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Nakao T, Kosai K, Akamatsu N, Ota K, Mitsumoto-Kaseida F, Hasegawa H, Izumikawa K, Mukae H, Yanagihara K. Molecular and phenotypic characterization of Streptococcus pneumoniae isolates in a Japanese tertiary care hospital. Front Cell Infect Microbiol 2024; 14:1391879. [PMID: 39104851 PMCID: PMC11298800 DOI: 10.3389/fcimb.2024.1391879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
This study aimed to investigate the bacterial characteristics of pneumococcal isolates obtained from a tertiary care hospital in Japan. We analyzed the antimicrobial susceptibility, possession of macrolide resistance genes, pneumococcal serogroup/serotype, and sequence type (ST) of pneumococcal isolates from patients aged 15 years or older between 2011 and 2020 at Nagasaki University Hospital. Of the 73 isolates analyzed, 86.3% showed resistance to macrolides, and 28.8%, 46.6%, and 11.0% harbored mefA, ermB, and both, respectively. Of the isolates possessing ermB, 97.6% showed high levels of macrolide resistance [minimal inhibitory concentration (MIC) range, > 16 µg/mL]. Solithromycin (MIC range, 0.03-0.25 µg/mL), regardless of the presence of macrolide resistance genes, and lascufloxacin (MIC range, 0.06-0.5 µg/mL) showed potent in vitro activity against pneumococci. Serotype 19A was the most prevalent (six isolates), followed by serotypes 10A, 15A, and 15B/C (five isolates each). Four serotypes (11A, 19A, 22F, and 23B) and five STs (36, 99, 433, 558, and 3111) were significantly correlated with the presence of macrolide resistance genes. All four isolates with serotype 11A/ST99 and three isolates with serotype 19A/ST3111 harbored both mefA and ermB. No macrolide resistance genes were detected in either of the two isolates with serotype 22F/ST433, while all ten isolates with serogroup 15 (serotypes 15A and 15B/C, five isolates each) possessed ermB alone. Our study revealed the bacterial characteristics of the pneumococcal isolates obtained from our hospital. In vitro activity of solithromycin and lascufloxacin against these isolates was confirmed.
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Affiliation(s)
- Takumi Nakao
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Kenji Ota
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Fujiko Mitsumoto-Kaseida
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
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Safari D, Daningrat WOD, Milucky JL, Khoeri MM, Paramaiswari WT, Tafroji W, Salsabila K, Winarti Y, Soebandrio A, Hadinegoro SR, Prayitno A, Childs L, Pimenta FC, Carvalho MDG, Pilishvili T. Nasopharyngeal carriage of Streptococcus pneumoniae among children <5 years of age in Indonesia prior to pneumococcal conjugate vaccine introduction. PLoS One 2024; 19:e0297041. [PMID: 38206916 PMCID: PMC10783721 DOI: 10.1371/journal.pone.0297041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/27/2023] [Indexed: 01/13/2024] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) prevent nasopharyngeal colonization with vaccine serotypes of Streptococcus pneumoniae, leading to reduced transmission of pneumococci and stronger population-level impact of PCVs. In 2017 we conducted a cross-sectional pneumococcal carriage study in Indonesia among children aged <5 years before 13-valent PCV (PCV13) introduction. Nasopharyngeal swabs were collected during visits to community integrated health service posts at one peri-urban and one rural study site. Specimens were analyzed by culture, and isolates were serotyped using sequential multiplex polymerase chain and Quellung reaction. Antibiotic susceptibility was performed by broth microdilution method. We enrolled 1,007 children in Gunungkidul District, Yogyakarta (peri-urban) and 815 in Southwest Sumba, East Nusa Tenggara (rural). Pneumococcal carriage prevalence was 30.9% in Gunungkidul and 87.6% in Southwest Sumba (combined: 56.3%). PCV13 serotypes (VT) carriage was 15.0% in Gunungkidul and 52.6% in Southwest Sumba (combined: 31.8%). Among pneumococcal isolates identified, the most common VT were 6B (16.4%), 19F (15.8%), and 3 (4.6%) in Gunungkidul (N = 323) and 6B (17.6%), 19F (11.0%), and 23F (9.3%) in Southwest Sumba (N = 784). Factors associated with pneumococcal carriage were age (1-2 years adjusted odds ratio (aOR) 1.9, 95% CI 1.4-2.5; 3-4 years aOR 1.5, 95% CI 1.1-2.1; reference <1 year), other children <5 years old in the household (aOR 1.5, 95% CI 1.1-2.0), and presence of ≥1 respiratory illness symptom (aOR 1.8, 95% CI 1.4-2.2). Overall, 61.5% of the pneumococcal isolates were non-susceptible to ≥1 antibiotic class and 13.2% were multi-drug non-susceptible (MDNS) (non-susceptible to ≥3 classes of antibiotics). Among 602 VT isolates, 73.9% were non-susceptible and 19.9% were MDNS. These findings are critical to establish a pre-PCV13 carriage prevalence and demonstrate the complexity in evaluating the impact of PCV13 introduction in Indonesia given the wide variability in the carriage prevalence as shown by the two study sites.
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Affiliation(s)
- Dodi Safari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wa Ode Dwi Daningrat
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer L. Milucky
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Miftahuddin Majid Khoeri
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wisiva Tofriska Paramaiswari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Wisnu Tafroji
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Korrie Salsabila
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Yayah Winarti
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | - Amin Soebandrio
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, West Java, Indonesia
| | | | - Ari Prayitno
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Lana Childs
- CDC Foundation, Atlanta, GA, United States of America
| | - Fabiana C. Pimenta
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Maria da Gloria Carvalho
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Tamara Pilishvili
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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3
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Lee J, Yoon Y, Kim EJ, Lee D, Baek Y, Takano C, Chang B, Iijima T, Kilgore PE, Hayakawa S, Hoshino T, Kim DW, Seki M. 23-valent polysaccharide vaccine (PPSV23)-targeted serotype-specific identification of Streptococcus pneumoniae using the loop-mediated isothermal amplification (LAMP) method. PLoS One 2021; 16:e0246699. [PMID: 33591996 PMCID: PMC7886117 DOI: 10.1371/journal.pone.0246699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/22/2021] [Indexed: 11/21/2022] Open
Abstract
Reports of invasive disease due to Streptococcus pneumoniae have declined since the introduction of pneumococcal conjugate vaccines (PCV7 and PCV13). The incidence of invasive diseases due to S. pneumoniae that are not addressed by the vaccines, however, has increased in children and adults, creating a global public health problem. Previously, we established the loop-mediated isothermal amplification (LAMP) method for a PCV13 serotype-specific assay. In the current study, we developed a rapid, simple, and cost-effective assay to detect serotypes in the 23-valent pneumococcal polysaccharide vaccine (PPSV23) using the LAMP method. In this study, LAMP primer sets for serotypes 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F of S. pneumoniae were developed. The reactivity, specificity, and sensitivity of LAMP assays were determined and compared to those of conventional PCR. The feasibility of LAMP assays in clinical application in patients with invasive pneumococcal diseases was validated by defining the detection limit of the LAMP assay with bacterial genomic DNA-spiked blood specimens. The specificity of each LAMP assay was determined using 44 serotypes of pneumococcal strains. Their sensitivity was 100 copies per reaction versus 103 to 106 copies per reaction for PCR assays. Using DNA-spiked blood specimens, excluding the LAMP assay that targeted serotype 22F (103 copies per reaction), the limit of detection of the LAMP assay was similar to that with purified DNA as the template (102 copies per reaction), compared with 103 to >106 copies per reaction for PCR assays. In conclusion, a rapid and simple LAMP-based PPSV23-targeted serotype detection assay was developed for use in many countries. This study is the first report of a LAMP-based assay for identification of PPSV23 serotypes. Further evaluation of this assay is needed through surveillance and vaccine efficacy studies.
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Affiliation(s)
- Jiwon Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Youngbae Yoon
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Eun Jin Kim
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Donghyun Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Yeongjun Baek
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Bin Chang
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takahiro Iijima
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Paul E. Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Mitsuko Seki
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Oliveira LMA, Souza ARV, Pinto TCA, Teixeira LM. Characterization of Streptococcus pneumoniae serotype 19F-variants occurring in Brazil uncovers a predominant lineage that can lead to misinterpretation in capsular typing. Int J Infect Dis 2021; 104:580-583. [PMID: 33476756 DOI: 10.1016/j.ijid.2021.01.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae (S. pneumoniae) of serogroup 19 are mainly represented by serotypes 19A and 19F, which are associated with antimicrobial resistance and disease. The wzy gene, a component of the pneumococcal capsular locus, is the target to differentiate serotypes 19A and 19F by PCR-based capsular typing. In the last decade, allelic variants of the wzy19F gene have been described, leading to misinterpretation of capsular typing results. METHODS A collection of 154 serotype 19F S. pneumoniae strains recovered from carriage and disease in Brazil was evaluated to identify and characterize wzy19F variant isolates. RESULTS Eleven (7%) wzy19F variant isolates were detected and identified as belonging to ST810 (n = 10) or ST13673 (n = 1; single-locus variant of ST810). They were mostly recovered from diseased patients, susceptible to the antimicrobial agents tested (except for one multidrug-resistant strain) and did not harbor pili genes. Sequences of the wzy19F gene of these variants were identical to each other and to those previously described in Brazil, but slightly different from wzy19F variants identified in other countries. CONCLUSION This study indicated that wzy19F variants present a geographically driven distribution and was the first to uncover phenotypic and genetic features of a wzy19F variant lineage occurring in Brazil since 1989.
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Affiliation(s)
- Laura M A Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aline R V Souza
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana C A Pinto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucia M Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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5
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Takano C, Kuramochi Y, Seki M, Kim DW, Omagari D, Sasano M, Chang B, Ohnishi M, Kim EJ, Fuwa K, Kilgore PE, Hoshino T, Hayakawa S. Molecular serotype-specific identification of Streptococcus pneumoniae using loop-mediated isothermal amplification. Sci Rep 2019; 9:19823. [PMID: 31882619 PMCID: PMC6934563 DOI: 10.1038/s41598-019-56225-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/09/2019] [Indexed: 11/14/2022] Open
Abstract
In children, the incidence of pneumococcal meningitis has decreased since the introduction of pneumococcal conjugate vaccine (PCV7 and PCV13). However, since the introduction of the vaccine, developed countries have seen the emergence of non-PCV13 serotypes. However, invasive pneumococcal disease (IPD) caused by PCV13-targeted serotypes still represents an important public health problem in resource-limited countries. To develop a rapid, simple, and cost-effective assay to detect serotypes of Streptococcus pneumoniae, we developed a novel loop-mediated isothermal amplification (LAMP) assay based on the sequences available for the 13 capsular types that are included in PCV13: 1, 3, 4, 5, 6 A, 6B, 7 F, 9 V, 14, 18 C, 19 A, 19 F, and 23 F. We evaluated test reactivity, specificity, sensitivity and performance, and compared the results between established LAMP and conventional PCR assays. To support its clinical use, the detection limits of the LAMP assay were evaluated using bacterial genomic DNA-spiked cerebrospinal fluid (CSF) and blood specimens. We confirmed the specificity of the LAMP assay using 41 serotypes of pneumococcal strains. The sensitivity of the LAMP assay was 10 to 100 copies per reaction, compared to 10 to 104 copies per reaction for PCR assays. The detection limits of the LAMP assay were comparable when using DNA-spiked CSF and blood specimens, as compared to using purified DNA as the template. In conclusion, a rapid and simple LAMP-based pneumococcal serotyping method has been developed. This is the first report of a LAMP method for a PCV13 serotype-specific identification assay, which could be a promising step to facilitate epidemiological studies of pneumococcal serotyping.
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Affiliation(s)
- Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yoko Kuramochi
- Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan. .,Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan.
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea. .,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Daisuke Omagari
- Nihon University School of Dentistry, Tokyo, 101-8310, Japan
| | - Mari Sasano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Neurological Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Bin Chang
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Makoto Ohnishi
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea
| | - Kazumasa Fuwa
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Paul E Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Tomonori Hoshino
- Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
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van Tonder AJ, Bray JE, Quirk SJ, Haraldsson G, Jolley KA, Maiden MCJ, Hoffmann S, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB. Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes. Microb Genom 2016; 2:000090. [PMID: 28133541 PMCID: PMC5266551 DOI: 10.1099/mgen.0.000090] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/20/2016] [Indexed: 01/14/2023] Open
Abstract
The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule ('serotype'), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted.
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Affiliation(s)
| | - James E. Bray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sigríður J. Quirk
- Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland
| | - Gunnsteinn Haraldsson
- Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland
| | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Steen Hoffmann
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ásgeir Haraldsson
- Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland
| | - Helga Erlendsdóttir
- Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland
| | - Karl G. Kristinsson
- Clinical Microbiology, University of Iceland and Landspitali University Hospital, Reykjavik, Iceland
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Nurse-Lucas M, McGee L, Hawkins PA, Swanston WH, Akpaka PE. Serotypes and genotypes of Streptococcus pneumoniae isolates from Trinidad and Tobago. Int J Infect Dis 2016; 46:100-6. [PMID: 27062986 PMCID: PMC5739879 DOI: 10.1016/j.ijid.2016.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/22/2016] [Accepted: 04/03/2016] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES There are currently 94 known pneumococcal capsular polysaccharide serotypes and their prevalence differs by geographic region and the period studied. Streptococcus pneumoniae infections have been diagnosed clinically in Trinidad and Tobago and other Caribbean countries, however data on the serotype and sequence type distributions in this country are limited. The objective of this study was to determine serotypes and multilocus sequence types (MLSTs) of invasive and non-invasive pneumococcal isolates from Trinidad and Tobago. METHODS Ninety-eight pneumococcal isolates from several regional hospitals in the country were analyzed using both standard microbiological methods and molecular analysis. These isolates included invasive (n=83) and selected non-invasive (n=15) strains recovered before (n=25) and after (n=73) the introduction of the pneumococcal conjugate vaccine. RESULTS More than half of the isolates (54.1%) were recovered from children under 15 years of age, with the largest proportion being from children under 2 years of age (24.5%). The most prevalent serotypes were 19F (18.4%), 6B (15.3%), 23F (14.3%), 3 (11.2%), 19A (6.1%), 6A (5.1%), 14 (5.1%), and 9V (4.1%). The most common serotype/MLST combinations were 6B/ST138 (n=10, 10.2%), 3/ST180 (n=5, 5.1%), 23F/ST629 (n=5, 5.1%), 19F/ST8398 (n=4, 4.1%), and three each of 6B/ST145, 14/9V/ST156, 9V/ST162, 19A/320, and 3/ST10440. CONCLUSIONS This report provides the first glimpse of the prevailing pneumococcal sequence types in the country. Most of the isolates represented serotypes in the 10-valent (61.2% of isolates) and 13-valent (83.7%) pneumococcal conjugate vaccines. A detailed population study is warranted to fully determine the circulating pneumococcal sequence types. Furthermore, the implementation of an effective and continuous surveillance system in Trinidad and Tobago is paramount to monitor vaccine impact.
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Affiliation(s)
- Michele Nurse-Lucas
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St Augustine, Trinidad and Tobago
| | - Lesley McGee
- Respiratory Disease Branch, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Paulina A Hawkins
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - William H Swanston
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St Augustine, Trinidad and Tobago
| | - Patrick Eberechi Akpaka
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St Augustine, Trinidad and Tobago.
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8
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Pneumococcus with the "6E" cps Locus Produces Serotype 6B Capsular Polysaccharide. J Clin Microbiol 2016; 54:967-71. [PMID: 26818670 DOI: 10.1128/jcm.03194-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/15/2016] [Indexed: 11/20/2022] Open
Abstract
Genetic studies of serogroup 6 isolates ofStreptococcus pneumoniaeidentified putative serotype 6E. Although its capsular polysaccharide structure has not been elucidated, putative serotype 6E is described in an increasing number of studies as a potentially new serotype. We show here that SPEC6B, which is widely used as a target strain for serotype 6B opsonophagocytosis assays, has the genetic features of the putative serotype 6E but produces capsular polysaccharide identical to 6B capsular polysaccharide as determined by one-dimensional (1D) and 2D nuclear magnetic resonance (NMR). Thus, putative serotype 6E is a mere genetic variant of serotype 6B. Also, SPEC6B is appropriate as a target strain for serotype 6B opsonophagocytosis assays. This example illustrates the difficulties of assigning new bacterial serotypes based on genetic findings alone.
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Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
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10
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Ziane H, Manageiro V, Ferreira E, Bektache S, Tazir M, Caniça M. Capsular typing of Streptococcus pneumoniae isolated in an Algerian hospital using a new multiplex PCR-based scheme. J Microbiol Methods 2015; 119:243-6. [PMID: 26546733 DOI: 10.1016/j.mimet.2015.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022]
Abstract
We developed a new sequential multiplex-PCR-based typing scheme (MPBTS) for pneumococcal capsular classification. The serogroup/type of 37 control isolates obtained by the Quellung reaction, MPBTS, and nucleotide sequencing, were fully concordant. The serogroups/types of 75 invasive isolates determined by MPBTS, presented 100% specificity and 96% sensitivity, when compared with the Quellung reaction.
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Affiliation(s)
- Hanifa Ziane
- Service de Microbiologie Clinique, Centre Hospitalo-Universitaire Mustapha Bacha, Faculté de Médecine, Algiers, Algeria
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; CECA-ICETA, Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, Oporto, Portugal.
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Soumia Bektache
- Service de Microbiologie Clinique, Centre Hospitalo-Universitaire Mustapha Bacha, Faculté de Médecine, Algiers, Algeria
| | - Mohamed Tazir
- Service de Microbiologie Clinique, Centre Hospitalo-Universitaire Mustapha Bacha, Faculté de Médecine, Algiers, Algeria
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
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11
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Satzke C, Dunne EM, Porter BD, Klugman KP, Mulholland EK. The PneuCarriage Project: A Multi-Centre Comparative Study to Identify the Best Serotyping Methods for Examining Pneumococcal Carriage in Vaccine Evaluation Studies. PLoS Med 2015; 12:e1001903; discussion e1001903. [PMID: 26575033 PMCID: PMC4648509 DOI: 10.1371/journal.pmed.1001903] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/09/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. METHODS AND FINDINGS Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. CONCLUSIONS Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail:
| | - Eileen M. Dunne
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Barbara D. Porter
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - E. Kim Mulholland
- Pneumococcal Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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12
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Detection and prediction of Streptococcus pneumoniae serotypes directly from nasopharyngeal swabs using PCR. J Med Microbiol 2015; 64:836-844. [DOI: 10.1099/jmm.0.000097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Dunne EM, Tikkanen L, Balloch A, Gould K, Yoannes M, Phuanukoonnon S, Licciardi PV, Russell FM, Mulholland EK, Satzke C, Hinds J. Characterization of 19A-like 19F pneumococcal isolates from Papua New Guinea and Fiji. New Microbes New Infect 2015; 7:86-8. [PMID: 26339490 PMCID: PMC4547413 DOI: 10.1016/j.nmni.2015.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 02/03/2023] Open
Abstract
Molecular identification of Streptococcus pneumoniae serotype 19F is routinely performed by PCR targeting the wzy gene of the capsular biosynthetic locus. However, 19F isolates with genetic similarity to 19A have been reported in the United States and Brazil. We screened 78 pneumococcal carriage isolates and found six 19F wzy variants that originated from children in Papua New Guinea and Fiji. Isolates were characterized using multilocus sequence typing and opsonophagocytic assays. The 19F wzy variants displayed similar susceptibility to anti-19F IgG antibodies compared to standard 19F isolates. Our findings indicate that these 19F variants may be more common than previously believed.
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Affiliation(s)
- E M Dunne
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - L Tikkanen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - A Balloch
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - K Gould
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - M Yoannes
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - S Phuanukoonnon
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - P V Licciardi
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - F M Russell
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - E K Mulholland
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - C Satzke
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - J Hinds
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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14
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Single-plex quantitative assays for the detection and quantification of most pneumococcal serotypes. PLoS One 2015; 10:e0121064. [PMID: 25798884 PMCID: PMC4370668 DOI: 10.1371/journal.pone.0121064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/27/2015] [Indexed: 12/04/2022] Open
Abstract
Streptococcus pneumoniae globally kills more children than any other infectious disease every year. A prerequisite for pneumococcal disease and transmission is colonization of the nasopharynx. While the introduction of pneumococcal conjugate vaccines has reduced the burden of pneumococcal disease, understanding the impact of vaccination on nasopharyngeal colonization has been hampered by the lack of sensitive quantitative methods for the detection of >90 known S. pneumoniae serotypes. In this work, we developed 27 new quantitative (q)PCR reactions and optimized 26 for a total of 53 qPCR reactions targeting pneumococcal serotypes or serogroups, including all vaccine types. Reactions proved to be target-specific with a limit of detection of 2 genome equivalents per reaction. Given the number of probes required for these assays and their unknown shelf-life, the stability of cryopreserved reagents was evaluated. Our studies demonstrate that two-year cryopreserved probes had similar limit of detection as freshly-diluted probes. Moreover, efficiency and limit of detection of 1-month cryopreserved, ready-to-use, qPCR reaction mixtures were similar to those of freshly prepared mixtures. Using these reactions, our proof-of-concept studies utilizing nasopharyngeal samples (N=30) collected from young children detected samples containing ≥2 serotypes/serogroups. Samples colonized by multiple serotypes/serogroups always had a serotype that contributes at least 50% of the pneumococcal load. In addition, a molecular approach called S6-q(PCR)2 was developed and proven to individually detect and quantify epidemiologically-important serogroup 6 strains including 6A, 6B, 6C and 6D. This technology will be useful for epidemiological studies, diagnostic platforms and to study the pneumobiome.
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15
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Genetic, biochemical, and serological characterization of a new pneumococcal serotype, 6H, and generation of a pneumococcal strain producing three different capsular repeat units. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:313-8. [PMID: 25589550 DOI: 10.1128/cvi.00647-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptococcus pneumoniae clinical isolates were recently described that produced capsular polysaccharide with properties of both serotypes 6A and 6B. Their hybrid serological property correlated with mutations affecting the glycosyltransferase WciP, which links rhamnose to ribitol by an α(1-3) linkage for serotypes 6A and 6C and an α(1-4) linkage for serotypes 6B and 6D. The isolates had mutations in the triad residues of WciP that have been correlated with enzyme specificity. The canonical triad residues of WciP are Ala192-Ser195-Arg254 for serotypes 6A and 6C and Ser192-Asn195-Gly254 for serotypes 6B and 6D. To prove that the mutations in the triad residues are responsible for the hybrid serotype, we introduced the previously described Ala192-Cys195-Arg254 triad into a 6A strain and found that the change made WciP bispecific, resulting in 6A and 6B repeat unit expression, although 6B repeat unit production was favored over production of 6A repeat units. Likewise, this triad permitted a 6C strain to express 6C and 6D repeat units. With reported bispecificity in WciN, which adds either glucose or galactose as the second sugar in the serogroup 6 repeat unit, the possibility exists for a strain to simultaneously produce all four serogroup 6 repeat units; however, when genes encoding both bispecific enzymes were introduced into a 6A strain, only 6A, 6B, and 6D repeat units were detected serologically. Nonetheless, this may be the first example of a bacterial polysaccharide with three different repeat units. This strategy of expressing multiple repeat units in a single polymer is a novel approach to broadening vaccine coverage by eliminating the need for multiple polysaccharide sources to cover multiple serogroup members.
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16
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Shakoor S, Kabir F, Khowaja AR, Qureshi SM, Jehan F, Qamar F, Whitney CG, Zaidi AKM. Pneumococcal serotypes and serogroups causing invasive disease in Pakistan, 2005-2013. PLoS One 2014; 9:e98796. [PMID: 24892937 PMCID: PMC4043782 DOI: 10.1371/journal.pone.0098796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
While pneumococcal conjugate vaccines have been implemented in most countries worldwide, use in Asia has lagged in part because of a lack of data on the amount of disease that is vaccine preventable in the region. We describe pneumococcal serotypes elicited from 111 episodes of invasive pneumococcal disease (IPD) from 2005 to 2013 among children and adults in Pakistan. Seventy-three percent (n = 81) of 111 IPD episodes were cases of meningitis (n = 76 in children 0–15 years and n = 5 among adults). Serotypes were determined by target amplification of DNA extracted from pneumococcal isolates (n = 52) or CSF specimens (n = 59). Serogroup 18 was the most common serogroup causing meningitis in children <5 years, accounting for 21% of cases (n = 13). The 10-valent pneumococcal conjugate vaccine (PCV 10) or PCV10- related serotypes were found in 61% (n = 47) of childhood (age 0–15 years) meningitis episodes. PCV-13 increased this coverage to 63% (one additional serotype 19A; n = 48). Our data indicate that use of PCVs would prevent a large proportion of serious pneumococcal disease.
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Affiliation(s)
- Sadia Shakoor
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
- Department of Pathology and Microbiology, the Aga Khan University Hospital, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Asif R. Khowaja
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Shahida M. Qureshi
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Farah Qamar
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
| | - Cynthia G. Whitney
- National Center for Immunization and Respiratory Diseases, CDC, Atlanta, Georgia, United States of America
| | - Anita K. M. Zaidi
- Department of Pediatrics and Child Health, the Aga Khan University Hospital, Karachi, Pakistan
- * E-mail:
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17
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Raymond F, Boucher N, Allary R, Robitaille L, Lefebvre B, Tremblay C, Corbeil J, Gervaix A. Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms. PLoS One 2013; 8:e76197. [PMID: 24086706 PMCID: PMC3782451 DOI: 10.1371/journal.pone.0076197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae serotype epidemiology is essential since serotype replacement is a concern when introducing new polysaccharide-conjugate vaccines. A novel PCR-based automated microarray assay was developed to assist in the tracking of the serotypes. Autolysin, pneumolysin and eight genes located in the capsular operon were amplified using multiplex PCR. This step was followed by a tagged fluorescent primer extension step targeting serotype-specific polymorphisms. The tagged primers were then hybridized to a microarray. Results were exported to an expert system to identify capsular serotypes. The assay was validated on 166 cultured S. pneumoniae samples from 63 different serotypes as determined by the Quellung method. We show that typing only 12 polymorphisms located in the capsular operon allows the identification at the serotype level of 22 serotypes and the assignation of 24 other serotypes to a subgroup of serotypes. Overall, 126 samples (75.9%) were correctly serotyped, 14 were assigned to a member of the same serogroup, 8 rare serotypes were erroneously serotyped, and 18 gave negative serotyping results. Most of the discrepancies involved rare serotypes or serotypes that are difficult to discriminate using a DNA-based approach, for example 6A and 6B. The assay was also tested on clinical specimens including 43 cerebrospinal fluid samples from patients with meningitis and 59 nasopharyngeal aspirates from bacterial pneumonia patients. Overall, 89% of specimens positive for pneumolysin were serotyped, demonstrating that this method does not require culture to serotype clinical specimens. The assay showed no cross-reactivity for 24 relevant bacterial species found in these types of samples. The limit of detection for serotyping and S. pneumoniae detection was 100 genome equivalent per reaction. This automated assay is amenable to clinical testing and does not require any culturing of the samples. The assay will be useful for the evaluation of serotype prevalence changes after new conjugate vaccines introduction.
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Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Nancy Boucher
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Robin Allary
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Lynda Robitaille
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Ste-Anne-de-Bellevue, Québec, Canada
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique, Ste-Anne-de-Bellevue, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie and Département de Microbiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Alain Gervaix
- Department of Pediatrics, University Hospitals of Geneva, Geneva, Switzerland
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18
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Evaluation of pneumococcal serotyping by multiplex PCR and quellung reactions. J Clin Microbiol 2013; 51:4193-5. [PMID: 24025905 DOI: 10.1128/jcm.01876-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Screening of 1,750 pneumococcal isolates for common serotypes by PCR was followed by Quellung reaction analysis of PCR-negative isolates with a comparison to the conventional (Quellung reaction only) approach. PCR agreed with Quellung reaction results for 99% of isolates. The sequential PCR/Quellung reaction algorithm is accurate and more cost-effective than the conventional approach.
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19
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Update of pneumococcal PCR serotyping assay for detection of a commonly occurring type 19F wzy variant in Brazil. J Clin Microbiol 2013; 51:2470-1. [PMID: 23658255 DOI: 10.1128/jcm.00743-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Collard JM, Alio Sanda AK, Jusot JF. Determination of pneumococcal serotypes in meningitis cases in Niger, 2003-2011. PLoS One 2013; 8:e60432. [PMID: 23555971 PMCID: PMC3610823 DOI: 10.1371/journal.pone.0060432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 02/26/2013] [Indexed: 11/19/2022] Open
Abstract
Background The epidemiology of pneumococcal meningitis in the African ‘meningitis belt’ is poorly studied. In order to ensure an effective vaccination strategy and post-vaccination surveillance, we examined the serotype distribution patterns of pneumococcal meningitis in Niger over the period 2003–2011. Methods Cerebrospinal fluid (CSF) samples were collected from different health facilities throughout Niger in the frame of the national microbiological surveillance of meningitis. Determination of the serotype of CSF positive for pneumococci was performed using a sequential multiplex PCR method (SM-PCR) adapted with a national algorithm in which 32 different serotypes were covered and grouped into eight consecutive PCR. Results The SM-PCR assay could predict the Sp serotype for 779 CSF (88.7%), 98 CSF (11.3%) were not-typeable in our national-adapted algorithm. In total, 26 different serotypes were identified. Serotype 1 (n = 393) was the most prevalent and accounted for 45.3% of infections, followed by serogroups/serotypes 12F/(12A)/(44)/(46) (7.3%), 6/(6A/6B/6C/6D) (5.4%), 14 (5.2%), 5 (4.6%), 23F (4.2%), 45 (3.6%), 2 (3.1%), 18/(18A/18B/18C/18F) (2.9%) and 17 others serotypes with a prevalence of less than 2%. The proportion of serotype 1 in infants(<2 years old) represented only 4.3% of the cases affected by this serotype. In contrast, serotypes 5, 6, 14, 19A and 23F were only detected in very young children. Conclusions The proportion of serotype 1 in the pneumococcal meningitis cases and the theoretical vaccine coverage across all age groups advocates for the introduction of a conjugate vaccine (PCV10 or 13) into the Expanded Programme on Immunization (EPI) in Niger. Post-vaccine introduction surveillance supported by molecular approaches will be essential to provide a comprehensive picture of the impact of the vaccine on the burden reduction of pneumococcal meningitis and on pneumococcal serotype distribution.
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Donkor ES. Molecular typing of the pneumococcus and its application in epidemiology in sub-Saharan Africa. Front Cell Infect Microbiol 2013; 3:12. [PMID: 23503978 PMCID: PMC3596783 DOI: 10.3389/fcimb.2013.00012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/25/2013] [Indexed: 01/15/2023] Open
Abstract
Molecular typing of the pneumococcus has played a crucial role in understanding the epidemiology of the organism. However, most of what is known about molecular epidemiology of the pneumococcus pertains to the developed world. The brunt of pneumococcal infections is borne by sub-Saharan African countries, which makes epidemiological monitoring of the pneumococcus essential in this region of the world. This review paper focuses on molecular typing of the pneumococcus and what is known about epidemiology of the organism in sub-Saharan Africa based on the various typing methods. Several molecular typing methods are available for typing the pneumococcus and the major ones include multilocus sequence typing (MLST), multilocus enzyme electrophoresis (MLEE), serotyping and DNA fingerprinting methods such as pulsed field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP). Currently, MLST is the most suitable method for typing the pneumococcus. The pneumococcal population structure in sub-Saharan Africa appears to be quite different from that of the developed world, and pneumococcal serotype 1 related to the ST 618 clone and clones of the ST 217 clonal complex are responsible for outbreaks in sub-Saharan Africa.
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Affiliation(s)
- Eric S Donkor
- Department of Microbiology, University of Ghana Medical School Accra, Ghana.
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22
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Dynamics of Streptococcus pneumoniae serotypes causing acute otitis media isolated from children with spontaneous middle-ear drainage over a 12-year period (1999-2010) in a region of northern Spain. PLoS One 2013; 8:e54333. [PMID: 23349853 PMCID: PMC3551958 DOI: 10.1371/journal.pone.0054333] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to determine the serotype and clonal distribution of pneumococci causing acute otitis media (AOM) and their relationship with recurrences and mixed infections with other microorganisms under the influence of the 7-valent pneumococcal conjugate vaccine (PCV7). To do this, all pneumococcal isolates collected from the spontaneous middle-ear drainage of children <5 years old diagnosed of AOM by their pediatrician or their general practitioner from 1999 to 2010 were phenotypically characterized and the most frequent serotypes were genotyped. In the 12-year study, 818 episodes of pneumococcal AOM were detected, mostly (70.5%) in children younger than 2 years old. In 262 episodes (32%), the pneumococci were isolated with another bacterium, mainly (n = 214) Haemophilus influenzae. Mixed infections were similar in children under or over 2 years old. The most frequent serotypes were 19A (n = 227, 27.8%), 3 (n = 92, 11.2%) and 19F (n = 74, 9%). Serotypes included in the PCV7 sharply decreased from 62.4% in the pre-vaccination (1999–2001) to 2.2% in the late post-vaccination period (2008–2010). Serotype diversity steadily increased after the introduction of the PCV7 but decreased from 2008–2010 due to the predominant role of serotype 19A isolates, mostly ST276 and ST320. The prevalence of serotype 3 doubled from 6.1% (20/326) in 1999–2004 to 14.6% (72/492) in 2005–2010. Relapses mainly occurred in male infants infected with isolates with diminished antimicrobial susceptibility. Reinfections caused by isolates with the same serotype but different genotype were frequent, highlighting the need for genetic studies to differentiate among similar strains. In conclusion, the main change in pneumococcal AOM observed after the introduction of the PCV7 was the sharp decrease in vaccine serotypes. Also notable was the high burden of serotype 19A in total pneumococcal AOM before and especially after the introduction of the PCV7, as well as in relapses and reinfections.
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23
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Gladstone RA, Jefferies JM, Faust SN, Clarke SC. Sampling methods for the study of pneumococcal carriage: a systematic review. Vaccine 2012; 30:6738-44. [PMID: 22981760 DOI: 10.1016/j.vaccine.2012.08.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/20/2012] [Accepted: 08/31/2012] [Indexed: 10/27/2022]
Abstract
Streptococcus pneumoniae is an important pathogen worldwide. Accurate sampling of S. pneumoniae carriage is central to surveillance studies before and following conjugate vaccination programmes to combat pneumococcal disease. Any bias introduced during sampling will affect downstream recovery and typing. Many variables exist for the method of collection and initial processing, which can make inter-laboratory or international comparisons of data complex. In February 2003, a World Health Organisation working group published a standard method for the detection of pneumococcal carriage for vaccine trials to reduce or eliminate variability. We sought to describe the variables associated with the sampling of S. pneumoniae from collection to storage in the context of the methods recommended by the WHO and those used in pneumococcal carriage studies since its publication. A search of published literature in the online PubMed database was performed on the 1st June 2012, to identify published studies that collected pneumococcal carriage isolates, conducted after the publication of the WHO standard method. After undertaking a systematic analysis of the literature, we show that a number of differences in pneumococcal sampling protocol continue to exist between studies since the WHO publication. The majority of studies sample from the nasopharynx, but the choice of swab and swab transport media is more variable between studies. At present there is insufficient experimental data that supports the optimal sensitivity of any standard method. This may have contributed to incomplete adoption of the primary stages of the WHO detection protocol, alongside pragmatic or logistical issues associated with study design. Consequently studies may not provide a true estimate of pneumococcal carriage. Optimal sampling of carriage could lead to improvements in downstream analysis and the evaluation of pneumococcal vaccine impact and extrapolation to pneumococcal disease control therefore further in depth comparisons would be of value.
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Affiliation(s)
- R A Gladstone
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
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Rapid and easy identification of capsular serotypes of Streptococcus pneumoniae by use of fragment analysis by automated fluorescence-based capillary electrophoresis. J Clin Microbiol 2012; 50:3451-7. [PMID: 22875895 DOI: 10.1128/jcm.01368-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The purpose of this study was to develop a high-throughput method for the identification of pneumococcal capsular types. Multiplex PCR combined with fragment analysis and automated fluorescent capillary electrophoresis (FAF-mPCR) was utilized. FAF-mPCR was composed of only 3 PCRs for the specific detection of serotypes 1, 2, 3, 4, 5, 6A/6B, 6C, 7F/7A, 7C/(7B/40), 8, 9V/9A, 9N/9L, 10A, 10F/(10C/33C), 11A/11D/11F, 12F/(12A/44/46), 13, 14, 15A/15F, 15B/15C, 16F, 17F, 18/(18A/18B/18C/18F), 19A, 19F, 20, 21, 22F/22A, 23A, 23B, 23F, 24/(24A/24B/24F), 31, 33F/(33A/37), 34, 35A/(35C/42), 35B, 35F/47F, 38/25F, and 39. In order to evaluate the assay, all invasive pneumococcal isolates (n = 394) characterized at Hospital Sant Joan de Déu, Barcelona, Spain, from July 2010 to July 2011 were included in this study. The Wallace coefficient was used to evaluate the overall agreement between two typing methods (Quellung reaction versus FAF-mPCR). A high concordance with Quellung was found: 97.2% (383/394) of samples. The Wallace coefficient was 0.981 (range, 0.965 to 0.997). Only 11 results were discordant with the Quellung reaction. However, latex reaction and Quellung results of the second reference laboratory agreed with FAF-mPCR for 9 of these 11 strains (82%). Therefore, we considered that only 2 of 394 strains (0.5%) were not properly characterized by the new assay. The automation of the process allowed the typing of 30 isolates in a few hours with a lower cost than that of the Quellung reaction. These results indicate that FAF-mPCR is a good method to determine the capsular serotype of Streptococcus pneumoniae.
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From Quellung to multiplex PCR, and back when needed, in pneumococcal serotyping. J Clin Microbiol 2012; 50:2727-31. [PMID: 22692742 DOI: 10.1128/jcm.00689-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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.
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Bowers JR, Driebe EM, Nibecker JL, Wojack BR, Sarovich DS, Wong AH, Brzoska PM, Hubert N, Knadler A, Watson LM, Wagner DM, Furtado MR, Saubolle M, Engelthaler DM, Keim PS. Dominance of multidrug resistant CC271 clones in macrolide-resistant streptococcus pneumoniae in Arizona. BMC Microbiol 2012; 12:12. [PMID: 22251616 PMCID: PMC3285076 DOI: 10.1186/1471-2180-12-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 01/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of resistance to macrolide antibiotics in Streptococcus pneumoniae are rising around the world due to the spread of mobile genetic elements harboring mef(E) and erm(B) genes and post-vaccine clonal expansion of strains that carry them. RESULTS Characterization of 592 clinical isolates collected in Arizona over a 10 year period shows 23.6% are macrolide resistant. The largest portion of the macrolide-resistant population, 52%, is dual mef(E)/erm(B)-positive. All dual-positive isolates are multidrug-resistant clonal lineages of Taiwan19F-14, mostly multilocus sequence type 320, carrying the recently described transposon Tn2010. The remainder of the macrolide resistant S. pneumoniae collection includes 31% mef(E)-positive, and 9% erm(B)-positive strains. CONCLUSIONS The dual-positive, multidrug-resistant S. pneumoniae clones have likely expanded by switching to non-vaccine serotypes after the heptavalent pneumococcal conjugate vaccine release, and their success limits therapy options. This upsurge could have a considerable clinical impact in Arizona.
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Affiliation(s)
- Jolene R Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA.
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Development of an automated and multiplexed serotyping assay for Streptococcus pneumoniae. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2011; 18:1900-7. [PMID: 21900529 DOI: 10.1128/cvi.05312-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptococcus pneumoniae expresses more than 90 capsule types, and currently available pneumococcal vaccines are designed to provide serotype-specific protection. Consequently, serotyping of pneumococcal isolates is important for determining the serotypes to be included in pneumococcal vaccines and to monitor their efficacy. Yet serotyping of pneumococcal isolates has remained a significant technical challenge. By multiplexing many assays, we have now developed a simple yet comprehensive serotyping assay system that can not only identify all known pneumococcal serotypes but also subdivide nontypeable (NT) isolates into those with or without the conventional capsule locus. We have developed this assay system to require only six key reagents: two are used in one multiplex inhibition-type immunoassay, and four are required in two multiplex PCR-based assays. The assay system is largely automated by a seamless combination of monoclonal antibody-based and PCR-based multiplex assays using the flow cytometric bead array technology from Luminex. The assay system has been validated with a panel of pneumococci expressing all known pneumococcal serotypes and was found to be easily transferable to another laboratory.
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Yun KW, Cho EY, Hong KB, Choi EH, Lee HJ. Streptococcus pneumoniae type determination by multiplex polymerase chain reaction. J Korean Med Sci 2011; 26:971-8. [PMID: 21860544 PMCID: PMC3154352 DOI: 10.3346/jkms.2011.26.8.971] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/25/2011] [Indexed: 12/25/2022] Open
Abstract
The purpose of this study was to develop pneumococcal typing by multiplex PCR and compare it with conventional serotyping by quellung reaction. Pneumococcal strains used in this study included 77 isolates from clinical specimens collected from children at Seoul National University Children's Hospital from 2006 to 2010. These strains were selected as they represented 26 different serotypes previously determined by quellung reaction. Molecular type was determined by 8 sequential multiplex PCR assays. Bacterial DNA extracted from cultured colonies was used as a template for PCR, and primers used in this study were based on cps operon sequences. Types 6A, 6B, 6C, and 6D were assigned based on the presence of wciN(β) and/or wciP genes in 2 simplex PCRs and sequencing. All 77 isolates were successfully typed by multiplex PCR assays. Determined types were as follows: 1, 3, 4, 5, 6A, 6B, 6C, 6D, 7C, 7F, 9V, 10A, 11A, 12F, 13, 14, 15A, 15B/15C, 19A, 19F, 20, 22F, 23A, 23F, 34, 35B, and 37. The results according to the PCR assays were in complete concordance with those determined by conventional quellung reaction. The multiplex PCR assay is highly reliable and potentially reduces reliance upon conventional serotyping.
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Affiliation(s)
- Ki Wook Yun
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Young Cho
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Bae Hong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Hoan Jong Lee
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
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Vernet G, Saha S, Satzke C, Burgess D, Alderson M, Maisonneuve JF, Beall B, Steinhoff M, Klugman K. Laboratory-based diagnosis of pneumococcal pneumonia: state of the art and unmet needs. Clin Microbiol Infect 2011; 17 Suppl 3:1-13. [DOI: 10.1111/j.1469-0691.2011.03496.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Association between nasopharyngeal load of Streptococcus pneumoniae, viral coinfection, and radiologically confirmed pneumonia in Vietnamese children. Pediatr Infect Dis J 2011; 30:11-8. [PMID: 20686433 DOI: 10.1097/inf.0b013e3181f111a2] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND The interplay between nasopharyngeal bacterial carriage, viral coinfection, and lower respiratory tract infections (LRTIs) is poorly understood. We explored this association in Vietnamese children aged less than 5 years. METHODS A hospital-based case-control study of pediatric LRTIs was conducted in Nha Trang, Vietnam. A total of 550 hospitalized children (274 radiologically confirmed pneumonia [RCP] and 276 other LRTIs) were enrolled and 350 healthy controls were randomly selected from the community. Polymerase chain reaction-based methods were used to measure bacterial loads of Streptococcus pneumoniae (SP), Haemophilus influenzae, and Moraxella catarrhalis and to detect 13 respiratory viruses and bacterial serotypes in nasopharyngeal samples of study participants. RESULTS The median nasopharyngeal bacterial load of SP was substantially higher in children with RCP compared with healthy controls or children with other LRTIs (P < 0.001). SP load was 15-fold higher in pneumonia children with viral coinfection compared with those children without viral coinfection (1.4 x 10⁷/mL vs. 9.1 x 10⁵/mL; P 0.0001). SP load was over 200-fold higher in serotypeable SP compared with nontypeable SP (2.5 x 10⁶/mL vs. 1 x 10⁴/mL; P < 0.0001). These associations were independent of potential confounders in multiple regression models. No clear association was found between nasopharyngeal load of Haemophilus influenzae or Moraxella catarrhalis and viral coinfection in either RCP or other LRTIs groups. CONCLUSIONS An increased load of SP in the nasopharynx was associated with RCP, viral coinfection, and presence of pneumococcal capsule.
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Revisiting pneumococcal carriage by use of broth enrichment and PCR techniques for enhanced detection of carriage and serotypes. J Clin Microbiol 2010; 48:1611-8. [PMID: 20220175 DOI: 10.1128/jcm.02243-09] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The measurement of pneumococcal carriage in the nasopharyngeal reservoir is subject to potential confounders that include low-density and multiple-strain colonization. To compare different methodologies, we picked a random sampling of 100 nasopharyngeal specimens recovered from infants less than 2 years of age who were previously assessed for pneumococcal carriage and serotypes by a conventional method that used direct plating from the transport/storage medium (50 specimens were culture negative and 50 specimens were culture positive for pneumococci). We used a broth enrichment approach and a conventional PCR approach (with and without broth enrichment) to determine pneumococcal carriage and serotypes, and the results were compared to the initial conventional culture-based results. Additionally, we used a lytA-targeted real-time PCR for pneumococcal detection. Broth enrichment for both the culture-based and the PCR-based methods enhanced the isolation of pneumococci and detection of serotype diversity, with the most effective serotype deduction method being one that used broth enrichment prior to sequential multiplex PCR. Similarly, we also found that broth enrichment followed by the lytA-specific real-time PCR was the most sensitive for the detection of apparent pneumococcal carriage. The broth enrichment, conventional multiplex PCR, and real-time PCR approaches used in this study were effective in detecting pneumococcal carriage in the 50 specimens that were negative by conventional direct plating from transport medium (range of numbers of positive specimens, 8/50 to 22/50 [16 to 44%]), and the three different serotyping approaches that used broth enrichment increased the number of serotype identifications from the 100 specimens (12 to 29 additional serotype identifications to be positive). A PCR-based approach that employed a broth enrichment step appeared to best enhance the detection of mixed serotypes and low-density pneumococcal carriage.
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Realtime PCR is more sensitive than multiplex PCR for diagnosis and serotyping in children with culture negative pneumococcal invasive disease. PLoS One 2010; 5:e9282. [PMID: 20174571 PMCID: PMC2824814 DOI: 10.1371/journal.pone.0009282] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 01/28/2010] [Indexed: 11/19/2022] Open
Abstract
Background Pneumococcal serotyping is usually performed by Quellung reaction, considered the gold standard test. However the method cannot be used on culture-negative samples. Molecular methods can be a useful alternative. The aim of the study was to evaluate the use of Multiplex-sequential-PCR (MS-PCR) or Realtime-PCR on blood samples for diagnosis and serotyping of invasive pneumococcal disease (IPD) in a pediatric clinical setting. Methodology/Principal Findings Sensitivity and specificity of MS-PCR and Realtime-PCR have been evaluated both on 46 well characterized pneumococcal isolates and on 67 clinical samples from children with culture-negative IPD. No difference in sensitivity and specificity between MS-PCR and Realtime PCR was found when the methods were used on isolates: both methods could type 100% isolates and the results were always consistent with culture-based methods. On the contrary, when used on clinical samples 43/67 (64.2%) were typeable by MS-PCR and 61/67 (91.0%) by Realtime-PCR (p = 0.0004,K Cohen 0.3, McNemar's p<0.001). Non-typeability by MS-PCR was associated in 18/20 cases (90.0%) with low bacterial load. The difference between the two methods was present both when they were used on normally sterile fluids (respectively 31/33 (93.9%) typeable samples for Realtime-PCR and 24/33 (72.7%) for MS-PCR, p = 0.047, 95%CL 0.03–0.98; K Cohen 0.3; McNemar's p = 0.0016) and when they were used on nasopharyngeal swabs (respectively 30/34 (88.2%) typeable samples for Realtime-PCR and 19/34 (55.9%) for MS-PCR, p = 0.007, 95%CL 0.04–0.66); the presence of multiple pneumococcal serotypes in nasopharyngeal swabs was found more frequently by Realtime PCR (19/30; 63.3%) than by Multiplex-sequential PCR (3/19; 15.8%; p = 0.003;95%CL 1.87–39.97). Conclusions/Significance In conclusion, both MS-PCR and Realtime PCR can be used for pneumococcal serotyping of most serotypes/serogroups directly on clinical samples from culture-negative patients but Realtime-PCR appears more sensitive.
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