Using whole genome sequencing to unravel the genetics underlying antimicrobial resistant pathogens

Taane Clark (primary)
Pathogen Molecular Biology
LSHTM
Martin Hibberd (secondary)
Pathogen Molecular Biology
LSHTM

Abstract

Antimicrobial resistance(AMR) threatens the effective prevention and treatment of a range of infections affecting humans and animals. It is a global public health threat, especially as healthcare practices, systems and economies rely on antimicrobial medicines. Across multiple bacterial species, genetic mutations are drivers of AMR. Whole-genome-sequencing can lead to rapid identification of AMR and virulence genes, and the determination of the diversity and spread of antimicrobial resistomes. We will use metagenomic, phylogenetic, bioinformatics and GWAS analytical methods across a range of pathogens to identify AMR mutations and transmission clusters. Large genomic datasets for Mycobacteria, Staphylococcus and Enterobacteriaceae (e.g. Salmonella, Klebsiella) are available immediately.


References

[1] https://amr-review.org/
[2] Coll et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015 May 27;7(1):51.
[3] Phelan J et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Med. 2016 Mar 23;14:31.
[4] Kumar et al. Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles Antimicrob Agents Chemother. 2011 Sep; 55(9): 4267–4276.
[5] Conceição T et al. First description of CTX-M-15-producing Klebsiella pneumoniae in Portugal.
Antimicrob Agents Chemother. 2005 Jan;49(1):477-8.


BBSRC Area
Animal disease, health and welfare
Area of Biology
GeneticsMicrobiology
Techniques & Approaches
BioinformaticsGeneticsMathematics / StatisticsSimulation / Modelling