MFF0065: Future of microbiology


MFF The future of microbiology Gary Lum

It’s Monday 15 May 2017. I’ve spent today in Sydney for work.

I was recently asked if I thought there is much of a future in microbiology for a specialist microbiologist.

It’s an interesting question. I grew up in an era of clinical specimens being looked at microscopically and set up on culture plates. The beauty of microscopy and culture is that you get a feel for quantity and quality of the specimen and the pathogens grown. For example, seeing lots of pus and one or two types of bacteria microscopically was good information to have when reading the cultures. If the bacteria growing matched the bacteria seen in the Gram’s stain, then the likelihood of a true infection is greater, especially with the presence of pus. Of course, there are some exceptions, like when Clostridium perfringens, which causes gas gangrene elaborates an α-toxin, it destroys leucocytes so in a Gram’s stain from a patient with gas gangrene all you see are these magnificent looking Gram-positive bacilli and no sign of pus anywhere.

In culture, heavy growth of a bacterium in pure culture has more significance than light growth of a predominant bacterium in a mixed culture.

With advances like PCR, we’re in an environment where we can make a diagnosis a whole lot more quickly from a clinical specimen but without a lot of the information, we used to get. For example, in the good old days when someone had a drippy dick, we’d get some pus, we’d look at it microscopically, we’d see the gonococci and then we’d grow it and then we’d perform antimicrobial susceptibility testing. These days, we get a first void urine which goes for PCR, we get a nucleic acid detected or not detected result. We don’t get microscopy, we don’t get antimicrobial resistance information in a time of growing problems with resistance. We also don’t have an isolate for public health epidemiology. Sure, you can go back to the urine as a reflex move, try to grow the gonococcus, but that takes time. PCR also removes the ability to perform a test of cure work because dead bacteria can be found for weeks after treatment and PCR may still detect nucleic acid from dead bacteria.

We have a similar situation with faeces specimens where culture independent diagnostic testing means we get faster results for identification but unless it’s managed holistically, we lose valuable information on microscopy, culture, antimicrobial resistance and epidemiological characterisation for outbreak management.

With the advent of metagenomics and whole genome sequencing, we may get back some information like the presence of antimicrobial resistance genes and full epidemiological characterisation, but will we be able to discern the quality of a specimen like we can now by having a look at it down the microscope.

With robotics and supercomputing, we may see a time when we don’t have a need for bench scientists and medically qualified specialist microbiologists. Hopefully, I will have moved on to something new before that era becomes the norm.

If you disagree with anything in these podcasts or if you would like to voice a different view, please feel free to write a comment. If I have said something incorrect I welcome correction. Please also feel free to share your comments on social media.

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