Microbiologists and Outbreak Preparedness

In this step, Martin Antonio (MRC) explains how microbiologists are involved in outbreak preparedness and response. He explains how microbiologists may be alerted to an outbreak, and the initial steps that would be taken to begin an outbreak response from the laboratory perspective.

How are Microbiologists Involved in Preparedness?

Microbiologists play a key role in infectious disease outbreak preparedness. Adequate laboratory capacity is an important component of health system preparedness and a cornerstone in rapid detection and identification of transmissible agents; monitoring and surveillance of infectious diseases; outbreak response; and providing scientific evidence to prevent and control infectious diseases. As part of preparedness and response, the microbiologist must be part of the Emergency Operations Centre (EOC) activities and ensure that laboratory staffing/expertise, resources and coordination are in place to respond to infectious disease threats. These include:

1. Biosafety and biosecurity: Designated laboratories must have adequate biosafety facilities and measures in place to work with any infectious agents, including personal protective equipment. Microbiologists must also ensure that shipment of infectious biological materials within or outside the country are handled appropriately and according to the International Health Regulations.
2. Reagent stockpile: Microbiologists must be ready to distribute diagnostic tests and critical laboratory supplies and equipment quickly to the field or a designated testing facility where they are needed. Stockpiling of reagents must be done carefully and in conjunction with the logistics team to ensure adequate storage for any reagents or biological material that may be sensitive to certain conditions (i.e. heat).
3. Laboratory surveillance of the infectious agents: Microbiologists must test diagnostic panels to verify that laboratories can accurately identify pathogens. Regular quality assurance programs can identify any issues with detecting pathogens in laboratories and ensure these are fixed so during an emergency, laboratories are prepared. Laboratories should also be ready to store samples from outbreaks for future research such as vaccine development. This should be planned in conjunction with epidemiologists and medical teams to ensure proper research protocols, including informed consent and ethics, are in place.

How Would a Microbiologist be Alerted to a Possible Outbreak?

By reviewing routine diagnostic laboratory clinical data, microbiologists may notice an unusual number of cases of a disease within a specified period and this may be indicative of an outbreak. Routine laboratory data may come through hospitals participating in a sentinel surveillance network or as part of a larger reference laboratory. Clinicians in local hospitals may also alert a microbiologist to an outbreak if they have been seeing a cluster of symptoms that need to be further investigated with laboratory tests.

Laboratories that are part of a sentinel surveillance network test regularly for certain pathogens, which may include epidemic-prone diseases. These laboratories may detect an increasing trend in cases of a disease in a particular subgroup or geographic location. The microbiologist would then work with a state or regional epidemiologist to confirm whether this is an abnormal number, which may indicate an outbreak.

Larger reference laboratories often have more equipment and specialised tests to detect different types of diseases. Specimen samples from patients with unknown disease or suspected illness with an epidemic-prone disease may be sent to a larger laboratory with more diagnostic capacity. In many cases, just one laboratory confirmed case with an epidemic-prone disease (for example, Ebola) can trigger the declaration of an outbreak.

First Steps a Microbiologist Will Take if Alerted to an Outbreak

Microbiologists must work with clinicians and epidemiologists to ascertain the cause(s) and source(s) of the syndromic outbreak following a ‘case definition’. A case definition is a specific set of signs and symptoms combined with the personal history (travel history, location at a specific time) of an individual.

The case definition is informed from other epidemiological aspects of the outbreak and may change in the early stages of the outbreak. For example, this may involve reviewing the “epidemic curve” to determine the time(s) of onset of cases; when, where, how people got sick; age groups affected; source of the outbreak; and type of clinical samples to be tested for confirmation of cases. Once an individual meets the case definition for the disease, they are considered a “suspect case”. The appropriate laboratory test (depending on the pathogen circulating) would be done and, if a positive laboratory test is detected, this case would now be “confirmed”.

The overarching goal is to perform laboratory tests on suspect cases in an outbreak in order to confirm true cases as rapidly as possible. Confirming cases allows clinicians to inform patient care and gives more information to decision makers to guide public health interventions.