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PubMed2025

Accurate serotype identification of Streptococcus pneumoniae using nanopore Cas9-targeted serotype identification (nCATSerotyping).

Streptococcus pneumoniae (pneumococcus) is a leading cause of community-acquired pneumonia and invasive diseases, particularly among children and the elderly. The introduction of pneumococcal conjugate vaccines has significantly reduced invasive pneumococcal disease, but the prevalence of non-vaccine serotypes and newly emerging serotypes is increasing globally. Thus, accurate serotyping is essential for epidemiological surveillance and the development of next-generation multivalent pneumococcal vaccines. Conventional serotyping methods, including multiplex polymerase chain reaction (mPCR), monoclonal antibody (mAb) assays, and Quellung reaction using rabbit antisera, are limited by serotype coverage and cross-reactivity, making the detection of new or emerging serotypes challenging. In this study, we developed a nanopore Cas9-targeted serotyping (nCATSerotyping) platform, which employs Cas9-mediated enrichment of the capsular polysaccharide synthesis locus followed by Oxford Nanopore sequencing. Applying this method to 276 clinical pneumococcal isolates collected in South Korea (2018-2020), we achieved a serotyping success rate of 97.10% (268/276), significantly outperforming conventional methods such as mAb and mPCR, which identified only 76.45% (211/276) of isolates. Whole-genome sequencing of the remaining eight non-typeable isolates revealed them to be non-pneumococcal (oral streptococci), confirming 100% accuracy for S. pneumoniae serotyping. Importantly, our method identified emerging and underrepresented serotypes, including serotype 13 and null capsule clade strains. nCATSerotyping offers a rapid, accurate, and comprehensive solution for pneumococcal serotyping, with significant advantages in identifying novel and non-typeable strains. This scalable platform will be a valuable tool for global serotype surveillance and next-generation multivalent pneumococcal vaccine development.IMPORTANCEAccurate pneumococcal serotyping is critical for vaccine development and epidemiological surveillance, particularly as non-vaccine serotypes emerge following widespread pneumococcal conjugate vaccine implementation. Current serotyping methods face significant limitations in coverage and accuracy, identifying around 76% of pneumococcal isolates and failing to detect emerging serotypes like serotype 13 and null capsule clades. The nanopore Cas9-targeted serotyping platform addresses these critical gaps by achieving 100% serotyping accuracy for confirmed Streptococcus pneumoniae isolates while identifying previously undetectable strains that conventional methods missed. This comprehensive approach is essential for monitoring vaccine effectiveness, understanding serotype replacement patterns, and informing next-generation vaccine development strategies. Furthermore, the identification of misclassified oral streptococci highlights the diagnostic precision needed for accurate pneumococcal surveillance, ensuring that epidemiological data accurately reflect true pneumococcal disease burden and serotype distribution patterns.

Streptococcus pneumoniae↗

PubMed1991

[T-serotype distribution of group A hemolytic streptococci in a rapidly expanding residential area in Sanda City, Hyogo Prefecture, with reference to an outbreak of serotype T-28 in autumn, 1988].

In the fall of 1988, an outbreak of streptococcal infections was observed at 2 pediatric clinics in Sanda City, Hyogo prefecture. The 2 clinics were independent of each other; one (clinic A) was located in the down town area, in the older part of the city, where there is little population turn over, while the other (clinic B) was in a newly developed-fast growing residential district. The strains and the distribution of T-serotypes isolated at each location are as follows: clinic A; 58 strains (34.5% serotype T-4, 31.0% serotype T-12, 10.3% serotype T-1, and 23.3% serotype T-28), clinic B; 43 strains (48.8% serotype T-28, 23.3% serotype T-12, 11.6% serotype T-4 and 7.0% serotype T-1). According to the data from Kobe City infectious disease surveillance center, there were a total of 102 group A hemolytic streptococci strains isolated in 1988, the T-serotypes distribution of which was as follows: 47.0% serotype T-4, 15.7% serotype the T-12, 10.8% serotype T-1 and 9.8% serotype T-28. Serotype T-4 was dominant here, as it was in location A of Sanda City. The epidemic proportion of serotype T-28 found at location B is considered to be due to the fact that location B has very little social interaction with location A and other areas. No difference was observed among the different serotypes on the drug susceptibility test: all strains showed a sensitivity to ampicillin and penicillin G, but were resistant to tetracycline and chloramphenicol.

Adolescent↗

PubMed1992

Characterization of the lipopolysaccharide O antigens of Actinobacillus pleuropneumoniae serotypes 9 and 11: antigenic relationships among serotypes 9, 11, and 1.

The antigenic lipopolysaccharide O polysaccharides of capsular serotypes 9 and 11 were examined by chemical, immunological, and nuclear magnetic resonance methods. Immunodiffusion tests carried out on these O antigens indicated that both contained common epitopes which were also shared by Actinobacillus pleuropneumoniae serotype 1. Chemical analysis and high-field nuclear magnetic resonance spectroscopy showed that the O antigens of serotypes 9 and 11 were high-molecular-weight polymers consisting of a backbone of repeating trisaccharide units composed of alpha-L-rhamnopyranosyl and alpha-D-glucopyranosyl residues (2:1). One of the alpha-L-rhamnose units forms a branch point and is stoichiometrically substituted with terminal 2-acetamido-2-deoxy-beta-D-glucose residues in the serotype 11 O polysaccharide, but only to the extent of 25% in the serotype 9 O polysaccharide. Thus, the serotype 9 O polysaccharide contains two different repeating units: a tetrasaccharide unit with the same structure as that of the serotype 11 O polysaccharide and a trisaccharide unit: [formula: see text] where R = beta-D-GlcpNAc for serotype 1 and 11 O polysaccharides, and R = H (75%) and R = beta-D-GlcpNAc (25%) for serotype 9. The structure of the previously determined serotype 1 O polysaccharide (E. Altman, J.-R. Brisson, and M. B. Perry, Biochem. Cell. Biol. 64:17-25, 1986) is identical to that of the serotype 11 O polysaccharide. We propose a more complete serotyping scheme for A. pleuropneumoniae which includes designation of both the capsular (K) and O antigens.

Actinobacillus pleuropneumoniae↗

PubMed1991

Operational overlapping of cross-reactive and serotype-specific neutralization epitopes on VP7 of human rotavirus serotype 3.

VP7-specific neutralizing monoclonal antibodies (N-MAbs) to serotype 3 human rotavirus were produced to analyze serotype 3-specific and cross-reactive neutralization epitopes on VP7. On the basis of the reactivity patterns in neutralization tests with various human and animal strains, a total of 10 N-MAbs could be classified into four groups; five antibodies specific to serotype 3 were divided into two groups, and five antibodies consisted of two groups which are cross-reactive with strain 69 M (serotype 8) or strain WI61 (serotype 9). Seven N-MAbs showed the same reactivity patterns to the virus strains in both neutralization tests and enzyme-linked immunosorbent assay (ELISA), while three N-MAbs specific to serotype 3 in neutralization showed a cross-reactivity with the serotype 8 strain in ELISA. Neutralization-resistant mutants of serotype 3 strains P and YO were selected by the N-MAbs. Cross-neutralization tests between the mutants and the MAbs indicated the presence of two serotype-specific (S1 and S2) and three cross-reactive (C1, C2, and C3) epitope groups. S1, S2, and C3 epitope groups overlapped operationally each other, and the S1 epitope group had an overlapping with the C1 epitope group. However, C2 epitope group identified by the MAbs which neutralized serotypes 3 and 9, had no operational overlapping with any other epitope groups.

Animals↗

PubMed1990

Serotype-related antigen of Trichosporon cutaneum in the induction of summer-type hypersensitivity pneumonitis: correlation between serotype of inhalation challenge-positive antigen and that of the isolates from patients' homes.

Inhalation challenge with the culture filtrate-antigens prepared from two strains of different serotype of Trichosporon cutaneum (TIMM 1573, serotype I; TIMM 1318, serotype II) was performed on patients with summer-type hypersensitivity pneumonitis and asymptomatic seropositive family members. Of the 17 patients, 12 were strongly positive, four were mildly so, and one was negative. Interestingly, of the 16 inhalation challenge-positive patients, four reacted to both serotypes I and II, five to serotype I only, and seven to serotype II only. There was a good correlation between the serotype inhalation challenge-positive antigen and that of T. cutaneum isolated from the homes of two patients' homes. A strain of T. cutaneum demonstrating a new serotype was isolated from the homes of two patients, one of whom was negative to both serotypes I and II. Specific antibody activity, lymphocyte proliferative response, and skin reaction to the antigens were also positive, but these findings were not useful to discriminate the inhalation challenge-positive from the inhalation challenge-negative antigen. Neither of the two asymptomatic family members responded. These results indicate that inhalation challenge in patients with summer-type hypersensitivity pneumonitis is provoked by the serotype-related antigen of T. cutaneum, reflecting the sensitization of these patients in their homes.

Alveolitis, Extrinsic Allergic↗

PubMed1992

Serotype specificity of immunological assays for the capsular polymer of Actinobacillus pleuropneumoniae serotypes 1 and 9.

The cross-reactivity of the purified polysaccharides of Actinobacillus pleuropneumoniae serotypes 1 and 9 were examined using a variety of highly sensitive assays, such as radioimmunoassay, latex agglutination, enzyme-linked immunosorbent assay (ELISA), and immunoblotting. In addition, conventional immunodiffusion was included for comparison. Latex agglutination, utilizing affinity-purified IgG to capsule, was also used to serotype whole cells. Agglutination or precipitation tests (radioimmunoassay, latex agglutination, and immunodiffusion) indicated no cross-reactivity between the capsules of serotypes 1 and 9, and no cross-reactivity between whole cells by latex agglutination. Assays that required binding of the capsule to a solid support (ELISA and immunoblotting) did demonstrate cross-reactions between serotypes 1 and 9 capsules, although reactions with the heterologous serotype were weaker than with the homologous serotype. The cross-reactivity could not be attributed solely to nonspecific factors because similar cross-reactivity did not occur with serotype 5 or 7 capsules by any assay. Reactivity of antisera with homologous or heterologous capsule was reduced, but not completely eliminated, by adsorption with washed, live bacteria of the heterologous serotype. Thus, the assay, as well as the antigen or specificity of the antibody reagent used, may influence the results of A. pleuropneumoniae serotyping or serological tests.

Actinobacillus pleuropneumoniae↗

PubMed1991

Serotyping of Canadian isolates of Treponema hyodysenteriae and description of two new serotypes.

A total of 30 isolates of Treponema hyodysenteriae collected in the Saint-Hyacinthe (Quebec, Canada) area were serotyped by agar gel double immunodiffusion by using extracted lipopolysaccharide and hyperimmune rabbit antisera. Only 17% (5 of 30) of the isolates were typed with antisera specific for each of the seven known serotypes of T. hyodysenteriae. Antisera raised against 11 untypeable local isolates were then produced and tested against each lipopolysaccharide extract. Results showed two serologically distinct groups among 21 of the 25 untypeable isolates. The isolates in each group shared identical antigens. No detectable reactions could be observed between antisera raised against these 11 isolates and the antigens extracted from 7 reference serotype strains. On the basis of these results, two new serotypes of T. hyodysenteriae, serotypes 8 and 9, are proposed. We also propose isolate FM 88-90 as the reference strain for serotype 8 and isolate FMV 89-3323 as the reference strain for serotype 9. These two new serotypes, which represented 70% of the isolates tested, seem to be the major serotypes found in the province of Quebec.

Animals↗

PubMed1992

Monoclonal antibodies as probes to examine serotype-specific and cross-reactive epitopes of lipopolysaccharides from serotypes O2, O5, and O16 of Pseudomonas aeruginosa.

Serotypes O2, O5, and O16 of Pseudomonas aeruginosa are chemically related, and the O antigens of their lipopolysaccharides share a similar trisaccharide repeat backbone structure. Serotype-specific monoclonal antibodies (MAbs) MF71-3, MF15-4, and MF47-4 against the O2, O5, and O16 serotypes, respectively, were isolated. MAb 18-19, which is cross-reactive with all strains of this chemically related serogroup, was also produced. When column chromatography or sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated lipopolysaccharide (LPS) samples from each of the serotypes were probed with the MAbs in Western immunoblots, each of the serotype-specific MAbs interacted only with high-molecular-weight bands of the homologous LPS, with a minimum O-antigen chain length of at least 6 to 10 repeats. In contrast, cross-reactive MAb 18-19 was shown to interact in Western immunoblots with the entire LPS banding pattern except the fastest-running band, which lacks O antigen. Chemical modification of P. aeruginosa LPS by alkali treatment and carboxyl reduction abolished reactions between LPS and MAb 18-19, while reactions of modified LPS with serotype-specific MAbs were not affected. Therefore, cross-reactive MAb 18-19 likely recognizes the chemical backbone structure of the O repeat that is common to all three serotypes of the O2-O5-O16 group, while the O-specific MAbs appeared to recognize LPS epitopes that could be presented when 6 to 10 or more O-antigen repeat units are present on the LPS molecule. Thus, the O-specific LPS epitopes likely involve unique chemical structures, glycosidic linkages, and some order of folding of the O side chains.

Antibodies, Bacterial↗

PubMed1992

The restriction endonuclease map of Marek's disease virus (MDV) serotype 2 and collinear relationship among three serotypes of MDV.

A BamHI, EcoRI, and XhoI restriction endonuclease map of Marek's disease virus (MDV) serotype 2 (MDV2) DNA was constructed by double-digest analyses of 28 cloned BamHI and 11 cloned EcoRI fragments of MDV2 DNA, followed by hybridization tests of these cloned BamHI DNA fragments with electrophoretically separated digests of MDV2-infected cell DNA. On this map, MDV2 genome consisted of two segments which have unique regions inserted between two inverted repeat regions as observed in MDV serotype 1 and 3 genomes. Further, the DNA homology among three serotypes of MDV was examined by hybridization under less stringent conditions using cloned BamHI fragments of MDV2 DNA. Most of the MDV2 fragments located within the unique regions hybridized with MDV serotype 1 and 3 DNAs, indicating the presence of the collinear relationship among three serotypes. In addition, MDV2 DNA fragments which hybridized with the DNA fragments encoding MDV1 gp57-65 (or A antigen) or MDV1 gp100, gp60, gp49 (or B antigen) were identified and these fragments of serotypes 1 and 2 found to be collinear.

Animals↗

PubMed1976

The stability of the serotypes of Bordetella pertussis with particular reference to serotype 1,2,3,4.

Strains of Bordetella pertussis in which all the organisms contain agglutinogens 1 and 3 or 1,2 and 4 are easy to identify as serotypes 1,0,3,0 and 1,2,0,4 respectively; and similarly, stable strains of serotype 1,0,3,4 are occasionally found. During repeated subcultures, passage in vivo, and lyophilization and preservation for many years, these serotypes do not change. Mixing 1,0,3,0 and 1,2,0,4 serotypes and culturing them together in vivo and in vitro produces cultures from which organisms of the same two serotypes can be isolated. In contrast, strains which type as 1,2,3,4 are often a heterogeneous group. We have attempted to classify these as "stable", "variable" and "mixed" cultures. Some strains comprise organisms all of which contain the four agglutinogens and are as easy to type as the strains described above. These we have called "stable" 1,2,3,4 strains. Other 1,2,3,4 strains are made up of colonies possessing all four agglutinogens, as shown by agglutinin production, but in amounts varying from day to day so that direct typing is inconsistent. These we have called "variable" 1,2,3,4 strains. The last category, "mixed", is made up of organisms most of which give rise to stable 1,2,3,4 cultures; a few of the component organisms, however, have one or two of the four agglutinogens missing. The importance of the "variable" cultures is emphasized for work on apparent change of serotype, e.g. during infection.

Agglutination Tests↗

PubMed1992

[Serotyping of 48 isolates of Candida albicans: predominance of serotype A over B in Venezuela].

The study of serotyping of isolates of Candida albicans of clinical material obtained from different geographic areas of Venezuela suggest that serotype A is predominant over type B. These results are in relation with results obtained in other countries. Type A serotype is predominant in 57 to 100% in the areas studied. Only in 2 cities serotype B was isolated. Both serotypes of Candida albicans were observed in intertriginous, mucosal, inguinal and lung forms. These studies have allowed us to have information about the predominance of serotypes in certain areas of the country.

Agglutination Tests↗

PubMed1977

Pathological changes in calves injected intradermally with Mycobacterium intracellulare serotype Davis and M. avium serotype 2.

Three strains of the M. intracellulare-M. avium complex were injected intradermally into 12 calves. M. intracellulare serotype Davis (M. avium complex serotype 8) was injected into five calves. One calf died with disseminated caseous granulomas at 79 days; three calves killed between 56 and 82 days after inoculation had widely disseminated caseous or caseous or caseocalcareous granulomas. One calf killed at 173 days had only encapsulated granulomas at the injection site and its regional lymph node. Two strains of M. avium serotype 2 (M. avium complex serotype 2) were injected intradermally into seven calves. Six had disseminated granulomas when killed 54-170 days after inoculation. One calf killed at 55 days had granulomas confined to the inoculation sites and their regional lymph nodes. Lesions induced by both M. avium serotype 2 and M. intracellulare serotype Davis were initially caseocalcareous granulomas which became encapsulated and nonprogressive after about 112 days. Two calves inoculated with similar doses of M. bovis and killed in extremis at 37 and 65 days after inoculation had disseminated progressive lesions without encapsulation.

Animals↗

PubMed1978

Antigens of Streptococcus mutans: isolation of a serotype-specific and a cross-reactive antigen from walls of strain V-100 (serotype e).

Two cell wall-associated polysaccharide antigens were extracted from purified cell walls of Streptococcus mutans serotype e strain V-100. One of these purified antigens (I) is specific for serotype e, whereas the other (II) has antigenic determinants reactive with both heterologous anti-serotype c serum (GS-5) and the homologous (e) serum. When crude formamide extracts of V-100 cell walls were loaded onto a Cellex-D column and eluted with a linear gradient of ammonium carbonate (0.02 to 0.40 M), the two products mentioned above could be recovered. The purified, antigenically reactive products (I and II) were each composed only of rhamnose and glucose in approximately a 2:1 molar ratio. Immunoelectrophoresis of the crude formamide extract, peak I, and peak II showed the purified fractions to have opposite mobilities and the crude extract to have a mobility that encompassed both purified peaks when reacted with homologous antiserum (V-100). When these three fractions were immunoelectrophoresed and reacted with heterologous anti-serotype c serum (GS-5), only the anodic portion of the crude V-100 formamide extract and purified peak II formed precipitates. Ouchterlony analysis with homologous antiserum produced precipitin patterns between the crude formamide extract and both purified peaks, indicating complete identity. However, only crude extracts of V-100 and the purified peak II material reacted with heterologous (c) antiserum; peak I did not cross-react in these Ouchterlony assays. Hapten inhibition studies revealed that a beta-glucosyl moiety is the immunodeterminant for serotype e and is present on each purified fraction. The basis of the cross-reaction between anti-c sera and the purified antigen II of e is discussed.

Cell Wall↗

PubMed1992

Characterization of lipopolysaccharides from four Pasteurella haemolytica serotype strains: evidence for presence of sialic acid in serotypes 1 and 5.

Highly purified lipopolysaccharides (LPS) obtained from four strains of Pasteurella haemolytica representative of four different serotypes were studied to ascertain their overall structural elements and sugar and fatty acid compositions. SDS-PAGE analysis revealed that each LPS was of the smooth-type although they differed in migration patterns. Somewhat unusual features of these LPS included the presence of: (a) rhamnose in the core oligosaccharides of serotypes 2 and 3; and (b) sialic acid in the LPS of serotypes 1 and 5. The fatty acids, myristic, hydroxymyristic and palmitic occur in essentially equivalent amounts in each of these LPS. In addition, stearic acid was present in small amounts of serotypes 1 and 5.

Amino Sugars↗

PubMed1976

The serotypes of Bordetella pertussis isolated in Great Britain between 1941 and 1968 and a comparison with the serotypes observed in other countries over this period.

Classification, by agglutinogens, of 634 isolates of Bordetella pertussis collected from 1971 to 1968 in Great Britain demonstrated that a change from a predominantly 1,2,0,4 serotype (75% of those examined during 1941-4) to a predominantly 1,0,3,0 serotype (73% of those examined during 1966-8) occurred sometime after 1953. Furthermore, evidence from the examination of isolates collected between 1941 and 1953 suggests that the change may have been gradual. Isolates of serotype 1,2,3,4 made up 20-30% of the total of our cross-country selection for the periods 1941-4, 1946-9, 1950-3 and 1966-8, but over shorter periods in individual areas the percentage varied from negligible to as high as half of those isolated. Results from other countries show a similar drift towards a 1,0,3 sertype but more often from a 1,2,3 than from 1,2,0 serotype. The value, in epidemiological studies, of extended information obtained by monospecific typing sera to all six, rather than only two or three agglutinogens, and confirmation of the results by agglutinin production is demonstrated: for instance not all 1,0,3 isolates were identical.

Agglutination Tests↗

PubMed1992

Protective efficacy against serotype 1 rotavirus diarrhea by live oral rhesus-human reassortant rotavirus vaccines with human rotavirus VP7 serotype 1 or 2 specificity.

Rhesus-human rotavirus (RV) reassortant vaccine strains D x RRV or DS 1 x RRV with VP7 serotype 1 or 2 specificity were evaluated for safety, immunogenicity and protective efficacy in a double blind placebo-controlled three cell trial involving 359 infants ages 2 to 5 months. The titer of the D x RRV vaccine was 10(4) and that of the DS 1 x RRV vaccine was 10(5) plaque-forming units/1-ml dose. The vaccines were acceptably reactogenic, each inducing a transient febrile response in fewer than one-third of the vaccinees. Seroconversion by RV enzyme-linked immunosorbent assay IgA antibody was detected in 61 and 75% of the vaccinees receiving a single dose of the serotype 1 or 2 reassortant vaccine, respectively. Efficacy against RV diarrhea was evaluated in two successive epidemic seasons; RV serotype 1 was prevalent in both. Clinical efficacy was observed with both vaccines and was associated with seroconversion after vaccination; considering only such vaccinees both vaccines showed equal efficacy. The overall rates of protection for the two vaccines combined against clinical RV disease in children with seroconversion after vaccination were 92 and 59% in the first and second RV epidemic seasons, respectively. Protection against asymptomatic RV infection, as measured by serologic responses, was 59% in the first season and nil in the second season. It is concluded that each of the reassortant RV vaccines was effective in inducing protection against symptomatic RV disease associated with RV serotype 1.

Administration, Oral↗

PubMed1978

A microagglutination test for Yersinia enterocolitica infection: recognition of multiple serotypes in experiments with stained suspensions of serotype O5,27.

When suspensions of Yersinia enterocolitica were stained with triphenyl-tetrazolium chloride (TTC) their antigenic specificity, as determined by tube and microtitre-plate agglutination tests, was altered. Thus, a TTC-stained suspension of serotype O5,27 detected antibodies to nine O serotypes of Y. enterocolitica in sera from experimentally infected animals but did not cross-react with antisera to organisms of five other unrelated genera including Brucella. The same suspension did, however, cross-react weakly with antisera to four serotypes of Yersinia pseudotuberculosis. The value of this antigen preparation in detecting antibodies to the wide range of Y. enterocolitica serotypes likely to cause infection in man should now be assessed.

Agglutination Tests↗

PubMed1992

Biochemical characterization of an antigenic saline extract of Actinobacillus pleuropneumoniae serotype 5 and identification of a serotype-specific antigen for ELISA serodiagnosis.

A saline extract of boiled-formalinized whole cells from a local strain (81-750; Quebec, Canada) of Actinobacillus pleuropneumoniae, serotype 5b was used as an antigen in an enzyme-linked immunosorbent assay (ELISA) for serodiagnosis of swine pleuropneumonia. Characterization of this crude extract was done and proteins, neutral sugars, hexosamines, and 2-keto-3-deoxyoctonate (KDO) were evaluated. On phenol extraction of the crude extract a serotype-specific antigen of polysaccharidic nature was recovered from the aqueous phase. This antigen was characterized using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) with Coomassie blue, silver and Schiff stainings. Immunoblots were done using sera of experimentally infected pigs that showed serotype specificity and cross-reactivity. Overall, the results indicate that the O-chain of lipopolysaccharides is a specific antigen that could be used in ELISA for the serodiagnosis of serotype 5 of A. pleuropneumoniae.

Actinobacillus Infections↗