolate soft agar penetrationdefective mutants which are useful vaccines. This table is not meant to be limiting, but rather is meant to provide examples of the types of strains which may be employed.

TABLE 2 STRAINS FOR VACCINE CONSTRUCTION
EMI14.1

<tb> <SEP> Strain <SEP> Serotype <SEP> Relevant <SEP> Genotype
<tb> Peru-2 <SEP> Inaba <SEP> Type-2 <SEP> CTX <SEP> deletion, <SEP> str
<tb> Peru-3 <SEP> Inaba <SEP> attRSI <SEP> deletion, <SEP> recA:: <SEP> htpP-ctxB, <SEP> str
<tb> Peru-4 <SEP> Inaba <SEP> Type-2 <SEP> CTX <SEP> deletion <SEP> recA <SEP> : <SEP> : <SEP> ctx-ctxB
<tb> Peru-5 <SEP> Inaba <SEP> attRS1 <SEP> deletion, <SEP> ZacZ:: <SEP> ctxP-ctxB, <SEP> str
<tb> Bang-2 <SEP> Ogawa <SEP> Type-2 <SEP> CTX <SEP> deletion, <SEP> str
<tb> Bang-3 <SEP> Ogawa <SEP> attRSI <SEP> deletion, <SEP> recA:: <SEP> htpP-ctxB, <SEP> str
<tb> Bang-5 <SEP> Ogawa <SEP> attRS1 <SEP> deletion, <SEP> lacZ:: <SEP> ctxP-ctxB, <SEP> str
<tb> Bah-2 <SEP> Inaba <SEP> Type-2 <SEP> CTX <SEP> deletion, <SEP> str
<tb> Bah-3 <SEP> Inaba <SEP> attRS1 <SEP> deletion, <SEP> recA::

<SEP> htpP-ctxB, <SEP> str
<tb> Bah-5 <SEP> Inaba <SEP> attRS1 <SEP> deletion, <SEP> recA <SEP> :: <SEP> ctxP-ctxB, <SEP> str
<tb> Bengal-2 <SEP> Bengal <SEP> Type-2 <SEP> CTX <SEP> deletion, <SEP> str
<tb> Bengal-3 <SEP> Bengal <SEP> attRS1 <SEP> deletion, <SEP> recA:: <SEP> htpP-ctxB, <SEP> str
<tb> Bengal-4 <SEP> Bengal <SEP> Type-2 <SEP> recA:: <SEP> ctx-ctxB
<tb> Bengal-5 <SEP> Bengal <SEP> attRSl <SEP> deletion, <SEP> recA:: <SEP> ctxP-ctxB, <SEP> str
<tb>
Note str under relevant genotype refers to streptomycin resistance.

This is a spontaneously mutated strain is resistant to 100 pg/ml of streptomycin as a result of a mutation in a ribosomal protein. All strains and the methods for making the same are described in
Mekalanos, U. S. Serial No. 08/083,388, filed June 28,1993. The parent strains are C6709-Sm (Peru-2), P27459-Sm (Bang-2), and E7946
Sm (Bah-2).

Construction of Vaccines with additional mutations.

In addition to the soft agar penetration-defective and ctxA mutations, the desirable vaccine may contain other mutations known to improve vaccine safety, reactogenicity and immunogenicity. The following are examples of useful mutations which may be employed.
attRSI deletions. In addition to having low reactogenicity, genetically engineered live attenuated cholerae vaccines are theoretically safe only if they cannot revert or otherwise regain the capacity to produce cholerae toxin. Strains which carry a single copy of the attRS1 sequence can efficiently acquire a new copy of the
CTX element through DNA transfer by either P factor conjugation or bacteriophage transduction. Thus, deletions which render V. cholerae devoid of RS1 and attRS1 sequences can prevent a vaccine strain from reacquiring the CTX genetic element in nature through its own site specific recombination system.

Methods of making RSI and attRSI deletions and parental vaccine strains containing these mutations are described in
Mekalanos, U. S. Serial No. 08/083,388, filed June 28, 1993, incorporated herein by reference. For example,
Peru-3, Bang-3, Bah-3 and Bengal-3 have these deletions and may be used as parental starting strains in the methods of the invention.

Rec-Mutations. The mutant strains described can be further improved as vaccine candidates by creating additional mutations within each strain that will serve to enhance the safety and immunogenicity of the vaccine.

With regard to safety, an additional mutation can be introduced into the recA gene of any of the strains described, which mutation is designed to inactivate that recA gene. Such double mutant strains will therefore be defective in recombination and will be unable to recombine with wild type strains of V. cholerae in the environment. Thus, they will be incapable of acquiring wild type toxin genes and expressing the CTX element.

Thus, a series of mutated derivatives can also be useful in the invention, each incorporating additional properties that render the strains safer, genetically more stable and more broadly immunogenic. The construction of such derivatives is described in
Mekalanos, U. S. Serial No. 08/083,388, filed June 28, 1993. icf and zot mutations. Recently, a new toxin called ZOT has been found to be encoded by the core region (Baudry et al., 1992, Infect. Immun. 60: 428-434). In addition, we have previously found evidence that Type-1 or Type-2
CTX deletion mutants described in Mekalanos, U. S. Serial
No. 08/083,388 filed June 28,1993, have decreased colonization and, therefore, enhanced vaccine characteristics. The gene deleted which causes decreased colonization is called icf (or"cep") and encodes ICF.

Icf is separate and distinct from zot and both may be useful in the preferred soft agar penetration-defective vaccine. Strains in Table 2 ending in"-2","-4"and"5" (e. g., Beng-2) contain the icf deletion and may be used as parental starting strains in the methods of the invention. In addition, the soft agar penetrationdefective strains in Examples 2,3 and 4 also contain icf deletions.

Isolation of spontaneous soft agar penetration-defective mutations of V. cholerae.

To obtain spontaneous soft agar penetrationdefective mutants, soft agar can be used to assess the ability of bacteria to penetrate a media of high viscosity (soft agar media which is 0.25-0.45% agar).

Spontaneous soft agar penetration-defective vaccines with a high therapeutic value include Peru-14, Peru-15, Bang15, Bah-15, and Bengal-15 (see Example 3, below).

Spontaneous soft agar penetration-defective strains may be isolated from any V. cholerae parent strain using the following method. V. cholerae cells are grown to stationary phase in test tubes in Luria broth (LB) without agitation (or are grown on LB plates) at 30 for 24-48 hours. The V. cholerae cells are then collected from the bottom of the test tube (or off the plate) and recultured by repeating the stationary 30 growth conditions. After the second cycle of growth cells are serially diluted sufficient to give one cell/1p1 and plated within 0.4% soft LB agar (100 1/plate) or repicked off the LB plate, onto soft agar if using the plate method. Plates are then incubated at 30 overnight (12-30 hours). Soft agar penetrating cells will give rise to spreading colonies, while soft agar penetration-defective mutants will yield pinpoint colonies of less than 2mM.

Cells from pinpoint colonies are then stabbed onto new soft agar plates. Those stabs which yield pinpoint colonies and not give rise to revertants (spreading cells) are useful soft agar penetration-defective mutant strains (for example, see
Figure 1).

Isolation of soft agar penetration-defective mutants by transposon mutagenesis.

Transposon mutagenesis allows the identification, sequencing, cloning and characterization of soft agar penetration-defective mutants without requiring any prior knowledge of the gene sequence, chromosomal location, etc. Furthermore, any gene useful for construction of soft agar penetration-defective vaccines may potentially be isolated using this technique. In addition, this technique allows an assessment of the nature of the soft agar penetration-defective phenotype prior to cloning, sequencing, etc., thereby minimizing laboratory effort required to construct vaccines. The protocol for transposon mutagenesis is depicted in Figure 2. The technique is described in Taylor et al., J. Bact.

171: 1870 (1989). Briefly, a transcriptional lacZ transposon carrying kanamycin resistance, is introduced into a soft agar penetrating parent V. cholerae strain which has an internal deletion of the lacZ gene. The transposon integrates randomly and integrants may be selected on LB media plates (1.5% agarase) with Kanamycin and XG indicator (5-bromo-4-chloro-3-indolyl- -Dgalactoside, Boehringer Mannheim, Indianapolis, IN).

Cells from Kanamycin resistant colonies are then individually stabbed onto 0.4% agarase medium, with
Kanamycin and XG indicator. Integrants with a soft agar penetration-defective phenotype are readily identified as non-spreading colonies (see below Figure 1). Soft agar penetration-defective colonies are then purified, retested, and chromosomal DNA is isolated. The transposon insertion junction may be sequenced, and the parent gene identified using inverse PCR (Lochman et al., in PCR Technology, H. A. Erlich ed., 1989. Stockton Press,
N. Y., N. Y. p. 105). Oligomeres useful for PCR sequencing are provided in Example 5, although other oligomeres may be readily synthesized and utilized using standard techniques. Once sequencing is performed the disrupted gene may be identified by homology to known enteric motility genes (see Table 2, below).

We have used this method to identify motB in cholerae (see Example 5). Once the gene conferring the desirable phenotype has been identified a knockout mutation which does not confer drug resistance may be generated using standard genetic engineering techniques, for example, those provided below.

Isolation of soft anar penetration-defective mutants by disruption of genes identified by homology cloning
The sequences of many genes encoding proteins necessary for mobility of enteric bacteria and thus penetration through soft agar are known. Because V. cholerae is so closely related (see Examples 5 and 6) to these enteric bacteria these sequences may be used to design degenerate oligonucleotides which may, in turn, be used to either sequence the V. cholerae homology by PCR or to isolate a clone bearing the gene from a V. cholerae
DNA library. If sequenced by PCR, the resulting sequence may be used to isolate a clone bearing the gene from a V. cholerae library. Using either method, a disruption of the gene by insertion or deletion may be made using standard molecular biology procedures (see Example 6) and the resulting mutant gene recombined into the vaccine strain.

Example 6 provides an additional cloning scheme which may be used to detect genes which may be mutated to confer SAP-D ph cap. Tweezers are then used to place a piece of carboncoated mica into the drop until the carbon lifts off and carbon is then caught on the mica and lifted into an inverted cap (from a Falcon 15 ml tube) full of stain (either 1% uranyl phosphate or 0.5% molybdenate.) Mica is allowed to fall to bottom of cap while carbon floats on surface. Floating carbon is picked up with small round copper grid and carefully blotted dry with Whatmann filter paper. The sample is then observed in the electron microscope and scored for the presence or absence of flagella.

Assay for HEp-2 adherence.

HEp-2 cells are commercially available from the
ATCC, Bethesda, MD (ATCC CCL23). Adherence may be determined relative to the parent-strain using the following protocol. V. cholerae cultures are grown overnight with aeration (in Rolodrum) in 5 mls LB at 30 C, then subcultured 1/100 and incubated at 30 C with aeration for approximately 2 hrs until the bacteria have reached midlog phase. V. cholerae cells are then washed 2 times in PBS (phosphate buffered saline) to remove any toxin. To achieve a multiplicity of infection (MOI) of 100, bacteria are added to wells with small round glass coverslips seeded with approximately 105 HEp-2 cells in
IMEM media with 5% fetal bovine serum and glutamine (2mM) without antibiotics.

V. cholerae cells are then spun down at 1000 rpm in desktop centrifuge for 10 minutes and
V. cholerae cells and HEp-2 cells are incubated for 20 minutes at temperature or 30 C. Suction is then used to remove fluid in wells and cells are washed by adding lml of PBS to each well, followed by suction removal. This washing is repeated 3 additional times. The slide is then fixed in methanol for 5 minutes at room temperature and then methanol is removed completely by suction.

Giemsa stain is added in a 1/12.5 dilution in H20 to each well and slides are allowed to sit for 25 minutes. Stain is then removed by suction and wells are washed 4 times with sterile water. Coverslips are then removed and slides are placed cell side up on paper towel and air dried. Coverslips are mounted cell side down onto glass slides using Pro-texx Mounting medium and allowed to set overnight. Cells are then observed and adherent bacteria are counted using light microscope.

Serological Characterization of Vaccine Strains.

Each derivative may be demonstrated to retain its expected serotype (i. e., the serotype of each of the mutants respective parental strain) by testing freshly harvested bacterial cells by slide agglutination using
Difco V. cholerae 01 Inaba or Ogawa typing serum or 0139 specific typing serum. We have tested all V. cholerae vaccine strains specifically described herein and these tests indicate that the strains still express the appropriate LPS antigens. Other tests may be used to demonstrate that mutant strains are prototrophic and still express Tcp pili (e. g., see Example 1). Thus, the mutants may be shown to express a number of properties that are important for their ability to be useful as live vaccine strains.

Colonization Properties of the Vaccine Strains.

To test the colonization properties of these vaccine strains, a mouse intestinal competition assay may be used as described in Taylor et al. (Proc. Natl. Acad.

Sci. USA. 84: 2833-2837,1987). This assay has been shown to yield results which correlate accurately with the colonization properties of mutant strains when they are subsequently tested in human volunteers (Herrington et al., J. Exper. Med. 168: 1487-1492,1988). The assay measures differences in colonization of a mutant strain by comparing its ability to compete for growth and survival with another closely related or isogenic strain.

In this assay, the mutant and competing strains are mixed in a ratio of approximately 1: 1 and then approximately one million cells of this mixture are introduced to the stomach of 3-5 day old suckling CD-1 mice. After 24 hours, the mice are sacrificed, the intestine was dissected, homogenized, and plated on bacteriological media containing an antibiotic which selects for both the strains. Colonies that grow after overnight incubation are then tested for additional markers which differentiate the mutant strain from the competing strain (i. e., resistance to kanamycin or hybridization with appropriate radioactive DNA probes).

Suckling mouse colonization assay.

Ratio of the fluid in the intestinal loops (ml) to the length (cm) (the FA ratio) may be determined as described by Baselski et al., Infect. Immun. 15: 704-712 (1977). Briefly, mice are inoculated with 2.5 x 106 to 6.0 x 108 CFU, as determined by plating dilutions of the inoculum on L agar. Both Swiss Webster (CFW) mice and
CD-1 mice may used for FA ratio determination.

The upper halves of the bowels from six to eight mice are pooled and homogenized with an Omni-Mixer, and the CFU per milliliter for each strain was determined by plating dilutions to appropriate antibiotic-containing Lagar plates. For determination of in vivo growth, the entire intestine is homogenized. The output ratio is then calculated.

III. Methods of Administering Soft Agar Penetration
Defective Vaccines.

Use of the Live Vaccine Strains
Vaccines derived from V. cholerae mutant strains
Peru-1, Peru-2, Bang-1, Bang-2, Bah-1, Bah-2, Bengal-2,
Bengal-3, or any of the additional mutants described herein are useful as sources of immunological protection against cholerae and other related toxigenic diseases when used as live vaccines. Other such diseases include, but are not limited to, those induced by enterotoxigenic
E. coli and other bacteria that produce toxins which are immunologically cross-neutralizable with cholerae B subunit.

When inoculated into the intestine of an experimental animal or human, mutant strains of V. cholerae should stimulate and induce a strong immunological response against all bacterial components that are elaborated by these strains including, but not limited to, the Ogawa and Inaba serotype 01 serogroup LPS antigens, flagella antigens, the antigenic domains of the
Tcp pili, and the outer membrane proteins. Based on published studies with other prototype cholerae vaccines, both IgA and IgG classes of antibodies directed against these bacterial components will be synthesized in the inoculated animal or human and will serve to protect the animal or human against subsequent challenge with virulent strains of V. cholerae.

Dosage
Determination of the appropriate dosage and administration of these vaccines is performed essentially as described in Herrington et al., (1988, J. Exper. Med.

168: 1487-1492). In general, such dosages are between, but are not limited to, 105-109 viable bacteria per dose.

Growth of Vaccine Strains
The bacteria to be used as the vaccine can be grown in a standard V. Cholerae laboratory media. The cells can be harvested and then lyophilized in a formulation that preserves viability (e. g., sterile skim milk or saline containing 5mM CaCl2 and 10% weight by volume of glycerol).

Administration
Administration of the vaccine involves combining the contents of two envelopes or vials, one containing the lyophilized vaccine strain or combination of strains, the other containing water and sufficient sodium bicarbonate or alternate buffer as to neutralize stomach acid (approximately 2 grams). The vaccine can then be swallowed by the vaccinee. Alternatively, the lyophilized vaccine can be incorporated into tablets which can be coated with an acid resistant"enteric coating". Such a form of vaccine can be administered to the vaccinee in one or more (up to three) doses spaced from a few days to several weeks apart. When used as a "booster"vaccine, the vaccine can also be administered to previously vaccinated individuals in one or more doses (up to three) spaced from a few days to several weeks apart.

When two or more strains are being administered they may be provided together, or in individual doses 728 days apart.

IV. Examples
The following examples are provided to illustrate not limit the invention.

Example 1: General features of motility and chemotaxis defective mutants
In order to determine the effects of motility on the expression of virulence factors, motility and chemotaxis mutants were isolated. Both spontaneous and transposon-induced mutants with altered swimming patterns were obtained. Spontaneous soft agar penetrationdefective (nonmotile) and hypermotile mutants were obtained, as were insertion induced soft agar penetration-defective mutants. Mutants were examined for cholerae toxin production, TCP expression, hemagglutination, hemolysis, adherence to HEp-2 cells, and ability to colonize infant mice.

In general, hypermotile mutants were defective in toxin and TCP production while nonmotile mutants showed increased toxin and TCP expression. These results suggest that virulence and motility are oppositely regulated. Although nonmotile mutants make TCP, they are unable to bind HEp-2 cells (see Fig. 3). Addition of agents that inhibit motility of wild-type bacteria were also found to abolish adherence to HED-2 cells, suggesting that motility itself is required for binding.

In vivo competitions between the mutants and wild-type V. cholerae in the infant mouse model reveal that both classes of mutants are dramatically attenuated.

These colonization defects exhibited by the hypermotile and soft agar penetration-defective mutants may result from the absence of toxin and TCP, the lack of adherence and motility, or the inability to reach the intestinal epithelium.

Example 2: Isolation filamentous mutants by spontaneous mutagenesis.

Peru-14 is soft agar penetration-defective, and, in addition, over 50% of Peru-14 cells are filamentous, with a spiral-like appearance and having a cell length of greater than 5 normal cell lengths (25nM, as opposed to the wild-type cells length of 5nM).

Peru-14 was isolated as a spontaneous soft agar penetration-defective derivative of the triply-deleted
Peru strain (Peru-3, ctxA-, att-, and recA") that was free from side effects but still retained the ability to colonize and act as a vaccine, as shown in below (Tables 3and 4).

Although Peru-14 was isolated based upon the theory stated above, this theory of function may or may not accurately and completely explain the effectiveness of Peru-14 as a vaccine. The usefulness of Peru-14 (or any other vaccine described herein) as an effective vaccine does not depend on the correctness of this theory.

Table 3
Outcome of Immunization with Freshly Harvested Peru-14
Cholerae Vaccine
Duration of
Dose Volunteer Symptoms Stool Excretion (cfu) if (days)/Peak day 2x106 28 Gas Formed 3/3
29 Cramps Formed 4/2
30 None Formed--
33 None Formed 4/4
34 None 336g 4/1
35 None Formed 3/3 gXlo8 25 None Formed 5/1
26 Gas Formed 3/1
27 Headache Formed 2/2
31 Nausea, Loss of Appetite Formed 7/4
32 None Formed 5/3
36 Cramps 63g+ 3/1
Volunteer had painless semi-solid stool at 72 hours post
immunization. Stool was culture-negative for Peru-14.

+ Volunteer had two small liquid stools at 48 hours post-immunization.

Stools were culture-positive for Peru-14.

Table 4
Comparison Reactogenicity with differing El TorO1 Vaccine
Strains
No. with significant
Strains No. with diarrhea other symtoms
Motile Strains 2/3 3/3
Bah-3 1/3 3/3
Bang-3 1/3 2/6
Peru-3 2/6 2/6
Motility-Deficient Strain2
Peru-14 1/21 2/21
Moderate to severe abdominal cramps, malaise, emesis, or
fever.

2 Peru-14 is a filamentous mutant of Peru-3 and is motilitydeficient
Specifically, the Peru-14 soft agar penetrationdefective strain was produced as follows. Peru-3 was grown overnight in LB broth containing 100 g streptomycin sulfate at 30 C. The culture was diluted to approximately 2000 cfu/ml and 0.1 ml was plated onto LB plates containing 100 Ag streptomycin. After incubating the plates overnight at 30 C, approximately 1000 colonies were toothpicked into soft agar plates (LB broth + 0.45%
Bacto-agar) and incubated overnight at 30 C. The inoculating toothpick is inserted only 1-2 mm into the surface of the soft agar plate. Of the 1000 colonies picked, 25 appeared to be non-penetrie ; Fing. Nonpenetrating isolates appear as colonies of approximately 2 mm in diameter, whereas penetrating isolates swarm on and within agar the agar to a diameter greater than 5 mm.

These colonies were repicked into soft agar once again, along with a known non-penetrating, non-motile cholerae strain and the original Peru-3 strain. One colony of the 25 was non-soft agar penetrating (when compared to the controls). This colony, designated Peru-14, was still
Inaba positive with agglutination sera, and produced the same level of B-subunit toxin as Peru-3 when tested in the B-subunit ELISA. The methods described above can be used for isolating soft agar penetration defective mutants of any V. cholerae strain. Non-revertible penetration-defective mutants, such as those harboring a genetic deletion, can be made using the methods described above.

Example 3: Isolation of spontaneous mutations which are soft agar penetration-defective and Mot-.

The spontaneous mutant isolation protocol described generally above has been used to isolate soft agar penetration-defective of Peru-2, Bang-2 and Bah-2 (all Rec+) Peru-3, Bah-3 and Bang-3, and Bengal-3 (all
Rec¯). All are Mot-Fla-by the electron microscopic assays. Rec-derivatives of Peru-3, Bah-3, Bang-3 and
Bengal-3 are termed Peru-15, Bah-15, Bang-15 and Bengal15, respectively, and have been further characterized.

The results of the mouse colonization assays are shown in
Table 6, below. All three strains showed a decrease in colonization relative to the soft agar penetrating parent strain.

Isolation of Peru-15
Peru-15 is a live attenuated oral cholera vaccine candidate derived from V. cholerae 01 El Tor Inaba (C6709) by deleting the cholera toxin CTX genetic element, introducing the gene encoding CT-B subunit into the rec A gene, and screening for non-motility. In a placebo-controlled clinical study, Peru-15 was orally administered to 11 North American volunteers at a dose of 2X108 cfu. No vaccinees developed diarrhea, and 10 shed vaccine organisms in stool. More than 200 Peru-15 stool isolates screened from all culture-positive volunteers showed no reversion to motility. Serologically, 10 vaccinees had > 4-fold increases in serum vibriocidal antibody titers (the correlate of cholera immunity); peak geometric mean titer (GMT) of 1710; range 400-6400. This results are tabulated in Table 4.

One month after vaccination, 5 random vaccinees and 5 control volunteers were challenged with virulent V. cholerae 01 (N6961). Four of the 5 controls developed cholera with a mean diarrheal volume of 1.9L. Two vaccinees developed diarrhea, 0.3 L and 1.0 L, respectively; the latter vaccinee had neither shed vaccine organisms nor responded serologically following
Peru-15 vaccination. Challenge data suggest that significant serum vibriocidal responses positively predict vaccine efficacy. These results are tabulated in
Table 5.

Table 4
Reactogenicity and Immunogenicity of Nonmotile
El Tor 01 Inaba Vaccine Strain Peru-15
Vaccinees Controls
No. with diarrhea 0/11 0.3
No. with severe symptoms1 1/11 0/3
No. positive for shedding2 8/11 0/3
No. seroconv. for vibriocidal Ab 10/11 0/3
Peak geometric mean vibriocidal 1,710 0/3
Ab titer 1 Defined as those symptoms interfering with normal
activities or requiring treatment. Single positive
vaccinee had a migraine headache and emesis at day 5.

2 Average peak geometric mean titer for vaccinees was
2X104 per gram of stool.

Table 5
Challenge Study of Vaccinees Immunized
with Nonmotile V. cholerae Strain Peru-15
Vaccinees Controls
No. of volunteers with diarrhea 2/5 4/5
Diarrheal stool volume 296/9611 458-3,830
No. with fever > 100.50/5 2/5
No. with emesis 0/5 2/5 1 The vaccinee producing 961 ml of diarrheal stool was also
the only vaccinee that did not seroconvert in vibiocidal
titer after vaccination.

Chemistry, Manufacturing and Control of Peru-15
At the wild-type (and Peru-2) recA locus, the mixture of BgIII and EcoRV, will generate two fragments: a-6.5kb fragment derived from the EcoRV site downstream of the recA locus and an EcoRV or BglII site further downstream in chromosome sequence; and an-3.5 kb
BglII/BglII fragment derived from a BglII site, upstream of, and a second BglII site, within, the recA locus.

Both fragments will hybridize with the recA probe: neither fragment will hybridize with the CTX core probes.

At the recA locus of successfully resolved merodiploids, these enzymes will generate a single, > 8kb, fragment derived from the BgIII site upstream of the RecA locus and an EcoRV or BgIII site further downstream in chromosome sequence. This fragment will hybridize with both the recA and CTX core probes.

Selection of a Motility Dysfunctional Isolate of Peru-3:
Isolation of Peru-15
A vial of the Peru-3 seed lot was sampled and used to inoculate a 3 ml suspension culture in Luria broth containing 100 Rg/ml streptomycin. Incubation at 30 C, without shaking, was continued for 16 to 18 hours.

Approximately 2.9 ml of the culture medium was aspirated from the culture in a manner such as to leave the cell suspension at the bottom of the tub minimally disturbed.

The residual cell suspension was removed from the tube and transferred into another culture tube containing 3 ml of Luria broth containing 100 yg/ml streptomycin.

Incubation, aspiration, and reinoculation was repeated four additional times.

Following the fifth passage, cells from the bottom of the culture tube were diluted and plated onto Luria agar plates containing 100 yg/ml streptomycin. Sixtyeight single colonies were sampled from the agar surface with sterile toothpicks and stabbed into motility agar plates (0.4% agar, Luria broth. 100 yg/ml streptomycin).

Dysfunctional motility was defined as reduced spreading from the site of inoculation, when compared to Peru-3, following overnight incubation at 30 C. 15 of sixtyeight isolates exhibited dysfunctional motility. Each of the 15 motility dysfunctional colonies were sampled from the motility plates and used to inoculate a 3 ml Luria broth. 100 yg/ml streptomycin, suspension culture, which was incubated overnight, at 30 C with shaking.

A 100/il aliquot of each overnight suspension was used to inoculate another 3 ml suspension culture which was incubated overnight, at 30 C without shaking.

Approximately 2.9 ml of the culture medium was aspirated from each of the 15 cultures in a manner such as to leave the cell suspension at the bottom of the tub minimally disturbed. Cells from the bottom of the 15 culture tubes ere streaked onto 15 Luria agar plates containing 100 g/ml streptomycin, which were incubated overnight at 30 C. From each of the 15 Luria agar plates, 25 single colonies were sampled with sterile toothpicks and stabbed into individual motility agar plates (0.4% agar, Luria broth. 100 yg/ml streptomycin). On two of the plates all colonies exhibited dysfunctional motility; the colonies on these plates had been derived from two of the original 15 isolated, #2-29 and #2-35.

Clinical Testing of Bengal-15
Bengal-15 has been tested in human trials with favorable results relative to the control strain M010, as shown in Table 7. Only one of the four human recipients of the vaccine developed any diarrhea, and this was minor. All four subjects showed significant intestinal colonization. Table 8 provides a detailed listing of systemic symptoms following ingestion of Bengal-15 by volunteers. Tables 9,10 and 11 show the favorable challenge results achieved when wild-type cholera was given to volunteers previously immunized with Bengal-15.
Results with unvaccinated volunteers also challenged with wild-type cholera are provided as a control.

TABLE 6
Mouse Colonization Data on Motile and Nonmotile
Vibrio cholerae Vaccine Strainsa
Serogroup/
Strain Motility Biotype/Average
Serotype CFU/mouse
Bah-3 Yes 01/E1 1.3 x 106
Tor/Ogawa
Bah-15 No 01/E1 5.2 x 105
Tor/Ogawa
Bang-3 Yes 01/E1 1.2 x 107
Tor/Inaba
Bang-15 No 01/E1 7.0 x 105
Tor/Inaba
Bengal-3 Yes 0139/Bengal/1.4 x 107
Bengal-15 No 0139/Bengal/6.3 x 106 a Strains were orally administered to 3-7 day old CD-1 mice. After 18 hours, mouse intestines were removed, homogenized, and plated for viable counts (colony forming units, CPU). Each strain was tested in 4-5 mice and the values reported are averages. Note also that in control experiments, non-colonizing strains (such as TcpA negative mutants) give average CFU/mouse values of less than 1 x 102.

TABLE 7
CLINICAL RESPONSE TO WILD TYPE (M010) AND
ATTENUATED 0139 Cholerae VACCINE PROTOTYPES
EMI35.1

<tb> <SEP> Volunteer <SEP> Age <SEP> Symptoms <SEP> Diarrheal <SEP> Number <SEP> of <SEP> Culture <SEP> TCN
<tb> <SEP> Letter <SEP> Race <SEP> Stool <SEP> Diarrheal <SEP> (Date <SEP> of <SEP> Treat
<tb> <SEP> Code <SEP> Sex <SEP> Volume <SEP> stools <SEP> Positive)

<SEP> ment
<tb> <SEP> M010
<tb> <SEP> A <SEP> 40/B/F <SEP> malaise <SEP> 276 <SEP> 2 <SEP> 12/2-3 <SEP> 12/1
<tb> <SEP> gurgling
<tb> <SEP> E <SEP> 30/B/M <SEP> malaise <SEP> 1257 <SEP> 7 <SEP> 11/30-12/1
<tb> <SEP> gurgling <SEP> 12/4
<tb> <SEP> cramps
<tb> <SEP> F <SEP> 18/W/F <SEP> malaise <SEP> 758 <SEP> 6 <SEP> 12/1-2 <SEP> 12/1
<tb> <SEP> gurgling
<tb> <SEP> cramps
<tb> <SEP> T <SEP> 100.4
<tb> <SEP> VRI-16
<tb> <SEP> B <SEP> 35/B/F <SEP> None <SEP> 0 <SEP> 0 <SEP> Negative <SEP> 12/5
<tb> <SEP> G <SEP> 22/B/M <SEP> None <SEP> 0 <SEP> 0 <SEP> 12/2,12/5
<tb> <SEP> 12/4
<tb> <SEP> K <SEP> 21/B/F <SEP> cramps <SEP> 0 <SEP> 0 <SEP> 12/2 <SEP> 12/5
<tb> <SEP> 0 <SEP> 37/B/F <SEP> None <SEP> 0 <SEP> 0 <SEP> 12/2 <SEP> 12/5
<tb> <SEP> BENGAL-3
<tb> <SEP> C <SEP> 36/B/M <SEP> gas <SEP> 0 <SEP> 0 <SEP> 12/3,

12/5
<tb> <SEP> 12/5
<tb> <SEP> I <SEP> 21/W/M <SEP> None <SEP> 0 <SEP> 0 <SEP> 12/2, <SEP> 12/5
<tb> <SEP> 12/4
<tb> <SEP> L <SEP> 26/B/M <SEP> cramps <SEP> 312 <SEP> 12/1-4 <SEP> 12/2
<tb> <SEP> N <SEP> 38/B/M <SEP> malaise, <SEP> 0 <SEP> 0 <SEP> 12/1 <SEP> 12/4
<tb> <SEP> cramps
<tb> <SEP> BENGAL-15
<tb> <SEP> D <SEP> 28/B/M <SEP> cramps <SEP> x <SEP> 3 <SEP> d <SEP> 0 <SEP> 0 <SEP> 12/1,

12/5
<tb> <SEP> 12/3
<tb> <SEP> H <SEP> 28/W/M <SEP> none <SEP> 0 <SEP> 0 <SEP> 12/4 <SEP> 12/5
<tb> <SEP> J <SEP> 24/W/M <SEP> malaise <SEP> 160* <SEP> 1 <SEP> 11/30-12/3
<tb> <SEP> 12/3
<tb> <SEP> M <SEP> 32/B/M <SEP> none <SEP> 0 <SEP> 0 <SEP> 12/1 <SEP> 12/5
<tb> * = not scored as diarrhea because volume less than 30mis
Table 8
Systemic Symptoms Following Ingestion of Nonmotile
0139 Vaccine Strain Bengal-15
Bengal-15 Butter Control
Number of volunteers 10 3 % excreting vaccine 90 0 % with diarrhea 0 0 % with other symptoms
Headache 50 33
Muscle aches 0 33
Malaise 30 66
Abdominal gurgling 40 33
Abdominal cramps 40 66
Stomach gas 70 100
Table 9
Bengal-15 Immunological Response in Volunteers
Vibriocidal antibody1 Peak anti-CT-B
Titers2
Day 0 Day 14 Day 28
Vaccinees
1 < 5 640 160 15
2 20 80 10 < 5
3 < 5 640 640 15
4 < 5 80 40 15
5 < 5 640 80 < 5

6 < 5 640 160 15
7 < 5 320 160 15
8 < 5 160 40 15
9 < 5 160 < 5 45
10 < 5 < 5 < 5 < 5
Controls
1 < 5 < 5 < 5 < 5
2 < 5 < 5 < 5 < 5
3 < 5 < 5 < 5 < 5
T M01OT4 used as the target strain in the vibriocidal assay.

2 Anti-CT-B titers are expressed as peak reciprocal values.

Table 10
Bengal-15 Challenge Studyl
Immunization status Bengal-15 Controls
Number of volunteers 7 6
Diarrhea attack rate 1 (14%) 5 (85%)
Mean no. diarrheal stools 3 12
Mean diarrheal output (L) 0.4 3.7
Incubation period (mean h) 95 h 26 h
Excretion of challenge strain 3 (42%)
Vaccine efficacy 83%
Fishers exact test 1-tail P=0.025 1 Challenge was a single 5x106 dose of V. cholerae 0139
strain M010
Table 11
Challenge Study1 Bengal-15 of Vaccinees and Control
Subjects
Diarrheal stool No. of
Incubation
Vaccinees output volume (ml) Diarrheal stools period (hrs)
1 0 -
2 0 -
3 394 395
4 85 122
5 0 ¯ ¯
60-
7 0 ¯ ¯
Controls
1 4876 1021
2 0 0 0
3 7800 22 45
4 1374 6 21
5 3015 13 22
6 1667 7 20 1 V. cholerae 0139 strain M010 was given at a dose of 5X106
cfu.

Example 4: Isolation of soft agar penetration-defective strains by transposon mutagenesis.

A. Identification and sequencing of motB in V. cholerae
Transposon insertions in V. cholerae strain 0395 (Lac-) were generated using the protocol provided above and depicted in Figure 2. Virtually any V. cholerae strain may, however, be used in with the Tnlac transposon used this protocol so long as it is Lac-.

Using this protocol, Mot-Fla+ and Mot-Fla-soft agar penetration-defective strains were obtained. We then sequenced the insertion joints from one of the Mot-Fla+ mutants.

DNA from Tnlac is sequenced using the following protocol. Chromosomal DNA was made from the Tnlac insertion strains using standard protocols. 1-2 Ag of
DNA was then cut overnight with an enzyme chosen from the following group: Pstl, Tagl, SacII, Xhol, Aval, Mscl,
BanL, Ddel, TthIII (those in bold are most preferable).

DNA was Phenol extracted with 2X phenol and 2X chloroform, then ethanol precipitated. Dried digested sample were resuspended in 10 l and 0.5 Zg of digested
DNA was then put in sterile Eppindorf tubes (1.5ml) with 150 Al sterile water, 50 l 10 x T4 DNA ligation buffer (with neither BSA nor spermidine) and 500 units of T4 DNA
Ligase were added. The test tube was then incubated 1216 hrs. at 14 C. 50p1 (1/10) of the mixture was used to do PCR. Ligated DNA was de-salted in spin columns followed by ethanol precipitation prior to PCR.

PRC conditions are as follows. 30 cycles were done at 95 C for 1', 50 C for 2'and 73 C 2.'The following primers may be used to sequence all Tnlac insertion junctions:
5'CCATCTCATCAGAGGGTAGT 3' (SEQ ID No. l)
(this oligonucleotide reads into the transposon)
5'ACCATGTTAGGAGGTCACAT 3' (SEQ ID No. 2)
(this oligonucleotide reads out the right end of the transposon).

Products of the PCR reaction were put over a column to remove primers and sequencing was done directly, although bands may be gel purified using low melting agarase run on a high % gel followed by cutting out on the band in a small volume and heating at 65 C for 10'. When bands are cut out using the later method 1 unit of agarase is used for every 100 l of gel, and the agarase mixture is then incubated for 1 hour at 37 C, and then sequencing is done directly.

B. Construction of deletions for use in V. cholerae vaccines.

Once the sequence of the gene of interest has been determined and the loss of function phenotype has been determined to be desirable for vaccine use, full length clones may be obtained from V. cholerae libraries and disruptions (deletions or insertions which have a low reversion frequency) may be constructed using standard protocols in molecular biology and as described herein.

These deletions may then be recombined into the chromosome using the techniques provided, for example, in
Mekalanos'U. S. Serial No. 08/083,388, filed June 28, 1993.

The insertion points of one soft agar penetrationdefective transposon insertion were sequenced to demonstrate the identification of these putative motility and chemotaxis genes. The gene was determined to be the
V. cholerae homolog of E. coli motB (see Table 2 and Fig.

4, SEQ ID No. 3). The accuracy of this determination is supported by the finding that this insertion mutation confers a Mot-Fla+ phenotype, as would be expected for a motB insertion in E. coli
Example 5: Isolation of soft agar penetration-defective mutants bv homology cloning and disruption: cloning of fliC.

The method used to isolate the V. cholerae fliC homologue is provided in Mekalanos and Camilli, U. S. patent application filed on September 28,1993, hereby incorporated by reference). Briefly, the method is as follows: a plasmid vector pIVET5 was constructed which allows one to screen for bacterial genes which are induced in host tissues. Random partially digested
Sau3AI DNA fragments of the V. cholerae chromosome were cloned into a single BamHI restriction site in pIVET5 immediately 5'to a promoterless synthetic operon consisting of a site-specific DNA recombinase and the E. coli lacZY reporter coding sequences. The recombinant plasmid library was moved into a V. cholerae reporter strain that contains a lacZ:: resi-tet-resl allele on the chromosome (V. cholerae lacZ gene not E. coli.

The plasmids behave as suicide vectors in V. cholerae and must therefore integrate into the chromosome by homologous recombination. Transcriptional fusions of V. cholerae chromosomal genes to the promoterless synthetic operon on the integrated plasmid can result, upon induction of the chromosomal gene promoter, in expression of the site specific recombinase and lacZY reporter genes. The recombinase specifically catalyzes recombination at the resl sequences flanking the tet gene, resulting in excision of the tet gene and subsequent loss of tetracycline resistance in descendent bacteria. To screen for V. cholerae genes which are induced in the suckling-mouse model of cholerae, we screened for and pooled tetracycline resistant, Laccolonies in vitro on L-agar plates supplemented with tetracycline and XG.

These represent bacteria having no or transcriptionally inactive gene fusions to the promoterless synthetic operon on the integrated plasmids.

These colonies were pooled together and used to orally infected suckling mice. After 24 hours bacteria were recovered form the small intestines and plated on L-agar.

Resultant colonies were replica-plated to L-agar supplemented with tetracycline to screen for colonies which were tetracycline sensitive. These represent bacterial clones having a chromosomal gene or operon fused to the synthetic operon on the integrated plasmid which was induced at some time during infection of the mice. The integrated plasmid was cloned from one such strain. The fusion junction was sequenced using an outward reading oligonucleotide primer complementary to the 5'end of the site-specific recombinase gene and standard techniques.

One such clone, designated AC-V45-2 had a transcriptional fusion of the synthetic operon on the integrated plasmid to a gene on the V. cholerae chromosome divergently transcribed from the V. cholerae fliC homologue (see homology figure below). FliC is the major protein, flagellin, which comprises the flagella in many bacterial species. The identity of the gene or operon fused to the synthetic operon is unknown at this time. However, it presumably is involved in motility as is the case for S. typhimurium where immediately upstream and divergently transcribed from fliC is the fliDST operon encoding a putative flagella cap protein and two regulatory genes, respectively (Macnab review). Thus, our method has indirectly identified the fliC homologue of V. cholerae by directly identifying physically linked gene (s) that may be involved in motility.

This method may allow identification of other gene (s) involved in motility of V. cholerae.

Deletion of the V. cholerae fliC gene to generate an aflagellate mutant strain can be easily accomplished as follows. The entire fliC gene can be cloned from AC
V45-2 by digesting chromosomal DNA with an infrequentcutting restriction enzyme such as SaII which has a site downstream of the synthetic operon on the integrated plasmid, but which does not have sites within the synthetic operon nor within the sequenced portion of fliC. This DNA fragment will contain most if not all of fliC as well as the synthetic operon. The entire chromosomal SaII digested DNA will be cloned into the
SaII site of pBR322 (Watson, N. (1988) Gene 70: 399-403) by ligation, electroporated into E. coli, DN5a, and LacZ+ bacteria screened for on L-agar supplemented with ampicillin and X-gal. Such LacZ+ clones will contain the sought-after recombinant plasmid containing fliC and the synthetic operon.

The fliC gene will be restriction enzyme mapped using standard techniques. A nonrevertible mutation in fliC consisting of a deletion of a large internal fliC DNA fragment will be made using the appropriate restriction enzymes followed by selfligation. The AfliC allele on the resulting plasmid will be used to replace the wild-type fliC gene on the bacterial chromosome by allele exchange using the previously described and commonly used technique of double crossover via homologous recombination (Hamilton,
C. (1989) J. Bacteriol. 171: 4617-4622). The AfliC mutation in the resulting V. cholerae strain will be confirmed by southern blot analysis using a fliCcontaining DNA plasmid probe. Such a strain will be nonmotile and aflaggellate because the flagellin protein will not be made due to deletion of fliC.

This technique of allelic exchange can be used to generate non-reverting deletion mutations in any of the motility genes of V. cholerae.

Example 6. Bivalent Vaccine Results
The most straightforward approach for testing a bivalent vaccine is to make determination of whether both vaccine candidates can co-colonize the mouse and rabbit intestine. The infant mouse colonization model has proven valuable in predicting the level of V. cholerae colonization in the human intesting Pearson et al., PNAS
USA, 90: 3750-3754, (1993)), and the adult rabbit immunogenicity model has proven valuable in predicting the immunogenicity of V. cholerae in humans, (Albert et al., Proceeding of the 29th Joint Conference, U. S.- Japan
Cooperative Medical Science Program and Related Diarrheal
Diseases. Monterey, CA (1993)).

The aim of the present experiment was to determine whether 01 vaccine candidates can colonize the mouse and rabbit intestine compatibly with 0139 vaccine candidate Bengal-15 and, most importantly, provoke 01-and 0139-specific immune responses in the rabbit. We have found that both cocolonization and immunogenicity can be achieved with a bivalent vaccine.

Infant mouse colonization study:
Administration protocol: three to five day old sucking
CD-1 mice housed 5 mice per group were inoculated orally with 50 Sl of V. cholerae in Luria broth using PE-10 tubing on the end of a lcc syringe. After 24 hours, the mice were sacrificed by CO2 narcosis, and the small intestines were harvested. Intestines were homogenized, diluted and plated on Luria agar containing 100 sol streptomycin sulfate. The results follow.

Input cfu Output cfu
Peru-14 3.4x105 4.8x105
Bengal-15 6.9x104 7.4x103
Five mice per group
Adult rabbit immunogenicity study:
Immunization protocol: 9-11 week old, 1.5-2 kg, male SPF
New Zealand white rabbits from either Hazelton Research
Products or Charles River Laboratories are housed individually in stainless steel caging allowing 4 square feet per rabbit. Rabbits are fasted overnight. Rabbits are then anesthetized with 30 mg/kg Ketamine and 3 mg/kg
Zylazine plus Acepromazine intramuscularly (IM). If needed, an additional 15 mg/kg Ketamine is delivered IM to maintain sedation. A prebleed is drawn from the auricular artery. A rectal swab using a sterile cotton tipped applicator is taken and plated on TCBS agar. At time 0,50 mg/kg cimetidine is delivered IV to the marginal ear vein.

At time=15 minutes 10 ml NaHCO3 is delivered by orogastric feeding tube attached to a 30 cc syringe. At time=30 minutes another 10 ml NaHCO3 is delivered orally, followed by immediately by the dose of
V. cholera in 10 ml LB media delivered orally. At time=60 minutes, 1 ml of tincture of opium containing 10 mg morphine is delivered intraperitoneally (IP). The rabbits are then returned to their cages are allowed to eat and drink. Rectal swabs are taken on days 1,3,5, 7,14,21, and 28. Weekly bleeds to recover sera are done on days 7,14,21, and 28 following inoculation. On day 28, animals are sacrificed by first sedating by IM injection of ketamine/xylazine (44 mg/kg ketamine, 2.5 mg/kg xylazine) followed by lateral ear vein injection of the lethal dose of sodium pentobarbital 1 ml/10 lbs. The results are shown in Table 12.

Example 4: Isolation of soft agar penetration-defective mutants by Streptomycin Selection: VR1-16
Vibrio choleraee serotype 0139 strain AI4456 was isolated from a cholerae patient in Dhaka, Bangladesh in
March, 1993. Approximately 109 cells were suspended in 1 ml Luria broth containing 100 pg/ml streptomycin, centrifuged, and resuspended in 1 ml Luria broth containing 100 Mg/ml streptomycin. A 0.1 ml aliquot was plated on Luria agar containing 100 ssg/ml streptomycin and incubate overnight at 37 C. Several thousand colonies were obtained. Eight colonies were picked and restreaked on Luria agar containing 100 ssg/ml streptomycin, and grown overnight at 37 C. One of the isolates was observed to be nonmotile on soft agar and on microscopic examination. (See Fig. 1).

Plasmid pAR62 was introduced to this isolate by conjugation as a means of generating a core att RSI deletion (see Mekalanos,
USSN 08/803,388, filed June 28,1993). A single exconjugate was picked and grown overnight at 37 in Luria broth containing 100 pg/ml streptomycin and 1.25 pg/ml tetracycline. This culture was plated on Luria agar containing 100 pg/ml streptomycin, and colony lifts were prepared and probed with the RS1 probe. From approximately 2000 colonies screened, one was identified as negative for RS1 hybridization. This isolate was also negative for hybridization with the CT-1 probe. It was designated VRI-2. The ctxB gene was reintroduced under the control of the htpG promoter using plasmid pDB6891, a derivative of pJM6891 containing the htpP-ctxB construct inserted into the V. cholerae lacZ gene.

Plasmid pDB6891 was introduced into VRI-2 by electrotransformation, and a single transformant was grown overnight in Luria broth containing 100 pg/ml ampicillin, subcultured into Luria broth containing 100 pg/ml streptomycin and 75Ag/ml Xgal.

White colonies were picked and scored for sensitivity to ampicillin. An ampicillin sensitive, white colony was picked and designated VRI-16. Integration of the htpctxB construct at lacZ was confirmed by Southern blot analysis and production of cholerae toxin B subunit was confirmed by GM1 ELISA.

In mouse colonization assays VR1 resulting in colonization at levels of 4.5 x 103 CFU/mouse.

Furthermore, human subjects who took VRI-16 showed no clinical symptoms and none of the four subjects had diarrheal stool. All but one subject had significant colonization of the intestine.

The method used to make VR1-16 may be used to obtain additional soft agar penetration-defective vaccine strains; we have found that streptomycine selection, as described, results in a soft agar penetration-defective phenotype in approximately 14% of the resistant mutants obtained.

SUMMARY OF RABBIT IMMUNE RESPONSE DATA
FROMPERU AND BENGAL ORAL IMMUNIZATIONS
VIBRIOCIDAL (01) VIBRIOCIDAL (0139) CtxB ELISA 0 13 21 28 0 13 21 28 0 14 21 28
Peru-14/Benga)-15 < 25 1600 1500 1600 < 25 100 200 400 < 10 < 10 80 160 (2X109) (8x109)
Peru-14/Bengal-15 < 25 200 200 200 < 25 200 200 200 < 10 < 10 80 160 (7x108) (1x1010)
Peru-14/Bengal-15 < 25 400 400 400 < 25 100 100 100 < 10 < 10 < 10 < 10 (4x109) (1x109)
Peru-15 < 25 3200 3t00 3200 < 25 < 2S < 25 < 25 < 10 < 10 < 10 < 10 (9x109)
Peru-15/Bengal-15 < 25 800 1600 3200 < 25 100 100 100 < 10 < 10 160 160 4x109)(6x109)
Peru-15/Bengal-15 < 25 200 nd nd < 25 < 25 nd nd nd nd nd nd @@@09) (3x109)
Peru-15/Bengal-15 < 25 25 nd nd < 25 200 nd nd nd nd nd nd (1x109) (6x109)
Peru-lS/Bengal-15 < 2S 401 nd nd < 25 200 nd nd ad nd nd nd (6u10 ! xl
V.

Deposits
Under the terms of the Budapest Treaty on the
International Recognition of the Deposit of
Microorganisms for the Purpose of Patent Procedure, deposit of V. cholerae strains C6709-Sm, P27459-Sm,
E7946-Sm, Bengal-2, Bengal-3, MO10, VRI-16, Bengal-15,
Peru-14, Peru-15, Bah-15, and Bang-15 have been made with the American Type Culture Collection (ATCC) of Rockville,
Maryland, USA, where the deposits were given ATCC
Accession Numbers ATCC 55331 (C6709-Sm) deposited June 24,1992; ATCC 55333 (P27459-Sm) deposited June 24,1992;
ATCC 55332 (E7946-Sm) deposited June 24,1992; ATCC 55436 (0139, Bengal-2) deposited June 14,1993; ATCC 55437 (0139, Bengal-3) deposited June 14,1993; ATCC 55438 (0139, M010) deposited June 14,1993; ATCC 55463 (Bengal15) deposited August 10,1993; ATCC 55446 (Peru-14) deposited June 30,1993; ATCC (Peru-15) deposited
December 2,1994;

ATCC (Bah-15) December 2,1994; deposited ATCC (Bang-15) deposited December 2, 1994.

Applicants'assignees, President and Fellows of
Harvard College and Virus Research Institute, Inc., represent that the ATCC is a depository affording permanence of the deposit and ready accessibility thereto by the public if a patent is granted. All restrictions on the availability to the public of the material so deposited will be irrevocably removed upon granting of a patent. The material will be available during the pendency of the patent application to one determined by the Commissioner to be entitled thereto under 37 C. F. R.

1.14 and 35 U. S. C. µ 122. The deposited material will be maintained with all the care necessary to keep it viable and uncontaminated for a period of at least five years after the most recent request for the furnishing of a sample of the deposited material, and in any case, for a period of at least thirty (30) years after the date of deposit or for the enforceable life of the patent, whichever period is longer. Applicants'assignees acknowledge their duty to replace the deposit should the depository be unable to furnish a sample when requested due to the condition of the deposit.

Further embodiments of the invention are within the following claims:

Claims

CLAIMS: 1. A vaccine comprising a nontoxinogenic genetically stable mutant strain of V. cholerae, said mutant strain being a mutant of a parental strain, said mutant strain lacking DNA encoding a functional CtxA subunit, and said mutant strain further exhibiting a soft agar penetration-defective phenotype relative to said parental strain.

2. The vaccine of claim 1, wherein said mutant strain is further lacking any functional attRSl sequences.

3. The vaccine of claim 1, wherein said mutant strain is derived from a parental strain belonging to the E1 Tor biotype.

4. The vaccine of claim 3, wherein said parental mutant strain is of the Inaba or Ogawa serotype.

5. The vaccine of claim 1, wherein said mutant strain is derived from a parental strain belonging to the non-01 serogroup.

6. The vaccine of claim 5, wherein said parental mutant strain is of the Bengal 0139 serogroup.

7. The vaccine of claim 6, wherein said parental strain is Bengal-2.

8. The vaccine of claim 7, wherein said parental strain is Bengal-3.

9. The vaccine of claim 4, wherein said parental strain is Peru-2.

10. The vaccine of claim 4, wherein said parental strain is Peru-3.

11. The vaccine of claim 10, wherein said mutant strian is Peru-15.

12. The vaccine of claim 4, wherein said parental strain is Bah-2.

13. The vaccine of claim 4, wherein said parental strain is Bah-3.

14. The vaccine of claim 13, wherein said mutant strain is Bah-15.

15. The vaccine of claim 4, wherein said parental strain is Bang-2.

16. The vaccine of claim 4, wherein said parental strain is Bang-3.

17. The vaccine of claim 16, wherein said mutant strain is Bang-15.

18. The vaccine strain of claim 1, wherein said mutant strain lacks CTX core sequences.

19. The vaccine strain of claim 1, wherein said mutant strain further lacks a functional recA gene.

20. The vaccine of claim 19, wherein said strain is ctx.

21. The vaccine strain of claim 1, wherein said strain further encodes a B subunit of cholerae toxin.

22. A vaccine comprising at least two different strains of V. cholerae according to claim 1.

23. The vaccine of claim 21, wherein one of said strains is derived from Peru-3 and one of said strains is derived from Bengal-3.

24. The vaccine of claim 22, one of said strains being Peru-14 and the other being Bengal-15.

25. The vaccine of claim 22, one of said strains being Peru-15 and the other being Bengal-15.

26. The V. cholerae strain of claim 1, wherein at least 25% of the cells of said strain are capable of forming filamentous structures of 15nM or greater under conditions of stationary phase growth.

27. The vaccine of claim 1 where said strain is in a physiologically acceptable carrier.

28. The vaccine of claim 26, wherein said strain is Bengal-15.

29. The vaccine strain of claim 1, wherein said mutant strain is Mot-.

30. The vaccine strain of claim 29, wherein said Mot-phenotype is resulting from a genetically engineered disruption of a motility gene.

31. The Mot-train of claim 29, wherein said Mot-phenotype is resulting from a disruption of the motB gene.

32. The vaccine of claim 1, wherein said mutant strain is Fla-.

33. A vaccine strain of claim 32 wherein said Fla-phenotype is resulting from a genetically engineered disruption of a flagellar gene.

34. The Fla-vaccine of claim claim 29, wherein said Fla-phenotype is resulting from a disruption in the fliC gene.

35. The vaccine of claim 1, wherein said strain has a 5-fold or greater decrease in HEp-2 binding relative to said parent strain.

36. A method of vaccinating against cholerae by administering any of the vaccines of claim 1.

37. A method of making a killed V. cholerae vaccine, said method comprising the steps of providing at least one of the mutant strains exhibiting a soft agar penetration-defective phenotype of claim 1, which strains have been killed; adding to said killed strains cholerae toxin B subunit produced by at least one of said strains, wherein said toxin B subunit is obtained from the medium in which said strain was propagated; and suspending said killed strains and said toxin B subunit in a physiologically acceptable carrier.

38. A method of making a genetically stable mutant strain of V. cholerae lacking DNA encoding a functional ctxA subunit, lacking any functional attRS1 sequences, and being soft-agar penetration defective, said method comprising the steps of: introducing into a V. cholerae strain a plasmid comprising a fragment of V. cholerae DNA which is mutated in its ctxA and attRS1 sequences, said DNA being capable of recombining with wild type V. cholerae inside said V. cholerae and introducing into said V. cholerae strain a mutation conferring a soft-agar penetration defective phenotype, said steps resulting in the generation of said mutant strain.

39. Purified V. cholerae motB DNA.

40. Purified V. cholerae motB DNA comprising flanking DNA sequence, said flanking DNA sufficient to promote recombination with V. cholerae chromosomal DNA.

41. The DNA of claim 39 or 40, said DNA comprising a deletion or disruption sufficient to confer a Mot-phenotype when said DNA is present in a V. cholera strain lacking an additional motB gene.

42. Purified V. cholerae fliC DNA.

43. Purified V. cholerae fliC DNA comprising flanking DNA sequence, said flanking DNA sufficient to promote recombination with V. cholerae chromosomal DNA.

44. The DNA of claim 42 or 43, said DNA comprising a deletion or disruption sufficient to confer a Fla-phenotype when said DNA is present in a V. cholera strain lacking an additional motB gene.

45. A cell containing the isolated DNA of any one of claims 39-44.

46. An essentially homogenous population of cells, each of which comprises the isolated DNA of any one of claims 39-44.

47. The vaccine of claim 10, wherein said mutant strain is VR1-16.