“Putting your job into perspective”

My baby daughter recently had open heart surgery at just two weeks of age, to repair a serious congenital heart defect (Tetralogy of Fallot). She was desperately sick in the days leading up to the surgery, and required several weeks of convalescence afterwards.

They don’t like doing open heart surgery at such a young age, but decided that this was the lesser of the evils…

On the day of the surgery she was really struggling, despite being in intensive care on maximal therapy. I never thought I would be glad to see my daughter wheeled off to theatre to be put on cardiac bypass.

Fortunately everything went well, and she is now 10 weeks old. She is doing all the things that 10 week old babies should be doing. Except for the scar on her chest, you would not even know what she has been through.

She is, quite literally, a little miracle.

Now things are getting back to normal. I am back at work, and able to think clearly again.

During the long days and nights in the neonatal intensive care unit, my microbiology job was the furthest thing from my mind.

But the whole experience has helped me put my job, and to a large extent my career into perspective.

And I am very aware that my family and I are not the only ones who have been through the emotional wringer. Most people have had major life events at some time or other; bereavements, births, severe illness, redundancy, divorce, etc., etc.

We all have our struggles…

So in future, whenever my workload is starting to feel heavy, I will think to myself “Compared to recent events in life, this is a walk in the park.”

And whenever I am asked to take on extra responsibilities, I will think to myself “I have a young baby to look after and care for. What work responsibilities can possibly be greater than that?”

And if I need to take the odd risk in order to develop and progress the microbiology department that I work in, I will think to myself “This is not a life or death situation. What is the worst that can happen…?”

Sometimes our mind plays tricks with us with regards to the challenges we face at work, to the degree that they start to become stressful and all encompassing.

When work life gets tough, then reflect on your other life, the more important one, and put your job into perspective. 


“The dark art of antibiotic resistance surveillance”

This post is best read with a glass of wine…

As a profession, I think we are really not very good at measuring antibiotic resistance/antibiotic susceptibility patterns…

We are very happy to proclaim at the start of presentations “Antibiotic resistance is increasing”, or “In the era of increasing antibiotic resistance.” without providing any data to support this claim.

We need to move away from this type of talk. We are after all, scientists, not politicians.

However antimicrobial resistance surveillance is deceptively difficult. Here are a few reasons why high quality surveillance data is hard work, and requires a lot of thought and planning…

  • It is actually the trends that are critical:- There is a big difference between providing an annual antibiogram to clinicians, and presenting graphs which show changes in antimicrobial susceptibility over time. For example a GP looks at an annual antibiogram provided by the microbiology laboratory and sees that organism X has a resistance rate to antibiotic Y of 10%. Doesn’t sound too bad and certainly a viable treatment option. But if we knew that the resistance rate was 5% last year and 2% the year before that, then we have a problem. It seems obvious, but antimicrobial resistance surveillance is all about trends, not snapshots.
  • Too many permutations:-  There are more than 50 different commercially available antibiotics, and many hundreds of microrganisms identifiable on MALDI-TOF. So the number of antibiotic:microbe combinations is well in to the thousands. So which ones should be measured? The obvious ones are those that are commonly encountered and used, e.g susceptibility of E. coli to trimethoprim, ones that are clinically very important, e.g. susceptibility of Streptoccus pneumoniae to penicillin, or those of great public health importance, e.g. susceptibility of E. coli to meropenem. The ones to be avoided is where the combination falls outside these groups, particularly those where the numbers seen are insufficent to get meaningful data. e.g. Selenomonas spp. susceptibility to ciprofloxacin.  The important thing here is to decide on the microbe:antibiotic combinations to be measured before you start your surveillance program. Otherwise the data is open to exploitation, with people picking antimicrobial resistance surveillance data to suit their particular agenda. e.g. Antibiotic resistance is increasing because Microbe A is becoming more resistant to antibiotic B, and ignore the fact that Microbe C is becoming less resistant to antimicrobial D…
  • Different Definitions:- Because there are different antimicrobial testing standards out there, e.g. CLSI, EUCAST, CDS, etc., one person’s definition of resistant may not be the same as anothers… It is very important to ensure everyone has the same “definitions” of what is resistant and what is not resistant, before you even start. Otherwise you are on a hiding to nothing…
  • Politics:- Everybody has their own wishes and desires, and it is no different when it comes to measuring antibiotic resistance surveillance. Everybody wants to look at different antibiotic:microbe combinations, use different testing methodologies, present the data differently. This can cause problems with not only the accuracy of the data, but also in getting any surveillance data at all, when multiple laboratories are required to work together. When antibiotic resistance data requires the political co-operation of different countries then the difficulties move onto a whole new level altogether. Despite there being a willingness to work together, getting multi-national agreement on surveillance is a monumental task.
  • The goalposts get moved. Every so often the breakpoints get changed, for various reasons, so that an isolate that was once susceptible can become resistant (on paper), and vice versa. This is why using MIC values for surveillance purposes is so important, as it is an objective measurement which has no interpretation applied to it. This facilitates the acquisition of accurate surveillance data over many years.
  • Memory is erased. Sometimes when the laboratory information sytem (LIS) in a microbiology laoratory gets changed, a lot of the historical susceptibility data can get lost, either because it is not compatible with the new system, or not thought to be important enough to keep. Although electronic storage of laboratory data has been around for at least 20 years, as far as I am aware many microbiology laboratories do not have 20 years of data, for exactly this reason. It is a very important point to consider when considering a change of LIS.
  • Biases:- So many things can lead to bias in the surveillance data… Participation bias, sampling bias, patient cohort bias, testing bias, etc.. The list is virtually endless. All these things need to be considered and corrected for as best as possible when performing antimicrobial resistance surveillance.

So it is not easy, by any stretch of the imagination.

Good antimicrobial stewardship programmes should be based on having sound, standardised and objective baseline antimicrobial resistance data against which any interventions can be audited.

The other big area of surveillance which is essential to antimicrobial stewardship programmes is antimicrobial usage data. This data goes hand in hand with antimicrobial resistance surveillance.

Although it’s easy to talk about increasing antibiotic resistance, it is actually very difficult to measure properly…


“Ageing methodology”

The laboratory detection of verotoxin/shigatoxin producing E. coli (sometimes called enterohaemorrhagic E. coli) has caused much grief for diagnostic microbiology laboratories over the decades. It is a relatively nasty infection, and it can cause bloody diarrhoea in a good proportion of patients. In a small minority it can cause severe complications such as Haemolytic Uraemic Syndrome (HUS) or Thrombotic Thrombocytopenic Purpura (TTP).

Diagnosis was initially centred on the culture of E. coli 0157 which can produce verotoxin/shiga toxin.

SMAC (Sorbitol MacConkey) agar plates were all the rage in the 1990s, taking advantage of the fact that E. coli 0157 does not ferment sorbitol. 

How lucky is that?

These were soon replaced by the more selective CTSMAC (Cefixime Tellurite Sorbitol MacConkey), with the cefixime and tellurite inhibiting other annoying non-sorbitol fermenters such as Proteus Spp.

The only problem is that E. coli 0157 is not the only E. coli serotype that can produce verotoxins. Lots of other E. coli serotypes are capable of doing this as well, e.g. 0111, 026, 045, 0145, etc.. As time passed, and our understanding of the infection improved, it became very apparent that a very significant proportion of VTEC induced diarrhoea was actually not due to E. coli 0157.

How inconvenient…

Nevertheless, CTSMAC plates were now entrenched in laboratories. And it was better than nothing.

As the years passed,  alternative methods came onto the scene.

ELISAs used for “direct” VTEC toxin detection in stool were employed in some labs in the early 2000s. At least they detected non-0157 associated disease, but sensitivity remained an issue when used directly on samples. They were not widely adopted by diagnostic laboratories.

Chromagar plates have also been developed to pick up the main VTEC serotypes. A little pricey however, and still need follow-up work for confirmation.

Then came PCR, and more recently multi-plex PCR, not only detecting (the toxins of) VTEC, but all the other common gastrointestinal pathogens as well.

In the molecular age, CTSMAC plates are starting to look a bit dated. What was seen as  modern methodology a generation ago no longer cuts the mustard.

As we move through this transition period for VTEC detection there is a real mish-mash of different VTEC methodologies used in laboratories worldwide. I don’t think this messy situation will last. In a decade or so I suspect 90% or more of microbiology laboratories will be using molecular methods for VTEC detection (and everything else stool related).

However at the moment, there are still plenty of CTSMAC plates being manufactured worldiwde. We still (guiltily) use them at our lab, as we continue to work out how to afford molecular testing for enteric pathogens…

But now they are used in the knowledge that they will clearly not pick up all VTEC strains in the patient samples, or anywhere close.

CTSMAC plates are getting old, and I for one can’t wait to see the back of them…


Note that the Infectious Diseases Society of America has just brought out updated guidelines on Infectious Diarrhoea, including quite a bit of detail on VTEC/STEC. Apart from the incorrect spelling of diarrhoea, they are very good!

I will add them to the guidelines section of this website also.