Monthly Archives: January 2017

“Flexible working: Confessions of a wanderer…”

Confessions of a Microbiologist,

I am not very good at following the rules… I never have been. I was much the same at school, at university and every other organisation I have been involved with.

And I am not very good at being told when I should be working, when I should take my breaks, when I should be here or there.

I ended up in trouble in school quite a few times because of this!

Nowadays I start work at anytime between 7am and 9am in the morning, depending on what is happening at home, and how much insomnia I had the night before. I am very much a morning person, so 90% of my productive work for the day usually happens before lunchtime. I don’t really trust myself with anything too complex as the afternoon progresses, and I leave all menial tasks until late in the afternoon, when I am good for nothing else..

Because my concentration span is relatively short I tend to take multiple breaks throughout the day. Sometimes my breaks are longer than my work periods! I usually work hard when I am working, and occasionally I even get myself into “the zone”… I give myself a specific task to complete in a certain timeframe (e.g. do presentation A, write letter B, sort out blood cultures X, Y & Z). I keep my emails switched completely off when I am doing specific tasks like this.

I finish up (in the lab) sometime between 3.30 & 5 pm. After the children go to bed in the evening I usually sit down for 20-30 minutes and clear/sort my emails. People seem to like sending emails between 5 and 6pm so there is usually a little cluster waiting for me… I adhere to a “Zero Inbox” policy.

Most of my strategic thinking for the microbiology laboratory happens whilst driving to or from work, or in the middle of the night!  This type of work needs an absolute minimum of interference.

I am very productivity focused as opposed to hours focused. I make no apologies whatsoever for the time I spend or don’t spend in the office/lab.

I am very fortunate in that my role allows me to be hyper-flexible with regards to work hours. I am extremely grateful for this. It may even partially explain the career path I have taken. But I am also aware that not everyone that works in the laboratory setting has this kind of freedom.

I am a strong proponent of flexible working hours for all laboratory staff, wherever the system can allow it. Any opportunity for flexible start and finish times, flexible breaks or off-site work should be both encouraged and embraced.

We are no longer at school…

Michael

“Staphylococcus aureus in sputum samples. A reporting conundrum.”

The Art of Microbiology, The Science of Microbiology,

When I worked in a microbiology laboratory in Glasgow we hardly ever reported antibiotic susceptibilities on Staphylococcus aureus when cultured from sputum. Now I am working in New Zealand, and we almost always do…

So who is right and who is wrong?

The problem is that Staphylococcus aureus in the sputum can mean several different things:

  • It may simply represent oropharyngeal contamination of the sample.
  • On the flipside it may signify a severe necrotising pneumonia in an immunocompromised or post-influenza patient.
  • And thirdly, we know that Staphylococcus aureus can colonise or occasionally cause “low level” infection in the architectually damaged lung (e.g. cystic fibrosis, COPD, bronchiectasis)

So in summary, it can mean absolutely nothing, or it could signify a life threatening illness…

The clinical context and sample quality are clearly key here to working out what is going on. However, in actual practice, the sputum sample often arrives into the laboratory without any clinical details, so we are processing blind.

“Just do your stuff, and give us the result…”

So how should we manage this problem from a laboratory point of view?

Here are a few potential solutions:

  • Reject sputum samples for culture where the Gram stain shows lots of squamous epithelial cells representative of oropharyngeal contamination. (A lot of labs have now adopted this approach, including my own)
  • Report susceptibilities routinely on Staphylococcus aureus from hospitalised (& cystic fibrosis) patients only.
  • Add a comment saying that close clinical correlation is required in the interpretation of this result & susceptibilities will be available on request only.

or all of the above…

The clinical context is always important for the laboratory to issue a correct report. However, for sputum samples growing Staphylococcus aureus, it is absolutely critical.

Or one could be even stricter, and just say, “no clinical details, no test”…

Michael

“Molecular diagnosis of wound infections: The Holy Grail.”

Future of Microbiology, The Science of Microbiology,

The slice of pie taken by the molecular department in the microbiology laboratory is increasing, slowly but surely.

On the contrary, the proportion of culture based microbiology is inexorably declining.

Many clinical microbiology laboratories are now switching, or looking at switching over to molecular diagnosis of enteric pathogens.

Molecular diagnosis of pathogens causing vaginitis and pharyngitis will not be far behind, and a few labs have already moved in this direction.

However diagnosis of wound infections remains firmly culture based. There is not even much in the literature with regards to molecular diagnosis of wound infections…

Is it even possible?

So what are the difficulties?:

  • Potential number of pathogens: There are several pathogens or putative pathogens that are able to cause wound infections. This makes PCR based molecular diagnosis more difficult. However, on the flip side, 95% of wound infections in a general clinical setting are caused by two pathogens, Staphylococcus aureus and Streptococcus pyogenes (Group A streptococcus).
  • Lack of susceptibility information: Molecular diagnosis of resistance determinants is still a little behind phenotypic culture based testing. However with regards to the two main pathogens as above, PCR analysis can easily differentiate between MSSA and MRSA, and susceptibility data for Streptococcus pyogenes is only required for a small proportion of patients who have anaphylactic reactions to penicillin.
  • “Over-sensitivity”: It is always nice to know which are the dominant organisms within a wound. Culture is relatively good at this. However molecular methods are starting to be able to quantify to some extent (e.g by playing with the cycle threshold cut-off).
  • Cost: The culture of a standard wound swab might cost $10 or so, even when overheads are included. In my experience molecular tests have to be performed in very large volumes to even get close to this kind of price. However wound swabs do arrive into the laboratory in very large volumes!

If it was easy it would have been done by now… I suspect it is the 4 things above acting together as a “bundle”, as opposed to any one insurmountable barrier which has contributed to the lack of progress up until now.

However it will come in some form or other, you can be sure of that…

Here is a potential solution I have thought of:

  • Any wound swab accompanied with clinical details suggesting an unusual pathogen e.g. animal bites (Pasteurella), water exposure (vibrios, aeromonas), immunocompromise,  would still undergo routine “catch-all” bacterial culture.
  • The rest (the vast majority) would be subjected to a multiplex PCR for the detection of MSSA, MRSA and Streptococcus pyogenes (and possibly Group G streptococcus also). A positive result would be reported routinely. A  negative result would have an accompanying comment to suggest contacting the laboratory if the patient’s symptoms were persisting, or if further susceptibilities are required, so that culture could be set up if necessary.

In this way molecular diagnostics could be performed on (a good proportion of) wound swabs at a relatively low cost.

In addition multiplex PCRs could be developed specifically for infections in specific clinical situations, e.g. post animal bite,  etc., etc.

Automated bacteriology culture systems like Kiestra TLA would not have happened if the industry didn’t think that there was at least another 20 years or so of culture based bacteriology left, and they are probably right. But I don’t think it will be too long before commercial laboratory diagnostics companies start looking closely at “wholesale” molecular options as above.

And who knows, whole genome sequencing might come in and completely disrupt PCR based molecular diagnostics, and the picture might change again…

“The future’s uncertain and the end is alway near“

Michael