{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T22:44:21Z","timestamp":1769640261511,"version":"3.49.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Antonie van Leeuwenhoek"],"published-print":{"date-parts":[[2025,1]]},"DOI":"10.1007\/s10482-024-02016-1","type":"journal-article","created":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T13:02:34Z","timestamp":1728478954000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Characterization of meningitis-causing bacteria, with focus on genomic and pangenomic study of multi-drug resistant Streptococcus pneumoniae from cerebrospinal fluid"],"prefix":"10.1007","volume":"118","author":[{"given":"Rehan","family":"Ali","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kashif","family":"Ali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad","family":"Aurongzeb","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khalid","family":"Al-Regaiey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junaid Ahmed","family":"Kori","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad","family":"Irfan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasmeen","family":"Rashid","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danah","family":"Al Abduljabbar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Imdad","family":"Kaleem","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shahid","family":"Bashir","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,10,9]]},"reference":[{"key":"2016_CR1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.590682","volume":"10","author":"A Anil","year":"2020","unstructured":"Anil A, Banerjee A (2020) Pneumococcal encounter with the blood-brain barrier endothelium. Front Cell Infect Microbiol 10:590682","journal-title":"Front Cell Infect Microbiol"},{"issue":"2","key":"2016_CR2","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.1016\/j.ygeno.2019.10.009","volume":"112","author":"M Aslam","year":"2020","unstructured":"Aslam M et al (2020) Potential druggable proteins and chimeric vaccine construct prioritization against Brucella melitensis from species core genome data. Genomics 112(2):1734\u20131745","journal-title":"Genomics"},{"issue":"11","key":"2016_CR3","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1111\/j.1462-5822.2010.01490.x","volume":"12","author":"A Banerjee","year":"2010","unstructured":"Banerjee A, Van Sorge NM, Sheen TR, Uchiyama S, Mitchell TJ, Doran KS (2010) Activation of brain endothelium by pneumococcal neuraminidase NanA promotes bacterial internalization. Cellullar Microbiol 12(11):1576\u20131588","journal-title":"Cellullar Microbiol"},{"issue":"2","key":"2016_CR4","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1016\/j.bjm.2016.06.014","volume":"48","author":"E\u00d6 Ba\u015fp\u0131nar","year":"2017","unstructured":"Ba\u015fp\u0131nar E\u00d6 et al (2017) Comparison of culture and PCR methods in the diagnosis of bacterial meningitis. Braz J Microbiol 48(2):232\u2013236","journal-title":"Braz J Microbiol"},{"issue":"12","key":"2016_CR5","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.3390\/microorganisms1012231623","volume":"10","author":"D Berbel","year":"2022","unstructured":"Berbel D, Gonz\u00e1lez-D\u00edaz A, L\u00f3pez de Egea G, C\u00e0mara J, Ardanuy C (2022) An overview of macrolide resistance in streptococci: prevalence. Mobile Elements and Dyn. Microorg 10(12):2316. https:\/\/doi.org\/10.3390\/microorganisms1012231623","journal-title":"Mobile Elements and Dyn. Microorg"},{"issue":"11","key":"2016_CR6","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.3390\/antibiotics12111580.PMID:37998782;PMCID:PMC10668849","volume":"12","author":"I Bianconi","year":"2023","unstructured":"Bianconi I, Aschbacher R, Pagani E (2023) Current uses and future perspectives of genomic technologies in clinical microbiology. Antibiotics (basel) 12(11):1580. https:\/\/doi.org\/10.3390\/antibiotics12111580.PMID:37998782;PMCID:PMC10668849","journal-title":"Antibiotics (basel)"},{"issue":"1","key":"2016_CR7","doi-asserted-by":"publisher","first-page":"24373","DOI":"10.1038\/srep24373","volume":"6","author":"NM Chaudhari","year":"2016","unstructured":"Chaudhari NM, Gupta VK, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6(1):24373","journal-title":"Sci Rep"},{"key":"2016_CR8","doi-asserted-by":"crossref","unstructured":"C Cill\u00f3niz, C Garcia-Vidal, A Ceccato, A Torres (2018) \u201cAntimicrobial Resistance Among Streptococcus pneumoniae.,\u201d Antimicrobial Resistance in the 21st Century. pp. 13\u201338","DOI":"10.1007\/978-3-319-78538-7_2"},{"key":"2016_CR9","unstructured":"CLSI (2020) Performance Standards for Antimicrobial Susceptibility, 30th ed. Clinical and Laboratory Standards Institute"},{"issue":"19","key":"2016_CR10","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinform 26(19):2460\u20132461","journal-title":"Bioinform"},{"key":"2016_CR11","doi-asserted-by":"publisher","DOI":"10.21767\/2171-6625.1000231","author":"A Erum","year":"2017","unstructured":"Erum A et al (2017) Different incidences of acute bacterial meningitis in children of Central Punjab in Pakistan. J Neurol Neurosci 8 (S4: 231)\u00a0https:\/\/doi.org\/10.21767\/2171-6625.1000231","journal-title":"J Neurol Neurosci"},{"issue":"3","key":"2016_CR12","doi-asserted-by":"publisher","first-page":"e1277","DOI":"10.1093\/cid\/ciac726","volume":"76","author":"BM Forde","year":"2023","unstructured":"Forde BM, Bergh H, Cuddihy T, Hajkowicz K, Hurst T, Playford EG, Henderson BC, Runnegar N, Clark J, Jennison AV, Moss S, Hume A, Leroux H, Beatson SA, Paterson DL, Harris PNA (2023) Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens. Clin Infect Dis: an Official Pub Infect Dis Soc Am 76(3):e1277\u2013e1284. https:\/\/doi.org\/10.1093\/cid\/ciac726","journal-title":"Clin Infect Dis: an Official Pub Infect Dis Soc Am"},{"key":"2016_CR13","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.jhin.2023.10.015","volume":"143","author":"H Hakim","year":"2024","unstructured":"Hakim H, Glasgow HL, Brazelton JN, Gilliam CH, Richards L, Hayden RT (2024) A prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients. J Hosp Infect 143:53\u201363. https:\/\/doi.org\/10.1016\/j.jhin.2023.10.015","journal-title":"J Hosp Infect"},{"issue":"10","key":"2016_CR14","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1136\/jnnp.2006.110023","volume":"78","author":"M Hoogman","year":"2007","unstructured":"Hoogman M, van de Beek D, Weisfelt M, de Gans J, Schmand B (2007) Cognitive outcome in adults after bacterial meningitis. J Neurol Neurosurg Psychiatry 78(10):1092\u20131096","journal-title":"J Neurol Neurosurg Psychiatry"},{"issue":"7","key":"2016_CR15","doi-asserted-by":"publisher","first-page":"68408","DOI":"10.1371\/journal.pone.0068408","volume":"8","author":"F Iovino","year":"2013","unstructured":"Iovino F, Orihuela CJ, Moorlag HE, Molema G, Bijlsma JJE (2013) Interactions between blood-borne Streptococcus pneumoniae and the blood-brain barrier preceding meningitis. PLoS ONE 8(7):68408","journal-title":"PLoS ONE"},{"issue":"4","key":"2016_CR16","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.tim.2015.12.012","volume":"24","author":"F Iovino","year":"2016","unstructured":"Iovino F, Seinen J, Henriques-Normark B, van Dijl JM (2016) How Does Streptococcus pneumoniae Invade the Brain? Trends in Microbiol 24(4):307\u2013315","journal-title":"Trends in Microbiol"},{"issue":"D1","key":"2016_CR17","doi-asserted-by":"publisher","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","volume":"44","author":"M Kanehisa","year":"2016","unstructured":"Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44(D1):D457\u2013D462","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2016_CR18","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s40121-018-0195-0","volume":"7","author":"F Khan","year":"2018","unstructured":"Khan F et al (2018) Molecular characterization of pneumococcal surface protein A (PspA), serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae strains isolated from Pakistan. Infectious Diseases and Therapy 7(2):277\u2013289","journal-title":"Infectious Diseases and Therapy"},{"key":"2016_CR19","volume-title":"Streptococcal Meningitis","author":"J Ma\u0144dziuk","year":"2022","unstructured":"Ma\u0144dziuk J, Kuchar EP (2022) Streptococcal Meningitis. StatPearls Publishing, Treasure Island (FL)"},{"issue":"2","key":"2016_CR20","doi-asserted-by":"publisher","first-page":"113","DOI":"10.36233\/0372-9311-2020-97-2-113-118","volume":"97","author":"KO Mironov","year":"2020","unstructured":"Mironov KO et al (2020) Characterization of Streptococcus pneumoniae strains causing invasive infections using whole-genome sequencing. J Microbiol Epidemiol Immunobiol 97(2):113\u2013118","journal-title":"J Microbiol Epidemiol Immunobiol"},{"issue":"1","key":"2016_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-019-40346-7","volume":"9","author":"U Obolski","year":"2019","unstructured":"Obolski U et al (2019) Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data. Sci Rep 9(1):1\u20139","journal-title":"Sci Rep"},{"issue":"1","key":"2016_CR22","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s13756-021-00895-x","volume":"10","author":"X Peng","year":"2021","unstructured":"Peng X et al (2021) Prevalence and antimicrobial resistance patterns of bacteria isolated from cerebrospinal fluid among children with bacterial meningitis in China from 2016 to 2018: a multicenter retrospective study. Antimicrob Resist Infect Control 10(1):24","journal-title":"Antimicrob Resist Infect Control"},{"issue":"14","key":"2016_CR23","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinform 30(14):2068\u20132069","journal-title":"Bioinform"},{"issue":"9","key":"2016_CR24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0024704","volume":"6","author":"N Segata","year":"2011","unstructured":"Segata N, Huttenhower C (2011) Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS ONE 6(9):e24704","journal-title":"PLoS ONE"},{"issue":"1","key":"2016_CR25","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/s13104-020-4895-7","volume":"13","author":"S Sharma","year":"2020","unstructured":"Sharma S, Acharya J, Banjara MR, Ghimire P, Singh A (2020) Comparison of acridine orange fluorescent microscopy and gram stain light microscopy for the rapid detection of bacteria in cerebrospinal fluid. BMC Res Notes 13(1):29","journal-title":"BMC Res Notes"},{"issue":"1","key":"2016_CR26","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3390\/idr13010019","volume":"13","author":"S Sharma","year":"2021","unstructured":"Sharma S, Acharya J, Caugant DA, Banjara MR, Ghimire P, Singh A (2021) Detection of streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae in culture negative cerebrospinal. Infect Dis Reports 13(1):173\u2013180","journal-title":"Infect Dis Reports"},{"key":"2016_CR27","unstructured":"SV Shikha (2022) \u201cMeningitis Workup,\u201d Medscape Logo [Online]. Available: https:\/\/emedicine.medscape.com\/article\/232915-workup?icd=login_success_gg_match_norm&isSocialFTC=true"},{"issue":"1","key":"2016_CR28","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1186\/s12879-022-07606-w","volume":"22","author":"SR Tabatabaei","year":"2022","unstructured":"Tabatabaei SR et al (2022) Co-infection with dual Streptococcus pneumoniae serotypes as a cause of pediatric bacterial meningitis in Iran: a multi-center cross-sectional study. BMC Infect Dis 22(1):625","journal-title":"BMC Infect Dis"},{"issue":"1","key":"2016_CR29","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","volume":"28","author":"RL Tatusov","year":"2000","unstructured":"Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33\u201336","journal-title":"Nucleic Acids Res"},{"key":"2016_CR30","unstructured":"Pharmacy Times, \u201cTop 300 Prescriptions for 2020 in the United States,\u201d (2021). [Online]. Available: https:\/\/www.pharmacytimes.com\/view\/top-300-prescriptions-for-2020-in-the-united-states"},{"issue":"9","key":"2016_CR31","doi-asserted-by":"publisher","first-page":"4551","DOI":"10.1128\/IAI.67.9.4551-4556.1999","volume":"67","author":"AM Whatmore","year":"1999","unstructured":"Whatmore AM, Dowson CG (1999) The autolysin-encoding gene (lytA) of Streptococcus pneumoniae displays restricted allelic variation despite localized recombination events with genes of pneumococcal bacteriophage encoding cell wall lytic enzymes. Infect Immun 67(9):4551\u20134556","journal-title":"Infect Immun"},{"key":"2016_CR32","unstructured":"WHO, \"The Selection and Use of Essential Medicines: Report of the WHO Expert Committee, 2019 (including the 21st WHO Model List of Essential Medicines and the 7th WHO Mode. \" (2019)."},{"key":"2016_CR33","unstructured":"WHO, \u201cMeningitis,\u201d World Health Organization (WHO), 2021. [Online]. Available: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/meningitis (2021)"},{"key":"2016_CR34","unstructured":"T Williams, C Kelley (2011) \u201cGnuplot: an Interactive Plotting Program,\u201d [Online]. Available: http:\/\/gnuplot.info\/"},{"issue":"11","key":"2016_CR35","doi-asserted-by":"publisher","first-page":"3555","DOI":"10.3390\/ijms19113555","volume":"19","author":"B Yau","year":"2018","unstructured":"Yau B, Hunt NH, Mitchell AJ, Too LK (2018) Blood-brain barrier pathology and CNS outcomes in Streptococcus pneumoniae meningitis. Int J Mol Sci 19(11):3555","journal-title":"Int J Mol Sci"},{"issue":"1","key":"2016_CR36","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1093\/jac\/dkw076]","volume":"71","author":"A Zafar","year":"2016","unstructured":"Zafar A, Hasan R, Nizamuddin S, Mahmood N, Mukhtar S, Ali F, Morrissey I, Barker K, Torumkuney D (2016) Antibiotic susceptibility in Streptococcus pneumoniae, Haemophilus influenza and Streptococcus pyogenes in Pakistan: a review of results from the survey of antibiotic resistance (SOAR) 2002\u201315. J Antimicrob Chemother 71(1):103\u2013109. https:\/\/doi.org\/10.1093\/jac\/dkw076]","journal-title":"J Antimicrob Chemother"},{"issue":"9","key":"2016_CR37","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1093\/bioinformatics\/btu017","volume":"30","author":"Y Zhao","year":"2014","unstructured":"Zhao Y et al (2014) PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinform 30(9):1297\u20131299","journal-title":"Bioinform"},{"issue":"6","key":"2016_CR38","first-page":"e01034","volume":"1","author":"S Zhihai","year":"2013","unstructured":"Zhihai S et al (2013) Complete genome sequence of streptococcus pneumoniae strain A026, a clinical multidrug-resistant isolate carrying Tn2010. Genome Announc 1(6):e01034-e1113","journal-title":"Genome Announc"}],"container-title":["Antonie van Leeuwenhoek"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10482-024-02016-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10482-024-02016-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10482-024-02016-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T13:01:06Z","timestamp":1737032466000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10482-024-02016-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,9]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1]]}},"alternative-id":["2016"],"URL":"https:\/\/doi.org\/10.1007\/s10482-024-02016-1","relation":{},"ISSN":["0003-6072","1572-9699"],"issn-type":[{"value":"0003-6072","type":"print"},{"value":"1572-9699","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,9]]},"assertion":[{"value":"27 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 October 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"16"}}