Investigating bacteria behind hospital infections with SMART Designs Tool

A new tool has been developed using SMART CRISPRi technology which is designed to help identify and tackle causes of E. faecalis-related diseases and drug resistance.

Researchers from the Antimicrobial Resistance (AMR) Interdisciplinary Research Group (IRG) at Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, and Nanyang Technological University (NTU), have developed the tool to understand and prevent biofilm development, drug resistance, and other physiological behaviours of bacteria such as Enterococcus faecalis.

In the paper published in the journal mBio, the researchers explain the scalable dual-vector nisin-inducible CRISPRi system which can identify genes that allow bacteria like E. faecalis to form biofilms, cause infections, acquire antibiotic resistance, and evade the host immune system. The team combined CRISPRi technology with rapid DNA assembly under controllable promoters, which enables rapid silencing of single or multiple genes, to investigate nearly any aspect of enterococcal biology.

Understanding infections

E. faecalis faecalis, which is a bacteria found in the human gut, is one of the most prevalent causes of hospital-associated infections and can lead to a variety of multidrug-resistant, life-threatening infections.

However, current methods for understanding and preventing E. faecalis biofilm formation and development are labour intensive and time consuming. The SMART AMR research team designed an easily modifiable genetic technique that allows rapid and efficient silencing of bacteria genes to prevent infections.

Dr Irina Afonina, Postdoctoral Associate at SMART AMR and lead author of the paper, said: “Infections caused by E. faecalis are usually antibiotic tolerant and more difficult to treat, rendering them a significant public health threat. Identifying the genes that are involved in these bacterial processes can help us discover new drug targets or propose antimicrobial strategies to effectively treat such infections and overcome antimicrobial resistance.”

The new tool will be valuable in rapid and efficient investigation of a wide range of aspects of enterococcal biology and pathogenesis, host-bacterium interactions, and interspecies communication, and the researchers say that the method can be scaled up to simultaneously silence multiple bacterial genes or perform full-genome studies.

Corresponding author, SMART AMR Principal Investigator, and NTU Associate Professor Kimberly Kline, added: “The system we designed enables us to easily interrogate various stages during the biofilm developmental cycle of E. faecalis. By selectively silencing certain genes in pre-formed, mature biofilms, we can erode the biofilm and force it to disperse.”

The scalable CRISPRi system uses high-throughput screens which can allow for rapid identification of gene combinations to be simultaneously targeted for novel and efficient antimicrobial combinatorial therapies.