Molecular Biology & Genomics Centre

Pathogen Identification


Molecular based methods like PCR, Real-Time PCR and more recently next generation sequencing (NGS) have revolutionized the field of veterinary diagnostics. At MBG, we offer detection of pathogenic viruses, bacteria and parasites using molecular methods, which are fast and highly sensitive to detect microbial pathogens in various specimens. MBG is an ISO 17025 accredited facility and benefits from an isolated containment level 3 facility for processing highly (level 3) contagious pathogens.


All Bacteria Virus Fungi Parasite

Validated
Assay Code See Below
Description Aspergillus spp. has been found worldwide in almost all domestic and wild animals, ranging from insects and corals to NHP. Aspergillosis is a common infection in birds, particularly pet parrots, penguins, captive raptors, mallards and other ducks, turkeys, and Japanese quail, in which it causes pulmonary and air sac infection. Aspergillosis has also been described in cats and dogs in which it affects only the nasal passages. In large animals, Aspergillus infection is assumed to be rare but has been reported with increasing frequency. It can lead to various diseases like mycotic abortion and gland infection in cows as well as guttural pouch involvement in horses. In marine mammals, airways are usually initially affected leading to pneumonia, but other organs including the brain may also be infected following fatal dissemination. The most frequently identified pathogens are Aspergillus fumigatus and Aspergillus flavus, ubiquitous organisms capable of living under extensive environmental stress.

Aspergillus fumigatus is an opportunistic pathogen and the primary cause of invasive aspergillosis. Triazole antifungals are used to treat aspergillosis. However, triazole-resistant A. fumigatus infections are increasingly reported worldwide and are associated with increased treatment failure and mortality. This fungus can acquire resistance to azole antifungals due to mutations in the azole target (Cyp51A). Cyp51A mutations typical for environmental azole resistance acquisition (for example, TR34/L98H) have been reported in many cases. These mutations can also be found in isolates recovered from patients.

Pathogens Tested
  • APA-098 : Aspergillus fumigatus/ terreus/ flavus
  • APA-189 : Azole-resistance profiling of Cyp51A gene

Method Aspergillus fumigatus / terreus / flavus by Multi Real-Time PCR (This assay includes the detection and differentiation of Aspergillus fumigatus / terreus / flavus)
Azole-resistance profiling of Cyp51A gene (This assay detects selected mutations in the Cyp51A gene related to azole-resistance, by PCR and sequencing).
Sample Type
Culture, EDTA Blood, Swab / Secretion (Respiratory), Tissue.
Transport Condition Sample should be transported at 4°C.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 3 working days.
Urgent Samples will be reported within half of the minimum test period & will be Charged Double.
Samples delivered after 11:00 AM will be processed next working day unless urgent.

Links

Validated
Assay Code See Below
Description Aspergillus is a type of fungus that is found indoors and outdoors. Most people breathe in Aspergillus spores every day without getting sick. However, health problems may arise in people with weakened immune systems or having underlying diseases. Aspergillosis, most often caused by Aspergillus fumigatus, occurs in humans in chronic or acute forms which are clinically very distinct. Most cases of acute aspergillosis occur in people with severely compromised immune systems, e.g. those undergoing bone marrow transplantation. Chronic colonization or infection can cause complications in people with underlying respiratory illnesses, such as asthma, cystic fibrosis, sarcoidosis, tuberculosis, or chronic obstructive pulmonary disease. The most frequently identified pathogens are Aspergillus fumigatus and Aspergillus flavus, ubiquitous organisms capable of living under extensive environmental stress.

Aspergillus fumigatus is the primary cause of invasive aspergillosis. Triazole antifungals are used to treat patients with high-risk conditions such as stem cell and organ transplant recipients as mortality exceeds 50%. However, triazole-resistant A. fumigatus infections frequently occur and are associated with increased treatment failure and mortality. Of particular concern are resistant A.fumigatus isolates carrying either TR34/L98H or TR46/Y121F/T289A genetic resistance markers in the azole target (Cyp51A) gene and these are mostly associated with triazole fungicide use. Reports of these triazole-resistant A.fumigatus strains are more common in Europe than in the US.Understanding the prevalence of azole resistant patient isolates is important to guide clinical and public health decision-making.

Pathogens Tested
  • HPA-189 : Azole-resistance profiling of Cyp51A gene

Method Aspergillus fumigatus / terreus / flavus by Multi Real-Time PCR (This assay includes the detection and differentiation of Aspergillus fumigatus / terreus / flavus)
Azole-resistance profiling of Cyp51A gene (This assay detects selected mutations in the Cyp51A gene related to azole-resistance, by PCR and sequencing).
Sample Type
Accredited : 1
Alternatives : Culture, EDTA Blood, Swab / Secretion (Respiratory), Tissue.
Transport Condition Sample should be transported at 4°C.
Turn Around Time (TAT) TAT for routine samples is within 10 working days. Urgent Samples will be charged double and will be reported within 7 working days.
Samples delivered before 11:00 AM will begin processing immediately resulting in shorter TAT.
Note 555

Links

Validated
Assay Code APH-123
Description Histoplasma capsulatum is an ascomycetous fungus and belongs to the fungal family Ajellomycetaceae. It causes Histoplasmosis which is a type of lung infection caused by inhaling the fungal spores of Histoplasma capsulatum . Histoplasma capsulatum is dimorphic and switches from a mould-like (filamentous) growth form in the natural habitat to a small budding yeast form in the warm-blooded animal host. Histoplasma capsulatum appears to be strongly associated with the droppings of certain bird species as well as bats. A mixture of these droppings and certain soil types is particularly conducive to proliferation. In highly endemic areas there is a strong association with soil under and around chicken houses, and with areas where soil or vegetation has become heavily contaminated with faecal material deposited by flocking birds such as starlings and blackbirds.

Method Real -Time PCR
Sample Type
Culture, EDTA blood, Swab / Secretion (Respiratory), Swab / Secretion (Organ/Abscess).
Transport Condition Samples should be transported at 4°C.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 3 working days.
Urgent Samples will be reported within half of the minimum test period & will be Charged Double.
Samples delivered after 11:00 AM will be processed next working day unless urgent.

Links




Molecular Biology & Genomics Centre

Pathogen Identification


Molecular based methods like PCR, Real-Time PCR and more recently next generation sequencing (NGS) have revolutionized the field of veterinary diagnostics. At MBG, we offer detection of pathogenic viruses, bacteria and parasites using molecular methods, which are fast and highly sensitive to detect microbial pathogens in various specimens. MBG is an ISO 17025 accredited facility and benefits from an isolated containment level 3 facility for processing highly (level 3) contagious pathogens.


All Bacteria Virus Fungi Parasite

Validated
Assay Code See Below
Description Aspergillus spp. has been found worldwide in almost all domestic and wild animals, ranging from insects and corals to NHP. Aspergillosis is a common infection in birds, particularly pet parrots, penguins, captive raptors, mallards and other ducks, turkeys, and Japanese quail, in which it causes pulmonary and air sac infection. Aspergillosis has also been described in cats and dogs in which it affects only the nasal passages. In large animals, Aspergillus infection is assumed to be rare but has been reported with increasing frequency. It can lead to various diseases like mycotic abortion and gland infection in cows as well as guttural pouch involvement in horses. In marine mammals, airways are usually initially affected leading to pneumonia, but other organs including the brain may also be infected following fatal dissemination. The most frequently identified pathogens are Aspergillus fumigatus and Aspergillus flavus, ubiquitous organisms capable of living under extensive environmental stress.

Aspergillus fumigatus is an opportunistic pathogen and the primary cause of invasive aspergillosis. Triazole antifungals are used to treat aspergillosis. However, triazole-resistant A. fumigatus infections are increasingly reported worldwide and are associated with increased treatment failure and mortality. This fungus can acquire resistance to azole antifungals due to mutations in the azole target (Cyp51A). Cyp51A mutations typical for environmental azole resistance acquisition (for example, TR34/L98H) have been reported in many cases. These mutations can also be found in isolates recovered from patients.

Pathogens Tested
  • APA-098 : Aspergillus fumigatus/ terreus/ flavus
  • APA-189 : Azole-resistance profiling of Cyp51A gene

Method Aspergillus fumigatus / terreus / flavus by Multi Real-Time PCR (This assay includes the detection and differentiation of Aspergillus fumigatus / terreus / flavus)
Azole-resistance profiling of Cyp51A gene (This assay detects selected mutations in the Cyp51A gene related to azole-resistance, by PCR and sequencing).
Sample Type
Culture, EDTA Blood, Swab / Secretion (Respiratory), Tissue.
Transport Condition Sample should be transported at 4°C.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 3 working days.
Urgent Samples will be reported within half of the minimum test period & will be Charged Double.
Samples delivered after 11:00 AM will be processed next working day unless urgent.

Links

Validated
Assay Code See Below
Description Aspergillus is a type of fungus that is found indoors and outdoors. Most people breathe in Aspergillus spores every day without getting sick. However, health problems may arise in people with weakened immune systems or having underlying diseases. Aspergillosis, most often caused by Aspergillus fumigatus, occurs in humans in chronic or acute forms which are clinically very distinct. Most cases of acute aspergillosis occur in people with severely compromised immune systems, e.g. those undergoing bone marrow transplantation. Chronic colonization or infection can cause complications in people with underlying respiratory illnesses, such as asthma, cystic fibrosis, sarcoidosis, tuberculosis, or chronic obstructive pulmonary disease. The most frequently identified pathogens are Aspergillus fumigatus and Aspergillus flavus, ubiquitous organisms capable of living under extensive environmental stress.

Aspergillus fumigatus is the primary cause of invasive aspergillosis. Triazole antifungals are used to treat patients with high-risk conditions such as stem cell and organ transplant recipients as mortality exceeds 50%. However, triazole-resistant A. fumigatus infections frequently occur and are associated with increased treatment failure and mortality. Of particular concern are resistant A.fumigatus isolates carrying either TR34/L98H or TR46/Y121F/T289A genetic resistance markers in the azole target (Cyp51A) gene and these are mostly associated with triazole fungicide use. Reports of these triazole-resistant A.fumigatus strains are more common in Europe than in the US.Understanding the prevalence of azole resistant patient isolates is important to guide clinical and public health decision-making.

Pathogens Tested
  • HPA-189 : Azole-resistance profiling of Cyp51A gene

Method Aspergillus fumigatus / terreus / flavus by Multi Real-Time PCR (This assay includes the detection and differentiation of Aspergillus fumigatus / terreus / flavus)
Azole-resistance profiling of Cyp51A gene (This assay detects selected mutations in the Cyp51A gene related to azole-resistance, by PCR and sequencing).
Sample Type
Accredited : 1
Alternatives : Culture, EDTA Blood, Swab / Secretion (Respiratory), Tissue.
Transport Condition Sample should be transported at 4°C.
Turn Around Time (TAT) TAT for routine samples is within 10 working days. Urgent Samples will be charged double and will be reported within 7 working days.
Samples delivered before 11:00 AM will begin processing immediately resulting in shorter TAT.
Note 555

Links

Validated
Assay Code APH-123
Description Histoplasma capsulatum is an ascomycetous fungus and belongs to the fungal family Ajellomycetaceae. It causes Histoplasmosis which is a type of lung infection caused by inhaling the fungal spores of Histoplasma capsulatum . Histoplasma capsulatum is dimorphic and switches from a mould-like (filamentous) growth form in the natural habitat to a small budding yeast form in the warm-blooded animal host. Histoplasma capsulatum appears to be strongly associated with the droppings of certain bird species as well as bats. A mixture of these droppings and certain soil types is particularly conducive to proliferation. In highly endemic areas there is a strong association with soil under and around chicken houses, and with areas where soil or vegetation has become heavily contaminated with faecal material deposited by flocking birds such as starlings and blackbirds.

Method Real -Time PCR
Sample Type
Culture, EDTA blood, Swab / Secretion (Respiratory), Swab / Secretion (Organ/Abscess).
Transport Condition Samples should be transported at 4°C.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 3 working days.
Urgent Samples will be reported within half of the minimum test period & will be Charged Double.
Samples delivered after 11:00 AM will be processed next working day unless urgent.

Links