Molecular Surveillance of Antimicrobial Resistance in Human Clinical Isolates : A Clinician- Scientist Growth Journey

Molecular Surveillance of Antimicrobial Resistance in Human Clinical Isolates : A Clinician- Scientist Growth Journey | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Molecular Surveillance of Antimicrobial Resistance in Human Clinical Isolates : A Clinician- Scientist Growth Journey Dr. Atul Amarshibhai Devganiya This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7695606/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Antimicrobial resistance (AMR) is a critical global health challenge, contributing to approximately 5 million deaths annually ( The Lancet , 2022, DOI: 10.1016/S0140-6736(21)02724-0). In India, high antibiotic consumption and inconsistent infection control amplify AMR’s impact, necessitating clinician-led surveillance ( The Lancet Infectious Diseases , 2025, DOI: 10.1016/S1473-3099(24)00512-1). This study, conducted primarily in Banaskantha, Gujarat, using discarded samples from Banas Civil Hospital, Palanpur, under ethical protocols approved by the Institutional Ethics Committee ( ICMR Guidelines , 2017, DOI: 10.4103/0971-5916.207231), integrates phenotypic and genotypic methods to track AMR trends. Concurrently, I contributed to Equity-First Community Resilience: Integrated Public Health Strategies for Chronic Disease Prevention, Mental Wellbeing, and Climate Adaptation with my brother, Rahul Devganiya (M.Sc. Software Engineering candidate, University of West London), reflecting my broader public health engagement. Objectives : 1. To conduct longitudinal surveillance (2021–2025) of AMR in bacterial pathogens from clinical isolates in Banaskantha, contributing to regional and global datasets. 2. To apply molecular techniques, including PCR and Sanger sequencing, to detect resistance genes ( bla CTX-M, bla NDM, bla OXA-48, mecA , vanA ), aligned with international standards ( Clinical Microbiology Reviews , 2023, DOI: 10.1128/cmr.00022-22). 3. To document the professional development of a medical student into a clinician-scientist, demonstrating the feasibility of molecular microbiology research in resource-limited settings ( The Lancet Global Health , 2025, DOI: 10.1016/S2214-109X(24)00487-6). Methods From January 2021 to August 2025, 242 non-duplicate clinical isolates (urine, blood, pus, sputum, cerebrospinal fluid) were collected from discarded samples at Banas Civil Hospital, Palanpur, and analyzed at laboratories affiliated with Banas Medical College (2019–2025) and Kiran Medical College (2025–present). Antimicrobial susceptibility testing (AST) adhered to Clinical and Laboratory Standards Institute guidelines (CLSI M100, 31st ed.) using Kirby-Bauer disk diffusion and broth microdilution. Molecular assays, initiated in 2023 during my fourth year, progressed from single-gene PCR to multiplex PCR, targeting bla CTX-M, bla NDM, bla OXA-48, mecA , and vanA genes. DNA extraction advanced from boiling lysis to commercial kits, with amplicons verified by Sanger sequencing ( Journal of Antimicrobial Chemotherapy , 2024, DOI: 10.1093/jac/dkad393). Data analysis utilized R (v4.3.2) with ggplot2, consistent with global benchmarks ( Nature Reviews Microbiology , 2023, DOI: 10.1038/s41579-022-00846-2). Results Across 2021–2025, 242 isolates were analyzed (2021: 64; 2022: 87; 2023: 51; 2024: 29; 2025: 11). Predominant pathogens included Escherichia coli (38%, n=92), Klebsiella pneumoniae (26%, n=64), Pseudomonas aeruginosa (17%, n=41), Staphylococcus aureus (10%, n=23), and Enterococcus spp. (9%, n=22), reflecting hospital-acquired infection patterns ( Clinical Infectious Diseases , 2024, DOI: 10.1093/cid/ciad683). Resistance to third-generation cephalosporins was high ( E. coli : 64%; K. pneumoniae : 59%), consistent with regional trends ( The Lancet Regional Health – Southeast Asia , 2025, DOI: 10.1016/j.lansea.2024.100362). Carbapenem resistance peaked at 17% in 2024 ( Journal of Infectious Diseases , 2024, DOI: 10.1093/infdis/jiad567). MRSA prevalence was 28%, with VRE at 6%. Molecular assays detected bla CTX-M (42%), bla NDM (11%), bla OXA-48 (7%), mecA (25% of S. aureus ), and vanA (2 isolates), with genotype-phenotype concordance exceeding 80% ( Nature Microbiology , 2024, DOI: 10.1038/s41564-023-01576-0). Conclusion This study maps AMR trends in Banaskantha’s clinical isolates, contributing to infection control strategies while documenting my growth from a medical student (2019–2024) to a clinician-scientist (2025). By integrating phenotypic and genotypic approaches, it aligns with the One Health framework ( The Lancet Planetary Health , 2023, DOI: 10.1016/S2542-5196(23)00062-8) and demonstrates the potential of early-career clinicians in resource-limited settings to advance global AMR research. Antimicrobial resistance molecular microbiology ESBL carbapenemase MRSA VRE whole genome sequencing One Health clinician-scientist surveillance Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7695606","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":519478607,"identity":"71df20e3-6930-4730-877c-6a9e0d1840a7","order_by":0,"name":"Dr. Atul Amarshibhai Devganiya","email":"data:image/png;base64,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","orcid":"https://orcid.org/0009-0003-1281-4079","institution":"Banas Medical College \u0026 Research Institute","correspondingAuthor":true,"prefix":"Dr.","firstName":"Atul","middleName":"Amarshibhai","lastName":"Devganiya","suffix":""}],"badges":[],"createdAt":"2025-09-23 14:40:49","currentVersionCode":1,"declarations":{"humanSubjects":true,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":true,"humanSubjectConsent":true,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-7695606/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7695606/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":92130660,"identity":"38b1fe1d-63fe-4d2b-bed2-ccf51c9bc7c5","added_by":"auto","created_at":"2025-09-25 02:58:43","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1228257,"visible":true,"origin":"","legend":"","description":"","filename":"AMRResearch.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7695606/v1_covered_cd8525c4-5314-48e4-8fde-f0ce7ff2b482.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eMolecular Surveillance of Antimicrobial Resistance in Human Clinical Isolates : A Clinician- Scientist Growth Journey\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Banas Medical College \u0026 Research Institute","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Antimicrobial resistance, molecular microbiology, ESBL, carbapenemase, MRSA, VRE, whole genome sequencing, One Health, clinician-scientist, surveillance","lastPublishedDoi":"10.21203/rs.3.rs-7695606/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7695606/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAntimicrobial resistance (AMR) is a critical global health challenge, contributing to approximately 5 million deaths annually (\u003cem\u003eThe Lancet\u003c/em\u003e, 2022, DOI: 10.1016/S0140-6736(21)02724-0). In India, high antibiotic consumption and inconsistent infection control amplify AMR’s impact, necessitating clinician-led surveillance (\u003cem\u003eThe Lancet Infectious Diseases\u003c/em\u003e, 2025, DOI: 10.1016/S1473-3099(24)00512-1). This study, conducted primarily in Banaskantha, Gujarat, using discarded samples from Banas Civil Hospital, Palanpur, under ethical protocols approved by the Institutional Ethics Committee (\u003cem\u003eICMR Guidelines\u003c/em\u003e, 2017, DOI: 10.4103/0971-5916.207231), integrates phenotypic and genotypic methods to track AMR trends. Concurrently, I contributed to \u003cem\u003eEquity-First Community Resilience: Integrated Public Health Strategies for Chronic Disease Prevention, Mental Wellbeing, and Climate Adaptation\u003c/em\u003e with my brother, Rahul Devganiya (M.Sc. Software Engineering candidate, University of West London), reflecting my broader public health engagement.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eObjectives\u003c/strong\u003e:\u003c/p\u003e\n\u003cp\u003e1. To conduct longitudinal surveillance (2021–2025) of AMR in bacterial pathogens from clinical isolates in Banaskantha, contributing to regional and global datasets.\u003c/p\u003e\n\u003cp\u003e2. To apply molecular techniques, including PCR and Sanger sequencing, to detect resistance genes (\u003cem\u003ebla\u003c/em\u003eCTX-M, \u003cem\u003ebla\u003c/em\u003eNDM, \u003cem\u003ebla\u003c/em\u003eOXA-48, \u003cem\u003emecA\u003c/em\u003e, \u003cem\u003evanA\u003c/em\u003e), aligned with international standards (\u003cem\u003eClinical Microbiology Reviews\u003c/em\u003e, 2023, DOI: 10.1128/cmr.00022-22).\u003c/p\u003e\n\u003cp\u003e3. To document the professional development of a medical student into a clinician-scientist, demonstrating the feasibility of molecular microbiology research in resource-limited settings (\u003cem\u003eThe Lancet Global Health\u003c/em\u003e, 2025, DOI: 10.1016/S2214-109X(24)00487-6).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFrom January 2021 to August 2025, 242 non-duplicate clinical isolates (urine, blood, pus, sputum, cerebrospinal fluid) were collected from discarded samples at Banas Civil Hospital, Palanpur, and analyzed at laboratories affiliated with Banas Medical College (2019–2025) and Kiran Medical College (2025–present). Antimicrobial susceptibility testing (AST) adhered to Clinical and Laboratory Standards Institute guidelines (CLSI M100, 31st ed.) using Kirby-Bauer disk diffusion and broth microdilution. Molecular assays, initiated in 2023 during my fourth year, progressed from single-gene PCR to multiplex PCR, targeting \u003cem\u003ebla\u003c/em\u003eCTX-M, \u003cem\u003ebla\u003c/em\u003eNDM, \u003cem\u003ebla\u003c/em\u003eOXA-48, \u003cem\u003emecA\u003c/em\u003e, and \u003cem\u003evanA\u003c/em\u003e genes. DNA extraction advanced from boiling lysis to commercial kits, with amplicons verified by Sanger sequencing (\u003cem\u003eJournal of Antimicrobial Chemotherapy\u003c/em\u003e, 2024, DOI: 10.1093/jac/dkad393). Data analysis utilized R (v4.3.2) with ggplot2, consistent with global benchmarks (\u003cem\u003eNature Reviews Microbiology\u003c/em\u003e, 2023, DOI: 10.1038/s41579-022-00846-2).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAcross 2021–2025, 242 isolates were analyzed (2021: 64; 2022: 87; 2023: 51; 2024: 29; 2025: 11). Predominant pathogens included \u003cem\u003eEscherichia coli\u003c/em\u003e (38%, n=92), \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e (26%, n=64), \u003cem\u003ePseudomonas aeruginosa\u003c/em\u003e (17%, n=41), \u003cem\u003eStaphylococcus aureus\u003c/em\u003e (10%, n=23), and \u003cem\u003eEnterococcus\u003c/em\u003e spp. (9%, n=22), reflecting hospital-acquired infection patterns (\u003cem\u003eClinical Infectious Diseases\u003c/em\u003e, 2024, DOI: 10.1093/cid/ciad683). Resistance to third-generation cephalosporins was high (\u003cem\u003eE. coli\u003c/em\u003e: 64%; \u003cem\u003eK. pneumoniae\u003c/em\u003e: 59%), consistent with regional trends (\u003cem\u003eThe Lancet Regional Health – Southeast Asia\u003c/em\u003e, 2025, DOI: 10.1016/j.lansea.2024.100362). Carbapenem resistance peaked at 17% in 2024 (\u003cem\u003eJournal of Infectious Diseases\u003c/em\u003e, 2024, DOI: 10.1093/infdis/jiad567). MRSA prevalence was 28%, with VRE at 6%. Molecular assays detected \u003cem\u003ebla\u003c/em\u003eCTX-M (42%), \u003cem\u003ebla\u003c/em\u003eNDM (11%), \u003cem\u003ebla\u003c/em\u003eOXA-48 (7%), \u003cem\u003emecA\u003c/em\u003e (25% of \u003cem\u003eS. aureus\u003c/em\u003e), and \u003cem\u003evanA\u003c/em\u003e(2 isolates), with genotype-phenotype concordance exceeding 80% (\u003cem\u003eNature Microbiology\u003c/em\u003e, 2024, DOI: 10.1038/s41564-023-01576-0).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study maps AMR trends in Banaskantha’s clinical isolates, contributing to infection control strategies while documenting my growth from a medical student (2019–2024) to a clinician-scientist (2025). By integrating phenotypic and genotypic approaches, it aligns with the One Health framework (\u003cem\u003eThe Lancet Planetary Health\u003c/em\u003e, 2023, DOI: 10.1016/S2542-5196(23)00062-8) and demonstrates the potential of early-career clinicians in resource-limited settings to advance global AMR research.\u003c/p\u003e","manuscriptTitle":"Molecular Surveillance of Antimicrobial Resistance in Human Clinical Isolates : A Clinician- Scientist Growth Journey","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-25 02:50:35","doi":"10.21203/rs.3.rs-7695606/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"c62e453e-a08e-414c-9413-eb05b7a4e034","owner":[],"postedDate":"September 25th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-25T02:50:35+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-25 02:50:35","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7695606","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7695606","identity":"rs-7695606","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}