Vaccines against intracellular bacterial pathogens

There is a long history of remarkable success in developing vaccines against bacteria that are extracellular pathogens. In general, the development of vaccines against intracellular bacterial pathogens has proven to be more challenging. Typically, such vaccines need to induce a range of immune responses, including antibody, CD4(+) and CD8(+) T cell responses. These responses can be induced by live attenuated vaccines, but eliciting these responses with non-living vaccines has proven to be difficult. The difficulties appear to be related partly to the problems associated with the identification of protective antigens and partly with the difficulties associated with inducing CD8(+) T cell responses.

A 55 kDa hypothetical membrane protein is an iron-regulated virulence factor of Francisella tularensis subsp. novicida U112

Iron is an important nutritional requirement for bacteria due to its conserved role in many essential metabolic processes. As a consequence of the lack of freely available iron in the mammalian host, bacteria upregulate a range of virulence factors during infection. Transcriptional analysis of Francisella tularensis subsp. novicida U112 grown in iron-deficient medium identified 21 genes upregulated in response to this condition, four of which were attributed to a siderophore operon. In addition, a novel iron-regulated gene, FTT0025, was identified which is part of this operon and encodes a 55 kDa hypothetical membrane protein. When grown on chrome azurol S agar, the F. tularensis subsp. novicida U112deltaFTT0025 mutant produced an increased reaction zone compared with the wild-type, suggesting that siderophore production was unaffected but that the bacteria may have a deficiency in their ability to re-sequester this iron-binding molecule. Furthermore, the deltaFTT0025 mutant was attenuated in a BALB/c mouse model of infection relative to wild-type F. tularensis subsp. novicida U112.

Phenotypic characterization of a virulence-associated protein, VagH, of Yersinia pseudotuberculosis reveals a tight link between VagH and the type III secretion system

Recently, a number of attenuated mutants of Yersinia pseudotuberculosis have been identified using a bioinformatics approach. One of the target genes identified in that study was vagH, which the authors now characterized further. VagH shows homology to HemK of Escherichia coli, possessing methyltransferase activity similar to that of HemK, and targeting release factors 1 and 2. Microarray studies comparing the wild-type and the vagH mutant revealed that the mRNA levels of only a few genes were altered in the mutant. By proteome analysis, expression of the virulence determinant YopD was found to be increased, indicating a possible connection between VagH and the virulence plasmid-encoded type III secretion system (T3SS). Further analysis showed that Yop expression and secretion were repressed in a vagH mutant. This phenotype could be suppressed by trans-complementation with the wild-type vagH gene or by deletion of the negative regulator yopD. Also, in a similar manner to a T3SS-negative mutant, the avirulent vagH mutant was rapidly cleared from Peyer's patches and could not reach the spleen after oral infection of mice. In a manner analogous to that of T3SS mutants, the vagH mutant could not block phagocytosis by macrophages. However, a vagH mutant showed no defects in the T3SS-independent ability to proliferate intracellularly and replicated to levels similar to those of the wild-type in macrophages. In conclusion, the vagH mutant exhibits a virulence phenotype similar to that of a T3SS-negative mutant, indicating a tight link between VagH and type III secretion in Y. pseudotuberculosis.

Structures of OppA and PstS from Yersinia pestis indicate variability of interactions with transmembrane domains

Bacterial ATP-binding cassette (ABC) transport systems couple ATP hydrolysis with the uptake and efflux of a wide range of substances across bacterial membranes. These systems are comprised of transmembrane domains, nucleotide binding domains and, in the case of uptake systems, periplasmic binding proteins responsible for binding and presentation of substrate to the transmembrane domains. In pathogenic bacteria, ABC systems are known to play roles in virulence and pathogenicity and the surface localization of some components has made them attractive targets for both vaccine and anti-infective development. Here, the crystallization of five proteins (OppA, PstS, PiuA, YrbD and CysP) from Yersinia pestis, the causative agent of plague, are reported that diffracted to resolution limits ranging from 1.6 to 5 A. The first crystal structures of ABC system components from Y. pestis, OppA and PstS, are also reported here as complexes with their substrates. Comparisons of these two structures with known structures of related proteins suggest that these proteins possess versatility in substrate recognition and variations in protein-protein interactions with their cognate transmembrane domains.

Analysis of protection afforded by a Clostridium perfringens α-toxoid against heterologous clostridial phospholipases C

The major virulence determinant in clostridial myonecrosis caused by Clostridium perfringens is a phospholipase C (PLC), the alpha-toxin. Previously, mice have been protected against challenge with heterologous alpha-toxin or Clostridium perfringens spores by immunisation with the C-domain (known as Cpa(247-370) or alpha-toxoid) of the alpha-toxin. In this study, we have determined the ability of the alpha-toxoid to protect against the lethal effects of a divergent C. perfringens alpha-toxin and against the PLCs of C. absonum or C. bifermentans, species which have been isolated from cases of clostridial myonecrosis. Protection against the C. perfringens alpha-toxin variant, the C. absonum alpha-toxin or the C. bifermentans PLC was elicited by immunisation with the alpha-toxoid in vivo.

Immunisation with anthrolysin O or a genetic toxoid protects against challenge with the toxin but not against Bacillus anthracis

Anthrolysin O (ALO) is a toxin produced by Bacillus anthracis, the causative agent of anthrax. It is a member of the cholesterol-dependent cytolysin (CDC) group of toxins, many of which are potential vaccine candidates that protect against their producing organisms. Pore formation by ALO was studied by transmission electron microscopy and pores were found to be consistent with those formed by other members of this toxin family. We constructed and characterised a novel genetic toxoid of anthrolysin O, Delta6mALO, which was able to bind to cells but was incapable of pore-formation or haemolysis. The capacity of the haemolytic and non-haemolytic forms of ALO to protect against challenge with the toxin or B. anthracis was determined. Immunisation with both active and non-haemolytic forms of ALO elicited protection against lethal i.v. challenge with ALO but neither was protective against B. anthracis in a murine i.p. challenge model. Immunisation with another CDC, pneumolysin, did not confer cross-protection against challenge with ALO. Histopathological investigation following lethal i.v. challenge with ALO revealed acute pathology in the lungs with occlusion of alveolar vessels by fibrin deposits.

Concomitant administration of Yersinia pestis specific monoclonal antibodies with plague vaccine has a detrimental effect on vaccine mediated immunity

Antibodies can be used to confer rapid immunity against infectious agents for short periods of time. By comparison, vaccine induced immunity is more protective, but takes a relatively long time to develop. Concomitant administration of antibody and vaccine by different routes was evaluated as a means of providing both rapid and long-term protection against plague. BALB/c mice were treated intraperitoneally with monoclonal antibodies, with specificities for Yersinia pestis LcrV and F1 antigens. A cohort of these mice was simultaneously vaccinated with rF1 and rLcrV by the intramuscular route. Antibody co-administration with vaccine reduced the level of vaccine mediated protection afforded against a high level Y. pestis challenge. Conversely, antibody-mediated protection was unaffected by vaccine co-administration and lasted for at least 8 weeks post administration. We also evaluated the effect of administering vaccine intradermally and antibody intratracheally and observed that, irrespective of administration route, concomitant administration of antibody reduced the effectiveness of vaccine mediated immunity. The results of passive transfer experiments supported the thesis that the development of protective antibody responses following vaccination is impaired by the presence of circulating monoclonal antibodies with specificities for important B-cell epitopes in the vaccine. We also noted that intradermal injection of LcrV antigen and cholera toxin adjuvant afforded good levels of protection against systemic and aerosol challenge with Y. pestis: intradermal injection might therefore be considered as a potential minimally invasive method of plague vaccine administration. These data have implications for the design of therapeutic strategies against plague infection.

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis

MOTIVATION

An important application of protein microarray data analysis is identifying a serodiagnostic antigen set that can reliably detect patterns and classify antigen expression profiles. This work addresses this problem using antibody responses to protein markers measured by a novel high-throughput microarray technology. The findings from this study have direct relevance to rapid, broad-based diagnostic and vaccine development.

RESULTS

Protein microarray chips are probed with sera from individuals infected with the bacteria Francisella tularensis, a category A biodefense pathogen. A two-step approach to the diagnostic process is presented (1) feature (antigen) selection and (2) classification using antigen response measurements obtained from F.tularensis microarrays (244 antigens, 46 infected and 54 healthy human sera measurements). To select antigens, a ranking scheme based on the identification of significant immune responses and differential expression analysis is described. Classification methods including k-nearest neighbors, support vector machines (SVM) and k-Means clustering are applied to training data using selected antigen sets of various sizes. SVM based models yield prediction accuracy rates in the range of approximately 90% on validation data, when antigen set sizes are between 25 and 50. These results strongly indicate that the top-ranked antigens can be considered high-priority candidates for diagnostic development.

AVAILABILITY

All software programs are written in R and available at http://www.igb.uci.edu/index.php?page=tools and at http://www.r-project.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Protection afforded against aerosol challenge by systemic immunisation with inactivated Francisella tularensis live vaccine strain (LVS)

BALB/c mice were immunised with inactivated Francisella tularensis live vaccine strain (LVS) and the level of protection afforded against aerosol challenge with virulent strains of F. tularensis ascertained. Intramuscular (IM) injection of inactivated LVS with an aluminium-hydroxide-based adjuvant-stimulated IgG1-biased LVS-specific antibody responses and afforded no protection against aerosol challenge with subspecies holarctica (strain HN63). Conversely, IM injection of inactivated LVS adjuvanted with preformed immune-stimulating complexes (ISCOMS) admixed with immunostimulatory CpG oligonucleotides afforded robust protection against aerosol-initiated infection with HN63. However, despite a significantly extended time-to-death relative to naïve controls, the majority of mice immunised with the most potent vaccine formulation were not protected against a low-dose aerosol challenge with subspecies tularensis (strain Schu S4). These data indicate that parenterally administered non-living vaccines can be used for effective immunisation against aerosol challenges with subspecies holarctica, although not high virulence strains of F. tularensis.

Polysaccharides and virulence of Burkholderia pseudomallei

Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease of humans and animals. Gene clusters which encode capsular polysaccharide (type I O-PS) and LPS (type II O-PS), both of which play roles in virulence, have previously been identified. Here, the identification of two further putative clusters, type III O-PS and type IV O-PS, is reported. Mice challenged with type III O-PS or type IV O-PS mutants showed increased mean times to death (7.8 and 11.6 days) compared to those challenged with wild-type B. pseudomallei (3 days). To investigate the possible roles of polysaccharides in protection, mice were immunized with killed cells of wild-type B. pseudomallei or killed cells of B. pseudomallei with mutations in the O antigen, capsular polysaccharide, type III O-PS or type IV O-PS gene clusters. Immunization with all polysaccharide mutant strains resulted in delayed time to death compared to the naïve controls, following challenge with wild-type B. pseudomallei strain K96243. However, immunization with killed polysaccharide mutant strains conferred different degrees of protection, demonstrating the immunological importance of the polysaccharide clusters on the surface of B. pseudomallei.

Identification of a LolC homologue in Burkholderia pseudomallei, a novel protective antigen for melioidosis

Melioidosis is an emerging disease of humans in Southeast Asia and tropical Australia. The bacterium causing this disease, Burkholderia pseudomallei, is also considered a bioterrorism agent, and as yet there is no licensed vaccine for preventing B. pseudomallei infection. In this study, we evaluated selected proteins (LolC, PotF, and OppA) of the ATP-binding cassette systems of B. pseudomallei as candidate vaccine antigens. Nonmembrane regions of the B. pseudomallei proteins were expressed and purified from Escherichia coli and then evaluated as vaccine candidates in an established mouse model of B. pseudomallei infection. When delivered with the monophosphoryl lipid A-trehalose dicorynomycolate adjuvant, the proteins stimulated antigen-specific humoral and cellular immune responses. Immunization with LolC or PotF protein domains afforded significant protection against a subsequent challenge with B. pseudomallei. The most promising vaccine candidate, LolC, provided a greater level of protection when it was administered with immune-stimulating complexes complexed with CpG oligodeoxynucleotide 10103. Immunization with LolC also protected against a subsequent challenge with a heterologous strain of B. pseudomallei, demonstrating the potential utility of this protein as a vaccine antigen for melioidosis.

Francisella tularensis genomics and proteomics

The availability of the genome sequences of different strains of Francisella tularensis is having a major impact on a wide range of research projects, from understanding the biology of this organism to devising vaccines and diagnostics. Comparative genomics and molecular typing methods suggest that the four different subspecies of F. tularensis are genetically distinct groups. Although there is a high degree of nucleotide identity between strains, there are numerous DNA rearrangements. IS elements appear to have played a major role in these chromosomal rearrangements. The different subspecies of F. tularensis appear to have evolved by vertical descent from a common ancestor, probably F. tularensis subspecies novicida. Comparative genomic and proteomic studies have revealed possible reasons for the different virulence of different strains and a range of candidate virulence genes have been identified including those located on the Francisella pathogenicity island. Proteomic studies have identified proteins which are produced at elevated levels in vivo, and proteins which are recognized by immune or convalescent sera. These proteins might be exploited as components of vaccines or diagnostic systems.

Biosafety and selectable markers

Francisella tularensis (F. tularensis) is one of the most infectious pathogens known. Although the disease caused by this bacterium is rarely fatal with appropriate antibiotic therapy, it is often severely debilitating. Laboratory work with F. tularensis poses a significant hazard, and it is essential that appropriate laboratory facilities, trained personnel, and suitable working practices are in place in any organization working with this pathogen. Work with human virulent strains should be carried out at containment level 3. Vaccines play an important potential role in the protection of individuals working with F. tularensis, but the live vaccine strain (LVS) vaccine is not currently licensed for use in humans. Because antibiotic therapy is central to the treatment of human tularemia, antibiotic resistance markers for use in genetic manipulation studies should be carefully selected.

Vincent G, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE, Guryčová D, Minton NP, Titball RW, Pallen MJ, Vipond R. Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4

Background

Francisella tularensis causes tularaemia, a life-threatening zoonosis, and has potential as a biowarfare agent. F. tularensis subsp. tularensis, which causes the most severe form of tularaemia, is usually confined to North America. However, a handful of isolates from this subspecies was obtained in the 1980s from ticks and mites from Slovakia and Austria. Our aim was to uncover the origins of these enigmatic European isolates.

Methodology/Principal Findings

We determined the complete genome sequence of FSC198, a European isolate of F. tularensis subsp. tularensis, by whole-genome shotgun sequencing and compared it to that of the North American laboratory strain Schu S4. Apparent differences between the two genomes were resolved by re-sequencing discrepant loci in both strains. We found that the genome of FSC198 is almost identical to that of Schu S4, with only eight SNPs and three VNTR differences between the two sequences. Sequencing of these loci in two other European isolates of F. tularensis subsp. tularensis confirmed that all three European isolates are also closely related to, but distinct from Schu S4.

Conclusions/Significance

The data presented here suggest that the Schu S4 laboratory strain is the most likely source of the European isolates of F. tularensis subsp. tularensis and indicate that anthropogenic activities, such as movement of strains or animal vectors, account for the presence of these isolates in Europe. Given the highly pathogenic nature of this subspecies, the possibility that it has become established wild in the heartland of Europe carries significant public health implications.

The identification of surface proteins of Burkholderia pseudomallei

Burkholderia pseudomallei, the causative agent of the disease melioidosis is a human pathogen endemic in Northern Australia and South-East Asia. At present there is no available vaccine or effective treatment for this disease. Surface proteins play crucial roles in the host-pathogen interaction and have been exploited as vaccine candidates and diagnostic targets. Therefore, we wished to identify immunogenic surface proteins of B. pseudomallei. To this end we used two proteomic-based approaches in parallel: a biotinylation approach for the detection of surface located proteins identified 35 proteins, while screening with human sera identified 12 immunogenic proteins. Nine of these proteins were identified by both methods indicating that they may be both surface located and immunogenic: these proteins will be evaluated further as vaccine candidates and diagnostic targets.

Francisella tularensis vaccines

Francisella tularensis is the causative agent of tularaemia, a disease which occurs naturally in some countries in the northern hemisphere. Recently, there has been a high level of interest in devising vaccines against the bacterium because of the potential for it to be used as a bioterrorism agent. Previous human volunteer studies have shown that a strain of F. tularensis [the live vaccine strain (LVS)] that has been attenuated by laboratory passage is effective in humans as a vaccine against airborne disease. However, for a variety of reasons it seems unlikely that the LVS strain will be licensed for use in humans. Against this background there is an effort to devise a licensable vaccine against tularaemia. The prospects for a killed whole-cell subunit of live attenuated vaccine are reviewed. A rationally attenuated mutant seems the most likely route to a new tularaemia vaccine.

Kinetics of the immune response to the (F1+V) vaccine in models of bubonic and pneumonic plague

Protection against aerosol challenge with > 300 MLD of Yersinia pestis was observed 7 days after a single immunisation of mice with the F1+V vaccine. At day 60, mice were protected against injected challenge (10(7)MLD) in a vaccine dose-related manner. Recall responses to rV in splenocytes ex vivo at day 98 correlated significantly (p<0.001) with the immunising dose-level of V antigen; no memory response or anti-V serum IgG was detected in killed whole cell vaccine (KWCV) recipients. This may explain the susceptibility of KWCV recipients to aerosol challenge and the enhanced protection conferred by the F1+V sub-unit vaccine, particularly since the anti-F1 responses induced by either vaccine were similarly IgG1-polarised.

Identification of outer membrane proteins of Yersinia pestis through biotinylation

The outer membrane of Gram-negative bacteria contains proteins that might be good targets for vaccines, antimicrobials or detection systems. The identification of surface located proteins using traditional methods is often difficult. Yersinia pestis, the causative agent of plague, was labelled with biotin. Tagged proteins were visualised through streptavidin probing of Western blots. Seven biotinylated proteins of Y. pestis were identified including two porins and the putative virulence factor catalase peroxidase.

Development of signature-tagged mutagenesis in Burkholderia pseudomallei to identify genes important in survival and pathogenesis

Burkholderia pseudomallei, the causative agent of melioidosis, is an important human pathogen in Southeast Asia and northern Australia for which a vaccine is unavailable. A panel of 892 double signature-tagged mutants was screened for virulence using an intranasal BALB/c mouse model of infection. A novel DNA tag microarray identified 33 mutants as being attenuated in spleens, while 6 were attenuated in both lungs and spleens. The transposon insertion sites in spleen-attenuated mutants revealed genes involved in several stages of capsular polysaccharide biosynthesis and DNA replication and repair, a putative oxidoreductase, ABC transporters, and a lipoprotein that may be important in intercellular spreading. The six mutants identified as missing in both lungs and spleens were found to have insertions in recA involved in the SOS response and DNA repair; putative auxotrophs of leucine, threonine, p-aminobenzoic acid, and a mutant with an insertion in aroB causing auxotrophy for aromatic compounds were also found. Murine challenge studies revealed partial protection in BALB/c mice vaccinated with the aroB mutant. The refined signature-tagged mutagenesis approach developed in this study was used to efficiently identify attenuating mutants from this highly pathogenic species and could be applied to other organisms.

A Francisella tularensis subspecies novicida purF mutant, but not a purA mutant, induces protective immunity to tularemia in mice

Francisella tularensis subspecies novicida mutants have been made with deletions introduced into the purA or purF genes. These mutants demonstrated the expected growth requirement for purines and complementation with the wild type genes restored the ability to grow on purine deficient media. The mutants were at least 10,000-fold attenuated by the ip challenge route in Balb/C mice and defective for survival in J774A.1 mouse macrophages. Immunisation with the purA mutant did not provide protection against a subsequent challenge with 100 median lethal doses of F. tularensis subspecies novicida. Immunisation of mice with the purF mutant provided protection against a subsequent challenge with F. tularensis subspecies novicida but not against a subspecies tularensis challenge. These findings suggest that purine auxotrophs of F. tularensis should be further evaluated as live attenuated vaccines against tularemia, but that differential effects are seen depending on which step in the biosynthetic pathway is inactivated.

Oral administration of a Salmonella enterica-based vaccine expressing Bacillus anthracis protective antigen confers protection against aerosolized B. anthracis

Bacillus anthracis is the causative agent of anthrax, a disease that affects wildlife, livestock, and humans. Protection against anthrax is primarily afforded by immunity to the B. anthracis protective antigen (PA), particularly PA domains 4 and 1. To further the development of an orally delivered human vaccine for mass vaccination against anthrax, we produced Salmonella enterica serovar Typhimurium expressing full-length PA, PA domains 1 and 4, or PA domain 4 using codon-optimized PA DNA fused to the S. enterica serovar Typhi ClyA and under the control of the ompC promoter. Oral immunization of A/J mice with Salmonella expressing full-length PA protected five of six mice against a challenge with 10(5) CFU of aerosolized B. anthracis STI spores, whereas Salmonella expressing PA domains 1 and 4 provided only 25% protection (two of eight mice), and Salmonella expressing PA domain 4 or a Salmonella-only control afforded no measurable protection. However, a purified recombinant fusion protein of domains 1 and 4 provided 100% protection, and purified recombinant 4 provided protection in three of eight immunized mice. Thus, we demonstrate for the first time the efficacy of an oral S. enterica-based vaccine against aerosolized B. anthracis spores.

Down-regulation of gene transcripts associated with ricin tolerance in human RPMI 2650 cells

The present study sought to determine if novel therapeutic approaches against ricin intoxication could be identified from human respiratory tract cells selected for increased resistance to this toxin. Initial studies indicated that the RPMI 2650 line was an appropriate model, owing to its sensitivity to ricin. Tolerant cultures were developed by exposing cells to a graded series of ricin concentrations from 6 to 192 pM. This resulted in the generation of cultures whose LC(50) values were increased by up to 4-fold following exposure to up to 96 pM ricin and by up to 6-fold following exposure to up to 192 pM ricin, compared to control cultures. DNA microarrays were employed to determine the gene transcript expression profile of cultures with increased resistance to ricin to investigate which gene products mediate ricin resistance. Transcripts (10) were identified that were greater than 2-fold down-regulated in the cells tolerant to 96 pM ricin, whereas 48 transcripts were seen to be down-regulated in cultures tolerant to 192 pM ricin. Gene transcripts (5) were up-regulated 2-fold or more in the 192 pM tolerant cultures in comparison to unexposed cells. The results indicate that ricin tolerance is the product of complex changes in gene expression profiles, most of which were found to involve down-regulation of transcript expression. It may be possible to modulate the gene expression profiles associated with ricin tolerance for potential therapeutic purposes using drugs and antisense technologies.