Molecular characterization and exploration of streptomycin resistance genes in Xanthomonas campestris pv. campestris isolates from diverse agro climatic regions of Karnataka state, southern India

Xanthomonas campestris pv. campestris (Xcc), which causes black rot, is a major pathogen of commercial importance affecting crucifers in India. Lack of resistant cultivars and effective management practices led to the use of antibiotics and copper-based compounds as a partially successful management practice. However, the decreased efficacy of antibiotic (Streptomycin) and copper compounds against Xcc can be attributed to the emergence of acquired genes that make antibacterials less effective. In the current investigation, black rot affected plant samples from Karnataka, India, were collected and a total of 42 Xcc isolates were confirmed by species specific primers viz., DLH and Dhrp. Further, the isolates were screened for the presence of genes conferring resistance to streptomycin (strA, strB and rpsL) and copper (copA, copB and copL). A total of 13, 34 and 21 isolates carried strA, strB and rpsL genes respectively, whereas three isolates were identified to have the copL gene. Molecular typing of the collected Xcc isolates was carried out by amplifying conserved repeated elements including the repetitive extragenic palindromic elements (rep-PCR), enterobacterial repetitive intergenic consensus region (ERIC-PCR) and BOX-repeats (BOX-PCR) which grouped the 42 isolates into three distinct clusters. Our study clearly indicated that the geographical location has no correlation with the grouping of Xcc isolates. Further, a better understanding of antibiotic resistance genes in pathogenic isolates can help in developing effective management practices against the pathogen based on their antibiotic resistance profile.