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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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Lee CY, Chan CK, Chida M, Miyashita M, Lee YS, Wu HC, Chang YC, Lin WT, Chen YS. Streptococcus taonis sp. nov., a novel bacterial species isolated from a blood culture of a patient. Arch Microbiol 2024; 206:168. [PMID: 38489085 DOI: 10.1007/s00203-024-03884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024]
Abstract
One Gram stain-positive, catalase-negative, α-hemolytic, chain-forming or paired cocci, designated ST22-14T, was isolated from a blood culture of a child with suspected infection. The results of 16S rRNA gene sequences analyses showed that the most closely related species to strain ST22-14T were "Streptococcus vulneris" DM3B3T (99.2%), Streptococcus mitis NCTC 12261T (99.0%), "Streptococcus gwangjuense" ChDC B345T, (99.0%), Streptococcus oralis subsp. dentisani 7747T (99.0%), Streptococcus downii CECT 9732T (99.0%), and Streptococcus infantis ATCC 700779T (98.9%). The genome of strain ST22-14T consists of 2,053,261 bp with a G + C content of 39.4%. Average nucleotide identity values between strain ST22-14T and Streptococcus mitis NCTC 12261T or other five species were from 82.2 to 88.0%. In silico DNA-DNA hybridization of ST22-14T showed an estimated DNA reassociation value of 34.6% with the closest species. The main cellular fatty acids of strain ST22-14T were 16:0, 18:0, 14:0, 18:1ω7c and 18:1ω6c. Based on these results, strain ST22-14T should be classified as a novel species of genus Streptococcus, for which the name Streptococcus taonis sp. nov. is proposed (type strain ST22-14T = NBRC 116002T = BCRC 81402T).
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Affiliation(s)
- Chien-Yu Lee
- Department of Pediatrics, Taoyuan General Hospital, Ministry of Health and Welfare, No.1492, Zhongshan Rd., Taoyuan Dist., Taoyuan City, 330, Taiwan ROC
| | - Chin-Kan Chan
- Department of Pediatrics, Taoyuan General Hospital, Ministry of Health and Welfare, No.1492, Zhongshan Rd., Taoyuan Dist., Taoyuan City, 330, Taiwan ROC
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Momoko Chida
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Hui-Chung Wu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Yu-Chung Chang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Wen-Ting Lin
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Yi-Sheng Chen
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC.
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Butler M, Breazeale G, Mwangi E, Dowell E, Dominguez SR, Lamberth L, Hultén KG, Jung SA. Development and validation of a multiplex real-time PCR assay for detection and quantification of Streptococcus pneumoniae in pediatric respiratory samples. Microbiol Spectr 2023; 11:e0211823. [PMID: 37937989 PMCID: PMC10715132 DOI: 10.1128/spectrum.02118-23] [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: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE Streptococcus pneumoniae (Spn) is the world's leading cause of lower respiratory tract infection morbidity and mortality in children. However, current clinical microbiological methods have disadvantages. Spn can be difficult to grow in laboratory conditions if a patient is pre-treated, and Spn antigen testing has unclear clinical utility in children. Syndromic panel testing is less cost-effective than targeted PCR if clinical suspicion is high for a single pathogen. Also, such testing entails a full, expensive validation for each panel target if used for multiple respiratory sources. Therefore, better diagnostic modalities are needed. Our study validates a multiplex PCR assay with three genomic targets for semi-quantitative and quantitative Spn molecular detection from lower respiratory sources for clinical testing and from upper respiratory sources for research investigation.
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Affiliation(s)
- Molly Butler
- Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Garrett Breazeale
- Children’s Hospital Colorado, Aurora, Colorado, USA
- University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric Mwangi
- Children’s Hospital Colorado, Aurora, Colorado, USA
| | | | - Samuel R. Dominguez
- Children’s Hospital Colorado, Aurora, Colorado, USA
- University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Kristina G. Hultén
- Texas Children’s Hospital, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
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Suleiman M, Elamin N, Nabor R, Roberts J, Tang P, Hasan MR, Pérez-López A. Evaluation of Immulex S. pneumoniae Omni test for the direct detection of S. pneumoniae from positive blood cultures. Heliyon 2023; 9:e22106. [PMID: 38027561 PMCID: PMC10658396 DOI: 10.1016/j.heliyon.2023.e22106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/06/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Rapid and early identification of Streptococcus pneumoniae from positive blood cultures is crucial for the management of patients with bloodstream infections (BSI). Many identification systems in microbiology laboratories have difficulty differentiating S. pneumoniae from other closely related species in the Streptococcus mitis group. To overcome this limitation, we developed a rapid workflow in our laboratory combining direct MALDI-TOF MS identification with the Immulex S. pneumoniae Omni test (SSI Diagnostica, Denmark) for rapid detection of S. pneumoniae directly from positive blood cultures. The workflow was evaluated using 51 Streptococcus isolates. Compared to conventional biochemical testing, our new workflow demonstrates 100 % specificity and sensitivity for the detection and differentiation of S. pneumoniae from other closely related species. Our new workflow is accurate, cost-effective, and can easily be implemented in microbiology laboratories that already perform direct MALDI-TOF identification from positive blood cultures to improve the management of patients with invasive pneumococcal disease. Importance Invasive pneumococcal disease remains a major public health problem worldwide. Reducing the time to identify Streptococcus pneumoniae in positive blood cultures allows patients to be treated sooner with more targeted and effective antibiotics. We evaluated a two-step protocol where positive blood cultures are first tested directly by MALDI-TOF MS and any samples containing Streptococcus species are tested by Immulex S. pneumoniae Omni test to both detect and differentiate S. pneumoniae from other closely related Streptococcus species. Our study results showed 100 % sensitivity and specificity, and a much faster turn-around time than conventional methods.
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Affiliation(s)
| | | | | | | | - Patrick Tang
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Mohammad Rubayet Hasan
- Medical Scientific Department, LifeLabs, Toronto, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Andrés Pérez-López
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
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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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Nasopharyngeal colonization by Streptococcus pneumoniae in children and adults before the introduction of the 10-valent conjugate vaccine, Paraguay. PLoS One 2023; 18:e0280722. [PMID: 36795644 PMCID: PMC9934358 DOI: 10.1371/journal.pone.0280722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/07/2023] [Indexed: 02/17/2023] Open
Abstract
Streptococcus pneumoniae is a cause of invasive diseases such as pneumonia, meningitis, and other serious infections among children and adults in Paraguay. This study was conducted to establish S. pneumoniae baseline prevalence, serotype distribution, and antibiotic resistance patterns in healthy children aged 2 to 59 months and adults ≥60 years of age prior to the introduction of PCV10 in the national childhood immunization program in Paraguay. Between April and July 2012, a total of 1444 nasopharyngeal swabs were collected, 718 from children aged 2 to 59 months and 726 from adults ≥60 years of age. The pneumococcal isolation, serotyping, and antibiotic susceptibility testing were performed using standard tests. Pneumococcal colonization prevalence was 34.1% (245/718) in children and 3.3% (24/726) in adults. The most frequent pneumococcal vaccine-types (VT) detected in the children were 6B (42/245), 19F (32/245), 14 (17/245), and 23F (20/245). Carriage prevalence with PCV10 serotypes was 50.6% (124/245) and PCV13 was 59.5% (146/245). Among colonized adults, prevalence of PCV10 and PCV13 serotypes were 29.1% (7/24) and 41.6% (10/24), respectively. Colonized children were more likely to share a bedroom, have a history of respiratory infection or pneumococcal infection compared to non-colonized children. no associations were found in adults. However, no significant associations were found in children and neither in adults. Vaccine-type pneumococcal colonization was highly prevalent in children and rare in adults in Paraguay prior to vaccine introduction, supporting the introduction of PCV10 in the country in 2012. These data will be useful to evaluate the impact of PCV introduction in the country.
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Eriksen HB, Fuursted K, Jensen A, Jensen CS, Nielsen X, Christensen JJ, Shewmaker P, Rebelo AR, Aarestrup FM, Schønning K, Slotved HC. Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci. Front Microbiol 2023; 14:1120023. [PMID: 36937294 PMCID: PMC10018206 DOI: 10.3389/fmicb.2023.1120023] [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: 12/09/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction For Streptococcus pneumoniae, β-lactam susceptibility can be predicted from the amino acid sequence of the penicillin-binding proteins PBP1a, PBP2b, and PBP2x. The combination of PBP-subtypes provides a PBP-profile, which correlates to a phenotypic minimal inhibitory concentration (MIC). The non-S. pneumoniae Mitis-group streptococci (MGS) have similar PBPs and exchange pbp-alleles with S. pneumoniae. We studied whether a simple BLAST analysis could be used to predict phenotypic susceptibility in Danish S. pneumoniae isolates and in internationally collected MGS. Method Isolates with available WGS and phenotypic susceptibility data were included. For each isolate, the best matching PBP-profile was identified by BLAST analysis. The corresponding MICs for penicillin and ceftriaxone was retrieved. Category agreement (CA), minor-, major-, and very major discrepancy was calculated. Genotypic-phenotypic accuracy was examined with Deming regression. Results Among 88 S. pneumoniae isolates, 55 isolates had a recognized PBP-profile, and CA was 100% for penicillin and 98.2% for ceftriaxone. In 33 S. pneumoniae isolates with a new PBP-profile, CA was 90.9% (penicillin) and 93.8% (ceftriaxone) using the nearest recognized PBP-profile. Applying the S. pneumoniae database to non-S. pneumoniae MGS revealed that none had a recognized PBP-profile. For Streptococcus pseudopneumoniae, CA was 100% for penicillin and ceftriaxone in 19 susceptible isolates. In 33 Streptococcus mitis isolates, CA was 75.8% (penicillin) and 86.2% (ceftriaxone) and in 25 Streptococcus oralis isolates CA was 8% (penicillin) and 100% (ceftriaxone). Conclusion Using a simple BLAST analysis, genotypic susceptibility prediction was accurate in Danish S. pneumoniae isolates, particularly in isolates with recognized PBP-profiles. Susceptibility was poorly predicted in other MGS using the current database.
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Affiliation(s)
- Helle Brander Eriksen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark
- *Correspondence: Helle Brander Eriksen,
| | - Kurt Fuursted
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Jensen
- Department of Clinical Microbiology, Sygehus Lillebælt, Vejle, Denmark
| | | | - Xiaohui Nielsen
- The Regional Department of Clinical Microbiology, Slagelse, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Slagelse, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ana Rita Rebelo
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Hans-Christian Slotved,
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Tabata A, Matsumoto A, Fujimoto A, Ohkura K, Ikeda T, Oda H, Yokohata S, Kobayashi M, Tomoyasu T, Takao A, Ohkuni H, Nagamune H. Dual functions of discoidinolysin, a cholesterol-dependent cytolysin with N-terminal discoidin domain produced from Streptococcus mitis strain Nm-76. J Oral Microbiol 2022; 14:2105013. [PMID: 35937899 PMCID: PMC9351568 DOI: 10.1080/20002297.2022.2105013] [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] [Indexed: 11/10/2022] Open
Abstract
Background Some strains of Streptococcus mitis exhibit β-hemolysis due to the β-hemolytic activity of cholesterol-dependent cytolysin (CDC). Recently, a gene encoding an atypical lectinolysin-related CDC was found in S. mitis strain Nm-76. However, the product of this gene remains uncharacterized. We aimed to characterize this atypical CDC and its molecular functions and contribution to the pathogenicity of S. mitis strain Nm-76. Methods Phylogenetic analysis of the CDC gene was conducted based on the web-deposited information. The molecular characteristics of CDC were investigated using a gene-deletion mutant strain and recombinant proteins expressed in Escherichia coli. Results The gene encoding CDC found in Nm-76 and its homolog are distributed among many S. mitis strains. This CDC is phylogenetically different from other previously characterized CDCs, such as S. mitis-derived human platelet aggregation factor (Sm-hPAF)/lectinolysin and mitilysin. Because this CDC possesses an additional N-terminal domain, including a discoidin motif, it was termed discoidinolysin (DLY). In addition to the preferential lysis of human cells, DLY displayed N-terminal domain-dependent facilitation of human erythrocyte aggregation and intercellular associations between human cells. Conclusion DLY functions as a hemolysin/cytolysin and erythrocyte aggregation/intercellular association molecule. This dual-function DLY could be an additional virulence factor in S. mitis.
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Affiliation(s)
- Atsushi Tabata
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Airi Matsumoto
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Ai Fujimoto
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Kazuto Ohkura
- Division of Clinical Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Japan
| | - Takuya Ikeda
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Hiroki Oda
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Shuto Yokohata
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Miho Kobayashi
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Toshifumi Tomoyasu
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Ayuko Takao
- Department of Oral Microbiology, School of Dental Medicine, Tsurumi University, Kanagawa, Japan
| | - Hisashi Ohkuni
- Research Institute, Health Science Research Institute East Japan Co., Ltd., Saitama, Japan
| | - Hideaki Nagamune
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
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Abstract
Oral commensal streptococci are primary colonizers of the oral cavity. These streptococci produce many adhesins, metabolites, and antimicrobials that modulate microbial succession and diversity within the oral cavity. Often, oral commensal streptococci antagonize cariogenic and periodontal pathogens such as Streptococcus mutans and Porphyromonas gingivalis, respectively. Mechanisms of antagonism are varied and range from the generation of hydrogen peroxide, competitive metabolite scavenging, the generation of reactive nitrogen intermediates, and bacteriocin production. Furthermore, several oral commensal streptococci have been shown to alter the host immune response at steady state and in response to oral pathogens. Collectively, these features highlight the remarkable ability of oral commensal streptococci to regulate the structure and function of the oral microbiome. In this review, we discuss mechanisms used by oral commensal streptococci to interact with diverse oral pathogens, both physically and through the production of antimicrobials. Finally, we conclude by exploring the critical roles of oral commensal streptococci in modulating the host immune response and maintaining health and homeostasis.
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Sayed ZI, Abdel-Ghany MF, Ahmed SH, Adawy AM, El–Hamid RFA. Streptococcus pseudopneumoniae as an emerging respiratory tract pathogen at Assiut University hospitals. IRANIAN JOURNAL OF MICROBIOLOGY 2022; 14:645-652. [PMID: 36531811 PMCID: PMC9723435 DOI: 10.18502/ijm.v14i5.10957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
BACKGROUND AND OBJECTIVES Streptococcus pseudopneumoniae is a member of viridans streptococci. It is non-capsulated, bile insoluble and optochin susceptible in ambient air but resistant in 5% CO2. This study aimed to isolate S. pseudopneumoniae from sputum specimens of patients admitted to Chest Department and Chest ICU of Assiut University hospitals, differentiate it from Streptococcus pneumoniae in addition, to evaluate the prevalence of Streptococcus pseudopneumoniae in clinical isolates by phenotypic and genotypic methods, to subject the isolates to antimicrobial susceptibility testing using agar disc diffusion method. MATERIALS AND METHODS Isolation of Streptococcus pseudopneumoniae from sputum sample and doing phenotypic test (optochin susceptibility test,bile susceptibility test and antimicrobial susceptibility test) and genotypic test by polymerase chain reaction (PCR) for five genes: CpsA, LytA, AliB-like ORF2, 16S rRNA and Spn9802 genes. RESULTS Twenty isolates of S. pseudopneumoniae were diagnosed phenotypically by optochin susceptibility and bile solubility tests followed by genotypic characterization by polymerase chain reaction (PCR) for five genes: CpsA, LytA, AliB-like ORF2, 16S rRNA and Spn9802 genes. The prevalence of S. pseudopneumoniae among studied patients was 10% (20/200). CONCLUSION The pure growth of S. pseudopneumoniae from sputum samples together with the great percentage of antibiotic resistance should raise attention to the clinical importance of this organism.
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Affiliation(s)
- Zeinab Ibraheem Sayed
- Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt
| | | | - Shabaan Hashem Ahmed
- Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt
| | - Amany Mohmed Adawy
- Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt
| | - Rawhia Fathy Abd El–Hamid
- Department of Medical Microbiology and Immunology, School of Medicine, Assiut University, Assiut, Egypt
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Streptococcus humanilactis sp.nov., isolated from healthy nursing mother's breast milk. Arch Microbiol 2022; 204:654. [PMID: 36175573 DOI: 10.1007/s00203-022-03249-2] [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: 12/21/2021] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022]
Abstract
Two bacterial strains were isolated from the breast milk of two healthy nursing mothers. The isolates were Gram-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of the 16S rRNA gene sequences of strain IMAU99125T shared 99.7 and 99.6% similarity with Streptococcus mitis ATCC 49456 T and Streptococcus pseudopneumoniae ATCC BAA-960 T, respectively. The nearly complete 16S rRNA gene sequences of IMAU99125T and IMAU99674 strains were very closely related (with only 0.06% difference between them). Sequence analysis of the gyrB and rpoB genes also indicated that IMAU99125T was closely related to S. mitis ATCC 49456 T (94.7% and 97.1%, respectively) and S. pseudopneumoniae ATCC BAA-960 T (94.4% and 97.1%, respectively). Average nucleotide identity (ANI) values between strain IMAU99125T and S. mitis ATCC 49456 T and S. pseudopneumoniae ATCC BAA-960 T, were 93.3% and 92.7%, respectively. Genome-to-genome distance (GGD) values between strain IMAU99125T and S. mitis ATCC 99125 T and S. pseudopneumoniae ATCC BAA-960 T were 53.4% (50.7-56.0) and 50.4% (47.7-53.0), respectively. The major fatty acids of the strain were C16:0 (51.4%). On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two strains be classified as representing a novel species of the genus Streptococcus, namely Streptococcus humanilactis sp.nov. The type strain is IMAU99125T (= GDMCC 1.1876 T = KCTC 21157 T). The genome of Streptococcus humanilactis sp. nov. is comprised of 2,027,143 bp. The DNA G + C content of the strain is 40.0 mol%.
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12
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Jia J, Shi W, Dong F, Meng Q, Yuan L, Chen C, Yao K. Identification and molecular epidemiology of routinely determined Streptococcus pneumoniae with negative Quellung reaction results. J Clin Lab Anal 2022; 36:e24293. [PMID: 35170080 PMCID: PMC8993597 DOI: 10.1002/jcla.24293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Background Some streptococci strains identified as Streptococcus pneumoniae (S. pneumoniae) by routine clinical methods exhibiting negative Quellung reaction results may belong to other species of viridans group streptococci or non‐typeable S. pneumoniae. The purpose of this study was to investigate the identification and molecular characteristics of S. pneumoniae with negative Quellung reaction results. Methods One hundred and five isolates identified as S. pneumoniae using routine microbiological methods with negative Quellung reaction results were included. Multilocus sequence analysis (MLSA) was used as a gold standard in species identification, and the capacity of matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS) in identification was evaluated. Capsular genes and sequence types of S. pneumoniae isolates were determined by sequential multiplex PCR and multilocus sequence typing. Antimicrobial susceptibility patterns were determined via broth microdilution with a commercialized 96‐well plate. Results Among the isolates, 81 were identified as S. pneumoniae and 24 were S. pseudopneumoniae by MLSA. MALDI‐TOF MS misidentified six S. pneumoniae isolates as S. pseudopneumoniae and nine S. pseudopneumoniae isolates as S. pneumoniae or S. mitis/S. oralis. Thirty‐one sequence types (STs) were detected for these 81 S. pneumoniae isolates, and the dominant ST was ST‐bj12 (16, 19.8%). The non‐susceptibility rates of S. pseudopneumoniae were comparable to those of NESp strains. Conclusions Some S. pneumoniae isolates identified by routine methods were S. pseudopneumoniae. Most NESp strains have a different genetic background compared with capsulated S. pneumoniae strains. The resistance patterns of S. pseudopneumoniae against common antibiotics were comparable to those of NESp.
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Affiliation(s)
- Ju Jia
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Wei Shi
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Fang Dong
- Clinical Laboratory, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Qingying Meng
- Clinical Laboratory, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Lin Yuan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Changhui Chen
- Department of Pediatrics, Youyang County People's Hospital, Chongqing, China
| | - Kaihu Yao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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13
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Streptococcus sputorum, a Novel Member of Streptococcus with Multidrug Resistance, Exhibits Cytotoxicity. Antibiotics (Basel) 2021; 10:antibiotics10121532. [PMID: 34943744 PMCID: PMC8698525 DOI: 10.3390/antibiotics10121532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022] Open
Abstract
We describe the genomic and phenotypic characteristics of a novel member of Streptococcus with multidrug resistance (MDR) isolated from hospital samples. Strains SP218 and SP219 were identified as a novel Streptococcus, S. sputorum, using whole-genome sequencing and biochemical tests. Average nucleotide identity values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 94.3% and 93.3%, respectively. Genome-to-genome distance values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 56.70% (54–59.5%) and 56.40% (52.8–59.9%), respectively. The biochemical test results distinguished these strains from S. pseudopneumoniae and S. pneumoniae, particularly hydrolysis of equine urate and utilization of ribose to produce acid. These isolates were resistant to six major classes of antibiotics, which correlated with horizontal gene transfer and mutation. Notably, strain SP219 exhibited cytotoxicity against human lung epithelial cell line A549. Our results indicate the pathogenic potential of S. sputorum, and provide valuable insights into mitis group of streptococci.
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Ganaie F, Branche AR, Peasley M, Rosch JW, Nahm MH. Oral streptococci expressing pneumococci-like cross-reactive capsule types can affect WHO recommended pneumococcal carriage procedure. Clin Infect Dis 2021; 75:647-656. [PMID: 34891152 DOI: 10.1093/cid/ciab1003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Carriage studies are fundamental to assess the effects of pneumococcal vaccines. Since a large proportion of oral streptococci carry homologs of pneumococcal genes, nonculture-based detection and serotyping of upper respiratory tract (URT) samples can be problematic. Herein, we investigated if culture-free molecular methods could differentiate pneumococci from oral streptococci carried by adults in URT. METHODS Paired nasopharyngeal (NP) and oropharyngeal (OP) samples were collected from 100 older adults twice a month for one year. Extracts from the combined NP+OP samples (n=2400) were subjected to lytA real-time PCR. Positive samples were subjected to pure culture isolation followed by species confirmation using multiple approaches. Multibead assay and whole-genome sequencing were used for serotyping. RESULTS lytA-PCR was positive in 301 combined NP+OP extracts, 20 of which grew probable pneumococcal-like colonies based on colony morphology and biochemical tests. Multiple approaches confirmed that four isolates were S. pneumoniae, three were S. psuedopneumoniae, and thirteen were S. mitis. Eight nonpneumococcal strains carried pneumococcus-like cps loci (size: ~18 to 25 kb) that showed >70% of nucleotide identity with their pneumococcal counterparts. While investigating the antigenic profile, we found some S. mitis strains (P066 and P107) reacted with both serotype-specific polyclonal (Type 39 and FS17b) and monoclonal (Hyp10AG1 and Hyp17FM1) antisera, whereas some strains (P063 and P074) reacted only with polyclonal antisera (Type 5 and FS35a). CONCLUSION The extensive capsular overlap suggests that pneumococcal vaccines could reduce carriage of oral streptococci expressing cross-reactive capsules. Further, direct use of culture-free PCR-based methods in URT samples has limited usefulness for carriage studies.
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Affiliation(s)
- Feroze Ganaie
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Angela R Branche
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Michael Peasley
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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15
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Tabata A, Nagamune H. Diversity of β-hemolysins produced by the human opportunistic streptococci. Microbiol Immunol 2021; 65:512-529. [PMID: 34591320 DOI: 10.1111/1348-0421.12936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
The genus Streptococcus infects a broad range of hosts, including humans. Some species, such as S. pyogenes, S. agalactiae, S. pneumoniae, and S. mutans, are recognized as the major human pathogens, and their pathogenicity toward humans has been investigated. However, many of other streptococcal species have been recognized as opportunistic pathogens in humans, and their clinical importance has been underestimated. In our previous study, the Anginosus group streptococci (AGS) and Mitis group streptococci (MGS) showed clear β-hemolysis on blood agar, and the factors responsible for the hemolysis were homologs of two types of β-hemolysins, cholesterol-dependent cytolysin (CDC) and streptolysin S (SLS). In contrast to the regular β-hemolysins produced by streptococci (typical CDCs and SLSs), genetically, structurally, and functionally atypical β-hemolysins have been observed in AGS and MGS. These atypical β-hemolysins are thought to affect and contribute to the pathogenic potential of opportunistic streptococci mainly inhabiting the human oral cavity. In this review, we introduce the diverse characteristics of β-hemolysin produced by opportunistic streptococci, focusing on the species/strains belonging to AGS and MGS, and discuss their pathogenic potential.
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Affiliation(s)
- Atsushi Tabata
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hideaki Nagamune
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
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16
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Nix ID, Idelevich EA, Schlattmann A, Sparbier K, Kostrzewa M, Becker K. MALDI-TOF Mass Spectrometry-Based Optochin Susceptibility Testing for Differentiation of Streptococcus pneumoniae from other Streptococcus mitis Group Streptococci. Microorganisms 2021; 9:microorganisms9102010. [PMID: 34683331 PMCID: PMC8537049 DOI: 10.3390/microorganisms9102010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Discrimination of Streptococcus pneumoniae from other Streptococcus mitis group (SMG) species is still challenging but very important due to their different pathogenic potential. In this study, we aimed to develop a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based optochin susceptibility test with an objective read-out. Optimal test performance was established and evaluated by testing consecutively collected respiratory isolates. Optochin in different concentrations as a potential breakpoint concentration was added to a standardized inoculum. Droplets of 6 µL with optochin and, as growth control, without optochin were spotted onto a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard. Spectra were acquired, and results were interpreted as S. pneumoniae in the case of optochin susceptibility (no growth), or as non-S. pneumoniae in the case of optochin non-susceptibility (growth). Highest test accuracy was achieved after 20 h incubation time (95.7%). Rapid testing after 12 h incubation time (optochin breakpoint 2 µg/mL; correct classification 100%, validity 62.5%) requires improvement by optimization of assay conditions. The feasibility of the MALDI-TOF MS-based optochin susceptibility test was demonstrated in this proof-of-principle study; however, confirmation and further improvements are warranted.
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Affiliation(s)
- Ilka D. Nix
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Evgeny A. Idelevich
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Andreas Schlattmann
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
| | - Katrin Sparbier
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Markus Kostrzewa
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
- Correspondence: ; Tel.: +49-3834-86-5560
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Gisch N, Peters K, Thomsen S, Vollmer W, Schwudke D, Denapaite D. Commensal Streptococcus mitis produces two different lipoteichoic acids of type I and type IV. Glycobiology 2021; 31:1655-1669. [PMID: 34314482 DOI: 10.1093/glycob/cwab079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 11/14/2022] Open
Abstract
The opportunistic pathogen Streptococcus mitis possesses, like other members of the Mitis group of viridans streptococci, phosphorylcholine (P-Cho)-containing teichoic acids (TAs) in its cell wall. Bioinformatic analyses predicted the presence of TAs that are almost identical with those identified in the pathogen S. pneumoniae, but a detailed analysis of S. mitis lipoteichoic acid (LTA) was not performed to date. Here we determined the structures of LTA from two S. mitis strains, the high-level beta-lactam and multiple antibiotic resistant strain B6 and the penicillin-sensitive strain NCTC10712. In agreement with bioinformatic predictions we found that the structure of one LTA (type IV) was like pneumococcal LTA, except the exchange of a glucose moiety with a galactose within the repeating units. Further genome comparisons suggested that the majority of S. mitis strains should contain the same type IV LTA as S. pneumoniae, providing a more complete understanding of the biosynthesis of these P-Cho-containing TAs in members of the Mitis group of streptococci. Remarkably, we observed besides type IV LTA an additional polymer belonging to LTA type I in both investigated S. mitis strains. This LTA consists of β-galactofuranosyl-(1,3)-diacylglycerol as glycolipid anchor and a poly-glycerol-phosphate chain at the O-6 position of the furanosidic galactose. Hence, these bacteria are capable of synthesizing two different LTA polymers, most likely produced by distinct biosynthesis pathways. Our bioinformatics analysis revealed the prevalence of the LTA synthase LtaS, most probably responsible for the second LTA version (type I), amongst S. mitis and S. pseudopneumoniae strains.
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Affiliation(s)
- Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Simone Thomsen
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany.,German Center for Infection Research (DZIF), Thematic Translational Unit Tuberculosis, Partner Site: Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
| | - Dalia Denapaite
- Department of Microbiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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Jensen CS, Dargis R, Shewmaker P, Nielsen XC, Christensen JJ. Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry. Diagn Microbiol Infect Dis 2021; 101:115487. [PMID: 34339919 DOI: 10.1016/j.diagmicrobio.2021.115487] [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: 01/27/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022]
Abstract
This study evaluated the ability of the MALDI-ToF MS from Bruker Daltonics to identify clinical Mitis-Group-Streptococcus isolates with a focus on Streptococcus pseudopneumoniae. The results were analyzed using the standard log(score) and the previously published list(score). Importantly, using the log(score) no misidentifications occurred and 27 of 29 (93%) S. pneumoniae and 27 of 30 (90%) S. oralis strains were identified, but only 1 of 31 (3%) S. pseudopneumoniae and 1 of 13 (8%) S. mitis strains were identified. However, our results show that 30 of 31 S. pseudopneumoniae strains had a S. pseudopneumoniae Main Spectral Profiles within the 3 best matches. Using the list(score) all S. oralis and S. pneumoniae strains were identified correctly, but list(score) misidentified 10 S. pseudopneumoniae and 5 S. mitis. We propose to use the log(score) for identification of S. pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis, but for some strains additional testing may be needed.
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Affiliation(s)
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | | | | | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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Liu D, Xiao C, Li X, Sun Y, Qi H, Zou Y. Streptococcus shenyangsis sp. nov., a New Species Isolated from the Oropharynx of a Healthy Child from Shenyang China. Curr Microbiol 2021; 78:2821-2827. [PMID: 34031726 DOI: 10.1007/s00284-021-02500-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2021] [Indexed: 12/25/2022]
Abstract
A Gram-positive, catalase-negative, coccus-shaped, chain-forming organism isolated from the oropharynx of a healthy child in Shenyang, China, was subjected to phenotypic and molecular taxonomic analyses. 16S rRNA sequence analysis indicated that this bacterium represents a new member of the genus Streptococcus and is closely related to Streptococcus oralis subsp. dentisani DSM 27088. According to DNA-DNA hybridization analysis, strain D19T was less than 70% similar to other strains with close genetic relationships. Fatty acid analysis, physiological, and biochemical tests showed that strain D19T was different from the published Streptococcus species. The genome of strain D19T is 2,023,003 bp long with a GC content of 39.9 mol%. It contains 1889 protein-coding genes and 50 RNA genes. These results show that Streptococcus shenyangsis sp. nov. strain D19T is a new species.
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Affiliation(s)
- Defeng Liu
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China
| | - Chunling Xiao
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China.
| | - Xinming Li
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China
| | - Ye Sun
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China
| | - He Qi
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China
| | - Yang Zou
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, People's Republic of China
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Volokhov DV, Zagorodnyaya TA, Shen Z, Blom J, Furtak VA, Eisenberg T, Fan P, Jeong KC, Gao Y, Zhang S, Amselle M. Streptococcus vicugnae sp. nov., isolated from faeces of alpacas ( Vicugna pacos) and cattle ( Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions ( Zalophus californianus). Int J Syst Evol Microbiol 2021; 71. [PMID: 33999792 DOI: 10.1099/ijsem.0.004826] [Citation(s) in RCA: 6] [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
Four novel independent strains of Streptococcus spp. were isolated from faeces of alpaca (SL1232T), cattle (KCJ4950), and from respiratory tract of wild California sea lions (CSL7508T, CSL7591T). The strains were indole-, oxidase- and catalase-negative, non-spore-forming, non-motile Gram-positive cocci in short and long chains, facultative anaerobes. The 16S rRNA gene of SL1232T and KCJ4950 shared 99.40-99.60% nucleotide similarity to strains of S. equinus, S. lutetiensis, S. infantarius, and the 16S rRNA gene of CSL7508T and CSL7591T demonstrated 98.72 and 98.92% similarity, respectively, to S. marimammalium. All other known Streptococcus species had the 16S rRNA gene sequence similarities of ≤95%. The genomes were sequenced for the novel strains. Average nucleotide identity (ANI) analysis for strains SL1232T and KCJ4950, showed the highest similarity to S. equinus, S. lutetiensis, and S. infantarius with 85.21, 87.17, 88.47, 85.54, 87.47 and 88.89%, respectively, and strains CSL7508T and CSL7591T to S. marimammalium with 87.16 and 83.97%, respectively. Results of ANI were confirmed by pairwise digital DNA-DNA hybridization and phylogeny, which also revealed that the strains belong to three novel species of the genus Streptococcus. Phenotypical features of the novel species were in congruence with closely related members of the genus Streptococcus and gave negative reactions with the tested Lancefield serological groups (A-D, F and G). MALDI-TOF mass spectrometry supported identification of the species. Based on these data, we propose three novel species of the genus Streptococcus, for which the name Streptococcus vicugnae sp. nov. is proposed with the type strain SL1232T (=NCTC 14341T=DSM 110741T=CCUG 74371T), Streptococcus zalophi sp. nov. is proposed with the type strain CSL7508T (=NCTC 14410T=DSM 110742T=CCUG 74374T) and Streptococcus pacificus sp. nov. is proposed with the type strain CSL7591T (=NCTC 14455T=DSM 111148T=CCUG 74655T). The genome G+C content is 36.89, 34.85, and 35.34 % and draft genome sizes are 1906993, 1581094 and 1656080 bp for strains SL1232T, CSL7508T, and CSL7591T, respectively.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Zhenyu Shen
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392, Giessen, Germany
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Frankfurter Strasse 89-91, 35392 Giessen, Germany.,Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392, Giessen, Germany
| | - Peixin Fan
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Kwangcheol Casey Jeong
- Department of Animal Sciences, Emerging Pathogens Institute, University of Florida, 2055 Mowry Road, Gainesville, FL 32611, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Shuping Zhang
- Department of Veterinary Pathobiology, Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 East Campus Loop, Columbia, MO 65211, USA
| | - Megan Amselle
- American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
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21
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Description of optochin-resistant Streptococcus pneumoniae due to an uncommon mutation in the atpA gene and comparison with previously identified atpC mutants from Brazil. Sci Rep 2021; 11:7936. [PMID: 33846478 PMCID: PMC8041871 DOI: 10.1038/s41598-021-87071-8] [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: 12/05/2020] [Accepted: 03/15/2021] [Indexed: 11/09/2022] Open
Abstract
Optochin susceptibility testing is a major assay used for presumptive identification of Streptococcus pneumoniae. Still, atypical optochin-resistant (Optr) pneumococci have been reported and this phenotype has been attributed to nucleotide substitutions in the genes coding for the F0F1ATPase. While substitutions in the atpC gene (c-subunit of ATPase) are more common and better characterized, data on mutations in the atpA (a-subunit) are still limited. We have characterized five Optr isolates presenting alterations in the atpA (Trp206Cys in four isolates and Trp206Ser in one isolate), constituting the first report of such mutations in Brazil. Most of the Optr isolates consisted of heterogeneous populations. Except for Opt MICs and the nucleotide changes in the atpA gene, Optr and Opts subpopulations originating from the same culture had identical characteristics. In addition, we compared phenotypic and genetic characteristics of these atpA mutants with those of atpC mutants previously identified in Brazil. No structural alterations were detected among predicted proteins, regardless of mutations in the coding gene, suggesting that, despite the occurrence of mutations, protein structures tend to be highly conserved, ensuring their functionalities. Phylogenetic analysis revealed that atypical Optr strains are true pneumococci and Opt resistance does not represent any apparent selective advantage for clinical isolates.
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The Formation of Biofilm and Bacteriology in Otitis Media with Effusion in Children: A Prospective Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073555. [PMID: 33808050 PMCID: PMC8037871 DOI: 10.3390/ijerph18073555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Otitis media with effusion (OME) can cause serious complications such as hearing impairment or development delays. The aim of the study was to assess the microbiological profile of organisms responsible for OME and to determine if a biofilm formation can be observed. METHODS Ninety-nine samples from 76 patients aged from 6 months to 12 years were collected for microbiological and molecular studies. RESULTS In microbiological studies, pathogenic bacteria Haemophilus influenzae (38.89%), Streptococcus pneumoniae (33.33%), and Staphylococcus aureus MSSA (27.78%), as well as opportunistic bacteria Staphylococcus spp. (74.14%), Diphtheroids (20.69%), Streptococcus viridans (3.45%), and Neisseria spp. (1.72%) were found. The average degree of hearing loss in the group of children with positive bacterial culture was 35.9 dB, while in the group with negative bacterial culture it was 25.9 dB (p = 0.0008). The type of cultured bacteria had a significant impact on the degree of hearing impairment in children (p = 0.0192). In total, 37.5% of Staphylococcus spp. strains were able to form biofilm. CONCLUSIONS Staphylococcus spp. in OME may form biofilms, which can explain the chronic character of the disease. Pathogenic and opportunistic bacteria may be involved in the etiopathogenesis of OME. The degree of hearing loss was significantly higher in patients from which the positive bacterial cultures were obtained.
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Reslan L, Finianos M, Bitar I, Moumneh MB, Araj GF, Zaghlout A, Boutros C, Jisr T, Nabulsi M, Kara Yaccoub G, Hamze M, Osman M, Bou Raad E, Hrabak J, Matar GM, Dbaibo G. The Emergence of Invasive Streptococcus pneumoniae Serotype 24F in Lebanon: Complete Genome Sequencing Reveals High Virulence and Antimicrobial Resistance Characteristics. Front Microbiol 2021; 12:637813. [PMID: 33746930 PMCID: PMC7967862 DOI: 10.3389/fmicb.2021.637813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Background Invasive pneumococcal disease (IPD) remains a global health problem. IPD incidence has significantly decreased by the use of pneumococcal conjugate vaccines (PCV). Nevertheless, non-PCV serotypes remain a matter of concern. Eight Streptococcus pneumoniae serotype 24F isolates, belonging to a non-PCV serotype, were detected through the Lebanese Inter-Hospital Pneumococcal Surveillance Program. The aim of the study is to characterize phenotypic and genomic features of the 24F isolates in Lebanon. Methods WGS using long reads sequencing (PacBio) was performed to produce complete circular genomes and to determine clonality, antimicrobial resistance and virulence determinants. Results The sequencing results yielded eight closed circular genomes. Three multilocus sequence typing (MLST) types were identified (ST11618, ST14184, ST15253). Both MLST and WGS analyses revealed that these isolates from Lebanon were genetically homogenous belonging to clonal complex CC230 and clustered closely with isolates originating from Canada, United States of America, United Kingdom and Iceland. Their penicillin binding protein profiles correlated with both β-lactam susceptibility patterns and MLST types. Moreover, the isolates harbored the macrolide and tetracycline resistance genes and showed a similar virulence gene profile. To our knowledge, this study represents the first report of complete phenotypic and genomic characterization of the emerging Streptococcus pneumoniae, serotype 24F, in the Middle East and North Africa region.
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Affiliation(s)
- Lina Reslan
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Mohamad Bahij Moumneh
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - George F Araj
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Alissar Zaghlout
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Celina Boutros
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon
| | - Tamima Jisr
- Department of Laboratory and Blood, Makassed General Hospital, Beirut, Lebanon
| | | | | | - Monzer Hamze
- Department of Microbiology, Nini Hospital, Tripoli, Lebanon
| | - Marwan Osman
- El-Youssef Hospital Center, Department of Clinical Laboratory, Halba, Lebanon
| | - Elie Bou Raad
- El-Youssef Hospital Center, Department of Clinical Laboratory, Halba, Lebanon
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
| | - Ghassan M Matar
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens, American University of Beirut, Beirut, Lebanon.,Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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24
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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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25
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Matsumoto A, Tabata A, Ohkura K, Oda H, Kodama C, Ohkuni H, Takao A, Kikuchi K, Tomoyasu T, Nagamune H. Molecular characteristics of an adhesion molecule containing cholesterol-dependent cytolysin-motif produced by mitis group streptococci. Microbiol Immunol 2021; 65:61-75. [PMID: 33331679 DOI: 10.1111/1348-0421.12868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 01/06/2023]
Abstract
Streptococcus pseudopneumoniae (SPpn) is a relatively new species closely related to S. pneumoniae (SPn) and S. mitis (SM) belonging to the Mitis group of the genus Streptococcus (MGS). Although genes encoding various pneumococcal virulence factors have been observed in the SPpn genome, the pathogenicity of SPpn against human, including the roles of virulence factor candidates, is still unclear. The present study focused on and characterized a candidate virulence factor previously reported in SPpn with deduced multiple functional domains, such as lipase domain, two lectin domains, and cholesterol-dependent cytolysin-related domain using various recombinant proteins. The gene was found not only in SPpn but also in the strains of SM and SPn. Moreover, the gene product was expressed in the gene-positive strains as secreted and cell-bound forms. The recombinant of gene product showed lipase activity and human cell-binding activity depending on the function of lectin domain(s), but no hemolytic activity. Thus, based on the distribution of the gene within the MGS and its molecular function, the gene product was named mitilectin (MLC) and its contribution to the potential pathogenicity of the MLC-producing strains was investigated. Consequently, the treatment with anti-MLC antibody and the mlc gene-knockout significantly reduced the human cell-binding activity of MLC-producing strains. Therefore, the multifunctional MLC was suggested to be important as an adhesion molecule in considering the potential pathogenicity of the MLC-producing strains belonging to MGS, such as SPpn and SM.
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Affiliation(s)
- Airi Matsumoto
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Tokushima, Japan
| | - Atsushi Tabata
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Tokushima, Japan
| | - Kazuto Ohkura
- Division of Clinical Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Mie, Japan
| | - Hiroki Oda
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Tokushima, Japan
| | - Chihiro Kodama
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Tokushima, Japan
| | - Hisashi Ohkuni
- Health Science Research Institute East Japan, Kounosu, Saitama, Japan
| | - Ayuko Takao
- Department of Oral Microbiology, School of Dental Medicine, Tsurumi University, Yokohama, Kanagawa, Japan
| | - Ken Kikuchi
- Department of Infectious Diseases, Tokyo Women's Medical University, Shinjyuku-ku, Tokyo, Japan
| | - Toshifumi Tomoyasu
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Tokushima, Japan
| | - Hideaki Nagamune
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.,Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Tokushima, Japan
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Qi H, Liu D, Zou Y, Wang N, Tian H, Xiao C. Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. Antonie van Leeuwenhoek 2021; 114:113-127. [PMID: 33387140 PMCID: PMC7878260 DOI: 10.1007/s10482-020-01505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Using the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).
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Affiliation(s)
- He Qi
- Liaoning University of Traditional Chinese Medicine, Shenyang, People's Republic of China
- Department of Medical technology, Medical Science Institute of Liaoning, Shenyang, People's Republic of China
| | - Defeng Liu
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Yang Zou
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Nan Wang
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Han Tian
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Chunling Xiao
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China.
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27
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Mosadegh M, Asadian R, Emamie AD, Rajabpour M, Najafinasab E, Azarsa M. Impact of Laboratory Methods and Gene Targets on Detection of Streptococcus pneumoniae in Isolates and Clinical Specimens. Rep Biochem Mol Biol 2020; 9:216-222. [PMID: 33178872 DOI: 10.29252/rbmb.9.2.216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Background Timely identification of Streptococcus pneumoniae infections can lead to a decrease in mortality rates. Differentiation of S. pneumoniae from other similar species using traditional culture-based and molecular methods is problematic. In this study, we assessed the efficacy of identifying the blpA and lytA for the detection of S. pneumoniae from isolates and various clinical samples using molecular methods. Methods A total of 440 clinical samples were collected from patients with suspected invasive pneumococcal infections during February 2016 to October 2018. Biochemical tests were used to confirm the dubious colonies on 5% sheep blood agar. Fifty-seven confirmed isolates, 57 culture-positive samples, and 57 culture-negative samples were analyzed for the presence of blpA and lytA using both conventional and real-time PCR. Results All the isolates and culture-positive samples were positive for blpA and lytA by both PCR methods. Of the 57 culture-negative samples, conventional and real-time PCR amplified blpA from six and two samples, and lytA from seven and two samples, respectively. Conclusion The specificity of real-time PCR assay was significantly higher than that of conventional PCR for the identification of S. pneumoniae. In addition, it is suggested that respiratory secretions are not suitable specimen for direct diagnosis of pneumococcal infections.
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Affiliation(s)
- Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Rozita Asadian
- Department of Medical Laboratory Sciences, School of Paramedicine, Guilan University of Medical Sciences, Langeroud, Iran
| | - Amir Darb Emamie
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Rajabpour
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Elmira Najafinasab
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
| | - Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
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28
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Kosecka-Strojek M, Wolska M, Żabicka D, Sadowy E, Międzobrodzki J. Identification of Clinically Relevant Streptococcus and Enterococcus Species Based on Biochemical Methods and 16S rRNA, sodA, tuf, rpoB, and recA Gene Sequencing. Pathogens 2020; 9:pathogens9110939. [PMID: 33187333 PMCID: PMC7696602 DOI: 10.3390/pathogens9110939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococci and enterococci are significant opportunistic pathogens in epidemiology and infectious medicine. High genetic and taxonomic similarities and several reclassifications within genera are the most challenging in species identification. The aim of this study was to identify Streptococcus and Enterococcus species using genetic and phenotypic methods and to determine the most discriminatory identification method. Thirty strains recovered from clinical samples representing 15 streptococcal species, five enterococcal species, and four nonstreptococcal species were subjected to bacterial identification by the Vitek® 2 system and Sanger-based sequencing methods targeting the 16S rRNA, sodA, tuf, rpoB, and recA genes. Phenotypic methods allowed the identification of 10 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains (Leuconostoc, Granulicatella, and Globicatella genera). The combination of sequencing methods allowed the identification of 21 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains. The 16S rRNA and rpoB genes had the highest identification potential. Only a combination of several molecular methods was sufficient for unambiguous confirmation of species identity. This study will be useful for comparison of several identification methods, both those used as a first choice in routine microbiology and those used for final confirmation.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
- Correspondence: ; Tel.: +48-12-664-6365
| | - Mariola Wolska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
| | - Dorota Żabicka
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Ewa Sadowy
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
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Zou Y, Sun Y, Qi H, Liu D, Tian H, Wang N, Li X. Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children. Front Microbiol 2020; 11:563213. [PMID: 33133039 PMCID: PMC7550633 DOI: 10.3389/fmicb.2020.563213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, α-hemolytic, catalase-negative, facultative anaerobic and non-motile coccus was isolated form throat swabs taken from the oropharynx of healthy children. The genome was shown to be 1.950,659 bp long and contained 42.03 mol% G + C bases with 1,942 protein-coding and 53 RNA coding genes. The results of 16S rRNA gene sequencing strongly suggested that the strain is a member of the Streptococcus genus, with 98.04, 98.11, and 97.34% similarities to Streptococcus australis ATCC 700641T, Streptococcus rubneri LMG 27207T and Streptococcus parasanguinis ATCC 15912T, respectively. A sodA gene comparison exhibited a sequence identity of 92.6% with the closest strain Streptococcus australis ATCC 700641T. In silico DNA-DNA hybridization showed a highest DNA similarity value of 52% with Streptococcus australis ATCC 700641T. Comparing 18 biochemical traits, the similarities of the Streptococcus strain E24 were 72% with Streptococcus rubneri LMG 27207T, 78% with Streptococcus australis ATCC 700641T and 44% with Streptococcus parasanguinis ATCC 15912T. We suggest that based on the genotypic and phenotypic results that the strain E24 is a novel species of the Streptococcus genus and propose the name Streptococcus xiaochunlingii sp. nov. E24.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Ye Sun
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - He Qi
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Defeng Liu
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Han Tian
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Nan Wang
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Xinming Li
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
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30
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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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Cytotoxic property of Streptococcus mitis strain producing two different types of cholesterol-dependent cytolysins. INFECTION GENETICS AND EVOLUTION 2020; 85:104483. [PMID: 32731044 DOI: 10.1016/j.meegid.2020.104483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023]
Abstract
Streptococcus mitis strain Nm-65 secretes an atypical 5-domain-type cholesterol-dependent cytolysin (CDC) called S. mitis-derived human platelet aggregation factor (Sm-hPAF) originally described as a platelet aggregation factor. Sm-hPAF belongs to Group III CDC that recognize both membrane cholesterol and human CD59 as the receptors, and shows preferential activity towards human cells. Draft genome analyses have shown that the Nm-65 strain also harbors a gene encoding another CDC called mitilysin (MLY). This CDC belongs to Group I CDC that recognizes only membrane cholesterol as a receptor, and it is a homolog of the pneumococcal CDC, pneumolysin. The genes encoding each CDC are located about 20 kb apart on the Nm-65 genome. Analysis of the genomic locus of these CDC-encoding genes in silico showed that the gene encoding Sm-hPAF and the region including the gene encoding MLY were both inserted into a specific locus of the S. mitis genome. The results obtained using deletion mutants of the gene(s) encoding CDC in Nm-65 indicated that each CDC contributes to both hemolysis and cytotoxicity, and that MLY is the major hemolysin/cytolysin in Nm-65. The present study aimed to determine the potential pathogenicity of an S. mitis strain that produces two CDC with different receptor recognition properties and secretion modes.
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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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33
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Streptococcus downii sp. nov., isolated from the oral cavity of a teenager with Down syndrome. Int J Syst Evol Microbiol 2020; 70:4098-4104. [DOI: 10.1099/ijsem.0.004180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A new α-haemolytic streptococcal strain has been isolated from the dental plaque of a teenager with Down syndrome. Genetic and taxonomic analyses place this
Streptococcus
within the oralis group. It is a Gram-stain-positive, non-motile, non-spore-forming spherical alpha-haemolytic coccus arranged in chains, and it ferments a large number of monosaccharides and disaccharides, as well as polymeric carbohydrates. It differs biochemically from closely related species of
Streptococcus
due to its production of α-galactosidase, β-galactosidase and N-acetyl-β-d-glucosaminidase and by the absence of arginine dihydrolase deiminase and IgA1-protease. It grows in a temperature range of 25 to 40 °C (optimal growth temperature at 37 °C) and in a pH range of 4.5 to 8 (optimal pH at 7.0). A phylogenetic analysis based on its 16S and 23S rRNA gene sequences placed it close to
Streptococcus dentisani
CECT 7747T. The ANIb and ANIm values were 93.19 and 93.61 %, respectively, both below the accepted threshold to designate it as a new species of bacteria. A phylogenetic tree based on its core genome placed it close to
Streptococcus oralis
subsp.
dentisani
strain CECT 7747T with a distance in the expanded core phylogeny of 0.1298. The in silico DNA–DNA hybridization value was 52.2 % with respect to the closest species,
S. oralis
subsp.
dentisani
CECT 7747T. Based on these data, a new species of bacteria within the genus
Streptococcus
, family
Streptococcaceae
and order
Lactobacillales
is described, for which the name of Streptococcus downii sp. nov. is proposed (type strain CECT 9732T=CCUG 73139T).
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Gonzales-Siles L, Karlsson R, Schmidt P, Salvà-Serra F, Jaén-Luchoro D, Skovbjerg S, Moore ERB, Gomila M. A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Front Cell Infect Microbiol 2020; 10:222. [PMID: 32509595 PMCID: PMC7248185 DOI: 10.3389/fcimb.2020.00222] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/22/2020] [Indexed: 01/28/2023] Open
Abstract
Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the “Xisco” gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S. pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Patrik Schmidt
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Biology-Microbiology, Universitat de les Illes Balears, Palma, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Margarita Gomila
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma, Spain
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35
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Haddar CH, Joly J, Carricajo A, Verhoeven PO, Grattard F, Mory O, Begaud E, Germani Y, Cantais A, Pozzetto B. Strategy using a new antigenic test for rapid diagnosis of Streptococcus pneumoniae infection in respiratory samples from children consulting at hospital. BMC Microbiol 2020; 20:79. [PMID: 32264834 PMCID: PMC7137283 DOI: 10.1186/s12866-020-01764-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Despite vaccination programs, Streptococcus pneumoniae remains among the main microorganisms involved in bacterial pneumonia, notably in terms of severity. The prognosis of pneumococcal infections is conditioned in part by the precocity of the diagnosis. The aim of this study was to evaluate the impact of a Rapid Diagnostic Test (RDT) targeting cell wall polysaccharide of Streptococcus pneumoniae and performed directly in respiratory samples, on the strategy of diagnosis of respiratory pneumococcal infections in children. Results Upper-respiratory tract samples from 196 children consulting at hospital for respiratory infection were tested for detecting S. pneumoniae using a newly-designed RDT (PneumoResp, Biospeedia), a semi-quantitative culture and two PCR assays. If positive on fluidized undiluted specimen, the RDT was repeated on 1:100-diluted sample. The RDT was found highly specific when tested on non-S. pneumoniae strains. By comparison to culture and PCR assays, the RDT on undiluted secretions exhibited a sensitivity (Se) and negative predictive value (NPV) of more than 98%. By comparison to criteria of S. pneumoniae pneumonia combining typical symptoms, X-ray image, and culture ≥107 CFU/ml, the Se and NPV of RDT on diluted specimens were 100% in both cases. Conclusions In case of negative result, the excellent NPV of RDT on undiluted secretions allows excluding S. pneumoniae pneumonia. In case of positive result, the excellent sensitivity of RDT on diluted secretions for the diagnosis of S. pneumoniae pneumonia allows proposing a suitable antimicrobial treatment at day 0.
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Affiliation(s)
- Cyrille H Haddar
- GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes), University of Lyon, 42023, Saint-Etienne, France.,BioSpeedia, Institut Pasteur, 75015, Paris, France
| | - Johan Joly
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | - Anne Carricajo
- GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes), University of Lyon, 42023, Saint-Etienne, France.,Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | - Paul O Verhoeven
- GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes), University of Lyon, 42023, Saint-Etienne, France.,Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | - Florence Grattard
- GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes), University of Lyon, 42023, Saint-Etienne, France.,Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | - Olivier Mory
- Pediatric Emergency Department, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | | | - Yves Germani
- BioSpeedia, Institut Pasteur, 75015, Paris, France
| | - Aymeric Cantais
- Pediatric Emergency Department, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France
| | - Bruno Pozzetto
- GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes), University of Lyon, 42023, Saint-Etienne, France. .,Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, 42055, Saint-Etienne Cedex 02, France.
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36
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Development of a novel MALDI-TOF MS-based bile solubility test for rapid discrimination of Streptococcus pneumoniae. Int J Med Microbiol 2020; 310:151413. [PMID: 32089435 DOI: 10.1016/j.ijmm.2020.151413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
Differentiation of Streptococcus pneumoniae from other Streptococcus mitis group streptococci (SMGS) remains challenging despite the introduction of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). While the bile solubility test (BST) provides most reliable discrimination of pneumococci, its practical implementation is limited by subjective visual interpretation and frequent inconclusive results. We aimed to develop a rapid confirmation BST based on direct-on-target MALDI-TOF MS assay. After establishment of optimal test conditions, test performance was evaluated on 36 consecutive clinical SMGS isolates. Colony material was suspended and pipetted onto a MALDI target. After drying, sodium deoxycholate in different concentrations (2%, 5%, and 10 %) was added. Incubation for 30 min (at room temperature or 35 °C) was followed by liquid removal and spot washing. After adding 70 % formic acid, spots were overlaid with matrix and measured (MALDI Biotyper smart, Bruker). The absence of microbial spectra (Biotyper score <1.7) in samples with sodium deoxycholate indicated efficient removal of bacterial biomass due to bile solubility, thus, identifying pneumococci. In contrast, scores ≥1.7 were interpreted as lack of bile solubility and confirmation as viridans streptococci other than S. pneumoniae. Highest test accuracy was achieved applying 5% sodium deoxycholate at 35 °C and 10 % sodium deoxycholate at room temperature. These test conditions provided 100 % sensitivity and 100 % specificity for discrimination of S. pneumoniae. The developed MALDI-TOF MS-based BST is an easy-to-perform assay with minimum hands-on time and objective readout. The promising results of this proof-of-principle study warrant confirmation with large collections of epidemiologically diverse strains.
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37
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Farfour E, Degand N, Muggeo A, Marcelino P, Vasse M, Guillard T. Accurate identification of S. pneumoniae using MALDI-TOF mass spectrometry, still a challenge for clinical laboratories? Eur J Clin Microbiol Infect Dis 2020; 39:209-211. [DOI: 10.1007/s10096-019-03716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
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38
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Yahiaoui RY, Goessens WH, Stobberingh EE, Verbon A. Differentiation between Streptococcus pneumoniae and other viridans group streptococci by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Clin Microbiol Infect 2019; 26:1088.e1-1088.e5. [PMID: 31811915 DOI: 10.1016/j.cmi.2019.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/20/2019] [Accepted: 11/24/2019] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is becoming the method of choice for bacterial identification. However, correct identification by MALDI-TOF of closely related microorganisms such as viridans streptococci is still cumbersome, especially in the identification of S. pneumoniae. By making use of additional spectra peaks for S. pneumoniae and other viridans group streptococci (VGS). We re-identified viridans streptococci that had been identified and characterized by molecular and phenotypic techniques by MALDI-TOF. METHODS VGS isolates (n = 579), 496 S. pneumoniae and 83 non-S. pneumoniae were analysed using MALDI-TOF MS and the sensitivity and specificity of MALDI-TOF MS was assessed. Hereafter, mass spectra analysis was performed. Presumptive identification of proteins represented by discriminatory peaks was performed by molecular weight matching and the corresponding nucleotides sequences against different protein databases. RESULTS Using the Bruker reference library, 495 of 496 S. pneumoniae isolates were identified as S. pneumoniae and one isolate was identified as non-S. pneumoniae. Of the 83 non-S. pneumoniae isolates, 37 were correctly identified as non-S. pneumoniae, and 46 isolates as S. pneumoniae. The sensitivity of the MALDI-TOF MS was 99.8% (95% confidence interval (CI) 98.9-100) and the specificity was 44.6% (95% CI 33.7-55.9). Eight spectra peaks were mostly present in one category (S. pneumoniae or other VGS) and absent in the other category and inversely. Two spectra peaks of these (m/z 3420 and 3436) were selected by logistic regression to generate three identification profiles. These profiles could differentiate between S. pneumoniae and other VGS with high sensitivity and specificity (99.4% and 98.8%, respectively). CONCLUSIONS Spectral peaks analysis based identification is a powerful tool to differentiate S. pneumoniae from other VGS species with high specificity and sensitivity and is a useful method for pneumococcal identification in carriage studies. More research is needed to further confirm our findings. Extrapolation of these results to clinical strains need to be deeply investigated.
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Affiliation(s)
- R Y Yahiaoui
- Erasmus MC University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, the Netherlands; Haga Hospital, Medical Microbiology, The Hague, the Netherlands.
| | - W H Goessens
- Erasmus MC University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, the Netherlands
| | - E E Stobberingh
- Maastricht University Medical Centre/CAPHRI, Maastricht, the Netherlands
| | - A Verbon
- Erasmus MC University Medical Centre Rotterdam, Department of Medical Microbiology & Infectious Diseases, Rotterdam, the Netherlands
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39
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Streptococcus pseudopneumoniae, an opportunistic pathogen in patients with cystic fibrosis. J Cyst Fibros 2019; 19:e28-e31. [PMID: 31759908 DOI: 10.1016/j.jcf.2019.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 11/24/2022]
Abstract
The pathogenic power of Streptococcus pseudopneumoniae has been specified over years, particularly in case of chronic respiratory diseases; S. pseudopneumoniae isolation has however not been characterized before in CF patients. Identification of S. pseudopneumoniae remains challenging due to the high simila-rity level between species of the Streptococcus mitis group. Twenty CF patients with S. pseudopneumoniae were included. Isolates initially identified by phenotypic routine methods were subjected to both recA sequencing and amplification of S. pseudopneumoniae specific markers. Microbiological and clinical data were reviewed for patients with confirmed S. pseudopneumoniae. Thirteen isolates actually belong to S. pseudopneumoniae. S. pseudopneumoniae was associated with pulmonary exacerbation in 46% of the patients, either as the sole pathogen or as part of a polymicrobial infectious process. S. pseudopneumoniae has to be considered as an additional opportunistic pathogen in CF and additional studies are needed to increase knowledge of its epidemiology and clinical significance in CF.
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40
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Ullberg M, Özenci V. Identification and antimicrobial susceptibility testing of Gram-positive and Gram-negative bacteria from positive blood cultures using the Accelerate Pheno™ system. Eur J Clin Microbiol Infect Dis 2019; 39:139-149. [PMID: 31641972 PMCID: PMC6962126 DOI: 10.1007/s10096-019-03703-y] [Citation(s) in RCA: 10] [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: 06/11/2019] [Accepted: 09/04/2019] [Indexed: 12/03/2022]
Abstract
Rapid identification and antimicrobial susceptibility testing remain a crucial step for early efficient therapy of bloodstream infections. Traditional methods require turnaround times of at least 2 days, while rapid procedures are often associated with extended hands-on time. The Accelerate Pheno™ System provides microbial identification results within 90 min and susceptibility data in approximately 7 h directly from positive blood cultures with only few minutes of hands-on time. The aim of this study was, therefore, to evaluate the performance of the Accelerate Pheno™ System in identification and antimicrobial susceptibility testing of both Gram-positive and Gram-negative bacteria directly from clinical blood culture samples. We analyzed 108 and 67 blood culture bottles using the Accelerate PhenoTest™ BC kit with software version v1.0 and the FDA-cleared version v1.2, respectively. Reliable identification was achieved for Enterobacteriaceae, staphylococci, and enterococci, with 76/80 (95%), 42/46 (91%), and 10/11 (91%) correct identifications. Limitations were observed in the identification of streptococci, including Streptococcus pneumoniae and Streptococcus pyogenes, and coagulase-negative staphylococci. Antimicrobial susceptibility results for Enterobacteriaceae, for amikacin, ertapenem, ciprofloxacin, gentamicin, meropenem, and piperacillin-tazobactam ranged between 86 and 100% categorical agreement. Using v1.2, results for ceftazidime showed 100% concordance with the reference method. For staphylococci, the overall performance reached 92% using v1.2. Qualitative tests for detection of methicillin or macrolide-lincosamide-streptogramin B (MLSB) resistance caused major and very major errors for isolates. Overall, the present data show that the Accelerate Pheno™ system can, in combination with Gram stain, be used as a rapid complementation to standard microbial diagnosis of bloodstream infections.
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Affiliation(s)
- Måns Ullberg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
| | - Volkan Özenci
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden.
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Lim YK, Park SN, Shin JH, Ji S, Jo E, Chang YH, Shin Y, Paek J, Kim H, Kook JK. Streptococcus koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion. Curr Microbiol 2019; 76:1531-1536. [PMID: 31570960 DOI: 10.1007/s00284-019-01778-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/18/2019] [Indexed: 01/29/2023]
Abstract
A novel facultative anaerobic, Gram-stain-positive coccus, strain JS71T, was isolated from the human subgingival dental plaque of a periodontitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence had high similarity with Streptococcus rubneri DSM 26920T (98.6%), Streptococcus parasanguinis ATCC 15912T (98.5%), and Streptococcus australis CCUG 45919T (98.3%). The genome of strain JS71T was 2,009,592 bp in length. The DNA G+C content of the strain was 42.1 mol%. Average nucleotide identity values between strain JS71T and S. rubneri DSM 26920T, S. parasanguinis ATCC 15912T, and S. australis CCUG 45919T were 88.9%, 80.8%, and 92.4%, respectively. Genome-to-genome distance values between strain JS71TS. rubneri DSM 26920T, S. parasanguinis ATCC 15912T, and S. australis CCUG 45919T were 36.5% (34-39%), 26.3% (23.9-28.7%), and 48.0% (45.4-50.6%), respectively. The major fatty acids of the strain were C16:0 (39.7%), C18:1 ω6c/C18:1 ω7c (15.5%), and C18:0 (10.4%). Based on these results, strain JS71T (= KCOM 2890T = JCM 33454T) should be a novel species of the genus Streptococcus, for which the name Streptococcus koreensis sp. nov. is proposed.
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Affiliation(s)
- Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Suk Ji
- Department of Periodontics, Institute of Oral Health Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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Peela SCM, Sistla S, Tamilarasu K, Krishnamurthy S, Adhishivam B. Validation of pneumococcal iron acquisition ( piaA) gene for accurate identification of Streptococcus pneumoniae. Indian J Med Microbiol 2019; 36:504-507. [PMID: 30880696 DOI: 10.4103/ijmm.ijmm_18_274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose The pneumococcal iron acquisition (piaA) gene is found to be highly specific and hence proposed as a diagnostic marker for identification of pneumococci. The objective of the present study was to evaluate the piaA gene as a genetic marker for the identification of pneumococci. Methods Twenty isolates were initially sequenced for lytA gene using published primers. PiaA-PCR (piaA polymerase chain reaction) was performed using in-house primers and protocol. Based on the sensitivity and specificity results, a final sample of 30 pneumococcal isolates and 11 non-pneumococcal isolates confirmed with lytA- sequencing were selected. Statistical analyses were performed using OpenEpi v3.01 and GraphPad Quickcalc at P < 0.05 as the level of statistical significance. Results Of the initial 20 samples tested, piaA PCR was positive in only 71.43% (10/14) of the pneumococcal isolates but was 100% specific (0/6 non-pneumococcal isolates) P = 0.011. When the PCR was performed on 41 samples, the sensitivity increased to 73.33% (95% of confidence interval [CI] = 55.55-85.82) and specificity remained the same P < 0.001. The level of agreement between the PCR and lytA-sequencing was found to be moderate (κ = 0.694; 95% CI = 0.432-0.955). Conclusions PiaA-PCR can be used as a specific marker for the identification of pneumococcus, though it is less sensitive. As the level of agreement was moderate, further analyses on a large number of samples can give conclusive evidence for its use as a diagnostic marker for pneumococcus.
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Affiliation(s)
- Sreeram Chandra Murthy Peela
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Sujatha Sistla
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Kadhiravan Tamilarasu
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Sriram Krishnamurthy
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - B Adhishivam
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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Streptococcus chosunense sp. nov., Isolated from Human Postoperative Maxillary Cyst. Curr Microbiol 2019; 76:1193-1198. [PMID: 31332483 DOI: 10.1007/s00284-019-01746-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/13/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
Abstract
A novel facultative anaerobic, non-spore forming, non-motile, and Gram-stain-positive coccus, designated strain ChDC B353T, was isolated from human postoperative maxillary cyst. The 16S ribosomal RNA gene (16S rDNA) sequence of the strain was most closely related to those of Streptococcus pseudopneumoniae ATCC BAA-960T (99.4%), Streptococcus mitis NCTC 12261T (99.3%), and Streptococcus pneumoniae NCTC 7465T (99.2%). The major fatty acids of the strain were C16:0 (43.2%) and C18:1 ω6c/C18:1 ω7c (20.2%). The genome of strain ChDC B353T was composed of 1,902,053 bps. The DNA G+C content of the strain was 40.2 mol%. Average nucleotide identity (ANI) values between strain ChDC B353T and S. pseudopneumoniae ATCC BAA-960T, S. mitis NCTC 12261T, and S. pneumoniae NCTC 7465T were 91.9%, 93.5%, and 91.3%, respectively. Genome-to-genome distance (GGD) values between strain ChDC B353T and S. pseudopneumoniae ATCC BAA-960T, S. mitis NCTC 12261T, or S. pneumoniae NCTC 7465T were 46.6% (44.0-49.2%), 53.2% (50.5-55.9%), and 46.0% (43.5-48.7%), respectively. The threshold values of ANI and GGD for species discrimination are 95-96% and 70%, respectively. These results reveal that strain ChDC B353T (= KCOM 1699T = JCM 33453T) is a novel species belonging to genus Streptococcus, for which a name of Streptococcus chosunense sp. nov. is proposed.
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44
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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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Abstract
S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae. Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.
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46
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Streptococcus gwangjuense sp. nov., Isolated from Human Pericoronitis. Curr Microbiol 2019; 76:799-803. [PMID: 31028412 DOI: 10.1007/s00284-019-01687-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 10/26/2022]
Abstract
A novel facultative anaerobic, Gram-stain-negative coccus, designated strain ChDC B345T, was isolated from human pericoronitis lesion and was characterized by polyphasic taxonomic analysis. The 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence of strain ChDC B345T was most closely related to those of Streptococcus mitis NCTC 12261T (99.5%) and Streptococcus pseudopneumoniae ATCC BAA-960T (99.5%). Complete genome of strain ChDC B345T was 1,972,471 bp in length and the G + C content was 40.2 mol%. Average nucleotide identity values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 92.17% and 93.63%, respectively. Genome-to-genome distance values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 47.8% (45.2-50.4%) and 53.0% (51.0-56.4%), respectively. Based on these results, strain ChDC B345T (= KCOM 1679T = JCM 33299T) should be classified as a novel species of genus Streptococcus, for which we propose the name Streptococcus gwangjuense sp. nov.
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47
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Kavalari ID, Fuursted K, Krogfelt KA, Slotved HC. Molecular characterization and epidemiology of Streptococcus pneumoniae serotype 24F in Denmark. Sci Rep 2019; 9:5481. [PMID: 30940899 PMCID: PMC6445336 DOI: 10.1038/s41598-019-41983-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/21/2019] [Indexed: 12/29/2022] Open
Abstract
Since 2012, have we in Denmark observed an increase of invasive pneumococcal infections (IPD) due to Streptococcus pneumoniae serotype 24F. We here present epidemiological data on 24F IPD cases, and characterization of 48 24F clinical isolates based on clonal relationship, antimicrobial resistance (AMR) determinants and virulence factors. IPD surveillance data from (1999-2016) were used to calculate the incidence and age-distribution of serotype 24F IPD and the effect of pneumococcal conjugated vaccines (PCV). Characterization of forty-eight 24F isolates (14.7% of all 24F isolates from the period) was based on whole-genome sequencing analysis (WGS). The IPD cases of serotype 24F showed a significant increase (p < 0.05) for all age groups after the PCV-13 introduction in 2010. The majority of tested 24F isolates consisted of two MLST types, i.e. the ST72 and the ST162. Serotype 24F IPD increased in Denmark after the PCV-13 introduction in parallel with an increase of the ST162 clone. The genotypic penicillin binding protein (PBP) profile agreed with the phenotypical penicillin susceptibility. The virulence genes lytA, ply, piaA, piaB, piaC, rspB and the cpsA/wzg were detected in all 24F isolates, while the pspA and zmpC genes were absent.
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Affiliation(s)
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - H-C Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
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48
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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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van Schaik ML, Duijkers R, Paternotte N, Jansen R, Rozemeijer W, van der Reijden WA, Boersma WG. Feasibility of a quantitative polymerase chain reaction assay for diagnosing pneumococcal pneumonia using oropharyngeal swabs. Mol Biol Rep 2019; 46:1013-1021. [PMID: 30569391 PMCID: PMC7089193 DOI: 10.1007/s11033-018-4558-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is the most important pathogen causing community-acquired pneumonia (CAP). The current diagnostic microbial standard detects S. pneumoniae in less than 30% of CAP cases. A quantitative polymerase chain reaction (PCR) targeting autolysin (lytA) is able to increase the rate of detection. The aim of this study is validation of this quantitative PCR in vitro using different available strains and in vivo using clinical samples (oropharyngeal swabs). The PCR autolysin (lytA) was validated by testing the intra- and inter-run variability. Also, the in vitro specificity and sensitivity, including the lower limit of detection was determined. In addition, a pilot-study was performed using samples from patients (n = 28) with pneumococcal pneumonia and patients (n = 28) with a pneumonia without detection of S. pneumoniae with the current diagnostic microbial standard, but with detection of either a viral and or another bacterial pathogen to validate this test further. The intra- and inter-run variability were relatively low (SD's ranging from 0.08 to 0.96 cycle thresholds). The lower limit of detection turned out to be 1-10 DNA copies/reaction. In-vitro sensitivity and specificity of the tested specimens (8 strains carrying lytA and 6 strains negative for lytA) were both 100%. In patients with pneumococcal and non-pneumococcal pneumonia a cut-off value of 6.000 copies/mL would lead to a sensitivity of 57.1% and a specificity of 85.7%. We were able to develop a quantitative PCR targeting lytA with good in-vitro test characteristics.
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Affiliation(s)
- M L van Schaik
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
- Department of Pulmonology, Isala clinics Zwolle, Dr. van Heesweg 2, 8025AB, Zwolle, The Netherlands
| | - R Duijkers
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - N Paternotte
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - R Jansen
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W Rozemeijer
- Department Medical Microbiology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands
| | - W A van der Reijden
- Department Molecular Biology, Regional Laboratory for Medical Microbiology and Public Health, Haarlem, The Netherlands
| | - W G Boersma
- Department Pulmonology, Noordwest Ziekenhuisgroep, Alkmaar, The Netherlands.
- Department of Pulmonary Diseases, Northwest Hospital Group, P.O. Box 501, 1800AM, Alkmaar, The Netherlands.
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50
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Croxen MA, Lee TD, Azana R, Hoang LM. Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Microb Genom 2018; 4:e000175. [PMID: 29629856 PMCID: PMC6113875 DOI: 10.1099/mgen.0.000175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The S. pneumoniae marker was detected in 8027 out of 8051 (>99.7 %) S. pneumoniae genomes. The S. pseudopneumoniae marker was specific for all genomes that clustered in the S. pseudopneumoniae clade, including unresolved species of the genus Streptococcus sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the S. pseudopneumoniae marker in six of 8051 (<0.08 %) S. pneumoniae genomes, both the S. pneumoniae and S. pseudopneumoniae markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus Streptococcus or to a panel of over 46 000 genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.
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Affiliation(s)
- Matthew A. Croxen
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Provincial Laboratory for Public Health (ProvLab), University of Alberta Hospital, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Present address: Provincial Laboratory for Public Health, Edmonton, Canada
- Present address: Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Canada
| | - Tracy D. Lee
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Robert Azana
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Linda M. Hoang
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, Canada
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