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Fiona M Russell - One of the best experts on this subject based on the ideXlab platform.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    PLOS ONE, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    bioRxiv, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    Objectives: As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated 33F-1). Here, we investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its impact on serotyping results. Methods: Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. Results: All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the cpsA, cpsB, cpsC, cpsD, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. Conclusions: We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This has important implications for molecular approaches measuring vaccine impact and disease surveillance, which continue to increase in popularity, particularly in low- and middle-income countries, where pneumococcal serotype diversity is poorly understood.

  • first report of putative streptococcus pneumoniae serotype 6d among nasopharyngeal isolates from fijian children
    The Journal of Infectious Diseases, 2009
    Co-Authors: Ping Jin, Shahin Oftadeh, Fanrong Kong, Meng Xiao, Fei Zhou, Chunyi Liu, Fiona M Russell, Gwendolyn L. Gilbert
    Abstract:

    BACKGROUND A putative Streptococcus pneumoniae serotype, 6D, resulting from the introduction of wciN(beta) into serotype 6B has been proposed. METHODS We studied 98 unique serogroup 6 isolates from Fijian children, two-thirds of whom had received at least 1 dose of 7-valent pneumococcal conjugate vaccine, and 51 invasive isolates from Australian children. We used a polymerase chain Reaction (PCR) system that targets both wciN(beta) and the single-nucleotide polymorphism that differentiates serotypes 6A and 6B-wciP584g (6A) and wciP584a (6B). RESULTS Two (9%) of 22 Australian isolates and 24 (38%) of 64 Fijian isolates previously identified as 6A by the Quellung Reaction and wciP584g PCR contained wciN(beta) and were designated as 6C; 14 (41%) of 34 Fijian isolates previously identified as 6B by the Quellung Reaction and wciP584a PCR contained wciN(beta) and were designated as the new putative serotype 6D. A significantly smaller proportion of children from whom serotype 6D was isolated (2/14 [14%]) had not received PCV-7, compared with the proportion of those from whom serotype 6B was isolated (11/20 [55%]) (P < .05). CONCLUSION This is the first report of naturally occurring S. pneumoniae serotype 6D.

Kim E Mulholland - One of the best experts on this subject based on the ideXlab platform.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    PLOS ONE, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    bioRxiv, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    Objectives: As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated 33F-1). Here, we investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its impact on serotyping results. Methods: Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. Results: All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the cpsA, cpsB, cpsC, cpsD, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. Conclusions: We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This has important implications for molecular approaches measuring vaccine impact and disease surveillance, which continue to increase in popularity, particularly in low- and middle-income countries, where pneumococcal serotype diversity is poorly understood.

Eileen M Dunne - One of the best experts on this subject based on the ideXlab platform.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    PLOS ONE, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    bioRxiv, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    Objectives: As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated 33F-1). Here, we investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its impact on serotyping results. Methods: Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. Results: All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the cpsA, cpsB, cpsC, cpsD, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. Conclusions: We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This has important implications for molecular approaches measuring vaccine impact and disease surveillance, which continue to increase in popularity, particularly in low- and middle-income countries, where pneumococcal serotype diversity is poorly understood.

Sam Manna - One of the best experts on this subject based on the ideXlab platform.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    PLOS ONE, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

  • discovery of a streptococcus pneumoniae serotype 33f capsular polysaccharide locus that lacks wcje and contains a wcyo pseudogene
    bioRxiv, 2018
    Co-Authors: Sam Manna, Fiona M Russell, Bd Ortika, Eileen M Dunne, Casey L Pell, Mike Kama, Tuya Mungun, Kim E Mulholland
    Abstract:

    Objectives: As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated 33F-1). Here, we investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its impact on serotyping results. Methods: Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung Reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. Results: All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the cpsA, cpsB, cpsC, cpsD, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. Conclusions: We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This has important implications for molecular approaches measuring vaccine impact and disease surveillance, which continue to increase in popularity, particularly in low- and middle-income countries, where pneumococcal serotype diversity is poorly understood.

Moon H Nahm - One of the best experts on this subject based on the ideXlab platform.

  • Differential circulation of Streptococcus pneumoniae serotype 6C clones in two Israeli pediatric populations
    2016
    Co-Authors: Nurith Porat, Moon H Nahm, In Ho Park, Ron Dagan
    Abstract:

    We genotyped Streptococcus pneumoniae serotype 6C (Sp6C) isolates collected from Jewish and Bedouin children in southern Israel during the decade before vaccination. Sp6C constituted 8.2 % of the presumed Sp6A isolates. All of the Sp6C clonal clusters were associated with serogroup 6, mainly Sp6A. Different clonal distributions were found in the two subpopulations. Streptococcus pneumoniae serotype 6C (Sp6C) has recently been identified using monoclonal antibodies (8, 13). This se-rotype was previously typed as Sp6A by the Quellung Reaction. Genetic studies have found that the capsule gene locus of Sp6C is very similar to that of Sp6A, except for wciN; wciN6A en-codes a galactosyltransferase, whereas wciN6C encodes a glu-cosyltransferase (12). Since the two genes are completely di-vergent in nucleotide sequence, they can be differentiated by a specific PCR assay (1, 12). Studies in the United States (9, 11) documented a stepwise annual increase in the incidence of invasive disease caused by Sp6C following the implementatio

  • Identification of Streptococcus pneumoniae Serotype 11E, Serovariant 11Av and Mixed Populations by High- Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) Spectroscopy and Flow
    2016
    Co-Authors: Cytometric Serotyping Assay, Moon H Nahm, Romina Camilli, Brady L. Spencer, Monica Moschioni, Vittoria Pinto, Francesco Berti, Annalisa Pantosti
    Abstract:

    Background: Recent studies have identified Streptococcus pneumoniae serotype 11E and serovariant 11Av among isolates previously typed as 11A by classical serotyping methods. Serotype 11E and serovariant 11Av differ from serotype 11A by having totally or partially inactive wcjE, a gene in cps locus coding for an O-acetyl transferase. Serotype 11E is rare among carriage isolates but common among invasive isolates suggesting that it survives better during invasion. Aim of this work was to investigate the epidemiology of serotype 11A in a pneumococcal collection using a new serotyping approach based on High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) spectroscopy to distinguish serotypes 11A and 11E. Methods: A collection of 48 (34 invasive and 14 carriage) S. pneumoniae isolates from Italy, previously identified as serotype 11A by the Quellung Reaction, were investigated by wcjE sequencing, HR-MAS NMR spectroscopy and the reference flow cytometric serotyping assay (FCSA) based on monoclonal antibodies. Results: HR-MAS NMR spectra from serotypes 11A and 11E showed different NMR peaks indicating that HR-MAS NMR could be used to distinguish these serotypes, although HR-MAS NMR could not distinguish serotype 11Av from serotype 11E unambiguously. Thirty-eight isolates were confirmed to be serotype 11A, 8 isolates with a mutated wcjE were serotype 11E, 1 isolate belonged to serovariant 11Av, and 1 isolate was a mixed population 11A/11Av. All 11E isolates were identifie

  • from Quellung to multiplex pcr and back when needed in pneumococcal serotyping
    Journal of Clinical Microbiology, 2012
    Co-Authors: Lotta Siira, Moon H Nahm, Tarja Kaijalainen, Lotte Lambertsen, Maija Toropainen, Anni Virolainen
    Abstract:

    All currently available vaccines against Streptococcus pneumoniae are based on selections of the over 90 different serotypes, which underlines the importance of serotyping for surveillance and vaccine efficacy monitoring. In this study, we modified and validated a PCR-based scheme for deducing the serotypes of the invasive pneumococci isolated in Finland. For validation, 170 isolates were serotyped using the new protocol with six sequential multiplex PCRs for the deduction of serotypes, supplemented with Quellung testing when needed. The results were compared with those obtained by traditional serotyping methods. We found that 98.8% (168/170) of the isolates were correctly serotyped by the new protocol. Subsequently, the scheme was taken into regular use for serotyping the invasive pneumococci isolated in Finland for serotype-specific surveillance purposes and has been applied in the serotyping of more than 1,500 invasive isolates so far. The sequential multiplex PCRs (mPCRs) have given a result for over 99% of the isolates and allowed us to both handle samples in bulk and noticeably reduce the cost of reagents. While serotyping primarily by PCR is precise and effective, Quellung testing remains the most reliable way to discover possible discrepancies between the DNA deduced and the phenotypic serotype of an isolate. Since implementing the protocol for regular use, two serotype 19F PCR-positive isolates were found to be serotype 19A by the Quellung Reaction. While a rare occurrence, this is an important observation, which prompted a revision of our serotyping protocol to prevent possible underreporting of serotype 19A, a potential replacement serotype following large-scale vaccination.

  • a rapid pneumococcal serotyping system based on monoclonal antibodies and pcr
    Journal of Medical Microbiology, 2008
    Co-Authors: M Da G S Carvalho, Bernard Beall, Moon H Nahm
    Abstract:

    Streptococcus pneumoniae expresses at least 91 different polysaccharide (PS) capsules and the currently available serotyping methods are tedious to perform. We have been developing a rapid pneumococcal serotyping assay (named the ‘multibead assay’) based on the capacity of pneumococcal lysates to inhibit the ability of 24 different anti-capsule antibodies to bind to latex beads coated with 24 different PSs (serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9N, 9V, 14, 18C, 19A, 19F, 23F, 2, 8, 10A, 11A, 12F, 15B, 17F, 20, 22F and 33F). Because the polyclonal antibodies used for 10 serotypes (2, 8, 10A, 11A, 12F, 15B, 17F, 20, 22F and 33F) had limited serotype specificity, we replaced them with monoclonal antibodies for the 10 serotypes. To extend the serotype coverage beyond the 24 serotypes, we have adapted multiplexed PCR for five additional serotypes (15A, 15C, 16F, 35B and 38) to be useful with the pneumococcal lysates prepared for the multibead assay. We then validated the combined assay with 157 clinical isolates from the Centers for Disease Control and Prevention and found that the new combined assay produced results that are concordant with the Quellung Reaction. The combined assay is robust and could be used to rapidly identify the serotypes of the majority of pneumococci (∼90 %). In addition, the assay validation study suggests the presence of serological subtypes within serotype 11A.

  • discovery of a new capsular serotype 6c within serogroup 6 of streptococcus pneumoniae
    Journal of Clinical Microbiology, 2007
    Co-Authors: In Ho Park, David G Pritchard, Rob Cartee, Angela Pires Brandao, Maria Cristina De Cunto Brandileone, Moon H Nahm
    Abstract:

    Using two monoclonal antibodies, we found subtypes among pneumococcal isolates that are typed as serotype 6A by the Quellung Reaction. The prevalent subtype bound to both monoclonal antibodies and was labeled here 6Aα, whereas the minor subtype bound to only one monoclonal antibody and was labeled 6Aβ. To determine the biochemical nature of the two serologically defined subtypes, we purified capsular polysaccharides (PSs) from the two subtypes and examined their chemical structures with gas-liquid chromatography and mass spectrometry. The study results for 6Aα PS are consistent with the previously published structure of 6A PS, which is →2) galactose (1→3) glucose (1→3) rhamnose (1→3) ribitol (5→phosphate. In contrast, the 6Aβ PS study results show that its repeating unit is →2) glucose 1 (1→3) glucose 2 (1→3) rhamnose (1→3) ribitol (5→phosphate. We propose to continue referring to 6Aα as serotype 6A but to refer to 6Aβ as serotype 6C. Serotype 6C would thus represent the 91st pneumococcal serotype, with 90 pneumococcal serotypes having previously been recognized. This study also demonstrates that a new serotype may exist within an established and well-characterized serogroup or serotype.