Normal Microbial Flora “ Microbiota” Prof. Khaled H. Abu-Elteen

1. Normal Microbial Flora “ Microbiota” Prof. Khaled H. Abu-Elteen

2. Microbial Habitats Normal flora: microorganisms normally living on or in the body without normally causing disease. Your body is a home to 1 x 1014 microbial cells (bacteria)

3. Outline • Definitions • Interactions between humans and bacteria • Changes in normal flora • Benefits of normal flora • Why care about the normal flora? • Normal flora • Throat and mouth • Skin and nose • Adult female genital tract • Large bowel • Harmful effects of gut flora • Harmful alterations in gut flora

4. Key Terms Resident Transient Contaminant • Commensalism: microbe benefits, host unaffected. • Mutualism: microbe benefits, host benefits. • Opportunism: change in host circumstance. Normal flora is a significant cause of both minor AND serious life threatening infections.

5. Definitions • Pathogen • an organism that can cause infection in individuals with normal host defences, e.g., Salmonella enteritidis, Vibrio cholerae • Commensal • an organism that is found normally on those parts of the body that are exposed to, or communicate with, the external environment, eg. Bacteroides fragilis, Staphylococcus epidermidis; the 'normal flora' • Opportunistic pathogen ('opportunist') • an organism that can cause infection in individuals with abnormal host defences. Commensals may be opportunistic pathogens.

6. Microbes and humans Very few microbes are always pathogenic Many microbes are potentially pathogenic Most microbes are never pathogenic

7. Acquisition of normal flora • Sterile at birth, but from then on we are continually exposed to microorganisms, some of which become established as normal flora. • During birth maternal • After birth dietary sources and direct contact • NOT static, but continually changing…. - may reflect your environment

8. Location, Location, Location NOT all body sites have normal flora • Sterile sites - inaccessible - unsuitable - protected “Most external body sites have normal flora” • Skin, mouth, URT, GIT, genitourinary tract • Nature of body SITE has a major influence on TYPE of normal flora - TROPISM

9. NORMALLY STERILE SITES IN THE HUMAN BODY • Colonization of one of these sites generally involves a defect or breach in the natural defenses that creates a portal of entry • Brain; Central nervous system, CSF • Blood; Tissues; Organ systems • Sinuses; Inner and Middle Ear • Lower Respiratory Tract: Larynx; Trachea; Bronchioles (bronchi); Lungs; Alveoli • Kidneys; Ureters; Urinary Bladder; Posterior Urethra • Uterus; Endometrium (Inner mucous membrane of uterus ); Fallopian Tubes;

10. Skin Flora • Relatively inhospitable- dry - low pH and temperature - inhibitory secretions • Location ?- surface or subsurface - dry or moist body site • Body odour - role of microbes and anti-perspirant staphylococci propionibacterium yeasts Handwashing: resident, transient, contaminant flora

12. Upper Respiratory Tract Flora • Sterile below larynx(bronchi and lungs are sterile) • Common organisms - streptococci - Neisseria - haemophilus • SPECIAL CONSIDERATION • Streptococcus pyogenes • Streptococcus pneumoniae • Neisseria meningitidis • Haemophilus influenzae All are potentially serious pathogens at this and other body sites.

13. saliva has approx. 108 bacteria/ml 'viridans streptococci' Strep. mutans, Strep. mitior, Strep. salivarius Neisseria spp. N. lactamica, N. flavescens, N. meningitidis Haemophilus influenzae Streptococcus pneumoniae Corynebacterium spp. inc. C. diphtheriae - toxigenic and non-toxigenic strains Spirochaetes Bacteroides melaninogenicus Fusobacteria anaerobic cocci Actinomyces spp. The normal floramouth and throat

14. Gastronitestinal flora 1 Various parts of organ system – pH, O2 tension, nutrients MOUTH - paradoxically is quite anaerobic - 100 billion per gram tissue (clenched fist injuries) - plaque and tooth decay STOMACH - ? Sterile site (microbes in transit) - What about Helicobacter?

15. E. coli as a faecal indicator organism. Gastrointestinal flora 2 • Small versus large bowel • 1011-12 bacteria per gram of bowel contents. - most are anaerobic bacteria (1000:1) - E. coli is a well known aerobic component. The bowel is an important source of organisms for infection.

16. The normal floralarge bowel • Density • Upper: Medium 108 - 1010/g • Lower: High >1010/g • Organisms • Bacteroides spp. • Enterobacteriaceae, esp E. coli • Enterococci • Clostridium spp. • Candida spp.

17. Genitourinary tract flora Urinary tract- sterile site ? (transient / protected) - distal urethra Vaginal flora • Pre-pubescent - pH 7 - skin and bowel flora • Post-pubescent - pH 5 - hormone / epithelial changes - lactobacilli Age is a strong predictor for nature of infection LOSS of normal vaginal flora: CAUSE and EFFECT

18. The normal floraadult female genital tract • Lactobacilli • Diphtheroids • Staphylococcus epidermidis • Streptococci • enterobacteriaceae

20. Summary • Normal flora is not present at all body sites. • The types of normal flora vary with the nature of the body site. • Normal flora is continually changing to reflect your environment and biological state. • Normal flora is primarily bacterial with occasional yeasts (fungi), but no viruses, moulds (fungi) or parasites. • Important to distinguish between resident, transient and contaminating flora.

21. Microbes and humans Disease can come about in several overlapping ways 1. Some bacteria are entirely adapted to the pathogenic way of life in humans. They are never part of the normal flora but may cause subclinical infection, e.g. M . tuberculosis 2. Some bacteria which are part of the normal flora acquire extra virulence factors making them pathogenic, e.g. E. coli 3. Some bacteria which are part of the normal flora can cause disease if they gain access to deep tissues by trauma, surgery, lines, e.g. S. epidermidis 4. In immunocompromised patients many free-living bacteria and components of the normal flora can cause disease, especially if introduced into deep tissues, e.g. Acinetobacter

22. How do we know that a given pathogen causes a specific disease? Diagnosis and effective treatment of infection depends not just on isolating an organism, but in establishing a plausible link between the laboratory findings, recognised syndromes and the patient's clinical condition Recognised syndromes e.g. septicaemia, endocarditis, osteomyelitis meningitis, UTI, pneumonia pharyngitis patient's clinical condition potential pathogen isolated from or detected in clinical samples

23. Microbes and humans • Evidence for a potential pathogen being clinical significant (particularly for bacteria) • Isolated in abundance • Isolated in pure culture • Isolated on more than one occasion • Isolated from deep tissues • Evidence of local inflammation • Evidence of immune response to pathogen • Fits with clinical picture

24. Changes in normal flora • with changes in hormal physiology and development • female genital tract and lactobacilli • when antibiotics select for a 'resistant flora’ • Candida overgrowth in mouth, vagina • Clostridium difficile (antibiotic-associated colitis) • new organisms may be acquired • neonate from maternal genital tract during birth • Gram-negative colonisation of gut and URT in hospitalised patients • Cross-infection with C. difficile, MRSA, VRE etc

25. Why care about the normal flora?it may be good for you! • colonization resistance: • competition for space and nutrients with pathogens • release of bacteriocins and colicins (antibacterial substances) to prevent pathogen growth • vitamin K production in gut • continued antigenic stimulation from commensals • cross-reacting protective immunity against pathogens • commensal neisseriaceae and Neisseria meningitidis

26. Why care about the normal flora? • commensal bacteria may cause disease at their site of carriage or nearby, e.g. • Streptococcus mutans (mouth) • causes dental caries • Streptococcus pneumoniae (upper airways) • causes otitis media, sinusitis • Some members of the normal flora can become pathogenic if they acquire additional virulence factors (e.g. E. coli) or are introduced into normally sterile sites (e. g. Staphylococcus aureus)

27. Harmful effects of gut bacteria • escape of normal flora to abnormal sites • perforated appendix leads to peritonitis with • Bacteroides spp. and facultative aerobes inc. E. coli • cholecystitis and cholangitis • often mixed infection, E. coli predominant, also including enterococci • urinary tract infection • most frequent organism in normal urinary tract is E. coli • vaginal candiosis

28. antibiotic use leads to sensitive gut flora killed leads to overgrowth with resistant flora inc. Clostridium difficile leads to C. difficile toxin production leads to Diarrhoea, pseudomembraneous colitis Treatment stop precipitating antibiotic give oral metronidazole or vancomycin recovery requires re-establishment of normal flora ? probiotics Harmful effects of alterations in normal gut flora