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So you want to be a clinical microbiologist?

Bring science from the bench to the bedside in a career that draws on your strengths in research and working with people

by Nicole Arbour

So you want to be a clinical microbiologist

A career in clinical microbiology offers the opportunity to let you keep one foot planted in academia and the other out, making it an attractive career path for many science graduates, so long as you can handle the microbes. The successful clinical microbiologist possesses the insatiable curiosity and problem-solving skills of the research scientist, as well as the articulate, managerial extrovert's ability to communicate effectively with the layperson. Can you relate to this description? Are you a detail-oriented person who enjoys teamwork? If you answered yes to these questions, a career in clinical microbiology might be right for you. If not, click here to consider another science career path.

A day in the life of a clinical microbiologist

A clinical microbiologist has two major duties: managing a team of medical technologists and consulting with physicians ordering tests. Managing medical technologists includes helping to analyze test results and answering questions pertaining to incoming patient samples, or samples that are in any way unusual or difficult to identify. It also requires dealing with administrative matters that may arise. Reporting test results and consulting with physicians on tests requested, making sure that the appropriate tests were ordered, and that unnecessary ones are cancelled - are also important parts of your day.

Being a clinical microbiologist also involves the creation, optimization and implementation of assays for use in clinical diagnostics, as well as keeping up with current literature. In addition to these duties and depending on the specific position, motivation and experience levels, a clinical microbiologist can also run a research lab, teach at an affiliated university, work on international projects involving infectious diseases, be involved in policy making and consult for industry.

As someone who has completed a PhD in academia, you're already aware of the rigours of academic life, as well as the time it can take to translate research into something available in a clinical setting. As a clinical microbiologist, "you get the satisfaction of knowing that you have helped someone today, and not in 10 years or maybe never," said Marc Desjardins, a clinical microbiologist at the Ottawa General Hospital. Not only are you working with a team of highly trained technologists to identify the pathogens affecting patients in the present, but with the ability to develop and implement assays for clinical diagnostics, clinical microbiology really brings science from the bench to the bedside in a very appreciable way.

What about the money?

After being accredited as a Fellow of the Canadian College of Microbiologists (FCCM) or receiving your American Board of Medical Microbiology (ABMM) accreditation (these certifications, which are mutually recognized, are explained in detail below), salaries start at around $100,000, a significant difference from what you'll find in academia. While the salary disparity between an (FCCM/ABMM) accredited PhD, and that of an MD (despite similar jobs done in the lab) might be considered a downside, once you consider what your peers are making following similar training in academia (PDF), this may not seem like such a big deal.

What kind of work/life balance can you expect on the job? "The hours are flexible, but tend to be long, usually between nine to 10 hours a day. Often you have to take work home on weekends - teaching, grading, protocol writing and reading," explained Dr. Desjardins. As you become more established you will also do more travelling, he said. This may be limited to one or two conferences a year at the start, but will likely become more frequent over time.

Meanwhile, advancement in this job, as with most, depends on the motivation of the individual, where they are employed, and how they personally define advancement. In clinical microbiology, there are many opportunities that can be taken advantage of. First, there is the possibility of teaching at a university and running a basic research lab. Research and development work, leading to presentations and publications on a national or international stage, will help to get your name out and establish your reputation in the community. From there, consulting opportunities may arise in the public, private or international development sectors.

Still with us? Great. It's time to learn how to find your way in the industry and, most importantly, how to get the accreditation you need to land the job.

Getting your foot in the door

Even before you graduate, if you've determined that clinical microbiology is a career path that interests you, there are a number of things you should be doing. For one, try to get in contact with and talk to the clinical microbiologists in your area. Most people will be more than happy to discuss their career path with someone interested in their line of work. You can check out both the Canadian College of Microbiologists (CCM) and American Society for Microbiology (ASM) websites for information and people to contact for more information on particular programs offered.

You'll also want to do as much networking as possible during your PhD training. Get to know your local microbiologists, both academic and clinical, as they will be indispensable sources of knowledge and support while applying to CCM-accredited or Committee on Postdoctoral Education Programs-accredited training programs (more on those in a moment). Become a student member of CCM or ASM, and get to know the organizations and how they work.

Meanwhile, following the completion of your PhD, you will still have to get your FCCM/ABMM accreditation to get through the door to a good clinical microbiology position. This certification also represents an internationally recognized accreditation that is sought after in both clinical and industrial settings internationally.

FCCM accreditation requires the completion of a three-year postdoctoral residency at the CCM-accredited program at Mount Sinai Hospital in Toronto. For more information on this program you can contact CCM registrar Raoul R. Korngold. An ABMM accreditation requires the completion of a two-year postdoctoral residency at a hospital in the United States that offers a Committee on Postdoctoral Educational Programs-accredited program in medical microbiology. A detailed list of approved postgraduate training programs can be found here. To apply to one of these postgraduate training programs, see the following ASM webpage for details. Following your residency you must write and pass an FCCM or an ABMM accreditation exam.

Finally, with your FCMM/ABMM accreditation in hand you're ready to start applying for positions. There are many excellent resources to start from, including the CCM, the ASM and the Canadian Association for Clinical Microbiology and Infectious Diseases (CACMID) websites, among others.

If you've made it this far, you may have what it takes to be a clinical microbiologist. But if you're still shopping around for other career ideas, check out some of our other science career profiles here and here.

Dr. Nicole Arbour is a recent graduate from the biochemistry graduate program at the University of Ottawa and currently works as a research scientist with Spartan Bioscience in Ottawa.

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Comments on this Article

I am still in high school and I am considering careers in biology but I haven't made up my mind of what to be. I am considering microbiology, biochemistry, epidemiology, immunology, pathology and virology I was hoping if anyone can provide more information about these subjects and how many years it takes to be each one and good universities providing programs for these including scholarship programs and advice on which is good. Thanks

Posted by Hana, Aug 6, 2014 2:45 PM

Hi.I hold a PhD degree in Microbiology from my back home. With more than 10 years experiences in the field of Clinical Microbiology fortunately, recently I got my eligibility for FCCM exam from Canadian Collage of Microbiologists. As I am eligible to apply for job I would like to find any position in the field of Clinical Microbiology in Canada. So, it would be appreciated if give me any information about any sites or sources that can help me to find any position in this field.

Posted by Shohreh, Jul 9, 2014 2:49 PM

I obviously do feel that the field of Clinical Microbiology will definitely be the next place where plenty of job opportunities will be available. SO, it is a field to look for the students as well as professionals.
Great Article, I had a pleasure to read everything about " A day in the life of a clinical microbiologist"
Keep up the Great Work.

Posted by The Microbes, Nov 13, 2013 11:11 PM

hi ,i hav a degree in microbiology.can i do masters in biotechnology?

Posted by pauline yiembow taku, Aug 19, 2012 10:13 AM

I have master in microbiology, and PhD in Biotechnology, and thesis work was on molecular basis of PGP bacterial cold physiology and their application for transgenic plant development. Could I can apply for FCCM/ABMM fellowship program. At present I am working as Research consultant for Medical graduate in Medical college.

Posted by General Microbiologist, Aug 15, 2012 6:47 PM

I am a doctor in Pakistan, about to start my postgraduate residency training in Medical Microbiology in a Pakistani hospital. This training will be of five years after which i plan to come to Canada. What course of action will I be needed to take to pursue my career as a Medical Microbiologist in Canada?

Posted by Iffat Khan, Jul 24, 2012 2:57 AM

Hi there,

I have almost completed my PhD in microbiology in Canada. I am considering applying to the programs at Toronto and Winnipeg for Clinical Microbiology, but that leaves very little options for my husband (PhD in oceanography).

Does anyone know if there is equivalent training available in Australia? Furthermore, are individuals still referred to as "clinical microbiologists" in Australia, or does the job title differ?

I appreciate any help!

Posted by Katy, Apr 9, 2012 2:38 PM

In response to the TM's comments above, I encourage him/her to click on the following link to understand the boundaries of ABMM certification which has full reciprocity with FCCM certification. FYI, most of the Public Health Labs in the U.S. are directed by Ph.D. Clinical Microbiologists; Canada is just traditionally being MD-centric!
Doing a “fellowship in Clinical Microbiology” prepared the incumbent for those duties that are required as a lab director, hence at the lab level there is zero difference between a Clinical and Medical microbiologist, and in fact considering patient management focus associated with Medical Microbiology, experience shows they act suboptimal in Clinical Microbiology labs besides they cannot be 100% devoted to the lab as they still tend to function as a physician. Here are two examples:

Posted by Clinical Microbiologist, Nov 30, 2011 10:59 AM

Dr. Arbour should understand the boundaries and limitations of her FCCM/ABMM degree. Her statement:

"While the salary disparity between an (FCCM/ABMM) accredited PhD, and that of an MD (despite similar jobs done in the lab) might be considered a downside"

is misplaced and misleading for the reader regarding the scope of practice of her Medical Microbiologists MD colleagues. She attempts to equate the scope of practice of two distinct disciplines for the unsuspecting reader when this is far from being the truth in real practice and in background training. Her statement is derogatory of the discipline of Medical Microbiology. In the Medical Professional Code of Conduct, this is considered unbecoming and an unprofessional conduct.

The following excerpt from the Royal College of Physicians and Surgeons of Canada (RCPSC) Medical Microbiology Certification Objective states 4 major roles of the Medical Microbiologist (see below). Although a Ph.D microbiologist's role may overlap in point #1 and partially in point #4, points #2 and #3 is where the difference is between an MD microbiologist and a Ph.D microbiologist. Even in roles #1 and #4 where activities might appear similar, the difference of having medical knowledge, training and experience in the clinical setting is what preserves safety and quality in patient care from a diagnostic and clinical laboratory standpoint.

Medical Microbiology is a branch of medicine concerned primarily with the diagnosis,
treatment and prevention of infectious diseases. The specialty of Medical Microbiology
consists primarily of four major spheres of activity:
1. Scientific and administrative direction of a clinical microbiology laboratory.
2. Creation and direction of a hospital infection control program.
3. Provision of clinical consultations on the investigation, diagnosis, and treatment of
patients suffering from infectious diseases.
4. Public health and communicable disease epidemiology and prevention

For more detail information, refer to:

Posted by TM, Jun 23, 2011 11:17 PM


I just would like to mention that beside CCM-accredited program at Mount Sinai Hospital in Toronto, another Clinical Microbiology training program exists in Winnipeg, Manitoba; so it'd be good if you could also add that to the above info for prospective candidates: here's the link:

Posted by Kamran Kadkhoda, Dec 8, 2010 11:01 AM

I am in my second year offering medical microbiology,i want to know if after my first degree I can continue with my masters and if any sponsorship package for students who want study with you.

Posted by sieh isaac kwame, Aug 10, 2010 6:07 AM

Dear University Affairs

I am a Medical Doctor and Pharmacist who is in Australia with the goal to study a Master Degree in Infectious Diseases at the University of Western Australia. I would like to know somethings concerning to Clinical Microbiologist career. First, what are the opportunities of job?
and salaries? Second, In relation with my background what you think, is a good combination?
Third, I am thinking after finish my Master in Infectious Diseases going to Canada. What coul be the opportunities for me there?

Thank you

Posted by Jose Ignacio Trujillo R, Mar 23, 2010 8:11 PM


Iam planning to immigrate to Canada by 2010.I found this information quite interesting as i am very much interested to pursue the career of clinical microbiologist.But i was not clear what opportunities do a person like me have as i have done a Master Degree in Microbiology from an Indian University.

Posted by Suseela Jacob, Oct 5, 2009 11:18 AM


This field sounds interesting. Where can I find the postdoctoral training sites in Canada?

Thank you

Posted by Chad Segel, Feb 20, 2009 9:22 AM

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