{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T02:23:03Z","timestamp":1784082183187,"version":"3.55.0"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,13]],"date-time":"2022-01-13T00:00:00Z","timestamp":1642032000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"College of Science, Rochester Institute of Technology"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    <jats:italic>Neisseria<\/jats:italic>\n                    commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage\n                    <jats:italic>in vitro<\/jats:italic>\n                    selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (\u2265 2 \u03bcg\/mL) in the\n                    <jats:italic>Neisseria<\/jats:italic>\n                    commensal,\n                    <jats:italic>N<\/jats:italic>\n                    .\n                    <jats:italic>elongata<\/jats:italic>\n                    . Across multiple lineages (n = 7\/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (\n                    <jats:italic>rpmH<\/jats:italic>\n                    ) and the intergenic region proximal to the 30S ribosomal S3 protein (\n                    <jats:italic>rpsC)<\/jats:italic>\n                    through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in\n                    <jats:italic>rpmH<\/jats:italic>\n                    is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in\n                    <jats:italic>N<\/jats:italic>\n                    .\n                    <jats:italic>gonorrhoeae<\/jats:italic>\n                    . Transformations into the ancestral\n                    <jats:italic>N<\/jats:italic>\n                    .\n                    <jats:italic>elongata<\/jats:italic>\n                    lineage confirmed the causality of both\n                    <jats:italic>rpmH<\/jats:italic>\n                    and\n                    <jats:italic>rpsC<\/jats:italic>\n                    mutations. Though most lineages inheriting duplications suffered\n                    <jats:italic>in vitro<\/jats:italic>\n                    fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0262370","type":"journal-article","created":{"date-parts":[[2022,1,13]],"date-time":"2022-01-13T14:03:32Z","timestamp":1642082612000},"page":"e0262370","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications"],"prefix":"10.1371","volume":"17","author":[{"given":"Jordan C.","family":"Raisman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Fiore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucille","family":"Tomin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3402-7781","authenticated-orcid":true,"given":"Joseph K. O.","family":"Adjei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia X.","family":"Aswad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina J.","family":"Domondon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben A.","family":"Donahue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia A.","family":"Masciotti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Connor G.","family":"McGrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo","family":"Melita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul A.","family":"Podbielski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madelyn R.","family":"Schreiner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren J.","family":"Trumpore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter C.","family":"Wengert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emalee A.","family":"Wrightstone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-4322","authenticated-orcid":true,"given":"Andr\u00e9 O.","family":"Hudson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9449-2418","authenticated-orcid":true,"given":"Crista B.","family":"Wadsworth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,1,13]]},"reference":[{"issue":"1","key":"pone.0262370.ref001","first-page":"1","article-title":"High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings","volume":"11","author":"E Nji","year":"2021","journal-title":"Sci Rep"},{"key":"pone.0262370.ref002","doi-asserted-by":"crossref","first-page":"173","DOI":"10.3389\/fmicb.2016.00173","article-title":"Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer","volume":"7","author":"CJ Von Wintersdorff","year":"2016","journal-title":"Front Microbiol"},{"issue":"8","key":"pone.0262370.ref003","doi-asserted-by":"crossref","first-page":"2720","DOI":"10.1128\/AAC.00026-07","article-title":"Rapid dissemination and diversity of CTX-M extended-spectrum \u03b2-lactamase genes in commensal Escherichia coli isolates from healthy children from low-resource settings in Latin America","volume":"51","author":"L Pallecchi","year":"2007","journal-title":"Antimicrob Agents Ch"},{"issue":"1670","key":"pone.0262370.ref004","doi-asserted-by":"crossref","first-page":"20140087","DOI":"10.1098\/rstb.2014.0087","article-title":"The human gut resistome","volume":"370","author":"W. Van Schaik","year":"2015","journal-title":"Philos T Roy Soc B"},{"key":"pone.0262370.ref005","article-title":"Non-clinical settings\u2013the understudied facet of antimicrobial drug resistance","author":"S Castillo-Ram\u00edrez","year":"2021","journal-title":"Environ Microbiol"},{"key":"pone.0262370.ref006","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1111\/j.1365-2958.2005.04964.x","article-title":"Natural transformation of Neisseria gonorrhoeae: From DNA donation to homologous recombination","volume":"59","author":"HL Hamilton","year":"2006","journal-title":"Mol Microbiol"},{"key":"pone.0262370.ref007","doi-asserted-by":"crossref","first-page":"e1003458","DOI":"10.1371\/journal.pgen.1003458","article-title":"Dialects of the DNA uptake sequence in Neisseriaceae","volume":"9","author":"SA Frye","year":"2013","journal-title":"PLoS 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gonorrhoeae alleles","author":"AC Retchless","year":"2018","journal-title":"BMC Genomics"},{"key":"pone.0262370.ref017","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1093\/molbev\/msz225","article-title":"Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen","volume":"37","author":"B Arnold","year":"2020","journal-title":"Mol Biol Evol"},{"key":"pone.0262370.ref018","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1098\/rsif.2011.0601","article-title":"Population structure in the Neisseria, and the biological significance of fuzzy species","volume":"9","author":"J Corander","year":"2011","journal-title":"J Roy Soc Interface"},{"key":"pone.0262370.ref019","first-page":"1793","article-title":"Carriage of Neisseria meningitidis and other Neisseria species among children and young adults in Paraguay","volume":"68","author":"G Chamorro","year":"2019","journal-title":"J Med Microbiol"},{"key":"pone.0262370.ref020","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1016\/j.jinf.2016.03.010","article-title":"Pharyngeal carriage of Neisseria species in the African meningitis belt","volume":"72","author":"K Diallo","year":"2016","journal-title":"J Infect"},{"key":"pone.0262370.ref021","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1128\/CMR.00040-10","article-title":"Review and international recommendation of methods for typing Neisseria gonorrhoeae isolates and their implications for improved knowledge of gonococcal epidemiology, treatment, and biology","volume":"24","author":"M Unemo","year":"2011","journal-title":"Clin Microbiol Rev"},{"key":"pone.0262370.ref022","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1099\/mic.0.000086","article-title":"Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus","volume":"161","author":"G Liu","year":"2015","journal-title":"Microbiol"},{"key":"pone.0262370.ref023","doi-asserted-by":"crossref","first-page":"13742","DOI":"10.1038\/s41598-019-50203-2","article-title":"Genomic characterization of novel Neisseria species","volume":"9","author":"K Diallo","year":"2019","journal-title":"Sci Rep"},{"issue":"2","key":"pone.0262370.ref024","doi-asserted-by":"crossref","first-page":"e01494","DOI":"10.1128\/AAC.01494-19","article-title":"Meningococcal Quinolone Resistance Originated from Several Commensal Neisseria Species","volume":"64","author":"M Chen","year":"2020","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"pone.0262370.ref025","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1056\/NEJMoa0806414","article-title":"Emergence of ciprofloxacin-resistant Neisseria meningitidis in North America","volume":"360","author":"HM Wu","year":"2009","journal-title":"N Engl J Med"},{"key":"pone.0262370.ref026","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1093\/cid\/ciz365","article-title":"decreased cephalosporin susceptibility of oropharyngeal Neisseria species in antibiotic-using men who have sex with men in Hanoi, Vietnam","volume":"70","author":"HV Dong","year":"2019","journal-title":"Clin Infect Dis"},{"issue":"5","key":"pone.0262370.ref027","doi-asserted-by":"crossref","first-page":"538","DOI":"10.3390\/antibiotics10050538","article-title":"Antimicrobial resistance profiles of human commensal Neisseria species","volume":"10","author":"M Goytia","year":"2021","journal-title":"Antibiotics"},{"key":"pone.0262370.ref028","doi-asserted-by":"crossref","first-page":"656","DOI":"10.3390\/antibiotics9100656","article-title":"Exploration of the Neisseria resistome reveals resistance mechanisms in commensals that may be acquired by N. gonorrhoeae through horizontal gene transfer","volume":"9","author":"MA Fiore","year":"2020","journal-title":"Antibiotics"},{"key":"pone.0262370.ref029","doi-asserted-by":"crossref","first-page":"384","DOI":"10.3390\/pathogens10030384","article-title":"WGS of commensal Neisseria reveals acquisition of a new ribosomal protection protein (MsrD) as a possible explanation for high level azithromycin resistance in Belgium","volume":"10","author":"T de Block","year":"2021","journal-title":"Pathogens"},{"key":"pone.0262370.ref030","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.drup.2014.02.002","article-title":"Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance","volume":"16","author":"G Jansen","year":"2013","journal-title":"Drug Resistance Updates"},{"key":"pone.0262370.ref031","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1128\/AAC.00149-15","article-title":"Novel genes related to ceftriaxone resistance found among ceftriaxone-resistant Neisseria gonorrhoeae strains selected in 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International journal of STD &","volume":"31","author":"H Fifer","year":"2020","journal-title":"AIDS"},{"key":"pone.0262370.ref035","first-page":"1","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"Clinical Laboratory Standards Institute","year":"2019","edition":"29"},{"issue":"4","key":"pone.0262370.ref036","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1093\/jac\/dkz535","article-title":"Susceptibility of invasive Neisseria meningitidis strains isolated in Germany to azithromycin, an alternative agent for post-exposure prophylaxis","volume":"75","author":"M Krone","year":"2020","journal-title":"J Antimicrobl Chem"},{"issue":"3","key":"pone.0262370.ref037","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofv117","article-title":"Population-Based Surveillance of Neisseria meningitidis Antimicrobial Resistance in the United States.","volume":"2","author":"BH Harcourt","year":"2015","journal-title":"Open Forum Infect Dis."},{"issue":"2","key":"pone.0262370.ref038","doi-asserted-by":"crossref","first-page":"e01699","DOI":"10.1128\/JCM.01699-20","article-title":"Genomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing","volume":"59","author":"KV Sukhum","year":"2021","journal-title":"J Clin Microbiol"},{"key":"pone.0262370.ref039","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1128\/AAC.00309-10","article-title":"High-level azithromycin resistance occurs in Neisseria gonorrhoeae as a result of a single point mutation in the 23S rRNA genes","volume":"54","author":"SA Chisholm","year":"2010","journal-title":"Antimicrob Agents Ch"},{"key":"pone.0262370.ref040","doi-asserted-by":"crossref","first-page":"3020","DOI":"10.1128\/AAC.46.9.3020-3025.2002","article-title":"Mutation in 23S rRNA associated with macrolide resistance in Neisseria gonorrhoeae","volume":"46","author":"LK Ng","year":"2002","journal-title":"Antimicrob Agents Ch"},{"key":"pone.0262370.ref041","doi-asserted-by":"crossref","first-page":"5374","DOI":"10.1038\/s41467-020-19250-6","article-title":"Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae","volume":"11","author":"KC Ma","year":"2020","journal-title":"Nat Commun"},{"key":"pone.0262370.ref042","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1128\/JCM.03195-15","article-title":"Genomic epidemiology and molecular resistance mechanisms of azithromycin-resistant Neisseria gonorrhoeae in Canada from 1997 to 2014","volume":"54","author":"W Demczuk","year":"2016","journal-title":"J Clin Microbiol"},{"key":"pone.0262370.ref043","doi-asserted-by":"crossref","first-page":"4162","DOI":"10.1128\/jb.177.14.4162-4165.1995","article-title":"Transcriptional control of the mtr efflux system of Neisseria gonorrhoeae","volume":"177","author":"KE Hagman","year":"1995","journal-title":"J Bacteriol"},{"key":"pone.0262370.ref044","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/jac\/47.5.651","article-title":"Decreased susceptibility to azithromycin and erythromycin mediated by a novel mtr(R) promoter mutation in Neisseria gonorrhoeae","volume":"47","author":"L Zarantonelli","year":"2001","journal-title":"J Antimicrob Chemoth"},{"key":"pone.0262370.ref045","doi-asserted-by":"crossref","first-page":"e00187-11","DOI":"10.1128\/mBio.00187-11","article-title":"A novel mechanism of high-level, broad-spectrum antibiotic resistance caused by a single base pair change in Neisseria gonorrhoeae","volume":"2","author":"EA Ohneck","year":"2011","journal-title":"mBio"},{"issue":"22","key":"pone.0262370.ref046","doi-asserted-by":"crossref","first-page":"3820","DOI":"10.1128\/JB.01896-14","article-title":"Defect in the formation of 70S ribosomes caused by lack of ribosomal protein L34 can be suppressed by 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Andrews","year":"2010","journal-title":"FASTQC: A quality control tool for high throughput sequence data."},{"key":"pone.0262370.ref054","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0262370.ref055","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"pone.0262370.ref056","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T. 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