introduction: Unwelcome Guests

An effective pathogen management program is top most concern for farmers to help manage outbreaks, drive down operating costs, and drive up yields. Pathogen management protocols vary from operation to operation and from species to species. From disinfection to biofloc to high loads of algae, the goal is always the same: stay on top of pathogen outbreaks. 

But pathogens can colonise systems both from within and without. If an operation relies on outside suppliers for fingerlings and PLs, for example, the risk is higher of accidentally importing some unwelcome guests along with the next shipment. 

We took a look at what, if any, pathogens, a shipment of red snapper fingerlings might be carrying. And the results might surprise you, as it did us. 

methodology: SwabGENius

swab genius

To carry out this study, we used SwabGENius, one of our sampling kits designed to take any swab-able sample imaginable from solids, to biofilm, to lesions, and for testing quarantined stock for pathogens. 

We then extracted the DNA from all samples, performed Next Gen sequencing, and analyzed the data using our AI-driven advanced algorithms.

results: Unsuprising Surprises

Once water has been disinfected and properly readied for grow out, pathogen loads can be introduced from quarantined stock. Many pathogens, especially Vibrio, are unwelcome hitchhikers that are accidentally introduced with newly imported stock.

And indeed, we found this batch of fingerlings to be infected with Vibrio harveyi

We also sequenced their genome and found that these fingerlings matched with Crimson Snapper, not Red Snapper. Since we’re the ‘microbiome people’ not the ‘fish people’ we’d love to hear the experts on this. Are they basically the same fish from a consumer standpoint and often switched? Or was this a swift play by the original supplier? Drop us a note.    

Quarantined Red Snapper Fingerlings 

Red snapper fingerlings were swabbed while in quarantine tanks prior to stocking into the main tanks at a local RAS operation. The fingerlings were found to be infected to be with Vibrio harveyi and carrying resistant genes to tetracycline, a common antibiotic used to treat a wide variety of bacterial pathogens, indicating a recent antibiotic treatment prior to shipment. 

Along with the fact that many countries now are banning antibiotics use in aquaculture, and rightfully so (antibiotics in water released into local waters cause serious environmental damage); it’s also important to understand what kind of resistant genes your stock is carrying so that any further antibiotics treatment (if any) is effective and doesn’t contribute to further resistance. 

Hybrid groupers waiting in quarantine for metagenomic testing

Swabs aside, we can also test for pathogens in water samples. Vibrio is free ‘swimming’ and found in water (not just lesions). If there aren’t any natural mortalities, no need to force one. Water is perfectly able to report on the pathogen load for us.  

Introducing Vibrio-infected Quarantined Stock to Water

A Recipe For Disaster

In our previous case study, we looked at how disinfection puts the aquatic microbiome on the back foot. So putting infected stock into water that has already lost the key drivers for health creates a recipe for disaster. 

But happens when infected quarantined stock are added to  stable, pathogen-free water? In this graph, we can see how this event impacts the microbiome. 

The microbiome in the tank water (sample 5.1) was stable leading up to the transfer of stock and showed good biodiversity. Biodiversity is a crucial driver of healthy water systems, and diversity means the tank or pond water is more resilient to changes and less prone to future disease events.

The day after infected stock was added (sample 5.1P), we can see a number of significant changes: microbial diversity dropped, abundance dropped, Alteromonas grew significantly, and Vibrio took up residence in the tank.

Taken together, we would consider this tank to be at high risk for a pathogen event, and indeed, very sadly, almost all of these fingerlings perished shortly after transfer. 

conclusion: Knowledge is Power

Understanding what’s in your water isn’t just an interesting exercise. 

Knowing if something is in your water and, more importantly, knowing what is in your water guides the management protocols put in place to best manage these eventualities. 

Pathogens can be successfully managed with the right protocols in place, but a vast many of the protocols are not optimised.

From the microbiological standpoint, when we look at risk, we consider the road to a full-blown pathogen event to be lined with a number of red flags. The more flags, the higher the chance of a disease outbreak.

In this case, the risk that this tank will experience a disease event has a number of red flags: the presence of Vibrio, reduced microbial diversity, reduced microbial abundance, and a higher overall pathogen load. 

But half the battle is won with awareness of the situation, followed by an effective management protocol that can bring the pathogen loads back down again to a low level and re-balance the microbiome.

Following effective protocols and tweaking them to best handle the new circumstances in your system found after testing is a great way to bring the pathogen loads back down again to a low level and restore balance to the microbiome.

Contact us today to find out if your
quarantined stock are pathogen free.