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Klebsiella aerogenes , is a Gram-negative bacterium, which was previously known as Enterobacter aerogenes . It is present in all environments such as water, soil, air and hospitals; and is an opportunistic pathogen that causes several types of infections. As compared to other clinically important pathogens included in the ESKAPE category ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species ), the pangenome and population structure of Klebsiella aerogenes is still poorly understood. For the present study, the bacterial sample was isolated from agricultural soils of Haryana, India. With an aim to identify the occurrence of multi-drug resistance genes in the agricultural field soil bacterial isolate, whole genome sequencing (WGS) of the bacteria was performed; and the antibiotic resistance causing genes, along with the genes responsible for other major functions of the cell; and the different Single Nuceotide Polymorphisms (SNPs) and Insertions and deletions (InDels) were identified. The data presented in this manuscript can be reused by researchers as a reference for determining the antibiotic resistance genes that could be present in different bacterial isolates, and it would also help in determination of functions of various other genes present in other genomes of Klebsiella species.

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Due to the prolonged use of antibiotics in agriculture, antibiotic resistance has become a major concern. Hence, the present study involved evaluation of the presence of antibiotic resistance genes in the bacterial isolates prevalent in agricultural soils of Haryana, India. Bacteria were isolated from agricultural soils collected from different districts of the state, and all the isolates were subjected to antibiotic resistance screening tests against four commonly used antibiotics viz. penicillin, tetracycline, streptomycin and erythromycin. On the basis of high resistance activity, six bacterial isolates were selected for molecular studies, and the isolate exhibiting maximum resistance was selected for whole genome sequencing (WGS). Based upon WGS analysis, resistance genes were identified in the selected isolate, out of which six genes were selected for wet lab analysis. These six genes when subjected to amplification studies in the other five identified bacteria, revealed their presence in some of these isolates as well. Apart from the 28 identified genes, “blaTEM” gene, was also identified using amplification studies in Klebsiella aerogenes. To the best of our knowledge blaTEM has not yet been reported in Klebsiella aerogenes. The presence of several multi-drug-resistance (MDR) genes has been confirmed in the bacterial microflora inhabiting the collected soils.

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