Is your diagnostic protocol missing the bigger picture? Learn why leading veterinarians are shifting from targeted PCR panels to whole-genome sequencing to solve complex herd health mysteries.
It is a frustrating scenario every swine veterinarian knows too well: You have a herd with clear clinical signs—respiratory distress, scouring piglets, or reproductive failure. You submit samples to the lab, checking the boxes for the "usual suspects." The results come back negative, or perhaps positive for a pathogen that doesn't fully explain the severity of the symptoms. You are left with a sick herd, a frustrated producer, and no clear path forward.
The problem often isn't your clinical judgment; it's the limitations of traditional diagnostics. As Prof. Guillermo Ramis puts it, we have been operating under a model of "Dime qué tengo" (Tell me what I have)—where we only find what we specifically look for.
But what if you didn't have to guess? What if you could see everything in the sample—viral clusters, unexpected bacteria, virulence factors, and even the microbiome—all at once?
This article dives deep into the revolution of Next-Generation Sequencing (NGS) in swine medicine. Drawing on insights from Prof. Guillermo Ramis (University of Murcia) and Dr. Gabriel Moyano (Farmfaes), we explore how moving beyond check-box diagnostics is saving piglets, optimizing antibiotic use, and solving the industry's toughest health challenges.
For decades, veterinary diagnostics have relied on a hypothesis-driven approach. You suspect E. coli, so you test for E. coli. You suspect PRRS, so you run a PCR for PRRS.
Prof. Ramis highlights a critical flaw in this system: "The probability to mark what is not necessary or not mark what is producing your problems is very high".
When you rely solely on targeted panels (PCR or qPCR), you are essentially gambling that your initial hypothesis is 100% correct. This approach creates several blind spots:
The Solution? Open-ended diagnostics. By using technologies that sequence all DNA and RNA in a sample (often called "metagenomics" or "shotgun sequencing"), you shift the paradigm from "Is X present?" to "Tell me everything that is here."
The core issue is that traditional diagnostics constrain your view to only what you think you should be looking for, forcing you to miss not only the current problem but also potential future threats.
"We are elevating the responsibility of the practitioners to make ticks in a list... With PathoSense, you are going to explore all the DNAs and RNAs you have in the sample. You are not going to miss nothing." — Prof. Guillermo Ramis
One of the most compelling arguments for advanced diagnostics comes from a real-world case shared by Dr. Gabriel Moyano.
A farm was experiencing respiratory issues in piglets. Standard logic dictates looking for respiratory pathogens: PRRS, Influenza, Mycoplasma hyopneumoniae.
Using Pathosense deep sequencing, the team found something unexpected in the lung samples: high loads of Escherichia coli.
"It was surprising because E. coli is usually linked to intestinal problems, not lung infections," Dr. Moyano notes. Even more fascinating was the genetic breakdown of the bacteria found in the farm:
Historically, finding E. coli in a lung sample might be dismissed as fecal cross-contamination during necropsy. However, the genomic data proved otherwise. The F17 virulence factor allows the bacteria to translocate—moving from the gut into the bloodstream and reaching the lungs, joints, or brain.
Why this matters:
Without sequencing virulence factors, this farm would have continued treating for respiratory viruses while the real killer—a translocating bacterium—went unchecked.
The Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a persistent and evolving threat, with the emergence of highly virulent strains like the Rosalia cluster in Spain. The Rosalia variant caused "serious" problems for the Spanish swine industry, resulting in big losses and great uncertainty for farmers who were not prepared for such a highly virulent strain.
The conventional method for characterizing PRRSV involves sequencing the ORF5 gene, which represents only about 1% of the entire viral genome.
Prof. Ramis recounts a case where a veterinarian was convinced their herd was stable because the lab results showed a "vaccine strain":
Because the lab sequenced the ORF5 and it matched a vaccine. However, when WGS was performed on the full genome, "the rest of the genome was a Rosalia cluster strain". The symptoms were Rosalia-related because 85% of the genome was from the highly virulent cluster, despite the ORF5 being from the vaccine. This was a recombinant virus—a "Frankenstein" mix of a vaccine and a wild-type strain.Actionable Insight: PathoSense, specifically the "deep dive technique" that can sequence the full genome of the PRRSV directly from the original sample, is crucial. It provides the necessary data to accurately characterize strains, track their evolution, and make informed decisions on biosecurity and vaccination strategy, especially in light of the continuous importation of piglets that may be untested for PRRS.
If you only look at ORF5, you might falsely believe your biosecurity is holding or that your vaccine is causing clinical signs. Whole genome sequencing is the only way to accurately track viral evolution, recombination, and origin.
"Rosalia is not a strain... we should start speaking about a cluster. Sequencing it is very important... finding the Rosalia symptom because the 85% of the genome was from PRRS, but exactly the ORF5 was from a vaccinal strain." — Dr. Gabriel Moyano
When you open the door to unbiased sequencing, you often find pathogens that aren't on any standard tick-sheet.
In a diagnostic investigation for diarrhea, Prof. Ramis took five rectal swabs. The sequencing confirmed the expected Rotavirus A and E. coli. But it also found:
Wait, respiratory pathogens in feces? Yes. Finding high loads of respiratory pathogens in fecal matter indicates a systemic load so high that the animal is shedding virus and bacteria through multiple routes. This fundamentally changes how you view the infection pressure in that pen. "You have much more problems than the intestinal problems," Ramis warns.
In high-health breeding farms, maintaining a negative status is paramount. During routine screening of blood samples using NGS, the team discovered Mycoplasma parvum.
This pathogen causes anemia and can be vertically transmitted. In a boar stud, this could be disastrous, spreading via semen to downstream sow farms. A standard PCR panel for reproductive failure likely would have missed this completely.
Beyond simply identifying a pathogen, PathoSense allows for the detection of virulence factors (VFs)—the specific genes that allow a pathogen to cause disease.
Dr. Moyano predicts that in the future, We won't just say "Positive for E. coli." We will say, "Positive for E. coli cluster X, carrying virulence genes Y and Z".
We are entering an era where identifying the bacteria species is no longer enough. We must identify what that bacteria can do. Streptococcus suis is a commensal organism found in almost all pigs. Finding it means nothing. Finding a Streptococcus suis with specific genes that allow it to cross the blood-brain barrier means everything.
Why Virulence Profiling is Critical:
Using VFs to Assess Vaccine Efficacy
"The virulence factors open an incredible frame of opportunities... identifying that the E. coli that is causing the problem is the one that is not covered by the vaccine." — Prof. Guillermo Ramis
The Future of Smart Vaccines
The ability to map virulence factors directly from field samples is pushing the industry toward a future of highly customized, smart vaccines. Why include dozens of factors in a vaccine if only a few are needed? Conversely, why use a vaccine if the key virulence factors causing problems on your farm are not even included? Sequencing provides the data to close this gap and drive the development of truly effective, targeted preventative measures.
Beyond pathogens, the total microbial community (microbiome) is the next frontier in herd health. Research from the University of Murcia and FarmFaes is shedding light on how we can "program" piglet health before they are even born.
Prof. Ramis dedicates 50% of his research time to the microbiome. His findings suggest that the sow's microbiome is the primary driver of the piglet's future health.
Actionable Insight: If you are struggling with gut health or respiratory immunity in the nursery, look at your sow feed. Modulating the dam's gut flora may be the most effective way to protect the litter during the critical first three weeks of life.
Ready to move beyond "Dime qué tengo"? Here is how to start integrating these advanced tools into your routine:
Q: What is the "Rosalia Cluster" and why does it matter? A: Rosalia is a highly virulent variant of PRRSV found in Spain, resulting from a recombination between a vaccine strain and a wild Italian strain. It causes severe losses. It is critical because standard ORF5 sequencing often misidentifies it as a vaccine strain, masking the true danger to the herd.
Q: Why is "Dime que tengo" better than PCR? A: "Dime que tengo" (Tell me what I have) refers to open-ended sequencing that detects everything in a sample. PCR only detects what you specifically look for. Sequencing prevents you from missing co-infections, rare pathogens (like Mycoplasma parvum), or unexpected virulence factors.
Q: Can sequencing detect Antimicrobial Resistance (AMR)? A: This is the next step. As Prof. Ramis mentioned, the "dream" is to predict antibiotic sensitivity (MIC values) directly from the genome. While detecting virulence factors is currently available, reliable genomic AMR prediction for clinical use is the immediate next frontier in this technology.
Q: Is this technology only for viruses? A: No. As demonstrated by the E. coli and Mycoplasma cases, NGS is incredibly powerful for bacteria, parasites, and analyzing the overall microbiome. It is particularly useful for differentiating between commensal and pathogenic bacteria via virulence factor analysis.
Q: Do I need special samples for this type of testing?
Standard diagnostic samples like lungs, feces, tissue work well. Samples should be processed with the PathoSense sampling kit. The key is that because the technology amplifies all genetic material, sample quality matters. However, you can often get a full viral genome from the same sample used for initial detection.
The days of guessing which box to check on a submission form are fading. As the Spanish swine industry has learned through the challenges of Rosalia and antibiotic reduction, the complexity of modern diseases requires a more sophisticated approach.
Diagnostics is no longer just about detection; it is about intelligence. It's about knowing not just who is there, but what they are capable of doing.
As Dr. Moyano summarizes, "It's like magic... with the original sample, if you find the PRRS, you can do the deep dive technique and you have the full sequence".
Are you ready to stop guessing and start diagnosing?