title: Challenges of using molecular serotyping for surveillance of pneumococcal disease.
abstract: Recent advances in the molecular identification and serotyping of Streptococcus pneumoniae are useful for culture-negative samples; however, there are limitations associated with these methods. We aimed to assess the value of molecular assays for invasive pneumococcal disease (IPD) surveillance in South Africa from 2010 through 2012. Nonviable isolates and culture-negative clinical specimens were tested for the lytA gene and, if positive, were serotyped, using real-time PCRs. Multinomial regression analysis was used to determine the maximum lytA cycle threshold (CT) value useful for predicting the ability to detect a serotype for the sample. The χ(2) test was used to compare the prevalence of serotypes between viable/nonviable isolates and culture-negative clinical specimens. Of 11,224 IPD cases reported, 1,091 (10%) were culture-negative samples and 981 (90%) of these were lytA positive. Samples with a lytA CT value of ≥35 were significantly less likely to be serotyped. A serotype/group was determined for 87% (737/844) of samples with a lytA CT value of <35, of which 60% (443/737) were identified as individual serotypes. The serotype prevalence did not differ significantly between isolates and culture-negative specimens. Although molecular serotyping added 7% (737/11,224) serotyping data, the inability to resolve 40% of samples to single serotypes remains a challenge for serotype-specific data analysis.
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Medical Research Council, Johannesburg, South Africa.
authors: Victoria
authors: V
authors: Magomani
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Medical Research Council, Johannesburg, South Africa nicolew@nicd.ac.za.
authors: Nicole
authors: N
authors: Wolter
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Influenza Division, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors: Stefano
authors: S
authors: Tempia
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Medical Research Council, Johannesburg, South Africa.
authors: Mignon
authors: M
authors: du Plessis
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Medical Research Council, Johannesburg, South Africa.
authors: Linda
authors: L
authors: de Gouveia
authors: National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Medical Research Council, Johannesburg, South Africa.
authors: Anne
authors: A
authors: von Gottberg
mesh_terms: D062665:Epidemiological Monitoring; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D011008:Pneumococcal Infections / Q000453:epidemiology / Q000382:microbiology*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012703:Serotyping / Q000379:methods*; D013019:South Africa / Q000453:epidemiology; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification