title: The Relevance of a Novel Quantitative Assay to Detect up to 40 Major Streptococcus pneumoniae Serotypes Directly in Clinical Nasopharyngeal and Blood Specimens.
abstract: For epidemiological and surveillance purposes, it is relevant to monitor the distribution and dynamics of Streptococcus pneumoniae serotypes. Conventional serotyping methods do not provide rapid or quantitative information on serotype loads. Quantitative serotyping may enable prediction of the invasiveness of a specific serotype compared to other serotypes carried. Here, we describe a novel, rapid multiplex real-time PCR assay for identification and quantification of the 40 most prevalent pneumococcal serotypes and the assay impacts in pneumonia specimens from emerging and developing countries. Eleven multiplex PCR to detect 40 serotypes or serogroups were optimized. Quantification was enabled by reference to standard dilutions of known bacterial load. Performance of the assay was evaluated to specifically type and quantify S. pneumoniae in nasopharyngeal and blood samples from adult and pediatric patients hospitalized with pneumonia (n = 664) from five different countries. Serogroup 6 was widely represented in nasopharyngeal specimens from all five cohorts. The most frequent serotypes in the French, South African, and Brazilian cohorts were 1 and 7A/F, 3 and 19F, and 14, respectively. When both samples were available, the serotype in blood was always present as carriage with other serotypes in the nasopharynx. Moreover, the ability of a serotype to invade the bloodstream may be linked to its nasopharyngeal load. The mean nasopharyngeal concentration of the serotypes that moved to the blood was 3 log-fold higher than the ones only found in the nasopharynx. This novel, rapid, quantitative assay may potentially predict some of the S. pneumoniae serotypes invasiveness and assessment of pneumococcal serotype distribution.
authors.affiliation: Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France.
authors.forename: Melina
authors.initials: M
authors.lastname: Messaoudi
authors.affiliation: Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France.
authors.forename: Milen
authors.initials: M
authors.lastname: Milenkov
authors.affiliation: Department of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.|Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Werner C
authors.initials: WC
authors.lastname: Albrich
authors.affiliation: National Reference Center for Streptococci, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany.
authors.forename: Mark P G
authors.initials: MP
authors.lastname: van der Linden
authors.affiliation: Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot - Hospices Civils de Lyon, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bénet
authors.affiliation: Faculty of Pharmacy, University of Health Sciences, Phnom Penh, Cambodia.
authors.forename: Monidarin
authors.initials: M
authors.lastname: Chou
authors.affiliation: CHU Gabriel Touré, Bamako, Mali.
authors.forename: Mariam
authors.initials: M
authors.lastname: Sylla
authors.affiliation: Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil.
authors.forename: Patricia
authors.initials: P
authors.lastname: Barreto Costa
authors.affiliation: Service de Réanimation Pédiatrique Médico-Chirurgicale, HFME, Groupement Hospitalier Est, Bron, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Richard
authors.affiliation: Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.|Hubert Department of Global Health and Division of Infectious Diseases, Emory University, Atlanta, Georgia, United States of America.
authors.forename: Keith P
authors.initials: KP
authors.lastname: Klugman
authors.affiliation: Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France.|Departement of Medical Microbiology & Infectious Diseases Erasmus MC, Rotterdam, The Netherlands.
authors.forename: Hubert P
authors.initials: HP
authors.lastname: Endtz
authors.affiliation: Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France.
authors.forename: Gláucia
authors.initials: G
authors.lastname: Paranhos-Baccalà
authors.affiliation: Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France.
authors.forename: Jean-Noël
authors.initials: JN
authors.lastname: Telles
mesh_terms: D000328:Adult; D001938:Brazil; D002160:Cambodia; D002675:Child, Preschool; D015331:Cohort Studies; D004269:DNA, Bacterial / Q000235:genetics; D005602:France; D006801:Humans; D008302:Mali; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D009305:Nasopharynx / Q000382:microbiology*; D011008:Pneumococcal Infections / Q000097:blood / Q000382:microbiology*; D015203:Reproducibility of Results; D065288:Serogroup; D012703:Serotyping / Q000379:methods*; D013019:South Africa; D013045:Species Specificity; D013291:Streptococcus / Q000145:classification / Q000235:genetics; D013296:Streptococcus pneumoniae / Q000145:classification / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial