Tag Archives: bacteriology benchwork

“Twenty Tips for people working on the Bacteriology Benches”

Apologies for the paucity of posts recently. Ultra-marathons (click here for update) and babies have seen to that! The post below is a combination of posts (with some extra points added) published a couple of years ago on this website, and will form the basis for a chapter in my forthcoming book “The Art of Clinical Microbiology”.

Feel free to disagree with any of the points made below, it is only personal opinion!

1)      The clinical value of a result is (in general) inversely proportional to the number of days spent generating it.

In the vast majority of cases, once you are 4 or 5 days down the line from the sample being taken, the clinical value of the result starts to wane. It is at this point that one must start to ask. “What difference is it going to make to the patient to get a definitive ID on this organism” or “Do I really need to know what the penicillin MIC on this difficult to grow Coryne is?”. Find out if the patient is still unwell, whether they have been discharged etc etc. Often the answer is that the patient has long since been treated and discharged and your time (and the laboratory’s resources) could have been better spent on other work. This is not always the case of course, but exactly this scenario occurs far too frequently to be ignored.


2)      The clinical value of a result is inversely proportional to the number of different organism types present in this sample.

Once 3 different organism types are found in a sample the clinical significance of each individual organism starts to decrease. Once you have 5 or 6 it is almost impossible to give any meaningful results from the sample. If you have such a sample, focus on the organisms that are the likely pathogens, and just mention the others. With multiple organism samples, it is easy to fall into the trap above and start spending several days working them all through. This is very important when you see what looks like enteric flora on the plates. In my opinion this should be reported as enteric flora (and yes, even in sterile sites). There are very few occasions where it is actually necessary to work up individual organisms in “enteric flora”.

With both these first two points I must emphasize, that I personally am happy for an “incomplete result” to be released, even as a final report. If it is taking too long to identify an organism that is unlikely to be pathogenic in the first place, don’t identify it!


3)      Once you have clinically useful lab information, release it to the clinicians.

This to some extent depends on how your laboratory information system is set up. In some cases your interim work will be released to the clinicians anyway. For some labs you will need to actively release the information. The point is, don’t hold useful information back just so that you can release the “perfect result” in a couple of days’ time. Trust me, the patient will not thank you for this. If you have information which suggests the likely ID but are awaiting confirmation, then often it is worthwhile releasing this as well. For example, If you have a CoNS from a blood culture, which is latex negative and you are awaiting a tube coagulase, then it is ok to add a comment to the interim result “Staphylococcal species. Likely to be a CoNS on the basis of current results. Confirmation awaited.” In most cases you will be right and possibly saved the patient unnecessary antibiotics. On the occasional case that you are wrong, you have not put out any misleading information on your report.


4)      Focus your time on the important samples.

There is a large range of samples which are received into the lab, anything from blood cultures/sterile site specimens on ICU patients to superficial wound swabs from chronic leg ulcers. Focus your time and efforts on samples that are likely to make a significant clinical difference. I would estimate that less than 10% of microbiology samples coming through the lab impact on a patients treatment, and of that 10 % less than half will have a significant, potentially life saving impact on treatment. (You might not want to hear that, but I believe it to be true!). Without ignoring the rest of the work completely, focus your time and energy on sterile site samples, blood cultures, samples from CF sufferers, samples from patients in ICU or not responding to treatment.


5)      Know when something is odd/does not look right.

This is to some extent common sense, but also boils down to experience and a degree of intuition. Every bench will have its bread and butter work but every so often something will crop up which does not fit; ie. An unusual organism, or an unusual antibiogram for a common organism. Stop and reflect when this happens. Is it laboratory error, or is this something genuine? Ask for help if necessary, regardless of your seniority. This is often where the interesting stuff in microbiology lies, and the art of spotting the odd and unusual is one that should be coveted by microbiology scientists and clinical microbiologists alike.


6)      Know when to ask for help

This is one I regard as critical in ensuring the production of quality results. If someone in your department has particular expertise on a particular organism or antibiogram, don’t be too proud or too afraid to use this expertise (even if they are more junior than you in the “pecking order”). They can often put you on the right course for a speedy and correct result, with ultimate benefit to the patient. Everyone has different strengths.(Personally I am useless at mycology, but I know the people who are good at it in my lab.)


7)      Take frequent breaks

Bench bacteriology is demanding and sometimes repetitive work. I am a big believer in short and frequent breaks. Don’t be afraid to take a few minutes out after a certain amount of time or a certain amount of plates. Struggling on until the “official” break may lead to mistakes being made. Negotiate with your manager if he/she doesn’t like this approach. I think you will find you will win. Everybody has different work patterns and works at different speeds. Categorisng everybody into the same work mode is neither helpful nor productive.


8)      Rotate and refresh.

If you are spending too long on one particular bench, then ask to rotate. “Bench fatigue” leads to mistakes as well as a de-skilling in the other benches, and is not desirable for the department as a whole. It is my belief that no-one should spend more than 3 months on any one bench before moving on. The de-skilling aspect of bench fatigue makes subsequent rostering more difficult and a vicious circle is set up.


9)      Document everything, and with respect.

A lot of labs have now moved to paperless audit trails and this is good. However it is important to remember that even your electronic documentation serves as a legal document which is potentially viewable by lawyers, clinicians and even the patient, in the case of any dispute. Ensure that your documentation is brief but thorough and that it represents a reproducible record of the work done on the sample, when and by whom. It is very important not to criticise the patient, the requestor or any of your colleagues’ previous work in such documentation. Such negative comments reflect poorly on the author and are ultimately unproductive.


10)      Find out People’s Names.

When phoning a result to the ward, it is very important to first elucidate who you are speaking to, their designation, and ensure they are qualified and appropriate to receive the result. When the result has been given it is equally as important to document this and also to document who you have spoken to so that the audit trail can be created. The same applies if the laboratory is receiving an incoming telephone request for extended incubation, extra susceptibilities etc. It can be very frustrating, not to mention potentially dangerous not to know who the person is on the other end of the phone….


11) Don’t “over-analyse” anaerobes…

I am not a big fan of identifying all anaerobes isolated, and in particular from superficial sites, where in many cases anaerobic culture should not even be undertaken. Whether the clinician includes anaerobic cover when treating the patient should depend much more on the clinical presentation and the site of infection, as opposed to any information the laboratory provides. Due to the difficulty in culturing anaerobes, a negative result from the laboratory should generally not be used “per se” by the clinician to cease anaerobic treatment.

If mixed anaerobes are present then it is usually pefectly acceptable to report as mixed anaerobes. Identifying each one individually is unlikely to be of benfit to the patient.

In sterile sites, then indeed it may be worthwhile spending time fully identifying anaerobes, particularly when they are a pure single isolate. Some anaerobes can give rise to very particular clinical scenarios, eg Fusobacterium necrophorum giving rise to Lemierre’s syndrome.


12) Think carefully about what organisms you perform susceptibilities on.

There is a lot of “just in case” antimicrobial susceptibility testing that goes on in microbiology laboratories. Ie doing susceptibilities on an organism “just in case” it is the pathogen, and then unnecessarily testing a large range of antimicrobials, “just in case” one of them might be used by the clinician. The third problem in this area is testing where the result is highly predictable; eg, testing beta-haemolytic streptococci against beta-lactams.

My advice is to only perform susceptibilities when:

i)  There is a significant chance that the organism is pathogenic,  and

ii)  The outcome of the susceptibility test is unpredictable.

If susceptibility testing needs to be performed, then only test a limited range of antimicrobials, ie the ones that are the most effective and most likely to be used.


13) Visit other laboratories.

If you spend all your time in just one laboratory, you are likely to start to believe that your laboratory’s “way” is the only way to do things. I think it is very important, regardless of whether you are a trainee or qualified, junior or senior, to spend time in other laboratories, observing or preferably working. In this way, you can find out different approaches to different problems that your laboratory faces, which you can then propose for your own laboratory. If you work in a diagnostic lab, then it is very important to visit referral labs that may be utilised by your laboratory for typing or identification of difficult organisms. This allows you to gain a better understanding of what happens to the sample or isolate when it leaves your lab.


14) Take note of Interesting Cases.

Every laboratory has its’ “bread and butter”, stuff that you will see lots of every day. You will know this type of work inside out. However when you do come across something that is unusual and that you might only encounter on that bench once a year or less, then it is worthwhile considering writing the case up for publication in either a scientific or medical journal, or presenting it at a conference. (Keep an Excel spreadsheet of such cases). I think it is important to stress here that I am not really interested in organisms that are so abstract that you are likely never to encounter them again, but ones that you may expect to see in your lab once every year or two, so that by writing it up, it is likely to benefit colleagues for future diagnosis and management. For example a Listeria monocytogenes bacteraemia in an immunocompetent individual, an Erysopelothrix wound infection, or a carbapenemase producer in an area where these are not endemic.


15) Be meticulous.

This is a tricky one for me. I am not a naturally meticulous person so I need to be “conciously” meticulous when needed..  However it is an important microbiology skill to have whilst working on the benches, in order to obtain the correct result and secondly to avoid contamination of both the sample and yourself. Because being meticulous can be both tedious and time consuming, it is important to value the importance of meticulousness and also to know why it is important. Some scientists are naturally meticulous, some need to learn how to be so.


16) Adapt to and embrace change.

Methods and processes change all the time in the microbiology laboratory. Huge changes are imminent with the arrival of Total Lab Automation for bacteriology. Understand why the change is being made and then learn how the change works. Don’t be scared to “forget” old methodologies to make room in your brain for the new ones.


17) Challenge your seniors.

Just because they have more reponsibility and a higher pay scale, they are not always right! Don’t be scared to (politely) question their decisions when there is reason to do so. In fact, please do! It should be mutually beneficial to both individuals. If something could be done better, say so. If you have been in one area of the lab too long, then make your feelings clear.


18) Help and respect your colleagues.

The best laboratories operate with the staff working as a team, with good communication and little gossip. Be very careful before criticising any of your colleagues, and in particular behind their back. These are people you will see day in day out for the forseeable future. Work through the issues and whatever you do, keep talking.


19) Learn from your mistakes, don’t dwell.

Everyone makes mistakes, you can be sure of that, and if you are processing upwards of 50 samples a day, you will probably slip up to some degree every day, no matter how competent you are. That’s just the way it is. However mistakes that have serious consequences for the patient are few and far between. Accept your mistakes, learn from them, and move on.


20) Never be totally content with what you have.

A controversial one to finish off with, and one that not everyone will agree with. Because bacteriology work can be quite mundane and repetitive at times, it can be easy to get into a rut. Always keep your eye out on the horizon for what other work opportunities are available, both within and outwith microbiology. The concept of a job for life is rapidly diminishing, partly because of technological changes and automation, but also because we as a society now accept better the concept of people spending their working career in a range of different jobs, sometimes covering different fields. Personally I am happy in my work, but I always have my eye on the next challenge!