Using pathogen genomic data to manage a disease outbreak

Based on our reference database and trained classifiers, users who generate new nanopore sequences from unknown bacterial DNA can derive clinically and epidemiologically relevant information to answer the three main questions that aquaculture producers have during a disease outbreak.

What is killing my aquatic animals?

Identify a bacterial pathogen at the genus and species levels. Fine epidemiology using multi-locus sequence type (MLST) data to determine the origin, track spread and evolution of bacterial disease outbreaks

How can I treat my aquatic animals?

To minimize disease outbreaks, potential preventative measures include the use of probiotics, vaccination, better management practices, monitoring of the environment, and improved biosecurity.

Treatment with antibiotics can be used to treat fish diseases caused by bacteria only. With ready access to antibiotics coupled to limited availability of veterinary support and diagnostic tools, aquatic disease control with antibiotics is poorly informed, often unrecorded and likely to be high in many countries where aquaculture growth is fastest.

There are over 67 antibiotics used in 11 aquaculture producing countries. Overuse and misuse of antibiotics present an increasing risk of developing antibiotic resistant bacteria, a phenomenon also known as antimicrobial resistance (AMR). AMR has been declared as one of the most serious threats to global public health with attention now focused on global food supply.

Watch this short video explaining why AMR in aquaculture matters for the One Health approach

Safe antibiotic use based on data-driven decisions under health professional supervision will be key to reduce their overall use in aquaculture.

  • Can raw nanopore reads be used to correctly infer AMR phenotype of streptococcal fish pathogens (Streptococcus iniae and S. agalactiae) from an in-house database? Work in progress (coming in 2022).

How can I prevent disease in the next crops?

Prevention of re-occurrence of a disease must be considered. Vaccination of farmed fish with locally produced autogenous vaccines against bacterial disease can provide a locally-driven, cost-effective means to protect those animals, reduce antibiotic use and therefore address the global antibiotic resistance problem.

Molecular serotyping/biotyping information is used to categorize pathogenic members from different bacterial groups. Such information is used to produce/re-formulate autogenous vaccines and is of primary importance to ensure that vaccines cover outbreak isolates in a particular region.

Read more about the benefits of autogenous vaccination in Aquaculture Open Access link

  • Our Lab in a Backpack reference database and in-built classifiers can now accurately identify multiple serotypes and biotypes of two major fish pathogens (S. agalactiae and Yersinia ruckeri).

Are my aquatic animals safe for human consumption?

Transmission of zoonotic and foodborne diseases between animals and humans through consumption or during handling and preparation of infected aquatic animals pose serious concerns for public health and food safety.

The non-cholera vibrio: Vibrio parahaemolyticus is a frequent cause of food poisoning and septicaemia in humans, although mostly via marine and brackish water shellfish.

S. iniae infections were reported in humans after handling or consuming infected fish. In 2015, S. agalactiae sequence type ST-283 was reported to cause foodborne disease outbreak in human through consumption of raw freshwater fish.

Currently our Lab in a Backpack’s reference database includes all the major known GBS sequence types (STs) and serotypes with our classifiers trained to detect them including ST-283, allowing for early detection of those zoonose risks in aquatic food products before reaching consumers.

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