The Ultimate Guide to Microbiology Test Requests: Unlocking the Secrets to Better Diagnosis

A Structured Framework for Ordering the Right Tests, Every Time

One of the biggest challenges faced by students and junior doctors rotating through the Infectious Diseases department is the lack of understanding and approach to requesting microbiology tests. It is one of the core foundations of medicine that is not taught well. If you often rely on recalling what your seniors have told you or what you read in the book, look no further.

Let’s walk through a practical, structured, and comprehensive approach to requesting microbiology tests — one that helps you provide the best patient care and makes you sound smart while doing it!

This is Step 4 of the 5-Step Infection Framework we’ve been working through together.

By this point, you've already done the groundwork: You've taken a thorough history using both the 5-Step Infection Framework and the paediatric ID history, and you've determined where the infection is likely located. Now it’s time to order the right microbiology tests to confirm your diagnosis or identify the pathogen responsible.

Here’s the key: the laboratory can only help as much as we help them.
Think of microbiology as a conversation — microbiologists are doctors too!
The more context you provide, the better they can process the specimen, select the right tests, and interpret the results meaningfully.

When writing your request, include:

• A brief summary of the patient's clinical story (e.g., medical history, travel, trauma, animal bites, water exposure etc)

• Risk factors: immunosuppression, pregnancy, medications

• Clinical signs and symptoms; progression over time

• Site of infection

• Recent or current treatment, and any relevant allergies (so alternative antibiotics can be suggested if needed)
  

Even though standard culture media like blood agar and chocolate agar support the growth of most organisms, the lab has access to a wide range of selective, differential, and specialised media — but we can only tailor the processing if we know what you're thinking.

Good communication directly translates to better care for our patients.

Reasons for Testing

When considering whether to request a microbiology test, it is helpful to frame your decision within one (or more) of the following key categories:

1. Diagnosis

• To identify the causative pathogen and confirm a suspected infection.

• This can strengthen your clinical diagnosis and guide initial management.
  

2. Guide or Change Management (Antimicrobial Stewardship)

• To direct treatment decisions, including:

  • Supporting or adjusting empiric therapy choices.

  • De-escalating or narrowing antibiotic therapy (e.g., stopping vancomycin when MRSA is ruled out).

  • Assessing the patient's response to treatment over time.

3. Infection Prevention and Control

• To screen for specific organisms that may pose a transmission risk to others, especially in healthcare settings (e.g., multi-resistant organisms (MRO) such as MRSA, VRE, ESBL-producing bacteria).

• Early identification supports isolation precautions and reduces the risk of outbreaks. If you think that MRO might be involved, please place your patients in appropriate precautions immediately.
  

4. Public Health Significance

• To identify pathogens that require mandatory public health actions, such as notification, case management, and outbreak control (e.g., measles, meningococcal disease, Hepatitis A). Identification of pathogens of public health significance also likely requires infection prevention and control measures.

Specimen Types by Organ System

To help you consider which samples to collect, here's a breakdown by organ systems. This is an oversimplification of specimen types and collection; many other nuances of specimen collection, transport, storage, timing of collection in relation to antibiotic administration, the appropriate container, and volume need to be factored in (a whole new topic for another day).

Understanding the Test

A broad categorisation of test types:

When investigating infections, it's essential to understand the different types of diagnostic tests—what they detect, how reliable they are, and how they guide clinical decision-making. Each method has its own strengths and limitations. Pathogens can be identified directly through microscopy, culture, detection of genetic material, or specific antigen components. In contrast, serological tests detect the body’s immune response, offering indirect evidence of infection and inferring causality. Below is an overview of each testing category.

The same process can be applied to various types of organisms—bacteria, viruses, fungi, and parasites—providing you with a complete framework to request microbiological testing for different organisms.

Putting it together

Let's use this case as an example to practice these steps:

Case: A previously well 5-year-old boy from Broome presented with fever and reduced level of consciousness. He also developed a widespread rash, some of which looked like a petechial rash. His family returned from Bali just four days ago. His father reported that “the mosquitoes went crazy”.

Step 1: Clinical history

This is what the 5-Step Infection Framework and Paediatric Infectious Diseases History is all about.

• Fever, reduced level of consciousness, rash

• From Broome, travel to Bali

• Mosquito exposure

• Previously well child

The microbiologist reads the clinical history and thinks

• Encephalitis, rash? HSV/ VZV/ Enterovirus

• Broome: MVE (Murray Valley encephalitis), JEV (Japanese encephalitis virus), Kunjin virus

• Bali: Dengue, malaria

• Influenza can cause a similar kind of picture; other sick contacts may give a clue

Step 2: Organ systems involved

Think about the organs involved and other organ systems that can provide clues. Try to obtain specimens relevant to the organ systems involved.

Step 3: Test Categories

Go through the categories of microscopy, culture, serology and molecular tests in a structured manner. So if you get asked by your consultant what tests you are going to request, you will appear calm, composed, thoughtful and intelligent :)

Below is an example, non-exhaustive list, of what might be requested using our structured three step process:

*The term PCR is commonly used in clinical practice, as it is widely recognized. However, the more precise terminology is NAAT (nucleic acid amplification test), of which PCR is one specific method.

Additional Tips:

1. Talk to People: If you’re unsure about the result, don’t hesitate to ask a senior colleague or reach out to the microbiology lab. They’re experts at interpreting results and can help guide you through the process. It is better to get it right the first time, rather than recollecting it (it’s hard getting specimens from kids!)
   

2. Document it: Be sure to document in the patient’s notes why you ordered the test and how you interpreted the results. This is especially helpful if the results don’t quite match your expectations.
   

3. Reflect: After receiving the results, take a moment to think about how the test impacted your clinical decision-making. Did it help you confirm your diagnosis? Or did it lead you to rethink your approach? This reflection will make you a better clinician the next time.

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I hope this provides you with a structured framework to guide your decisions when requesting microbiology tests. Of course, you don’t need to order every test possible—often, a single test can provide the definitive diagnosis. This framework becomes especially helpful when initial tests return negative. In such cases, you may consider repeating the test or exploring other testing options. And, if you're ever unsure, don't hesitate to reach out to your friendly microbiologist!