The use of genomics in carbapenamase producing Enterobacteriaceae outbreak
Lex EX Leong1
1Public Health and Epidemiology, Microbiology and Infectious Diseases, SA Pathology
Enterobacteriaceae is a family of Gram-negative bacteria and consists of a wide range of clinically relevant pathogens. These include beneficial commensal bacteria, opportunistic pathogens that can cause significant disease in immunocompromised patients, and primary pathogens capable of initiating disease in healthy individuals. Antibiotics have been used to prevent and treat infections caused by the two latter groups, however, Enterobacteriaceae are increasingly resistant to antibiotics, especially beta-lactams. This resistance is largely due to the acquisition of mobile genes elements with antimicrobial resistance, over-expression of efflux pump, and inducible chromosomal antibiotic-modifying enzymes.
Traditionally, the detection and identification of the antimicrobial resistance (AMR) was performed using phenotypic susceptibility testing in combination with simple genotypic molecular approaches. These methods lacked the fine discrimination required to track outbreaks due to the transmission of bacteria or gene elements. Outbreaks of carbapenemase-producing Enterobacteriaceae were particularly problematic.
Whole genome sequencing of these pathogens has emerged as a powerful tool for outbreak investigation, along with the identification of AMR genes and mobile genetic elements such as plasmids. The utility of genomics will be illustrated with specific examples from recent outbreaks.
Biography:
Dr Lex Leong is a molecular microbiologist leading a team within the SA Pathology’s Public Health and Epidemiology Laboratory. He is also an adjunct research fellow with University of South Australia, and associate research fellow with South Australian Health and Medical Research Institute. His work is focused on the translation of pathogen genomic to clinical and public health microbiology. These studies include the genomic examination of tuberculosis and SARS-CoV-2 to reveal true levels of genetic diversity, the coordination of multi-jurisdictional outbreak investigations associated with foodborne diseases, and antimicrobial resistance characterisation to aid in infection control measures.