01 09-2017 gut microbiology

MICROBIOLOGY OF GUT

Dr. R. Someshwaran, MBBS, MD., Assistant Professor, Department of Microbiology,

Karpagam Faculty of Medical Sciences and Research.

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

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

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

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

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.

HOSPITAL SETTING

GUT MICROBIOTA

• Our GUT is an

extremely

complex

ecosystem

harboring more

than 100 trillion

micro-organisms

FACTORS AFFECTING NORMAL FLORA

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.


• 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.


• 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


• 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


• 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.


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

DISTRIBUTION OF GUT MICROBIOTA

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.

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.

DICTIM TO ALWAYS REMEMBER

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

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

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.

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

http://www.cdc.gov/ncidod/dhqp/hai.html

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

ANAL ABSCESS

• Infected cavity filled with pus near the anus

• Risk factors: Fistula-in-ano, Diabetes, Crohn’sdisease and Immunosuppression.

ETIOLOGY

GRAM POSITIVE COCCI

Staphylococcus aureus (MSSA, MRSA)

Enterococci (VSE, VRE)

CONS (MR/MS)

Streptococci (Non hemolytic)

Streptococci (Hemolytic)

Anaerobic Streptococci

ETIOLOGY

GRAM NEGATIVE BACILLI (Aerobic)

Escherichia coli (Most common)

Klebsiella pneumoniae

Proteus mirabilis, proteus vulgaris

Pseudomonas aeruginosa

Acinetobacter baumannii

Enterobacter aerogenes, E. cloacae

Mycoplasma

ETIOLOGY

GRAM NEGATIVE BACILLI (Anaerobic)

Bacteroides fragilis

Lactobacillus bifidus, L. acidophilus

Clostridium difficile

Clostridium perfringens

ETIOLOGY

Miscellaneous

Candida albicans

HSV 1 & 2

Hepatitis B virus

HIV

Donovaniosis

Syphilis

LABORATORY DIAGNOSIS

Gram stain of smear

CULTURE

Specimen inoculation - Surface plating

SUPERBUG?

• ESBL

• AmpC

• Carbapenemases

• MRSA

• VRSA

• VRE

HOW TO TREAT SUPERBUGS???

PREVENTION

“All disease begins in the gut”

Hippocrates

The Father of Modern Medicine40