{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T07:41:51Z","timestamp":1740123711917,"version":"3.37.3"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2022,7,1]],"date-time":"2022-07-01T00:00:00Z","timestamp":1656633600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,7,1]],"date-time":"2022-07-01T00:00:00Z","timestamp":1656633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["World J Microbiol Biotechnol"],"published-print":{"date-parts":[[2022,9]]},"DOI":"10.1007\/s11274-022-03338-w","type":"journal-article","created":{"date-parts":[[2022,7,1]],"date-time":"2022-07-01T02:03:18Z","timestamp":1656640998000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host"],"prefix":"10.1007","volume":"38","author":[{"given":"Indrani","family":"Sarkar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prateek","family":"Dey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saurabh Singh","family":"Rathore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gyan Dev","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3238-5086","authenticated-orcid":false,"given":"Ram Pratap","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,7,1]]},"reference":[{"issue":"6","key":"3338_CR1","doi-asserted-by":"publisher","first-page":"3695","DOI":"10.1073\/pnas.062526999","volume":"99","author":"H Akashi","year":"2002","unstructured":"Akashi H, Gojobori T (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci 99(6):3695\u20133700","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"3338_CR2","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1074\/jbc.M309891200","volume":"279","author":"C Albenne","year":"2004","unstructured":"Albenne C, Skov LK, Mirza O, Gajhede M, Feller G, d\u2019Amico S, Remaud-Simeon M (2004) Molecular basis of the amylose-like polymer formation catalyzed by Neisseria polysaccharea amylosucrase. J Biol Chem 279(1):726\u2013734","journal-title":"J Biol Chem"},{"key":"3338_CR3","doi-asserted-by":"publisher","first-page":"e00904","DOI":"10.1016\/j.idcr.2020.e00904","volume":"21","author":"N Al Mahmeed","year":"2020","unstructured":"Al Mahmeed N, El Nekidy WS, Langah R, Nusair AR (2020) Meningitis as the initial manifestation of systemic lupus erythematosus. Idcases 21:e00904","journal-title":"Idcases"},{"issue":"2","key":"3338_CR4","doi-asserted-by":"publisher","first-page":"3938","DOI":"10.1093\/gbe\/evaa023","volume":"12","author":"BA Al Suwayyid","year":"2020","unstructured":"Al Suwayyid BA, Rankine-Wilson L, Speers DJ, Wise MJ, Coombs GW, Kahler CM (2020) Meningococcal disease-associated prophage-like elements are present in Neisseria gonorrhoeae and some commensal Neisseria species. Genome Biol Evol 12(2):3938\u20133950","journal-title":"Genome Biol Evol"},{"issue":"9","key":"3338_CR5","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1093\/molbev\/msq103","volume":"27","author":"D Amor\u00f3s-Moya","year":"2010","unstructured":"Amor\u00f3s-Moya D, Bedhomme S, Hermann M, Bravo IG (2010) Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage. Mol Biol Evol 27(9):2141\u20132151","journal-title":"Mol Biol Evol"},{"issue":"9","key":"3338_CR6","doi-asserted-by":"publisher","first-page":"2456","DOI":"10.1128\/jcm.31.9.2456-2466.1993","volume":"31","author":"BM Andersen","year":"1993","unstructured":"Andersen BM, Steigerwalt AG, O\u2019Connor SP, Hollis DG, Weyant RS, Weaver RE, Brenner DJ (1993) Neisseria weaveri sp. nov., formerly CDC group M-5, a gram-negative bacterium associated with dog bite wounds. J Clin Microbiol 31(9):2456\u20132466","journal-title":"J Clin Microbiol"},{"issue":"1","key":"3338_CR7","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1128\/jcm.33.1.76-78.1995","volume":"33","author":"BM Andersen","year":"1995","unstructured":"Andersen BM, Weyant RS, Steigerwalt AG, Moss CW, Hollis DG, Weaver RE, Brenner DJ (1995) Characterization of Neisseria elongata subsp. glycolytica isolates obtained from human wound specimens and blood cultures. J Clin Microbiol 33(1):76\u201378","journal-title":"J Clin Microbiol"},{"key":"3338_CR8","doi-asserted-by":"publisher","DOI":"10.1136\/bcr-2016-214937","author":"V Batra","year":"2016","unstructured":"Batra V, Khararjian A, Wheat J, Zhang SX, Crain B, Baras A (2016) From suspected Creutzfeldt-Jakob disease to confirmed histoplasma meningitis. Case Rep. https:\/\/doi.org\/10.1136\/bcr-2016-214937","journal-title":"Case Rep"},{"key":"3338_CR9","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1100\/tsw.2011.70","volume":"11","author":"J Bohlin","year":"2011","unstructured":"Bohlin J (2011) Genomic signatures in microbes\u2014properties and applications. Sci World J 11:715\u2013725","journal-title":"Sci World J"},{"issue":"1","key":"3338_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-017-3543-7","volume":"18","author":"J Bohlin","year":"2017","unstructured":"Bohlin J, Eldholm V, Pettersson JH, Brynildsrud O, Snipen L (2017) The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes. BMC Genomics 18(1):1\u201311","journal-title":"BMC Genomics"},{"issue":"10","key":"3338_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2011-12-10-r109","volume":"12","author":"M Botzman","year":"2011","unstructured":"Botzman M, Margalit H (2011) Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol 12(10):1\u201311","journal-title":"Genome Biol"},{"issue":"1","key":"3338_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/emi.2016.106","volume":"5","author":"AM Butt","year":"2016","unstructured":"Butt AM, Nasrullah I, Qamar R, Tong Y (2016) Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect 5(1):1\u201314","journal-title":"Emerg Microbes Infect"},{"issue":"4","key":"3338_CR13","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.canep.2014.06.002","volume":"38","author":"S Caini","year":"2014","unstructured":"Caini S, Gandini S, Dudas M, Bremer V, Severi E, Gherasim A (2014) Sexually transmitted infections and prostate cancer risk: a systematic review and meta-analysis. Cancer Epidemiol 38(4):329\u2013338","journal-title":"Cancer Epidemiol"},{"key":"3338_CR14","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000423","author":"A Calder","year":"2020","unstructured":"Calder A, Menkiti CJ, \u00c7a\u011fda\u015f A, Santos JL, Streich R, Wong A et al (2020) Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the Neisserial gene repertoire. Microbial Genomics. https:\/\/doi.org\/10.1099\/mgen.0.000423","journal-title":"Microbial Genomics"},{"issue":"5","key":"3338_CR15","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1093\/bioinformatics\/btr721","volume":"28","author":"R Carr","year":"2012","unstructured":"Carr R, Borenstein E (2012) NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. Bioinformatics 28(5):734\u2013735","journal-title":"Bioinformatics"},{"key":"3338_CR16","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-75936-4","volume-title":"Software for data analysis: programming with R","author":"J Chambers","year":"2008","unstructured":"Chambers J (2008) Software for data analysis: programming with R. Springer Science & Business Media, Berlin"},{"key":"3338_CR17","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000208","author":"MEA Clemence","year":"2018","unstructured":"Clemence MEA, Maiden MCJ, Harrison OB (2018) Characterization of capsule genes in non-pathogenic Neisseria species. Microbial Genomics. https:\/\/doi.org\/10.1099\/mgen.0.000208","journal-title":"Microbial Genomics"},{"key":"3338_CR18","doi-asserted-by":"publisher","first-page":"128","DOI":"10.3389\/fmicb.2017.00128","volume":"8","author":"F Cornejo-Granados","year":"2017","unstructured":"Cornejo-Granados F, Zatarain-Barr\u00f3n ZL, Cantu-Robles VA, Mendoza-Vargas A, Molina-Romero C, S\u00e1nchez F et al (2017) Secretome prediction of two M. tuberculosis clinical isolates reveals their high antigenic density and potential drug targets. Front Microbiol 8:128","journal-title":"Front Microbiol"},{"issue":"6","key":"3338_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2008-9-6-225","volume":"9","author":"GD Ehrlich","year":"2008","unstructured":"Ehrlich GD, Hiller NL, Hu FZ (2008) What makes pathogens pathogenic. Genome Biol 9(6):1\u20137","journal-title":"Genome Biol"},{"key":"3338_CR20","doi-asserted-by":"publisher","DOI":"10.1128\/9781555817381.ch34","author":"J Elias","year":"2015","unstructured":"Elias J, Frosch M, Vogel U (2015) Neisseria. Manual Clin Microbiol. https:\/\/doi.org\/10.1128\/9781555817381.ch34","journal-title":"Manual Clin Microbiol"},{"issue":"1","key":"3338_CR21","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1093\/nar\/gkg004","volume":"31","author":"S Garcia-Vallve","year":"2003","unstructured":"Garcia-Vallve S, Guzm\u00e1n E, Montero MA, Romeu A (2003) HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 31(1):187\u2013189","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"3338_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-9-62","volume":"9","author":"A Garg","year":"2008","unstructured":"Garg A, Gupta D (2008) VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics 9(1):1\u201312","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"3338_CR23","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1093\/nar\/8.1.197-c","volume":"8","author":"R Grantham","year":"1980","unstructured":"Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8(1):197\u2013197","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"3338_CR24","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1183\/09031936.93.02070685","volume":"2","author":"P Gris","year":"1989","unstructured":"Gris P, Vincke G, Delmez JP, Dierckx JP (1989) Neisseria sicca pneumonia and bronchiectasis. Eur Respir J 2(7):685\u2013687","journal-title":"Eur Respir J"},{"issue":"9","key":"3338_CR25","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1056\/NEJM197808312990924","volume":"299","author":"D Hansman","year":"1978","unstructured":"Hansman D (1978) Meningitis caused by Neisseria lactamica. N Engl J Med 299(9):491","journal-title":"N Engl J Med"},{"key":"3338_CR26","volume-title":"Nucleotide metabolism: an introduction","author":"JF Henderson","year":"2014","unstructured":"Henderson JF, Paterson ARP (2014) Nucleotide metabolism: an introduction. Academic Press"},{"issue":"9","key":"3338_CR27","doi-asserted-by":"publisher","first-page":"e1001115","DOI":"10.1371\/journal.pgen.1001115","volume":"6","author":"R Hershberg","year":"2010","unstructured":"Hershberg R, Petrov DA (2010) Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet 6(9):e1001115","journal-title":"PLoS Genet"},{"issue":"1","key":"3338_CR28","first-page":"20312","volume":"3","author":"A Heydecke","year":"2013","unstructured":"Heydecke A, Andersson B, Holmdahl T, Melhus \u00c5 (2013) Human wound infections caused by Neisseria animaloris and Neisseria zoodegmatis, former CDC Group EF-4a and EF-4b. Infect Ecol Epidemiol 3(1):20312","journal-title":"Infect Ecol Epidemiol"},{"issue":"9","key":"3338_CR29","doi-asserted-by":"publisher","first-page":"e1001107","DOI":"10.1371\/journal.pgen.1001107","volume":"6","author":"F Hildebrand","year":"2010","unstructured":"Hildebrand F, Meyer A, Eyre-Walker A (2010) Evidence of selection upon genomic GC-content in bacteria. PLoS Genet 6(9):e1001107","journal-title":"PLoS Genet"},{"issue":"5","key":"3338_CR30","first-page":"553","volume":"6","author":"L Huang","year":"2014","unstructured":"Huang L, Ma L, Fan K, Li Y, Xie L, Xia W et al (2014) Necrotizing pneumonia and empyema caused by Neisseria flavescens infection. J Thorac Dis 6(5):553","journal-title":"J Thorac Dis"},{"issue":"14","key":"3338_CR31","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1016\/S0960-9822(99)80334-0","volume":"9","author":"LD Hurst","year":"1999","unstructured":"Hurst LD, Smith NG (1999) Do essential genes evolve slowly? Curr Biol 9(14):747\u2013750","journal-title":"Curr Biol"},{"issue":"6","key":"3338_CR32","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1101\/gr.87702","volume":"12","author":"IK Jordan","year":"2002","unstructured":"Jordan IK, Rogozin IB, Wolf YI, Koonin EV (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12(6):962\u2013968","journal-title":"Genome Res"},{"issue":"6","key":"3338_CR33","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1128\/jb.85.6.1274-1279.1963","volume":"85","author":"DS Kellogg Jr","year":"1963","unstructured":"Kellogg DS Jr, Peacock WL Jr, Deacon WE, Brown L, Pirkle CI (1963) Neisseria gonorrhoeae I: virulence genetically linked to clonal variation. J Bacteriol 85(6):1274\u20131279","journal-title":"J Bacteriol"},{"issue":"1","key":"3338_CR34","doi-asserted-by":"publisher","first-page":"81","DOI":"10.7845\/kjm.2015.4083","volume":"54","author":"EM Kim","year":"2018","unstructured":"Kim EM, Seong CN (2018) Complete genome sequence of Neisseria sp. KEM232 isolated from a human smooth surface caries. Korean J Microbiol 54(1):81\u201383","journal-title":"Korean J Microbiol"},{"issue":"6","key":"3338_CR35","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","volume":"35","author":"S Kumar","year":"2018","unstructured":"Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547","journal-title":"Mol Biol Evol"},{"issue":"4","key":"3338_CR36","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1007\/PL00006158","volume":"44","author":"JG Lawrence","year":"1997","unstructured":"Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44(4):383\u2013397","journal-title":"J Mol Evol"},{"key":"3338_CR37","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1007\/978-1-4614-3567-9_15","volume-title":"Evolutionary systems biology","author":"R Levy","year":"2012","unstructured":"Levy R, Borenstein E (2012) Reverse ecology: from systems to environments and back. Evolutionary systems biology. Springer, New York, pp 329\u2013345"},{"key":"3338_CR38","doi-asserted-by":"publisher","DOI":"10.1155\/2019\/6015730","author":"QF Lu","year":"2019","unstructured":"Lu QF, Cao DM, Su LL, Li SB, Ye GB, Zhu XY, Wang JP (2019) Genus-wide comparative genomics analysis of Neisseria to identify new genes associated with pathogenicity and niche adaptation of Neisseria pathogens. Int J Genomics. https:\/\/doi.org\/10.1155\/2019\/6015730","journal-title":"Int J Genomics"},{"issue":"D1","key":"3338_CR39","doi-asserted-by":"publisher","first-page":"D115","DOI":"10.1093\/nar\/gkr1044","volume":"40","author":"VM Markowitz","year":"2012","unstructured":"Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Kyrpides NC (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40(D1):D115\u2013D122","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"3338_CR40","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","volume":"57","author":"AG McArthur","year":"2013","unstructured":"McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348\u20133357","journal-title":"Antimicrob Agents Chemother"},{"key":"3338_CR41","first-page":"1471","volume-title":"Molecular medical microbiology","author":"GG McSheffrey","year":"2015","unstructured":"McSheffrey GG, Gray-Owen SD (2015) Neisseria gonorrhoeae. Molecular medical microbiology. Academic Press, Cambridge, pp 1471\u20131485"},{"issue":"4","key":"3338_CR42","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1111\/apm.12144","volume":"122","author":"A Mechergui","year":"2014","unstructured":"Mechergui A, Achour W, Baaboura R, Ouertani H, Lakhal A, Torjemane L, Hassen AB (2014) Case report of bacteremia due to Neisseria mucosa. APMIS 122(4):359\u2013361","journal-title":"APMIS"},{"issue":"2","key":"3338_CR43","doi-asserted-by":"publisher","first-page":"366","DOI":"10.3201\/eid2602.190191","volume":"26","author":"MM Mustapha","year":"2020","unstructured":"Mustapha MM, Lemos APS, Griffith MP, Evans DR, Marx R, Coltro ES, Sacchi CT (2020) Two cases of newly characterized Neisseria species. Brazil Emerg Infect Dis 26(2):366","journal-title":"Brazil Emerg Infect Dis"},{"issue":"7","key":"3338_CR44","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/ng1381","volume":"36","author":"Y Nakamura","year":"2004","unstructured":"Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36(7):760\u2013766","journal-title":"Nat Genet"},{"issue":"1","key":"3338_CR45","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1101\/gr.200901","volume":"12","author":"A Nekrutenko","year":"2002","unstructured":"Nekrutenko A, Makova KD, Li WH (2002) The KA\/KS ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res 12(1):198\u2013202","journal-title":"Genome Res"},{"key":"3338_CR46","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw943","author":"J Pi\u00f1ero","year":"2016","unstructured":"Pi\u00f1ero J, Bravo \u00c0, Queralt-Rosinach N, Guti\u00e9rrez-Sacrist\u00e1n A, Deu-Pons J, Centeno E, Furlong LI (2016) DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. https:\/\/doi.org\/10.1093\/nar\/gkw943","journal-title":"Nucleic Acids Res"},{"key":"3338_CR47","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/147648","author":"VS Rao","year":"2014","unstructured":"Rao VS, Srinivas K, Sujini GN, Kumar GN (2014) Protein-protein interaction detection: methods and analysis. Int J Proteomics. https:\/\/doi.org\/10.1155\/2014\/147648","journal-title":"Int J Proteomics"},{"issue":"17","key":"3338_CR48","doi-asserted-by":"publisher","first-page":"5036","DOI":"10.1093\/nar\/gkh834","volume":"32","author":"MD Reis","year":"2004","unstructured":"Reis MD, Savva R, Wernisch L (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32(17):5036\u20135044","journal-title":"Nucleic Acids Res"},{"key":"3338_CR49","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-61779-346-2_1","author":"NG Rouphael","year":"2012","unstructured":"Rouphael NG, Stephens DS (2012) Neisseria meningitidis: biology, microbiology, and epidemiology. Neisseria Meningitidis. https:\/\/doi.org\/10.1007\/978-1-61779-346-2_1","journal-title":"Neisseria Meningitidis"},{"issue":"1","key":"3338_CR50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11274-017-2388-1","volume":"34","author":"A Roy","year":"2018","unstructured":"Roy A, Sen A, Chakrobarty S, Sarkar I (2018) Comprehensive profiling of functional attributes, virulence potential and evolutionary dynamics in mycobacterial secretomes. World J Microbiol Biotechnol 34(1):1\u201319","journal-title":"World J Microbiol Biotechnol"},{"issue":"8","key":"3338_CR51","first-page":"221","volume":"23","author":"S Safton","year":"1999","unstructured":"Safton S, Cooper G, Harrison M, Wright L, Walsh P (1999) Neisseria canis infection: a case report. Commun Dis Intell 23(8):221","journal-title":"Commun Dis Intell"},{"issue":"3","key":"3338_CR52","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.ygeno.2018.02.019","volume":"111","author":"MS Saha","year":"2019","unstructured":"Saha MS, Pal S, Sarkar I, Roy A, Mohapatra PKD, Sen A (2019) Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex. Genomics 111(3):426\u2013435","journal-title":"Genomics"},{"issue":"1","key":"3338_CR53","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1128\/CMR.17.1.14-56.2004","volume":"17","author":"H Schmidt","year":"2004","unstructured":"Schmidt H, Hensel M (2004) Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev 17(1):14\u201356","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"3338_CR54","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","volume":"27","author":"ME Smoot","year":"2011","unstructured":"Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431\u2013432","journal-title":"Bioinformatics"},{"issue":"18","key":"3338_CR55","doi-asserted-by":"publisher","first-page":"3442","DOI":"10.1093\/nar\/28.18.3442","volume":"28","author":"B Snel","year":"2000","unstructured":"Snel B, Lehmann G, Bork P, Huynen MA (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28(18):3442\u20133444","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"3338_CR56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-7-128","volume":"7","author":"LA Snyder","year":"2006","unstructured":"Snyder LA, Saunders NJ (2006) The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as\u2019 virulence genes\u2019. BMC Genomics 7(1):1\u201311","journal-title":"BMC Genomics"},{"issue":"34","key":"3338_CR57","doi-asserted-by":"publisher","first-page":"20354","DOI":"10.1073\/pnas.2013559117","volume":"117","author":"F Soncin","year":"2020","unstructured":"Soncin F, Parast MM (2020) Role of Hippo signaling pathway in early placental development. Proc Natl Acad Sci 117(34):20354\u201320356","journal-title":"Proc Natl Acad Sci"},{"issue":"9580","key":"3338_CR58","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1016\/S0140-6736(07)61016-2","volume":"369","author":"DS Stephens","year":"2007","unstructured":"Stephens DS, Greenwood B, Brandtzaeg P (2007) Epidemic meningitis, meningococcaemia, and Neisseria meningitidis. The Lancet 369(9580):2196\u20132210","journal-title":"The Lancet"},{"issue":"3","key":"3338_CR59","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1093\/jpids\/piaa085","volume":"10","author":"G Taormina","year":"2021","unstructured":"Taormina G, Campos J, Sweitzer J, Retchless AC, Lunquest K, McNamara LA et al (2021) \u03b2-lactamase\u2013producing, ciprofloxacin-resistant Neisseria meningitidis isolated from a 5-month-old boy in the United States. J Pediatric Infect Dis Soc 10(3):379\u2013381","journal-title":"J Pediatric Infect Dis Soc"},{"key":"3338_CR60","first-page":"2","volume":"1","author":"JD Thompson","year":"2003","unstructured":"Thompson JD, Gibson TJ, Higgins DG (2003) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 1:2\u20133","journal-title":"Curr Protoc Bioinformatics"},{"issue":"3","key":"3338_CR61","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1128\/CMR.00010-14","volume":"27","author":"M Unemo","year":"2014","unstructured":"Unemo M, Shafer WM (2014) Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. Clin Microbiol Rev 27(3):587\u2013613","journal-title":"Clin Microbiol Rev"},{"issue":"4","key":"3338_CR62","doi-asserted-by":"publisher","first-page":"e6012","DOI":"10.1371\/journal.pone.0060120","volume":"8","author":"T Vesth","year":"2013","unstructured":"Vesth T, Lagesen K, Acar \u00d6, Ussery D (2013) CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS ONE 8(4):e6012","journal-title":"PLoS ONE"},{"issue":"5","key":"3338_CR63","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1007\/s00203-018-1499-x","volume":"200","author":"DV Volokhov","year":"2018","unstructured":"Volokhov DV, Amselle M, Bodeis-Jones S, Delmonte P, Zhang S, Davidson MK et al (2018) Neisseria zalophi sp. Nov., isolated from oral cavity of California sea lions (Zalophus californianus). Arch Microbiol 200(5):819\u2013828","journal-title":"Arch Microbiol"},{"issue":"1","key":"3338_CR64","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1146\/annurev.bi.46.070177.003041","volume":"46","author":"AC Wilson","year":"1977","unstructured":"Wilson AC, Carlson SS, White TJ (1977) Biochemical evolution. Annu Rev Biochem 46(1):573\u2013639","journal-title":"Annu Rev Biochem"},{"issue":"4","key":"3338_CR65","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1093\/jhered\/92.4.371","volume":"92","author":"X Xia","year":"2001","unstructured":"Xia X, Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. J Hered 92(4):371\u2013373","journal-title":"J Hered"},{"issue":"2","key":"3338_CR66","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1093\/nar\/gkj454","volume":"34","author":"P Yakovchuk","year":"2006","unstructured":"Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34(2):564\u2013574","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"3338_CR67","first-page":"555","volume":"13","author":"Z Yang","year":"1997","unstructured":"Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13(5):555\u2013556","journal-title":"Comput Appl Biosci"},{"key":"3338_CR68","doi-asserted-by":"publisher","DOI":"10.1097\/IM9.0000000000000024","author":"F Yang","year":"2020","unstructured":"Yang F, Yan J, van der Veen S (2020) Antibiotic resistance and treatment\u00a0options for multidrug-resistant gonorrhea. Infect Microbes Dis. https:\/\/doi.org\/10.1097\/IM9.0000000000000024","journal-title":"Infect Microbes Dis"}],"container-title":["World Journal of Microbiology and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11274-022-03338-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11274-022-03338-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11274-022-03338-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T02:22:27Z","timestamp":1668478947000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11274-022-03338-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,1]]},"references-count":68,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2022,9]]}},"alternative-id":["3338"],"URL":"https:\/\/doi.org\/10.1007\/s11274-022-03338-w","relation":{},"ISSN":["0959-3993","1573-0972"],"issn-type":[{"type":"print","value":"0959-3993"},{"type":"electronic","value":"1573-0972"}],"subject":[],"published":{"date-parts":[[2022,7,1]]},"assertion":[{"value":"24 November 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 June 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2022","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 conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"149"}}