Outbreak response: Microbiologist

In this step, Martin Antonio (MRC) outlines the key activities of microbiologists during an outbreak response. He explains what tools are needed in a laboratory to respond to an outbreak and how microbiologists can be involved in research to improve both current and future outbreak responses.

1) What are the key activities of microbiologists in an outbreak?

The role of the microbiologist during a disease outbreak is to provide trusted laboratory confirmation of clinically suspected (probable) cases using appropriate and validated laboratory methods.

This involves coordination and receipt of all clinical samples from the field, which then get logged and properly stored in the laboratory. Storage is critical and the temperature must be properly maintained to ensure the integrity of clinical specimens. Specimens may need to be tested again in the future, so microbiologists need to work with logistics to ensure adequate facilities are maintained throughout an outbreak.

Appropriate diagnostic tests should be performed on the clinical samples in the field, if possible; however, clinical samples may be sent to a designated local laboratory for further diagnostic testing. Microbiology capacity should be established as close to the site of the outbreak as possible, while ensuring full biosafety precautions, however this is not always possible. Furthermore, clinical samples may be transferred to a national or regional reference laboratory for further confirmatory testing including antibiotic susceptibility testing, serotyping, and/or genotyping.

Microbiologists also need to be involved in building local capacity at public health laboratories for detection and surveillance of the infectious pathogens. This is needed to ensure sufficient microbiology capacity at a local level to detect the infectious agents in a timely and accurate manner.

2) What other activities do microbiologists perform during an outbreak?

Scientific research in laboratories is a critical part of outbreak control. Research during outbreaks can lead to discoveries that save lives. For example, a laboratory can support research for tracking genetic mutations that occur in strains during Ebola outbreaks, which can change the clinical severity of the disease. Similarly, laboratory identification and molecular tracing of epidemiologically linked strains can help to confirm transmission chains contributing to outbreak control and informing the design and assessment of policies to contain the disease. For example, whole-genome sequence data may provide information about the source of the outbreak, identify dissemination routes, and exclude or confirm the possibility of genetic modifications. Genomic findings can also be used to create rapid diagnostic tests, effective therapies, and vaccines.

3) What are the key tools microbiologists use in outbreak control?

The microbiologist must, if possible, deploy the most rapid, cutting-edge technology (e.g. genomics) as part of the outbreak response. Rapid diagnostic tests (RDTs) are diagnostic assays designed for use at the point-of-care (POC) and can be adapted for use in low-resource settings. The strength of RDTs is that the device is low-cost, simple to operate in the field (and therefore close to the source of outbreak), and results are simple to interpret. However, the assay must be sensitive, specific and stable at extreme temperatures.

4) Who are microbiologists’ main counterparts and collaborators during outbreak response?

Microbiologists must work closely with logisticians to ensure laboratories are properly prepared, through the stocking of reagents and other laboratory supplies, to respond to an outbreak. They also need to ensure cold chain is maintained for biological specimens collected in the field and those specimens sent to other laboratories for testing. Furthermore, if biological specimens are sent across international borders for testing, the logistics team supports microbiologists by ensuring the correct permits are secured.

Microbiologists also work closely with epidemiologists and clinicians to inform and refine the case definition being used in the outbreak. Epidemiologists will incorporate laboratory data into their analysis of the clinical data and need to maintain a close relationship with the microbiologist in order to access and understand the data being sent to them.