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Gonzales-Siles L, Salvà-Serra F, Degerman A, Nordén R, Lindh M, Skovbjerg S, Moore ERB. Identification and capsular serotype sequetyping of Streptococcus pneumoniae strains. J Med Microbiol 2019; 68:1173-1188. [PMID: 31268417 DOI: 10.1099/jmm.0.001022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Anna Degerman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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2
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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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3
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Kim W, Park HK, Hwang WJ, Shin HS. Simultaneous detection of Streptococcus pneumoniae, S. mitis, and S. oralis by a novel multiplex PCR assay targeting the gyrB gene. J Clin Microbiol 2013; 51:835-40. [PMID: 23269740 PMCID: PMC3592088 DOI: 10.1128/jcm.02920-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/17/2012] [Indexed: 01/05/2023] Open
Abstract
A multiplex PCR (mPCR) protocol was developed for simultaneous detection of the gyrB gene in Streptococcus pneumoniae, Streptococcus mitis, and Streptococcus oralis, and the specificity was evaluated using 141 coccus strains. Genomic DNAs purified from S. pneumoniae, S. mitis, and S. oralis strains were efficiently detected with size differences, whereas no PCR products were amplified from any of the reference strains tested. A pilot study of 47 human oral swab specimens was conducted in parallel, and the mPCR assay identified S. pneumoniae in 1 sample, S. mitis in 8 samples, and S. oralis in 2 samples, providing a powerful means for characterization at the level of species compared with traditional culture analysis. Our results suggest that the mPCR protocol presented here is a sensitive and promising tool for the rapid detection and discrimination of S. pneumoniae, S. mitis, and S. oralis from clinical specimens.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hee Kuk Park
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo-Jin Hwang
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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Identification of a pheA gene associated with Streptococcus mitis by using suppression subtractive hybridization. Appl Environ Microbiol 2012; 78:3004-9. [PMID: 22307284 DOI: 10.1128/aem.07510-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We performed suppression subtractive hybridization to identify genomic differences between Streptococcus mitis and Streptococcus pneumoniae. Based on the pheA gene, a primer set specific to S. mitis detection was found in 18 out of 103 S. mitis-specific clones. Our findings would be useful for discrimination of S. mitis from other closely related cocci in the oral environment.
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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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6
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Misidentification of alpha-hemolytic streptococci by routine tests in clinical practice. INFECTION GENETICS AND EVOLUTION 2011; 11:1709-15. [PMID: 21798371 DOI: 10.1016/j.meegid.2011.07.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/06/2011] [Accepted: 07/08/2011] [Indexed: 11/21/2022]
Abstract
Accurate species-level identification of viridans group streptococci (VGS) is very important for understanding of their pathogenicity and virulence. However, an extremely high level of the similarity between VGS, especially Streptococcus pneumoniae, Streptococcus mitis, Streptococcus oralis and Streptococcus pseudopneumoniae, often results in misidentification of these organisms, so there is an urgent need of novel approaches to species identification. A set of 50 randomly selected clinical isolates of alpha-hemolytic streptococci from upper respiratory tract were characterized by the routine phenotypic methods (alpha-hemolysis, colony morphology, Gram stain and optochin susceptibility). Modern proteomic and genetic approaches - the direct bacterial profiling (DBP) by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique and multilocus sequence analysis (MLSA) scheme (http://viridans.emlsa.net/) - were applied for the accurate species identification. After that all isolates were stored at -70°C. Later they were re-inoculated, and a number of additional tests (bile solubility, latex agglutination by commercial "Slidex® pneumo-kit" and repeated optochin test) were performed. A considerable discrepancy was discovered in the results of the different approaches. Looking in the future, one could say that MLSA-like schemes based on the analysis of the nucleotide sequences of seven or more loci of the bacterial genome, appeared to be the most useful instrument in the VGS discrimination, in contrast to the numerous one-target identification schemes, which have been introduced into practice by now.
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Borovskaya AD, Il’ina EN, Savinova TA, Sidorenko SV, Grudinina SA, Govorun VM. Differentiation of α-hemolytic streptococci by direct mass spectrometric profiling. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:61-9. [DOI: 10.1134/s1068162011010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Waterer GW, Rello J, Wunderink RG. Management of Community-acquired Pneumonia in Adults. Am J Respir Crit Care Med 2011; 183:157-64. [DOI: 10.1164/rccm.201002-0272ci] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Park HK, Lee HJ, Jeong EG, Shin HS, Kim W. The rgg gene is a specific marker for Streptococcus oralis. J Dent Res 2010; 89:1299-303. [PMID: 20739692 DOI: 10.1177/0022034510378426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Although the pathogenesis of Streptococcus oralis may be different from that of other viridans group streptococci, S. oralis shares a high degree of DNA sequence similarity with these streptococci. As a result, discrimination of S. oralis from its close relatives has long been considered difficult. This study was conducted to find specific genes that allow for the in vitro identification of S. oralis, but not other oral commensals. Four hundred ninety S. oralis clones obtained by suppressive subtractive hybridization were used for Southern hybridization, and positive clones were sequenced. Of 5 S. oralis-specific clones, newly designed primer sets based on the glucosyltransferase regulatory gene amplified genomic DNA only from S. oralis strains, but not from any of the other 125 strains tested. Our findings may be useful for the future development of efficient diagnostic tools for the rapid identification and differentiation of S. oralis from other oral streptococci strains.
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Affiliation(s)
- H K Park
- Department of Microbiology & Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-ku, Seoul 156-756, Republic of Korea
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Park HK, Lee HJ, Kim W. Real-time PCR assays for the detection and quantification of Streptococcus pneumoniae. FEMS Microbiol Lett 2010; 310:48-53. [DOI: 10.1111/j.1574-6968.2010.02044.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Park HK, Lee SJ, Yoon JW, Shin JW, Shin HS, Kook JK, Myung SC, Kim W. Identification of the cpsA gene as a specific marker for the discrimination of Streptococcus pneumoniae from viridans group streptococci. J Med Microbiol 2010; 59:1146-1152. [PMID: 20616191 DOI: 10.1099/jmm.0.017798-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae, the aetiological agent of pneumonia and non-gonococcal urethritis, shares a high degree of DNA sequence identity with the viridans group of streptococci, particularly Streptococcus mitis and Streptococcus oralis. Although their clinical and pathological manifestations are different, discrimination between S. pneumoniae and its close viridans cocci relatives is still quite difficult. Suppression subtractive hybridization was performed to identify the genomic differences between S. pneumoniae and S. mitis. Thirty-four resulting S. pneumoniae-specific clones were examined by sequence determination and comparative DNA sequence analysis using blast. S. pneumoniae-specific primers were subsequently designed from one of the clonal DNA sequences containing the cps gene (coding for capsular polysaccharide biosynthesis). The primer specificities were evaluated using 49 viridans streptococci including 26 S. pneumoniae, 54 other streptococci, 14 Lactococcus species, 14 Enterococcus species and three Vagococcus species, and compared with the specificities of previously described autolysin (lytA), pneumolysin (ply), Spn9802 and Spn9828 primers. The newly designed cpsA-specific primer set was highly specific to S. pneumoniae and was even better than the existing primers. These findings may help improve the rapid identification and differentiation of S. pneumoniae from closely related members of the viridans group streptococci.
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Affiliation(s)
- Hee Kuk Park
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Sang-Jae Lee
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan 570-749, Republic of Korea
| | - Jang Won Yoon
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jong Wook Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan 570-749, Republic of Korea
| | - Joong-Ki Kook
- Department of Biochemistry, Chosun University College of Dentistry, Gwangju 501-825, Republic of Korea
| | - Soon Chul Myung
- Department of Urology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Wonyong Kim
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, 221 Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
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12
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Park HK, Yoon JW, Shin JW, Kim JY, Kim W. rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 2010; 305:58-64. [DOI: 10.1111/j.1574-6968.2010.01913.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Cherkaoui A, Emonet S, Ceroni D, Candolfi B, Hibbs J, Francois P, Schrenzel J. Development and validation of a modified broad-range 16S rDNA PCR for diagnostic purposes in clinical microbiology. J Microbiol Methods 2009; 79:227-31. [PMID: 19782706 DOI: 10.1016/j.mimet.2009.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 09/15/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
Abstract
Broad-range PCR followed by sequencing identifies bacterial pathogens, even in challenging settings such as patients receiving antibiotics or infected with fastidious or non-cultivable organisms. The major problem with broad-range PCR is the risk of sample contamination. Risk is present at every step of the procedure, starting from sample collection. Contaminating bacterial DNA may be present not only in laboratory reagents but also at the surface of plastic consumables and containers used for specimen drawing and transport to the diagnostic laboratory. Contaminating DNA is amplified efficiently, leading to false-positive results. Thus, high specificity depends on eliminating such spurious targets, an awkward problem given the abundance of such targets and a highly sensitive method that detects very small numbers of molecules. Several investigators have reported strategies for eliminating the amplification of contaminating DNA sequences. So far, none of these methods has been entirely effective and reproducible. Here we describe a method that uses Exonuclease III (ExoIII) to disable contaminating sequences from acting as templates, while maintaining the high sensitivity of PCR for pathogen DNA. We use this assay in 144 clinical specimens from normally sterile sites, identifying pathogens from 24 (17%). Conventional methods identified pathogens in only four of these specimens, all of which were positive for the same pathogen by PCR. Compared with conventional methods, broad-range PCR with ExoIII pre-treatment of reagents substantially improves the diagnostic yield of bacterial pathogen identification from normally sterile sites.
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Affiliation(s)
- Abdessalam Cherkaoui
- Clinical Microbiology Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva 14, Switzerland
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Do T, Jolley KA, Maiden MCJ, Gilbert SC, Clark D, Wade WG, Beighton D. Population structure of Streptococcus oralis. MICROBIOLOGY-SGM 2009; 155:2593-2602. [PMID: 19423627 PMCID: PMC2885674 DOI: 10.1099/mic.0.027284-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Streptococcus oralis is a member of the normal human oral microbiota, capable of opportunistic pathogenicity; like related oral streptococci, it exhibits appreciable phenotypic and genetic variation. A multilocus sequence typing (MLST) scheme for S. oralis was developed and the resultant data analysed to examine the population structure of the species. Analysis of 113 isolates, confirmed as belonging to the S. oralis/mitis group by 16S rRNA gene sequencing, characterized the population as highly diverse and undergoing inter- and intra-species recombination with a probable clonal complex structure. ClonalFrame analysis of these S. oralis isolates along with examples of Streptococcus pneumoniae, Streptococcus mitis and Streptococcus pseudopneumoniae grouped the named species into distinct, coherent populations and did not support the clustering of S. pseudopneumoniae with S. mitis as reported previously using distance-based methods. Analysis of the individual loci suggested that this discrepancy was due to the possible hybrid nature of S. pseudopneumoniae. The data are available on the public MLST website (http://pubmlst.org/soralis/).
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Affiliation(s)
- Thuy Do
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, Guy's Campus, London SE1 9RT, UK
- Biomedical Research Centre, Guy's and St Thomas' Hospital NHS Foundation Trust, London SE1 9RT, UK
| | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | - Steven C. Gilbert
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, Guy's Campus, London SE1 9RT, UK
- Biomedical Research Centre, Guy's and St Thomas' Hospital NHS Foundation Trust, London SE1 9RT, UK
| | - Douglas Clark
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, Guy's Campus, London SE1 9RT, UK
| | - William G. Wade
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, Guy's Campus, London SE1 9RT, UK
| | - David Beighton
- King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, Guy's Campus, London SE1 9RT, UK
- Biomedical Research Centre, Guy's and St Thomas' Hospital NHS Foundation Trust, London SE1 9RT, UK
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Ding JJ, Su X, Guo FM, Shi Y, Shao HF, Meng XZ. Comparison of three different PCR-based methods to predict the penicillin nonsusceptibleStreptococcus pneumoniaeisolates from China. Lett Appl Microbiol 2009; 48:105-11. [DOI: 10.1111/j.1472-765x.2008.02497.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Duplex real-time PCR assay for detection of Streptococcus pneumoniae in clinical samples and determination of penicillin susceptibility. J Clin Microbiol 2008; 46:2751-8. [PMID: 18562586 DOI: 10.1128/jcm.02462-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a duplex real-time PCR for the rapid diagnosis of Streptococcus pneumoniae infection from culture-negative clinical samples with the simultaneous determination of penicillin susceptibility. The assay amplifies a lytA gene target and a penicillin binding protein 2b (pbp2b) gene target in penicillin-susceptible organisms. The assay was shown to be sensitive (detects 0.5 CFU per PCR) and specific for the detection of S. pneumoniae DNA. The assay was validated by comparing pbp2b PCR results with MIC data for 27 S. pneumoniae isolates. All 5 isolates with penicillin MICs of > 1.0 mg/liter were pbp2b real-time PCR negative, as were 9 of the 10 isolates with penicillin MICs of 0.12 to 1.0 mg/liter. One isolate with a penicillin MIC of 0.12 to 1.0 mg/liter gave an equivocal pbp2b real-time PCR result. Twelve isolates were penicillin susceptible (MICs of < or = 0.06 mg/liter) and pbp2b real-time PCR positive. These data were used to establish an algorithm for the interpretation of penicillin susceptibility from the duplex PCR result. pbp2b real-time PCR results were also compared to an established PCR-restriction fragment length polymorphism (RFLP) method previously applied to these 27 isolates and 46 culture-negative clinical samples (containing S. pneumoniae DNA by broad-range 16S rRNA gene PCR). Discordant results were seen for four isolates and six culture-negative clinical samples, as PCR-RFLP could not reliably detect penicillin MICs of 0.12 to 1.0 mg/liter. We report prospective application of the duplex PCR assay to the diagnosis of S. pneumoniae infection from 200 culture-negative clinical specimens sent to the laboratory for diagnostic broad-range 16S rRNA gene PCR. One hundred six were negative in the duplex PCR. Ninety-four were lytA PCR positive, and 70 of these were also pbp2b PCR positive and interpreted as penicillin susceptible. Fourteen were pbp2b PCR negative and interpreted as having reduced susceptibility to penicillin. For the remaining 10 samples, susceptibility to penicillin was not determined.
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Suzuki N, Yuyama M, Maeda S, Ogawa H, Mashiko K, Kiyoura Y. Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae. J Med Microbiol 2006; 55:709-714. [PMID: 16687588 DOI: 10.1099/jmm.0.46296-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It was previously reported that two oligonucleotide primer sets (spn9802 and spn9828) for discriminating Streptococcus pneumoniae from pneumococcus-like oral streptococcal isolates using PCR had been developed. In this study, PCR amplification of the lytA, ply, spn9802 and spn9828 genes was used to identify presumptive S. pneumoniae. Two genetic groups were identified by analysing sputum samples from 28 patients with community-acquired pneumonia: the lytA-positive, ply-positive, spn9802-positive and spn9828-negative group, and the lytA-positive, ply-positive, spn9802-positive and spn9828-positive group. Isolates of the former group were resistant to optochin, while those of the latter group showed susceptibility to optochin. The lytA-positive, ply-positive, spn9802-negative and spn9828-negative isolates, and lytA-positive, ply-positive, spn9802-negative and spn9828-positive isolates, were not detected in sputum from patients with pneumonia. Subsequently, a total of 92 saliva samples from healthy individuals was screened by PCR using these primer sets. The lytA-positive, ply-positive, spn9802-positive and spn9828-negative group was identified more frequently in saliva from healthy children than in saliva from older healthy individuals and patients with pneumonia. The lytA-positive, ply-positive, spn9802-positive and spn9828-positive group was found frequently in saliva from healthy children, and in saliva and sputum from patients with pneumonia. This study demonstrates a rapid, optimal screening method for the genotypic identification of presumptive S. pneumoniae by PCR using four genes highly specific for S. pneumoniae.
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Affiliation(s)
- Nao Suzuki
- Division of Oral Bacteriology, Department of Oral Medical Science, Ohu University School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama 963-8611, Japan
| | - Mayumi Yuyama
- Jusendo General Hospital, 1-8-16 Ekimae, Koriyama 963-8585, Japan
| | - Sinsaku Maeda
- Jusendo General Hospital, 1-8-16 Ekimae, Koriyama 963-8585, Japan
| | - Haruhiko Ogawa
- Division of Pulmonary Medicine, Saiseikai Kanazawa Hospital, 2-13-6 Akatsuchimachi, Kanazawa 920-0353, Japan
| | - Kazuyuki Mashiko
- Jusendo General Hospital, 1-8-16 Ekimae, Koriyama 963-8585, Japan
| | - Yusuke Kiyoura
- Division of Oral Bacteriology, Department of Oral Medical Science, Ohu University School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama 963-8611, Japan
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Zettler EW, Scheibe RM, Dias CAG, Santafé P, Santos DS, Moreira JDS, Fritscher CC. Determination of penicillin resistance in Streptococcus pneumoniae isolates from southern Brazil by PCR. Int J Infect Dis 2005; 10:110-5. [PMID: 16310395 DOI: 10.1016/j.ijid.2005.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Revised: 04/07/2005] [Accepted: 04/14/2005] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To demonstrate the potential clinical applicability of the PCR technique to the early detection of bacterial resistance in Streptococcus pneumoniae. METHODS We studied 153 samples of S. pneumoniae, isolated from different anatomic sites, using polymerase chain reaction (PCR) for the detection of specific amplicons from genes that code for penicillin-binding proteins (PBP) 1a, 2b and 2x, which are responsible for penicillin resistance in this organism. The occurrence of these mutated genes was correlated with the minimum inhibitory concentration (MIC) of penicillin, determined by the agar dilution test. RESULTS The rate of penicillin resistance in S. pneumoniae in Porto Alegre, Brazil was 22.8% (16.3% intermediate resistance and 6.5% high resistance). In a statistically significant proportion of cases (p < 0.05), penicillin-susceptible samples had no amplicons, intermediate samples had only one (generally from PBP 2x), and highly resistant samples had amplicons from all three PBPs investigated. CONCLUSION These results suggest that penicillin resistance in S. pneumoniae in southern Brazil is on the increase, but is still lower than in other countries, and that PCR could be used for its early detection.
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Affiliation(s)
- Eduardo Walker Zettler
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga, 6690 - conjunto 501, Bairro Jardim Botânico, Porto Alegre - RS, CEP: 90660-000, Brazil.
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19
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Suzuki N, Seki M, Nakano Y, Kiyoura Y, Maeno M, Yamashita Y. Discrimination of Streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization. J Clin Microbiol 2005; 43:4528-34. [PMID: 16145102 PMCID: PMC1234109 DOI: 10.1128/jcm.43.9.4528-4534.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two oligonucleotide primer sets for the discrimination of Streptococcus pneumoniae from "pneumococcus-like" oral streptococcal isolates by PCR were developed. Genomic subtractive hybridization was performed to search for differences between Streptococcus pneumoniae strain WU2 and the most closely related oral streptococcus, Streptococcus mitis strain 903. We identified 19 clones that contained S. pneumoniae-specific nucleotide fragments that were absent from the chromosomal DNA of typical laboratory strains of S. mitis and other oral bacteria. Subsequently, oligonucleotide PCR primers for the detection of S. pneumoniae were designed from the sequences of the subtracted DNA fragments, and the specificities of the 19 primer sets were evaluated by PCR using chromosomal DNAs extracted from four S. pneumoniae clinical isolates and from 20 atypical organisms classified as S. mitis or S. oralis, which harbored genes encoding the pneumococcal virulence factors autolysin (lytA) or pneumolysin (ply), as templates. Of the 19 primer sets, two (Spn9802 and Spn9828) did not amplify PCR products from any of the pneumococcus-like streptococcal strains that we examined. The genes containing the Spn9802 and Spn9828 sequences encoded proteins of unknown function that did not correspond to any previously described proteins in other bacteria. These new oligonucleotide primers may be very useful for early and correct diagnosis of S. pneumoniae infections.
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Affiliation(s)
- Nao Suzuki
- Department of Oral Medical Science, School of Dentistry, Tomitamachi, Koriyama, Japan
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20
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Abstract
BACKGROUND An increase in the incidence of thoracic empyema in children has been reported. The causative pathogen is often unknown as pleural fluid is frequently sterile at the time of culture. The role of unusual organisms is unclear. AIMS (1) To compare the detection of organisms in pleural fluid from children with empyema using a molecular technique (16S rDNA polymerase chain reaction (PCR)) and bacterial culture. (2) To compare the concordance of organisms identified using the two techniques and the influence of prior antibiotic treatment on positive detection rate. METHODS Pleural fluid from children admitted with empyema between January 2000 and February 2002 was cultured and additionally analysed using broad range 16S rDNA PCR. RESULTS Pleural fluid was cultured from 32 patients, aged 1 month-16 years. Median duration of previous antibiotic therapy was 8 days (range 1-42 days). Six samples were culture positive and 22 were PCR positive. A causal organism was detected by PCR alone, after considering results from the local hospital, in 14 patients. There was complete concordance in organisms cultured and detected by PCR. Additional organisms detected by PCR were predominantly S pneumoniae, S pyogenes, and anaerobes. CONCLUSIONS Analysis of pleural fluid by broad range 16S rDNA PCR in addition to culture, increases organism identification in empyema.
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Affiliation(s)
- S Saglani
- Department of Respiratory Paediatrics, Great Ormond Street Hospital for Children, Great Ormond Street, London, UK
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21
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Isabel Viciana M, Victoria García-López M, Mariscal A, Antonia Sánchez-Bernal M, Clavijo E, Martín E, Rodríguez-Ortega R, Pinedo A. Aspectos microbiológicos y clinicoepidemiológicos de los aislados de Streptococcus pneumoniae durante dos años. Enferm Infecc Microbiol Clin 2004. [DOI: 10.1016/s0213-005x(04)73024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Harris KA, Hartley JC. Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service. J Med Microbiol 2003; 52:685-691. [PMID: 12867563 DOI: 10.1099/jmm.0.05213-0] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of the present study was to develop a broad-range PCR based on bacterial 16S rDNA for use in the routine diagnostic clinical microbiology service. The optimization and validation of the assay for use on clinical specimens from normally sterile sites is described, and preliminary results are reported on the use of the assay in the clinical diagnosis of bacterial infection in 382 paediatric specimens over a 2-year period. These results are compared to those obtained by standard culture techniques and show increased diagnosis of bacterial infection when both culture and PCR are used together; 16S rDNA PCR provided the sole evidence of pathogenic infection in 71 cases. Key stages in the assay development and potential pitfalls of the technique are highlighted and the improvement the assay offers in the diagnosis of infection in the paediatric setting is discussed.
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Affiliation(s)
- Kathryn A Harris
- Department of Microbiology, Level 4 Camelia Botnar Laboratories, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - John C Hartley
- Department of Microbiology, Level 4 Camelia Botnar Laboratories, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
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23
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Mlynarczyk G, Mlynarczyk A, Jeljaszewicz J. Epidemiological aspects of antibiotic resistance in respiratory pathogens. Int J Antimicrob Agents 2001; 18:497-502. [PMID: 11738335 PMCID: PMC7173210 DOI: 10.1016/s0924-8579(01)00455-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Respiratory infections are the most frequent reason for primary health care consultation. The main causes of respiratory tract infections in children are viruses and the most common types are upper respiratory tract infections: common cold, pharyngitis, otitis media and sinusitis. Pneumonia is much more serious. As well as viruses, bacteria are often involved in respiratory tract infections. Three bacterial species are most commonly isolated: Streptococcus pneumoniae, non-encapsulated Haemophilus influenzae and Moraxella (Branhamella) catarrhalis. The most common bacterial cause of pharyngitis is Streptococcus pyogenes. Bacteria isolated from community-acquired infection usually are sensitive to the majority of suitable drugs, but during the past two decades, significant antibiotic resistance has emerged. Resistance to penicillins has spread among H. influenzae and S. pneumoniae. The mechanism of penicillin resistance in H. influenzae is mainly by production of beta-lactamases TEM-1 and ROB-1, whereas in S. pneumoniae resistance is an effect of the changes in penicillin binding proteins. Among respiratory pathogens, resistance to tetracyclines, macrolides, trimethoprim-sulphamethoxazole and fluoroquinolones has also appeared. Several mechanisms depending on changes in target, active efflux and modifying enzymes are involved.
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Affiliation(s)
- G Mlynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, 5 Chalubinskiego, 02-004, Warsaw, Poland
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24
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Fluit AC, Visser MR, Schmitz FJ. Molecular detection of antimicrobial resistance. Clin Microbiol Rev 2001; 14:836-71, table of contents. [PMID: 11585788 PMCID: PMC89006 DOI: 10.1128/cmr.14.4.836-871.2001] [Citation(s) in RCA: 257] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art.
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Affiliation(s)
- A C Fluit
- Eijkman-Winkler Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
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25
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McAvin JC, Reilly PA, Roudabush RM, Barnes WJ, Salmen A, Jackson GW, Beninga KK, Astorga A, McCleskey FK, Huff WB, Niemeyer D, Lohman KL. Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR. J Clin Microbiol 2001; 39:3446-51. [PMID: 11574554 PMCID: PMC88370 DOI: 10.1128/jcm.39.10.3446-3451.2001] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Molecular surveillance of pathogens has shown the need for rapid and dependable methods for the identification of organisms of clinical and epidemiological importance. As the leading cause of community-acquired pneumonia, Streptococcus pneumoniae was used as a model organism to develop and refine a real-time fluorescence PCR assay and enhanced DNA purification method. Seventy clinical isolates of S. pneumoniae, verified by latex agglutination, were screened against 26 negative control clinical isolates employing a TaqMan assay on a thermocycler (LightCycler). The probe, constructed from the lytA gene, correctly detected all S. pneumoniae genomes without cross-reaction to negative controls. The speed and ease of this approach will make it adaptable to identification of many bacterial pathogens and provide potential for adaptation to direct detection from patient specimens.
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Affiliation(s)
- J C McAvin
- Molecular Epidemiology Branch, Air Force Institute for Environment and Occupational Health Risk Analysis/Epidemiology Surveillance Division, Brooks Air Force Base, San Antonio, Texas 78235, USA
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26
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Abstract
DNA amplification techniques are now available for all of the major respiratory bacterial pathogens. The most important recent developments have been in the application of these techniques to routine clinical practice. A major problem for rapid techniques is the need to provide susceptibility results. Effective susceptibility techniques have now been described for Streptococcus pneumoniae and Mycobacterium tuberculosis. It has also been possible to use amplification techniques to monitor the response to antituberculosis chemotherapy by monitoring mRNA in sputum samples. The added sensitivity the amplification-based techniques give over conventional culture techniques is valuable not only in enhancing diagnosis, which allows the use of less invasive specimens, but also in opening new investigative areas in the pathogenesis of respiratory conditions.
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Affiliation(s)
- S Gillespie
- Royal Free and University College Medical School, London, UK
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