{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T13:24:10Z","timestamp":1782739450015,"version":"3.54.5"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T00:00:00Z","timestamp":1710720000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T00:00:00Z","timestamp":1710720000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Antimicrobial resistance (AMR) of <jats:italic>Neisseria gonorrhoeae<\/jats:italic> is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of <jats:italic>N. gonorrhoeae<\/jats:italic> is sparse in Zambia. This study aimed to determine the genetic diversity of <jats:italic>N. gonorrhoeae<\/jats:italic> isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A cross-sectional study that sequenced 38 <jats:italic>N. gonorrhoeae<\/jats:italic> isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cge.cbs.dtu.dk\/services\/CGEpipeline-1.1\">https:\/\/cge.cbs.dtu.dk\/services\/CGEpipeline-1.1<\/jats:ext-link> was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The most frequent STs with 18.4% of isolates each were ST<jats:sup>7363<\/jats:sup>, ST<jats:sup>1921<\/jats:sup> and ST<jats:sup>1582<\/jats:sup>, followed by ST<jats:sup>1583<\/jats:sup> (13%), novel ST<jats:sup>17026<\/jats:sup> (7.9%), ST<jats:sup>1588<\/jats:sup> (7.9%), ST<jats:sup>1596<\/jats:sup> (5.3%), ST<jats:sup>11181<\/jats:sup> (5.3%), ST<jats:sup>11750<\/jats:sup> (2.6\/%) and ST<jats:sup>11241<\/jats:sup> (2.6%) among the 38 genotyped isolates. The <jats:italic>blaTeM-1B<\/jats:italic> and <jats:italic>tetM<\/jats:italic> (55%) was the most prevalent combination of AMR genes, followed by <jats:italic>blaTeM-1B<\/jats:italic> (18.4%), <jats:italic>tetM<\/jats:italic> (15.8%), and the combination of <jats:italic>blaTeM-1B<\/jats:italic>, <jats:italic>ermT<\/jats:italic>, and <jats:italic>tetL<\/jats:italic> was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was <jats:italic>gryA<\/jats:italic> (S91F), <jats:italic>parC<\/jats:italic> (E91G), <jats:italic>ponA<\/jats:italic> (L421) and <jats:italic>rpsJ<\/jats:italic> (V57M), followed by 18.4% in <jats:italic>gyrA<\/jats:italic> (S91F), <jats:italic>ponA<\/jats:italic> (L421P), <jats:italic>rpsJ<\/jats:italic> (V57M), and 18.4% in <jats:italic>gyrA<\/jats:italic> (D95G, S91F), <jats:italic>ponA<\/jats:italic> (L421P), and <jats:italic>rpsJ<\/jats:italic> (V57M). The combinations in <jats:italic>gyrA<\/jats:italic> (D95G, S91F) and rpsJ (V57M), and <jats:italic>gyrA<\/jats:italic> (D95G, S91F), <jats:italic>parC<\/jats:italic> (E91F), <jats:italic>ponA<\/jats:italic> (L421P) and <jats:italic>rpsJ<\/jats:italic> (V57M) were 13.2% each of the isolates. Plasmid <jats:italic>TEM-1<\/jats:italic> (84.2%), <jats:italic>tetM (<\/jats:italic>15.8%), and gonococcal genetic island (GGI) was detected in all isolates.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This study revealed remarkable heterogeneity of <jats:italic>N. gonorrhoeae<\/jats:italic> with <jats:italic>bla<\/jats:italic><jats:sub>TEM\u22121<\/jats:sub>, <jats:italic>tetM, ponA, gyrA<\/jats:italic>, and <jats:italic>parC<\/jats:italic> genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-024-10155-y","type":"journal-article","created":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T15:02:33Z","timestamp":1710774153000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia"],"prefix":"10.1186","volume":"25","author":[{"given":"Kelvin Lutambo","family":"Sarenje","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"van Zwetselaar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Happiness","family":"Kumburu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tolbert","family":"Sonda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blandina","family":"Mmbaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Owen","family":"Ngalamika","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret C.","family":"Maimbolwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amon","family":"Siame","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sody","family":"Munsaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoffrey","family":"Kwenda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,18]]},"reference":[{"key":"10155_CR1","first-page":"412","volume":"16","author":"M Unemo","year":"2019","unstructured":"Unemo M, Lahra MM, Cole M, Mike S, Galarza P, Ndowa F, Martin, et al. World Health Organisation Global Gonococcal Antimicrobial Surveillance Program (WHO GASP): review of new data and evidence to inform international collaborative actions and research efforts. J PubMed Cent. 2019;16:412\u201325.","journal-title":"J PubMed Cent"},{"key":"10155_CR2","unstructured":"WHO. Global progress report on HIV, viral hepatitis and sexually transmitted infections, May 20., 2021. https:\/\/www.who.int\/publications\/i\/item\/9789240027077 (accessed Aug 18, 2021)."},{"key":"10155_CR3","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. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st Century: past, evolution, and future. Clin Microbiol Rev. 2014;27:587\u2013613.","journal-title":"Clin Microbiol Rev"},{"key":"10155_CR4","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s13073-021-00860-8","volume":"13","author":"K Yahara","year":"2021","unstructured":"Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama S, Hirabayashi A, et al. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoae. BMC Genome Med. 2021;13:51.","journal-title":"BMC Genome Med"},{"key":"10155_CR5","doi-asserted-by":"publisher","first-page":"1816","DOI":"10.1093\/infdis\/jiaa002","volume":"222","author":"OB Harrison","year":"2020","unstructured":"Harrison OB, Cehovin A, Skett J, Jolley KA, Massari P, et al. Neisseria gonorrhoeae population genomics: use of the gonococcal core genome to improve surveillance of antimicrobial resistance. J Infect Dis. 2020;222:1816\u201325.","journal-title":"J Infect Dis"},{"key":"10155_CR6","doi-asserted-by":"crossref","unstructured":"Unemo M, del Rio C, Shafer WM. Antimicrobial resistance expressed by Neisseria gonorrhoeae: a major global public health problem in the 21st century. Microbiol. Spectr. 4, 2016. https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4920088\/. Accessed April 17, 2019.","DOI":"10.1128\/microbiolspec.EI10-0009-2015"},{"key":"10155_CR7","unstructured":"World Health Organization (WHO). Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. http:\/\/www.who.int\/medicines\/publications\/WHO-PPL-Short_Summary_25Feb-ET_NM_WHO.pdf. 2017."},{"key":"10155_CR8","doi-asserted-by":"publisher","first-page":"17596","DOI":"10.1038\/s41598-018-35750-4","volume":"8","author":"D Golparian","year":"2018","unstructured":"Golparian D, Don\u00e0 V, S\u00e1nchez-Bus\u00f3 L, Foerster S, Harris S, Endimiani A, Low N, Unemo M. Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Sci Rep. 2018;8:17596. https:\/\/doi.org\/10.1038\/s41598-018-35750-4.","journal-title":"Sci Rep"},{"key":"10155_CR9","doi-asserted-by":"publisher","first-page":"e02005","DOI":"10.1128\/AAC.02005-19","volume":"64","author":"W Demczuk","year":"2020","unstructured":"Demczuk W, Martin I, Sawatzky P, Allen V, Lefebvre B, Hoang L, Naidu P, Minion J, VanCaeseele P, Haldane D, Eyre DW, Mulvey MR. Equations to predict antimicrobial MICs in Neisseria gonorrhoeae using molecular antimicrobial resistance determinants. J Antimicrob Agents Chemother. 2020;64:e02005\u201319. https:\/\/doi.org\/10.1128\/AAC.02005-19.","journal-title":"J Antimicrob Agents Chemother"},{"key":"10155_CR10","doi-asserted-by":"publisher","first-page":"mgen000359","DOI":"10.1099\/mgen.0.000359","volume":"6","author":"K Alfsnes","year":"2020","unstructured":"Alfsnes K, Eldholm V, Olsen AO, Brynildsrud OB, Bohlin J, Steinbakk M, Caugant DA. Genomic epidemiology and population structure of Neisseria gonorrhoeae in Norway, 2016\u20132017. Microb Genomics. 2020;6:mgen000359. https:\/\/doi.org\/10.1099\/mgen.0.000359.","journal-title":"Microb Genomics"},{"key":"10155_CR11","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.1128\/JCM.00100-17","volume":"55","author":"W Demczuk","year":"2017","unstructured":"Demczuk W, Sidhu S, Unemo M, Whiley DM, Allen VG, Dillon JR, Cole M, Seah C, Trembizki E, Trees DL, Kersh EN, Abrams AJ, de Vries HJC, van Dam AP, Medina I, Bharat A, Mulvey MR, Van Domselaar G, Martin I. Neisseria gonorrhoeae sequence typing for antimicrobial resistance, a novel antimicrobial resistance multilocus typing scheme for tracking global dissemination of N. gonorrhoeae strains. J Clin Microbiol. 2017;55:1454\u201368. https:\/\/doi.org\/10.1128\/JCM.00100-17.","journal-title":"J Clin Microbiol"},{"key":"10155_CR12","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1741-7007-5-35","volume":"5","author":"JS Bennett","year":"2007","unstructured":"Bennett JS, Jolley KA, Sparling PF, Saunders NJ, Hart CA, Feavers IM, Maiden MC. Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing. BMC Biol. 2007;5:35. https:\/\/doi.org\/10.1186\/1741-7007-5-35.","journal-title":"BMC Biol"},{"key":"10155_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijid.2020.01.020","volume":"39","author":"B Shaskolskiya","year":"2020","unstructured":"Shaskolskiya B, Dementievaa E, Kandinova I, Chestkovb A, Kubanovb A, Deryabinb D, Gryadunova D. Genetic diversity of Neisseria gonorrhoeae multi-antigen sequence types in Russia and Europe. Int J Infect Dis. 2020;39:1\u20138.","journal-title":"Int J Infect Dis"},{"issue":"8","key":"10155_CR14","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1086\/383047","volume":"189","author":"IMC Martin","year":"2004","unstructured":"Martin IMC, Ison CA, Aanensen DM, Fenton KA, Spratt BG. Rapid sequence-based identification of gonococcal transmission clusters in a large metropolitan area. Jour Infect Dis. 2004;189(8):1497\u2013505.","journal-title":"Jour Infect Dis"},{"issue":"9","key":"10155_CR15","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1097\/01.olq.0000431356.80840.d4","volume":"40","author":"AE Singh","year":"2013","unstructured":"Singh AE, Gratrix J, Read R, Lovgren M, Drews SJ, Romanowski B, et al. Neisseria gonorrhoeae multiantigen sequence typing is beneficial in further characterizing gonococcal populations in Alberta, Canada. Sex Trans Dis. 2013;40(9):745\u201350.","journal-title":"Sex Trans Dis"},{"issue":"10","key":"10155_CR16","doi-asserted-by":"publisher","first-page":"e0223598","DOI":"10.1371\/journal.pone.0223598","volume":"14","author":"N Attram","year":"2019","unstructured":"Attram N, Agbodzi B, Dela H, Behene E, Nyarko EO, Kyei NNA, et al. Antimicrobial resistance (AMR) and molecular characterization of Neisseria gonorrhoeae in Ghana, 2012\u20132015. PLoS ONE. 2019;14(10):e0223598. https:\/\/doi.org\/10.1371\/journal.pone.0223598.","journal-title":"PLoS ONE"},{"key":"10155_CR17","doi-asserted-by":"publisher","first-page":"e02311","DOI":"10.1128\/AAC.02311-20","volume":"65","author":"Y Li","year":"2021","unstructured":"Li Y, Li Y, Xiu L, Zeng Y, Zhang C, Sun L, Zhang L, Wang F, Peng J. Typing of Neisseria gonorrhoeae isolates in Shenzhen, China, from 2014 to 2018 reveals the shift of genotypes significantly associated with antimicrobial resistance. Antimicrob Agents Chemother. 2021;65:e02311\u201320. https:\/\/doi.org\/10.1128\/AAC.02311-20.","journal-title":"Antimicrob Agents Chemother"},{"key":"10155_CR18","doi-asserted-by":"publisher","first-page":"e00759","DOI":"10.1128\/AAC.00759-21","volume":"65","author":"N Mitchev","year":"2021","unstructured":"Mitchev N, Singh R, Allam M, Kwenda S, Ismail A, Garrett N, Ramsuran V, Niehaus AJ, Mlisana KP. Antimicrobial resistance mechanisms, multilocus sequence typing, and NG-STAR sequence types of diverse Neisseria gonorrhoeae isolates in KwaZulu-Natal, South Africa. Antimicrob Agents Chemother. 2021;65:e00759\u201321. https:\/\/doi.org\/10.1128\/AAC.00759-21.","journal-title":"Antimicrob Agents Chemother"},{"key":"10155_CR19","unstructured":"WHO. Report on global sexually transmitted infection surveillance 2018. https:\/\/www.who.int\/publications\/i\/item\/9789241565691."},{"key":"10155_CR20","doi-asserted-by":"publisher","first-page":"548","DOI":"10.2471\/BLT.18.228486","volume":"97","author":"J Rowley","year":"2019","unstructured":"Rowley J, Vander Hoorn S, Korenromp E, Low N, Unemo M, Abu-Raddad LJ, Chico RM, Smolak A, Newman L, Gottlieb S, Thwin SS, Broutet N, Taylor MM. Chlamydia, Gonorrhoea, trichomoniasis and syphilis: global prevalence and incidence estimates, 2016. Bull World Health Organ. 2019;97:548\u2013562P. https:\/\/doi.org\/10.2471\/BLT.18.228486.","journal-title":"Bull World Health Organ"},{"key":"10155_CR21","doi-asserted-by":"publisher","first-page":"e1002366","DOI":"10.1371\/journal.pmed.1002366","volume":"14","author":"E Alirol","year":"2017","unstructured":"Alirol E, Wi TE, Bala M, Bazzo ML, Chen XS, Deal C, Dillon JR, Kularatne R, Heim J, van Hooft R, Hook EW, Lahra MM, Lewis DA, Ndowa F, Shafer WM, Tayler L, Workowski K, Unemo M, Balasegaram M. Multidrug-resistant gonorrhea: a research and development roadmap to discover new medicines. PLoS Med. 2017;14:e1002366.","journal-title":"PLoS Med"},{"issue":"Suppl 6","key":"10155_CR22","doi-asserted-by":"publisher","first-page":"e25355","DOI":"10.1002\/jia2.25355","volume":"22","author":"MS Cohen","year":"2019","unstructured":"Cohen MS, Council OD, Chen JS. Sexually transmitted infections and HIV in the era of antiretroviral treatment and prevention: the biologic basis for epidemiologic synergy. J Int AIDS Soc. 2019;22(Suppl 6):e25355.","journal-title":"J Int AIDS Soc"},{"key":"10155_CR23","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1097\/00002030-199301000-00015","volume":"7","author":"M Laga","year":"1993","unstructured":"Laga M, Manoka A, Kivuvu M, Malele B, Tuliza M, Nzila N, et al. Non-ulcerative sexually transmitted diseases as risk factors for HIV- 1 transmission in women: results from a cohort study [see comments]. Aids. 1993;7:95\u2013102. https:\/\/doi.org\/10.1097\/00002030-199301000-00015. [PubMed] [CrossRef] [Google Scholar].","journal-title":"Aids"},{"issue":"2","key":"10155_CR24","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1136\/sti.2004.010249","volume":"81","author":"ST Sadiq","year":"2005","unstructured":"Sadiq ST, Taylor S, Copas AJ, Bennett J, Kaye S, Drake SM, et al. The effects of urethritis on seminal plasma HIV-1 RNA loads in homosexual men not receiving antiretroviral therapy. Sex Transm Infect. 2005;81(2):120\u20133.","journal-title":"Sex Transm Infect"},{"key":"10155_CR25","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1097\/MOH.0000000000000394","volume":"25","author":"JS Stevens","year":"2018","unstructured":"Stevens JS, Criss AK. Pathogenesis of Neisseria gonorrhoeae in the female reproductive tract: neutrophilic host response, sustained infection, and clinical sequelae. Curr Opin Hematol. 2018;25:13\u201321.","journal-title":"Curr Opin Hematol"},{"issue":"4","key":"10155_CR26","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1097\/QAI.0b013e3181c3ef29","volume":"53","author":"KT Bernstein","year":"2010","unstructured":"Bernstein KT, Marcus JL, Nieri G, Philip SS, Klausner JD. Rectal gonorrhoea and chlamydia reinfection is associated with increased risk of HIV seroconversion. J Acquir Immune Defic Syndr. 2010;53(4):537\u201343.","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"1","key":"10155_CR27","doi-asserted-by":"publisher","first-page":"849","DOI":"10.4102\/sajhivmed.v20i1.849","volume":"20","author":"S Lowe","year":"2019","unstructured":"Lowe S, Mudzviti T, Mandiriri A, Shamu T, Mudhokwani P, Chimbetete C, et al. Sexually transmitted infections, the silent partner in HIV-infected women in Zimbabwe. South Afr J HIV Med. 2019;20(1):849.","journal-title":"South Afr J HIV Med"},{"key":"10155_CR28","doi-asserted-by":"publisher","first-page":"e25343","DOI":"10.1002\/jia2.25343","volume":"22","author":"TE Wi","year":"2019","unstructured":"Wi TE, Ndowa FJ, Ferreyra C, Kelly-Cirino C, Taylor MM, Toskin I, Kiarie J, Santesso N, Unemo M. Diagnosing sexually transmitted infections in resource-constrained settings: challenges and ways forward. J Intern Aids Soc. 2019;22:e25343. https:\/\/doi.org\/10.1002\/jia2.25343.","journal-title":"J Intern Aids Soc"},{"key":"10155_CR29","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1097\/OLQ.0000000000000943","volume":"46","author":"A Y\u00e9o","year":"2019","unstructured":"Y\u00e9o A, Kouam\u00e9-Blavo B, Kouam\u00e9 CE, Ouattara A, Yao AC, Gbed\u00e9 BD, Bazan F, Faye-Kett\u00e9 H, Dosso M, Wi T, Unemo M. Establishment of a gonococcal antimicrobial surveillance programme, in accordance with World Health Organization standards, in C\u00f4te d\u2019Ivoire, western Africa, 2014\u20132017. Sex Transm Dis. 2019;46:179\u201384. https:\/\/doi.org\/10.1097\/OLQ.0000000000000943.","journal-title":"Sex Transm Dis"},{"issue":"2","key":"10155_CR30","doi-asserted-by":"publisher","first-page":"139","DOI":"10.4103\/0255-0857.180278","volume":"34","author":"R Verma","year":"2016","unstructured":"Verma R, Sood S. Gonorrhoea diagnostics: an update. Indian J Med Microbiol. 2016;34(2):139.","journal-title":"Indian J Med Microbiol"},{"key":"10155_CR31","unstructured":"Ministry of Health, Zambia National Formulary Committee. (2020). Standard Treatment Guidelines, Essential Medicines List, Essential Laboratory Supplies for Zambia, 5th edition. Zambia Ministry of Health, Lusaka. https:\/\/www.moh.gov.zm."},{"key":"10155_CR32","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1186\/s12879-022-07674-y","volume":"22","author":"KL Sarenje","year":"2022","unstructured":"Sarenje KL, Ngalamika O, Maimbolwa MC, Siame A, Munsaka SM, Kwenda G. Antimicrobial resistance of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Urban hospitals, Lusaka, Zambia. BMC Infect Dis. 2022;22:688. https:\/\/doi.org\/10.1186\/s12879-022-07674-y.","journal-title":"BMC Infect Dis"},{"key":"10155_CR33","volume-title":"Performance standards for antimicrobial susceptibility testing. CLSI-M100, 31st editions","author":"Clinical and Laboratory Standards Institute","year":"2021","unstructured":"Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing. CLSI-M100, 31st editions. Wayne (PA): Clinical and Laboratory Standards Institute; 2021."},{"key":"10155_CR34","unstructured":"Andrews S, FastQC:. A Quality Control Tool for High Throughput Sequence Data. Available: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"10155_CR35","doi-asserted-by":"publisher","unstructured":"Wingett SW, Andrews S. FastQ screen: a tool for multi-genome mapping and quality control. F1000Research; 2018. https:\/\/doi.org\/10.12688\/f1000research.15931.2.","DOI":"10.12688\/f1000research.15931.2"},{"key":"10155_CR36","unstructured":"Kneaddata. Available: https:\/\/huttenhower.sph.harvard.edu\/kneaddata\/."},{"key":"10155_CR37","unstructured":"van Zwetselaar M, BAP - KCRI CGE Bacterial Analysis Pipeline. 2022. Available: https:\/\/github.com\/kcri-tz\/kcri-cge-bap."},{"key":"10155_CR38","doi-asserted-by":"publisher","unstructured":"Thomsen MCF, Ahrenfeldt J, Cisneros JLB, Jurtz V, Larsen MV, Hasman H, et al. PLoS ONE. 2016;11:e0157718. https:\/\/doi.org\/10.1371\/journal.pone.0157718. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance.","DOI":"10.1371\/journal.pone.0157718"},{"key":"10155_CR39","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","volume":"19","author":"A Souvorov","year":"2018","unstructured":"Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol. 2018;19:153. https:\/\/doi.org\/10.1186\/s13059-018-1540-z.","journal-title":"Genome Biol"},{"key":"10155_CR40","unstructured":"van Zwetselaar M. unfasta - Command-line pipes and filters for genomic sequence data. zwets.it; 2022. Available: http:\/\/io.zwets.it\/2016\/01\/22\/introducing-unfasta\/."},{"key":"10155_CR41","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/JCM.02452-13","volume":"52","author":"H Hasman","year":"2014","unstructured":"Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-M\u00f8ller N, et al. Rapid Whole-Genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol. 2014;52:139\u201346. https:\/\/doi.org\/10.1128\/JCM.02452-13.","journal-title":"J Clin Microbiol"},{"key":"10155_CR42","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1128\/JCM.02981-13","volume":"52","author":"MV Larsen","year":"2014","unstructured":"Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, et al. Benchmarking of methods for genomic taxonomy. J Clin Microbiol. 2014;52:1529\u201339. https:\/\/doi.org\/10.1128\/JCM.02981-13.","journal-title":"J Clin Microbiol"},{"key":"10155_CR43","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1186\/s12859-018-2336-6","volume":"19","author":"PTLC Clausen","year":"2018","unstructured":"Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics. 2018;19:307. https:\/\/doi.org\/10.1186\/s12859-018-2336-6.","journal-title":"BMC Bioinformatics"},{"key":"10155_CR44","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","volume":"50","author":"MV Larsen","year":"2012","unstructured":"Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. Multilocus sequence typing of total-genome-sequenced Bacteria. J Clin Microbiol. 2012;50:1355\u201361. https:\/\/doi.org\/10.1128\/JCM.06094-11.","journal-title":"J Clin Microbiol"},{"key":"10155_CR45","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","volume":"11","author":"KA Jolley","year":"2010","unstructured":"Jolley KA, Maiden MC, BIGSdb. Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595. https:\/\/doi.org\/10.1186\/1471-2105-11-595.","journal-title":"BMC Bioinformatics"},{"key":"10155_CR46","unstructured":"van Zwetselaar M. KCST-Kmer-counting sequence typing. 2021. Available: https:\/\/io.zwets.it\/kcst."},{"key":"10155_CR47","doi-asserted-by":"publisher","unstructured":"Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother [cited 12 Aug 2020]. https:\/\/doi.org\/10.1093\/jac\/dkaa345.","DOI":"10.1093\/jac\/dkaa345"},{"key":"10155_CR48","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garc\u00eda-Fern\u00e1ndez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895\u2013903. https:\/\/doi.org\/10.1128\/AAC.02412-14.","journal-title":"Antimicrob Agents Chemother"},{"key":"10155_CR49","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043\u201355. https:\/\/doi.org\/10.1101\/gr.186072.114.","journal-title":"Genome Res"},{"key":"10155_CR50","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s13059-021-02393-0","volume":"22","author":"A Orakov","year":"2021","unstructured":"Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021;22:178. https:\/\/doi.org\/10.1186\/s13059-021-02393-0.","journal-title":"Genome Biol"},{"key":"10155_CR51","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114. https:\/\/doi.org\/10.1038\/s41467-018-07641-9.","journal-title":"Nat Commun"},{"key":"10155_CR52","doi-asserted-by":"publisher","first-page":"4868","DOI":"10.1093\/bioinformatics\/btab","volume":"37","author":"A Rempel","year":"2021","unstructured":"Rempel A, Wittler R. SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction. Bioinformatics. 2021;37:4868\u201370. https:\/\/doi.org\/10.1093\/bioinformatics\/btab.","journal-title":"Bioinformatics"},{"issue":"11","key":"10155_CR53","doi-asserted-by":"publisher","first-page":"1762","DOI":"10.1093\/infdis\/jiaa079","volume":"222","author":"CM Kahler","year":"2020","unstructured":"Kahler CM. The goldilocks zone: searching for a phylogenetic approach for the recombinogenic Neisseria gonorrhoeae. J Infect Dis. 2020;222(11):1762\u20133.","journal-title":"J Infect Dis"},{"key":"10155_CR54","unstructured":"https:\/\/pubmlst.org\/organisms\/neisseria-spp."},{"key":"10155_CR55","doi-asserted-by":"publisher","first-page":"e00906","DOI":"10.1128\/AAC.00906-20","volume":"64","author":"LD Maduna","year":"2020","unstructured":"Maduna LD, Kock MM, van der Veer BMJW, Radebe O, McIntyre J, van Alphen LB, Peters RPH. Antimicrobial resistance of Neisseria gonorrhoeae isolates from high-risk men in Johannesburg, South Africa. Antimicrob Agents Chemother. 2020;64:e00906\u201320. https:\/\/doi.org\/10.1128\/AAC.00906-20.","journal-title":"Antimicrob Agents Chemother"},{"key":"10155_CR56","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s13073-021-00858-2","volume":"13","author":"L Sanchez-Buso","year":"2021","unstructured":"Sanchez-Buso L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, et al. A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch. Genome Med. 2021;13:61. https:\/\/doi.org\/10.1186\/s13073-021-00858-2.","journal-title":"Genome Med"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10155-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-024-10155-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10155-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T15:04:29Z","timestamp":1710774269000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-024-10155-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,18]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["10155"],"URL":"https:\/\/doi.org\/10.1186\/s12864-024-10155-y","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,18]]},"assertion":[{"value":"23 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 February 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 March 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":"All examined gonococcal isolates were analyzed and preserved as part of the routine diagnostics, and information obtained during the study was kept confidential. Informed consent was obtained for all participants in the study. The study including its protocol was approved by the Zambia National Health Research Ethics Board (ZNHREB Ref No.E17020), and the University of Zambia Health Sciences Research Ethics Committee (UNZAHREC Ref No. 20190624004). The whole study was carried out following the Zambian STI guidelines and regulations which are in agreement with the Declaration of Helsinki.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"290"}}