1. Opportunistic Gastrointestinal
Pathogens

2. Introduction
What is Opportunistic Infection?
Opportunistic infections are infections caused by pathogens that
exploit a weakened immune system. These infections primarily affect
individuals with compromised immune function.

3. Risk factors
HIV/AIDS
Cancer Chemotherapy
Bone marrow suppression
Antibiotic treatment leading to disruption
of the physiological microbiome
Organ transplant patients
Pregnancy
Genetic predisposition

4. Microbial agents causing opportunistic
infections
Bacterial agents:
• Campylobacter jejuni
• Helicobacter spp.
• Clostridium difficile
• E. coli
• Aeromonas spp.
• Plesiomonas spp
• Mycobacterium tuberculosis
• Non-tubercular mycobacterium

5. Viral agents
• Herpes virus family: Cytomegalovirus, Herpes simplex,
HHV-8, HHV-6
• Adenovirus
• Enterovirus
• Astrovirus
• Norovirus

6. Fungal agents
• Candida spp
• Histoplasma capsulatum

7. Parasitic agents
• Cryptosporidium parvum
• Isospora belli
• Cyclospora cayetanensis
• Giardia lamblia
• Strongyloides stercoralis
• Entamoeba histolytica
• Trichuris trichiura
• Ascaris lumbricoides

8. Bacterial agents

9. Campylobacter jejuni

10. Contd…
• Most common disease is acute enteritis, with diarrhoea,
fever, and abdominal pain
• Factors that decrease or neutralize gastric acid secretion
favour disease
• GI disease characteristically produces histologic damage
to the mucosal surface of the duodenum

11. Diagnosis
 Specimen:
1. Diarrheal stool- preferred sample
2. Rectal swab
 Microscopic examination:
 Gram-staining: Comma shape/ “Gull-wing” appearance
 Dark-field microscopy- darting movement

12.  Culture:
Skirrow’s media- colorless or gray dew-drop colony
 Biochemical:
 Oxidase +ve
 Catalase +ve
 Urease -ve

13. Helicobacter spp.
• Small, Spiral shape, Gram-negative, micro-aerophilic rods
• Highly motile with cork-screw movement
• Multiple, sheathed polar flagella
• Feco-oral and person-to-person spread occur

14. Virulence factors

15. Symptoms of H. pylori infection

16. Lab diagnosis
 Specimen:
 Endoscopic biopsy from multiple sites including healthy
tissue surrounding ulcers
 Specimen should be fresh, not delayed >3 hours
 Kept in 1-3 mL isotonic saline for culture and formalin for
histopathology

17.  Invasive test:
 Histopathology
 Rapid urease test
 Culture
 PCR
 Non-invasive test:
 Serological test- ELISA,
ICT, LAT
 Urea breath test
 Antigen detection in stool
(HPSA test)

18. Clostridium difficile
• Anaerobic, motile, Gram-negative bacteria, ubiquitous in nature,
and especially prevalent in soil
• May colonize the human colon without symptom; approximately 2–
5% of the adult population are carriers
• The use of systemic antibiotics, including broad-spectrum
penicillins/cephalosporins, fluoroquinolones, and clindamycin,
causes the normal microbiota of the bowel to be altered

20. Laboratory diagnosis
 Colonoscopy or sigmoidoscopy- (pseudomembranous colitis)
 LAT to detect antigens in stool
 Cytotoxic assay to detect cytotoxicity of toxin B
 ELISA for toxin A and B
 PCR

21.  M. tuberculosis may cause extrapulmonary disease affecting the GI tract
as a result of disseminated disease or primary intestinal involvement
 The most common mycobacterial infections causing GI disease in the
compromised host are those caused by Mycobacterium avium-
intracellulare complex (MAC).
 Gastric ulceration, enterocolitis, enteric fistulae, and intra-abdominal
abscess and hemorrhage are common manifestations of disseminated
MAC
M. Tuberculosis & NTM

22.  The most common sites are the ileocecal and jejuni-ileum sites,
and less commonly include the esophagus, stomach, and
duodenum
 Patients may have signs suggestive of acute appendicitis or
intestinal obstruction and can have rectal lesions presenting as
perirectal abscess, fistulae, or fissures

23. Lab Diagnosis
Culture & Microscopy
 Z-N stain, Auramin/ Rhodamin stain
 Lowenstein-Jensen media, Middle
brook media
Immunological & Molecular
 Gene Xpert
 QuantiFERON-TB Gold test
 PCR
Specimen: Biopsy from endoscopy & colonoscopy, blood, ascetic fluid
Other supportive investigations
 Plain X-ray abdomen
 Sonography of abdomen
 CT scan abdomen
 ADA

25. Herpes virus family
 Herpes-simplex virus can cause esophagitis in HIV infected
patients and solid-organ transplant patients
 It is usually seen in the oropharynx in patients receiving bone
marrow transplants. There may be vesicles and punched-out
ulcerations with an adherent pseudomembrane

26.  Epstein-Barr virus associated post-transplant lymphoproliferative
disorder (PTLD) may have a GI component; the clinical
presentation of which may include GI bleeding, obstruction, and
perforation
 HHV-6 has been reported to cause colitis in patients following
renal transplant and is suggested as an etiologic agent of gastro-
duodenal disease and colitis following stem cell transplantation

27.  Human herpes virus (HHV)-8, associated with Kaposi’s sarcoma,
may cause gastritis as a complication of primary skin disease
 Varicella-zoster virus is a less common cause of GI disease in
the compromised host, and may cause esophagitis and
enterocolitis

28. Cytomegalovirus

29.  Cytomegalovirus is by far the most common viral agent causing GI
disease in the immunocompromised host
 It may cause esophagitis, gastritis, and enterocolitis.
 CMV enterocolitis is common in advanced HIV, solid-organ, bone-
marrow and HSCT recipients, and common-variable
immunodeficiency

30.  Esophagitis may occur in <5% to 10% of patients with AIDS
 The most common site affected is the colon, occasionally
affecting more than one GI site and sometimes becoming
disseminated

31.  Norovirus is the most common cause of gastroenteritis
 Infection is characterized by non-bloody diarrhea, vomiting, and
stomach pain. Fever or headaches may also occur
 The virus is usually spread by the fecal-oral route, through
contaminated food or water or person-to-person contact
 It is commonly associated with infection and gastroenteritis in
both immunocompromised as well as immunocompetents
Noro viruses

32.  It is potentially causing more significant disease in compromised
individuals
 The characteristics of norovirus illness include persistent diarrhea
with prolonged viral shedding, particularly in immunosuppressed
children
 Noroviruses have also been associated with chronic diarrhea in
transplant recipients
Contd…

33. Adenovirus

34. Adenovirus
 Adenovirus GIT infections often present with symptoms like
nausea, vomiting, diarrhea, and abdominal pain
 It may cause diarrhea and hemorrhagic colitis in bone-marrow
transplant patients and solid-organ transplant recipients,
particularly small-bowel
 The compromised host is susceptible to GI infection with rotavirus
and infection may be associated with prolonged diarrhea and
dehydration

35.  The diagnosis of viral infections of the GI tract may be
accomplished by histopathologic analysis of tissue and immunologic
and molecular methods for detection
 Adenovirus and norovirus can be detected in stool by PCR
 Among HIV patients with CMV GI disease, characteristic
inclusions of CMV by histopathologic analysis of duodenal/ rectal
biopsies were detected
Lab diagnosis of viral agents

36. B. Immunosuppressed patients may not mount
much of an inflammatory response to CMV
infection as seen in this biopsy. Two enlarged,
CMV-infected endothelial cells are present (arrows).
A B
A. Two infected cells (arrows) are seen: one
exhibits enlargement and the classic glassy
nuclear inclusion, and another displays subtler
features with coarse, eosinophilic cytoplasmic
inclusions
Fig: Cytomegalovirus (CMV)-infected cells (H&E stain)

37.  In patients with lesions in the oral cavity or esophagitis, the most
common agent herpes simplex virus (HSV) detected by direct
immunofluorescent staining of smears, culture, or molecular testing
of material from the lesions
 Testing for community-acquired viral infections, such as
adenoviruses, can be performed using commercially available
immunoassays for detection of viral antigen

38.  Norovirus detection is accomplished by RT-PCR assays and is
usually available in commercial-reference laboratories or
local/state public health laboratories

39. Fungal
Agents

40. • Candidiasis is caused by the yeast Candida albicans and
other Candida species
• Oral candidiasis is frequently associated with radiotherapy
and chemotherapy for treatment of solid tumors and
hematologic malignancies
• It is particularly common in HIV-positive patients with low
CD4+ T-cell counts, occurring in about 10% to 15% of
patients and associated with frequent recurrences
Candida spp.

41. Lab diagnosis:
Samples
• Whitish patches from the mucous membrane of the mouth
• Sputum
Method of collection
• Sterile swab
Direct examination (Microscopy)
• KOH wet mount
• Gram staining (presence of yeast cell & pseudohyphae)
Culture
• In SDA media- whitish creamy colony

42. Histoplasma capsulatum
• GI histoplasmosis, caused by Histoplasma capsulatum, occurs
mostly in the competent host, but risk increases in patients with
HIV and is predominant in males
• Patients receiving anti-TNF-α therapy for diseases like
inflammatory bowel disease (IBD) are also at increased risk for
histoplasmosis
• The first year following solid-organ transplants is also a high
risk for histoplasmosis

43. Histoplasma capsulatum
• The organism may affect all sites of the GI tract, but primarily
affects the colon
• There is high mortality associated with GI histoplasmosis and
the disease is fatal in about one-fourth of cases

44. Lab Diagnosis:
• Histopathology: Endoscopic biopsy from affected site examined under
microscope- Intracellular yeast within macrophages
• Culture: In SDA media.
 At 25°- Slow growing, granular to cottony appearance
 At 37°- Creamy, moist yeast-like colony
 Microscopy from Culture showed- tuberculate macroconidia
 Antigen detection: By EIA
25°C 37°C

46. Cryptosporidium parvum
 Cryptosporidium parvum is a microscopic parasite that can cause
a diarrheal illness called cryptosporidiosis
 It's considered an opportunistic infection, particularly in
individuals with weakened immune systems, such as those with
HIV/AIDS or certain other underlying health conditions
 C. parvum inhabits the small intestine. It may also be found in
stomach, appendix, colon, rectum and pulmonary tree

47.  Involvement of sites other than small intestine like – pharynx,
stomach, large intestine and respiratory tract is quite common in
HIV positive pts
 Involvement of biliary tract can cause papillary stenosis - is a
disturbance of the sphincter of Oddi
 Obstruction of the valve can cause: pancreatic pain, jaundice

48.  Stool examination
 Wet mount preparation
 Modified Z-N staining
 Fluorescent staining
 IIF
 Histopathological examination
 Molecular diagnosis: PCR, Western blot
 Serodiagnosis: Antibody and antigen can be detected by ELISA
Laboratory Diagnosis
Cryptosporidium spp.
oocysts (pink arrows) in
Cryptosporidium spp.
oocysts in modified Z-N
stain

49. Isospora belli
 Isospora belli cause severe diarrhea in patients with AIDS, affecting
primarily the small intestine, and is often associated with severe
dehydration
 Infection and symptoms may occur 2 days after infectious oocysts
are ingested leading to destruction of intestinal epithelial cells and
causes watery diarrhea and vomiting

50. Laboratory diagnosis
Direct evidence
 Demonstration of transparent oocyst
in saline preparation
 Modified ZN stain
Indirect evidence
 High fecal fat content
 Charcot-Leyden crystals in
stool
A. Stool examination
A. Duodenal aspirates
 If stool examination reveals negative results, duodenal
aspirates and enterotest performed to demonstrate oocyst

51. Cyclospora caytanensis
 Cyclospora cayetanensis is a foodborne illness causing persistent
diarrhea in the compromised host, but usually self-limited in
competent hosts
 It causes prolong diarrhea with abdominal pain, low grade fever and
fatigue
 In patients with AIDS, symptoms may persist for as long as 12
weeks, biliary disease has also been detected in this group

52.  Stool examination:
 3 consecutive days sample should be screened
 Oocyst can be stained by ZN stain
 The oocyst under UV illumination, unstained oocyst are auto-fluorescent
 Histopathology:
 Acute and chronic inflammation
 Villous atrophy
 Hyperplasia of crypts
Laboratory diagnosis

53.  Strongyloides causes severe hyperinfection in immunosuppressed
patients
 Patients at risk include those treated with immunosuppressive drug
therapies and patients with other conditions such as leukemia,
lymphoma, and solid-organ transplants and also in HSCT
 Presence of worm and filariform larva in intestine may cause
epigastric pain, nausea, diarrhea and blood loss
Strongyloides stercoralis

54.  It causes intractable diarrhea with blood and mucus
 Repeated autoinfection occurs in an immunocompromised host
which leads to generate large number of worms in the intestine
and caused “Hyperinfection syndrome”
Saline mount of stool sample showing larvae of
Strongyloides stercoralis

55. Laboratory
Diagnosis
Microscopy
1. Dried wet mount
of stool:
Rhabditiform larva
2. Stool
concentration method
by formol ether conc.
3. Demonstration of
larva in duodenal
aspirates or jejunal
biopsies
Stool culture
1. Done when
larvae are scanty in
stools
Methods used:
-Agar plate culture
-Charcoal culture
method
Serology
1. Done using
Strongyloides or
filarial antigens
Methods used:
-Complement
fixation
-Indirect
hemagglutination
-ELISA
Blood examination
1.Peripheral eosinophilia
2. Raised serum IgE

56. Giardia lamblia
 Giardia lamblia infections may have a chronic course in patients
with immunodeficiencies, particularly patients with IgA
deficiency or other disorders associated with immunoglobulin
deficiencies
 Often they are asymptomatic, but in some cases, Giardia may
lead to mucus diarrhea, fat malabsorption (steatorrhea), dull
epigastric pain, belching and flatulence

57. In immunocompromised patients as hypogammaglobulinemia,
decreased IgA in small intestine, decreased gastric acidity or
achlorhydria
Severe manifestations
 Persistent diarrhea, steatorrhea, Fatty dyspepsia hypoproteinemia,
deficiency of fat-soluble vitamins (vit. A, D, E, K), folic acid
 Chronic malabsorption syndrome
 Stunted growth
 Cholangitis, cholecystitis jaundice Biliary colic

58. Laboratory
Diagnosis
Stool
examination
1.Macroscopic exam
2.Microscopic exam.
of stained pathogen
Entero test Serology
1. Antigen test:
-ELISA
-IIF test
2. Antibody detection:
-ELISA
-IIF test
Molecular test
1. DNA probe
2. PCR

59. Saline mount of stool sample showing
cyst of Giardia lamblia
From left to right: Entero-Test device prior to
swallowing, Entero-Test in situ(image source: Guiney
WJ et al British Journal of Clinical Pharmacology)

60.  E. histolytica causes enterocolitis and extraintestinal disease (liver
abscess) and may be more common in immunocompromised
patients, particularly in malnourished children
 Acute necrotizing colitis is a rare complication with high mortality
seen predominantly in developing countries
 Toxic megacolon is also a rare complication and assisociated with
corticosteroid use
Entamoeba histolytica

61. Lab diagnosis of intestinal
amoebiasis
Stool
examination
-Microscopy
-Macroscopy
-Iodine prep.
-Trichome stained
prep.
Stool
culture
Media used:
-NIH polygenic
-Nelson’s
-Robinson’s
Mucosal
scraping
-Wet mount
-Stained prep.
Sero-
diagnosis
-IHA
-ELISA
-LAT
Molecular
diagnosis
DNA
probe

62. Fig: Cyst of E. histolytica
in a concentrated wet
mount stained with
iodine
Fig: Trophozoites of E. histolytica
with ingested erythrocytes stained
with trichrome

63. Enteric parasites Indian World
Cryptosporidium parvum 10.8% to 82.0% 0.6% to 18.3%
Giardia spp. 2.2% to 8.3% 1.5% to 17.7%
Isospora belli 2.5% to 31.0% 0.8% to 16.0%
E. histolytica 1.7% to 7.7% 1.4% to 10.3%
Cyclospora cayatenensis 1.5% to 31.0% 0.1% to 10.0%
Table: Prevalence of opportunistic enteric parasites in HIV-infected
patients- Indian and world scenario