Salmonella DNA adenine methylase mutants prevent colonization of newly hatched chickens by homologous and heterologous serovars

Genetic engineering of Salmonella spp. for novel vaccine strategies and therapeutics

Salmonella enterica is a diverse species that infects both humans and animals. S. enterica subspecies enterica consists of more than 1,500 serovars. Unlike typhoidal Salmonella serovars which are human host-restricted, non-typhoidal Salmonella (NTS) serovars are associated with foodborne illnesses worldwide and are transmitted via the food chain. Additionally, NTS serovars can cause disease in livestock animals causing significant economic losses. Salmonella is a well-studied model organism that is easy to manipulate and evaluate in animal models of infection. Advances in genetic engineering approaches in recent years have led to the development of Salmonella vaccines for both humans and animals. In this review, we focus on current progress of recombinant live-attenuated Salmonella vaccines, their use as a source of antigens for parenteral vaccines, their use as live-vector vaccines to deliver foreign antigens, and their use as therapeutic cancer vaccines in humans. We also describe development of live-attenuated Salmonella vaccines and live-vector vaccines for use in animals.

Vaccines to Control Salmonella in Poultry

This review is focused on describing and analyzing means by which Salmonella enterica serotype strains have been genetically modified with the purpose of developing safe, efficacious vaccines to present Salmonella-induced disease in poultry and to prevent Salmonella colonization of poultry to reduce transmission through the food chain in and on eggs and poultry meat. Emphasis is on use of recently developed means to generate defined deletion mutations to eliminate genetic sequences conferring antimicrobial resistance or residual elements that might lead to genetic instability. Problems associated with prior means to develop vaccines are discussed with presentation of various means by which these problems have been lessened, if not eliminated. Practical considerations are also discussed in hope of facilitating means to move lab-proven successful vaccination procedures and vaccine candidates to the marketplace to benefit the poultry industry.

Bacterial vaccines in poultry

BACKGROUND

Poultry bacterial pathogens are mainly controlled by using high-cost sanitary measures and medical treatment. However, the drug-resistant strains of pathogens continuously emerge, and medical treatments are often ineffective. Moreover, there is increasing public objections to drug residues in poultry products. The other important type of control is the vaccination which depends on immunity. This immunological control is the major practical alternative to chemotherapy. Success of vaccines in combating poultry diseases depends mainly on the choice of the proper type of vaccines, correct time of its usage, and method of administration.The types of vaccines include attenuated live vaccines, and these vaccines were shown to be effective in inducing protection. The second type is killed vaccine or whole bacteria extracts which is less successful in providing protection compared to live vaccines. The metabolic product vaccine (toxoids) is the third type of vaccine. The recombinant DNA technique was adopted to produce the protective antigens in a sufficient amount and in cost-effective ways.

CONCLUSIONS

Protection studies against bacterial diseases were performed by using several trials: living vaccines (live attenuated vaccines; live, non-pathogenic microorganisms; live, low virulence microorganism), inactivated (killed) vaccines (heat-inactivated, chemical inactivates, radiation), metabolic product vaccines (toxoids), subunit vaccines (whole cell proteins, outer membrane proteins, purified flagellar proteins (flagellin), fimbrial proteins, pilus proteins, lipopolysaccharides), vaccines produced by recombinant deoxyribonucleic acid (DNA) technology, and DNA vaccines.

Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection

Since poultry is a very common source of non-typhoid Salmonella for humans, different interventions aimed at decreasing the prevalence of Salmonella in chickens are understood as an effective measure for decreasing the incidence of human salmonellosis. One such intervention is the use of probiotic or competitive exclusion products. In this study we tested whether microbiota from donor hens of different age will equally protect chickens against Salmonella Enteritidis infection. Newly hatched chickens were therefore orally inoculated with cecal extracts from 1-, 3-, 16-, 28-, and 42-week-old donors and 7 days later, the chickens were infected with S. Enteritidis. The experiment was terminated 4 days later. In the second experiment, groups of newly hatched chickens were inoculated with cecal extracts of 35-week-old hens either on day 1 of life followed by S. Enteritidis infection on day 2 or were infected with S. Enteritidis infection on day 1 followed by therapeutic administration of the cecal extract on day 2 or were inoculated on day 1 of life with a mixture of the cecal extract and S. Enteritidis. This experiment was terminated when the chickens were 5 days old. Both Salmonella culture and chicken gene expression confirmed that inoculation of newly hatched chickens with microbiota from 3-week-old or older chickens protected them against S. Enteritidis challenge. On the other hand, microbiota from 1-week-old donors failed to protect chickens against S. Enteritidis challenge. Microbiota from 35-week-old hens protected chickens even 24 h after administration. However, simultaneous or therapeutic microbiota administration failed to protect chickens against S. Enteritidis infection. Gut microbiota can be used as a preventive measure against S. Enteritidis infection but its composition and early administration is critical for its efficacy.

DNA Methylation

The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during the repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and the regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential, and, in C. crescentus, it is important for temporal gene expression, which, in turn, is required for coordinating chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage, decrease transformation frequency in certain bacteria, and decrease the stability of short direct repeats and are necessary for site-directed mutagenesis and to probe eukaryotic structure and function.

Refined live attenuated Salmonella enterica serovar Typhimurium and Enteritidis vaccines mediate homologous and heterologous serogroup protection in mice

Invasive nontyphoidal Salmonella (NTS) infections constitute a major health problem among infants and toddlers in sub-Saharan Africa; these infections also occur in infants and the elderly in developed countries. We genetically engineered a Salmonella enterica serovar Typhimurium strain of multilocus sequence type 313, the predominant genotype circulating in sub-Saharan Africa. We evaluated the capacities of S. Typhimurium and Salmonella enterica serovar Enteritidis ΔguaBA ΔclpX live oral vaccines to protect mice against a highly lethal challenge dose of the homologous serovar and determined protection against other group B and D serovars circulating in sub-Saharan Africa. The vaccines S. Typhimurium CVD 1931 and S. Enteritidis CVD 1944 were immunogenic and protected BALB/c mice against 10,000 50% lethal doses (LD50) of S. Typhimurium or S. Enteritidis, respectively. S. Typhimurium CVD 1931 protected mice against the group B serovar Salmonella enterica serovar Stanleyville (91% vaccine efficacy), and S. Enteritidis CVD 1944 protected mice against the group D serovar Salmonella enterica serovar Dublin (85% vaccine efficacy). High rates of survival were observed when mice were infected 12 weeks postimmunization, indicating that the vaccines elicited long-lived protective immunity. Whereas CVD 1931 did not protect against S. Enteritidis R11, CVD 1944 did mediate protection against S. Typhimurium D65 (81% efficacy). These findings suggest that a bivalent (S. Typhimurium and S. Enteritidis) vaccine would provide broad protection against the majority of invasive NTS infections in sub-Saharan Africa.

Characterization of a Salmonella Typhimurium ghost carrying an adjuvant protein as a vaccine candidate for the protection of chickens against virulent challenge

In this study we describe the generation of a safe, immunogenic, genetically inactivated Salmonella Typhimurium ghost vaccine candidate carrying the Escherichia coli heat-labile enterotoxin B subunit (LTB) protein as an adjuvant molecule. An asd(+) p15A ori(-) plasmid pJHL187-LTB harbouring the E lysis gene cassette and a foreign antigen delivery cassette containing the eltB gene was used to transform a Δasd Salmonella Typhimurium (JOL1311) strain to construct the ghost strain, JOL1499. Incubation of mid-logarithmic phase JOL1499 cultures at 42°C resulted in co-expression of the eltB and E lysis genes, leading to the generation of Salmonella Typhimurium ghost cells carrying the LTB protein (Salmonella Typhimurium-LTB ghost). The production of LTB in Salmonella Typhimurium-LTB ghost preparations was confirmed by western blot analysis, and functional activity of the LTB protein to bind with GM1 receptors was determined by means of GM1 enzyme-linked immunosorbent assay. Efficacy of the Salmonella Typhimurium-LTB ghost as a vaccine candidate was evaluated in a chicken model using 56 chickens at 5 weeks old, which were divided into four groups (n = 14): group A was designated the non-vaccinated control group, whereas the birds in groups B, C, and D were immunized intramuscularly with 10(9), 10(8), and 10(7) ghost cells, respectively. Compared with the non-immunized chickens (group A), immunized chickens (groups B, C and D) exhibited increased titres of plasma IgG and intestinal secretory IgA antibodies. After oral challenge with 10(9) colony-forming units of a virulent Salmonella Typhimurium strain, the vaccinated group B birds showed a decrease in internal organ colonization with the challenge strain.

Alteration in lymphocytes responses, cytokine and chemokine profiles in laying hens infected with Salmonella Typhimurium

Salmonella Typhimurium has been reported to contaminate egg production across the world, but the exact nature of the immune mechanisms protective against Salmonella infection in laying hens has not been characterized at the molecular level. The experiment was conducted to determine Salmonella colonization and lymphocytes subpopulation in the ileum and spleen, and the mRNA expression of pro-inflammatory cytokines [interleukin (IL)-1β and IL-6], chemokine IL-8, and T helper (Th)1/Th2 cytokines [Interferon (IFN)-γ, IL-12 and IL-18; IL-4 and IL-10 respectively] in the cecal tonsil and spleen of Salmonella challenged hens. Forty Salmonella-free laying hens were challenged orally with Salmonella Typhimurium or phosphate-buffered saline (PBS; control). The Salmonella challenged or non-challenged hens (n=10) were sacrificed at 2 and 7 days post-infection (DPI). The lymphocyte subpopulation was determined via flow cytometric analysis in the ileum and spleen. The cecal tonsil and spleen samples were collected for mRNA expression through quantitative-RT-PCR. The Salmonella counts were higher (P<0.05) in the ileum than that in the spleen at 2 and 7DPI, and were higher (P<0.05) at 7DPI than that at 2DPI in the spleen. Salmonella challenge increased (P<0.05) ileal CD4+ and CD8α+ cells ratios at 2 and 7DPI, whereas it increased (P<0.05) splenic CD8α+ cells ratio only at 7DPI. The magnitude of increase in ileal CD8α+ cells ratio was higher (P<0.05) than that in CD4+ cells ratio. The mRNA expression of IL-1β, IL-6, IL-8, IFN-γ, IL-12 and IL-18 were significantly up-regulated in the cecal tonsil of Salmonella challenged hens, and the magnitude of increases in IL-6, IL-8 and IL-12 were significantly higher at 7DPI than that at 2DPI. However, Salmonella challenge increased (P<0.05) the mRNA expression of IL-1β, IL-10 and IL-18 at 2 and 7DPI, and IL-8 and IFN-γ mRNA only at 7DPI in the spleen. These findings demonstrated that there appeared the induction of cellular immune responses, and a Th1-cytokines reaction in the intestine and spleen of laying hens infected with Salmonella Typhimurium.

Transcriptional Profiling of a Cross-Protective Salmonella enterica serovar Typhimurium UK-1 dam Mutant Identifies a Set of Genes More Transcriptionally Active Compared to Wild-Type, and Stably Transcribed across Biologically Relevant Microenvironments

Vaccination with Salmonella enterica serovar Typhimurium lacking DNA adenine methyltransferase confers cross-protective immunity against multiple Salmonella serotypes. The mechanistic basis is thought to be associated with the de-repression of genes that are tightly regulated when transiting from one microenvironment to another. This de-repression provides a potential means for the production of a more highly expressed and stable antigenic repertoire capable of inducing cross-protective immune responses. To identify genes encoding proteins that may contribute to cross-protective immunity, we used a Salmonella Typhimurium DNA adenine methyltransferase mutant strain (UK-1 dam mutant) derived from the parental UK-1 strain, and assessed the transcriptional profile of the UK-1 dam mutant and UK-1 strain grown under conditions that simulate the intestinal or endosomal microenvironments encountered during the infective process. As expected, the transcriptional profile of the UK-1 dam mutant identified a set of genes more transcriptionally active when compared directly to UK-1, and stably transcribed in biologically relevant culture conditions. Further, 22% of these genes were more highly transcribed in comparison to two other clinically-relevant Salmonella serovars. The strategy employed here helps to identify potentially conserved proteins produced by the UK-1 dam mutant that stimulate and/or modulate the development of cross-protective immune responses toward multiple Salmonella serotypes.

Immunization with a DNA adenine methylase over-producing Yersinia pseudotuberculosis vaccine confers robust cross-protection against heterologous pathogenic serotypes

Yersinia pseudotuberculosis is a foodborne pathogen that can cause serious human illness. Although the source and route of transmission often remain obscure, livestock have been implicated in some cases. The diversity of yersiniae present on farms and their widespread distribution in animal and environmental reservoirs necessitates the use of broad prophylactic strategies that are efficacious against many serotypes simultaneously. Herein, immunization of mice with a modified, live attenuated Y. pseudotuberculosis vaccine that overproduces the DNA adenine methylase (Dam(OP)) conferred robust protection against virulent challenge (150-fold LD50) with homologous and heterologous serotypes that have been associated with human disease (O:1, O:1a, O:3). Further, the dam gene was shown to be essential for cell viability in all (7 of 7) Y. pseudotuberculosis strains tested. Direct selection for the inheritance of dam mutant alleles in Y. pseudotuberculosis resulted in dam strain variants that contained compensatory (second-site suppressor) mutations in genes encoding methyl-directed mismatch repair proteins (mutHLS) that are involved in suppression of the non-viable cell phenotype in all (19/19) strains tested. Such dam mutH variants exhibited a significant increase in virulence and spontaneous mutation frequency relative to that of a Dam(OP) vaccine strain. These studies indicate that Y. pseudotuberculosis Dam(OP) strains conferred potent cross-protective efficacy as well as decreased virulence and spontaneous mutation frequency relative to those that lack Dam, which have compensatory mutations in mutHLS loci. These data suggest that development of yersiniae livestock vaccines based on Dam overproduction is a viable mitigation strategy to reduce these potential foodborne contaminants.

Influence of bacteriophage P22 on the inflammatory mediator gene expression in chicken macrophage HD11 cells infected with Salmonella Typhimurium

This study was designed to evaluate the effects of bacteriophage on the intracellular survival and immune mediator gene expression in chicken macrophage-like HD11 cells. The invasive ability and intracellular survival of Salmonella Typhimurium (ST(P22-) ) and lysogenic S. Typhimurium (ST(P22+) ) in HD11 cells were evaluated at 37 °C for 24 h postinfection (hpi). The expression of inflammatory mediator genes was determined in ST(P22-) - and ST(P22+) -infected HD11 cells treated with and without bacteriophage P22 at 1 and 24 hpi using quantitative RT-PCR. The ability of ST(P22-) and ST(P22+) to invade HD11 cells was significantly decreased by bacteriophage P22 at 1 hpi. The numbers of intracellular ST(P22-) and ST(P22+) were significantly decreased from 2.39 to 1.62 CFU cm(-2) and from 3.40 to 1.72 CFU cm(-2) in HD11 cells treated with bacteriophage P22, respectively, at 24 hpi. The enhanced expression of inflammatory mediators was observed in ST(P22-) - and ST(P22+) -infected HD11 cells treated with and without bacteriophage P22. These results suggest that the application of bacteriophage could be an effective way to control the intracellular infection.

SPI1 defective mutants of Salmonella enterica induce cross-protective immunity in chickens against challenge with serovars Typhimurium and Enteritidis

In this study we were interested in the serovar cross-protection potential of Salmonella Pathogenicity Island 1 (SPI1) attenuated vaccine strains of Salmonella enterica serovars Enteritidis and Typhimurium and immune response of vaccinated and naive chickens to Salmonella infection. The immune response was characterized by real time PCR quantifying transcripts of interleukins IL1β, IL17, IL22, interferon gamma (IFNγ), inducible NO synthase (iNOS), immunoglobulins IgM, IgA, IgY and Ig light chain, and six genes of acute phase response including avidin, serum amyloid A, extracellular fatty acid-binding protein (Ex-FABP), immune responsive gene 1, chemokine AH221 and trappin-6. Vaccination with SPI1 mutants of both serovars protected chickens against Salmonella infection, independent of the serovar used for the challenge and the time post infection. However, expressions of all interleukins, iNOS and Ex-FABP showed that protection against homologous serovars was significantly higher than against heterologous serovars after intravenous challenge at 4 days post infection. The vaccination with a mixture of S. Enteritidis and S. Typhimurium SPI1 mutants induced an intermediate protection against challenge with both serovars, i.e. the mixed vaccine provided an additional protective effect when compared with the chickens vaccinated with a vaccine formed by only a single Salmonella serovar.

Dam methylation participates in the regulation of PmrA/PmrB and RcsC/RcsD/RcsB two component regulatory systems in Salmonella enterica serovar Enteritidis

The absence of Dam in Salmonella enterica serovar Enteritidis causes a defect in lipopolysaccharide (LPS) pattern associated to a reduced expression of wzz gene. Wzz is the chain length regulator of the LPS O-antigen. Here we investigated whether Dam regulates wzz gene expression through its two known regulators, PmrA and RcsB. Thus, the expression of rcsB and pmrA was monitored by quantitative real-time RT-PCR and Western blotting using fusions with 3×FLAG tag in wild type (wt) and dam strains of S. Enteritidis. Dam regulated the expression of both rcsB and pmrA genes; nevertheless, the defect in LPS pattern was only related to a diminished expression of RcsB. Interestingly, regulation of wzz in serovar Enteritidis differed from that reported earlier for serovar Typhimurium; RcsB induces wzz expression in both serovars, whereas PmrA induces wzz in S. Typhimurium but represses it in serovar Enteritidis. Moreover, we found that in S. Enteritidis there is an interaction between both wzz regulators: RcsB stimulates the expression of pmrA and PmrA represses the expression of rcsB. Our results would be an example of differential regulation of orthologous genes expression, providing differences in phenotypic traits between closely related bacterial serovars.

Development of a novel in-water vaccination protocol for DNA adenine methylase deficient Salmonella enterica serovar Typhimurium vaccine in adult sheep

Intensive livestock production is associated with an increased incidence of salmonellosis. The risk of infection and the subsequent public health concern is attributed to increased pathogen exposure and disease susceptibility due to multiple stressors experienced by livestock from farm to feedlot. Traditional parenteral vaccine methods can further stress susceptible populations and cause carcass damage, adverse reactions, and resultant increased production costs. As a potential means to address these issues, in-water delivery of live attenuated vaccines affords a low cost, low-stress method for immunization of livestock populations that is not associated with the adverse handling stressors and injection reactions associated with parenteral administration. We have previously established that in-water administration of a Salmonella enterica serovar Typhimurium dam vaccine conferred significant protection in livestock. While these experimental trials hold significant promise, the ultimate measure of the vaccine will not be established until it has undergone clinical testing in the field wherein environmental and sanitary conditions are variable. Here we show that in-water administration of a S. Typhimurium dam attenuated vaccine was safe, stable, and well-tolerated in adult sheep. The dam vaccine did not alter water consumption or vaccine dosing; remained viable under a wide range of temperatures (21-37°C); did not proliferate within fecal-contaminated trough water; and was associated with minimal fecal shedding and clinical disease as a consequence of vaccination. The capacity of Salmonella dam attenuated vaccines to be delivered in drinking water to protect livestock from virulent Salmonella challenge offers an effective, economical, stressor-free Salmonella prophylaxis for intensive livestock production systems.

Evaluation of recombinant Salmonella expressing the flagellar protein fliC for persistence and enhanced antibody response in commercial turkeys

Salmonella enterica serovar Enteritidis (SE) is one of the most common causes of human foodborne illness in the United States. Previous research indicates that antibodies against the fliC protein can provide protection against Salmonella challenge in mice. To generate a vaccine that effectively protects poultry against multiple Salmonella serotypes, novel attenuated strains of SE were developed to express a fliC peptide sequence on the outer membrane protein lamB in association with an M2e (marker) epitope. In 3 separate trials, poults were immunized with 10(7) to 10(8) cfu/poult of the appropriate recombinant Salmonella strains (ΔSE-M2e or ΔSE-M2e-fliC) via oral gavage on the day of hatch and again on d 21 posthatch. Liver, spleen, and cecal tonsils were aseptically removed on d 7, 14, 21, 28, 35, and 42 posthatch for detection of Salmonella, and blood samples were obtained at these same time points for determination of an M2e-specific antibody response. In all 3 trials, the ΔSE-M2e-fliC strain exhibited significantly less invasion of the liver and spleen at d 7 and 14 when compared with ΔSE-M2e or SE phage type 13A (P < 0.05). Similarly, colonization of the cecal tonsils was decreased in the poults immunized with the ΔSE-M2e-fliC strain. By d 21, the ΔSE-M2e-fliC strain exhibited a significantly higher M2e-specific antibody response when compared with the negative control and SE phage type 13A groups (P < 0.05). However, no significant differences in M2e-specific antibody responses were observed between the ΔSE candidate vaccine strains throughout the study. Overall, these data suggest that oral live attenuated Salmonella-vectored vaccines expressing a fliC peptide sequence are able to elicit a humoral immune response in commercial poults and may contribute to a reduction in Salmonella organ invasion and colonization.

Protective immunity conferred by a DNA adenine methylase deficient Salmonella enterica serovar Typhimurium vaccine when delivered in-water to sheep challenged with Salmonella enterica serovar Typhimurium

Stimulation of acquired immunity to Salmonella in livestock is not feasible in neonates (which can be infected within 24h of birth) and is challenging in feedlots, which typically source animals from diverse locations and vendors. Induction of innate immune mechanisms through mass vaccination of animals upon arrival to feedlots is an alternative approach. Transport, environmental conditions, changes in social grouping, and further handling during feedlot assembly are significant stressors. These factors, as well as concurrent exposure to a diversity of pathogens, contribute to the risk of disease. We have shown that oral immunization of calves with a modified live Salmonella enterica serovar Typhimurium vaccine strain, which lacks the DNA adenine methylase gene (S. Typhimurium dam), attenuates the severity of clinical disease, reduces fecal shedding, and promotes clearance of salmonellae following virulent homologous and heterologous challenge. This study examines the safety and efficacy of a S. Typhimurium dam vaccine in sheep via oral delivery in drinking water (ad libitum), as a means to effectively vaccinate large groups of animals. Adult merino sheep were vaccinated in drinking water -28 days, -7 days and 24h pre and 24h post-virulent Salmonella Typhimurium challenge which was administered via the oral route. Significant attenuation of clinical disease (temperature, appetite, and attitude) and reduction in mortality and virulent Salmonella Typhimurium fecal shedding and tissue colonization was observed in animals that received the vaccine 28 and 7 days pre-challenge. Further, vaccination did not pose a risk to stock previously infected with virulent salmonellae as mortalities and clinical disease in sheep vaccinated prior to or following virulent challenge did not differ significantly from the non-vaccinated controls. The capacity of S. Typhimurium dam vaccines delivered in drinking water to protect livestock from virulent Salmonella challenge offers an effective, economical, stressor free Salmonella prophylaxis for intensive livestock production systems.

Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein

We reported previously that a Salmonella enterica serovar Enteritidis dam mutant expressing a truncated Dam protein does not agglutinate in the presence of specific antibodies against O9 polysaccharide. Here we investigate the participation of Dam in lipopolysaccharide (LPS) synthesis in Salmonella. The LPS O-antigen profiles of a dam null mutant (SEDeltadam) and the Salmonella serovar Enteritidis parental strain were examined by using electrophoresis and silver staining. Compared to the parental strain, SEDeltadam produced LPS with shorter O-antigen polysaccharide chains. Since Wzz is responsible for the chain length distribution of the O antigen, we investigated whether Dam methylation is involved in regulating wzz expression. Densitometry analysis showed that the amount of Wzz produced by SEDeltadam is threefold lower than the amount of Wzz produced by the parental strain. Concomitantly, the activity of the wzz promoter in SEDeltadam was reduced nearly 50% in logarithmic phase and 25% in stationary phase. These results were further confirmed by reverse transcription-PCR showing that wzz gene expression was threefold lower in the dam mutant than in the parental strain. Our results demonstrate that wzz gene expression is downregulated in a dam mutant, indicating that Dam methylation activates expression of this gene. This work indicates that wzz is a new target regulated by Dam methylation and demonstrates that DNA methylation not only affects the production of bacterial surface proteins but also the production of surface polysaccharides.

DNA Methylation

The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcmmethyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholera and Caulobactercrescentus) adenine methylation is essential, and in C.crescentus it is important for temporal gene expression which, in turn, is required for coordination of chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage,decrease transformation frequency in certain bacteria,and decrease the stability of short direct repeats andare necessary for site-directed mutagenesis and to probe eukaryotic structure and function.

Regulation of the Salmonella enterica std fimbrial operon by DNA adenine methylation, SeqA, and HdfR

DNA adenine methylase (dam) mutants of Salmonella enterica serovar Typhimurium grown under laboratory conditions express the std fimbrial operon, which is tightly repressed in the wild type. Here, we show that uncontrolled production of Std fimbriae in S. enterica serovar Typhimurium dam mutants contributes to attenuation in mice, as indicated by the observation that an stdA dam strain is more competitive than a dam strain upon oral infection. Dam methylation appears to regulate std transcription, rather than std mRNA stability or turnover. A genetic screen for std regulators showed that the GATC-binding protein SeqA directly or indirectly represses std expression, while the poorly characterized yifA gene product serves as an std activator. YifA encodes a putative LysR-like protein and has been renamed HdfR, like its Escherichia coli homolog. Activation of std expression by HdfR is observed only in dam and seqA backgrounds. These data suggest that HdfR directly or indirectly activates std transcription. Since SeqA is unable to bind nonmethylated DNA, it is possible that std operon derepression in dam and seqA mutants may result from unconstrained HdfR-mediated activation of std transcription. Derepression of std in dam and seqA mutants of S. enterica occurs in only a fraction of the bacterial population, suggesting the occurrence of either bistable expression or phase variation.

Salmonella enterica serovar Enteritidis dam mutant induces low NOS-2 and COX-2 expression in macrophages via attenuation of MAPK and NF-kappaB pathways

Although dam mutants of Salmonella have been proposed as live vaccines, their capacity to trigger cell inflammatory cascades has not been fully elucidated. We investigated in detail the ability of Salmonella enterica dam mutant to activate the signalling pathways of the inflammatory response in RAW 264.7 cells. Apoptosis in macrophages treated with Salmonella dam mutant was low. Similarly, the expression of both NOS-2 and COX-2 and subsequently the production of NO and PGE(2) was significantly reduced. Also, Salmonella dam mutant induced an attenuated activation of the inflammatory signalling pathway as indicated by the reduced degradation of IkappaBalpha and IkappaBbeta and the low IkappaBalpha phosphorylation found. In addition, translocation of p65 to the nucleus was notably impaired and the amount of phosphorylated p44, p42 and p38 MAPKs was clearly reduced in extracts from dam-infected macrophages. These results indicate that the lack of ERK and p38 phosphorylation at the proper time in dam-infected cells notably reduces the engagement of subsequent signalling pathways involved in the full activation of NF-kappaB in response to infection. Taken together, these results suggest that Salmonella activation of both signalling cascades in the inflammatory response is a mechanism requiring Dam protein participation.

Innate interferon response in macrophage and epithelial cells infected with wild-type compared to DNA adenine methylase and flagellin mutant Salmonella enterica serovar Typhimurium

Salmonella enterica serovar Typhimurium is highly virulent and mediates robust interferon (IFN)-stimulated gene (ISG) induction, whereas bacterial mutants that lack the DNA adenine methylase (Dam) are attenuated, elicit a reduced ISG activation profile, and establish immunity to murine typhoid fever. We show here that in contrast to observations in mice, infection of macrophage cell cultures with either wild-type (WT) or dam(-) mutant Salmonella resulted in surprisingly similar kinetics and amplitudes of induction of IFN-beta, the type I IFN-alpha,beta beacon gene Mx, and the type II IFN-gamma beacon inducible nitric oxide synthase (iNOS). Likewise, activation of NF-kappaB-dependent gene expression in epithelial cells was comparable with WT and dam(-) mutant Salmonella. In contrast, the flagellin-deficient flhC(-) mutant did not activate NF-kappaB in epithelial cells but activated ISG expression comparable to that of WT Salmonella in macrophage cells. WT and dam(-) strains displayed a similar Toll-like receptor 5 (TLR5)-dependent NF-kappaB activation, whereas the flhC(-) mutant lacked this activity. UV-inactivated Salmonella elicited similar ISG induction to that of viable Salmonella in macrophages and mediated the establishment of a functional antiviral state but displayed decreased cytocidal activity. These results establish that the inherent IFN system-inducing capacities of dam(-) and WT Salmonella strains in cultured macrophage and epithelial cells, unlike the mouse, are indistinguishable.

In vivo-selected mutations in methyl-directed mismatch repair suppress the virulence attenuation of Salmonella dam mutant strains following intraperitoneal, but not oral, infection of naïve mice

Salmonella enterica serovar Typhimurium that lacks the DNA adenine methylase (Dam) ectopically expresses multiple genes that are preferentially expressed during infection, is attenuated for virulence, and confers heightened immunity in vaccinated hosts. The safety of dam mutant Salmonella vaccines was evaluated by screening within infected mice for isolates that have an increased capacity to cause disease relative to the attenuated parental strain. Since dam mutant strains are sensitive to the DNA base analog 2-aminopurine (2-AP), we screened for 2-AP-resistant (2-AP(r)) isolates in systemic tissues of mice infected with dam mutant Salmonella. Such 2-AP(r) derivatives were isolated following intraperitoneal but not oral administration and were shown to be competent for infectivity via intraperitoneal but not oral infection of naïve mice. These 2-AP(r) derivatives were deficient in methyl-directed mismatch repair and were resistant to nitric oxide, yet they retained the bile-sensitive phenotype of the parental dam mutant strain. Additionally, introduction of a mutH null mutation into dam mutant cells suppressed the inherent defects in intraperitoneal infectivity and nitric oxide resistance, as well as overexpression of SpvB, an actin cytotoxin required for Salmonella systemic survival. These data suggest that restoration of intraperitoneal virulence of dam mutant strains is associated with deficiencies in methyl-directed mismatch repair that correlate with the production of systemically related virulence functions.

Salmonella infections: immune and non-immune protection with vaccines

Salmonella enterica in poultry remains a major political issue. S. enterica serovar Enteritidis, particularly, remains a world-wide problem. Control in poultry by immunity, whether acquired or innate, is a possible means of containing the problem. Widespread usage of antibiotics has led to the emergence of multiple antibiotic-resistant bacteria. This problem has indicated an increasing requirement for effective vaccines to control this important zoonotic infection. An attempt is made in the present review to explain the relatively poor success in immunizing food animals against these non-host-specific Salmonella serotypes that usually produce food-poisoning, compared with the success obtained with the small number of serotypes that more typically produce systemic "typhoid-like" diseases. New examinations of old problems such as the carrier state and vertical transmission, observed with S. Pullorum, is generating new information of relevance to immunity. Newer methods of attenuation are being developed. Live vaccines, if administered orally, demonstrate non-specific and rapid protection against infection that is of biological and practical interest. However, from the point of view of consumer safety, there is a school of thought that considers inactivated or sub-unit vaccines to be the safest. The benefits of developing effective killed or sub-unit vaccines over the use of live vaccines are enormous. Recently, there have been significant advances in the development of adjuvants (e.g. microspheres) that are capable of potent immuno-stimulation, targeting different arms of the immune system. The exploitation of such technology in conjunction with the ongoing developments in identifying key Salmonella virulence determinants should form the next generation of Salmonella sub-unit vaccines for the control of this important group of pathogens. There are additional areas of concern associated with the use of live vaccines, particularly if these are generated by genetic manipulation.

Cross-reactive cellular and humoral immune responses to Salmonella enterica serovars Typhimurium and Enteritidis are associated with protection to heterologous re-challenge

Chickens infected with Salmonella enterica serovars Typhimurium (ST) and Enteritidis (SE) still represent a major source of human food poisoning via consumption of contaminated meat and eggs. Vaccination represents a sustainable approach to control Salmonella in the chicken and the serovar specificity of immunity has the potential to impact on the need for multivalent vaccines. The issue of cross-reactive immune responses and cross-serovar protection was examined in these experiments. Cellular and humoral immune responses were measured by antigen-specific ELISA and splenocyte proliferation assays during primary infections (with ST and SE) and during a second challenge with homologous or heterologous serovars. Primary infection with ST or SE induced strong lymphocyte proliferation and high levels of specific antibody (IgM, IgG and IgA) responses with substantial serovar cross-reactivity. The occurrence of high levels of splenocyte proliferation and strong antibody responses corresponded to the initiation of clearance with both ST and SE. Re-challenge of ST and SE infection-primed chickens with either serovar resulted in significant levels of protection (assessed by bacterial numbers and rate of clearance) with little difference between homologous or heterologous challenge schedules. Relatively low levels of antigen-specific splenocyte proliferation were detected during secondary infection, which may be caused by splenic T cells exiting to the gut. In contrast, the more rapid specific antibody responses (compared with primary infection controls) indicate the development of a secondary antigen-specific adaptive response. The substantial level of cross-protection between serovars and the level of antigenic cross-reactivity indicates the potential for single serovar live vaccines to protect against both group B and D salmonellae.

Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase

The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with cognate DNA was determined at 1.89 A resolution in the presence of S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments. Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts to the non-target strand in the second (3') half of the GATC site are established by R124 to the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119 intercalates into the DNA between the second and third base-pairs, which is essential for base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam, three major new observations are made in E.coli Dam. (1) The first Gua is recognized by K9, removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds to the surface of EcoDam in the absence of S-adenosyl-L-methionine, which illustrates a possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays structural flexibility by adopting an extrahelical or intrahelical position where it is in contact to N120.

Increased excision of the Salmonella prophage ST64B caused by a deficiency in Dam methylase

Salmonella enterica mutants defective in Dam methylase are strongly attenuated in virulence and release a large amount of proteins to the extracellular medium. The extent to which these two phenotypes are linked is unknown. Using a proteomic approach, we identified Sb6, Sb13, and Sb36 as proteins present in larger amounts in culture supernatants of an S. enterica serovar Typhimurium dam mutant than in those of the wild-type strain. These three proteins are encoded in the Salmonella prophage ST64B. Higher amounts of ST64B phage DNA and tailless viral capsids were also detected in supernatant extracts of the dam mutant, suggesting that Dam methylation negatively regulates the excision of ST64B. Reverse transcription-PCR analysis revealed that the expression of two ST64B genes encoding a putative antirepressor and a phage replication protein increases in the dam mutant. The SOS response also augments the excision of ST64B. Infection assays performed with phage-cured strains demonstrated that ST64B does not carry genes required for virulence in the mouse model. Evidence was also obtained discarding a relationship between the high excision of ST64B and the envelope instability or virulence attenuation phenotype. Taken together, these data indicate that ST64B excises at a high rate in dam mutants due to the loss of repression exerted by Dam on phage genes and induction of the SOS response characteristic of these mutants. The exacerbated excision of ST64B does not however contribute to the incapacity of dam mutants to cause disease.

Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase

DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.

Cytokine and chemokine responses associated with clearance of a primary Salmonella enterica serovar Typhimurium infection in the chicken and in protective immunity to rechallenge

Infection of poultry with Salmonella enterica serovar Typhimurium poses a significant risk to public health through contamination of meat from infected animals. Vaccination has been proposed to control infections in chickens. However, the vaccines are currently largely empirical, and our understanding of the mechanisms that underpin immune clearance and protection in avian salmonellosis is not complete. In this study we describe the cytokine, chemokine, and antibody responses and cellular changes in primary and secondary infections of chickens with Salmonella serovar Typhimurium. Infection of 1-week-old chickens induced early expression of a macrophage inflammatory protein (MIP) family chemokine in the spleen and liver, followed by increased expression of gamma interferon accompanied by increased numbers of both CD4(+) and CD8(+) T cells and the formation of granuloma-like follicular lesions. This response correlated with a Th1-mediated clearance of the systemic infection. Primary infection also induced specific immunoglobulin M (IgM), IgG, and IgA antibody responses. In contrast to previously published studies performed with newly hatched chicks, the expression levels of proinflammatory cytokines in the gastrointestinal tract were not greatly increased following infection. However, significant expression of the anti-inflammatory cytokine transforming growth factor beta4 was detected in the gut early in infection. Following secondary challenge, the birds were fully protected against systemic infection and showed a high level of protection against gastrointestinal colonization. Rapid expression of the MIP family chemokine and interleukin-6 was detected in the guts of these birds and was accompanied by an influx of lymphocytes. Increased levels of serum IgA-specific antibodies were also found following rechallenge. These findings suggest that cellular responses, particularly Th1 responses, play a crucial role in immune clearance in avian salmonellosis and that protection against rechallenge involves the rapid recruitment of cells to the gastrointestinal tract. Additionally, the high levels of inflammatory response found following Salmonella serovar Typhimurium infection of newly hatched chicks were not observed following infection of older birds (1 week old), in which the expression of regulatory cytokines appeared to limit inflammation.

Vaccines against Infections Caused by Salmonella, Shigella, and Pathogenic Escherichia coli

Infectious diseases represent one of the most common causes of death worldwide, with the enteropathogenic bacteria Salmonella and Shigella and pathogenic Escherichia coli being among the most detrimental. Currently, vaccination represents the preferred method of preventing such infections. For stimulating the adaptive immune response, immunizations are frequently based on formulations which include inactivated whole-cell vaccines, live attenuated vaccines, or subunit vaccines. These can be administered via a parenteral or mucosal route, the latter having the advantage that it most closely mimics the actual course of infection. In addition to the type of vaccine and method of application, important consideration needs to be paid to safety, efficacy, and cost, which are often major bottlenecks in the successful implementation of vaccines. In this chapter we take a limited look at the history surrounding vaccinations involving Salmonella, Shigella, and pathogenic E. coli. Salmonella infections, which can lead to typhoid fever, are becoming increasing difficult to treat with antibiotics due to multi-drug-resistant strains. At present, the parenteral Vi-based subunit vaccines and the live attenuated oral vaccine Ty21a have proven to be the vaccines of choice, with high levels of protective efficacy and limited side effects. Shigella infections are responsible for the diarrheal disease shigellosis. Various live and nonliving mucosal and parenteral vaccines have been tested, with the most promising candidates evolving around those that stimulate the production of O-antigen-specific antibodies. Pathogenic Escherichia coli infections can lead to severe diseases due to the bacterium's production of several specific toxins. Vaccines against this bacterium target its toxins, as well as surface-exposed antigens, all of which have been found to be effective as immunogens.

Structure of the bacteriophage T4 DNA adenine methyltransferase

DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a beta-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA.

Salmonella DNA adenine methylase mutants elicit early and late onset protective immune responses in calves

Salmonellosis is an important disease of livestock and Salmonella contamination of livestock-derived food products and effluents pose a significant risk to human health. Salmonella vaccines currently available to prevent salmonellosis in cattle have limited efficacy. Here we evaluated a Salmonella enterica serovar Typhimurium vaccine strain lacking the DNA adenine methylase (Dam) for safety and efficacy in calves. Vaccination was safe in calves, and following challenge with virulent Typhimurium 4 weeks post-immunization, vaccinated animals exhibited significantly lower mortality, diarrhea, and rectal temperatures, as well as reduced colonization of gastrointestinal tract and visceral organs compared to non-vaccinated control animals. Additionally, early onset protection (competitive exclusion) in vaccinated neonatal calves was demonstrated by attenuated clinical disease (as measured by rectal temperatures and attitude scores) and reduced mortality when challenged with virulent Typhimurium 24h after immunization. Taken together, these data suggest that vaccination with Salmonella Dam mutant strains confer significant protection against Salmonella infections in cattle via both adaptive immunity and competitive exclusion mechanisms.

Tissue selectivity of interferon-stimulated gene expression in mice infected with Dam(+) versus Dam(-) Salmonella enterica serovar Typhimurium strains

The host interferon (IFN) system plays an important role in protection against microbial infections. Salmonella enterica serovar Typhimurium is highly virulent in the mouse model, whereas mutants that lack DNA adenine methylase (Dam(-)) are highly attenuated and elicit fully protective immune responses against murine typhoid fever. We examined the expression of IFN-responsive genes in several mouse tissues following infection with Dam(+) or Dam(-) Salmonella. Infection of mice with Dam(+) Salmonella resulted in the induction of host genes known to be indicators of IFN bioactivity and regulated by either IFN-alpha/beta (Mx1) or IFN-gamma (class II transactivator protein [CIITA] and inducible nitric oxide synthase [iNOS]) or by both IFN-alpha/beta and IFN-gamma (RNA-specific adenosine deaminase [ADAR1] and RNA-dependent protein kinase [PKR]) in a tissue-specific manner compared to uninfected animals. Since the Mx1 promoter is IFN-alpha/beta specific and the Mx1 gene is not inducible directly by IFN-gamma, these data suggest a role of IFN-alpha/beta in the host response to Salmonella infection. Mice infected with Dam(-) Salmonella showed reduced expression of the same set of IFN-stimulated genes (ISGs) as that observed after infection with wild-type Salmonella. The reduced capacity to induce ISGs persisted in Dam(-)-vaccinated mice after challenge with the virulent (Dam(+)) strain. Finally, although no Dam(-) organisms were recovered from the liver or spleen after oral infection of mice, ADAR, PKR, Mx, and CIITA expression levels were elevated in these tissues relative to those in uninfected mice, suggestive of the distant action of a signaling molecule(s) in the activation of ISG expression.