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Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005–2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005–2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.

Background Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them. Methods Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating. Results Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0–2 SNPs) with the common ancestor dated around 2017. Conclusion The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011–June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance. Most genomes contained genes encoding B (n = 525; 65.7%) or C (n = 163; 20.4%) capsules; isolates were genetically highly diverse, with >20 genomic lineages, five of which comprising 60.7% (n = 485) of isolates. There were >350 antigenic fine-types: 307 were present once, the most frequent (P1.7-2,4:F5-1) comprised 8% (n = 64) of isolates. Each genome was characterised for Bexsero Antigen Sequence Typing (BAST): 25.5% (n = 204) of isolates contained alleles encoding the fHbp and/or the PorA VR1 vaccine component, but most genomes (n = 513; 64.2%) did not contain the NadA component. EMSC-GL will support an integrated surveillance of disease-associated genotypes in Europe, enabling the monitoring of hyperinvasive lineages, outbreak identification, and supporting vaccine programme implementation.

International audience; The objectives of our study were to describe the epidemiology of invasive disease from 1993 to 2008 in Slovenia, a country with routine serotype b (Hib) conjugate vaccination since the year 2000. A total of 292 isolates of , recovered from a normally sterile site, were collected in the study period. The isolates were serotyped by slide agglutination and antibiotic susceptibility was determined. One hundred and eight isolates received after the year 2000 were serotyped by slide agglutination and by polymerase chain reaction (PCR) capsule typing, and both methods were compared. After the introduction of the routine Hib vaccination, the incidence of disease in children under the age of 5 years has decreased by 87.6% and type b was replaced by non-typeable as the predominant serotype. The proportion of serotype b decreased from 85.3% in the pre-vaccination period to 13.0% in the vaccination period and the proportion of non-capsulated isolates increased from 12.0 to 85.2%. The study of genetic relatedness by pulsed-field gel electrophoresis (PFGE) demonstrated that the isolates of serotypes b and f were genetically homogeneous within the serotype. The results of our national surveillance showed that the vaccine has been very efficient in preventing Hib invasive disease in Slovenia. Nevertheless, we see a need for further monitoring of invasive infections at a national level.

Invasive strains of Neisseria meningitidis isolated from sterile body fluids of children aged 0-14 years were intentionally collected in nine Slovenian laboratories, and sent to the laboratory of the National Institute of Public Health, Ljubljana for final evaluation. From 1993-1999 we collected 53 invasive strains from children presented in this study. The incidence rate of invasive diseases in children shows that there is a rapid fall from 4.74/100,000 in 1993 to 0.90/100,000 in 1999. Invasive diseases predominated in children in the age group 0-1 year (19.6 cases per 100,000 children); followed by the age groups 2-4 years, 5-9 years and 10-14 years. The results of serogrouping indicate that the largest proportion of meningococci isolated (90%) were group B, while 8% of isolates were group C and only 2% group Y. The serotype/serosubtype distribution shows that the most frequent serotype (excluding 19 non-typable NT strains) was serotype 22, which was expressed in 9 strains and the most frequent serosubtype (excluding 11 NST strains) was P1.5,2 found in 7 strains. The most frequently isolated strains (excluding NT/NST strains) were B:22:P1.14; B:NT:P1.5 and B:NT:P1.16. Thirty-one strains collected during 1993-1995 were analysed by multilocus enzyme electrophoresis (MEE). There were 25 electrophoretic types (ETs) among 31 strains; the strains were very heterogeneous with only four ETs being represented by more than one strain. Study shows that meningococcal disease is still endemic in Slovenia.

Several lines of evidence indicate that suicidal behaviour is partly heritable, with multiple genes implicated in its aetiology. We focused on nine genes (S100A13, EFEMP1, PCDHB5, PDGFRB, CDCA7L, SCN2B, PTPRR, MLC1 and ZFP36) which we previously detected as differentially expressed in the cortex of suicide victims compared to controls. We investigated 84 variants within these genes in 495 suicidal subjects (299 completers and 196 attempters) and 1513 controls (109 post-mortem and 1404 healthy). We evaluated associations with: 1) suicidal phenotype; 2) possible endophenotypes for suicidal behaviour. Overall positive results did not survive the correction threshold. However, we found a nominally different distribution of EFEMP1 genotypes, alleles and haplotypes between suicidal subjects and controls, results that were partially replicated when we separately considered the subgroup of suicide completers and post-mortem controls. A weaker association emerged also for PTPRR. Both EFEMP1 and PTPRR genes were also related to possible endophenotypes for suicidal behaviour such as anger, depression-anxiety and fatigue. Because of the large number of analyses performed and the low significance values further replication are mandatory. Nevertheless, neurotrophic gene variants, in particular EFEMP1 and PTPRR, may have a role in the pathogenesis of suicidal behaviour.