Multiple Sequence Alignment of NDM-1 DNA Sequence of Different Carbapenemases Producing Gram-Negatives




Journal Title

Journal ISSN



Volume Title




Peer reviewed



Multiple Sequence Alignment of NDM-1 DNA Sequence of Different Carbapenemase Producing Gram-Negatives Baho S.1 and Samarasinghe S.2 1,2 De Montfort University/Leicester/LC/United Kingdom

Background- NDM-1 is an enzyme that confers resistance to bacteria against a broad range of β-lactam antibiotics. It is one of the most effective Carbapenemases in terms of carbapenem hydrolysis and geographical spread. Therefore, learn how its DNA sequence evolved through testing its sequence in some organisms might give an idea about the effect of geographical distribution and other environmental effects. In our work, we are trying to find out how the wide spreading of DNM-1 among different Gram-negatives could affect the conservatively of its DNA sequence i.e. the percentage of similarity and differences among NDM-1 DNA sequence. This might give possible insights into the development of new resistance against current effective antibiotics which in turns might help to the precedent event for a possible treatment.

Methods From GenBank, the complete DNA coding sequences of NDM-1 of Acinetobacter (johnsonii NF114, sp. NF111, sp. NF116), Klebsiella pneumoniae (Res2011-182, K.P-UC-13, K.P-UC-14, K.P-UC-15), Citrobacter freundii NF109, Escherichia coli NF113, Providencia vermicola NF115 and Pseudomonas sp. NF117 were obtained (813 bp for each). DNA sequence analysis was carried out by means of multiple sequence alignment using EMBOSS Clustal Omega and aligned using default setting with all mentioned strains.

Results Percent identity matrix showed a 100% of similarity between all Klebsiella strains, it also showed a 100% similarity between Acinetobacter strains, C. freundii NF109, E. coli NF113, P.vermicola NF115 and Pseudomonas sp. NF117. But showed only 44.12% of similarity between all the above-mentioned strains with K. pneumoniae strains. The cladogram showed unexpected evolutionary pathway of NDM-1 between Klebsiella strains and A. johnsonii and A. sp. NF111, compared with A. sp. NF116 and other tested strains.

Conclusion NDM-1 sequence evolved dramatically when transferred to some species while still conserved with others. The evolution might arise as a result of a mutation in the resistance sequence while being conserved among different species could be attributed to the convergent evolution.



Antibiotic Resistance in Urinary Tract Pathogens


Baho, S. and Samarasinghe, S. (2018) Multiple Sequence Alignment of NDM-1 DNA Sequence of Different Carbapenemases Producing Gram-Negatives. ASM Microbe 2018. Atlanta, June 2018.


Research Institute

Leicester Institute for Pharmaceutical Innovation - From Molecules to Practice (LIPI)