{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:48:36Z","timestamp":1791852516284,"version":"4.3.4"},"reference-count":35,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T00:00:00Z","timestamp":1643328000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The uropathogens is the main cause of urinary tract infection (UTI). The aim of the study was to isolate bacteria from urine samples of UTI patients and find out the susceptibility of isolated bacteria. Bacteria were identified using both conventional and molecular methods. Sanger sequence procedure used for 16S ribosomal RNA and phylogenetic analysis was performed using Molecular Evolutionary Genetics Analysis (MEGA-7) software. In this study,<jats:italic>Escherichia coli<\/jats:italic>,<jats:italic>Klebsiella pneumonia<\/jats:italic>,<jats:italic>Staphylococcus<\/jats:italic>were reported as 58, 28 and 14.0% respectively. Phylogenetic tree revealed that 99% of sample No. Ai (05) is closely related to<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>to (NR 114042.1<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>strain NBRC 102203). Aii (23) is 99% similar to<jats:italic>K<\/jats:italic>.<jats:italic>pneumoniae<\/jats:italic>to (NR 117686.1<jats:italic>K<\/jats:italic>.<jats:italic>pneumonia<\/jats:italic>strain DSM 30104) and 90% Bi (48) is closely linked to<jats:italic>S<\/jats:italic>.<jats:italic>aureus<\/jats:italic>to (NR 113956.1<jats:italic>S<\/jats:italic>.<jats:italic>aureus<\/jats:italic>strain NBRC 100910). The antibiotic susceptibility of<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>recorded highest resistance towards ampicillin (90%) and least resistant to ofloxacin (14%). Some of the other antibiotics such amoxicillin, ciprofloxacin, gentamicin, ceftazidime, cefuroxime and nitrofurantoin resistance were observed 86, 62, 24, 55, 48 and 35% respectively. The cefuroxime showed the highest antibiotic resistance against<jats:italic>K<\/jats:italic>.<jats:italic>pneumoniae<\/jats:italic>with 85% followed by amoxicillin, ciprofloxacin, gentamicin, ceftazidime, ampicillin and nitrofurantoin resulted in 60, 45, 67, 70, 75 and 30% respectively. The resistance of<jats:italic>S<\/jats:italic>.<jats:italic>aureus<\/jats:italic>against erythromycin, cefuroxime and ampicillin were found with 72%. The resistance against amoxicillin, gentamicin, ceftazidime and ceftriaxone found 57, 43, 43 and 15% respectively. Phylogenetic analysis shows that sequences are closely related with the reference sequences and<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>is the dominant bacteria among UTI patients and is resistant to the commercially available antibiotics.<\/jats:p>","DOI":"10.1371\/journal.pone.0262952","type":"journal-article","created":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T18:25:41Z","timestamp":1643394341000},"page":"e0262952","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens"],"prefix":"10.1371","volume":"17","author":[{"given":"Hanif","family":"Ullah","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kashif","family":"Bashir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Idrees","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amin","family":"Ullah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neelma","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bilal","family":"Nasir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tariq","family":"Nadeem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hina","family":"Ahsan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Islam","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3160-4830","authenticated-orcid":true,"given":"Qurban","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sher","family":"Muhammad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Afzal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,1,28]]},"reference":[{"issue":"39","key":"pone.0262952.ref001","doi-asserted-by":"crossref","first-page":"15530","DOI":"10.1073\/pnas.1315203110","article-title":"Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation","volume":"110","author":"D. J. Schwartz","year":"2013","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6","key":"pone.0262952.ref002","doi-asserted-by":"crossref","first-page":"e450","DOI":"10.1016\/j.ijid.2013.01.025","article-title":"Distribution of uropathogenic virulence genes in Escherichia coli isolated from patients with urinary tract infection","volume":"17","author":"M. Tarchouna","year":"2013","journal-title":"International Journal of Infectious Diseases"},{"issue":"1","key":"pone.0262952.ref003","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3923\/crb.2011.9.15","article-title":"Emerging of multidrug resistance human pathogens from urinary tract infections","volume":"4","author":"S. Manikandan","year":"2011","journal-title":"Current Research in Bacteriology"},{"issue":"1","key":"pone.0262952.ref004","first-page":"1","article-title":"Catheter associated urinary tract infection and obstinate biofilm producers","volume":"1","author":"G Maharjan","year":"2018","journal-title":"Candian Journal of Infectious Diseases and Medical Microbiology"},{"issue":"6","key":"pone.0262952.ref005","first-page":"61","article-title":"Bacteriological profile and antimicrobial susceptibility pattern of community acquired urinary tract infection in children: a tertiary care experience","volume":"15","author":"P Sargiary","year":"2016","journal-title":"Journal of Dental and Medical Science"},{"issue":"f2","key":"pone.0262952.ref006","first-page":"13","article-title":"Incidence of urinary tract infections (UTI) among children and adolescents in Ile-Ife, Nigeria","volume":"1","author":"O Aiyegoro","year":"2007","journal-title":"African Journal of Microbiology Research"},{"issue":"3","key":"pone.0262952.ref007","doi-asserted-by":"crossref","first-page":"e0174199","DOI":"10.1371\/journal.pone.0174199","article-title":"Contribution of urinary tract infection to the burden of febrile illnesses in young children in rural Kenya","volume":"12","author":"WG Masika","year":"2017","journal-title":"PLoS One"},{"issue":"2","key":"pone.0262952.ref008","doi-asserted-by":"crossref","first-page":"187","DOI":"10.4314\/ejhs.v28i2.10","article-title":"Pediatric urinary tract infection as a cause of outpatient clinic visits in southern Ethiopia: a cross sectional study","volume":"28","author":"E Mitiku","year":"2018","journal-title":"Ethiop J Health Sci."},{"issue":"Suppl 2","key":"pone.0262952.ref009","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1111\/j.1365-2362.2008.01986.x","article-title":"Mechanisms and consequences of bladder cell invasion by uropathogenic Escherichia coli","volume":"38","author":"BK Dhakal","year":"2008","journal-title":"European Journal of Clinical Investigation"},{"key":"pone.0262952.ref010","first-page":"153","article-title":"the clinical features and antibiotic susceptibility of causative bacters of pyelonephritis of children in Mongolia","volume":"3","author":"L Dashiimaa","year":"2010","journal-title":"Journal of Mongolian Medicine"},{"key":"pone.0262952.ref011","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1128\/AEM.06921-11","article-title":"Multiplex PCR-based reverse line blot assay for simultaneous detection of 22 virulence genes in uropathogenic Escherichia coli","volume":"78","author":"T Kudinha","year":"2012","journal-title":"Applied Environmental Microbiology"},{"issue":"1","key":"pone.0262952.ref012","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.bjid.2015.09.003","article-title":"Follow-up after infants younger than 2 months of age with urinary tract infection in Southern Israel: epidemiologic, microbiologic and disease recurrence characteristics","volume":"20","author":"E. Gurevich","year":"2016","journal-title":"Brazilian Journal of Infectious Diseases"},{"issue":"1","key":"pone.0262952.ref013","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1128\/microbiolspec.VMBF-0017-2015","article-title":"Evolution of bacterial pathogens within the human host","volume":"4","author":"K. A. Bliven","year":"2016","journal-title":"Microbiology Spectrum"},{"issue":"10","key":"pone.0262952.ref014","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1111\/j.1469-0691.2008.02070.x","article-title":"Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories","volume":"14","author":"P.C. Woo","year":"2008","journal-title":"Clinical Microbiology Infections"},{"key":"pone.0262952.ref015","doi-asserted-by":"crossref","first-page":"5975","DOI":"10.5897\/AJB2013.12057","article-title":"Bacterial species identification getting easier","volume":"12","author":"T. Phumudzo","year":"2013","journal-title":"African Journal of Biotechonlogy"},{"key":"pone.0262952.ref016","doi-asserted-by":"crossref","first-page":"2761","DOI":"10.1128\/JCM.01228-07","article-title":"16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls","volume":"45","author":"J. Michael","year":"2007","journal-title":"Journal of clinical Microbiology"},{"issue":"4","key":"pone.0262952.ref017","first-page":"69","article-title":"Isolation, Identification, Molecular Characterization and Antibiotic Susceptibility Testing of Uro-Pathogenic E. Coli (UPEC) Isolated From Non-Hospitalized Urinary tract infections (UTI)","volume":"2","author":"Z. A. Badini","year":"2019","journal-title":"Pak-Euro Journal of Medical and Life Sciences"},{"issue":"06","key":"pone.0262952.ref018","doi-asserted-by":"crossref","first-page":"459","DOI":"10.3855\/jidc.8257","article-title":"Analysis of diarrheagenic potential of uropathogenic Escherichia coli isolates in Dhaka, Bangladesh","volume":"11","author":"M. Khaleque","year":"2017","journal-title":"The Journal of Infection in Developing Countries"},{"issue":"2","key":"pone.0262952.ref019","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1128\/jmbe.v11i2.205","article-title":"Review of three DNA analysis applications for use in the microbiology or genetics classroom","volume":"11","author":"D. S. Treves","year":"2010","journal-title":"Journal of Microbiology & Biology Education: JMBE"},{"key":"pone.0262952.ref020","doi-asserted-by":"crossref","first-page":"100727","DOI":"10.1016\/j.nmni.2020.100727","article-title":"Phenotypic and genotypic characterization of clinical carbapenem-resistant Enterobacteriaceae isolates from Sokoto, northwest Nigeria","volume":"37","author":"A. Olowo-okere","year":"2020","journal-title":"New Microbes and New Infections"},{"issue":"7","key":"pone.0262952.ref021","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"S. Kumar","year":"2016","journal-title":"Molecular biology and evolution"},{"issue":"4","key":"pone.0262952.ref022","doi-asserted-by":"crossref","first-page":"16","DOI":"10.54530\/jcmc.268","article-title":"Knowledge, attitude and practice on antibiotic use and its resistance among medical students in a tertiary care hospital","volume":"10","author":"S. Panthi","year":"2020","journal-title":"Journal of Chitwan Medical College"},{"issue":"5","key":"pone.0262952.ref023","first-page":"411","article-title":"Antibiotic resistance of urinary tract infection of children under 14 years admitted to the pediatric clinic of Imam Sajjad hospital, 2012","volume":"19","author":"F F. Asadi Manesh","year":"2014","journal-title":"Armaghane danesh"},{"issue":"1","key":"pone.0262952.ref024","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13104-018-3910-8","article-title":"Bacterial profile, antibiotic susceptibility pattern and associated factors among pregnant women with Urinary Tract Infection in Goba and Sinana Woredas, Bale Zone, Southeast Ethiopia","volume":"11","author":"S. Taye","year":"2018","journal-title":"BMC Research Notes"},{"issue":"1","key":"pone.0262952.ref025","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-27342-z","article-title":"Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae)","volume":"8","author":"W. S. Mohammed","year":"2018","journal-title":"Scientific Reports"},{"issue":"3","key":"pone.0262952.ref026","doi-asserted-by":"crossref","DOI":"10.5812\/archcid.101136","article-title":"Molecular Detection and Identification of Bacteria in Urine Samples of Asymptomatic and Symptomatic Pregnant Women by 16S rRNA Gene Sequencing","volume":"15","author":"P. Lakshmi","year":"2020","journal-title":"Archives of Clinical Infectious Diseases"},{"issue":"1","key":"pone.0262952.ref027","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-22660-8","article-title":"Microbial metagenome of urinary tract infection","volume":"8","author":"A. Moustafa","year":"2018","journal-title":"Scientific reports"},{"issue":"1","key":"pone.0262952.ref028","doi-asserted-by":"crossref","DOI":"10.54112\/bcsrj.v2021i1.51","article-title":"Perception regarding self-medication of antibiotics in general public sector university of southern Punjab: a comparison between medical and non-medical students","volume":"2021","author":"S. Khalid","year":"2021","journal-title":"Biological and Clinical Sciences Research Journal"},{"issue":"1","key":"pone.0262952.ref029","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4102\/phcfm.v7i1.800","article-title":"Antimicrobial susceptibility profile of uropathogens in Maluti Adventist Hospital patients, 2011","volume":"7","author":"P. Mubanga","year":"2015","journal-title":"African journal of Primary Health Care & Family medicine"},{"issue":"1","key":"pone.0262952.ref030","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-67732-w","article-title":"Efficacy of Acacia nilotica aqueous extract in treating biofilm-forming and multidrug resistant uropathogens isolated from patients with UTI syndrome","volume":"10","author":"R. B. Elamary","year":"2020","journal-title":"Scientific Reports"},{"issue":"1","key":"pone.0262952.ref031","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-19690-7","article-title":"A urine-dependent human urothelial organoid offers a potential alternative to rodent models of infection","volume":"8","author":"H. Horsley","year":"2018","journal-title":"Scientific Reports"},{"issue":"1","key":"pone.0262952.ref032","article-title":"A Sonographic evaluation of pediatric acute abdominal pain: A systematic review","volume":"2021","author":"U. Nadeem","year":"2021","journal-title":"Biological and Clinical Sciences Research Journal"},{"issue":"14","key":"pone.0262952.ref033","doi-asserted-by":"crossref","first-page":"3165","DOI":"10.1007\/s00216-019-01784-4","article-title":"A micro-Raman and chemometric study of urinary tract infection-causing bacterial pathogens in mixed cultures","volume":"411","author":"M. Yogesha","year":"2019","journal-title":"Analytical and bioanalytical chemistry"},{"issue":"1","key":"pone.0262952.ref034","doi-asserted-by":"crossref","DOI":"10.54112\/bcsrj.v2020i1.23","article-title":"Uterine artery doppler indices as predictive measures for the pre-eclampsia and intrauterine growth restriction","volume":"2020","author":"M. Rashid","year":"2020","journal-title":"Biological and Clinical Sciences Research Journal"},{"issue":"1","key":"pone.0262952.ref035","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-020-05402-y","article-title":"Bacterial profile, antibiotic susceptibility pattern and associated risk factors of urinary tract infection among clinically suspected children attending at Felege-Hiwot comprehensive and specialized hospital, Northwest Ethiopia. A prospective study","volume":"20","author":"A. Fenta","year":"2020","journal-title":"BMC Infectious Diseases"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0262952","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T03:09:57Z","timestamp":1674616197000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0262952"}},"subtitle":[],"editor":[{"given":"Muhammad Hussnain","family":"Siddique","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,1,28]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0262952","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,28]]}}}