Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods

go back to reference Facklam R (2002) What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613–630PubMedPubMedCentral Facklam R (2002) What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15:613–630PubMedPubMedCentral

go back to reference Jensen A, Scholz CFP, Kilian M (2016) Re-evaluation of the taxonomy of the mitis group of the genus Streptococcus based on the whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus. Int J Syst Evol Microbiol 66:4803–4820. https://doi.org/10.1099/ijsem.0.001433CrossRefPubMed Jensen A, Scholz CFP, Kilian M (2016) Re-evaluation of the taxonomy of the mitis group of the genus Streptococcus based on the whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus. Int J Syst Evol Microbiol 66:4803–4820. https://​doi.​org/​10.​1099/​ijsem.​0.​001433CrossRefPubMed

go back to reference Patel S, Gupta RS (2018) Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. Infect Genet Evol 66:130–151. https://doi.org/10.1016/j.meegid.2018.09.020CrossRefPubMed Patel S, Gupta RS (2018) Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. Infect Genet Evol 66:130–151. https://​doi.​org/​10.​1016/​j.​meegid.​2018.​09.​020CrossRefPubMed

go back to reference Troeger C, Forouzanfar M, Rao PC, Khalil I, Brown A, Swartz S, Fullman N, Mosser J, Thompson RL, Reiner RC Jr, Abajobir A, Alam N, Alemayohu MA, Amare AT, Antonio CA, Asayesh H, Avokpaho E, Barac A, Beshir MA, Boneya DJ, Brauer M, Dandona L, Dandona R, Fitchett JRA, Gebrehiwot TT, Hailu GB, Hotez PJ, Kasaeian A, Khoja T, Kissoon N, Knibbs L, Kumar GA, Rai RK, El Razek HMA, Mohammed MSK, Nielson K, Oren E, Osman A, Patton G, Qorbani M, Roba HS, Sartorius B, Savic M, Shigematsu M, Sykes B, Swaminathan S, Topor-Madry R, Ukwaja K, Werdecker A, Yonemoto N, El Sayed ZM, Lim SS, Naghavi M, Vos T, Hay SI, Murray CJL, Mokdad AH (2017) Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the global burden of disease study 2015. Lancet Infect Dis 17:1133–1161. https://doi.org/10.1016/S1473-3099(17)30396-1CrossRef Troeger C, Forouzanfar M, Rao PC, Khalil I, Brown A, Swartz S, Fullman N, Mosser J, Thompson RL, Reiner RC Jr, Abajobir A, Alam N, Alemayohu MA, Amare AT, Antonio CA, Asayesh H, Avokpaho E, Barac A, Beshir MA, Boneya DJ, Brauer M, Dandona L, Dandona R, Fitchett JRA, Gebrehiwot TT, Hailu GB, Hotez PJ, Kasaeian A, Khoja T, Kissoon N, Knibbs L, Kumar GA, Rai RK, El Razek HMA, Mohammed MSK, Nielson K, Oren E, Osman A, Patton G, Qorbani M, Roba HS, Sartorius B, Savic M, Shigematsu M, Sykes B, Swaminathan S, Topor-Madry R, Ukwaja K, Werdecker A, Yonemoto N, El Sayed ZM, Lim SS, Naghavi M, Vos T, Hay SI, Murray CJL, Mokdad AH (2017) Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the global burden of disease study 2015. Lancet Infect Dis 17:1133–1161. https://​doi.​org/​10.​1016/​S1473-3099(17)30396-1CrossRef

go back to reference Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L, Chu Y, Lukšić I, Nair H, McAllister DA, Campbell H, Rudan I, Black R, Knoll MD (2018) Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15. Lancet Glob Health 6:e744–e757PubMedPubMedCentral Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L, Chu Y, Lukšić I, Nair H, McAllister DA, Campbell H, Rudan I, Black R, Knoll MD (2018) Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15. Lancet Glob Health 6:e744–e757PubMedPubMedCentral

go back to reference van Aalst M, Lötsch F, Spijker R, van der Meer JTM, Langendam MW, Goorhuis A, Grobusch MP, de Bree GJ (2018) Incidence of invasive pneumococcal disease in immunocompromised patients: a systematic review and meta-analysis. Travel Med Infect Dis 24:89–100. https://doi.org/10.1016/j.tmaid.2018.05.016CrossRefPubMed van Aalst M, Lötsch F, Spijker R, van der Meer JTM, Langendam MW, Goorhuis A, Grobusch MP, de Bree GJ (2018) Incidence of invasive pneumococcal disease in immunocompromised patients: a systematic review and meta-analysis. Travel Med Infect Dis 24:89–100. https://​doi.​org/​10.​1016/​j.​tmaid.​2018.​05.​016CrossRefPubMed

go back to reference Cherazard R, Epstein M, Doan TL, Salim T, Bharti S, Smith MA (2017) Antimicrobial resistant Streptococcus pneumoniae: prevalence, mechanisms, and clinical implications. Am J Ther 24:e361–e369. https://doi.org/10.1097/MJT.0000000000000551CrossRefPubMed Cherazard R, Epstein M, Doan TL, Salim T, Bharti S, Smith MA (2017) Antimicrobial resistant Streptococcus pneumoniae: prevalence, mechanisms, and clinical implications. Am J Ther 24:e361–e369. https://​doi.​org/​10.​1097/​MJT.​0000000000000551​CrossRefPubMed

go back to reference Weinberger DM, Malley R, Lipsitch M (2011) Serotype replacement in disease following pneumococcal vaccination: a discussion of the evidence. Lancet 378:1962–1973. https://doi.org/10.1016/S0140-6736(10)62225-8CrossRefPubMedPubMedCentral Weinberger DM, Malley R, Lipsitch M (2011) Serotype replacement in disease following pneumococcal vaccination: a discussion of the evidence. Lancet 378:1962–1973. https://​doi.​org/​10.​1016/​S0140-6736(10)62225-8CrossRefPubMedPubMedCentral

go back to reference Koelman DLH, Brouwer MC, van de Beek D (2020) Resurgence of pneumococcal meningitis in Europe and Northern America. Clin Microbiol Infect 26:199–204. https://doi.org/10.1016/j.cmi.2019.04.032CrossRefPubMed Koelman DLH, Brouwer MC, van de Beek D (2020) Resurgence of pneumococcal meningitis in Europe and Northern America. Clin Microbiol Infect 26:199–204. https://​doi.​org/​10.​1016/​j.​cmi.​2019.​04.​032CrossRefPubMed

go back to reference Doern CD, Burnham CAD (2010) It’s not easy being green: the viridans group streptococci, with a focus on pediatric clinical manifestations. J Clin Microbiol 48:3829–3835. https://doi.org/10.1128/JCM.01563-10CrossRefPubMedPubMedCentral Doern CD, Burnham CAD (2010) It’s not easy being green: the viridans group streptococci, with a focus on pediatric clinical manifestations. J Clin Microbiol 48:3829–3835. https://​doi.​org/​10.​1128/​JCM.​01563-10CrossRefPubMedPubMedCentral

go back to reference Beynon RP, Bahl VK, Prendergast BD (2006) Infective endocarditis. BMJ 333:334–339PubMedPubMedCentral Beynon RP, Bahl VK, Prendergast BD (2006) Infective endocarditis. BMJ 333:334–339PubMedPubMedCentral

go back to reference Murdoch DR, Corey GR, Hoen B, Miró JM, Fowler VG Jr, Bayer AS, Karchmer AW, Olaison L, Pappas PA, Moreillon P, Chambers ST, Chu VH, Falcó V, Holland DJ, Jones P, Klein JL, Raymond NJ, Read KM, Tripodi MF, Utili R, Wang A, Woods CW, Cabell CH, International Collaboration on Endocarditis-Prospective Cohort Study (ICE-PCS) Investigators (2009) Clinical presentation, etiology, and outcome of infective endocarditis in the 21st century: the international collaboration on endocarditis-prospective cohort study. Arch Intern Med 169:463–473. https://doi.org/10.1001/archinternmed.2008.603CrossRefPubMedPubMedCentral Murdoch DR, Corey GR, Hoen B, Miró JM, Fowler VG Jr, Bayer AS, Karchmer AW, Olaison L, Pappas PA, Moreillon P, Chambers ST, Chu VH, Falcó V, Holland DJ, Jones P, Klein JL, Raymond NJ, Read KM, Tripodi MF, Utili R, Wang A, Woods CW, Cabell CH, International Collaboration on Endocarditis-Prospective Cohort Study (ICE-PCS) Investigators (2009) Clinical presentation, etiology, and outcome of infective endocarditis in the 21^st century: the international collaboration on endocarditis-prospective cohort study. Arch Intern Med 169:463–473. https://​doi.​org/​10.​1001/​archinternmed.​2008.​603CrossRefPubMedPubMedCentral

go back to reference Shelburne SA, Sahasrabhojane P, Saldana M, Yao H, Su X, Horstmann N, Thompson E, Flores AR (2014) Streptococcus mitis strains causing severe clinical disease in cancer patients. Emerg Infect Dis 20:762–771. https://doi.org/10.3201/eid2005.130953CrossRefPubMedPubMedCentral Shelburne SA, Sahasrabhojane P, Saldana M, Yao H, Su X, Horstmann N, Thompson E, Flores AR (2014) Streptococcus mitis strains causing severe clinical disease in cancer patients. Emerg Infect Dis 20:762–771. https://​doi.​org/​10.​3201/​eid2005.​130953CrossRefPubMedPubMedCentral

go back to reference Mundy LS, Janoff EN, Schwebke KE, Shanholtzer CJ, Willard KE (1998) Ambiguity in the identification of Streptococcus pneumoniae. Optochin, bile solubility, quellung, and the AccuProbe DNA probe tests. Am J Clin Pathol 109:55–61PubMed Mundy LS, Janoff EN, Schwebke KE, Shanholtzer CJ, Willard KE (1998) Ambiguity in the identification of Streptococcus pneumoniae. Optochin, bile solubility, quellung, and the AccuProbe DNA probe tests. Am J Clin Pathol 109:55–61PubMed

go back to reference Martín-Galiano AJ, Balsalobre L, Fenoll A, de la Campa AG (2003) Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. Antimicrob Agents Chemother 47:3187–3194PubMedPubMedCentral Martín-Galiano AJ, Balsalobre L, Fenoll A, de la Campa AG (2003) Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. Antimicrob Agents Chemother 47:3187–3194PubMedPubMedCentral

go back to reference Arbique JC, Poyart C, Trieu-Cuot P, Quesne G, da Gloria CM, Steigerwalt AG, Morey RE, Jackson D, Davidson RJ, Facklam RR (2004) Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42:4686–4696PubMedPubMedCentral Arbique JC, Poyart C, Trieu-Cuot P, Quesne G, da Gloria CM, Steigerwalt AG, Morey RE, Jackson D, Davidson RJ, Facklam RR (2004) Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42:4686–4696PubMedPubMedCentral

go back to reference Balsalobre L, Hernández-Madrid A, Llull D, Martín-Galiano AJ, García E, Fenoll A, de la Campa AG (2006) Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. J Clin Microbiol 44:4163–4171PubMedPubMedCentral Balsalobre L, Hernández-Madrid A, Llull D, Martín-Galiano AJ, García E, Fenoll A, de la Campa AG (2006) Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible. J Clin Microbiol 44:4163–4171PubMedPubMedCentral

go back to reference Richter SS, Heilmann KP, Dohrn CL, Riahi F, Beekmann SE, Doern GV (2008) Accuracy of phenotypic methods for identification of Streptococcus pneumoniae isolates included in surveillance programs. J Clin Microbiol 46:2184–2188. https://doi.org/10.1128/JCM.00461-08CrossRefPubMedPubMedCentral Richter SS, Heilmann KP, Dohrn CL, Riahi F, Beekmann SE, Doern GV (2008) Accuracy of phenotypic methods for identification of Streptococcus pneumoniae isolates included in surveillance programs. J Clin Microbiol 46:2184–2188. https://​doi.​org/​10.​1128/​JCM.​00461-08CrossRefPubMedPubMedCentral

go back to reference Leegaard TM, Bootsma HJ, Caugant DA, Eleveld MJ, Mannsaker T, Frøholm LO, Gaustad P, Høiby EA, Hermans PWM (2010) Phenotypic and genomic characterization of pneumococcus-like streptococci isolated from HIV-seropositive patients. Microbiology 156:838–848. https://doi.org/10.1099/mic.0.035345-0CrossRefPubMed Leegaard TM, Bootsma HJ, Caugant DA, Eleveld MJ, Mannsaker T, Frøholm LO, Gaustad P, Høiby EA, Hermans PWM (2010) Phenotypic and genomic characterization of pneumococcus-like streptococci isolated from HIV-seropositive patients. Microbiology 156:838–848. https://​doi.​org/​10.​1099/​mic.​0.​035345-0CrossRefPubMed

go back to reference Das A, Behera B, Madan M, Mathur P, Pandey A (2010) Empyema caused by optochin sensitive Streptococcus mitis in the course of varicella. Indian J Pediatr 77:464. https://doi.org/10.1007/s12098-010-0024-2CrossRefPubMed Das A, Behera B, Madan M, Mathur P, Pandey A (2010) Empyema caused by optochin sensitive Streptococcus mitis in the course of varicella. Indian J Pediatr 77:464. https://​doi.​org/​10.​1007/​s12098-010-0024-2CrossRefPubMed

go back to reference Simões AS, Sá-Leão R, Eleveld MJ, Tavares DA, Carriço JA, Bootsma HJ, Hermans PW (2010) Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children in Oeiras, Portugal: genomic characteristics and implications for surveillance. J Clin Microbiol 48:238–246. https://doi.org/10.1128/JCM.01313-09CrossRefPubMed Simões AS, Sá-Leão R, Eleveld MJ, Tavares DA, Carriço JA, Bootsma HJ, Hermans PW (2010) Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children in Oeiras, Portugal: genomic characteristics and implications for surveillance. J Clin Microbiol 48:238–246. https://​doi.​org/​10.​1128/​JCM.​01313-09CrossRefPubMed

go back to reference Ikryannikova LN, Lapin KN, Malakhova MV, Filimonova AV, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM (2011) Misidentification of alpha-hemolytic streptococci by routine tests in clinical practice. Infect Genet Evol 11:1709–1715. https://doi.org/10.1016/j.meegid.2011.07.010CrossRefPubMed Ikryannikova LN, Lapin KN, Malakhova MV, Filimonova AV, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM (2011) Misidentification of alpha-hemolytic streptococci by routine tests in clinical practice. Infect Genet Evol 11:1709–1715. https://​doi.​org/​10.​1016/​j.​meegid.​2011.​07.​010CrossRefPubMed

go back to reference Rolo D, Simões SA, Domenech A, Fenoll A, Liñares J, de Lencastre H, Ardanuy C, Sá-Leão R (2013) Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 8:e57047. https://doi.org/10.1371/journal.pone.0057047CrossRefPubMedPubMedCentral Rolo D, Simões SA, Domenech A, Fenoll A, Liñares J, de Lencastre H, Ardanuy C, Sá-Leão R (2013) Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 8:e57047. https://​doi.​org/​10.​1371/​journal.​pone.​0057047CrossRefPubMedPubMedCentral

go back to reference Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R (2016) lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 85:141–148. https://doi.org/10.1016/j.diagmicrobio.2016.03.018CrossRefPubMed Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R (2016) lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 85:141–148. https://​doi.​org/​10.​1016/​j.​diagmicrobio.​2016.​03.​018CrossRefPubMed

go back to reference Yahiaoui RY, den Heijer CD, Wolfs P, Bruggeman CA, Stobberingh EE (2016) Evaluation of phenotypic and molecular methods for identification of Streptococcus pneumoniae. Future Microbiol 11:43–50. https://doi.org/10.2217/fmb.15.124CrossRefPubMed Yahiaoui RY, den Heijer CD, Wolfs P, Bruggeman CA, Stobberingh EE (2016) Evaluation of phenotypic and molecular methods for identification of Streptococcus pneumoniae. Future Microbiol 11:43–50. https://​doi.​org/​10.​2217/​fmb.​15.​124CrossRefPubMed

go back to reference Sadowy E, Bojarska A, Kuch A, Skoczyńska A, Jolley KA, Maiden MCJ, van Tonder AJ, Hammerschmidt S, Hryniewicz W (2020) Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae. Eur J Clin Microbiol Infect Dis. https://doi.org/10.1007/s10096-020-03916-6 [online ahead of print] Sadowy E, Bojarska A, Kuch A, Skoczyńska A, Jolley KA, Maiden MCJ, van Tonder AJ, Hammerschmidt S, Hryniewicz W (2020) Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae. Eur J Clin Microbiol Infect Dis. https://​doi.​org/​10.​1007/​s10096-020-03916-6 [online ahead of print]

go back to reference Wester CW, Ariga D, Nathan C, Rice TW, Pulvirenti J, Patel R, Kocka F, Ortiz J, Weinstein RA (2002) Possible overestimation of penicillin resistant Streptococcus pneumoniae colonization rates due to misidentification of oropharyngeal streptococci. Diagn Microbiol Infect Dis 42:263–268PubMed Wester CW, Ariga D, Nathan C, Rice TW, Pulvirenti J, Patel R, Kocka F, Ortiz J, Weinstein RA (2002) Possible overestimation of penicillin resistant Streptococcus pneumoniae colonization rates due to misidentification of oropharyngeal streptococci. Diagn Microbiol Infect Dis 42:263–268PubMed

go back to reference Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107. dx.doi.org. https://doi.org/10.1186/gb-2010-11-10-r107CrossRefPubMedPubMedCentral Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107. dx.​doi.​org. https://​doi.​org/​10.​1186/​gb-2010-11-10-r107CrossRefPubMedPubMedCentral

go back to reference Sanguinetti L, Toti S, Reguzzi V, Bagnoli F, Donati C (2012) A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae. PLoS Comput Biol 8:e1002668 dx.doi.org. https://doi.org/10.1371/journal.pcbi.1002668CrossRefPubMedPubMedCentral Sanguinetti L, Toti S, Reguzzi V, Bagnoli F, Donati C (2012) A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae. PLoS Comput Biol 8:e1002668 dx.​doi.​org. https://​doi.​org/​10.​1371/​journal.​pcbi.​1002668CrossRefPubMedPubMedCentral

go back to reference Sherman JM (1937) The streptococci. Bacteriol Rev 1:3–97PubMedPubMedCentral Sherman JM (1937) The streptococci. Bacteriol Rev 1:3–97PubMedPubMedCentral

go back to reference Bentley RW, Leigh JA, Collins MD (1991) Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41:487–494PubMed Bentley RW, Leigh JA, Collins MD (1991) Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41:487–494PubMed

go back to reference Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T (1995) Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45:406–408PubMed Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T (1995) Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45:406–408PubMed

go back to reference Hardie JM, Whiley RA (1997) Classification and overview of Streptococcus and Enterococcus. J Appl Microbiol Symp Sup 83:1S–11S Hardie JM, Whiley RA (1997) Classification and overview of Streptococcus and Enterococcus. J Appl Microbiol Symp Sup 83:1S–11S

go back to reference Ruoff KL, Whiley RA, Beighton D (2003) Streptococcus. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH (eds) Manual of clinical microbiology, 8th edn. ASM Press, Washington, DC, pp 405–421 Ruoff KL, Whiley RA, Beighton D (2003) Streptococcus. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH (eds) Manual of clinical microbiology, 8th edn. ASM Press, Washington, DC, pp 405–421

go back to reference Lund E, Henrichsen J (1978) Chapter XI laboratory diagnosis, serology and epidemiology of Streptococcus pneumoniae. Methods Microbiol 12:241–262 Lund E, Henrichsen J (1978) Chapter XI laboratory diagnosis, serology and epidemiology of Streptococcus pneumoniae. Methods Microbiol 12:241–262

go back to reference Phillips G, Barker R, Brogan O (1988) Optochin-resistant Streptococcus pneumoniae. Lancet 2:281PubMed Phillips G, Barker R, Brogan O (1988) Optochin-resistant Streptococcus pneumoniae. Lancet 2:281PubMed

go back to reference Pinto TC, Souza AR, de Pina SE, Costa NS, Borges Neto AA, Neves FP, Merquior VL, Dias CA, Peralta JM, Teixeira LM (2013) Phenotypic and molecular characterization of optochin-resistant Streptococcus pneumoniae isolates from Brazil, with description of five novel mutations in the atpC gene. J Clin Microbiol 51:3242–3249. https://doi.org/10.1128/JCM.01168-13CrossRefPubMedPubMedCentral Pinto TC, Souza AR, de Pina SE, Costa NS, Borges Neto AA, Neves FP, Merquior VL, Dias CA, Peralta JM, Teixeira LM (2013) Phenotypic and molecular characterization of optochin-resistant Streptococcus pneumoniae isolates from Brazil, with description of five novel mutations in the atpC gene. J Clin Microbiol 51:3242–3249. https://​doi.​org/​10.​1128/​JCM.​01168-13CrossRefPubMedPubMedCentral

go back to reference Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O’Brien KL, WHO Pneumococcal Carriage Working Group (2013) Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 32:165–179. https://doi.org/10.1016/j.vaccine.2013.08.062CrossRefPubMed Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O’Brien KL, WHO Pneumococcal Carriage Working Group (2013) Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 32:165–179. https://​doi.​org/​10.​1016/​j.​vaccine.​2013.​08.​062CrossRefPubMed

go back to reference Slotved HC, Facklam RR, Fuursted K (2017) Assessment of a novel bile solubility test and MALDI-TOF for the differentiation of Streptococcus pneumoniae from other mitis group streptococci. Sci Rep 7:7167. https://doi.org/10.1038/s41598-017-07772-xCrossRefPubMedPubMedCentral Slotved HC, Facklam RR, Fuursted K (2017) Assessment of a novel bile solubility test and MALDI-TOF for the differentiation of Streptococcus pneumoniae from other mitis group streptococci. Sci Rep 7:7167. https://​doi.​org/​10.​1038/​s41598-017-07772-xCrossRefPubMedPubMedCentral

go back to reference Teles C, Smith A, Ramage G, Lang S (2011) Identification of clinically relevant viridans group streptococci by phenotypic and genotypic analysis. Eur J Clin Microbiol Infect Dis 30:243–250. https://doi.org/10.1007/s10096-010-1076-yCrossRefPubMed Teles C, Smith A, Ramage G, Lang S (2011) Identification of clinically relevant viridans group streptococci by phenotypic and genotypic analysis. Eur J Clin Microbiol Infect Dis 30:243–250. https://​doi.​org/​10.​1007/​s10096-010-1076-yCrossRefPubMed

go back to reference Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T (2020) Rapid and accurate species identification of mitis group streptococci using the MinION Nanopore sequencer. Front Cell Infect Microbiol 10:11. https://doi.org/10.3389/fcimb.2020.00011CrossRefPubMedPubMedCentral Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T (2020) Rapid and accurate species identification of mitis group streptococci using the MinION Nanopore sequencer. Front Cell Infect Microbiol 10:11. https://​doi.​org/​10.​3389/​fcimb.​2020.​00011CrossRefPubMedPubMedCentral

go back to reference Murray PR (2010) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: usefulness for taxonomy and epidemiology. Clin Microbiol Infect 16:1626–1630. https://doi.org/10.1111/j.1469-0691.2010.03364.xCrossRefPubMed Murray PR (2010) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: usefulness for taxonomy and epidemiology. Clin Microbiol Infect 16:1626–1630. https://​doi.​org/​10.​1111/​j.​1469-0691.​2010.​03364.​xCrossRefPubMed

go back to reference Ikryannikova LN, Filimonova AV, Malakhova MV, Savinova T, Filimonova O, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM (2012) Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra. Clin Microbiol Infect 19:1066–1071. https://doi.org/10.1111/1469-0691.12113CrossRef Ikryannikova LN, Filimonova AV, Malakhova MV, Savinova T, Filimonova O, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM (2012) Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra. Clin Microbiol Infect 19:1066–1071. https://​doi.​org/​10.​1111/​1469-0691.​12113CrossRef

go back to reference Zhou M, Yang Q, Kudinha T, Zhang L, Xiao M, Kong F, Zhao Y, Xu YC (2016) Using Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) complemented with selected 16S rRNA and gyrB genes sequencing to practically identify clinical important Viridans Group Streptococci (VGS). Front Microbiol 7:1328. https://doi.org/10.3389/fmicb.2016.01328CrossRefPubMedPubMedCentral Zhou M, Yang Q, Kudinha T, Zhang L, Xiao M, Kong F, Zhao Y, Xu YC (2016) Using Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) complemented with selected 16S rRNA and gyrB genes sequencing to practically identify clinical important Viridans Group Streptococci (VGS). Front Microbiol 7:1328. https://​doi.​org/​10.​3389/​fmicb.​2016.​01328CrossRefPubMedPubMedCentral

go back to reference Harju I, Lange C, Kostrzewa M, Maier T, Rantakokko-Jalava K, Haanperä M (2017) Improved differentiation of Streptococcus pneumoniae and other S. mitis group streptococci by MALDI Biotyper using an improved MALDI Biotyper database content and a novel result interpretation algorithm. J Clin Microbiol 55:914–922. https://doi.org/10.1128/JCM.01990-16CrossRefPubMedPubMedCentral Harju I, Lange C, Kostrzewa M, Maier T, Rantakokko-Jalava K, Haanperä M (2017) Improved differentiation of Streptococcus pneumoniae and other S. mitis group streptococci by MALDI Biotyper using an improved MALDI Biotyper database content and a novel result interpretation algorithm. J Clin Microbiol 55:914–922. https://​doi.​org/​10.​1128/​JCM.​01990-16CrossRefPubMedPubMedCentral

go back to reference Paton JC, Trappetti C (2019) Streptococcus pneumoniae capsular polysaccharide. Microbiol Spectr 7. https://doi.org/10.1128/microbiolspec.GPP3-0019-2018 Paton JC, Trappetti C (2019) Streptococcus pneumoniae capsular polysaccharide. Microbiol Spectr 7. https://​doi.​org/​10.​1128/​microbiolspec.​GPP3-0019-2018

go back to reference Skov Sørensen UB, Yao K, Yang Y, Tettelin H, Kilian M (2016) Capsular polysaccharide expression in commensal Streptococcus species: genetic and antigenic similarities to Streptococcus pneumoniae. mBio 7:e01844–e01816. https://doi.org/10.1128/mBio.01844-16CrossRefPubMedPubMedCentral Skov Sørensen UB, Yao K, Yang Y, Tettelin H, Kilian M (2016) Capsular polysaccharide expression in commensal Streptococcus species: genetic and antigenic similarities to Streptococcus pneumoniae. mBio 7:e01844–e01816. https://​doi.​org/​10.​1128/​mBio.​01844-16CrossRefPubMedPubMedCentral

go back to reference Lessa FC, Milucky J, Rouphael NG, Bennett NM, Talbot HK, Harrison LH, Farley MM, Walston J, Pimenta F, Gertz RE, Rajam G, da Gloria CM, Beall B, Whitney CG (2018) Streptococcus mitis expressing pneumococcal serotype 1 capsule. Sci Rep 8:17959. https://doi.org/10.1038/s41598-018-35921-3CrossRefPubMedPubMedCentral Lessa FC, Milucky J, Rouphael NG, Bennett NM, Talbot HK, Harrison LH, Farley MM, Walston J, Pimenta F, Gertz RE, Rajam G, da Gloria CM, Beall B, Whitney CG (2018) Streptococcus mitis expressing pneumococcal serotype 1 capsule. Sci Rep 8:17959. https://​doi.​org/​10.​1038/​s41598-018-35921-3CrossRefPubMedPubMedCentral

go back to reference Pimenta F, Gertz RE Jr, Park SH, Kim E, Moura I, Milucky J, Rouphael N, Farley MM, Harrison LH, Bennett NM, Bigogo G, Feikin DR, Breiman R, Lessa FC, Whitney CG, Rajam G, Schiffer J, da Gloria CM, Beall B (2019) Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis strains with highly similar cps5 loci and antigenic relatedness to serotype 5 pneumococci. Front Microbiol 9:3199. https://doi.org/10.3389/fmicb.2018.03199CrossRefPubMedPubMedCentral Pimenta F, Gertz RE Jr, Park SH, Kim E, Moura I, Milucky J, Rouphael N, Farley MM, Harrison LH, Bennett NM, Bigogo G, Feikin DR, Breiman R, Lessa FC, Whitney CG, Rajam G, Schiffer J, da Gloria CM, Beall B (2019) Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis strains with highly similar cps5 loci and antigenic relatedness to serotype 5 pneumococci. Front Microbiol 9:3199. https://​doi.​org/​10.​3389/​fmicb.​2018.​03199CrossRefPubMedPubMedCentral

go back to reference Slotved HC, Kaltoft M, Skovsted IC, Kerrn MB, Espersen F (2004) Simple, rapid latex agglutination test for serotyping of pneumococci (Pneumotest-Latex). J Clin Microbiol 42:2518–2225PubMedPubMedCentral Slotved HC, Kaltoft M, Skovsted IC, Kerrn MB, Espersen F (2004) Simple, rapid latex agglutination test for serotyping of pneumococci (Pneumotest-Latex). J Clin Microbiol 42:2518–2225PubMedPubMedCentral

go back to reference Kuch A, Gołębiewska A, Waśko I, Ronkiewicz P, Markowska M, Hryniewicz W, Skoczyńska A (2014) Usefulness of Pneumotest-latex for direct serotyping of Streptococcus pneumoniae isolates in clinical samples. J Clin Microbiol 52:2647–2649. https://doi.org/10.1128/JCM.00451-14CrossRefPubMedPubMedCentral Kuch A, Gołębiewska A, Waśko I, Ronkiewicz P, Markowska M, Hryniewicz W, Skoczyńska A (2014) Usefulness of Pneumotest-latex for direct serotyping of Streptococcus pneumoniae isolates in clinical samples. J Clin Microbiol 52:2647–2649. https://​doi.​org/​10.​1128/​JCM.​00451-14CrossRefPubMedPubMedCentral

go back to reference Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD (2014) Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet 46:305–309. https://doi.org/10.1038/ng.2895CrossRefPubMedPubMedCentral Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD (2014) Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet 46:305–309. https://​doi.​org/​10.​1038/​ng.​2895CrossRefPubMedPubMedCentral

go back to reference Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Eser ÖK, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD (2014) Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol 6:3281–3294. https://doi.org/10.1093/gbe/evu263CrossRefPubMedPubMedCentral Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Eser ÖK, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD (2014) Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol 6:3281–3294. https://​doi.​org/​10.​1093/​gbe/​evu263CrossRefPubMedPubMedCentral

go back to reference Varghese R, Jayaraman R, Veeraraghavan B (2017) Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 141:48–54. https://doi.org/10.1016/j.mimet.2017.07.015CrossRefPubMed Varghese R, Jayaraman R, Veeraraghavan B (2017) Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 141:48–54. https://​doi.​org/​10.​1016/​j.​mimet.​2017.​07.​015CrossRefPubMed

go back to reference da Gloria CM, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, Steigerwalt A, Whaley M, Facklam RR, Fields B, Carlone G, Ades EW, Dagan R, Sampson JS (2007) Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 45:2460–2466 da Gloria CM, Tondella ML, McCaustland K, Weidlich L, McGee L, Mayer LW, Steigerwalt A, Whaley M, Facklam RR, Fields B, Carlone G, Ades EW, Dagan R, Sampson JS (2007) Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 45:2460–2466

go back to reference Book M, Lehmann LE, Zhang X, Stüber F (2013) Monitoring infection: from blood culture to polymerase chain reaction (PCR). Best Pract Res Clin Anaesthesiol 27:279–288. https://doi.org/10.1016/j.bpa.2013.06.010CrossRefPubMed Book M, Lehmann LE, Zhang X, Stüber F (2013) Monitoring infection: from blood culture to polymerase chain reaction (PCR). Best Pract Res Clin Anaesthesiol 27:279–288. https://​doi.​org/​10.​1016/​j.​bpa.​2013.​06.​010CrossRefPubMed

go back to reference da Gloria CM, Pimenta FC, Jackson D, Roundtree A, Ahmad Y, Millar EV, O’Brien KL, Whitney CG, Cohen AL, Beall BW (2010) Revisiting pneumococcal carriage by use of broth enrichment and PCR techniques for enhanced detection of carriage and serotypes. J Clin Microbiol 48:1611–1618. https://doi.org/10.1128/JCM.02243-09CrossRef da Gloria CM, Pimenta FC, Jackson D, Roundtree A, Ahmad Y, Millar EV, O’Brien KL, Whitney CG, Cohen AL, Beall BW (2010) Revisiting pneumococcal carriage by use of broth enrichment and PCR techniques for enhanced detection of carriage and serotypes. J Clin Microbiol 48:1611–1618. https://​doi.​org/​10.​1128/​JCM.​02243-09CrossRef

go back to reference Strålin K, Herrmann B, Abdeldaim G, Olcén P, Holmberg H, Mölling P (2014) Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol 52:83–89. https://doi.org/10.1128/JCM.01742-13CrossRefPubMedPubMedCentral Strålin K, Herrmann B, Abdeldaim G, Olcén P, Holmberg H, Mölling P (2014) Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol 52:83–89. https://​doi.​org/​10.​1128/​JCM.​01742-13CrossRefPubMedPubMedCentral

go back to reference Gillis HD, Lang ALS, ElSherif M, Martin I, Hatchette TF, McNeil SA, LeBlanc JJ, Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) (2017) Assessing the diagnostic accuracy of PCR-based detection of Streptococcus pneumoniae from nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study. BMJ Open 7:e015008. https://doi.org/10.1136/bmjopen-2016-015008CrossRefPubMedPubMedCentral Gillis HD, Lang ALS, ElSherif M, Martin I, Hatchette TF, McNeil SA, LeBlanc JJ, Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) (2017) Assessing the diagnostic accuracy of PCR-based detection of Streptococcus pneumoniae from nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study. BMJ Open 7:e015008. https://​doi.​org/​10.​1136/​bmjopen-2016-015008CrossRefPubMedPubMedCentral

go back to reference Sundell N, Andersson LM, Brittain-Long R, Sundvall PD, Alsiö Å, Lindh M, Gustavsson L, Westin J (2019) PCR detection of respiratory pathogens in asymptomatic and symptomatic adults. J Clin Microbiol 57:e00716–e00718. https://doi.org/10.1128/JCM.00716-18CrossRefPubMedPubMedCentral Sundell N, Andersson LM, Brittain-Long R, Sundvall PD, Alsiö Å, Lindh M, Gustavsson L, Westin J (2019) PCR detection of respiratory pathogens in asymptomatic and symptomatic adults. J Clin Microbiol 57:e00716–e00718. https://​doi.​org/​10.​1128/​JCM.​00716-18CrossRefPubMedPubMedCentral

go back to reference Virolainen A, Salo P, Jero J, Karma P, Eskola J, Leinonen M (1994) Comparison of PCR assay with bacterial culture for detecting Streptococcus pneumoniae in middle ear fluid of children with acute otitis media. J Clin Microbiol 32:2667–2670PubMedPubMedCentral Virolainen A, Salo P, Jero J, Karma P, Eskola J, Leinonen M (1994) Comparison of PCR assay with bacterial culture for detecting Streptococcus pneumoniae in middle ear fluid of children with acute otitis media. J Clin Microbiol 32:2667–2670PubMedPubMedCentral

go back to reference Salo P, Ortqvist A, Leinonen M (1995) Diagnosis of bacteremic pneumococcal pneumonia by amplification of pneumolysin gene fragment in serum. J Infect Dis 171:479–482PubMed Salo P, Ortqvist A, Leinonen M (1995) Diagnosis of bacteremic pneumococcal pneumonia by amplification of pneumolysin gene fragment in serum. J Infect Dis 171:479–482PubMed

go back to reference Kaijalainen T, Rintamäki S, Herva E, Leinonen M (2002) Evaluation of gene-technological and conventional methods in the identification of Streptococcus pneumoniae. J Microbiol Methods 51:111–118PubMed Kaijalainen T, Rintamäki S, Herva E, Leinonen M (2002) Evaluation of gene-technological and conventional methods in the identification of Streptococcus pneumoniae. J Microbiol Methods 51:111–118PubMed

go back to reference Whatmore AM, Efstratiou A, Pickerill AP, Broughton K, Woodard G, Sturgeon D, George R, Dowson CG (2000) Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of “atypical” pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes. Infect Immun 68:1374–1382PubMedPubMedCentral Whatmore AM, Efstratiou A, Pickerill AP, Broughton K, Woodard G, Sturgeon D, George R, Dowson CG (2000) Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of “atypical” pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes. Infect Immun 68:1374–1382PubMedPubMedCentral

go back to reference Neeleman C, Klaassen CH, Klomberg DM, de Valk HA, Mouton JW (2004) Pneumolysin is a key factor in misidentification of macrolide-resistant Streptococcus pneumoniae and is a putative virulence factor of S. mitis and other streptococci. J Clin Microbiol 42:4355–4357PubMedPubMedCentral Neeleman C, Klaassen CH, Klomberg DM, de Valk HA, Mouton JW (2004) Pneumolysin is a key factor in misidentification of macrolide-resistant Streptococcus pneumoniae and is a putative virulence factor of S. mitis and other streptococci. J Clin Microbiol 42:4355–4357PubMedPubMedCentral

go back to reference Johnston C, Hinds J, Smith A, van der Linden M, Van Eldere J, Mitchell TJ (2010) Detection of large numbers of pneumococcal virulence genes in streptococci of the mitis group. J Clin Microbiol 48:2762–2769. https://doi.org/10.1128/JCM.01746-09CrossRefPubMedPubMedCentral Johnston C, Hinds J, Smith A, van der Linden M, Van Eldere J, Mitchell TJ (2010) Detection of large numbers of pneumococcal virulence genes in streptococci of the mitis group. J Clin Microbiol 48:2762–2769. https://​doi.​org/​10.​1128/​JCM.​01746-09CrossRefPubMedPubMedCentral

go back to reference Mosser JL, Tomasz A (1970) Choline-containing teichoic acid as a structural component of pneumococcal cell wall and its role in sensitivity to lysis by an autolytic enzyme. J Biol Chem 245:287–298PubMed Mosser JL, Tomasz A (1970) Choline-containing teichoic acid as a structural component of pneumococcal cell wall and its role in sensitivity to lysis by an autolytic enzyme. J Biol Chem 245:287–298PubMed

go back to reference Gillespie SH, Ullman C, Smith MD, Emery V (1994) Detection of Streptococcus pneumoniae in sputum samples by PCR. J Clin Microbiol 32:1308–1311PubMedPubMedCentral Gillespie SH, Ullman C, Smith MD, Emery V (1994) Detection of Streptococcus pneumoniae in sputum samples by PCR. J Clin Microbiol 32:1308–1311PubMedPubMedCentral

go back to reference Llull D, López R, García E (2006) Characteristic signatures of the lytA gene provide a basis for rapid and reliable diagnosis of Streptococcus pneumoniae infections. J Clin Microbiol 44:1250–1256PubMedPubMedCentral Llull D, López R, García E (2006) Characteristic signatures of the lytA gene provide a basis for rapid and reliable diagnosis of Streptococcus pneumoniae infections. J Clin Microbiol 44:1250–1256PubMedPubMedCentral

go back to reference Tavares DA, Handem S, Carvalho RJ, Paulo AC, de Lencastre H, Hinds J, Sá-Leão R (2019) Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020. Sci Rep 9:3285. https://doi.org/10.1038/s41598-019-39791-1CrossRefPubMedPubMedCentral Tavares DA, Handem S, Carvalho RJ, Paulo AC, de Lencastre H, Hinds J, Sá-Leão R (2019) Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020. Sci Rep 9:3285. https://​doi.​org/​10.​1038/​s41598-019-39791-1CrossRefPubMedPubMedCentral

go back to reference Morrison KE, Lake D, Crook J, Carlone GM, Ades E, Facklam R, Sampson JS (2000) Confirmation of psaA in all 90 serotypes of Streptococcus pneumoniae by PCR and potential of this assay for identification and diagnosis. J Clin Microbiol 38:434–437PubMedPubMedCentral Morrison KE, Lake D, Crook J, Carlone GM, Ades E, Facklam R, Sampson JS (2000) Confirmation of psaA in all 90 serotypes of Streptococcus pneumoniae by PCR and potential of this assay for identification and diagnosis. J Clin Microbiol 38:434–437PubMedPubMedCentral

go back to reference Verhelst R, Kaijalainen T, De Baere T, Verschraegen G, Claeys G, Van Simaey L, De Ganck C, Vaneechoutte M (2003) Comparison of five genotypic techniques for identification of optochin-resistant pneumococcus-like isolates. J Clin Microbiol 41:3521–3525PubMedPubMedCentral Verhelst R, Kaijalainen T, De Baere T, Verschraegen G, Claeys G, Van Simaey L, De Ganck C, Vaneechoutte M (2003) Comparison of five genotypic techniques for identification of optochin-resistant pneumococcus-like isolates. J Clin Microbiol 41:3521–3525PubMedPubMedCentral

go back to reference Messmer TO, Sampson JS, Stinson A, Wong B, Carlone GM, Facklam RR (2004) Comparison of four polymerase chain reaction assays for specificity in the identification of Streptococcus pneumoniae. Diagn Microbiol Infect Dis 49:249–254PubMed Messmer TO, Sampson JS, Stinson A, Wong B, Carlone GM, Facklam RR (2004) Comparison of four polymerase chain reaction assays for specificity in the identification of Streptococcus pneumoniae. Diagn Microbiol Infect Dis 49:249–254PubMed

go back to reference Jado I, Fenoll A, Casal J, Pérez A (2001) Identification of the psaA gene, coding for pneumococcal surface adhesin A, in viridans group streptococci other than Streptococcus pneumoniae. Clin Diagn Lab Immunol 8:895–898PubMedPubMedCentral Jado I, Fenoll A, Casal J, Pérez A (2001) Identification of the psaA gene, coding for pneumococcal surface adhesin A, in viridans group streptococci other than Streptococcus pneumoniae. Clin Diagn Lab Immunol 8:895–898PubMedPubMedCentral

go back to reference Zhang Q, Ma Q, Su D, Li Q, Yao W, Wang C (2010) Identification of horizontal gene transfer and recombination of PsaA gene in Streptococcus mitis group. Microbiol Immunol 54:313–319. https://doi.org/10.1111/j.1348-0421.2010.00216.xCrossRefPubMed Zhang Q, Ma Q, Su D, Li Q, Yao W, Wang C (2010) Identification of horizontal gene transfer and recombination of PsaA gene in Streptococcus mitis group. Microbiol Immunol 54:313–319. https://​doi.​org/​10.​1111/​j.​1348-0421.​2010.​00216.​xCrossRefPubMed

go back to reference Park HK, Lee SJ, Yoon JW, Shin JW, Shin HS, Kook JK, Myung SC, Kim W (2010) Identification of the cpsA gene as a specific marker for the discrimination of Streptococcus pneumoniae from viridans group streptococci. J Med Microbiol 59:1146–1152. https://doi.org/10.1099/jmm.0.017798-0CrossRefPubMed Park HK, Lee SJ, Yoon JW, Shin JW, Shin HS, Kook JK, Myung SC, Kim W (2010) Identification of the cpsA gene as a specific marker for the discrimination of Streptococcus pneumoniae from viridans group streptococci. J Med Microbiol 59:1146–1152. https://​doi.​org/​10.​1099/​jmm.​0.​017798-0CrossRefPubMed

go back to reference Mavroidi A, Aanensen DM, Godoy D, Skovsted IC, Kaltoft MS, Reeves PR, Bentley SD, Spratt BG (2007) Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol 189:7841–7855. https://doi.org/10.1128/JB.00836-07CrossRefPubMedPubMedCentral Mavroidi A, Aanensen DM, Godoy D, Skovsted IC, Kaltoft MS, Reeves PR, Bentley SD, Spratt BG (2007) Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol 189:7841–7855. https://​doi.​org/​10.​1128/​JB.​00836-07CrossRefPubMedPubMedCentral

go back to reference da Gloria CM, Pimenta FC, Moura I, Roundtree A, Gertz RE Jr, Li Z, Jagero G, Bigogo G, Junghae M, Conklin L, Feikin DR, Breiman RF, Whitney CG, Beall BW (2013) Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract. PeerJ 1:e97. https://doi.org/10.7717/peerj.97CrossRef da Gloria CM, Pimenta FC, Moura I, Roundtree A, Gertz RE Jr, Li Z, Jagero G, Bigogo G, Junghae M, Conklin L, Feikin DR, Breiman RF, Whitney CG, Beall BW (2013) Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract. PeerJ 1:e97. https://​doi.​org/​10.​7717/​peerj.​97CrossRef

go back to reference Whalan RH, Funnell SG, Bowler LD, Hudson MJ, Robinson A, Dowson CG (2006) Distribution and genetic diversity of the ABC transporter lipoproteins PiuA and PiaA within Streptococcus pneumoniae and related streptococci. J Bacteriol 188:1031–1038PubMedPubMedCentral Whalan RH, Funnell SG, Bowler LD, Hudson MJ, Robinson A, Dowson CG (2006) Distribution and genetic diversity of the ABC transporter lipoproteins PiuA and PiaA within Streptococcus pneumoniae and related streptococci. J Bacteriol 188:1031–1038PubMedPubMedCentral

go back to reference Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp GJ, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A (2017) Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 7:170074. https://doi.org/10.1098/rsob.170074CrossRefPubMedPubMedCentral Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp GJ, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A (2017) Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 7:170074. https://​doi.​org/​10.​1098/​rsob.​170074CrossRefPubMedPubMedCentral

go back to reference Peela SCM, Sistla S, Tamilarasu K, Krishnamurthy S, Adhishivam B (2018) Validation of pneumococcal iron acquisition (piaA) gene for accurate identification of Streptococcus pneumoniae. Indian J Med Microbiol 36:504–507. https://doi.org/10.4103/ijmm.IJMM_18_274CrossRefPubMed Peela SCM, Sistla S, Tamilarasu K, Krishnamurthy S, Adhishivam B (2018) Validation of pneumococcal iron acquisition (piaA) gene for accurate identification of Streptococcus pneumoniae. Indian J Med Microbiol 36:504–507. https://​doi.​org/​10.​4103/​ijmm.​IJMM_​18_​274CrossRefPubMed

go back to reference Zbinden A, Köhler N, Bloemberg GV (2011) recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci. J Clin Microbiol 49:523–527. https://doi.org/10.1128/JCM.01450-10CrossRefPubMedPubMedCentral Zbinden A, Köhler N, Bloemberg GV (2011) recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci. J Clin Microbiol 49:523–527. https://​doi.​org/​10.​1128/​JCM.​01450-10CrossRefPubMedPubMedCentral

go back to reference Sistek V, Boissinot M, Boudreau DK, Huletsky A, Picard FJ, Bergeron MG (2012) Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene. Clin Microbiol Infect 18:1089–1096. https://doi.org/10.1111/j.1469-0691.2011.03684.xCrossRefPubMed Sistek V, Boissinot M, Boudreau DK, Huletsky A, Picard FJ, Bergeron MG (2012) Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene. Clin Microbiol Infect 18:1089–1096. https://​doi.​org/​10.​1111/​j.​1469-0691.​2011.​03684.​xCrossRefPubMed

go back to reference Scholz CF, Poulsen K, Kilian M (2012) Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J Clin Microbiol 50:1968–1973. https://doi.org/10.1128/JCM.00365-12CrossRefPubMedPubMedCentral Scholz CF, Poulsen K, Kilian M (2012) Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J Clin Microbiol 50:1968–1973. https://​doi.​org/​10.​1128/​JCM.​00365-12CrossRefPubMedPubMedCentral

go back to reference Suzuki N, Seki M, Nakano Y, Kiyoura Y, Maeno M, Yamashita Y (2005) Discrimination of Streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization. J Clin Microbiol 43:4528–4534PubMedPubMedCentral Suzuki N, Seki M, Nakano Y, Kiyoura Y, Maeno M, Yamashita Y (2005) Discrimination of Streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization. J Clin Microbiol 43:4528–4534PubMedPubMedCentral

go back to reference Suzuki N, Yuyama M, Maeda S, Ogawa H, Mashiko K, Kiyoura Y (2006) Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae. J Med Microbiol 55:709–714PubMed Suzuki N, Yuyama M, Maeda S, Ogawa H, Mashiko K, Kiyoura Y (2006) Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae. J Med Microbiol 55:709–714PubMed

go back to reference Wessels E, Schelfaut JJ, Bernards AT, Claas EC (2012) Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 50:1171–1177. https://doi.org/10.1128/JCM.06609-11CrossRefPubMedPubMedCentral Wessels E, Schelfaut JJ, Bernards AT, Claas EC (2012) Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 50:1171–1177. https://​doi.​org/​10.​1128/​JCM.​06609-11CrossRefPubMedPubMedCentral

go back to reference Croxen MA, Lee TD, Azana R, Hoang LM (2018) Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Microb Genom 4. https://doi.org/10.1099/mgen.0.000175 Croxen MA, Lee TD, Azana R, Hoang LM (2018) Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Microb Genom 4. https://​doi.​org/​10.​1099/​mgen.​0.​000175

go back to reference Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107. https://doi.org/10.1186/gb-2010-11-10-r107CrossRefPubMedPubMedCentral Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107. https://​doi.​org/​10.​1186/​gb-2010-11-10-r107CrossRefPubMedPubMedCentral

go back to reference Andam CP, Hanage WP (2015) Mechanisms of genome evolution of Streptococcus. Infect Genet Evol 33:334–342. https://doi.org/10.1016/j.meegid.2014.11.007CrossRefPubMed Andam CP, Hanage WP (2015) Mechanisms of genome evolution of Streptococcus. Infect Genet Evol 33:334–342. https://​doi.​org/​10.​1016/​j.​meegid.​2014.​11.​007CrossRefPubMed

go back to reference Velsko IM, Perez MS, Richards VP (2019) Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core- and pan-genome analyses. Genome Biol Evol 11:1077–1087. https://doi.org/10.1093/gbe/evz049CrossRefPubMedPubMedCentral Velsko IM, Perez MS, Richards VP (2019) Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core- and pan-genome analyses. Genome Biol Evol 11:1077–1087. https://​doi.​org/​10.​1093/​gbe/​evz049CrossRefPubMedPubMedCentral

go back to reference Kilian M, Tettelin H (2019) Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. mBio 10:e01985–e01919. https://doi.org/10.1128/mBio.01985-19CrossRefPubMedPubMedCentral Kilian M, Tettelin H (2019) Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. mBio 10:e01985–e01919. https://​doi.​org/​10.​1128/​mBio.​01985-19CrossRefPubMedPubMedCentral

go back to reference Salvadori G, Junges R, Morrison DA, Petersen FC (2019) Competence in Streptococcus pneumoniae and close commensal relatives: mechanisms and implications. Front Cell Infect Microbiol 9:94. https://doi.org/10.3389/fcimb.2019.00094CrossRefPubMedPubMedCentral Salvadori G, Junges R, Morrison DA, Petersen FC (2019) Competence in Streptococcus pneumoniae and close commensal relatives: mechanisms and implications. Front Cell Infect Microbiol 9:94. https://​doi.​org/​10.​3389/​fcimb.​2019.​00094CrossRefPubMedPubMedCentral

go back to reference Gonzales-Siles L, Karlsson R, Schmidt P, Salvà-Serra F, Jaén-Luchoro D, Skovbjerg S, Moore ERB, Gomila M (2020) A pangenome approach for discerning species-unique gene markers for identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Front Cell Infect Microbiol 10:222. https://doi.org/10.3389/fcimb.2020.00222CrossRefPubMedPubMedCentral Gonzales-Siles L, Karlsson R, Schmidt P, Salvà-Serra F, Jaén-Luchoro D, Skovbjerg S, Moore ERB, Gomila M (2020) A pangenome approach for discerning species-unique gene markers for identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Front Cell Infect Microbiol 10:222. https://​doi.​org/​10.​3389/​fcimb.​2020.​00222CrossRefPubMedPubMedCentral

go back to reference Poyart C, Quesne G, Coulon S, Berche P, Trieu-Cuot P (1998) Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36:41–47PubMedPubMedCentral Poyart C, Quesne G, Coulon S, Berche P, Trieu-Cuot P (1998) Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36:41–47PubMedPubMedCentral

go back to reference Kawamura Y, Whiley RA, Shu SE, Ezaki T, Hardie JM (1999) Genetic approaches to the identification of the mitis group within the genus Streptococcus. Microbiology 145:2605–2613PubMed Kawamura Y, Whiley RA, Shu SE, Ezaki T, Hardie JM (1999) Genetic approaches to the identification of the mitis group within the genus Streptococcus. Microbiology 145:2605–2613PubMed

go back to reference Drancourt M, Roux V, Fournier PE, Raoult D (2004) rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42:497–504PubMedPubMedCentral Drancourt M, Roux V, Fournier PE, Raoult D (2004) rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 42:497–504PubMedPubMedCentral

go back to reference Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG (2004) Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42:3686–3695PubMedPubMedCentral Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG (2004) Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42:3686–3695PubMedPubMedCentral

go back to reference Galloway-Peña J, Sahasrabhojane P, Tarrand J, Han XY, Shelburne SA (2014) gyrB polymorphisms accurately assign invasive viridans group streptococcal species. J Clin Microbiol 52:2905–2912. https://doi.org/10.1128/JCM.01068-14CrossRefPubMedPubMedCentral Galloway-Peña J, Sahasrabhojane P, Tarrand J, Han XY, Shelburne SA (2014) gyrB polymorphisms accurately assign invasive viridans group streptococcal species. J Clin Microbiol 52:2905–2912. https://​doi.​org/​10.​1128/​JCM.​01068-14CrossRefPubMedPubMedCentral

go back to reference Rasmunssen LH, Dargis R, Hojholt K, Christensen JJ, Skovgaard O, Justensen US, Rosenvinge FS, Moser C, Lukjancenko O, Rasmunssen S, Nielsen XC (2016) Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of mitis group streptococci. Eur J Clin Microbiol Infect Dis 35:1615–1625. https://doi.org/10.1007/s10096-016-2700-2CrossRef Rasmunssen LH, Dargis R, Hojholt K, Christensen JJ, Skovgaard O, Justensen US, Rosenvinge FS, Moser C, Lukjancenko O, Rasmunssen S, Nielsen XC (2016) Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of mitis group streptococci. Eur J Clin Microbiol Infect Dis 35:1615–1625. https://​doi.​org/​10.​1007/​s10096-016-2700-2CrossRef

go back to reference Westling K, Julander I, Ljungman P, Vondracek M, Wretlind B, Jalal S (2008) Identification of species of viridans group streptococci in clinical blood culture isolates by sequence analysis of the RNase P RNA gene, rnpB. J Inf Secur 56:204–210 Westling K, Julander I, Ljungman P, Vondracek M, Wretlind B, Jalal S (2008) Identification of species of viridans group streptococci in clinical blood culture isolates by sequence analysis of the RNase P RNA gene, rnpB. J Inf Secur 56:204–210

go back to reference Park HK, Yoon JW, Shin JW, Kim JY, Kim W (2010) rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 305:58–64. https://doi.org/10.1111/j.1574-6968.2010.01913.xCrossRefPubMed Park HK, Yoon JW, Shin JW, Kim JY, Kim W (2010) rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 305:58–64. https://​doi.​org/​10.​1111/​j.​1574-6968.​2010.​01913.​xCrossRefPubMed

go back to reference Glazunova OO, Raoult D, Roux V (2010) Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus. Int J Syst Evol Microbiol 60:2140–2148. https://doi.org/10.1099/ijs.0.018176-0CrossRefPubMed Glazunova OO, Raoult D, Roux V (2010) Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus. Int J Syst Evol Microbiol 60:2140–2148. https://​doi.​org/​10.​1099/​ijs.​0.​018176-0CrossRefPubMed

go back to reference Maeda Y, Goldsmith CE, Coulter WA, Mason C, Dooley JS, Lowery CJ, Millar BC, Moore JE (2011) Comparison of five gene loci (rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ) to aid the molecular identification of viridans-group streptococci and pneumococci. Br J Biomed Sci 68:190–196PubMed Maeda Y, Goldsmith CE, Coulter WA, Mason C, Dooley JS, Lowery CJ, Millar BC, Moore JE (2011) Comparison of five gene loci (rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ) to aid the molecular identification of viridans-group streptococci and pneumococci. Br J Biomed Sci 68:190–196PubMed

go back to reference Enright MC, Spratt BG (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144:3049–3060PubMed Enright MC, Spratt BG (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144:3049–3060PubMed

go back to reference Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG (2009) Assigning strains to bacterial species via the internet. BMC Biol 7:3. https://doi.org/10.1186/1741-7007-7-3CrossRefPubMedPubMedCentral Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG (2009) Assigning strains to bacterial species via the internet. BMC Biol 7:3. https://​doi.​org/​10.​1186/​1741-7007-7-3CrossRefPubMedPubMedCentral

go back to reference Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG (2005) Using multilocus sequence data to define the pneumococcus. J Bacteriol 187:6223–6230PubMedPubMedCentral Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG (2005) Using multilocus sequence data to define the pneumococcus. J Bacteriol 187:6223–6230PubMedPubMedCentral

go back to reference Enright MC, Knox K, Griffiths D, Crook DW, Spratt BG (2000) Molecular typing of bacteria directly from cerebrospinal fluid. Eur J Clin Microbiol Infect Dis 19:627–630PubMed Enright MC, Knox K, Griffiths D, Crook DW, Spratt BG (2000) Molecular typing of bacteria directly from cerebrospinal fluid. Eur J Clin Microbiol Infect Dis 19:627–630PubMed

go back to reference Hanage WP, Fraser C, Spratt BG (2006) Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond Ser B Biol Sci 361:1917–1927. https://doi.org/10.1098/rstb.2006.1917CrossRef Hanage WP, Fraser C, Spratt BG (2006) Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond Ser B Biol Sci 361:1917–1927. https://​doi.​org/​10.​1098/​rstb.​2006.​1917CrossRef

go back to reference Fuursted K, Littauer PJ, Greve T, Scholz CF (2016) Septicemia with Streptococcus pseudopneumoniae: report of three cases with an apparent hepatic or bile duct association. Infect Dis (Lond) 48:636–639. https://doi.org/10.3109/23744235.2016.1157896CrossRef Fuursted K, Littauer PJ, Greve T, Scholz CF (2016) Septicemia with Streptococcus pseudopneumoniae: report of three cases with an apparent hepatic or bile duct association. Infect Dis (Lond) 48:636–639. https://​doi.​org/​10.​3109/​23744235.​2016.​1157896CrossRef

go back to reference Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15:R46. https://doi.org/10.1186/gb-2014-15-3-r46CrossRefPubMedPubMedCentral Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15:R46. https://​doi.​org/​10.​1186/​gb-2014-15-3-r46CrossRefPubMedPubMedCentral

go back to reference Zhang XX, Guo LY, Liu LL, Shen A, Feng WY, Huang WH, Hu HL, Hu B, Guo X, Chen TM, Chen HY, Jiang YQ, Liu G (2019) The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis. BMC Infect Dis 19:495. https://doi.org/10.1186/s12879-019-4132-yCrossRefPubMedPubMedCentral Zhang XX, Guo LY, Liu LL, Shen A, Feng WY, Huang WH, Hu HL, Hu B, Guo X, Chen TM, Chen HY, Jiang YQ, Liu G (2019) The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis. BMC Infect Dis 19:495. https://​doi.​org/​10.​1186/​s12879-019-4132-yCrossRefPubMedPubMedCentral

go back to reference Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:1005–1015. https://doi.org/10.1099/mic.0.055459-0CrossRefPubMedPubMedCentral Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:1005–1015. https://​doi.​org/​10.​1099/​mic.​0.​055459-0CrossRefPubMedPubMedCentral

go back to reference Juul S, Izquierdo F, Hurst A, Dai X, Wright A, Kulesha E, Pettett R, Turner DJ (2015) What’s in my pot? Real-time species identification on the MinION™. bioRxiv [Preprint]. https://doi.org/10.1101/030742 Juul S, Izquierdo F, Hurst A, Dai X, Wright A, Kulesha E, Pettett R, Turner DJ (2015) What’s in my pot? Real-time species identification on the MinION™. bioRxiv [Preprint]. https://​doi.​org/​10.​1101/​030742