Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 5 2021 10 08 583 591 Ajanta Sharma Department of Microbiology, Gauhati Medical College, Guwahati, Assam Bornali Dutta Department of Microbiology, Gauhati Medical College, Guwahati, Assam Debajit Rabha Department of Microbiology, Gauhati Medical College, Guwahati, Assam Elmy Rasul Department of Microbiology, Fakaruddin Ali Ahmed Medical College, Barpeta, Assam Naba Hazarika Department of Microbiology, Gauhati Medical College, Guwahati, Assam 2020 12 20 2021 08 06 Background and Objectives: Information on the genetic epidemiology of cholera in Assam, a northeastern state of India is lacking despite cholera being a major public health problem. The study aimed to determine the virulence genes and genes encoding antibiotic resistance in Vibrio cholerae isolates and to determine the prevalent genotypes based on the presence or absence of the virulence genes and ctxB genotype. Materials and Methods: Twenty-five V. cholerae strains were subjected to conventional biotyping and serotyping followed by multiplex PCR to detect ctxA, ctxB, zot, ace, O1rfb, tcpA, ompU, ompW, rtxC, hly and toxR and antibiotic resistance genes. Cholera toxin B (ctxB) gene was amplified followed by sequencing. Results: All the V. cholerae O1 isolates were El Tor Ogawa and showed the presence of the core toxin region representing the genome of the filamentous bacteriophage CTXø. The complete cassette of virulence genes was seen in 48% of the isolates which was the predominant genotype. All the isolates possessed amino acid sequences identical to the El Tor ctxB subunit of genotype 3. sulII gene was detected in 68% of the isolates, dfrA1 in 88%, strB in 48% and SXT gene was detected in 36% of the isolates. Conclusion: Toxigenic V. cholerae O1 El Tor Ogawa strains of ctxB genotype 3 carrying a large pool of virulence genes are prevailing in Assam. Presence of a transmissible genetic element SXT in 36% of the strains is of major concern as it indicates the emergence of multiple drug resistance among the V. cholerae isolates. https://ijm.tums.ac.ir/index.php/ijm/article/view/2891 https://ijm.tums.ac.ir/index.php/ijm/article/download/2891/1382