1. Microbial ecology Dr Edet E Udo Department of Microbiology Faculty of Medicine. Kuwait University. Kuwait.

2. Objectives Describe the different types of microbes- host relationship Describe the mode of acquisition and transmission of pathogens Define normal flora and its significance in health and disease Understand the distribution of bacteria in different body sites

3. Host Parasite relationships Microorganisms Non parasitic Non pathogens (Microbes that do not cause disease) Non parasitic Non pathogens (Microbes that do not cause disease) Parasitic Pathogens (Microbes that cause disease) Parasitic Pathogens (Microbes that cause disease)

4. Sources and reservoirs of infection

5. Source and spread of infection Reservoirs A continuous source of infection (habitat).Reservoirs can be human, animals or non-living things. Source : immediate origin of infection Human reservoirs the principal living reservoir of human disease is the human body itself. Human reservoirs are also carriers. Carrier A person or animal with asymptomatic infection that can be transmitted to another susceptible person or animal.

6. Spread of infection Asymptomatic carriers : A person who is infected but without symptoms Incubation carriers: are in the early stages of infection. e.g. sexually transmitted diseases, AIDS Convalescent carrier: in the late stages of recovery. E.g, typhoid. (typhoid Mary). A passive carrier : a person who is contaminated but not infected e.g. hospital staff Chronic carrier : carries infection long periods after recovery

7. Spread of infection Animal reservoirs: Both wild and domestic animals. Zoonoses: are diseases that occur primarily in animals and can be transmitted to humans. E.g. some types of influenza,(avian flu,) SARS virus anthrax, rabies, brucellosis, Salmonellosis, Lyme disease, pneumonic plague etc. A vector is a a live animal that transmits an infectious agent from one host to another. Arthropods such as fleas, mosquitoes, flies, ticks and cockroaches Larger animals: birds and bats.`

8. A biological vector – participates in the pathogen’s life cycle A mechanical vector – not necessary to the life cycle of the infectious agent. Non living reservoirs – Soil: harbors such pathogens as Clostridium botulinum, Cl. Tetani, fungi etc. – Water: may be contaminated with human and animal faeces and act as reservoir for several pathogens.

9. Acquisition of infection Communicable disease: – Occurs when a pathogen is transmitted from host to host directly or indirectly Contagious diseases: – Are readily transmissible through direct contact Non communicable disease are not spread from host to host acquired from host flora (e.g) pneumonia from non living environmental reservoir

10. Mode of transmissionExamples of disease spread Contact transmission Direct contact e.g. handshaking, Kissing, bites, sexual intercourse Cutaneous anthrax, genital warts, gonorrhea, syphilis, rabies, etc. Indirect contact e.g. drinking glasses, toothbrush, stethoscopes, cell phones, Common cold, enterovirus infections, influenza, etc Droplet transmission- sneezing Whooping cough, Tb, strep throat Vehicle transmission Airborne: e.g. dust particles or droplets carries more than 1 meter Chicken pox, influenza, Tb, pulmonary anthrax, histoplasmosis etc Waterborne e.g stream, swimming Cholera, Giardia diarrhea, etc. Foodborne- poultry, seafood, meatFood poisoning, tapeworms Vector transmission Mechanical-on body flies, cockroachesE.Coli diarrhea, Salmonellosis etc Biological e.g. mosquito, lice, ticksMalaria, denque fever, lyme disease

11. Mode of transmission of microbes. Handshake Dirty door handle Contaminated meat Droplets Air travel

12. Portal of exit of microbes

13. Prevention and control of Diseases The prevention and control of diseases depends on the identification of the components of the infectious disease cycle that are primarily responsible for a particular epidemic. Three kinds of control measures (a) those directed towards reducing or eliminating the source or reservoir of infection – 1. quarantine and isolation of cases and carriers – 2. destruction of animal reservoir of infection – 3. treatment of sewage to reduce water contamination – 4. therapy that reduces or eliminates infectivity of the individual

14. Prevention and control of Diseases (b). Those designed to break the connection between the source of infection and susceptible individuals – 1. chlorination of water supplies, – 2. pasteurization of milk – 3. supervision and inspection of food and people who handle food – 4. destruction of vectors by spraying with insecticides (c) Control measures to reduce the number of susceptible individuals and raise the general level of herd immunity. – 1. Passive immunization to give a temporary immunity following exposure to a pathogen or when a disease threatens to take an epidemic form – 2.Active immunization to protect the individual from the pathogen and the host population from the epidemic.

15. Microbial ecology Ecology comes from the Greek words : Oikos– household or dwelling and Logos– law Term first defined by Ernst Hoeckel (1866) Microbial ecology is:- The study of interactions between microbes and their environment.

16. Types of Microbial associations 1. Pathogens Microbial pathogens are microorganisms that have structures or products that allow them to cause disease – Primary pathogen – Opportunistic pathogens 2. Non pathogens – Do not normally cause disease

17. Types of microbial associations Opportunist – resident or transient flora that can cause disease under certain conditions. Commensalisms – a relationship in which one organism benefits while the other is neither harmed nor helped. – – The commensal is sheltered by the host but is not directly dependent on the host metabolically and causes it no harm – The commensal can survive if separated from the host e.g E. coli lives in the human colon and benefits from the nutrients, warmth and shelter but usually causes no disease or discomfort.

18. Non pathogenic microorganisms

19. Benefits of non pathogenic microorganisms 1. Contribution to health e.g. normal flora 2. Food production e.g. yogurt, bread, spreads e.g vegemite 3. Chemical production- enzymes, antibiotics, vitamins 4. Genetic engineering- production of hormones, insulin etc 5. Elimination of pollution- – bioremediation, degradation of toxic compounds e.g. polychlorinated biophenyls (PCB), cleaning up of oil spills

20. Normal bacterial flora The normal flora or microbiota of humans includes bacteria, fungi, and protozoans that resides permanently on the body without causing disease. Normal flora can be found in the gastrointestinal (GI) tract, respiratory tract, genitourinary tract, and on the skin. Normal flora protect us from invasion and proliferation of pathogenic (disease-causing) microbes by competing for space and nutrients.

21. Benefits of Normal bacterial flora – They: – Aid in the digestion of food – compete with pathogens for nutrients and adhesion sites – inactivate pathogenic bacterial toxins or metabolites – produce substances that inhibit pathogens’ growth – stimulate non specific immunity.

22. Why study microbial normal flora Understanding the different microorganisms at specific locations provides insight into possible infections that might result from injury to these body sites A knowledge of the normal flora in the infected part of the body gives the physician perspective on the possible source and significance of microorganisms isolated from the infected site. Provides understanding of the causes and consequences of overgrowth by microorganisms normally absent at a specific body site Increases awareness of the role normal flora play in stimulating the host immune response.

23. Distribution of Normal flora of the human body The Skin – Resident flora grow normally on the skin. – vary from one body site to another reflecting variation in anatomy and physiology of the body Most skin bacteria are found on the superficial cells, colonizing dead cells or closely associated with the oil and sweat glands. – Common skin flora are: S. epidermidis and aerobic Corynebacteria, S. aureus, dermatophytic fungi, Propionibacterium acnes, Pityrosporum ovale Some Gram -negative bacteria generally prefer moist areas of the skin

24. Nose and Nasopharynx. – The normal flora of the Nose include: – S. aureus and S. epidermidis are prominent. Strep pneumoniae, Neiserria meningitidis Haemophilus influenzae and Diphtheroids. Throat – the most important bacteria in the oropharynx are alpha-haemolytic streptococci, S. oralis, S. milleri, S. salivarius; N. meningitidis, Haemophilus species, Mycobacterium species, anaerobes, Porphyromonas, prevotella and Fusobacterium, – S. aureus and S. epidermidis.

25. Oral Cavity Initially consists of Streptococcus, Neisseria, Actinomyces, Veillonella and Lactobacillus As the first teeth erupts anaerobes become dominant, then streptococcus. The Eyes – The bacteria flora consist of S. epidermidis, S. aureus, aerobic corynebacteria (diphtheroids), Strep pneumoniae, Branhamella cataarhalis. – External Ear Predominant organisms are coagulase-negative staphylococci and Corynebacteria

26. Stomach Many microorganisms are washed from the oral cavity into the stomach and are killed by the acidic pH of the gastric contents Normally the number of microorganisms increase after a meal but quickly falls as the acid pH takes its toll.

27. Small Intestine Enterococcus faecalis, lactobacilli, diphtheroids and Candida are occasionally present in the jejunum. Large intestine (Colon). Over 300 different bacterial species have been isolated from human faeces and they consists primarily of anaerobic, gram-negative, non sporing bacteria and gram-positive spore forming and non sporing rods. Yeast (Candida albican) and protozoa may occur as harmless commensal – E.g. T. hominis, Entamoeba hartmani, Endolimax nana and Iodema butschlii.

28. Genitourinary Tract The upper genitourinary track- kidneys, ureters and urinary bladder, is usually free of microorganisms In both males and females,S. epidermidis, E. faecalis and Corynebacterium spp. are usually present in the distal portion of the urethra. Neisseria and Enterobacteriacae are found occasionally. In the adult female genital tract, the acid-tolerant lactobacilli, Lactobacillus acidophilus are dominant. They maintain the pH of the vagina an cervical orifice at between 4.4 and 4.6 Others are Candida albicans, Gardnerella vaginalis