Summary Background Invasive meningococcal disease (IMD) is a worldwide health issue that is potentially preventable with vaccination. In view of its sporadic nature and the high diversity of ...Neisseria meningitidis , epidemiological surveillance incorporating detailed isolate characterisation is crucial for effective control and understanding the evolving epidemiology of IMD. The Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL) exploits whole-genome sequencing (WGS) for this purpose and presents data on a comprehensive and coherent IMD isolate collection from England and Wales via the internet. We assessed the contribution of these data to investigating IMD epidemiology. Methods WGS data were obtained for all 899 IMD isolates available for England and Wales in epidemiological years 2010–11 and 2011–12. The data had been annotated at 1720 loci, analysed, and disseminated online. Information was also available on meningococcal population structure and vaccine (Bexsero, GlaxoSmithKline, Brentford, Middlesex, UK) antigen variants, which enabled the investigation of IMD-associated genotypes over time and by patients' age groups. Population genomic analyses were done with a hierarchical gene-by-gene approach. Findings The methods used by MRF-MGL efficiently characterised IMD isolates and information was provided in plain language. At least 20 meningococcal lineages were identified, three of which (hyperinvasive clonal complexes 41/44 lineage 3, 269 lineage 2, and 23 lineage 23) were responsible for 528 (59%) of IMD isolates. Lineages were highly diverse and showed evidence of extensive recombination. Specific lineages were associated with IMD in particular age groups, with notable diversity in the youngest and oldest individuals. The increased incidence of IMD from 1984 to 2010 in England and Wales was due to successive and concurrent epidemics of different lineages. Genetically, 74% of isolates were characterised as encoding group B capsules: 16% group Y, 6% group W, and 3% group C. Exact peptide matches for individual Bexsero vaccine antigens were present in up to 26% of isolates. Interpretation The MRF-MGL represents an effective, broadly applicable model for the storage, analysis, and dissemination of WGS data that can facilitate real-time genomic pathogen surveillance. The data revealed information crucial to effective deployment and assessment of vaccines against N meningitidis. Funding Meningitis Research Foundation, Wellcome Trust, Public Health England, European Union.
Nosocomial transmission and outbreaks of carbapenemase-producing Enterobacterales (CPE) represent a challenge to healthcare systems. In July 2018, a CPE hospital ward outbreak was declared. Our aim ...was to investigate transmission patterns, using social network analysis and genomics in a nosocomial CPE outbreak.
A retrospective descriptive analysis of all patients (cases and contacts) admitted to a ward experiencing a CPE outbreak (2018–2019) was undertaken. A case had a negative CPE admission screen, and subsequent positive test. A contact shared a multi-bed area and/or facility with a case (>4 hours). Social networks, including genomics data and ward locations, were constructed. Network metrics were analysed.
Forty-five cases and 844 contacts were analysed. The median age of cases was 78 years (IQR 67-83), 58% (n=26) were male and 100% had co-morbidities. The median outbreak ward length-of-stay (LOS) was 17 days (IQR 10-34). OXA-48 CPE was confirmed in all cases and from 26 environmental samples. Social networks identified clusters by time, gender and species/sequence type/plasmid. Network metrics indicated potential superspreading involving a subset of patients with behavioural issues.
Social networks elucidated high resolution transmission patterns involving two related OXA-48 plasmids, multiple species/genotypes and potential super-spreading. Interventions prevented intra-hospital spread. An older patient cohort, extended hospital LOS and frequent intra-ward bed transfers, coupled with suboptimal ward infrastructure, likely prolonged this outbreak. We recommend social network analysis contemporaneously with genomics (on case and environmental samples) for complex nosocomial outbreaks and bespoke care plans for patients with behavioural issues on outbreak wards.
The diversity and dynamics of Neisseria meningitidis populations generate a requirement for high resolution, comprehensive, and portable typing schemes for meningococcal disease surveillance. ...Molecular approaches, specifically DNA amplification and sequencing, are the methods of choice for various reasons, including: their generic nature and portability, comprehensive coverage, and ready implementation to culture negative clinical specimens. The following target genes are recommended: (1) the variable regions of the antigen-encoding genes porA and fetA and, if additional resolution is required, the porB gene for rapid investigation of disease outbreaks and investigating the distribution of antigenic variants; (2) the seven multilocus sequence typing loci-these data are essential for the most effective national, and international management of meningococcal disease, as well as being invaluable in studies of meningococcal population biology and evolution. These targets have been employed extensively in reference laboratories throughout the world and validated protocols have been published. It is further recommended that a modified nomenclature be adopted of the form: serogroup: PorA type: FetA type: sequence type (clonal complex), thus: B: P1.19,15: F5-1: ST-33 (cc32).
Abstract Background In September, 2015, the meningococcal group B vaccine (Bexsero, GlaxoSmithKline) was introduced into the UK childhood immunisation schedule. Prelicensure coverage estimates used ...Meningococcal Antigen Typing System (MATS) to determine phenotype and function of circulating meningococci. Using whole-genome sequencing, we aimed to perform rapid, scalable, high-resolution analysis of peptide vaccine antigens in disease-causing meningococci before and after vaccine implementation. Methods All culture-confirmed invasive meningococcal disease isolates from July 1, 2010, to June 30, 2016, from the UK underwent whole-genome sequencing (n=2994), representing 56·7% of cases reported to Public Health England. Genomes were hosted on the PubMLST database. The Bexsero Antigen Sequence Type (BAST) scheme was used to catalogue antigenic variants for comparison with the Bexsero type, BAST-1 (fHbp:1, NHBA:2, NadA:8, PorA VR1:7-2, PorA VR2:4). Statistical analysis was performed with R software (v3.2.4). Findings Complete BASTs were obtained for 2915 isolates (97·4%). Within the fHbp family 1, variant 1 was only present in 105 (3·5%) of 2994 isolates. Variant 4 dominated since 2010–11 in BASTs 220, 226, and 229. From 2013–14 onwards, family 2 variants were more frequent than family 1 variants. NHBA variant 2 decreased from 373 (15·3%) of 2441 prevaccine isolates to 45 (9·4%) of 479 postvaccine isolates (p=0·001). The most common variant was 29 (557/2994). NadA was absent in 2049 (70·1%) of 2921 isolates. PorA VR2 had 106 variants, most frequently variants 2 (n=542), 9 (350), and 4 (333). Genotypic matches to BAST-1 (≥1 antigen) decreased from 30·4% (167/550) to 15·5% (83/536) over a 6 year period. Coverage including cross-reactive antigens was 60·2–69·0%. Genotype–phenotype modelling estimated coverage of 62·1% (95% CI 60·9–63·3), with no significant change before or after vaccine implementation. Interpretation Recent clonal expansion of South American/UK serogroup W strain accounts for many antigenic changes, such as the increase in family 2 fHbp and NHBA variant 29. Cross-reactivity within the fHbp family 1 is a key determinant of vaccine immunogenicity. MATS coverage estimates of 73% (95% CI 57–87) were key to policy decisions for introduction of the vaccine in the UK. Analysis of recent disease isolates with genomic and genotype–phenotype correlations suggests that coverage estimates are lower but within the limits of previous MATS studies. Funding Wellcome Trust.
surveillance network for meningococcal disease in Europe Trotter, Caroline L; Chandra, Manosree; Cano, Rosa ...
FEMS microbiology reviews,
2007, 20070101, January 2007, 2007-Jan, 2007-01-00, Letnik:
31, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Between 1999 and 2004, the European Union Invasive Bacterial Infections Surveillance Network (EU-IBIS) received c. 50 000 reports of meningococcal disease from 27 participating countries. Analysis ...has demonstrated a major decline in the incidence of invasive disease in those countries that have introduced routine vaccination against serogroup C infection. The establishment of rapid reporting of W135 and B2a/B2b strains has been able to provide early reassurance that these strains are not emerging as major public health problems in Europe. Between September 2001 and February 2005, the EU-MenNet project offered further opportunities for enhancing this data resource. Collaborative projects included: improving the EU-IBIS website; reviewing case ascertainment in Europe; reviewing cost-effectiveness studies for meningococcal serogroup C conjugate (MCC) vaccination; international comparisons of MCC vaccine efficacy; and mathematical modelling studies. In addition, linking of data from the European Meningococcal Multi-locus Sequence Type Centre to epidemiological data was performed. Particular clonal complexes were found to be preferentially associated with certain serogroups. Case fatality was also found to vary with clonal complex, suggesting that genotype can be a marker for hypervirulence. The importance of close collaboration between networks of epidemiologists, microbiologists, and the wider scientific and public health community is demonstrated.
Following the introduction of effective protein-polysaccharide conjugate vaccines against capsular group C meningococcal disease in Europe, meningococci of capsular group B remain a major cause of ...death and can result in debilitating sequelae. The outer membrane proteins PorA and FetA have previously been shown to induce bactericidal antibodies in humans. Despite considerable antigenic variation among PorA and FetA OMPs in meningococci, systematic molecular epidemiological studies revealed this variation is highly structured so that a limited repertoire of antigenic types is congruent with the hyperinvasive meningococcal lineages that have caused most of the meningococcal disease in Europe in recent decades. Here we describe the development of a prototype vaccine against capsular group B meningococcal infection based on a N. meningitidis isolate genetically engineered to have constitutive expression of the outer membrane protein FetA. Deoxycholate outer membrane vesicles (dOMVs) extracted from cells cultivated in modified Frantz medium contained 21.8% PorA protein, 7.7% FetA protein and 0.03 μg LPS per μg protein (3%). The antibody response to the vaccine was tested in three mouse strains and the toxicological profile of the vaccine was tested in New Zealand white rabbits. Administration of the vaccine, MenPF-1, when given by intramuscular injection on 4 occasions over a 9 week period, was well tolerated in rabbits up to 50 μg/dose, with no evidence of systemic toxicity. These data indicated that the MenPF-1 vaccine had a toxicological profile suitable for testing in a phase I clinical trial.
Abstract
Objectives:
Molecular epidemiological description of an OXA-48 CPE outbreak affecting a tertiary-care hospital ward in Ireland over an extended period (2018–2019).
Methods:
Microbiological ...testing and whole-genome sequencing (WGS) were performed on all 56 positive OXA-48 outbreak case isolates.
Results:
In total, 7 different species were identified:
Enterobacter hormaechei
(n = 35, 62.5%),
Escherichia coli
(n = 12, 21.4%),
Klebsiella pneumoniae
(n = 5, 8.9%),
Klebsiella oxytoca
(n = 1, 1.8%),
Klebsiella michiganensis
(n = 1, 1.8%),
Citrobacter freundii
(n = 1, 1.8%), and
Serratia marcesens
(n = 1, 1.8%).
E. hormaechei
ST78 was the most common genotype (n = 14, 25%). Two major pOXA-48 plasmid types were identified throughout the outbreak, ‘types’ 1 and 2, and 5 major
E. hormaechei
clonal groupings were identified: ST78, ST108, ST1126, ST135, and ST66. Within each of the ST108, ST1126, ST135 and ST66 groups, the pOXA-48 harbored within each isolate were the same. Within ST78, 9 isolates contained the pOXA48 ‘type 2’ plasmid and 5 contained the ‘type 1’ plasmid. Environmental specimens were taken from different outbreak ward locations: handwash basins, sink and shower drains, and taps. Of 394 environmental specimens, OXA-48 CPE was isolated from 26 (6.6%).
Conclusions:
This prolonged outbreak of OXA-48 CPE was confined to one ward, but it exemplifies the complexity and difficulty in the control of these organisms. With multiple species and genotypes involved, they may be better described as ‘plasmid outbreaks.’ WGS provided insights into this diversity and potential transmission among cases, though its usefulness would be enhanced by analysis as close as possible to real time so that interventions can be implemented as soon as data are available.
Antimicrobial resistance is a major public health concern. Carbapenemase-producing Enterobacterales (CPE) represent a significant health threat as some strains are resistant to almost all available ...antibiotics. The aim of this research was to examine hospital effluent and municipal wastewater in an urban area in Ireland for CPE. Samples of hospital effluent (n = 5), municipal wastewater before (n = 5) and after (n = 4) the hospital effluent stream joined the municipal wastewater stream were collected over a nine-week period (May–June 2017). All samples were examined for CPE by direct plating onto Brilliance CRE agar. Isolates were selected for susceptibility testing to 15 antimicrobial agents in accordance with EUCAST criteria. Where relevant, isolates were tested for carbapenemase-encoding genes by real-time PCR. CPE were detected in five samples of hospital effluent, one sample of pre-hospital wastewater and three samples of post-hospital wastewater. Our findings suggest hospital effluent is a major contributor to CPE in municipal wastewater. Monitoring of hospital effluent for CPE could have important applications in detection and risk management of unrecognised dissemination of CPE in both the healthcare setting and the environment.
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•The impact of untreated hospital effluent on municipal sewage was investigated.•Higher prevalence of CPE detected in hospital effluent versus municipal sewage.•blaOXA-48, blaKPC, blaVIM and blaIMP present in hospital and post-hospital sewage•blaNDM present in municipal sewage•Releasing untreated hospital sewage may fuel CPE dissemination in the environment.
The aim of this work was the establishment of a national laboratory sentinel surveillance service for human clinical Campylobacter in Ireland. This included detailed genomic molecular epidemiology of ...Campylobacter for 2019. For February‐December 2019, 24 clinical microbiology laboratories in Ireland submitted all PCR/culture‐positive clinical Campylobacter spp. specimens to Public Health Laboratory (PHL) Dublin one week out of every four. Antimicrobial susceptibility testing (AST) according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria was carried out for Campylobacter spp. isolates for ciprofloxacin, tetracycline and erythromycin. Batch whole genome sequencing (WGS) was carried out on cultures and analysis was performed to determine species, genotype, identify antimicrobial resistance (AMR) and virulence determinants and identify clusters. A total of 75 isolates and 366 PCR‐positive stools were received, and 277 isolates recovered (55.7% recovery from stools). Of 257 isolates characterized by WGS, 86.4% (n = 222) were Campylobacter jejuni, 11.7% (n = 30) Campylobacter coli and 1.9% (n = 5) Campylobacter lari. There were 20 clonal complexes with ST‐21 clonal complex most prevalent at 26.8% (n = 69). 50.5% (n = 140) of isolates were susceptible to all three antimicrobials tested. 39.3% (n = 109) isolates were ciprofloxacin resistant, 26.3% (n = 73) tetracycline resistant and two isolates erythromycin resistant. Congruence between phenotypic and genotypic AST was observed. There was 95.9% and 95.6% sensitivity and specificity for WGS to predict ciprofloxacin sensitivity and 98.6% and 99.5% sensitivity and specificity for WGS to predict tetracycline sensitivity. Virulence factors flaA, racR, ciaB and cdtB were detected in all isolates. WGS identified 31 potential clusters for public health alert. This sentinel surveillance of human campylobacteriosis in Ireland establishes the basis for a national reference service. Linking with other partners in a ‘One Health’ framework will help us better understand sources of infection to reduce disease burden and the threat of AMR.
No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an ...approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.
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