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


Accredited
Assay Code APN-020
Description In September 2012, health authorities were notified of several cases of severe hCoV infection caused by a novel virus type hCoV-EMC. The strain was redefined by the International Committee on Taxonomy of Viruses into Middle East respiratory syndrome coronavirus (MERS-CoV) since it was first reported in Saudi Arabia.

MERS-CoV is a beta coronavirus and causes respiratory infection of humans and dromedary camels. Several studies have confirmed that Dromedary camels (Camelus dromedarius) are the natural host and zoonotic source of the MERS-CoV infection in humans. Other animal species may also be susceptible to infection with MERS-CoV. However, their epidemiological significance has not been proven.

Positive RT-PCR results for MERS-CoV or isolation of the virus from dromedary camels are notifiable to the OIE . While the impact of MERS-CoV on animal health is very low, human infections have a significant public health impact.

Method Real-Time RT-PCR.
Sample Type
Accredited : Swab / Secretion (Respiratory).
Alternatives : Culture, Serum.
Transport Condition Samples should be transported at 4°C.
Specimens must be sent in RNA preservative media.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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 Monkeypox is a viral zoonotic disease, caused by Monkeypox virus which is recognized as the most important orthopoxvirus infecton after the eradication of smallpox.
Monkeypox virus belongs to the Orthopoxvirus genus in the family Poxviridae. The Orthopoxvirus genus also includes variola virus (which causes smallpox), vaccinia virus (used in the smallpox vaccine), and cowpox virus.
Monkeypox was first discovered in 1958 when two outbreaks of a pox-like disease occurred in colonies of monkeys kept for research, hence the name Monkeypox. The first human case of Monkeypox was recorded in 1970 in the Democratic Republic of the Congo (DRC) during a period of intensified effort to eliminate smallpox
Monkeypox is an infectious viral disease that can occur in both humans and some other animals.

Method APM-215: Orthopox virus detection & confirmation by PCR & Sequencing.
APM-216: Monkeypox virus detection by Real-Time PCR.


Sample Type
Tissue (Skin lesions), Swabs/Secretions(Abscess/lesions)
Transport Condition Samples should be transported at 4°C and delivered within 24 hours.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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 Mycobacterium is a genus of Actinobacteria, family Mycobacteriaceae. Over 190 species are recognized in this genus. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis (Mycobacterium tuberculosis) and leprosy (Mycobacterium leprae) in humans. Bovine tuberculosis is a chronic disease of animals and humans caused by Mycobacterium bovis. In a large number of countries it is a major infectious disease among cattle, other domesticated animals, and certain wildlife species. Other members of the Mycobacterium genus include M. caprae (considered to be a primary pathogen of goats) and M. pinnipedii, a pathogen of fur seals and sea lions. Aerosol exposure to M. bovis is considered to be the most frequent route of infection of cattle, but infection by ingestion of contaminated material also occurs. After infection, nonvascular nodular granulomas known as tubercles may develop. Characteristic tuberculous lesions occur most frequently in the lungs and the retropharyngeal, bronchial and mediastinal lymph nodes as well as liver, spleen and other organs. Clinical signs include weakness, anorexia, emaciation, dyspnoea, enlargement of lymph nodes, and cough, particularly with advanced tuberculosis.

Mycobacterium avium subspecies paratuberculosis (MAP) is an obligate pathogenic bacterium and the causative agent of Johne's disease, which affects ruminants such as cattle, and also causes Crohn's disease in humans.

Avian tuberculosis, or avian mycobacteriosis, is an important disease that affects companion, captive exotic, wild and domestic birds and mammals and is most often caused by Mycobacterium avium subsp. avium (M. a. avium).The disease is characterized by chronic and progressive wasting, weakness and diarrhoea. The primary lesions of avian tuberculosis in birds are nearly always in the intestinal tract. Diagnosis of avian tuberculosis in birds depends on the demonstration of M. avium avium) in excretions or secretions of live birds or liver and spleen of dead birds.

Pathogens Tested
  • APM-037 : Mycobacterium avium subspecies avium (This assay includes the detection of Mycobacterium species and Mycobacterium avium subspecies avium.)
  • APM-038 : Mycobacterium Species (This assay includes the detection of Mycobacterium species only. This Assay can detect M. austroafricanum, M.avium subsp. avium,M.bovis BCG, M.chelonae,M.gordonae, M.fortuitum subsp.fortuitum, M.insubricum, M.intracellulare, M.kansasii, M.marium, M.mucogenicum, M.peregrinum, M.porcinum, M.scrofulaceum, M.setense, M.simiae, M.smegmatis, M.terrae, M.tuberculosis, M.ulcerans, M.xenopi)
  • APM-039 : Mycobacterium avium subspecies paratuberculosis (This assay includes the detection of Mycobacterium species and Mycobacterium avium subspecies paratuberculosis.)
  • APM-100: Mycobacterium tuberculosis (This assay includes the detection of Mycobacterium species and Mycobacterium tuberculosis.)

Method Real- Time PCR.
Sample Type
Tissue (Intestinal tract, liver, spleen), Stool, Culture, Swab/Secretion (Respiratory), EDTA Blood, Milk, CSF, Gastric Lavage, Tissue on FTA Card.
Transport Condition Samples should be transported at 4°C. Stool and milk must be frozen after collection.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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

Accredited
Assay Code See Below
Description This test checks for different species of Mycoplasma. Mycoplasma refers to a genus of bacteria that are the smallest living cells known. They can be parasitic or saprotrophic. Several species are pathogenic in humans, including M. pneumoniae, which is an important cause of atypical pneumonia and other respiratory disorders, and M. genitalium, which is believed to be involved in pelvic inflammatory diseases.

Mycoplasma genitalium - M.genitalium is a small parasitic bacterium that lives on ciliated epithelial cells of the genital tract and is sexually transmitted. In women symptoms such as vaginal itching, burning while urinating, discharge, pain during intercourse may appear. In the long term, this infection is suspected to cause pelvic inflammatory disease and cervicitis. In men it causes urogenital tract disease.

Mycoplasma bovis - M.bovis is a bacteria-like organism that causes persistent, chronic infections in calves and cows. The clinical manifestations of M.bovis include mastitis in cows and arthritis and pneumonia in young animals, genital disorders, abscess, conjunctivitis, otitis, and meningitis. The mechanisms of the pathogenesis of M. bovis are still unknown, but it uses complex strategies to invade the host organism. It adheres to the neutrophils and the macrophages, persisting and multiplying on the surface of these cells.

Pathogens Tested
  • APM-040 : Mycoplasma bovis (This Assay includes the detection of Mycoplasma bovis only.)
  • APM-041 : Mycoplasma Species (This Assay includes the detection of Mycoplasma Species only. This Assay can detect many Mycoplasma species including Mycoplasma agassizii,Mycoplasma anatis, Mycoplasma anseris, Mycoplasma arginini,Mycoplasma arthritidis,Mycoplasma auris, Mycoplasma buccale, Mycoplasma canadense,Mycoplasma cloacale,Mycoplasma collis, Mycoplasma columborale, Mycoplasma cricetuli, Mycoplasma cynos,Mycoplasma falconis,Mycoplasma faucium, Mycoplasma felis, Mycoplasma gateae,Mycoplasma gypis, Mycoplasma hominis, Mycoplasma hyopharyngis, Mycoplasma hyorhinis,Mycoplasma hyosynoviae, Mycoplasma iguana, Mycoplasma lagogenitalium, Mycoplasma leonicaptivi, Mycoplasma molare, Mycoplasma mustelae, Mycoplasma neophronis,Mycoplasma neurolyticum, Mycoplasma orale, Mycoplasma phocicerebrale, Mycoplasma phocidae, Mycoplasma salivarium, Mycoplasma spumans, Mycoplasma timone, and Mycoplasma zalophi .
    The assay cannot detect M. pneumoniae, M. gallisepticum and M.pulmonis.
.

Method Real-Time PCR.
Sample Type
Accredited : Culture, Milk, Swab/Secretion (Respiratory), Tissue (esophagus, trachea, cloaca, eyes, phallus).
Alternatives : Swab / Secretions (Genital), Swab/Secretion (Organ/Abscess)
Transport Condition Samples should be transported at 4°C. Milk must be frozen after collection.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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


Accredited
Assay Code APN-020
Description In September 2012, health authorities were notified of several cases of severe hCoV infection caused by a novel virus type hCoV-EMC. The strain was redefined by the International Committee on Taxonomy of Viruses into Middle East respiratory syndrome coronavirus (MERS-CoV) since it was first reported in Saudi Arabia.

MERS-CoV is a beta coronavirus and causes respiratory infection of humans and dromedary camels. Several studies have confirmed that Dromedary camels (Camelus dromedarius) are the natural host and zoonotic source of the MERS-CoV infection in humans. Other animal species may also be susceptible to infection with MERS-CoV. However, their epidemiological significance has not been proven.

Positive RT-PCR results for MERS-CoV or isolation of the virus from dromedary camels are notifiable to the OIE . While the impact of MERS-CoV on animal health is very low, human infections have a significant public health impact.

Method Real-Time RT-PCR.
Sample Type
Accredited : Swab / Secretion (Respiratory).
Alternatives : Culture, Serum.
Transport Condition Samples should be transported at 4°C.
Specimens must be sent in RNA preservative media.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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 Monkeypox is a viral zoonotic disease, caused by Monkeypox virus which is recognized as the most important orthopoxvirus infecton after the eradication of smallpox.
Monkeypox virus belongs to the Orthopoxvirus genus in the family Poxviridae. The Orthopoxvirus genus also includes variola virus (which causes smallpox), vaccinia virus (used in the smallpox vaccine), and cowpox virus.
Monkeypox was first discovered in 1958 when two outbreaks of a pox-like disease occurred in colonies of monkeys kept for research, hence the name Monkeypox. The first human case of Monkeypox was recorded in 1970 in the Democratic Republic of the Congo (DRC) during a period of intensified effort to eliminate smallpox
Monkeypox is an infectious viral disease that can occur in both humans and some other animals.

Method APM-215: Orthopox virus detection & confirmation by PCR & Sequencing.
APM-216: Monkeypox virus detection by Real-Time PCR.


Sample Type
Tissue (Skin lesions), Swabs/Secretions(Abscess/lesions)
Transport Condition Samples should be transported at 4°C and delivered within 24 hours.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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 Mycobacterium is a genus of Actinobacteria, family Mycobacteriaceae. Over 190 species are recognized in this genus. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis (Mycobacterium tuberculosis) and leprosy (Mycobacterium leprae) in humans. Bovine tuberculosis is a chronic disease of animals and humans caused by Mycobacterium bovis. In a large number of countries it is a major infectious disease among cattle, other domesticated animals, and certain wildlife species. Other members of the Mycobacterium genus include M. caprae (considered to be a primary pathogen of goats) and M. pinnipedii, a pathogen of fur seals and sea lions. Aerosol exposure to M. bovis is considered to be the most frequent route of infection of cattle, but infection by ingestion of contaminated material also occurs. After infection, nonvascular nodular granulomas known as tubercles may develop. Characteristic tuberculous lesions occur most frequently in the lungs and the retropharyngeal, bronchial and mediastinal lymph nodes as well as liver, spleen and other organs. Clinical signs include weakness, anorexia, emaciation, dyspnoea, enlargement of lymph nodes, and cough, particularly with advanced tuberculosis.

Mycobacterium avium subspecies paratuberculosis (MAP) is an obligate pathogenic bacterium and the causative agent of Johne's disease, which affects ruminants such as cattle, and also causes Crohn's disease in humans.

Avian tuberculosis, or avian mycobacteriosis, is an important disease that affects companion, captive exotic, wild and domestic birds and mammals and is most often caused by Mycobacterium avium subsp. avium (M. a. avium).The disease is characterized by chronic and progressive wasting, weakness and diarrhoea. The primary lesions of avian tuberculosis in birds are nearly always in the intestinal tract. Diagnosis of avian tuberculosis in birds depends on the demonstration of M. avium avium) in excretions or secretions of live birds or liver and spleen of dead birds.

Pathogens Tested
  • APM-037 : Mycobacterium avium subspecies avium (This assay includes the detection of Mycobacterium species and Mycobacterium avium subspecies avium.)
  • APM-038 : Mycobacterium Species (This assay includes the detection of Mycobacterium species only. This Assay can detect M. austroafricanum, M.avium subsp. avium,M.bovis BCG, M.chelonae,M.gordonae, M.fortuitum subsp.fortuitum, M.insubricum, M.intracellulare, M.kansasii, M.marium, M.mucogenicum, M.peregrinum, M.porcinum, M.scrofulaceum, M.setense, M.simiae, M.smegmatis, M.terrae, M.tuberculosis, M.ulcerans, M.xenopi)
  • APM-039 : Mycobacterium avium subspecies paratuberculosis (This assay includes the detection of Mycobacterium species and Mycobacterium avium subspecies paratuberculosis.)
  • APM-100: Mycobacterium tuberculosis (This assay includes the detection of Mycobacterium species and Mycobacterium tuberculosis.)

Method Real- Time PCR.
Sample Type
Tissue (Intestinal tract, liver, spleen), Stool, Culture, Swab/Secretion (Respiratory), EDTA Blood, Milk, CSF, Gastric Lavage, Tissue on FTA Card.
Transport Condition Samples should be transported at 4°C. Stool and milk must be frozen after collection.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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

Accredited
Assay Code See Below
Description This test checks for different species of Mycoplasma. Mycoplasma refers to a genus of bacteria that are the smallest living cells known. They can be parasitic or saprotrophic. Several species are pathogenic in humans, including M. pneumoniae, which is an important cause of atypical pneumonia and other respiratory disorders, and M. genitalium, which is believed to be involved in pelvic inflammatory diseases.

Mycoplasma genitalium - M.genitalium is a small parasitic bacterium that lives on ciliated epithelial cells of the genital tract and is sexually transmitted. In women symptoms such as vaginal itching, burning while urinating, discharge, pain during intercourse may appear. In the long term, this infection is suspected to cause pelvic inflammatory disease and cervicitis. In men it causes urogenital tract disease.

Mycoplasma bovis - M.bovis is a bacteria-like organism that causes persistent, chronic infections in calves and cows. The clinical manifestations of M.bovis include mastitis in cows and arthritis and pneumonia in young animals, genital disorders, abscess, conjunctivitis, otitis, and meningitis. The mechanisms of the pathogenesis of M. bovis are still unknown, but it uses complex strategies to invade the host organism. It adheres to the neutrophils and the macrophages, persisting and multiplying on the surface of these cells.

Pathogens Tested
  • APM-040 : Mycoplasma bovis (This Assay includes the detection of Mycoplasma bovis only.)
  • APM-041 : Mycoplasma Species (This Assay includes the detection of Mycoplasma Species only. This Assay can detect many Mycoplasma species including Mycoplasma agassizii,Mycoplasma anatis, Mycoplasma anseris, Mycoplasma arginini,Mycoplasma arthritidis,Mycoplasma auris, Mycoplasma buccale, Mycoplasma canadense,Mycoplasma cloacale,Mycoplasma collis, Mycoplasma columborale, Mycoplasma cricetuli, Mycoplasma cynos,Mycoplasma falconis,Mycoplasma faucium, Mycoplasma felis, Mycoplasma gateae,Mycoplasma gypis, Mycoplasma hominis, Mycoplasma hyopharyngis, Mycoplasma hyorhinis,Mycoplasma hyosynoviae, Mycoplasma iguana, Mycoplasma lagogenitalium, Mycoplasma leonicaptivi, Mycoplasma molare, Mycoplasma mustelae, Mycoplasma neophronis,Mycoplasma neurolyticum, Mycoplasma orale, Mycoplasma phocicerebrale, Mycoplasma phocidae, Mycoplasma salivarium, Mycoplasma spumans, Mycoplasma timone, and Mycoplasma zalophi .
    The assay cannot detect M. pneumoniae, M. gallisepticum and M.pulmonis.
.

Method Real-Time PCR.
Sample Type
Accredited : Culture, Milk, Swab/Secretion (Respiratory), Tissue (esophagus, trachea, cloaca, eyes, phallus).
Alternatives : Swab / Secretions (Genital), Swab/Secretion (Organ/Abscess)
Transport Condition Samples should be transported at 4°C. Milk must be frozen after collection.
Turn Around Time (TAT) Normal Turnaround time for pathogen Identification is within 5 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