A common gene pool for the Neisseria FetA antigen

Europe PMC Funders Group Author Manuscript Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Published in final edited form as: Int J Med Microbiol. 2009 February ; 299(2): 133–139. doi:10.1016/j.ijmm.2008.06.010. Europe PMC Funders Author Manuscripts A common gene pool for the Neisseria FetA antigen Julia S. Bennetta,*, Emily A. L. Thompsona, Paula Krizb, Keith A. Jolleya, and Martin C. J. Maidena aThe Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK bNational Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic Abstract Meningococcal FetA is an iron-regulated, immunogenic outer membrane protein and vaccine component. The most diverse region of this protein is a previously defined variable region (VR) that has been shown to be immunodominant. In this analysis, a total of 275 Neisseria lactamica isolates, collected during studies of nasopharyngeal bacterial carriage in infants were examined for the presence of a fetA gene. The fetA VR nucleotide sequence was determined for 217 of these isolates, with fetA apparently absent from 58 isolates, the majority of which belonged to the ST-624 clonal complex. The VR in N. lactamica was compared to the same region in Neisseria meningitidis, Neisseria gonorrhoeae and a number of other commensal Neisseria. Identical fetA variable region sequences were identified among commensal and pathogenic Neisseria, suggesting a common gene pool, differing from other antigens in this respect. Carriage of commensal Neisseria species, such as N. lactamica, that express FetA may be involved in the development of natural immunity to meningococcal disease. Europe PMC Funders Author Manuscripts Keywords FetA; Neisseria meningitidis; commensal Neisseria; gene pool Introduction Neisseria meningitidis is a major cause of meningitis and septicaemia. Although vaccines based on serogroups A, C, Y and W135 are effective, a comprehensive vaccine is not yet available, and the development of a vaccine against serogroup B meningococci is hampered by the similarity of its capsule to host antigens and its poor immunological reactivity (Finne et al., 1987). Serogroup B meningococci are responsible for a large burden of disease in North America and Europe, causing over 85% of meningococcal disease in England and Wales since the introduction of a serogroup C conjugate vaccine (Gray et al., 2006) and so the development of an effective vaccine based on these organisms is a priority for many public health authorities. Approaches to designing vaccines that protect against serogroup B meningococcal disease have focused on immunogenic non-capsular outer membrane proteins. Some vaccine formulations include the immunodominant outer membrane protein FetA (Wedege et al., * Corresponding author. Mailing address: The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK. Telephone: +44 (0)1865 281537, Fax: +44 (0)1865 281275, [email protected]. Bennett et al. Page 2 Europe PMC Funders Author Manuscripts 1998; Vipond et al., 2005), an iron regulated, TonB-dependent enterobactin receptor (Pettersson et al., 1990; Ala’Aldeen et al., 1994; Beucher & Sparling, 1995). A recent topology model of FetA, also known as FrpB, predicts a 22-stranded β-barrel with 11 surface exposed loops and an N-terminal plug domain that closes the barrel (Kortekaas et al., 2007). Loop 5 of this model corresponds to a variable region (VR) previously shown to contain epitopes for mouse monoclonal antibodies (van der Ley et al., 1996) and currently used in high resolution molecular typing of meningococci (Jolley et al., 2007). Although FetA is known to be diverse in meningococci, with allelic variants generated by both point mutation and horizontal genetic exchange (Thompson et al., 2003), research suggests that it could be a valuable component of vaccines that combine variant sequences from both FetA and PorA (Urwin et al., 2004). Acquisition of natural immunity to meningococcal disease in childhood may follow nasopharyngeal colonization by non-pathogenic species of Neisseria such as N. lactamica that express immunologicallycross-reactive surface antigens shared with the meningococcus (Gold et al., 1978; Griffiss et al., 1987). N. lactamica expresses FetA (Sanchez et al., 2006) and the N. lactamica isolate (020-06) that has been completely sequenced at The Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/Projects/N_lactamica/) has a FetA antigen with around 90% sequence identity to meningococcal strains Z2491 (Parkhill et al., 2000), MC58 (Tettelin et al., 2000) and FAM18 (Bentley et al., 2007), and is of similar size. Vaccines based on N. lactamica whole cells, outer membrane proteins, or outer membrane vesicles have been proposed (Griffiss et al., 1991; Oliver et al., 2002) and a vaccine based on N. lactamica outer membrane vesicles is being developed, with FetA as a component (Finney et al., 2007). However, the antigenic determinants in commensal Neisseria that induce cross-reactive immune responses to meningococcal infection, have not been defined (Tang et al., 1999), and the variability of FetA in commensal Neisseria and its relationship to meningococcal FetA has not been documented. Europe PMC Funders Author Manuscripts In this study, 275 N. lactamica isolates, collected from infants and a small number of siblings and parents during studies of nasopharyngeal bacterial carriage, were examined to assess the diversity of the FetA VR in this species. These isolates, collected in the UK, had previously been characterized by multilocus sequence typing (MLST) (Maiden et al., 1998; Bennett et al., 2005) with 72 distinct sequence types (STs) identified. The FetA VR sequences from N. lactamica were compared to the VR sequences from other nonpathogenic and pathogenic Neisseria to investigate relatedness and the potential for this commensal Neisseria antigen contributing to meningococcal immunity. Materials and methods Isolates Details of the 275 N. lactamica isolates, collected in Oxfordshire, UK, are available from the Neisseria MLST database: http://pubmlst.org/neisseria/ (Jolley et al., 2004). The genetic diversity of these N. lactamica isolates was similar to that seen in N. lactamica from other locations and likely to be representative of the global diversity. There is no evidence that these isolates form a separate population and the collection contained representatives from five of six clonal complexes currently defined for N. lactamica (Bennett, 2006). Nucleotide sequences of the fetA VR from these isolates were compared to sequences determined for a study of antigenic diversity in meningococcal FetA (Thompson, et al., 2003). These sequences were obtained from the 107 meningococcal isolates used to validate MLST (Maiden, et al., 1998), and assembled to represent the global diversity of meningococci in the mid to latter part of the twentieth century. Also included were fetA VR nucleotide sequences from a collection of meningococci obtained in the Czech Republic and characterized using MLST, which comprised 339 carried meningococci isolated between Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Bennett et al. Page 3 1992 and 1997 (Jolley et al., 2002; Yazdankhah et al., 2004; Jolley et al., 2005; Bennett et al., 2007) and 53 disease related meningococci, collected during 1993. Gene sequences from nine other meningococcal isolates were obtained from GenBank with the following accession numbers: AL162753; AE002548; U55377; U55378; U67310; U67311; U67312; U67313 and U67314. Europe PMC Funders Author Manuscripts Nucleotide sequences of the fetA VR were also determined for a collection of 33 nonpathogenic members of the genus Neisseria which had undergone microbiological and biochemical characterization (Barrett & Sneath, 1994), The collection included six Neisseria cinerea; one Neisseria flava; three Neisseria flavescens; 10 N. lactamica; six Neisseria mucosa; five Neisseria polysaccharea and two Neisseria subflava. A total of 11 fetA VR nucleotide sequences were available for Neisseria gonorrhoeae, including nine obtained from isolates provided by Prof. C. A. Hart, University of Liverpool, UK, and two from GenBank with accession numbers U13980 and AF115385. The VR nucleotide and peptide sequences used are available from the Neisseria FetA database: http://neisseria.org/nm/ typing/feta/. Nucleotide sequence determination Nucleotide sequence determination of the FetA VR was undertaken as described previously (Thompson, et al., 2003). Briefly, sequence templates were generated using PCRs with primers 12 and 4 (van der Ley, et al., 1996), and occasionally A14 (Carson et al., 1999), and then purified by precipitation with polyethylene glycol and sodium chloride (Embley, 1991). The termination products were generated by cycle sequencing using combinations of the primers S1, S8, S12, S13, S15 (Thompson, et al., 2003), and BigDye terminators (Applied Biosystems). The products were then separated with either a Prism 3700 DNA analyser or a Prism 377 DNA analyser (Applied Biosystems). The sequence of each strand was determined at least once, and the resultant DNA sequences were assembled using the STADEN suite of computer programs (Staden, 1996). Analysis of sequence data Europe PMC Funders Author Manuscripts Nucleotide sequences were manually aligned and translated using the SeqLab program, part of the GCG Wisconsin package, version 10.3 (Womble, 2000). Alignments were based on amino acid sequence similarity, and codon integrity was maintained. The sequence data was imported into MEGA 3.1 (Kumar et al., 2004) to construct Neighbour-joining trees from amino acid p-distances. The VR nucleotide sequences from N. lactamica were compared with those from N. meningitidis, using DnaSP 4.0 (Rozas et al., 2003) to calculate shared polymorphisms and fixed differences, and Arlequin 2.0 (Schneider et al., 2000) to compute pairwise FST. FST values indicate levels of gene flow between populations, with a value of one indicating no gene flow (100% differentiated populations) and zero indicating free genetic exchange (no population differentiation). Results and discussion Nucleotide sequences of the fetA VR were determined for 217 N. lactamica isolates collected in Oxfordshire, with fetA apparently absent from 58 isolates. The fetA gene was considered absent if it could not be amplified by the PCR employing combinations of the fetA PCR and sequencing primers which are complimentary to conserved DNA sequences within Neisseria. Particular VRs were associated with MLST STs, and the majority of the isolates that lacked fetA belonged to the ST-624 clonal complex, with fetA apparently absent from all isolates belonging to this complex. Lack of fetA has also been reported among meningococcal isolates (Claus et al., 2007; Marsh et al., 2007), with deletions mediated by repeat arrays flanking the gene. Deletion in the meningococcus, however, is considered to be Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Bennett et al. Page 4 a rare occurrence. The majority of N. lactamica isolates used in this study were obtained from UK population studies and it is not known whether fetA deletion is common in other isolate collections. Isolates of N. lactamica belonging to the ST-624 clonal complex have also been collected in Germany and Malawi (http://pubmlst.org/neisseria/), although it has not been established whether fetA is absent from these related isolates. Europe PMC Funders Author Manuscripts Among the Oxfordshire N. lactamica isolates, 28 unique fetA VR nucleotide sequences, corresponding to 28 unique peptide sequences, were determined. These were grouped on the basis of peptide sequence similarity and sequence length into five VR families, as previously defined for the meningococcus and designated F1-F5 (Thompson, et al., 2003). A total of 14 VR sequences were identified as family F1 variants, two as family F2, five as family F3, three as family F4 and four as family F5. Of the 28 variants, 17 were present in isolates obtained from single individuals. The most common variant was F1-25, found among N. lactamica isolates with seven different STs obtained from 10 unrelated individuals. Neighbour-joining trees, one for each of the five VR families, were constructed from FetA amino acid sequences from all eight species analysed (Figure 1). The phylogenies produced show that sequences from named species could be more closely related to sequences from other Neisseria, than to their own defined species and that identical peptide sequences were distributed among many neisseriae. There was little evidence for distinct, species specific clusters and examples of both commensals and pathogens were present within each family. An interrogation of the FetA database (http://neisseria.org/nm/typing/feta/) provided other examples of VR sharing between species. For example, the fetA VR sequence from FAM18, a representative of the ST-11 complex and a disease causing serogroup C strain (Bentley, et al., 2007), is the same as the fetA VR from N. lactamica isolates obtained from an infant between the age of 10 weeks and six months. The majority of amino acid sequences were encoded by single nucleotide sequences, apart from five family F5 variants (5-1, 5-6, 5-8, 5-12, 5-19), which differed by one to two nucleotides. The sharing of identical nucleotide sequences among species could be a consequence of either shared ancestry, which seems unlikely for a gene sequence under positive selection, or recent interspecies genetic exchange. Europe PMC Funders Author Manuscripts VR nucleotide sequences from N. lactamica and N. meningitidis were compared to determine gene flow and genetic similarity (Table 1). The nucleotide sequences from the other Neisseria were not included in this analysis as there were too few examples from each species in the dataset. The frequency of polymorphisms shared between N. lactamica and N. meningitidis indicated a high level of genetic similarity. There were no fixed differences between the nucleotide sequences in any of the five VR families examined, and FST values of zero indicated high gene flow between N. lactamica and N. meningitidis, with sequences not statistically genetically different (p>0.05). The high levels of diversity among the VRs, the sharing of identical nucleotide sequences, the sharing of polymorphisms, the absence of fixed differences and a FST value of zero between N. lactamica and N. meningitidis, indicate a common gene pool for the fetA VR, with frequent genetic exchange among neisseriae at this locus. A common gene pool has also been described for tbpB (Linz et al., 2000), although it differs from fetA in that imports of DNA from commensal species into meningococci are from a distinct tbpB family and reduce variant fitness (Zhu et al., 2001). Horizontal genetic exchange must be sufficiently rare among the Neisseria to maintain species as distinct biological entities (Maiden et al., 1996) and not all antigens have common gene pools. The N. lactamica porin for example, is distinct from the porins of N. meningitidis and N. gonorrhoeae (Derrick et al., 1999) (Bennett et al., in press), and some meningococcal antigens, such as TspA (Oldfield et al., 2007) and NadA (Comanducci et al., 2002), may not be expressed by N. lactamica. Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Bennett et al. Page 5 Europe PMC Funders Author Manuscripts Commensal Neisseria expressing immunologically cross-reactive surface antigens shared with meningococci are vaccine candidates, although at present only N. lactamica and its antigens have been studied intensively as components in vaccines against meningococcal disease (Oliver, et al., 2002; Gorringe et al., 2005; Sardinas et al., 2006). As N. lactamica is acapsular (Griffiss, et al., 1987) and does not possess the immunodominant antigen PorA (Derrick, et al., 1999), other antigens would be necessary to induce anti-meningococcal immunity. Antigens from N. lactamica and other commensal species, that have a high degree of sequence similarity to N. meningitidis, such as the FetA VR, are likely to be the most effective. It has been proposed that carriage of commensal Neisseria, such as N. lactamica contributes to the development of natural immunity to meningococcal disease (Gold, et al., 1978). Expression of outer membrane proteins such as FetA could be involved in this immunity. This should be taken into consideration when designing vaccines that include these crossreactive antigens, as it has been suggested that their use could impede the acquisition of natural immunity to meningococcal disease by preventing colonization by commensals (Sanchez et al., 2002). However, the effect of vaccination on commensals related to N. meningitidis has yet to be established in humans. Acknowledgments Julia Bennett was funded by the Meningitis Research Foundation. Emily Thompson was funded by a Biotechnology and Biological Sciences Research Council CASE studentship awarded to the University of Oxford and the National Institute for Biological Standards and Control. Paula Kriz was supported by grant No. 1A8688-3/05 of the Internal Grant Agency of Ministry of Health of the Czech Republic. Martin Maiden is a Wellcome Trust Senior Research Fellow and Keith Jolley is funded by The Wellcome Trust. The N. lactamica samples were obtained from studies carried out by the Oxford Vaccine Group supported by the Wellcome Trust, reference number: 056886/2/994/Z. We would like to thank the staff of the Oxford Vaccine Group for supporting the collection of samples and the families and children who participated in the studies. The authors are grateful to Tony Hart for providing the gonococcal samples. Europe PMC Funders Author Manuscripts References Ala’Aldeen D, Davies HA, Borriello SP. Vaccine potential of meningococcal FrpB: studies on surface exposure and functional attributes of common epitopes. Vaccine. 1994; 12:535–541. [PubMed: 7518627] Barrett SJ, Sneath PHA. A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology. 1994; 140:2867–2891. [PubMed: 8000550] Bennett, JS. 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Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc. Natl. Acad. Sci. USA. 2001; 98:5234–9. [PubMed: 11287631] Europe PMC Funders Author Manuscripts Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Bennett et al. Page 9 Europe PMC Funders Author Manuscripts Europe PMC Funders Author Manuscripts Figure 1. Neighbour-joining trees showing the relationships among five families of FetA VR sequences from Neisseria. Model: Amino acid p-distance. Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28. Bennett et al. Page 10 Table 1 Genetic variation of fetA VR families from N. lactamica and N. meningitidis Europe PMC Funders Author Manuscripts fetA family F1 F2 F3 F4 F5 No. of N. lactamica isolates 88 6 49 42 43 No. of N. meningitidis isolates 224 2 153 30 99 No. of N. lactamica nucleotide variants 17 2 5 3 5 No. of N. meningitidis nucleotide variants 22 2 9 6 19 Length of aligned nucleotide sequences 96 78 117 120 126 Total no. of polymorphic sites 58 6 52 38 67 Total no. of polymorphisms 79 7 62 42 77 Fst within family* 0.00 0.00 0.00 0.00 0.00 Shared polymorphisms 59 0 50 16 55 Fixed differences 0 0 0 0 0 * p>0.05, indicating that the populations were not significantly genetically different Europe PMC Funders Author Manuscripts Int J Med Microbiol. Author manuscript; available in PMC 2014 March 28.