Strain coverage
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BACKGROUND: The Meningococcal Antigen Typing System (MATS) was developed to identify meningococcus group B strains with a high likelihood of being covered by the 4CMenB vaccine, but is limited by the requirement for viable isolates from culture-confirmed cases. We examined if antigen genotyping could complement MATS in predicting strain coverage by the 4CMenB vaccine. METHODS: From a panel of 3912 MATS-typed invasive meningococcal disease isolates collected in England and Wales in 2007-2008, 2014-2015 and 2015-2016, and in 16 other countries in 2000-2015, 3481 isolates were also characterized by antigen genotyping. Individual associations between antigen genotypes and MATS coverage for each 4CMenB component were used to define a genetic MATS (gMATS). gMATS estimates were compared with England and Wales human complement serum bactericidal assay (hSBA) data and vaccine effectiveness (VE) data from England. RESULTS: Overall, 81% of the strain panel had genetically predictable MATS coverage, with 92% accuracy and highly concordant results across national panels (Lin's accuracy coefficient, 0.98; root-mean-square deviation, 6%). England and Wales strain coverage estimates were 72-73% by genotyping (66-73% by MATS), underestimating hSBA values after four vaccine doses (88%) and VE after two doses (83%). The gMATS predicted strain coverage in other countries was 58-88%. CONCLUSIONS: gMATS can replace MATS in predicting 4CMenB strain coverage in four out of five cases, without requiring a cultivable isolate, and is open to further improvement. Both methods underestimated VE in England. Strain coverage predictions in other countries matched or exceeded England and Wales estimates.
- MeSH
- antigeny bakteriální genetika MeSH
- celosvětové zdraví MeSH
- genotyp * MeSH
- genotypizační techniky metody MeSH
- lidé MeSH
- meningokoková meningitida epidemiologie mikrobiologie MeSH
- meningokokové vakcíny imunologie MeSH
- molekulární epidemiologie metody MeSH
- Neisseria meningitidis séroskupiny B klasifikace genetika izolace a purifikace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
Cíl práce: Aktuální data ukazují, že Neisseria meningitidis B působí kolem 70 % invazivního meningokokového onemocnění (IMO) v Evropě a dostupnost vakcíny účinné proti N. meningitidis B je žádoucí. Nová MenB vakcína byla registrovaná v Evropě v lednu 2013. Byl vyvinut nový systém typizace meningokokových antigenů (MATS) s cílem určit pokrytí kmenů touto vakcínou. Recentně byla publikována data pro evropské konsorcium včetně agregovaných dat pro Českou republiku. Cílem tohoto sdělení je prezentace detailních výsledků MATS pro české izoláty N. meningitidis B. Materiál a metodiky: Bylo vybráno 108 izolátů N. meningitidis B získaných z IMO v České republice v období 2007–2010. Metoda MATS byla provedena podle publikovaných metod. Výsledky: Podle analýzy MATS pokrytí všech českých 108 izolátů N. meningitidis B je 74% (95% CI: 59–87%). Bylo pozorováno, že 39 kmenů (36 %) je pokryto jedním antigenem, zatímco 41 kmenů (38 %) je pokryto více než jedním antigenem. U 28 kmenů (26 %) nebylo zjištěno pokrytí žádným antigenem. Závěry: Analýza MATS ukázala, že nová MenB proteinová vakcína může v České republice chránit proti podstatné části IMO způsobených N. meningitidis B. Pokud v České republice bude MenB vakcína zavedena, je nezbytné pokračování detailní surveillance IMO.
Background: Recent data indicate that Neisseria meningitidis B strains cause about 70% of invasive meningococcal disease (IMD) cases in Europe and the availability of a vaccine effective against N. meningitidis B is desirable. A new protein-based MenB vaccine was licensed for use in Europe in January 2013. Meningococcal antigen typing system (MATS) was developed to predict strain coverage of this vaccine. Reports have recently been published for a European consortium, including aggregated data for the Czech Republic. The aim of this paper is to provide a detailed breakdown of MATS results for the Czech N. meningitidis B isolates. Materials and methods: One hundred and eight N. meningitidis B isolates from IMD collected in the Czech Republic during 2007–2010 were selected. MATS analysis was done according to the method previously published. Results: Based on MATS analysis, the overall estimate of strain coverage of the new MenB vaccine for a panel of 108 Czech N. meningitidis B strains is 74% (95% CI: 59–87%). Thirty-nine strains (36%) are predicted to be covered by a single antigen and 41 strains (38%) by more than one antigen. For 28 strains (26%), no antigen coverage was found. Conclusions: MATS analysis showed that the new protein-based MenB vaccine could protect against a substantial proportion of IMD caused by N. meningitidis B in the Czech Republic. Continued detailed surveillance of IMD will be essential if the MenB vaccine is introduced to the country.
- MeSH
- antigeny bakteriální imunologie MeSH
- ELISA MeSH
- infekce bakteriemi čeledi Neisseriaceae * prevence a kontrola MeSH
- lidé MeSH
- meningokokové vakcíny MeSH
- multilokusová sekvenční typizace * MeSH
- Neisseria meningitidis séroskupiny B * MeSH
- očkovací programy MeSH
- surveillance populace MeSH
- techniky typizace bakterií * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
Cíl práce: Cílem práce je Multiple-locus variable number tandem repeat analýza (MLVA) souboru kmenů B. pertussis ze sbírky Národní referenční laboratoře pro pertusi a difterii (NRL/DIPE) Státního zdravotního ústavu (SZÚ) Praha. Jedná se o kmeny získané ze vzorků klinického materiálu převážně na území ČR v téměř padesátiletém období 1967–2015 (červen). Je porovnávána genetická diverzita a zastoupení detekovaných MLVA typů (MT) ve třech obdobích lišících se vakcinační strategií a trendem výskytu pertuse. Na podkladě získaných výsledků je posouzena vhodnost použití metody MLVA pro analýzu epidemických výskytů B. pertussis v ČR. Materiál a metodiky: Vzorky DNA extrahované z kmenů B. pertussis studovaného souboru byly analyzovány metodou MLVA podle standardizovaného postupu. Data byla zpracována pomocí algoritmu eBURST, pro statistické zpracování byl zvolen výpočet Simpsonova indexu diverzity (DI). Data byla zpracována pro celý soubor a též odděleně pro skupiny kmenů z tří období: 1967–1980, 1990–2007 a 2008–2015 (červen). Výsledky: V souboru bylo detekováno 14 různých MT, z toho 3 dosud nezjištěné. Nejčetnější byly v celém souboru MT27 a MT29. MT29 převládal v období 1967–1980, MT27 v obdobích 1990–2007 a 2008–2015 (červen). Hodnota DI byla nejnižší (0,49) pro období 2008–2015 (červen), pro dvě předchozí období byly hodnoty vyšší a vzájemně srovnatelné (0,667 pro období 1967–1980 a 0,654 pro období 1990–2007). Závěr: MLVA analýzou souboru kmenů B. pertussis izolovaných z klinického materiálu na území ČR v období 1967–2015 (červen) byl prokázán pokles genetické diverzity ve studované populaci a změny v zastoupení a četnosti jednotlivých MT. Tyto změny lze charakterizovat jako postupný nárůst výskytu celosvětově rozšířených MT v České republice na úkor MT regionálně unikátních. Převažujícím MT, stejně jako ve většině geografických oblastí s dlouhodobě proočkovanou populací, je MT27. Výsledky MLVA analýzy souboru 136 kmenů B. pertussis mohou být podkladem pro účelné využití metody k molekulárně epidemiologickému zpracování souborů menšího rozsahu.
Aim: To perform multiple-locus variable number tandem repeat analysis (MLVA) of B. pertussis strains from the collection of the National Reference Laboratory for Diphtheria and Pertussis (NRL/DIPE), National Institute of Public Health (NIPH), Prague. The study strains were isolated from clinical specimens collected mostly in the Czech Republic over a nearly 50-year period from 1967 to 2015 (June). The isolates from three periods characterized by different vaccination strategies and trends in pertussis are compared for genetic diversity and distribution of MLVA types (MT). Based on the results obtained, the suitability for use of MLVA in the analysis of epidemic outbreaks of B. pertussis in the Czech Republic is considered. Material and methods: DNA samples extracted from B. pertussis strains included in the present study were examined by MLVA using the standard protocol. Data were processed by means of the eBURST algorithm and the calculation of the Simpson diversity index (DI) was used for the statistical analysis. Data were analyzed as a whole and also separately for strains from the three periods: 1967–1980, 1990–2007, and 2008–2015 (June). Results: Fourteen different MT were detected in the study strains, with three of them not being reported before. The most common MTs were MT27 and MT29. MT29 was predominant in 1967–1980 while MT27 was the most prevalent in 1990–2007 and 2008–2015 (June). The DI was the lowest (0.49) in 2008–2015 (June), and comparably higher DIs were calculated for the two previous periods (i.e. 0.667 for 1967–1980 and 0.654 for 1990–2007). Conclusion: MLVA revealed a decrease in genetic diversity and shifts in MT distribution of B. pertussis strains isolated from clinical specimens in the Czech Republic from 1967 to 2015 (June). These shifts in the Czech Republic can be characterized as a progressive increase in global MTs at the expense of the locally unique ones. The most common MT, similarly to other geographical areas with long-term high vaccination coverage, is MT27. The results of MLVA of 136 B. pertussis strains can provide a background for using this method in molecular epidemiological analysis of smaller groups of strains.
- MeSH
- acelulární vakcíny imunologie MeSH
- bakteriální geny genetika MeSH
- Bordetella pertussis * genetika MeSH
- časové faktory MeSH
- DNA bakterií genetika MeSH
- genetická variace genetika MeSH
- hromadná vakcinace MeSH
- lidé MeSH
- minisatelitní repetice * genetika MeSH
- multilokusová sekvenční typizace * MeSH
- pertuse epidemiologie mikrobiologie prevence a kontrola MeSH
- pertusová vakcína imunologie MeSH
- tandemové repetitivní sekvence genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
- Československo MeSH
BACKGROUND: Recombinant vaccines containing factor H-binding protein (fHBP) have been developed for the purpose of protection from invasive meningococcal serogroup B disease. Neisseria meningitidis fHBP sequences can be divided into 2 genetically and immunologically distinct subfamilies (A and B); thus, cross protection is conferred within but not between subfamilies. A comprehensive understanding of fHBP epidemiology is required to accurately assess the potential vaccine impact when considering different vaccination implementation strategies. METHODS: Systematically collected invasive meningococcal serogroup B isolates from England, Wales, Northern Ireland, the United States, Norway, France and the Czech Republic were previously characterized for fHBP sequence. This study expanded the evaluation with additional meningococcal serogroup B disease isolates from Spain (n = 346) and Germany (n = 205). This expanded set (n = 1841), collected over a 6-year period (2001 to 2006), was evaluated for fHBP sequence and fHBP subfamily relative to patient age. RESULTS: All 1841 isolates contained fhbp. fHBP sequences from Spain and Germany fell within the previously described subfamilies, with 69% of isolates belonging to subfamily B and 31% to subfamily A; prevalent sequence variants were also similar. Stratification of data by age indicated that disease in infants <1 year of age was caused by a significantly higher proportion of isolates with fHBP subfamily A variants than that seen in adolescents and young adults 11-25 years (47.7% versus 19.5%, P < 0.0001, respectively). CONCLUSIONS: These observations highlight a difference in epidemiology of fHBP subfamilies in different age groups, with fHBP subfamily A strains causing more disease in vulnerable populations, such as infants, than in adolescents.
- MeSH
- antigeny bakteriální analýza genetika imunologie MeSH
- bakteriální proteiny analýza genetika imunologie MeSH
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- meningokokové infekce epidemiologie imunologie mikrobiologie prevence a kontrola MeSH
- meningokokové vakcíny aplikace a dávkování imunologie MeSH
- mladiství MeSH
- Neisseria meningitidis chemie imunologie izolace a purifikace MeSH
- předškolní dítě MeSH
- senioři MeSH
- věkové faktory MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- předškolní dítě MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Spojené státy americké MeSH
3 sv.
- MeSH
- hodnocení stavu výživy MeSH
- nemoci výživy a metabolismu MeSH
- poruchy výživy MeSH
- Publikační typ
- encyklopedie MeSH
Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). Until now, only a single TEN strain, Bosnia A, has been completely sequenced. The only other laboratory TEN strain available, Iraq B, was isolated in Iraq in 1951 by researchers from the US Centers for Disease Control and Prevention. In this study, the complete genome of the Iraq B strain was amplified as overlapping PCR products and sequenced using the pooled segment genome sequencing method and Illumina sequencing. Total average genome sequencing coverage reached 3469×, with a total genome size of 1,137,653 bp. Compared to the genome sequence of Bosnia A, a set of 37 single nucleotide differences, 4 indels, 2 differences in the number of tandem repetitions, and 18 differences in the length of homopolymeric regions were found in the Iraq B genome. Moreover, the tprF and tprG genes that were previously found deleted in the genome of the TEN Bosnia A strain (spanning 2.3 kb in length) were present in a subpopulation of TEN Iraq B and Bosnia A microbes, and their sequence was highly similar to those found in T. p. subsp. pertenue strains, which cause the disease yaws. The genome sequence of TEN Iraq B revealed close genetic relatedness between both available bejel-causing laboratory strains (i.e., Iraq B and Bosnia A) and also genetic variability within the bejel treponemes comparable to that found within yaws- or syphilis-causing strains. In addition, genetic relatedness to TPE strains was demonstrated by the sequence of the tprF and tprG genes found in subpopulations of both TEN Iraq B and Bosnia A. The loss of the tprF and tprG genes in most TEN microbes suggest that TEN genomes have been evolving via the loss of genomic regions, a phenomenon previously found among the treponemes causing both syphilis and rabbit syphilis.
- MeSH
- bakteriální geny MeSH
- frambézie mikrobiologie MeSH
- fylogeneze MeSH
- genom bakteriální MeSH
- infekce bakteriemi rodu Treponema mikrobiologie MeSH
- proteiny vnější bakteriální membrány genetika MeSH
- sekvenování celého genomu MeSH
- syfilis mikrobiologie MeSH
- Treponema pallidum genetika MeSH
- Treponema genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Bosna a Hercegovina MeSH
BACKGROUND: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes. CONCLUSIONS/SIGNIFICANCE: The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.
- MeSH
- druhová specificita MeSH
- frambézie mikrobiologie MeSH
- genom bakteriální genetika MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- přenos genů horizontální MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční seřazení MeSH
- shluková analýza MeSH
- syfilis mikrobiologie MeSH
- syntenie MeSH
- Treponema pallidum klasifikace genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Bosna a Hercegovina MeSH
BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques. METHODOLOGY/PRINCIPAL FINDINGS: The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related. CONCLUSION/SIGNIFICANCE: We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.
- MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom genetika MeSH
- molekulární sekvence - údaje MeSH
- sekvence aminokyselin MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA metody MeSH
- sekvenční seřazení MeSH
- syfilis genetika parazitologie MeSH
- Treponema pallidum genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. METHODOLOGY/PRINCIPAL FINDINGS: The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. CONCLUSIONS/SIGNIFICANCE: Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
- MeSH
- genom bakteriální * MeSH
- lidé MeSH
- pořadí genů MeSH
- rekombinace genetická MeSH
- repetitivní sekvence nukleových kyselin MeSH
- sekvenční analýza DNA * MeSH
- Treponema pallidum genetika MeSH
- výpočetní biologie MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Indonésie MeSH
The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence, coverage and conservation of integrated MGEs are apparent between sublineages. Differential MGE-associated gene cargo pertained to the functional categories of energy metabolism, ion transport, cell surface modification, and defense mechanisms. Inferred functional differences have the potential to impact long-term adaptive processes and may underpin the basis of the subspecies-level differentiation uncovered within A. ferrooxidans. Genome resequencing of iron- and sulfur-adapted cultures of a selected 2A sublineage strain (CCM 4253) showed that both episomal and large integrated MGEs are conserved over twenty generations in either growth condition. In turn, active insertion sequences profoundly impact short-term adaptive processes. The ISAfe1 element was found to be highly active in sublineage 2A strain CCM 4253. Phenotypic mutations caused by the transposition of ISAfe1 into the pstC2 encoding phosphate-transport system permease protein were detected in sulfur-adapted cultures and shown to impair growth on ferrous iron upon the switch of electron donor. The phenotypic manifestation of the △pstC2 mutation, such as a loss of the ability to oxidize ferrous iron, is likely related to the inability of the mutant to secure the phosphorous availability for electron transport-linked phosphorylation coupled to iron oxidation. Depletion of the transpositional △pstC2 mutation occurred concomitantly with a shortening of the iron-oxidation lag phase at later transfers on a ferrous iron-containing medium. Therefore, the pstII operon appears to play an essential role in A. ferrooxidans when cells oxidize ferrous iron. Results highlight the influence of insertion sequences and both integrated and episomal mobile genetic elements in the short- and long-term adaptive processes of A. ferrooxidans strains under changing growth conditions.