The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.  Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes.  Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications.  The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation.  Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes.  There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question.  In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.

Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.

BACKGROUND The meningococcal group B vaccine 4CMenB is a new, recombinant protein-based vaccine that is licensed to protect against invasive group B meningococcal disease. However, its role in preventing transmission and, therefore, inducing population (herd) protection is uncertain. METHODS We used cluster randomization to assign, according to school, students in years 10 to 12 (age, 15 to 18 years) in South Australia to receive 4CMenB vaccination either at baseline (intervention) or at 12 months (control). The primary outcome was oropharyngeal carriage of disease-causing Neisseria meningitidis (group A, B, C, W, X, or Y) in students in years 10 and 11, as identified by polymerase-chain-reaction assays for PorA (encoding porin protein A) and N. meningitidis genogroups. Secondary outcomes included carriage prevalence and acquisition of all N. meningitidis and individual disease-causing genogroups. Risk factors for carriage were assessed at baseline. RESULTS A total of 237 schools participated. During April through June 2017, a total of 24,269 students in years 10 and 11 and 10,220 students in year 12 were enrolled. At 12 months, there was no difference in the prevalence of carriage of disease-causing N. meningitidis between the vaccination group (2.55%; 326 of 12,746) and the control group (2.52%; 291 of 11,523) (adjusted odds ratio, 1.02; 95% confidence interval [CI], 0.80 to 1.31; P = 0.85). There were no significant differences in the secondary carriage outcomes. At baseline, the risk factors for carriage of disease-causing N. meningitidis included later year of schooling (adjusted odds ratio for year 12 vs. year 10, 2.75; 95% CI, 2.03 to 3.73), current upper respiratory tract infection (adjusted odds ratio, 1.35; 95% CI, 1.12 to 1.63), cigarette smoking (adjusted odds ratio, 1.91; 95% CI, 1.29 to 2.83), water-pipe smoking (adjusted odds ratio, 1.82; 95% CI, 1.30 to 2.54), attending pubs or clubs (adjusted odds ratio, 1.54; 95% CI, 1.28 to 1.86), and intimate kissing (adjusted odds ratio, 1.65; 95% CI, 1.33 to 2.05). No vaccine safety concerns were identified. CONCLUSIONS Among Australian adolescents, the 4CMenB vaccine had no discernible effect on the carriage of disease-causing meningococci, including group B. (Funded by GlaxoSmith-Kline; ClinicalTrials.gov number, NCT03089086.

Of 830 Neisseria meningitidis isolates obtained from healthy carriers in Bavaria, Germany, 136 (164 %) lacked the operons necessary for the synthesis, lipid modification, and transport of capsular polysaccharide. These operons were replaced by a non-coding intergenic region either 113 or 114 bp in length, termed here the capsule null locus (cnl). Comparisons of the nucleotide sequence of this region in the meningococcus and its acapsulate relatives, Neisseria gonorrhoeae and Neisseria lactamica, revealed six distinct sequence variants (cnl-1 to cnl-6), with a total of 10 nucleotide substitutions and three indels. With the exception of one 4 bp insertion, which was unique to a gonococcal isolate, all of the individual sequence changes were present in the N. lactamica isolates examined. The meningococcal isolates with a cnl belonged to one of four otherwise genetically diverse genetic groupings : the ST-53 and ST-1117 complexes (75 isolates) ; the ST-845 complex (12 isolates) ; the ST-198 and 1136 complexes (46 isolates), and the ST-44 complex (one isolate).These data demonstrated that a substantial proportion of carried meningococci were incapable of capsule production, that the cnl circulated within Neisseria populations by horizontal genetic exchange, and that the expression of a polysaccharide capsule was not a requirement for person-to-person transmission of certain meningococcal lineages.Keywords : Neisseria meningitidis, multilocus sequence typing, transmission, capsule null locus INTRODUCTIONThe causative organism of meningococcal disease, Neisseria meningitidis, is primarily a commensal bacterium which can be cultured from up to 40 % of human nasopharyngeal swab samples (Broome, 1986). This figure, which is likely to be an underestimate of the actual carriage rate (Sim et al., 2000), is dependent on a number of factors particular to the individuals sampled, including age and social status, together with population factors such as geographical location and climatic conditions (Rosenstein et al., 2001 The GenBank accession number for the sequence of the cnl-1 allele is AJ308327.species being harmless inhabitants of the mucosal surfaces of animals and humans (Morse & Knapp, 1992). Within the genus, the expression of a capsular polysaccharide is unique to N. meningitidis, and it is tempting to speculate that the acquisition of the genetic material necessary for the expression of a capsule was an important step in the evolution of the meningococcus from other Neisseria species.Immunochemical differences among meningococcal capsules define the serogroups of the organism (Vedros, 1987). Five of the 13 recognized capsular polysaccharides, those conferring serogroups A, B, C, W-135 and Y, can be thought of as virulence determinants, as virtually all meningococcal disease is caused by organisms expressing one of these capsular antigens (Poolman et al., 1995). These capsules are capable of protecting the bacterium against opsonophagocytosis during disseminated infection (Kahler et al., 1998 ; Masson & Holbein, 1985...

Volume 38, no. 12, p. 4492-4498, 2000. We described the genetic characterization of 156 Neisseria meningitidis isolates obtained from healthy young adults in the Czech Republic during 1993. Subsequent work has established that a further 61 isolates collected during that year had been stored separately and had been overlooked. These isolates were not a random sample of those collected, as isolates with a phenotype resembling the strain responsible for a disease outbreak that year were overrepresented. All but one of the additional meningococci were isolated from individuals who were 20 to 24 years old, giving a total of 190 isolates from this age group, rather than the 130 isolates originally reported; the other isolate was from the younger cohort (age range, 15 to 19 years).The revised multilocus sequence typing (MLST) data are available at the Neisseria MLST website (http://neisseria.mlst.net/ links.htm). These data show a total of 88 sequence types (STs), which were resolved into 16 clonal complexes (lineages), with the remaining STs not presently assigned to clonal complexes. The six most prevalent clonal complexes were the ST-11 complex (33 isolates . Since the original publication, some minor changes have been made to the assignment and names of the clonal complexes; for example, the ST-41 complex has been renamed the ST-44 complex. The present assignments are available at the PubMLST isolate database website (http://neisseria .mlst.net).The principal conclusions of the paper, that the population was diverse and that this diversity was principally generated by recombination, are unaltered (Table 1; Fig. 1). However, the revised data show that the prevalence of meningococci belonging to the ST-11 (ET-37) complex was almost six times higher than that calculated on the basis of the data from the 156 original isolates and much greater than any previously measured prevalence of this complex among carriage isolates. This affects estimates of the overrepresentation of ST-11 complex meningococci among isolates from invasive disease. Of the 27 meningococcal isolates carried by members of the younger cohort (age range, 15 to 19 years), 3 (11.1%) belonged to the ST-11 complex. As 10 (22.7%) of the 44 cases of invasive disease in this age group were caused by ST-11 complex organisms, this clonal complex was overrepresented approximately twofold among disease-causing meningococci, as originally reported. However, meningococcus carriage data for individuals in the older cohort (age range, 20 to 24 years) indicated that a total of 30 (15.8%) of the 190 isolates belonged to the ST-11 complex, with 2 out of 9 cases of disease having been caused by . This clonal complex was therefore overrepresented by approximately 1.4-fold (not the originally reported 16-fold) among the disease-associated meningococci isolated from this age group. The ST-11 complex meningococci were found in five of the geographical regions sampled, suggesting that the distribution of these meningococci was widespread. At present, it is unclear why the ...

Separate proteins for proton-linked transport of D-xylose, L-arabinose, D-galactose, L-rhamnose and L-fucose into Escherichia coli are being studied. By cloning and sequencing the appropriate genes, the amino acid sequences of proteins for D-xylose/H+ symport (XylE), L-arabinose/H+ symport (AraE), and part of the protein for D-galactose/H+ symport (GalP) have been determined. These are homologous, with at least 28% identical amino acid residues conserved in the aligned sequences, although their primary sequences are not similar to those of other E. coli transport proteins for lactose, melibiose, or D-glucose. However, they are equally homologous to the passive D-glucose transport proteins from yeast, rat brain, rat adipocytes, human erythrocytes, human liver, and a human hepatoma cell line. The substrate specificity of GalP from E. coli is similar to that of the mammalian glucose transporters. Furthermore, the activities of GalP, AraE and the mammalian glucose transporters are all inhibited by cytochalasin B and N-ethylmaleimide. Conserved residues in the aligned sequences of the bacterial and mammalian transporters are identified, and the possible roles of some in sugar binding, cation binding, cytochalasin binding, and reaction with N-ethylmaleimide are discussed. Each protein is independently predicted to form 12 hydrophobic, membrane-spanning alpha-helices with a central hydrophilic segment, also comprised of alpha-helix. This unifying structural model of the sugar transporters shares features with other ion-linked transport proteins for citrate or tetracycline.

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.