Distribution of Bexsero® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation.

Serogroup B is the only major disease-associated capsular group of Neisseria meningitidis for which no protein-polysaccharide conjugate vaccine is available. This has led to the development of multi-component protein-based vaccines that target serogroup B invasive meningococcal disease (IMD), including Bexsero®, which was implemented for UK infants in 2015, and Trumenba®. Given the diversity of meningococcal protein antigens, post-implementation surveillance of IMD isolates, including characterisation of vaccine antigens, is essential for assessing the effectiveness of such vaccines. Whole genome sequencing (WGS), as realised in the Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL), provides a rapid, comprehensive, and cost-effective approach to this. To facilitate the surveillance of the antigen targets included in Bexsero® (fHbp, PorA, NHBA and NadA) for protective immunity, a Bexsero® Antigen Sequence Type (BAST) scheme, based on deduced peptide sequence variants, was implemented in the PubMLST.org/neisseria database, which includes the MRF-MGL and other isolate collections. This scheme enabled the characterisation of vaccine antigen variants and here the invasive meningococci isolated in Great Britain and Ireland in the epidemiological years 2010/11 to 2013/14 are analysed. Many unique BASTs (647) were present, but nine of these accounted for 39% (775/1966) of isolates, with some temporal and geographic differences in BAST distribution. BASTs were strongly associated with other characteristics, such as serogroup and clonal complex (cc), and a significant increase in BAST-2 was associated with increased prevalence of serogroup W clonal complex 11 meningococci. Potential coverage was assessed by the examination of the antigen peptide sequences present in the vaccine and epidemiological dataset. There were 22.8-30.8% exact peptide matches to Bexsero® components and predicted coverage of 66.1%, based on genotype-phenotype modelling for 63.7% of serogroup B isolates from 2010/14 in UK and Ireland. While there are many caveats to this estimate, it lies within the range of other published estimates

Variation of the factor H-binding protein of Neisseria meningitidis

There is currently no comprehensive meningococcal vaccine, due to difficulties in immunizing against organisms expressing serogroup B capsules. To address this problem, subcapsular antigens, particularly the outer-membrane proteins (OMPs), are being investigated as candidate vaccine components. If immunogenic, however, such antigens are often antigenically variable, and knowledge of the extent and structuring of this diversity is an essential part of vaccine formulation. Factor H-binding protein (fHbp) is one such protein and is included in two vaccines under development. A survey of the diversity of the fHbp gene and the encoded protein in a representative sample of meningococcal isolates confirmed that variability in this protein is structured into two or three major groups, each with a substantial number of alleles that have some association with meningococcal clonal complexes and serogroups. A unified nomenclature scheme was devised to catalogue this diversity. Analysis of recombination and selection on the allele sequences demonstrated that parts of the gene are subject to positive selection, consistent with immune selection on the protein generating antigenic variation, particularly in the C-terminal region of the peptide sequence. The highest levels of selection were observed in regions corresponding to epitopes recognized by previously described bactericidal monoclonal antibodies

The temporal and geographical distribution and diversity of disease-associated Neisseria meningitidis genetic types in Europe

Meningococcal disease, caused by the bacterium Neisseria meningitidis, is an important cause of morbidity and mortality in young children and adolescents worldwide. There are 12 serogroups with most disease due to meningococci expressing one of five capsular polysaccharide antigens corresponding to serogroups A, B, C, Y and W135. In Europe, the majority of disease-causing strains are of serogroups B and C. No comprehensive vaccine is available against the bacterium due to the difficulty in producing serogroup B vaccines. A number of countries, e.g. UK and the Republic of Ireland have implemented routine meningococcal conjugate C (MCC) vaccine strategies. Due to the high proportion of disease accounted for by serogroup B in Europe and other developed countries, much research is currently being carried out to unearth vaccine candidates that would be protective and give as wide coverage as possible. Such candidates include the antigens PorA, FetA and factor H-binding protein. Potential drawbacks with antigens such as these which are under immune selection are high degrees of variability and lack of cross-immunity. Determination of the distribution, both geographically and temporally, of antigens and their association with clonal complex can aid in the formulation of novel vaccines and assess their potential coverage across Europe. Serological typing schemes involving characterisation of the polysaccharide capsule (serogroup) and outer membrane proteins such as PorA (serosubtype) and PorB (serotype) have been used for a number of years with some success. However, drawbacks associated with these methods include insufficient discrimination, limitations in panels of monoclonal antibodies used in the typing procedures and difficulty in comparison of results among labs. Consequently, in recent years genotypic methods such as multi-locus enzyme electrophoresis (MLEE) and subsequently multi-locus sequence typing (MLST) have been developed. These methods measure the variation in slowly evolving housekeeping genes whereas serological methods measure variation in antigens which are under immune pressure and are therefore more diverse. Combination of phenotypic and genotypic typing methods can offer high levels of discrimination. Molecular studies into meningococcal diversity have offered many important insights into its population biology, which have implications for prevention and control of meningococcal disease. These have included the identification of hyperinvasive lineages and the correlation of genetic type with antigenic type and disease epidemiology. The EU-MenNet programme was established as a pan-European infrastructure for the research and surveillance of European meningococcal disease. Its aim was to coordinate and disseminate the latest molecular isolate characterisation techniques (MLST) and electronic data transfer via the Internet to exploit epidemiological and population genetic studies. Within the EU-MenNet, the European Meningococcal MLST Centre (EMMC) was set up to carry out molecular typing — MLST, PorA and FetA — of European disease isolates from 18 countries over three years 2000, 2001 and 2002. The output of this project will be the largest representative molecular epidemiological study of meningococcal disease in Europe. Assessment of the data produced will give insights into the geographic and temporal distribution and structuring of disease-associated clonal complexes and antigens and their associations. This will give an indication of the meningococcal disease population in Europe and will be invaluable for the current, and ongoing, development and introduction of new meningococcal vaccines

The temporal and geographical distribution and diversity of disease-associated Neisseria meningitidis genetic types in Europe

Meningococcal disease, caused by the bacterium Neisseria meningitidis, is an important cause of morbidity and mortality in young children and adolescents worldwide. There are 12 serogroups with most disease due to meningococci expressing one of five capsular polysaccharide antigens corresponding to serogroups A, B, C, Y and W135. In Europe, the majority of disease-causing strains are of serogroups B and C. No comprehensive vaccine is available against the bacterium due to the difficulty in producing serogroup B vaccines. A number of countries, e.g. UK and the Republic of Ireland have implemented routine meningococcal conjugate C (MCC) vaccine strategies. Due to the high proportion of disease accounted for by serogroup B in Europe and other developed countries, much research is currently being carried out to unearth vaccine candidates that would be protective and give as wide coverage as possible. Such candidates include the antigens PorA, FetA and factor H-binding protein. Potential drawbacks with antigens such as these which are under immune selection are high degrees of variability and lack of cross-immunity. Determination of the distribution, both geographically and temporally, of antigens and their association with clonal complex can aid in the formulation of novel vaccines and assess their potential coverage across Europe. Serological typing schemes involving characterisation of the polysaccharide capsule (serogroup) and outer membrane proteins such as PorA (serosubtype) and PorB (serotype) have been used for a number of years with some success. However, drawbacks associated with these methods include insufficient discrimination, limitations in panels of monoclonal antibodies used in the typing procedures and difficulty in comparison of results among labs. Consequently, in recent years genotypic methods such as multi-locus enzyme electrophoresis (MLEE) and subsequently multi-locus sequence typing (MLST) have been developed. These methods measure the variation in slowly evolving housekeeping genes whereas serological methods measure variation in antigens which are under immune pressure and are therefore more diverse. Combination of phenotypic and genotypic typing methods can offer high levels of discrimination. Molecular studies into meningococcal diversity have offered many important insights into its population biology, which have implications for prevention and control of meningococcal disease. These have included the identification of hyperinvasive lineages and the correlation of genetic type with antigenic type and disease epidemiology. The EU-MenNet programme was established as a pan-European infrastructure for the research and surveillance of European meningococcal disease. Its aim was to coordinate and disseminate the latest molecular isolate characterisation techniques (MLST) and electronic data transfer via the Internet to exploit epidemiological and population genetic studies. Within the EU-MenNet, the European Meningococcal MLST Centre (EMMC) was set up to carry out molecular typing — MLST, PorA and FetA — of European disease isolates from 18 countries over three years 2000, 2001 and 2002. The output of this project will be the largest representative molecular epidemiological study of meningococcal disease in Europe. Assessment of the data produced will give insights into the geographic and temporal distribution and structuring of disease-associated clonal complexes and antigens and their associations. This will give an indication of the meningococcal disease population in Europe and will be invaluable for the current, and ongoing, development and introduction of new meningococcal vaccines.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Shiga toxigenic Escherichia coli incidence is related to small area variation in cattle density in a region in Ireland

Shiga toxigenic Escherichia coli (STEC) are pathogenic E. coli that cause infectious diarrhoea. In some cases infection may be complicated by renal failure and death. The incidence of human infection with STEC in Ireland is the highest in Europe. The objective of the study was to examine the spatial incidence of human STEC infection in a region of Ireland with significantly higher rates of STEC incidence than the national average and to identify possible risk factors of STEC incidence at area level. Anonymised laboratory records (n = 379) from 2009 to 2015 were obtained from laboratories serving three counties in the West of Ireland. Data included location and sample date. Population and electoral division (ED) data were obtained from the Irish 2011 Census of Population. STEC incidence was calculated for each ED (n = 498) and used to map hotspots/coldspots using the Getis-Ord Gi* spatial statistic and significant spatial clustering using the Anselin\u27s Local Moran\u27s I statistic. Multivariable regression analysis was used to consider the importance of a number of potential predictors of STEC incidence. Incidence rates for the seven-year period ranged from 0 to 10.9 cases per 1000. A number of areas with significant local clustering of STEC incidence as well as variation in the spatial distribution of the two main serogroups associated with disease in the region i.e. O26 and O157 were identified. Cattle density was found to be a statistically significant predictor of STEC in the region. GIS analysis of routine data indicates that cattle density is associated STEC infection in this high incidence region. This finding points to the importance of agricultural practices for human health and the importance of a “one-health” approach to public policy in relation to agriculture, health and environment.Thanks to the Division of Clinical Microbiology for their help in particular Belinda Hanahoe. This work was funded through an Irish Research Council (GOIPD/2015/610) Government of Ireland Postdoctoral Fellowship. Icons in graphical abstract made by Freepik (www.freepik.com) from Flaticon (www.flaticon.com). Flaticon is licensed by Creative Commons BY 3.0.2020-05-1

Indistinguishable NDM-producing escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017

In this study, New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae were identified in Irish recreational waters and sewage. Indistinguishable NDM-producing Escherichia coli by pulsed-field gel electrophoresis were isolated from sewage, a fresh water stream and a human source. NDM-producing Klebsiella pneumoniae isolated from sewage and seawater in the same area were closely related to each other and to a human isolate. This raises concerns regarding the potential for sewage discharges to contribute to the spread of carbapenemase-producing Enterobacteriaceae.peer-reviewe

Resolution of a protracted serogroup b meningococcal outbreak with whole-genome sequencing shows interspecies genetic transfer

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher\u27s exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24-to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis. One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-toperson transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates