In the past few years I have worked on and off (i.e. doing pilot experiments, having a grant proposal rejected) on a very simple, but I believe quite powerful, assay to detect pathogenic bacteria in environmental samples. As it stands, microbial water and food safety is based on the quantication of faecal indicator bacteria: more poo-related bacteria in your sample=bad. The problem is that some poo-related bacteria are not as harmful as others, and more importantly, there are some very harmful bacteria that are not associated with poo and thus are completely missed by this approach. Alternative ways to detect pathogens have their own limitations: for instance, molecular markers are restricted to a (small) set of ‘known knowns’ and are usually costly.
It would be much more useful to directly screen for bacteria able to cause disease, whatever their identity. Visiting student Rafael Hernandez took water and sediment samples and directly injected these in the the wax moth larva Galleria mellonella, a model for the innate immune system. There are many studies that inject particular pathogen strains in Galleria to quantify the rate of killing, and this has been shown to correlate well with death in infected mice. What is novel about our approach is that we inoculated Galleria not with specific strains but with samples containing entire microbial communities to detect where pathogens might be present.
Most samples from local beaches (water and sediment) we assayed did not result in Galleria death after injection, but for some samples, mortality after overnight incubation at 37C was very high. Rafael could isolate clones from infected Galleria, which then were used to infect Galleria again to confirm that they were the cause of death, and were subsequently whole-genome sequenced. The results were exciting. We found usual suspect E. coli, as well as another well known (but not gastro-intestinal-associated) human pathogen Pseudomonas aeruginosa, both harbouring many virulence and antibiotic resistance genes. However, the most virulent clone was a Proteus mirabilis strain harbouring a Salmonella Genomic Island that has been reported in recent years from human and animal infections but (to my knowledge) not from the natural environment or from the UK. We also found Vibrio injenensis, a species only very recently described from human patients in Korea and not reported from anywhere else. The figure above shows on the left panel Galleria cumulative death (inoculation with 100, 10.000 and 1.000.000 cells) and on the right genome characteristics (virulence genes in blue, antibiotic resistance genes in red) for the four characterised clones.
The combination of climate change, changing farming practices, increased exposure through water-based recreation and rising levels of antibiotic resistance is expected to lead to an increase in hard-to-treat opportunistic infections. The approach described here looks promising to uncover the prevalence and identity of pathogenic bacteria in the environment, including potential emerging pathogens, which is key to assessing environmental transmission risks.
This study is out but not ‘out out’; I have used bioarxiv for the first time to make results accessible before peer-reviewed publication. Read it here: