Monthly Archives: May 2015

“Perfecting the Pick-up Line”

Future of Microbiology, The Science of Microbiology, ,

 220px-Pickolo_-_Automatic_colony_picker_add-on_for_Tecan_EVO_robot

In a recent post a month or two ago I noted that the current, so called “Total Laboratory Automation” systems still had a few gaps in them (Click here for the article), one of them being the ability to automatically pick colonies off a plate and inoculate MALDITOF plates and susceptibility broths.

It therefore came as somewhat of a surprise to me as I wandered around the Trade Exhibition at the ECCMID in Copenhagen. The sign “Automated Colony Picking” caught my eye..

And sure enough, there it was, a robotic system that could automatically pick a digitally marked colony, and inoculate a Maldi plate and a susceptibility broth. The company was called “Sci-Robotics”, and the hardware called “Pickolo”. It was being trialled at a laboratory in Italy, apparently with good success, even for small or mucoid colonies. 

The big corporates involved in bacteriology automation (you know who they are…) were showing a considerable degree of interest in the hardware!

Somehow I don’t think it will be very long before automated colony pickers are added to the big laboratory automation platforms.

In fact I don’t think it will be long (less than 10 years) before the manual work that the microbiology scientists will be performing will be restricted to the weird, the complex, and the bits and pieces which don’t easily automate.

….and that is exactly the way it should be.

Michael

Click here for a You-tube video on the automated colony picker as described above.

TB or not TB – that is the question?

"One world" Microbiology, Antimicrobial Resistance, History of Microbiology, The Science of Microbiology,

As usual my delving into family history has prompted a post … I’ve been researching my Great-great-Uncle who was killed in action at Somme, France whilst serving as a WW1 ANZAC and discovered that his father, my great-great-grandfather died from (and I shall quote from the Marlborough newspaper that it was printed in) … “that dread disease consumption“.

Now you may consider TB to be a third world, old-fashioned type of disease and to a degree you would be right however TB remains the second greatest killer globally (HIV/AIDS is number one) due to a single infectious agent.  In 2013, 9 million people fell ill with tuberculosis and 1.5 million died as a result – 480,000 of these cases were MDR-TB (multi drug resistant).  There is an upside to all this in that 37 million lives were saved due to effective diagnosis and treatment between 2000-2013 and the number falling ill to the disease each year is declining albeit slowly.  New Zealand statistics show 305 cases nationwide during 2014 and this number has been relatively stable over the past five years.

MDR-TB is defined as those strains that are resistant to at least Isoniazid and Rifampicin (the two most powerful and standard first line drugs for treatment of TB).   XDR-TB are strains that are extensively drug resistant and are defined as MDR-TB with additional resistance to any fluoroquinolone and at least one of the second line agents (Amikacin, Capreomycin or Kanamycin).  Of the 480,000 MDR-TB cases in 2013 about 9.0% of these were determined to be XDR-TB.  Within New Zealand the rate of resistance is much lower, on average only 1-2% of isolates each year showing this level of resistance.  In the past 10 years there have been 33 cases of MDR-TB in good ol’ NZ and all but two of these cases were born overseas where it has been assumed they contracted it – 29 of these 31 cases were born in an Asian country.  Only one case of XDR-TB has ever been identified in New Zealand, this was in 2010.  I think this is one time were our geographical isolation from a large part of the world is to our benefit.

Tuberculosis was a disease that the WHO considered dropping from their watchlist in the 1960’s/1970’s due to it’s decline however it made a huge resurgence in the 1990’s with the number of HIV/AIDS cases increasing and is certainly a disease which we cannot afford to ignore.

You can view a copy of the 2014 WHO global TB report here.

“The dogma of day 1 and day 2”

Confessions of a Microbiologist, Future of Microbiology, The Science of Microbiology,

Readers who work in a clinical microbiology lab will be familiar with day 1 and day 2 reading. That is the way it has always been. Regardless of when the specimen was put up, the plates are incubated overnight and then read on day 1, re-incubated and then read again the next day, on day 2. This old-fashioned system is so non-standardised, it is actually a wonder that we still get away with it with regards to accreditation.

However not to worry. Smart incubators are becoming increasingly prevalent (e.g. WASP, Kiestra).These systems know when each plate enters the incubator, and thus allows plates to be incubated for a specific pre-programmed time, before automatic imaging occurs, and the scientist is notified that they are ready to be read.

As these automated systems become increasingly common, we need to move away from the day 1, day 2 dogma. Most plates will only need incubated for somewhere between 12 and 18 hrs before bacterial growth is visible.

Instead we should be talking about 1st reading and 2nd reading, or something similar. We should simply stop referring to plate reads as day 1 and day 2…..

The other area that Day 1, day 2 dogma is seen is with regards to enrichment broths. Enrichment broths such as MRSA/Gp B broths tend to get incubated for a day before being subbed onto plates. Of course 1 day/24 hrs is a completely arbitrary figure. With smart incubators and 24 hr rosters we need to start validating shorter enrichment periods, in order to decrease turnaround times.

Continuous put-up, continuous reading, continuous reporting. That should be the vision of all clinical microbiology laboratories.

Michael