This project has a microbiological component which seeks to assess the extent of antimicrobial resistance (AMR) in bacteria attached to dust in Ghanaian homes. This is a problem as resistance, if found in infectious bacteria, may hinder treatment of infectious disease. However it may be lurking in non-infectious bacteria as well. No problem? Well there is… this resistance might be mobile and transfer from non-infectious to infections bacteria. So we are going to assess the extent of AMR in all the bacteria we can. No matter which environment we look at there are common microbiological problems: We can culture bacteria directly from dust and we can test them for their resistance or sensitivity to a range of antibiotics commonly used in the treatment of infectious disease.
The sting is the tail is we can only culture usually less than 1% of all the bacteria present. The remaining >99% cannot be cultured but are still active, they may contain infectious bacteria that are resistant to antibiotics. So how do were find these unculturable microbes?
Two strategies can be adopted in addition to culture: one for identifying bacteria and the other for identifying AMR. Both involve taking a dust sample and extracting all DNA from all the attached bacteria. For bacteria we will use next generation sequencing which generates signatures of bacterial species from which we can identify and quantify (within limits) species and this will tell us about bacterial diversity in a number of homes. For AMR, we will detect the signatures of different genes that will tell us which antibiotic resistances are present.
By combining the sequencing and culturing we will obtain a picture of AMR is different households.
*Photo Credit: Dr. Graham Beards, CC BY-SA