π Interactive example based on a real PathoSense report. Click any field, bar, or section label to learn what it means.
EXAMPLE LAB
Animal owner:Example Farmβ
Links the result to a specific farm. PathoSense can track pathogen trends per farm over time, useful for herd health monitoring and outbreak follow-up.
Date of registration:27 February 2026β
The date the sample was received and registered at the partner lab. Turnaround time is calculated from this date.
Veterinarian:Dr. Vetβ
The submitting vet receives the result directly in the PathoSense app and by email as soon as the annotated report is ready.
Date of report:6 March 2026β
Typical turnaround is approximately 1 week from sample receipt at lab.
Email:vet@example.comβ
Result notifications are sent to this address. The full report is accessible in the PathoSense app.
Company:Swine technical servicesβ
The veterinary practice or technical service associated with the submission. Used for invoicing and practice-level reporting.
Animal:Pigβ
PathoSense covers 50+ animal species. Species context is used to filter pathogen relevance and calibrate the annotation.
Organ system:General Clinic, Respirationβ
The clinical signs selected in the PathoSense app at submission. Used by the diagnostics team to contextualise the annotation. The more specific the clinical description, the more targeted the interpretation.
Analysis type:Sickβ
Indicates whether samples come from clinically affected animals, healthy controls, or a mix.
Ages:Suckling piglet: 25 daysβ
Age is a critical filter for pathogen relevance. Suckling piglets have maternal immunity but face growing susceptibility as it wanes. At 25 days, PRRSV and Streptococcus suis are particularly concerning.
Animals in sample:Pool of 5 animalsβ
PathoSense recommends a maximum pool of 5 animals. For livestock diagnostics, pooling is especially advised: it increases the probability of detecting the causative pathogen and gives a herd-level view rather than a single-animal snapshot.
Sample type:TBS swabsβ
Tracheobronchial swab (TBS) β a tracheal sample collected at necropsy or via transtracheal approach in live animals. TBS is the preferred sample for lower respiratory disease in pigs, as it samples directly from the site of infection rather than the nasal cavity.
PathoSense uses a patented swab with a unique tip that purifies the sample on-site: it removes host cells and other genetic background material, so the sequencing focuses on what is actively causing the infection. Each kit includes the patented swab, a 50 mL collection tube, a pre-filled syringe with fluid, and a QR code for registration in the app.
Results
PathoSense reports pathogen load on a semi-quantitative scale from Low to High. The scale is calibrated against an internal control added to every sample before sequencing β giving a consistent, run-independent reference point across all analyses.
Low β pathogen present at low abundance. Actively replicating (genetic remnants are removed before analysis). Roughly equivalent to Ct 28β30 on conventional PCR.
Medium β significant presence, likely contributing to the clinical picture. Roughly equivalent to Ct 20β25.
High β dominant pathogen in the sample, strongly consistent with active infection. Roughly equivalent to Ct 10β15.
Why this differs from PCR: Non-viable genetic material (from dead pathogens or resolved infections) is removed by filtration and enzymatic treatment before sequencing. A Low result on PathoSense represents an actively replicating pathogen β not a remnant from a past infection.
1-2345678 (respiratory group 1) Β· Healthy Β· pool of 5 animals Β· Pooled TBS swabs
Routine PCR panels would only detect the following pathogens: PRRSV, Pasteurella, Glaasserella parasuis, Streptococcus suis
Hover or click a view to compare what each diagnostic approach would show:
SOV is an emerging swine pathogen first described in North America and since detected in European herds. It is not included in any standard PCR panel. SOV belongs to the same family as bovine respiratory syncytial virus and causes respiratory disease in pigs, particularly in the nursery and growing phase.
In this case
Low load in a surveillance sample from healthy control animals suggests subclinical carriage. Detection alongside PRRSV and other respiratory pathogens contributes to the PRDC picture. This finding would not have appeared on a standard PCR panel.
This pathogen β also known as PRV1 or porcine respirovirus 1 β is an emerging PRDC contributor not included in any standard diagnostic PCR panel. It has been detected on 76.7% of Polish farms (WoΕΊniak et al., 2022) and is likely similarly prevalent across Europe. No vaccines are currently available.
In this case
Low load alongside SOV, PRRSV, and the bacterial complex is consistent with a background respiratory pathogen load. The co-detection of two pathogens not on standard panels (SOV + PRV1) in the same sample illustrates how conventional diagnostics can underestimate the full infectious picture.
Astroviruses are frequently detected in both respiratory and enteric samples from sick and healthy pigs. Their clinical relevance is generally low in the absence of high load or specific clinical signs.
In this case
Low load in a mixed sick/healthy cohort is consistent with routine background detection. The annotation classifies this as an incidental finding in this context.
PHEV is a betacoronavirus (same genus as SARS-CoV-2) that was previously associated with "vomiting and wasting syndrome" in suckling piglets. It replicates in the respiratory system during the primary phase of infection before spreading to the nervous system. It is now considered widespread and mostly subclinical in older pigs.
In this case
Low load in 25-day suckling piglets warrants monitoring β this age group is the most susceptible to neurological sequelae. The absence of neurological signs in the submitted clinical description is reassuring, but severity depends on strain and herd immune status.
PRRSV is a primary pathogen and important as a trigger for co-infections. It causes immunosuppression that allows secondary bacterial pathogens to proliferate β even when PRRSV itself is present at low load. The dominant Streptococcus suis finding in this sample is consistent with PRRSV-driven immunosuppression.
In this case
Low PRRSV load does not mean PRRSV is not clinically relevant here. Its role as an immune trigger explains the high S. suis load and the broad bacterial complex. Further PRRSV typing (whole genome sequencing via PathoSense DeepDive) can identify the circulating lineage and inform vaccination strategy.
Streptococcus suis
Streptococcus suis
S. suis is the dominant pathogen in this sample. It is a major cause of meningitis, septicemia, arthritis, and pneumonia in pigs, and a zoonotic risk for people in close contact with infected pigs or pork. Medium load strongly suggests active infection rather than commensal carriage.
In this case
The combination of PRRSV-driven immunosuppression and medium-high S. suis load is clinically significant. The VF detection of Epf (Extracellular protein factor) indicates a virulent strain β Epf is present in serotypes associated with invasive disease including meningitis and polyserositis. Treatment decisions and bacterial sensitivity testing are advised.
Neisseria shayeganii
Neisseria shayeganii
N. shayeganii is a gram-negative bacterium found in the upper respiratory tract of pigs and other animals. Its role as a primary pathogen in pigs is not well established. Low load in a mixed sample is consistent with commensal carriage rather than active disease.
Rothia nasimurium
Rothia nasimurium
A gram-positive commensal of the upper respiratory tract. Rarely a primary pathogen in pigs. Low load in a respiratory pool is consistent with background nasal flora and does not indicate active infection.
Actinobacillus minor
Actinobacillus minor
A member of the Actinobacillus genus found in the respiratory tract of pigs. A. minor has low virulence compared to A. pleuropneumoniae and is typically considered part of the normal respiratory flora. Low load here is not clinically significant in isolation.
Trueperella pyogenes
Trueperella pyogenes
T. pyogenes is an opportunistic pathogen commonly found in abscess material and pyogenic infections in pigs. In the respiratory tract, it typically acts as a secondary invader following mucosal damage. Low load here suggests early opportunistic presence rather than active pyogenic disease.
Bergeyella zoohelcum
Bergeyella zoohelcum
A gram-negative rod found in the respiratory tract and oral cavity of animals. It has zoonotic potential (associated with wound infections in humans after animal bites) but is rarely a primary respiratory pathogen in pigs. Low load here is an incidental finding.
Fusobacterium necrophorum
Fusobacterium necrophorum
F. necrophorum is an anaerobic gram-negative bacterium associated with necrotic processes β liver abscesses in cattle and necrotic laryngitis ("calf diphtheria") in calves. In pigs it can contribute to oral and pharyngeal necrosis. Low load in a respiratory pool is part of the broader bacterial complex and not a dominant driver here.
Pasteurella multocida
Pasteurella multocida
P. multocida is an important secondary respiratory pathogen in pigs, commonly associated with enzootic pneumonia and atrophic rhinitis. It proliferates when the respiratory mucosa is already compromised β in this case by PRRSV and the PRDC viral complex.
In this case
Low load here represents early or secondary colonisation. Combined with the rest of the bacterial complex and PRRSV as immune driver, it contributes to the overall PRDC picture. Monitor for increasing load on re-sampling if clinical signs worsen.
Glaesserella parasuis
Glaesserella parasuis
G. parasuis (formerly Haemophilus parasuis) is the causative agent of GlΓ€sser's disease β polyserositis, meningitis, and arthritis in pigs. It is a common upper respiratory tract commensal that can become invasive when immunosuppressed. Low load here suggests commensal carriage in the context of PRRSV-driven immune compromise.
Escherichia coli
Escherichia coli
E. coli is primarily an enteric pathogen in pigs, where specific pathotypes cause post-weaning diarrhoea and oedema disease. Detection at low load in a respiratory pool may reflect contamination from the gastrointestinal tract during sample collection, or opportunistic respiratory presence. The VF panel for E. coli in this sample provides important context β see Virulence factors below.
LowMediumHigh
Animal anamnesis
The anamnesis is a free-text field where the vet can add clinical context beyond the structured dropdown fields. This is the most valuable field for producing a targeted annotation β the diagnostics team uses this information to contextualise findings and flag what is most clinically relevant in this specific case.
Respiratory pool samples pooled from 5 suckling piglets.
Annotation
Every PathoSense result is reviewed by a trained scientist or veterinarian before delivery. The annotation contextualises the findings in relation to the submitted clinical information β it explains what the results mean, flags notable findings, and suggests follow-up steps. The annotation does not include a treatment plan or prescription; clinical decision-making remains the responsibility of the attending veterinarian.
PRRSV is a primary pathogen and important as a trigger for co-infections.
This annotation note applies regardless of PRRSV load level. PRRSV's primary role is immunosuppression β it impairs alveolar macrophages and other innate immune cells, creating the conditions for the bacterial complex observed in this sample. Low load does not mean low clinical impact when it comes to PRRSV.
PHEV or porcine haemagglutinating encephalomyelitis virus is a betacoronavirus that was previously associated with "vomiting and wasting syndrome"; it replicates in the respiratory system during the primary phase of the infection.
PHEV is in the same genus (Betacoronavirus) as SARS-CoV-2. In suckling piglets, it can spread from the respiratory system to the nervous system via retrograde axonal transport, causing vomiting, progressive wasting, and death. In this 25-day cohort, the respiratory phase detection is worth noting β the absence of neurological signs in the submitted clinical description is a positive sign, but the piglets should be monitored.
Astrovirus is frequently detected in respiratory and enteric samples from sick and healthy animals.
This is a standard annotation note indicating astrovirus is an incidental finding β not a driver of the clinical picture in this case. PathoSense includes it in the report for completeness but explicitly contextualises it to avoid diagnostic over-interpretation.
Respiratory bacterial complex detected.
This note covers the broad set of bacterial species detected at low load. In PRDC, it is common to detect multiple bacteria simultaneously at low to medium load β this is the bacterial complex. The individual species are listed in the results chart above. The dominant bacterium (Streptococcus suis at medium load) is the primary focus for clinical action. The others represent opportunistic colonisation in the context of viral immune damage.
Pasteurella multocida is singled out here because it is a known primary contributor to enzootic pneumonia and secondary bacterial pneumonia in PRDC. Even at low load, the diagnostics team flags it as clinically relevant given its role as an opportunistic secondary pathogen in immunocompromised animals.
Glaesserella parasuis can be found in healthy animals. When combined with virulence factors, this bacterium can cause respiratory problems and GlΓ€sser's disease.
Bergeyella and Rothia are respiratory bacteria that are frequently found in sick animals.
Streptococcus suis is a major pathogen found in the respiratory tract. S. suis can also cause systemic infections such as arthritis and encephalomyelitis if virulence factors are present.
The annotation provides scientific interpretation of the results in the context of the submitted clinical information. Treatment decisions, antibiotic selection, and on-farm management remain the responsibility of the attending veterinarian.
Virulence factors detection
Virulence factor (VF) detection is included in the newest version of the PathoSense Diagnostics reports. For bacteria, VF genes encode mechanisms that enhance pathogenicity such as adhesins, toxins, serum resistance factors, and immune evasion genes. Detecting specific VF genes helps predict clinical severity, inform treatment selection, and assess zoonotic risk. Click on any VF gene below to learn what it means.
1-2345678
Escherichia:
fimC-I (Type I fimbriae)
Type I fimbriae mediate attachment of E. coli to host epithelial cells β the first step in colonisation. Their detection in a respiratory pool at low E. coli load does not confirm active disease, but indicates that the E. coli strains present have adhesive capacity. Type I fimbriae are found in a wide range of E. coli pathotypes.
Streptococcus:
Epf (Extracellular protein factor)
Epf (extracellular protein factor) is a virulence marker of highly virulent S. suis strains β originally described by Vecht et al. (1991, Infect Immun 59:3156) in serotype 2 strains responsible for invasive disease (meningitis, septicemia, polyserositis, endocarditis). Its detection in a sample with medium-high S. suis load is clinically significant and supports prioritising this finding for follow-up. Epf is also a zoonotic risk marker: virulent S. suis serotype 2 causes severe meningitis in people handling infected pigs or pork.