GUT MICRO FLORA NORMAL FLORA MICROBIOTA MBBS UG THEORY LECTURE CLASS COMMENSALS PATHOGENS DISEASE HOST

1. MICROBIOLOGY OF GUT
Dr. R. Someshwaran, MBBS, MD., Assistant Professor,
Department of Microbiology,
Karpagam Faculty of Medical Sciences and Research.

2. Objectives of today’s session
• To define and enlist normal flora of GUT
• To understand beneficial and harmful effects
of normal flora of GUT
• To list the etiology of Perianal sepsis
• To describe the Laboratory diagnosis of
Perianal sepsis
• To understand and substantiate the diagnosis
of treatment of super bugs

3. NORMAL FLORA
• Human beings harbour a wide array of
microorganisms both on and in their body
Classified into Residents and Transients
• Resident flora: Constitute a constant
population which cannot be completely
removed permanently
• Transient flora: Vary from time to time and are
temporary

4. ROLE OF NORMAL MICROBIAL FLORA
• Can become pathogenic when host defences falter
• Prevent or interfere with colonisation/invasion of
the body by pathogens
• Raise the overall immune status of the host against
pathogens having related or shared antigens
• Can cause confusion in diagnosis due to their
ubiquitous presence and their resemblance to
some pathogens

5. ROLE OF NORMAL MICROBIAL FLORA
• Microflora of intestinal tract synthesise
vitamin K and several B vitamins
• Antibiotic substances like colicins produced
have harmful effect on pathogens
• Endotoxins liberated by them help host defence
mechanism by triggering alternate
complement pathway
• Opportunistic pathogens cause disease
when host immune system fails

6. Hospital settings laden with pathogens
• A shift in Normal flora can cause an increase
in carriage of antibiotic resistant
Staphylococci.
• Reversal can be achieved by recolonization of
harmless Penicillin susceptible Staphylococci
502A strain.

7. Hospital settings laden with pathogens
• A shift in Normal flora can cause an increase
in carriage of antibiotic resistant
Staphylococci.
• Reversal can be achieved by recolonization of
harmless Penicillin susceptible Staphylococci
502A strain.

8. HOSPITAL SETTING

9. GUT MICROBIOTA
• Our GUT is an
extremely
complex
ecosystem
harboring more
than 100 trillion
micro-organisms

10. FACTORS AFFECTING NORMAL FLORA

11. NORMAL FLORA OF GUT 1
• Meconium is sterile in 80-90% of newborn GUT
• But in 10-20% few organisms may be acquired
during labour.
• Intestinal flora is established within 4-24 hours of
birth
• In breastfed children the intestine contains
Lactobacilli (L. bifidus 99% of total organism in
feces), Enterococci, colon bacilli and
Staphylococci.

12. NORMAL FLORA OF GUT 2
• In artificially bottlefed children Lactobacillus
acidophilus and colon bacilli and in part
Enterococci, Gram positive aerobic and
anaerobic bacilli are seen.
• Diet has the marked influence on relative
composition of intestinal and fecal flora.

13. NORMAL FLORA OF GUT 3
• In normal adults, Microorganism on surface of
esophageal wall are those swallowed from
saliva and food.
• Because of low pH of the stomach, it is
virtually sterile except soon after eating.
• In patients with Carcinoma stomach or
Achlorhydria or Pyloric obstruction there is
proliferation of Gram positive cocci and bacilli

14. NORMAL FLORA OF GUT 4
• Number of bacteria increases progressively
beyond the duodenum to the colon, being
comparatively low in the small intestine.
• In the adult Duodenum there are 103-106
bacteria per gram
• In the jejunum and proximal ileum 105-108
bacteria per gram
• In the lower ileum and cecum 108-1010
bacteria per gram

15. NORMAL FLORA OF GUT 5
• In the duodenum and upper ileum: Lactobacilli
and Enterococci predominate
• But in the lower ileum and cecum the flora
resemble fecal flora.
• In colon and Rectum: 1011 bacteria per gram of
contents constituting 10-20% of fecal mass.
• In the adult normal colon, resident bacterial flora
are mostly anaerobes (95-99%) viz., Anaerobic
Streptococci, Lactobacilli, Clostridia and
Bacteroides.

16. NORMAL FLORA OF GUT 6
• In adult normal colon: About 1-4% aerobes
viz., Enterococci, Coliforms and small number
of Proteus, Pseduomonas, Lactobacilli,
Mycoplasma, Candida and others.

17. DISTRIBUTION OF GUT MICROBIOTA

18. Bacteriological analysis of fecal flora
Anaerobic Aerobic
- Bacteroides - Escherichia coli
- Bifidobacterium - Enterobacter
- Eubacterium - Enterococcus
- Clostridia - Klebsiella
- Peptocercus - Lactobacillus
- Peptostreptocercus - Proteus
Note: Anaerobic bacteria outnumber aerobic bacteria by a
factor of 100–1000.

19. Bacteria in Blood and Tissues
• Commensal from intestinal tract may get into
blood and tissues
• Usually quickly eliminated by normal defence
mechanisms of the body.
• Occassional isolation of Diphtheroids or Non
hemolytic Streptococci from normal and
abnormal lymph nodes may be those with
escaped elimination.

20. DICTIM TO ALWAYS REMEMBER
• Unless Isolation of organisms with doubtful
pathogenicity more then once in serial blood
cultures, they have little significance.

21. Pseudomembranous colitis 1
• Indiscriminate administration of antibacterial
agents may completely alter the normal flora
and its functions
• Thus permitting exogenous and endogenous
pathogens to gain the upper hand and to cause
disease
• Broad spectrum antibiotic oral – Diarrhoea
(side effect) due to overgrowth of Yeast or
Staphylococci

22. Pseudomembranous colitis 2
• When Clindamycin is given, Anaerobic Gram
Positive Bacillus (Clostridium difficile- minor
member) may be allowed to multiply due to
suppression of other members.
• This results in serious life threatening condition
called Pseudomembranous colitis.
• Hence wherever possible, narrow spectrum
antibiotics at correct dosage and for correct
duration of time to be used to prevent suppression
of gut flora.

23. The Centers for Disease Control and Prevention
(CDC) & Healthcare-Associated Infections.
Link: http://www.cdc.gov/ncidod/dhqp/hai.html
The CDC estimates these account for 1.7 million
infections & 99,000 associated deaths each year
in American hospitals. Of these infections:
32% are urinary tract infections
22% are surgical site infections
15% are lung infections (pneumonia)
14% are bloodstream infections

24. PERINANAL SEPSIS
• Anorectal abscess
• Rectal abscess
• Perianal abscess
• Anal abscess

26. ANAL ABSCESS
• Infected cavity filled with pus near the anus
• Risk factors: Fistula-in-ano, Diabetes, Crohn’s
disease and Immunosuppression.

27. ETIOLOGY
GRAM POSITIVE COCCI
Staphylococcus aureus (MSSA, MRSA)
Enterococci (VSE, VRE)
CONS (MR/MS)
Streptococci (Non hemolytic)
Streptococci (Hemolytic)
Anaerobic Streptococci

28. ETIOLOGY
GRAM NEGATIVE BACILLI (Aerobic)
Escherichia coli (Most common)
Klebsiella pneumoniae
Proteus mirabilis, proteus vulgaris
Pseudomonas aeruginosa
Acinetobacter baumannii
Enterobacter aerogenes, E. cloacae
Mycoplasma

29. ETIOLOGY
GRAM NEGATIVE BACILLI
(Anaerobic)
Bacteroides fragilis
Lactobacillus bifidus, L. acidophilus
Clostridium difficile
Clostridium perfringens

30. ETIOLOGY
Miscellaneous
Candida albicans
HSV 1 & 2
Hepatitis B virus
HIV
Donovaniosis
Syphilis

31. LABORATORY DIAGNOSIS

32. Gram stain of smear

33. CULTURE

34. Specimen inoculation - Surface plating

35. AST

36. SUPERBUG?
• ESBL
• AmpC
• Carbapenemases
• MRSA
• VRSA
• VRE

37. HOW TO TREAT SUPERBUGS???

38. PREVENTION

40. “All disease begins in the gut”
Hippocrates
The Father of Modern Medicine
40