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Marimuthu S, Damiano RB, Wolf LA. Performance Characteristics of a Real-Time PCR Assay for Direct Detection of Streptococcus pneumoniae in Clinical Specimens. J Mol Diagn 2024; 26:552-562. [PMID: 38677549 DOI: 10.1016/j.jmoldx.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 04/29/2024] Open
Abstract
Community-acquired pneumonia and complications, such as bacteremia and meningitis due to Streptococcus pneumoniae infection, still occur in at-risk populations, despite the availability of effective vaccines. Laboratory confirmation of S. pneumoniae remains challenging despite advances in blood culture techniques and the availability of nucleic acid-amplification tests. The goal of this study was to determine the performance characteristics of a molecular assay designed as a diagnostic test using primary clinical specimens for invasive pneumococcal disease. The molecular assay adapted for the Luminex Aries instrument targets an S. pneumoniae-specific gene (autolysin, lytA) in clinical specimens. Using real-time PCR MultiCode technology, four different clinical specimen types were evaluated. Specimen types included bronchoalveolar lavage, whole blood, cerebrospinal fluid, and urine to cover the various presentations and appropriate specimen types for invasive pneumococcal infections. The lower limit of detection in urine was 10 colony forming units (CFU)/mL, while in bronchoalveolar lavage, cerebrospinal fluid, and whole blood, it was 100 CFU/mL. Accuracy and specificity were both 100%, and all specimen types were stable for 8 days at 4°C. Finally, 38 clinical specimens were tested to further evaluate the assay. The performance characteristics met Clinical Laboratory Improvement Amendments standards for a clinical diagnostic assay, and the assay offers a sensitive and specific real-time PCR test for direct detection of S. pneumoniae in relevant clinical specimens.
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Affiliation(s)
- Subathra Marimuthu
- Division of Infectious Diseases, Infectious Diseases Laboratory, School of Medicine, University of Louisville, Louisville, Kentucky
| | - Rocio B Damiano
- Division of Infectious Diseases, Infectious Diseases Laboratory, School of Medicine, University of Louisville, Louisville, Kentucky
| | - Leslie A Wolf
- Division of Infectious Diseases, Infectious Diseases Laboratory, School of Medicine, University of Louisville, Louisville, Kentucky.
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2
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Wahid B, Tiwana MS. Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics. Future Microbiol 2024:1-14. [PMID: 38900594 DOI: 10.2217/fmb-2023-0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/01/2024] [Indexed: 06/22/2024] Open
Abstract
Bacteriophages, as abundant and specific agents, hold significant promise as a solution to combat the growing threat of antimicrobial resistance. Their unique ability to selectively lyse bacterial cells without harming humans makes them a compelling alternative to traditional antibiotics and point-of-care diagnostics. The article reviews the current landscape of diagnostic technologies, identify gaps and highlight emerging possibilities demonstrates a comprehensive approach to advancing clinical diagnosis of microbial pathogens and covers an overview of existing phage-based bioassays. Overall, the provided data in this review effectively communicates the potential of bacteriophages in transforming therapeutic and diagnostic paradigms, offering a holistic perspective on the benefits and opportunities they present in combating microbial infections and enhancing public health.
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Affiliation(s)
- Braira Wahid
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton VIC Australia
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3
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Katayama Y, Morita M, Chang B, Katagiri D, Ishikane M, Yamada G, Mezaki K, Kurokawa M, Takano H, Akeda Y. Identification and characterization of a novel α-haemolytic streptococci, Streptococcus parapneumoniae sp. nov., which caused bacteremia with pyelonephritis. Int J Med Microbiol 2024; 315:151625. [PMID: 38824713 DOI: 10.1016/j.ijmm.2024.151625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/04/2024] Open
Abstract
OBJECTIVES We report a case of bacteremia with pyelonephritis in an adult male with an underlying disease caused by α-hemolytic streptococci. α-Hemolytic streptococci were isolated from blood, but it was challenging to identify its species. This study aimed to characterize the causative bacterium SP4011 and to elucidate its species. METHODS The whole-genome sequence and biochemical characteristics of SP4011 were determined. Based on the genome sequence, phylogenetic analysis was performed with standard strains of each species of α-hemolytic streptococci. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated. RESULTS SP4011 showed optochin susceptibility and bile solubility, but did not react with pneumococcal omni antiserum. Phylogenetic analysis of the whole-genome sequence showed that SP4011 clustered with S. pneumoniae and S. pseodopneumoniae and was most closely related to S. pseodopneumoniae. Genomic analysis revealed that ANI and dDDH values between SP4011 and S. pseodopneumoniae were 94.0 % and 56.0 %, respectively, and between SP4011 and S. pneumoniae were 93.3 % and 52.2 %, respectively. Biochemical characteristics also showed differences between SP4011 and S. pseodopneumoniae and between SP4011 and S. pneumoniae. These results indicate that SP4011 is a novel species. CONCLUSION Our findings indicate that SP4011 is a novel species of the genus Streptococcus. SP4011 has biochemical characteristics similar to S. pneumoniae, making it challenging to differentiate and requiring careful clinical diagnosis. This isolate was proposed to be a novel species, Streptococcus parapneumoniae sp. nov. The strain type is SP4011T (= JCM 36068T = KCTC 21228T).
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Affiliation(s)
- Yuri Katayama
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Katagiri
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Masahiro Ishikane
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Gen Yamada
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuhisa Mezaki
- Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masami Kurokawa
- Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hideki Takano
- Department of Nephrology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Colomba C, Garbo V, Boncori G, Albano C, Bagarello S, Condemi A, Giordano S, Canduscio LA, Gallo C, Parrinello G, Cascio A. Streptococcus mitis as a New Emerging Pathogen in Pediatric Age: Case Report and Systematic Review. Antibiotics (Basel) 2023; 12:1222. [PMID: 37508318 PMCID: PMC10376791 DOI: 10.3390/antibiotics12071222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Streptococcus mitis, a normal inhabitant of the oral cavity, is a member of Viridans Group Streptococci (VGS). Generally recognized as a causative agent of invasive diseases in immunocompromised patients, S. mitis is considered to have low pathogenic potential in immunocompetent individuals. We present a rare case of sinusitis complicated by meningitis and cerebral sino-venous thrombosis (CSVT) caused by S. mitis in a previously healthy 12-year-old boy with poor oral health status. With the aim of understanding the real pathogenic role of this microorganism, an extensive review of the literature about invasive diseases due to S. mitis in pediatric patients was performed. Our data define the critical role of this microorganism in invasive infections, especially in immunocompetent children and in the presence of apparently harmful conditions such as sinusitis and caries. Attention should be paid to the choice of therapy because of VGS's emerging antimicrobial resistance patterns.
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Affiliation(s)
- Claudia Colomba
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Valeria Garbo
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Giovanni Boncori
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Chiara Albano
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Sara Bagarello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Anna Condemi
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Salvatore Giordano
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Laura A Canduscio
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Cristina Gallo
- Division of Radiology, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Gaspare Parrinello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Antonio Cascio
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Infectious and Tropical Diseases Unit, AOU Policlinico "P. Giaccone", 90100 Palermo, Italy
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Kielbik K, Pietras A, Jablonska J, Bakiera A, Borek A, Niedzielska G, Grzegorczyk M, Grywalska E, Korona-Glowniak I. Impact of Pneumococcal Vaccination on Nasopharyngeal Carriage of Streptococcus pneumoniae and Microbiota Profiles in Preschool Children in South East Poland. Vaccines (Basel) 2022; 10:vaccines10050791. [PMID: 35632547 PMCID: PMC9143411 DOI: 10.3390/vaccines10050791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
In 2017, Poland introduced the 10-valent pneumococcal conjugate vaccine (PCV) into its national immunization schedule. This prospective study was conducted between March and June 2020 to determine the impact of vaccination on prevalence of the nasopharyngeal carriage of S. pneumoniae in 176 healthy children and to determine how conjugate vaccines indirectly affect colonization of nasopharyngeal microbiota. Pneumococcal isolates were analyzed by serotyping and antimicrobial resistance tests. Nasopharyngeal microbiota were detected and identified using the culture method and real-time PCR amplification primers and hydrolysis-probe detection with the 16S rRNA gene as the target. In the vaccinated group of children, colonization was in 24.2% of children, compared to 21.4% in the unvaccinated group. Serotypes 23A and 23B constituted 41.5% of the isolates. Serotypes belonging to PCV10 and PCV13 constituted 4.9% and 17.1% of the isolates, respectively. S. pneumoniae isolates were resistant to penicillin (34.1%), erythromycin (31.7%), and co-trimoxazole (26.8%). Microbial DNA qPCR array correlated to increased amounts of Streptococcus mitis and S. sanguinis in vaccinated children, with reduced amounts of C. pseudodiphtericum, S. aureus, and M. catarrhalis. Introduction of PCV for routine infant immunization was associated with significant reductions in nasopharyngeal carriage of PCV serotypes and resistant strains amongst vaccine serotypes, yet carriage of non-PCV serotypes increased modestly, particularly serotype 23B.
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Affiliation(s)
- Karolina Kielbik
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
- Correspondence: (K.K.); (I.K.-G.)
| | - Aleksandra Pietras
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Joanna Jablonska
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Adrian Bakiera
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
| | - Anna Borek
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
| | - Grazyna Niedzielska
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Michal Grzegorczyk
- Department of Rehabilitation and Physiotherapy, Medical University of Lublin, 20-081 Lublin, Poland;
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Izabela Korona-Glowniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
- Correspondence: (K.K.); (I.K.-G.)
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Molecular surveillance of pneumococcal carriage following completion of immunization with the 13-valent pneumococcal conjugate vaccine administered in a 3 + 1 schedule. Sci Rep 2021; 11:24534. [PMID: 34969968 PMCID: PMC8718523 DOI: 10.1038/s41598-021-03720-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022] Open
Abstract
In a cross-sectional study, with the use of molecular methods, we aimed to gain insight into oropharyngeal pneumococcal colonization over time in 1212 Greek children recruited in general pediatric settings throughout the country; they were fully vaccinated with PCV13 (3 + 1 schedule). A single sample was obtained from each child at a time interval of 26 days to 70 months after administration of the 4th (booster) PCV13 dose; sampling time was divided into six time intervals. Carriage of Streptococcus pneumoniae was detected by real-time PCR targeting the lytA gene and isolates were serotyped by singleplex real-time PCR assays. Multiple control procedures to avoid false-positive results were applied. We showed an overall S. pneumoniae carriage rate of 48.6%. Serotyping identified typeable isolates in 82% of the total lytA-positive samples. Non-PCV13 serotypes represented 83.8% of total isolates when excluding serogroups with mixed PCV13 and non-PCV13 serotypes. In multivariate analysis daycare/school attendance emerged as the main contributing factor. Notably, serotypes 19A and 3 were the only two PCV13 serotypes the colonization rate of which increased over time (χ2 for trend P < 0.001 and P = 0.012, respectively). The application of the SP2020 gene on lytA-positive serotyped samples showed pneumococcal colonization in 97% of cases, and the overall colonization profile over time closely resembled that of the lytA gene. With the provisions of the methodological approach and age group of our study, the use of the oropharynx emerges as a reliable alternative to the nasopharynx in estimating pneumococcal carriage in epidemiological studies.
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Pneumococcal Choline-Binding Proteins Involved in Virulence as Vaccine Candidates. Vaccines (Basel) 2021; 9:vaccines9020181. [PMID: 33672701 PMCID: PMC7924319 DOI: 10.3390/vaccines9020181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 01/25/2023] Open
Abstract
Streptococcus pneumoniae is a pathogen responsible for millions of deaths worldwide. Currently, the available vaccines for the prevention of S. pneumoniae infections are the 23-valent pneumococcal polysaccharide-based vaccine (PPV-23) and the pneumococcal conjugate vaccines (PCV10 and PCV13). These vaccines only cover some pneumococcal serotypes (up to 100 different serotypes have been identified) and are unable to protect against non-vaccine serotypes and non-encapsulated pneumococci. The emergence of antibiotic-resistant non-vaccine serotypes after these vaccines is an increasing threat. Therefore, there is an urgent need to develop new pneumococcal vaccines which could cover a wide range of serotypes. One of the vaccines most characterized as a prophylactic alternative to current PPV-23 or PCVs is a vaccine based on pneumococcal protein antigens. The choline-binding proteins (CBP) are found in all pneumococcal strains, giving them the characteristic to be potential vaccine candidates as they may protect against different serotypes. In this review, we have focused the attention on different CBPs as vaccine candidates because they are involved in the pathogenesis process, confirming their immunogenicity and protection against pneumococcal infection. The review summarizes the major contribution of these proteins to virulence and reinforces the fact that antibodies elicited against many of them may block or interfere with their role in the infection process.
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Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods. J Clin Microbiol 2021; 59:JCM.02503-20. [PMID: 33208473 DOI: 10.1128/jcm.02503-20] [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: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
A correct identification of Streptococcus pseudopneumoniae is a prerequisite for investigating the clinical impact of the bacterium. The identification has traditionally relied on phenotypic methods. However, these phenotypic traits have been shown to be unreliable, with some S. pseudopneumoniae strains giving conflicting results. Therefore, sequence-based identification methods have increasingly been used for identification of S. pseudopneumoniae In this study, we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify S. pseudopneumoniae Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to their respective species. It was not possible to identify all S. pseudopneumoniae strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, which could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae, and fastANI differentiated between S. pseudopneumoniae and S. pneumoniae using an ANI cutoff of 96%.
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Sadowy E, Bojarska A, Kuch A, Skoczyńska A, Jolley KA, Maiden MCJ, van Tonder AJ, Hammerschmidt S, Hryniewicz W. Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae. Eur J Clin Microbiol Infect Dis 2020; 39:1865-1878. [PMID: 32409955 PMCID: PMC7497345 DOI: 10.1007/s10096-020-03916-6] [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: 12/28/2019] [Accepted: 04/24/2020] [Indexed: 01/18/2023]
Abstract
The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as Streptococcus pneumoniae, obtained over 20 years from hospital patients in Poland. Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests, lytA and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the lytA 3' terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of psaA and ply were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from S. pneumoniae and demonstrated the polyclonal character of misID streptococci, associated with the Streptococcus pseudopneumoniae and Streptococcus mitis groups. While the S. pseudopneumoniae clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among S. mitis-like bacteria and support the notion that this group may in fact consist of several distinct species.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Agnieszka Bojarska
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | | | | | | | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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Abstract
Streptococcus pneumoniae (the pneumococcus) carriage is commonly used to measure effects of pneumococcal vaccines. Based on findings from culture-based studies, the World Health Organization recommends both nasopharyngeal (NP) and oropharyngeal (OP) sampling for detecting adult carriage. Given evidence of potential confounding by other streptococci, we evaluated molecular methods for pneumococcal identification and serotyping from 250 OP samples collected from adults in Fiji, using paired NP samples for comparison. Samples were screened using lytA quantitative PCR (qPCR), as well as pneumococcal identification and serotyping conducted by DNA microarray. A subset of OP samples were characterized by latex sweep agglutination and multiplex PCR. Alternate qPCR assays (piaB and bguR) for pneumococcal identification were evaluated. The lytA qPCR was less specific and had poor positive predictive value (PPV) in OP samples (88% and 26%, respectively) compared with NP samples (95% and 64%, respectively). Using additional targets piaB and/or bguR improved qPCR specificity in OP, although the PPV (42 to 53%) was still poor. Using microarray, we found that 102/107 (95%) of OP samples contained nonpneumococcal streptococci with partial or divergent complements of pneumococcal capsule genes. We explored 91 colonies isolated from 11 OP samples using various techniques, including multiplex PCR, latex agglutination, and microarray. We found that nonpneumococcal streptococci contribute to false positives in pneumococcal serotyping and may also contribute to spurious identification by qPCR. Our results highlight that molecular approaches should include multiple loci to minimize false-positive results when testing OP samples. Regardless of method, pneumococcal identification and serotyping results from OP samples should be interpreted with caution.IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a significant global pathogen. Accurate identification and serotyping are vital. In contrast with World Health Organization recommendations based on culture methods, we demonstrate that pneumococcal identification and serotyping with molecular methods are affected by sample type. Results from oropharyngeal samples from adults were often inaccurate. This is particularly important for assessment of vaccine impact using carriage studies, particularly in low- and middle-income countries where there are significant barriers for disease surveillance.
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Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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Schaumburg F, Flamen A, Ehrhardt J, Alabi AS, van der Linden MPG. Colonization dynamics of Streptococcus pneumoniae in a remote African population: A prospective cohort study. Vaccine 2020; 38:5413-5417. [PMID: 32600915 DOI: 10.1016/j.vaccine.2020.06.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/26/2020] [Accepted: 06/18/2020] [Indexed: 10/24/2022]
Abstract
The aim of this study was to analyze the population dynamics of Streptococcus pneumoniae in a remotely living African Pygmy population. The same pygmy population (Gabon) was prospectively screened for nasopharyngeal S. pneumoniae colonization in 2011 (n = 103), 2013 (n = 104) and 2017 (n = 107). Non-duplicate isolates (n = 126) were serotyped and tested for antimicrobial resistance (broth microdilution). At the three sampling time points, resistance rates were highest for tetracycline (36-58%), followed by penicillin (parenteral, meningitis-breakpoints, 6-39%) and chloramphenicol (3-15%). The majority of isolates was non-typeable (NT, n = 18/126, 14.3%) followed by serotype 6B (n = 17/126, 13.5%), 21 and 15A (n = 9/126, 7.1%, each). The distribution of serotypes was highly dynamic as only three serotypes (14, 17F, NT) were detected during all three visits. Resistance rates and serotypes of nasopharyngeal S. pneumoniae markedly changed in the remote Babongo population. This rapid change in serotypes could challenge the selection of pneumococcal vaccine.
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Affiliation(s)
- Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon.
| | | | - Jonas Ehrhardt
- Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon; Institut für Tropenmedizin, Eberhard-Karls-Universität Tübingen, Deutsches Zentrum für Infektionsforschung, Germany
| | - Abraham S Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon; Institut für Tropenmedizin, Eberhard-Karls-Universität Tübingen, Deutsches Zentrum für Infektionsforschung, Germany
| | - Mark P G van der Linden
- German National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
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Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T. Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer. Front Cell Infect Microbiol 2020; 10:11. [PMID: 32083020 PMCID: PMC7002467 DOI: 10.3389/fcimb.2020.00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance. The most reliable method of MGS species identification is multilocus sequence analysis (MLSA) with seven house-keeping genes; however, because this method is time-consuming, it is deemed unsuitable for use in most clinical laboratories. In this study, we established a scheme for identifying 12 species of MGS (S. pneumoniae, S. pseudopneumoniae, S. mitis, S. oralis, S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, and S. cristatus) using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK) with the taxonomic aligner “What's in My Pot?” (WIMP; Oxford Nanopore's cloud-based analysis platform) and Kraken2 pipeline with the custom database adjusted for MGS species identification. The identities of the species in reference genomes (n = 514), clinical isolates (n = 31), and reference strains (n = 4) were confirmed via MLSA. The nanopore simulation reads were generated from reference genomes, and the optimal cut-off values for MGS species identification were determined. For 31 clinical isolates (S. pneumoniae = 8, S. mitis = 17 and S. oralis = 6) and 4 reference strains (S. pneumoniae = 1, S. mitis = 1, S. oralis = 1, and S. pseudopneumoniae = 1), a sequence library was constructed via a Rapid Barcoding Sequencing Kit for multiplex and real-time MinION sequencing. The optimal cut-off values for the identification of MGS species for analysis by WIMP and Kraken2 pipeline were determined. The workflow using Kraken2 pipeline with a custom database identified all 12 species of MGS, and WIMP identified 8 MGS bacteria except S. infantis, S. australis, S. peroris, and S. sinensis. The results obtained by MinION with WIMP and Kraken2 pipeline were consistent with the MGS species identified by MLSA analysis. The practical advantage of whole genome analysis using the MinION nanopore sequencer is that it can aid in MGS surveillance. We concluded that MinION sequencing with the taxonomic aligner enables accurate MGS species identification and could contribute to further epidemiological surveys.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Rina Nemoto
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Toru Kawamura
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kenji Ikebuchi
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Taku Fujiwara
- Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
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14
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Chang B, Akeda H, Nakamura Y, Hamabata H, Ameku K, Toma T, Miyagi M, Ohnishi M. Impact of thirteen-valent pneumococcal conjugate vaccine on nasopharyngeal carriage in healthy children under 24 months in Okinawa, Japan. J Infect Chemother 2020; 26:465-470. [PMID: 31926843 DOI: 10.1016/j.jiac.2019.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]
Abstract
In November 2013, a 13-valent pneumococcal conjugate vaccine (PCV13) for all infants aged younger than 5 years was incorporated into the Japan national immunization program. An annual survey of nasopharyngeal carriage rates was performed on healthy infants aged 2-24 months from Okinawa, Japan to evaluate the effect of PCV13 on pneumococcal colonization. Of 756 evaluable infants, 203 pneumococcal strains were detected in 193 infants. The overall nasopharyngeal carriage rate was 25.5%, which was not different from our previously reported isolation rate before the introduction of PCV13. The main serotypes of the Streptococcus pneumoniae strains are 15A (18.2%), non-typeable (14.8%), and 15B (11.8%). The carriage rates of pneumococcal strains with 7-valent pneumococcal conjugate vaccine serotypes and PCV13 serotypes were 3.0% and 9.9%, respectively. These values were significantly lower than we reported before the introduction of PCV13. However, the carriage rates of non-PCV13 serotypes have increased. Multivariate logistic regression analysis suggested that siblings and day care attendance are risk factors for pneumococcal carriage.
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Affiliation(s)
- Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Hideki Akeda
- The Okinawa Society of Child Health, Okinawa, Japan
| | - Yoshihisa Nakamura
- Nakamura Clinic Pediatric, Dermatology and Internal Medicine, Okinawa, Japan
| | | | | | | | | | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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15
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Càmara J, Cubero M, Martín-Galiano AJ, García E, Grau I, Nielsen JB, Worning P, Tubau F, Pallarés R, Domínguez MÁ, Kilian M, Liñares J, Westh H, Ardanuy C. Evolution of the β-lactam-resistant Streptococcus pneumoniae PMEN3 clone over a 30 year period in Barcelona, Spain. J Antimicrob Chemother 2019; 73:2941-2951. [PMID: 30165641 DOI: 10.1093/jac/dky305] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/03/2018] [Indexed: 11/14/2022] Open
Abstract
Objectives To analyse the epidemiology and genetic evolution of PMEN3 (Spain9V-156), a penicillin-non-susceptible clone of Streptococcus pneumoniae, causing invasive pneumococcal disease (IPD) in Barcelona during 1987-2016. Methods WGS was performed on 46 representative isolates and the data were used to design additional molecular typing methods including partial MLST, PCR-RFLP and detection of surface-exposed proteins and prophages, to assign the remaining isolates to lineages. The isolates were also subjected to antimicrobial susceptibility testing. Results Two hundred and twenty-seven adult cases of IPD caused by PMEN3 were identified. PMEN3 caused mainly pneumonia (84%) and the 30 day mortality rate was 23.1%. Evidence of recombination events was found, mostly in three regions, namely the capsular operon (associated with capsular switching) and adjacent regions containing pbp2x and pbp1a, the murM gene and the pbp2b-ddl region. Some of these genetic changes generated successful new variant serotype lineages, including one of serotype 11A that is not included in the current PCV13 vaccine. Other genetic changes led to increased MICs of β-lactams. Notably, most isolates also harboured prophages coding for PblB-like proteins. Despite these adaptations, the ability of this clone to cause IPD remained unchanged over time, highlighting the importance of its core genetic background. Conclusions Our study demonstrated successful adaptation of PMEN3 to persist over time despite the introduction of broader antibiotics and conjugate vaccines. In addition to enhancing understanding of the molecular evolution of PMEN3, these findings highlight the need for the development of non-serotype-based vaccines to fight pneumococcal infection.
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Affiliation(s)
- Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Antonio J Martín-Galiano
- Bacterial Genetics, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Ernesto García
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Imma Grau
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Infectious Diseases Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jesper B Nielsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Peder Worning
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Román Pallarés
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Infectious Diseases Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Ángeles Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Mogens Kilian
- Department of Biomedicine Health, Aarhus University, Aarhus, Denmark
| | - Josefina Liñares
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge-Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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16
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Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, Three S. oralis Subspecies, and S. infantis. mBio 2019; 10:mBio.01985-19. [PMID: 31481387 PMCID: PMC6722419 DOI: 10.1128/mbio.01985-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pneumoniae is one of the most important human pathogens but is closely related to Streptococcus mitis, with which humans live in harmony. The fact that the two species evolved from a common ancestor provides a unique basis for studies of both infection-associated properties and properties important for harmonious coexistence with the host. By detailed comparisons of genomes of the two species and other related streptococci, we identified 224 genes associated with virulence and 25 genes unique to the mutualistic species. The exclusive presence of the virulence factors in S. pneumoniae enhances their potential as vaccine components, as a direct impact on beneficial members of the commensal microbiota can be excluded. Successful adaptation of S. mitis and other commensal streptococci to a harmonious relationship with the host relied on genetic stability and properties facilitating life in biofilms. From a common ancestor, Streptococcus pneumoniae and Streptococcus mitis evolved in parallel into one of the most important pathogens and a mutualistic colonizer of humans, respectively. This evolutionary scenario provides a unique basis for studies of both infection-associated properties and properties important for harmonious coexistence with the host. We performed detailed comparisons of 60 genomes of S. pneumoniae, S. mitis, Streptococcus pseudopneumoniae, the three Streptococcus oralis subspecies oralis, tigurinus, and dentisani, and Streptococcus infantis. Nonfunctional remnants of ancestral genes in both S. pneumoniae and in S. mitis support the evolutionary model and the concept that evolutionary changes on both sides were required to reach their present relationship to the host. Confirmed by screening of >7,500 genomes, we identified 224 genes associated with virulence. The striking difference to commensal streptococci was the diversity of regulatory mechanisms, including regulation of capsule production, a significantly larger arsenal of enzymes involved in carbohydrate hydrolysis, and proteins known to interfere with innate immune factors. The exclusive presence of the virulence factors in S. pneumoniae enhances their potential as vaccine components, as a direct impact on beneficial members of the commensal microbiota can be excluded. In addition to loss of these virulence-associated genes, adaptation of S. mitis to a mutualistic relationship with the host apparently required preservation or acquisition of 25 genes lost or absent from S. pneumoniae. Successful adaptation of S. mitis and other commensal streptococci to a harmonious relationship with the host relied on genetic stability and properties facilitating life in biofilms.
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17
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Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study. Int J Med Microbiol 2019; 309:151338. [PMID: 31444101 DOI: 10.1016/j.ijmm.2019.151338] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/20/2019] [Accepted: 08/10/2019] [Indexed: 12/13/2022] Open
Abstract
Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailored antibiotic treatment. We investigated if the 16S amplicon sequencing performed by MinION, a nanopore sequencer, was capable of rapid pathogen identification in bacterial meningitis. Six retrospective cases of confirmed bacterial meningitis and two prospective cases were included. The initial cerebrospinal fluid (CSF) samples of these patients were used for the experiments. DNA was extracted from the CSF, and PCR was performed on the 16S ribosomal DNA (16S rDNA). Sequencing libraries were prepared using the PCR products, and MinION sequencing was performed for up to 3 h. The reads were aligned to the bacterial database, and the results were compared to the conventional culture studies. Pathogenic bacteria were successfully detected from the CSF by 16S sequencing in all retrospective cases. 16S amplicon sequencing was more sensitive than conventional diagnostic tests and worked properly even in antibiotics-treated samples. MinION sequencing significantly reduced the turnaround time, and even 10 min of sequencing was sufficient for pathogen detection in certain cases. Protocol adjustment could further increase the sensitivity and reduce the turnaround time for MinION sequencing. Finally, the prospective application of MinION 16S sequencing was successful. Nanopore 16S amplicon sequencing is capable of rapid bacterial identification from the CSF of the bacterial meningitis patients. It may have many advantages over conventional diagnostic tests and should therefore be applied in a larger number of patients in the future.
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18
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Complete Genome Sequence of a Sequence Type 4846 Streptococcus pneumoniae Serotype 12F Strain Isolated from a Meningitis Case in Japan. Microbiol Resour Announc 2019; 8:8/11/e01632-18. [PMID: 30938327 PMCID: PMC6424211 DOI: 10.1128/mra.01632-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae serotype 12F rarely colonizes the nasopharynx but commonly causes invasive pneumococcal disease. Here, we report the complete genome sequence of a sequence type 4846 (ST4846) S. pneumoniae serotype 12F strain isolated from a cluster of invasive pneumococcal disease patients in Japan. Streptococcus pneumoniae serotype 12F rarely colonizes the nasopharynx but commonly causes invasive pneumococcal disease. Here, we report the complete genome sequence of a sequence type 4846 (ST4846) S. pneumoniae serotype 12F strain isolated from a cluster of invasive pneumococcal disease patients in Japan.
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19
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Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020. Sci Rep 2019; 9:3285. [PMID: 30824850 PMCID: PMC6397248 DOI: 10.1038/s41598-019-39791-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/21/2019] [Indexed: 11/15/2022] Open
Abstract
Real-time PCR targeting lytA (the major autolysin gene) and piaB (permease gene of the pia ABC transporter) are currently used as the gold-standard culture-independent assays for Streptococcus pneumoniae identification. We evaluated the performance of a new real-time PCR assay – targeting SP2020 (putative transcriptional regulator gene) – and compared its performance with the assays previously described. A collection of 150 pneumococci, 433 non-pneumococci and 240 polymicrobial samples (obtained from nasopharynx, oropharynx, and saliva; 80 from each site) was tested. SP2020 and lytA-CDC assays had the best performance (sensitivity of 100% for each compared to 95.3% for piaB). The specificity for lytA and piaB was 99.5% and for SP2020 was 99.8%. Misidentifications occurred for the three genes: lytA, piaB and SP2020 were found in non-pneumococcal strains; piaB was absent in some pneumococci including a serotype 6B strain. Combining lytA and SP2020 assays resulted in no misidentifications. Most polymicrobial samples (88.8%) yielded concordant results for the three molecular targets. The remaining samples seemed to contain non-typeable pneumococci (0.8%), and non-pneumococci positive for lytA (1.7%) or SP2020 (8.7%). We propose that combined detection of both lytA-CDC and SP2020 is a powerful strategy for the identification of pneumococcus either in pure cultures or in polymicrobial samples.
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20
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A versatile loop-mediated isothermal amplification microchip platform for Streptococcus pneumoniae and Mycoplasma pneumoniae testing at the point of care. Biosens Bioelectron 2019; 126:373-380. [DOI: 10.1016/j.bios.2018.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/20/2018] [Accepted: 11/10/2018] [Indexed: 01/15/2023]
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21
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Assessment of Postvaccine Immunity against Streptococcus pneumoniae in Patients with Asplenia, including an Analysis of Its Impact on Bacterial Flora of the Upper Respiratory Tract and Incidence of Infections. J Immunol Res 2018; 2018:1691347. [PMID: 30687764 PMCID: PMC6330813 DOI: 10.1155/2018/1691347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/29/2018] [Indexed: 11/29/2022] Open
Abstract
S. pneumoniae is a microorganism that may cause a serious threat in postsplenectomy patients due to a potentially invasive course of infection. In order to assess a protective activity after vaccination with the 23-valent vaccine, we made an analysis of the level of antibodies in patients with asplenia compared to a control group of healthy donors. Additionally, colonization by potentially pathogenic microorganisms of the upper respiratory tract was analyzed to determine the carrier state by strains with vaccine serotype. No such strains were found in the research, yet three non-vaccine-serotype strains were found. Colonization of the upper respiratory tract by potentially pathogenic microorganisms may be connected with increased susceptibility observed and incidence of infections in patients with asplenia. However, colonization by S. pneumoniae may not have an effect on the level of specific antibodies with the 23-valent vaccine against S. pneumoniae (PPV23) in postsplenectomy patients and healthy people. The response to vaccination against S. pneumoniae showed a lower level of specific antibodies in patients with splenectomy performed more than 2 years before the test than in patients with a recently removed spleen, i.e., from 1 month to 2 years before the test. Vaccination against pneumococci also has positive effects on incidence of other etiology infections, which is of high significance in the prophylaxis of infectious diseases in this group of patients.
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22
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Chang B, Morita M, Lee KI, Ohnishi M. Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections. J Clin Microbiol 2018; 56:e01822-17. [PMID: 29444837 PMCID: PMC5925718 DOI: 10.1128/jcm.01822-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/04/2018] [Indexed: 12/22/2022] Open
Abstract
Streptococcus pneumoniae colonizes the nasopharyngeal mucus in healthy individuals and can cause otitis media, pneumonia, and invasive pneumococcal diseases. In this study, we analyzed S. pneumoniae strains that caused 19 pneumonia episodes in long-term inpatients with severe underlying disease in a hospital during a period of 14 months (from January 2014 to February 2015). Serotyping and whole-genome sequencing analyses revealed that 18 of the 19 pneumonia cases were caused by S. pneumoniae strains belonging to 3 genetically distinct groups: clonal complex 9999 (CC9999), sequence type 282 (ST282), and ST166. The CC9999 and ST282 strains appeared to have emerged separately by a capsule switch from the pandemic PMEN 1 strain (Spain23F-ST81). After all the long-term inpatients were inoculated with the 23-valent pneumococcal polysaccharide vaccine, no other nosocomial pneumonia infections occurred until March 2016.
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Affiliation(s)
- Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken-Ichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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23
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Oodate M, Kimura K, Banno H, Yokoyama S, Jin W, Wachino JI, Hasegawa Y, Arakawa Y. Predominance of Serogroup 19 CC320/271 among Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates after Introduction of the PCV7 Vaccine in Several Regions of Japan. Jpn J Infect Dis 2017; 71:14-20. [PMID: 29093321 DOI: 10.7883/yoken.jjid.2017.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multidrug-resistant Streptococcus pneumoniae serogroup 19, including serotypes 19A and 19F, associated with clonal complex 320/271 (CC320/271), has been previously shown to be predominant in many countries after introduction of a 7-valent pneumococcal conjugate vaccine (PCV7). However, in Japan there has been no epidemiological research focused on penicillin-nonsusceptible isolates after this event. Therefore, we aimed to characterize penicillin-nonsusceptible S. pneumoniae (PNSSP; penicillin minimum inhibitory concentration [MIC] ≥ 4.0 μg/ml) after the introduction of PCV7 in Japan. Throughout Japan, we collected 1,057 pneumococcal isolates from 2010 to 2014. We then evaluated MICs and performed serotyping, multilocus sequence typing, and sequencing of penicillin-binding protein genes in 51 isolates (penicillin MIC ≥ 2.0 μg/ml). Twenty-three isolates (2.2%) showed penicillin nonsusceptibility (penicillin MIC ≥ 4.0 μg/ml). Serotypes 19F (14 isolates, 60.9%) and 23F (4 isolates, 17.4%), which are covered by the vaccine, were predominant among PNSSP strains. Only 3 isolates belonged to nonvaccine serotype 19A. Among the PNSSP isolates, CC320/271 (16/23 strains, 69.6%) was the most prevalent clone. Moreover, CC320/271 clones showed high MIC values of a third-generation cephalosporin. Thus, we demonstrated clonal predominance of serogroup 19 CC320/271 with strong resistance to β-lactams including a third-generation cephalosporin among PNSSP isolates.
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Affiliation(s)
- Mitsuru Oodate
- Department of Bacteriology, Nagoya University Graduate School of Medicine.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Hirotsugu Banno
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Satoru Yokoyama
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Wanchun Jin
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine
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24
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Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 2017; 141:48-54. [DOI: 10.1016/j.mimet.2017.07.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022]
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25
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Brotons P, Bassat Q, Lanaspa M, Henares D, Perez-Arguello A, Madrid L, Balcells R, Acacio S, Andres-Franch M, Marcos MA, Valero-Rello A, Muñoz-Almagro C. Nasopharyngeal bacterial load as a marker for rapid and easy diagnosis of invasive pneumococcal disease in children from Mozambique. PLoS One 2017; 12:e0184762. [PMID: 28910402 PMCID: PMC5599037 DOI: 10.1371/journal.pone.0184762] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Current diagnostic methods for detection of Streptococcus pneumoniae in children with suspected invasive pneumococcal disease have limitations of accuracy, timeliness, and patient convenience. This study aimed to determine the performance of pneumococcal load quantified with a real-time polymerase-chain reaction in nasopharyngeal samples to diagnose invasive pneumococcal disease in children. METHODS Matched case-control study of patients <5 years of age with invasive pneumococcal disease admitted to the Manhiça District Hospital (Mozambique) and asymptomatic controls recruited in different periods between 2006 and 2014. Cases were confirmed by a positive bacterial culture for S. pneumoniae in blood or cerebrospinal fluid. Nasopharyngeal aspirates were collected from cases and controls and pneumococcal density was quantified by lytA real-time polymerase-chain reaction. RESULTS Thirty cases (median age 12.8 months) and sixty controls (median age 11.7 months) were enrolled and 70% of them were male. Nasopharyngeal pneumococcal carriage was high in both groups: 28/30 (93.3%) for cases vs. 53/60 (88.3%) for controls (p = 0.71). Mean nasopharyngeal pneumococcal load was identified as a marker for invasive pneumococcal disease (7.0 log10 copies/mL in cases vs. 5.8 log10 copies/mL in controls, p<0.001) and showed good discriminatory power (AUC-ROC: 82.1%, 95% CI 72.5%-91.8%). A colonization density of 6.5 log10 copies/mL was determined as the optimal cut-off value to distinguish cases from controls (sensitivity 75.0%, specificity 73.6%). CONCLUSION Use of non-invasive nasopharyngeal aspirates coupled with rapid and accurate quantification of pneumococcal load by real-time polymerase chain reaction has the potential to become a useful surrogate marker for early diagnosis of invasive pneumococcal disease in children.
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Affiliation(s)
- Pedro Brotons
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | - Miguel Lanaspa
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Desiree Henares
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Amaresh Perez-Arguello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
| | - Lola Madrid
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | | | | | - Maria Andres-Franch
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Angeles Marcos
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ana Valero-Rello
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, University Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail:
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El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000503] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Grace El Moujaber
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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Morpeth SC, Deloria Knoll M, Scott JAG, Park DE, Watson NL, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Howie SRC, Kotloff KL, Levine OS, Madhi SA, O'Brien KL, Thea DM, Adrian PV, Ahmed D, Antonio M, Bunthi C, DeLuca AN, Driscoll AJ, Githua LP, Higdon MM, Kahn G, Karani A, Karron RA, Kwenda G, Makprasert S, Mazumder R, Moore DP, Mwansa J, Nyongesa S, Prosperi C, Sow SO, Tamboura B, Whistler T, Zeger SL, Murdoch DR. Detection of Pneumococcal DNA in Blood by Polymerase Chain Reaction for Diagnosing Pneumococcal Pneumonia in Young Children From Low- and Middle-Income Countries. Clin Infect Dis 2017; 64:S347-S356. [PMID: 28575371 PMCID: PMC5447841 DOI: 10.1093/cid/cix145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND. We investigated the performance of polymerase chain reaction (PCR) on blood in the diagnosis of pneumococcal pneumonia among children from 7 low- and middle-income countries. METHODS. We tested blood by PCR for the pneumococcal autolysin gene in children aged 1-59 months in the Pneumonia Etiology Research for Child Health (PERCH) study. Children had World Health Organization-defined severe or very severe pneumonia or were age-frequency-matched community controls. Additionally, we tested blood from general pediatric admissions in Kilifi, Kenya, a PERCH site. The proportion PCR-positive was compared among cases with microbiologically confirmed pneumococcal pneumonia (MCPP), cases without a confirmed bacterial infection (nonconfirmed), cases confirmed for nonpneumococcal bacteria, and controls. RESULTS. In PERCH, 7.3% (n = 291/3995) of cases and 5.5% (n = 273/4987) of controls were blood pneumococcal PCR-positive (P < .001), compared with 64.3% (n = 36/56) of MCPP cases and 6.3% (n = 243/3832) of nonconfirmed cases (P < .001). Blood pneumococcal PCR positivity was higher in children from the 5 African countries (5.5%-11.5% among cases and 5.3%-10.2% among controls) than from the 2 Asian countries (1.3% and 1.0% among cases and 0.8% and 0.8% among controls). Among Kilifi general pediatric admissions, 3.9% (n = 274/6968) were PCR-positive, including 61.7% (n = 37/60) of those with positive blood cultures for pneumococcus. DISCUSSION. The utility of pneumococcal PCR on blood for diagnosing childhood pneumococcal pneumonia in the 7 low- and middle-income countries studied is limited by poor specificity and by poor sensitivity among MCPP cases.
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Affiliation(s)
- Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
- Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University
| | | | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura L Hammitt
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Stephen R C Howie
- Department of Paediatrics, University of Auckland
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Medical Research Council Unit, Basse, The Gambia
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Peter V Adrian
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom ; Departments of
| | - Charatdao Bunthi
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Epidemiology
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Geoff Kahn
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Mental Health
| | - Angela Karani
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Ruth A Karron
- International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia
- Zambia Center for Applied Health Research and Development, Lusaka
| | - Sirirat Makprasert
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Razib Mazumder
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka and Matlab
| | - David P Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, Johannesburg, South Africa
| | - James Mwansa
- Zambia Center for Applied Health Research and Development, Lusaka
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Sammy Nyongesa
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | | | - Toni Whistler
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David R Murdoch
- Department of Pathology, University of Otago, and
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci. Antimicrob Agents Chemother 2017; 61:AAC.02646-16. [PMID: 28193649 PMCID: PMC5404556 DOI: 10.1128/aac.02646-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/20/2022] Open
Abstract
The identification of commensal streptococci species is an everlasting problem due to their ability to genetically transform. A new challenge in this respect is the recent description of Streptococcus pseudopneumoniae as a new species, which was distinguished from closely related pathogenic S. pneumoniae and commensal S. mitis by a variety of physiological and molecular biological tests. Forty-one atypical S. pneumoniae isolates have been collected at the German National Reference Center for Streptococci (GNRCS). Multilocus sequence typing (MLST) confirmed 35 isolates as the species S. pseudopneumoniae. A comparison with the pbp2x sequences from 120 commensal streptococci isolated from different continents revealed that pbp2x is distinct among penicillin-susceptible S. pseudopneumoniae isolates. Four penicillin-binding protein x (PBPx) alleles of penicillin-sensitive S. mitis account for most of the diverse sequence blocks in resistant S. pseudopneumoniae, S. pneumoniae, and S. mitis, and S. infantis and S. oralis sequences were found in S. pneumoniae from Japan. PBP2x genes of the family of mosaic genes related to pbp2x in the S. pneumoniae clone Spain23F-1 were observed in S. oralis and S. infantis as well, confirming its global distribution. Thirty-eight sites were altered within the PBP2x transpeptidase domains of penicillin-resistant strains, excluding another 37 sites present in the reference genes of sensitive strains. Specific mutational patterns were detected depending on the parental sequence blocks, in agreement with distinct mutational pathways during the development of beta-lactam resistance. The majority of the mutations clustered around the active site, whereas others are likely to affect stability or interactions with the C-terminal domain or partner proteins.
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30
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Morioka H, Iguchi M, Oodate M, Yoneda M, Ushijima F, Hirabayashi A, Tetsuka N, Tomita Y, Kato D, Yagi T. Pneumococcal biliary tract infections - How rare are they? J Infect Chemother 2016; 23:415-418. [PMID: 28024739 DOI: 10.1016/j.jiac.2016.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 10/30/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022]
Abstract
Pneumococcal biliary tract infections (PBTIs) were reported as rare due to the bacterium's bile solubility. The purpose of this study was to determine the occurrence and clinical characteristics of PBTIs. A retrospective case series review was conducted from January 2006 to August 2014 at a tertiary referral university hospital in Japan. Patients with a blood or bile culture positive for Streptococcus pneumoniae diagnosed with definite cholangitis or cholecystitis according to Tokyo Guideline 2013 were enrolled in this study. Data on clinical information, treatments, and outcomes were collected. During 104 months, 48 cases of positive blood cultures and 13 cases of positive bile cultures were recorded, and after excluding 43 and 5 of these, respectively, a total of 10 patients were diagnosed with PBTI. Most patients (9/10) had biliary tract problems and biliary devices in place. PBTIs were not rare; conversely, they were a relatively common cause of pneumococcal bacteremia in this center treating a high volume of biliary tract illnesses.
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Affiliation(s)
- Hiroshi Morioka
- Department of Infectious Diseases, Nagoya University Hospital, Japan; Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan
| | - Mitsutaka Iguchi
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Mitsuru Oodate
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Japan; Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan
| | - Masaki Yoneda
- Department of Psychiatry, Nagoya University Hospital, Japan
| | - Futoshi Ushijima
- Department of Respiratory Medicine and Clinical Immunology, Toyota Kosei Hospital, Japan
| | - Aki Hirabayashi
- Department of Infectious Diseases, Nagoya University Hospital, Japan; Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan
| | - Nobuyuki Tetsuka
- Department of Infectious Diseases, Nagoya University Hospital, Japan; Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan
| | - Yuka Tomita
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Daizo Kato
- Department of Infectious Diseases, Nagoya University Hospital, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Japan; Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan.
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Molecular Epidemiology of Streptococcus pneumoniae Isolates from Children with Recurrent Upper Respiratory Tract Infections. PLoS One 2016; 11:e0158909. [PMID: 27415833 PMCID: PMC4945090 DOI: 10.1371/journal.pone.0158909] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/23/2016] [Indexed: 11/23/2022] Open
Abstract
A total of 125 isolates were recovered from adenoids and/or nasopharynx of 170 children aged 2 to 5 from south-east Poland; they had undergone adenoidectomy for recurrent and/or persistent symptoms of upper respiratory tract infections. Pneumococcal isolates were analyzed by phenotyping (serotyping and antimicrobial resistance tests) and genotyping together with the clonality of the pneumococcal isolates based on resistance determinants, transposon distribution and multilocus sequence typing (MLST). Serotypes 19F, 6B and 23F constituted 44.8% of the isolates. Among all of the strains, 44.8% showed decreased susceptibility to penicillin and resistance to co-trimoxazole (52.8%), tetracycline (38.4%), erythromycin (53.6%), clindamycin (52.8%) and chloramphenicol (27.2%) was observed. Tn6002 was found in 34.8% of erythromycin-resistant isolates while composite Tn2010—in 16.7% of erm(B)-carrying isolates that harboured also mef(E) gene. Tn3872-related elements were detected in 27.3% of erythromycin-resistant strains. In the majority of chloramphenicol-resistant catpC194-carrying isolates (79.4%), ICESp23FST81-family elements were detected. The genotyping showed that pneumococcal population was very heterogeneous; 82 sequence types (STs) were identified, and the most frequent contributed to not more than 8% of the isolates. Nearly 44% STs were novel, each of them was recovered only from one child. Four STs belonged to one of the 43 worldwide spread resistant pneumococcal clones currently accepted by Pneumococcal Molecular Epidemiology Network (PMEN), i.e. Spain 9V-3, Spain 23F-1, Norway NT-42 and Poland 6B-20, accounting for 12 (16.7%) of the 75 nonususceptible isolates, and five STs were single-locus variants of PMEN resistant clones (England 14–9, Spain 9V-3, Spain 23F-1, Greece 21–30, Denmark 14–32), accounting 9 (12%) of nonsusceptible isolates. A few MDR clones belonging to 6B and 19F serotypes found among preschool children emphasizes rather the role of clonal dissemination of local strains in the community than international clones spreading in the increase of resistance among pneumococcal strains.
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Choline Binding Proteins from Streptococcus pneumoniae: A Dual Role as Enzybiotics and Targets for the Design of New Antimicrobials. Antibiotics (Basel) 2016; 5:antibiotics5020021. [PMID: 27314398 PMCID: PMC4929436 DOI: 10.3390/antibiotics5020021] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/04/2016] [Accepted: 05/16/2016] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is an important pathogen responsible for acute invasive and non-invasive infections such as meningitis, sepsis and otitis media, being the major cause of community-acquired pneumonia. The fight against pneumococcus is currently hampered both by insufficient vaccine coverage and by rising antimicrobial resistances to traditional antibiotics, making necessary the research on novel targets. Choline binding proteins (CBPs) are a family of polypeptides found in pneumococcus and related species, as well as in some of their associated bacteriophages. They are characterized by a structural organization in two modules: a functional module (FM), and a choline-binding module (CBM) that anchors the protein to the choline residues present in the cell wall through non-covalent interactions. Pneumococcal CBPs include cell wall hydrolases, adhesins and other virulence factors, all playing relevant physiological roles for bacterial viability and virulence. Moreover, many pneumococcal phages also make use of hydrolytic CBPs to fulfill their infectivity cycle. Consequently, CBPs may play a dual role for the development of novel antipneumococcal drugs, both as targets for inhibitors of their binding to the cell wall and as active cell lytic agents (enzybiotics). In this article, we review the current state of knowledge about host- and phage-encoded pneumococcal CBPs, with a special focus on structural issues, together with their perspectives for effective anti-infectious treatments.
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Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R. lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 2016; 85:141-8. [PMID: 27107535 DOI: 10.1016/j.diagmicrobio.2016.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/19/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Abstract
During surveillance studies we detected, among over 1500 presumptive pneumococci, 11 isolates displaying conflicting or novel results when characterized by widely accepted phenotypic (optochin susceptibility and bile solubility) and genotypic (lytA-BsaAI-RFLP and MLST) identification methods. We aimed to determine the genetic basis for the unexpected results given by lytA-BsaAI-RFLP and investigate the accuracy of the WHO recommended lytA real-time PCR assay to classify these 11 isolates. Three novel lytA-BsaAI-RFLP signatures were found (one in pneumococcus and two in S. mitis). In addition, one pneumococcus displayed the atypical lytA-BsaAI-RFLP signature characteristic of non-pneumococci and two S. pseudopneumoniae displayed the typical lytA-BsaAI-RFLP pattern characteristic of pneumococci. lytA real-time PCR misidentified these three isolates. In conclusion, identification of pneumococci by lytA real-time PCR, and other lytA-based methodologies, may lead to false results. This is of particular relevance in the increasingly frequent colonization studies relying solely on culture-independent methods.
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Affiliation(s)
- Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Dora Rolo
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Herman Goossens
- Department of Medical Microbiology, University of Antwerp, Antwerp, Belgium; Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Josefina Linares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB, UNL, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Morales M, Martín-Galiano AJ, Domenech M, García E. Insights into the Evolutionary Relationships of LytA Autolysin and Ply Pneumolysin-Like Genes in Streptococcus pneumoniae and Related Streptococci. Genome Biol Evol 2015; 7:2747-61. [PMID: 26349755 PMCID: PMC4607534 DOI: 10.1093/gbe/evv178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a major human pathogen. The main pneumococcal autolysin LytA and the pneumolysin Ply are two of the bacterium's most important virulence factors. The lytA- and ply-related genes are also found in other streptococci of the Mitis group (SMG). The precise characteristics of the lytA-related-but not the ply-related-genes of SMG and their prophages have been previously described. A search of the more than 400 SMG genomic sequences available in public databases (ca. 300 for S. pneumoniae), showed Streptococcus pseudopneumoniae IS7493 to harbor four ply-related genes, two of which (plyA and plyB) have 98% identical nucleotides. The plyA homolog of S. pseudopneumoniae is conserved in all S. pneumoniae strains, and seems to be included in a pathogenicity island together with the lytA gene. However, only nonencapsulated S. pneumoniae strains possess a plyB gene, which is part of an integrative and conjugative element. Notably, the existence of a bacterial lytA-related gene in a genome is linked to the presence of plyA and vice versa. The present analysis also shows there are eight main types of plyA-lytA genomic islands. A possible stepwise scenario for the evolution of the plyA-lytA island in S. pneumoniae is proposed.
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Affiliation(s)
- María Morales
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain Centro Nacional de Microbiología, ISCIII, Majadahonda, Madrid, Spain
| | - Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ernesto García
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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35
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Nationwide population-based surveillance of invasive pneumococcal disease in Japanese children: Effects of the seven-valent pneumococcal conjugate vaccine. Vaccine 2015; 33:6054-60. [PMID: 26235372 DOI: 10.1016/j.vaccine.2015.07.069] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/02/2015] [Accepted: 07/20/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND In Japan, the seven-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2010. PCV13 has replaced PCV7 since November 2013. METHODS The effectiveness of PCV7 in protecting against invasive pneumococcal disease (IPD) in children aged <5 years was evaluated in a nationwide active population-based surveillance of IPD in 2008-2013 in 10 prefectures in Japan. RESULTS 1181 cases were identified; 711 pneumococcal strains were analyzed for serotyping and antimicrobial resistance. Compared with the baseline IPD incidence (25.0 per 100,000), a 98% decline in IPD caused by PCV7 serotypes was found after the introduction of PCV7. This was partially offset by an increased incidence of IPD caused by PCV13 minus PCV7 and non-PCV13 serotypes, resulting in a 57% decline in overall IPD incidence. Absolute increases in the incidence rates of IPD caused by PCV13 minus PCV7 and non-PCV13 serotypes were 2.1 and 2.8 per 100,000 during the study period, respectively. The proportion of meropenem-nonsusceptible strains, especially with serotypes 19A and 15A, increased significantly after PCV7 introduction. CONCLUSIONS Our data confirmed a 98% decline in IPD incidence caused by PCV7 serotypes in children aged <5 years and serotype replacement after PCV7 introduction. This shows the importance of continuing surveillance of serotypes responsible for IPD and their antimicrobial resistance in Japan.
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Ueno M, Ishii Y, Tateda K, Anahara Y, Ebata A, Iida M, Inamura S, Takahata K, Suzuki Y, Chang B, Wada A, Sugita M, Tanaka T, Nishiwaki Y. Prevalence and risk factors of nasopharyngeal carriage of Streptococcus pneumoniae in healthy children in Japan. Jpn J Infect Dis 2015; 66:22-5. [PMID: 23429080 DOI: 10.7883/yoken.66.22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The findings of this study revealed a 22% prevalence of Streptococcus pneumoniae among healthy children in Japan; the prevalence tended to increase with age. We identified attendance at day-care facilities and the presence of older siblings as the major risk factors associated with pneumococcal carriage. A significant decrease in pneumococcal colonization was observed among children during the summer; however, a seasonal variation was independent of various factors. Our findings suggest that prior immunization with heptavalent pneumococcal conjugate vaccine within the current recommended schedule is required for children exposed to these risk factors.
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Affiliation(s)
- Masahiro Ueno
- Department of Pediatrics, Hasuda Issinkai Hospital, Saitama 349-0123, Japan.
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Ueno M, Ishii Y, Tateda K, Anahara Y, Ebata A, Iida M, Mizuno F, Inamura S, Takahata K, Suzuki Y, Chang B, Wada A, Sugita M, Tanaka T, Nishiwaki Y. Changes in Streptococcus pneumoniae serotypes in the nasopharynx of Japanese children after inoculation with a heptavalent pneumococcal conjugate vaccine. Jpn J Infect Dis 2014; 67:40-3. [PMID: 24451100 DOI: 10.7883/yoken.67.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, we prospectively investigated changes in Streptococcus pneumoniae serotypes among Japanese children after heptavalent pneumococcal conjugate vaccine (PCV7) inoculation. We acquired nasopharyngeal swabs from the children at each routine PCV7 inoculation and again at least 2 months after the last PCV7 inoculation. We defined 2 periods with regard to each culture: the inoculation period as "the period of pre- or incomplete vaccination" and post-inoculation as "the period of post- or completed vaccination." The prevalence of vaccine-type (VT) pneumococci was significantly reduced from 9.5% in the inoculation-period cultures to 2.9% in the post-inoculation cultures (P < 0.01). There was no statistical difference in the prevalence of non-vaccine-type pneumococci between the inoculation-period and post-inoculation cultures (24.1% versus 23.4%). The protection of PCV7 against nasopharyngeal colonization was inferred from the decrease in VT carriage post-inoculation. The decrease in VT carriage may be conducive to reducing VT transmission within the study area.
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Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O'Brien KL. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2014; 32:165-79. [PMID: 24331112 DOI: 10.1016/j.vaccine.2013.08.062] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia.
| | - Paul Turner
- Microbiology Department, Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia; Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anni Virolainen-Julkunen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Peter V Adrian
- MRC/Wits Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Respiratory and Meningeal Pathogens Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Barbara D Porter
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - J Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Hanna Nohynek
- Vaccine Programme Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Moscoso M, Esteban-Torres M, Menéndez M, García E. In vitro bactericidal and bacteriolytic activity of ceragenin CSA-13 against planktonic cultures and biofilms of Streptococcus pneumoniae and other pathogenic streptococci. PLoS One 2014; 9:e101037. [PMID: 25006964 PMCID: PMC4090064 DOI: 10.1371/journal.pone.0101037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022] Open
Abstract
Ceragenin CSA-13, a cationic steroid, is here reported to show a concentration-dependent bactericidal/bacteriolytic activity against pathogenic streptococci, including multidrug-resistant Streptococcus pneumoniae. The autolysis promoted by CSA-13 in pneumococcal cultures appears to be due to the triggering of the major S. pneumoniae autolysin LytA, an N-acetylmuramoyl-L-alanine amidase. CSA-13 also disintegrated pneumococcal biofilms in a very efficient manner, although at concentrations slightly higher than those required for bactericidal activity on planktonic bacteria. CSA-13 has little hemolytic activity which should allow testing its antibacterial efficacy in animal models.
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Affiliation(s)
- Miriam Moscoso
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Mallorca, Illes Balears, Spain
| | - María Esteban-Torres
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Mallorca, Illes Balears, Spain
| | - Margarita Menéndez
- Departamento de Química-Física Biológica, Instituto Química-Física Rocasolano, CSIC, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Mallorca, Illes Balears, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Mallorca, Illes Balears, Spain
- * E-mail:
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Clinical evaluation of a disposable amperometric magneto-genosensor for the detection and identification of Streptococcus pneumoniae. J Microbiol Methods 2014; 103:25-8. [PMID: 24858449 DOI: 10.1016/j.mimet.2014.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 11/22/2022]
Abstract
A disposable PCR-based amperometric magneto-genosensor for detection and identification of Streptococcus pneumoniae was evaluated. ROC curve analysis used to determine optimal signal cutoff values yielded a sensitivity of 91% and a specificity of 90%. The method was also tested for the direct detection of pneumococci in clinical samples.
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Almeida ST, Nunes S, Santos Paulo AC, Valadares I, Martins S, Breia F, Brito-Avô A, Morais A, de Lencastre H, Sá-Leão R. Low prevalence of pneumococcal carriage and high serotype and genotype diversity among adults over 60 years of age living in Portugal. PLoS One 2014; 9:e90974. [PMID: 24604030 PMCID: PMC3946249 DOI: 10.1371/journal.pone.0090974] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 02/06/2014] [Indexed: 11/27/2022] Open
Abstract
Pneumococcal disease is frequent at the extremes of age. While several studies have looked at colonization among young children, much less is known among the elderly. We aimed to evaluate pneumococcal carriage among elderly adults living in Portugal. Between April 2010 and December 2012, nasopharyngeal and oropharyngeal swabs of adults over 60 years of age, living in an urban area (n = 1,945) or in a rural area (n = 1,416), were obtained. Pneumococci were isolated by culture-based standard procedures, identified by optochin susceptibility, bile solubility and PCR screening for lytA and cpsA, and characterized by antibiotype, serotype, and MLST. Associations between pneumococcal carriage, socio-demographic and clinical characteristics were evaluated by univariate analysis and multiple logistic regression. The global prevalence of carriage was 2.3% (95% CI: 1.8-2.8). In the multiple logistic regression analysis, smoking, being at a retirement home, and living in a rural area increased the odds of being a pneumococcal carrier by 4.4-fold (95% CI: 1.9-9.2), 2.0-fold (95% CI: 1.1-3.6) and 2.0-fold (95% CI: 1.2-3.5), respectively. Among the 77 pneumococcal isolates, 26 serotypes and 40 STs were identified. The most prevalent serotypes were (in decreasing order) 19A, 6C, 22F, 23A, 35F, 11A, and 23B, which accounted, in total, for 60.0% of the isolates. Most isolates (93.5%) had STs previously described in the MLST database. Resistance to macrolides, non-susceptibility to penicillin and multidrug resistance were found in 19.5%, 11.7%, and 15.6% of the isolates, respectively. We conclude that the prevalence of pneumococcal carriage in the elderly, in Portugal, as determined by culture-based methods, is low. Serotype and genotype diversity is high. Living in a rural area, in a retirement home, and being a smoker increased the risk of pneumococcal carriage. This study contributes to the establishment of a baseline that may be used to monitor how novel pneumococcal vaccines impact on colonization among the elderly.
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Affiliation(s)
- Sónia T. Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sónia Nunes
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana Cristina Santos Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Idalina Valadares
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Sara Martins
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Fátima Breia
- Agrupamento de Centros de Saúde Alentejo Central II, Évora, Portugal
| | - António Brito-Avô
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Ana Morais
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology of Infectious Diseases, The Rockefeller University, New York, New York, United States of America
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Shahinas D, Thornton CS, Tamber GS, Arya G, Wong A, Jamieson FB, Ma JH, Alexander DC, Low DE, Pillai DR. Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics. PLoS One 2013; 8:e65670. [PMID: 23840352 PMCID: PMC3686770 DOI: 10.1371/journal.pone.0065670] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/26/2013] [Indexed: 01/31/2023] Open
Abstract
Streptococcus pseudopneumoniae (SPPN) is a recently described species of the viridans group streptococci (VGS). Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease. S. pseudopneumoniae can be distinguished from the closely related species, S. pneumoniae and S. mitis, by phenotypic characteristics, including optochin resistance in the presence of 5% CO2, bile insolubility, and the lack of the pneumococcal capsule. Previously, we reported the draft genome sequence of S. pseudopneumoniae IS7493, a clinical isolate obtained from an immunocompromised patient with documented pneumonia. Here, we use comparative genomics approaches to identify similarities and key differences between S. pseudopneumoniae IS7493, S. pneumoniae and S. mitis. The genome structure of S. pseudopneumoniae IS7493 is most closely related to that of S. pneumoniae R6, but several recombination events are evident. Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci. The presence of loci for competence, iron transport, pneumolysin production and antimicrobial resistance reinforce the phylogenetic position of S. pseudopneumoniae as an intermediate species between S. pneumoniae and S. mitis. Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.
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Affiliation(s)
- Dea Shahinas
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- * E-mail:
| | - Christina S. Thornton
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | | | | | | | - Frances B. Jamieson
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Public Health Ontario, Toronto, Canada
| | - Jennifer H. Ma
- Public Health Ontario, Toronto, Canada
- DNA Core Facility, Public Health Ontario, Toronto, Canada
| | - David C. Alexander
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Public Health Ontario, Toronto, Canada
- DNA Core Facility, Public Health Ontario, Toronto, Canada
| | - Donald E. Low
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Dylan R. Pillai
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
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Simultaneous direct identification of genital microorganisms in voided urine using multiplex PCR-based reverse line blot assays. Methods Mol Biol 2013; 943:229-45. [PMID: 23104293 DOI: 10.1007/978-1-60327-353-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Our aim was to develop and evaluate sensitive methods that would allow simultaneous direct identification of multiple potential pathogens in clinical specimens for diagnosis and epidemiological studies, using a multiplex PCR-based reverse line blot assay. We have previously developed assays suitable for detection of bacterial respiratory and systemic pathogens. In this chapter we describe, in detail, a method developed to identify 14 genital microorganisms, for use in epidemiological studies of genital infection or colonization, using first voided urine specimens. The 14 urogenital pathogens or putative pathogens studied were Trichomonas vaginalis, Streptococcus pneumoniae, Neisseria gonorrhoeae, N. meningitidis, Chlamydia trachomatis, Ureaplasma parvum, U. urealyticum, Mycoplasma hominis, M. genitalium, Gardnerella vaginalis, Haemophilus influenzae, herpes simplex virus 1 and 2, and adenovirus. Two species-specific primer pairs and probes were designed for each target. The method was validated using a reference strain or a well-characterized clinical isolate of each target organism. In a clinical study among men attending sexual health clinics in Sydney, we used the assay to compare rates of detection of the 14 organisms in men with urethritis with those in asymptomatic controls and found the method to be sensitive, specific, convenient, and relatively inexpensive.
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Rolo D, S. Simões A, Domenech A, Fenoll A, Liñares J, de Lencastre H, Ardanuy C, Sá-Leão R. Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 2013; 8:e57047. [PMID: 23437306 PMCID: PMC3578818 DOI: 10.1371/journal.pone.0057047] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/16/2013] [Indexed: 11/27/2022] Open
Abstract
We aimed to obtain insights on the nature of a collection of isolates presumptively identified as atypical Streptococcus pneumoniae recovered from invasive and non-invasive infections in Spain. One-hundred and thirty-two isolates were characterized by: optochin susceptibility in ambient and CO2-enriched atmosphere; bile solubility; PCR-based assays targeting pneumococcal genes lytA, ply, pspA, cpsA, Spn9802, aliB-like ORF2, and a specific 16S rRNA region; multilocus sequence analysis; and antimicrobial susceptibility. By multilocus sequence analysis, 61 isolates were S. pseudopneumoniae, 34 were pneumococci, 13 were S. mitis, and 24 remained unclassified as non-pneumococci. Among S. pseudopneumoniae isolates, 51 (83.6%) were collected from respiratory tract samples; eight isolates were obtained from sterile sources. High frequency of non-susceptibility to penicillin (60.7%) and erythromycin (42.6%) was found. Only 50.8% of the S. pseudopneumoniae isolates displayed the typical optochin phenotype originally described for this species. None harbored the cpsA gene or the pneumococcal typical lytA restriction fragment length polymorphism. The Spn9802 and the specific 16S rRNA regions were detected among the majority of the S. pseudopneumoniae isolates (n = 59 and n = 49, respectively). The ply and pspA genes were rarely found. A high genetic diversity was found and 59 profiles were identified. Among the S. pneumoniae, 23 were capsulated and 11 were non-typeable. Three non-typeable isolates, associated to international non-capsulated lineages, were recovered from invasive disease sources. In conclusion, half of the atypical pneumococcal clinical isolates were, in fact, S. pseudopneumoniae and one-fourth were other streptococci. We identified S. pseudopneumoniae and non-typeable pneumococci as cause of disease in Spain including invasive disease.
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Affiliation(s)
- Dora Rolo
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra S. Simões
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Arnau Domenech
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Asunción Fenoll
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Liñares
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Carmen Ardanuy
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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Kim SA, Kim DW, Dong BQ, Kim JS, Anh DD, Kilgore PE. An expanded age range for meningococcal meningitis: molecular diagnostic evidence from population-based surveillance in Asia. BMC Infect Dis 2012; 12:310. [PMID: 23164061 PMCID: PMC3519641 DOI: 10.1186/1471-2334-12-310] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/05/2012] [Indexed: 12/27/2022] Open
Abstract
Background To understand epidemiologic patterns of meningococcal disease in Asia, we performed a retrospective molecular analysis of cerebrospinal fluid (CSF) specimens collected in prospective surveillance among children aged < 5 years of age in China, South Korea, and Vietnam. Methods A total of 295 isolates and 2,302 CSFs were tested by a meningococcal species- and serogroup-specific polymerase chain reaction (PCR) assay targeting the Neisseria meningitidis (Nm) ctrA gene. Multi-locus sequence typing (MLST) was performed in Nm gene amplification analysis and incidence rates for meningococcal meningitis were estimated. Results Among 295 isolates tested, 10 specimens from Vietnam were confirmed as serogroup B and all were Sequence Type (ST) 1576 by MLST. Among the 2,032 CSF specimen tested, 284 (14%) were confirmed by PCR (ctrA gene), including 67 (23.6%) from China, 92 (32.4%) from Korea, and 125 (44.0%) from Vietnam. Neonates and infants aged < 6 months of age accounted for more than 50% of Nm-PCR positive CSF. Two CSF specimens from Vietnam were identified as serogroup B using MLST. In addition, 44 specimens underwent sequencing to confirm meningococcal serogroup; of these, 21 (48%) were serogroup C, 12 (27%) were serogroup X, 9 (20%) were serogroup Y and 2 (5%) were serogroup B. The incidence rates of meningococcal meningitis among children < 5 years of age was highest in Vietnam (7.4/100,000 [95% CI, 3.6—15.3] followed by Korea (6.8/100,000 [95% CI, 3.5-13.5] and China (2.1/100,000) [95% CI, 0.7-6.2]). Conclusions These results suggest that there is a previously undetected, yet substantial burden of meningococcal meningitis among infants and young children. Standardized, sensitive and specific molecular diagnostic assays with Nm serogrouping capacity are needed throughout Asia to understand the true burden of N. meningitidis disease.
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Affiliation(s)
- Soon Ae Kim
- Translational Research Division, International Vaccine Institute, SNU Research Park, San 4-8 Nakseongdae-Dong, Kwanak Gu, Seoul 151-919, South Korea.
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Sistek V, Boissinot M, Boudreau D, Huletsky A, Picard F, Bergeron M. Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene. Clin Microbiol Infect 2012; 18:1089-96. [DOI: 10.1111/j.1469-0691.2011.03684.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Kim DW, Kilgore PE, Kim EJ, Kim SA, Anh DD, Dong BQ, Kim JS, Seki M. The enhanced pneumococcal LAMP assay: a clinical tool for the diagnosis of meningitis due to Streptococcus pneumoniae. PLoS One 2012; 7:e42954. [PMID: 22900070 PMCID: PMC3416792 DOI: 10.1371/journal.pone.0042954] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a leading cause of invasive bacterial disease in developed and developing countries. We studied the loop-mediated isothermal amplification (LAMP) technique to assess its suitability for detecting S. pneumoniae nucleic acid in cerebrospinal fluid (CSF). METHODOLOGY/PRINCIPAL FINDINGS We established an improved LAMP assay targeting the lytA gene (Streptococcus pneumoniae [Sp] LAMP). The analytical specificity of the primers was validated by using 32 reference strains (10 Streptococcus and seven non-Streptococcus species) plus 25 clinical alpha-hemolytic streptococcal strains, including four S. pneumoniae strains and 21 other strains (3 S. oralis, 17 S. mitis, and one Streptococcus species) harboring virulence factor-encoding genes (lytA or ply). Within 30 minutes, the assay could detect as few as 10 copies of both purified DNA and spiked CSF specimens with greater sensitivity than conventional polymerase chain reaction (PCR). The linear determination range for this assay is 10 to 1,000,000 microorganisms per reaction mixture using real-time turbidimetry. We evaluated the clinical sensitivity and specificity of the Sp LAMP assay using 106 randomly selected CSF specimens from children with suspected meningitis in Korea, China and Vietnam. For comparison, CSF specimens were also tested against conventional PCR and culture tests. The detection rate of the LAMP method was substantially higher than the rates of PCR and culture tests. In this small sample, relative to the LAMP assay, the clinical sensitivity of PCR and culture tests was 54.5% and 33.3%, respectively, while clinical specificity of the two tests was 100%. CONCLUSIONS/SIGNIFICANCE Compared to PCR, Sp LAMP detected S. pneumoniae with higher analytical and clinical sensitivity. This specific and sensitive LAMP method offers significant advantages for screening patients on a population basis and for diagnosis in clinical settings.
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Affiliation(s)
- Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Molecular Bacteriology Laboratory, International Vaccine Institute, Seoul, Republic of Korea
| | - Paul E. Kilgore
- Translational Research Division, International Vaccine Institute, Seoul, Republic of Korea
- Wayne State University, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Pharmacy Practice, Detroit, Michigan, United States of America
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Molecular Bacteriology Laboratory, International Vaccine Institute, Seoul, Republic of Korea
| | - Soon Ae Kim
- Translational Research Division, International Vaccine Institute, Seoul, Republic of Korea
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Bai Qing Dong
- Guangxi Zhuang Autonomous Region, Center for Disease Prevention and Control, Nanning, Guangxi, People’s Republic of China
| | - Jung Soo Kim
- Chonbuk National University School of Medicine, Jeonju, Republic of Korea
| | - Mitsuko Seki
- Department of Oral Health Sciences, Nihon University School of Dentistry, Tokyo, Japan
- Dental Research Center, Nihon University School of Dentistry, Tokyo, Japan
- * E-mail:
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49
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Greve T, Møller JK. Accuracy of using the lytA gene to distinguish Streptococcus pneumoniae from related species. J Med Microbiol 2012; 61:478-482. [DOI: 10.1099/jmm.0.036574-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Thomas Greve
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark
| | - Jens Kjølseth Møller
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark
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50
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Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 2012; 50:1171-7. [PMID: 22278834 DOI: 10.1128/jcm.06609-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The identification and detection of mitis group streptococci, which contain Streptococcus pneumoniae, have been hampered by the lack of sensitive and specific assays. In this study, we evaluated several biochemical and molecular assays for the identification of S. pneumoniae and Streptococcus pseudopneumoniae and their distinction from other mitis group streptococci using a collection of 54 isolates obtained by the routine culturing of 53 respiratory specimens from patients with community-acquired pneumonia. The combined results of the biochemical and molecular assays indicated the presence of 23 S. pneumoniae, 2 S. pseudopneumoniae, and 29 other mitis group streptococcal isolates. The tube bile solubility test that is considered gold standard for the identification of S. pneumoniae showed concordant results with optochin susceptibility testing (CO(2) atmosphere) and a real-time multiplex PCR assay targeting the Spn9802 fragment and the autolysin gene. Optochin susceptibility testing upon incubation in an O(2) atmosphere, bile solubility testing by oxgall disk, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and sequence analysis of the tuf and rpoB genes resulted in several false-positive, false-negative, or inconclusive results. The S. pseudopneumoniae isolates could be identified only by molecular assays, and the multiplex real-time PCR assay was concluded to be most convenient for the identification of S. pneumoniae and S. pseudopneumoniae isolates. Using this method, S. pneumoniae and S. pseudopneumoniae DNA could be detected in the respiratory samples from which they were isolated and in an additional 11 samples from which only other streptococci were isolated.
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