Medical Specialties - Medical Microbiology (12 Apr 2023)

SPEAKER_01 0:00

If you enjoy listening to career conversations, why not become a member of the Royal College of Physicians of Edinburgh? Our membership provides you with access to the RCPE educational portal, the live evening medical updates, and you have options to view the symposia both in person or online. If you would like to learn more about this, please go to the Royal College of Physicians of Edinburgh website. Hello everyone, and welcome to another episode of Career Conversations brought to you by the Trainee and Members Committee of the Royal College of Physicians of Edinburgh. My name's Dr. Marilena Gianudi, and I am a cardiology registrar based in West Yorkshire, and I'm on the TMC. Today I am delighted to be joined by Dr. Chris Rooney, who's a medical and microbiology registrar based in West Yorkshire, and he's going to be talking to us about medical microbiology. So, Chris, welcome.

SPEAKER_00 1:01

Hi, thanks very much for inviting me on.

SPEAKER_01 1:04

Thank you for coming along. So, for our listeners, we use this podcast as a way of trying to promote group two specialties, especially for people who won't necessarily have had exposure to specialties that they're potentially interested in exploring later down the line. So, could you please just maybe start by telling us a bit about what medical microbiology is and how you got into it?

SPEAKER_00 1:29

Yeah, sure. So I think medical microbiology can be really diverse. It's rooted in laboratory-based diagnostics, but as the clinician, it's your role to integrate those diagnostics with the clinical team. But also you have roles in infection prevention and control and antimicrobial stewardship. And so I think it can be quite varied in terms of what you would do on a daily basis. And it gives you the opportunity to work with patients both on an individual level but also on a hospital-wide level or a community level.

SPEAKER_01 2:01

Okay. And what's the difference between microbiology and infectious diseases training?

SPEAKER_00 2:08

So training, I think, has gone through a lot of changes actually since I graduated. So initially for medical microbiology, you could have gone into the specialty straight away from F2. And then that changed a couple of years ago, where you had to do CMT and have MRCP. And so they created what was called or still is called combined infection training. So everyone who's interested in an infection specialty will do combined infection training, which will encompass virology, microbiology, infectious diseases, and clinics, which how they're kind of integrated or how it works out will be deanary specific. But after two years of that, then you will enter higher specialist training in one or two of those specialties. So when you initially apply, you will be applying for core infection training, but it will be a view towards a specific CCT. So in my case, I always knew that I was CCTing in microbiology, but my first two years will be kind of a broad infection training. So you can just do microbiology like I'm doing, or you could do microbiology and ID, or you could do general medicine and ID, or I think virology and ID. So it's varied, but at the start, you will always know what you're CCTing in, but everyone will do kind of the first two years the same.

SPEAKER_01 3:25

And how did you decide to just do microbiology? Because obviously, did you have exposure to virology and infectious diseases, or at what point do you need to decide that?

SPEAKER_00 3:36

Why I chose micro, I think is I was trying to think about this, and I think it's because I was quite greedy, to be honest. And I really liked the laboratory-based pathology specialties, but I knew that I was really interested in medicine and I wanted to maintain that link, not just kind of advising clinicians, but still having some patient interactions. And for me, I think microbiology offered that nice mix for those that are maybe even more clinically oriented and want to do specialist clinics, then ID might be more of a mix for them. But for me personally, I knew that I wanted to keep a large portion of the laboratory work and the clinical size with medical microbiology. In terms of exposure, so before I did medicine, I actually did a degree in microbiology. So I had that kind of stronger laboratory background and exposure, I suppose, than maybe other individuals wouldn't have. But I think in terms of exposure, there's rotations definitely in foundation year that you can do to get exposure to microbiology. And I think now that it's become integrated into, as you say, like a tier two specialty, then maybe it's time opening the conversation of whether you could have a microbiology specialty in CMT. But currently it's not offered, I don't think, in my deanery, but it may be offered elsewhere.

SPEAKER_01 4:47

And what is a typical day in your work life like then?

SPEAKER_00 4:54

Yeah, so again, it will vary, I suppose, depending on where you're training. Broadly speaking, I guess your day could be initially divided into whether you're going to be reactive or proactive. And so if you're proactive, you might be calling out important results. So that would include blood cultures or any results from sterile sites and trying to kind of advise the teams with the results that you already have and making a plan for further investigations that you might do. And then the other aspect is being more reactive where you're there to take consults. So you might be on the phones, for example, taking all of the variety of calls that might come in, or you may be going on ward rounds. And I suppose within those two broad spheres, then there's also opportunities in infection prevention. So if there were outbreaks going on at the hospital at that time, you might get involved in those, or if there's root cause analysis for certain infections, you might be involved in those. So it can be quite varied as to how your day will go. And then again, depending on how it's broken down in the proactive or reactive spheres, you might be on a placement, for example, in pediatrics. And so you might be tailored that the calls that you're going to receive that day would be all from pediatric specialties when they call in. So it can be really varied. And I think you never know who or what's going to pop up when you go out in the wards or when you receive that phone call and where that set of discussions and investigations might lead you.

SPEAKER_01 6:23

And obviously, you mentioned that you can go on ward rounds. From my, again, very limited experience, I've only really been in close contact with microbiologists when I did a hematology job. And I know speaking to kind of some trainees, that they potentially hadn't even thought of it as a career simply because of the perceived lack of patient interaction. Is there an opportunity to be relatively patient-facing if you want that? And then if you don't want it, then you can be more, you know, laboratory-based? How does that work?

SPEAKER_00 6:57

That's a great question. I think we're in this transition period. So traditionally, the microbiologists, I suppose, was seen more in the laboratory. And our training and your daily activities probably reflected that, and especially the exams. So it used to be that you were heavily based in the laboratory, actually doing maybe some of the testing yourself. And so the exams would have been actually over five days, and you would have gotten a sample and worked that up. Now it's changing. So there's an appreciation, obviously, that laboratory medicine, and that there's a lot of very highly skilled clinical scientists that run that aspect more autonomously now. And so the role of the medical microbiologist is switching more and more towards that consult, I think, and being more present on the wards. But again, it's kind of what you make it and what you want to do. But there's different avenues and sub-specialties that you could get involved in that require kind of daily input. So again, it can be varied in the hospital, but most hospitals that have an ICU would have a daily ward round and microbiologists that would be sub-specialising in intensive care, microbiology. And then other kinds of specialties, such as neonatal intensive care as well, also gets a daily ward round. And then you have, I think, sub-specialization in any specialty really, but we tend to have kind of ward rounds maybe three times a week in other specialties that maybe the patient aren't as critical, but there's still that aspect. And I think as it changes more and more, I think there's more emphasis on the microbiology going out. So now we've done what's called a bacteremia review. So there's research that shows that if you have direct interventions on the ward with the microbiologist, that there's better outcomes from patients that have bacteremias. And so currently we would see all patients that have MSSA bacteremias in our trusts. And I think that's something that's happening in a lot of trusts. And whether that would open up to include different bugs, I'm not sure, but it's definitely changing that we're becoming more and more present on the wards. I think if you asked microbiologists, they would say they were always present on the wards, but I suppose it's increasing presence.

SPEAKER_01 9:02

And with regards to your skills off the ward and off-patient-facing medicine and actually being in the lab, obviously you were potentially in a very good position because you mentioned that your first degree was in microbiology. But how does it work if someone hasn't had the exposure? How does training work to actually learn how to undertake the techniques that are needed in the lab?

SPEAKER_00 9:24

So we have DOPs, laboratory-based DOPs. So, like you would with your procedures in CMT, there will be a core set of kind of DOPs that you would be expected to do. And so generally what happens is that at the start, you have more laboratory sessions. So you understand the processes that are going on in the lab. And that would start from plating out agar plates and basic microscopy, then working up through different stains and sensitivity testing. And the idea is that you would have a laboratory-based training would occur early on in your ST3. And so, because the idea is that as we authorize samples out, you're the kind of last chain, as it was, to check everything to make sure that the sample has gone through the correct processes and the correct tests have been done on that sample. And so, in order to get to a position to be able to do that at the start, you would have a lot more laboratory-based sessions. So, in those sessions, how it's happened for me is that you're assigned to a specific biomedical scientist for that day or that morning and you kind of follow them around, see what they're doing. Again, it depends on what bench you've been assigned to. But the idea would be that you would have a number of sessions and that you would work up, maybe not to be autonomous in that bench, but definitely to be able to understand all of the processes and the rationale behind those laboratory tests. So when it comes back to the authorization of that sample, you're able to see any anomalies or have that discussion with the biomedical scientists as to why a test was done this way rather than another way, for example.

SPEAKER_01 10:57

Right. You mentioned that there are different benches. If we keep it really simple for us, you know, maybe listeners that haven't had any exposure to the lab setting at all. Could you talk us through the different benches in the environment in the lab?

SPEAKER_00 11:11

Yeah, so again, I guess it will vary depending on what hospital you're in, but generally you would have a urine bench, for example, that would process all of the urine samples, a general's bench that would take all of your skin swabs or any more general microbiology, such as your screening tests or your MRSA plates and things like that, would also be done in generals. Then you would have a respiratory bench. And so that might have different isolation associated with it for respiratory or airborne pathogens. And so you would need extra training before going in there. And then you would generally have a kind of blood culture bench. So that's kind of the obvious working up the blood cultures and depending on the site, but that would also include maybe sterile sites as well. So any kind of CSF or any samples that were taken from surgeries will be worked up there as well. And then you might have some automation as well. So someone will be looking at those benches. So again, it depends on what kind of procedures you have in your laboratory, but you may have automated processes. For example, we have for screening. And so there's someone kind of running, looking after the computer essentially. So rather than actually doing the specific kind of plating out, they're more looking at the whole pathway of those samples.

SPEAKER_01 12:20

Right. And do you think you need to have a really thorough understanding of basic science past what we get taught at medical school? Or do you think that the training is sufficient to kind of get you up to scratch?

SPEAKER_00 12:32

Yeah, I think the training should be sufficient to get you up to scratch. The curriculum is constantly changing, I think. And so it can be difficult, I suppose, to feel that you're getting everything and it's quite broad. But as I say, that intensive period at the start should bring you up to scratch in terms of what you need to know for the laboratory processes that are going on. I think, as I've said, we're kind of in this transition period where we're looking more towards the wards. And so the exams are also changing a lot more as well. And the emphasis on the practical aspects of medical microbiology, I suppose, are reducing. And so there's more emphasis on the clinical side and complex clinical cases in the exams and long cases where you would have multiple interactions with the team rather than what I suppose traditionally would have been maybe identifying an organism that was hard to grow or hard to classify. It's kind of moving away from that aspect into the more kind of complex clinical cases. But the training should be there to give you that knowledge to be able to understand all of the laboratory processes. But as I said, you probably wouldn't be expected to do them autonomously anymore.

SPEAKER_01 13:38

So what skills do you think are needed for a clinician wanting to follow this career?

SPEAKER_00 13:45

I think communication skills. I think there's an idea that a microbiologist, as you say, maybe isn't present on the ward so much and maybe likes to stay in the lab. But actually, I think you need really good communication skills to be able to lead or kind of advise the team as to what you think might be the cause of infection, what you think the treatments could be, because sometimes there might be different ideas or different things at play that you have to come to an agreed decision as to what's the best route for that patient. And that is really the nuts and bolts. You are that interface between the laboratory and the clinical team. And so it's being able to navigate those difficult decisions. And so, for example, if someone had a line infection, it's a really difficult line to remove, then the team will be understandably hesitant to remove that line. And whether there is a possibility of line salvage or whether you feel given what the laboratory results have shown that this line needs to be removed. And that's, I suppose, just one small example, but it's those kind of discussions that you have on a daily basis. So I think really good communication skills is important. Having a keen eye for detail probably is important as well. So if we think about mechanisms of resistance, I think the terminology in microbiology sometimes can be a barrier in terms of the language that is used, but also how those things are defined as well, in terms of an ESBL, CPE, all of those terms can be hard to wrap your head around. And they all come down to maybe millimeters of changes on sensitivity plates and so having that kind of ability, I suppose, or want to kind of get down to that nitty-gritty of testing is something maybe some people are more big picture. So I think maybe you need a certain level of detail as well in microbiology.

SPEAKER_01 15:26

And how would you advise anyone that's keen to pursue this career? What advice would you give them to get started into looking into it and to applying and following through with it?

SPEAKER_00 15:42

Yeah, so what worked well for me, even though I'd done a degree in microbiology through medical school, I didn't really all the way through on to do microbiology. And it was in my foundation year when there was a I was in cardiology and I was speaking about an endocarditis case to the microbiologist that I kind of sparked my interest again. And so I approached that microbiologist and asked if I could do a taster week with them. So we were allowed five days in different specialties. So I went there and then we did a little project about screening different check-in desks in outpatients because of his concerns about them being a source of infection. And so that gave me the week in the specialty and also a kind of side project to show commitment to specialty. And so those are definitely things that I would suggest. I think if you were to approach the microbiology department and say that you're interested in the specialty, there's definitely loads of projects, loads of audits and things that need to be done. And they can give you an insight into the specialty and fulfill that commitment to specialty. I suppose, in terms of placements, then you're obviously more tied in terms of getting the exposure if they don't offer the placement there. But again, I think having that conversation with the teams, then they can usually try to come up with something that you can get exposure, both on the clinical side and within the laboratory.

SPEAKER_01 17:03

I guess this is more for my selfish benefits, but I'm sure that, well, hopefully that other people will find this useful as well. For those of us that don't want to do microbiology, when we ring a microbiologist, which we all do, if it's not on a daily basis, it's at least once a week to get advice. What are your heart sink questions that we may ask? Or what are the kind of questions that are appropriate for us to ask?

SPEAKER_00 17:31

Yeah, that's a tricky one. Um, I think a clear rationale as to why you're calling or can be useful. So I think often the most frustrating of conversations can be that there's no real source of infection, and also there's no the investigations that have been completed. So it's really difficult to give advice if you don't have the swabs, you don't have the sputum cultures, you don't have the PCR tests requested. So it's really hard to know, and then you want to cover multiple sources. So having that really detailed history and examination from the patient and being able to say this patient has, I think, you know, a pneumonia and they have really complex sputums in the past. What do you think they should be on? I would think is an appropriate call. What's difficult is because we can't see the patient, is to make the diagnosis for you. That's kind of something that clinical diagnosis has to come from, I suppose, your side, and then helping you confirm or refute that diagnosis or treat that infection is why we're there. I think other triggers will be just knowing the antibiotic exposure, so in the community as well, and not just what they've had in secondary care, and knowing that the dates of when everything has been given is really helpful and knowing allergies, so it can be really frustrating if you go through a plan and then suddenly you realize that the patient is actually penicillin allergic. So having those things really quickly to pop out straight away in the conversation is just really helpful because I think, like all specialties, there's increasing pressure. And so while we appreciate that you've been waiting for a long time, we've also been going through a lot of different phone calls as well. And so if that information is to hand, it just really expedites that conversation.

SPEAKER_01 19:08

I think that's really useful and certainly something that I will take away when I'm ringing about endocarditis health. And one thing that we haven't covered is work-life balance and on-call commitment. Because again, I think that's something that's really important for anyone, you know, considering a group two specialty, especially, but I guess for all of us when we're making our career choices. So, what are your on-calls like? And how do you think this specialty helps you balance your work-life commitments?

SPEAKER_00 19:40

Yeah, I think that was one of the aspects as well that I took into account when I was choosing microbiology, in that we do have non-resident on calls. So you can be on call from home with the laptop, and so you can access the different servers. I think it really varies depending on what hospital you work in, just from meeting other trainees at national meetings. For me, we do do 24 hours kind of on call. So you would do your nine to five, then you would be on call all night, and then you would be expected to be available the next day at nine as well. The road has gone through multiple iterations, so that's currently how it stands. But I know in other centres the trainees may not do nights on call. And so there's kind of that variation there, but generally your on call can be from home. There is a laboratory process I kind of mentioned becoming more automated. There is an idea that there will be results coming at all times throughout the night. And so that may change how microbiologists work. I imagine it would. So again, depending on your trust or the department there, the hospital that you're working in, you would authorize samples up to a certain time. So we wouldn't be expected to call out positive blood cultures, we'll say at midnight. But again, that would vary depending on what trust you work in.

SPEAKER_01 20:57

And then weekends, is it just the same thing if your on call is just a 24-hour on call, obviously based in your deanery?

SPEAKER_00 21:04

Yeah, so generally there'll be more support for the weekends. So while we think that there's less samples coming through, for example, a lot of primary care centres are closed, and so you don't get the same volume of samples coming through from those. So in theory, there's less of a workload because there's less of you that's actually it feels like there's a lot more. But you would usually do a long day and then half of the next day, and then the other person would do the the opposite of that, and then usually there's the zero the day, then after the weekend. But again, it's kind of changing more. I think the consultants are becoming more present at the weekends given the increase in complexity of infections in general, and so that need to have a consultant on site as well at the weekends. So I think it's changing, and I think as ID and micro become a bit more blended, we may see also a combined infection service of on-call, which I'm not sure exactly how that might look, but again, it may change the ability to be non-resident on call.

SPEAKER_01 22:04

Okay. Chris, I think to be honest, that's all my questions. Do you have any parting comments for our listeners?

SPEAKER_00 22:13

I just think it can be hard to get the exposure maybe to micro, but it's definitely if you're kind of thinking about it, I would definitely reach out to the microbiology department. I think from in Leeds, anyway, we're always really keen to speak to people who are interested in microbiology. And it's just the I think we've discussed that exposure to the specialty can be lacking depending on lots of different factors. So don't be afraid to reach out and ask for the exposure. And if it's not for you, then that's fine. At least you've had a look.

SPEAKER_01 22:40

Yeah, definitely. And I think that's why we are doing these podcasts to try and help people even just consider specialties that they hadn't even heard of or considered. And so far, everyone is saying, look, we're more than happy to have people that might potentially want to train in this specialty come and have a look around. So I don't think there's a single specialty that wouldn't want new blood almost coming in. So for anyone that's interested, please reach out to your local service.

SPEAKER_00 23:10

Yeah, totally agree.

SPEAKER_01 23:11

So, Chris, I think that's my turn to say thank you. That's been really insightful. I'm sure our listeners would have gained a lot, and thank you for your time.

SPEAKER_00 23:20

Thank you.