Microbial Ecology Lecture 5 PDF

M ICROBIOLOGY Course Microbial Ecology CPC C L O W N I N P L U S C R O W N  Microbial ecology Science of systematic study of inter-relationships which exist between living organisms & ecosystem (environment) of 2 components : 1- Biotic (living) : plants, animals &...

M ICROBIOLOGY Course Microbial Ecology CPC C L O W N I N P L U S C R O W N  Microbial ecology Science of systematic study of inter-relationships which exist between living organisms & ecosystem (environment) of 2 components : 1- Biotic (living) : plants, animals & other organisms 2- Abiotic (non-living) : water, soil & atmosphere Symbiosis (symbiotic relationship) : Inter-species biological interaction Two dissimilar organisms (Symbionts) living together or in close association. A- Neutralism : Neutralistic symbiotic relationship Neither symbiont is affected by relationship Occupying same ecologic niche B- Commensalism : Commensalistic symbiotic relationship Beneficial to only one symbiont & of NO consequence (neither beneficial nor harmful) to other. Neither organism is physiologically dependent on the other. Examples : 1- Indigenous microflora (space & nutrients) of humans (none). 2- Blackhead Mite (Demodex) : — Tiny elongated body — D.folliculorum : in human facial hair follicles — D.brevis : in pilosebaceous glands (eyelashes) — Seldom cause much pathology (Demodicosis) — Cylindrical dandruff at base of eyelashes are pathognomonic of demodicosis. 3- Dermatobia hominis (human bot fly) : — Cause Furuncular myiasis — Endemic in Central & South America — The female lay & attach eggs on other zoophilic blood-feeding porter vectors (mostly flies, mosquitoes or ticks) — Porter vectors bite host, eggs hatch & released larvae — Introduced into skin of human host through bite wound → Boil-like lesions. — Treated by extraction of fly larvae (maggots). C- Mutualism : Mutualistic symbiotic relationship Beneficial to both symbionts (mutually beneficial) Examples : 1- Humans : — Many MOs of indigenous intestinal normal microflora (space & nutrients) ,such as : E. coli : vitamin K production Others : colonization resistance 1  2- Medicinal Leeches : — Used in the past for abscesses & wounds — Recently used to prevent venous congestion after plastic surgery — Aeromonas spp: GNB, normal flora in gut of leeches Essential for digestion of blood → nutrients to both — Note : Using leeches as a medical therapy may lead to wound infections by Aeromonas To prevent these infections, prophylactic antibiotics 3- Wolbachia (pipientis) : — Intracellular GN bacteria related to Rickettsia — The most common reproductive parasite (infects ONLY ovaries & testes) — Its host cannot reproduce, or even survive, without Wolbachia colonization — Live mainly within many arthropod spp & some filarial nematodes : — a- Onchocerca volvulus (onchocerciasis / river blindness) : Wolbachia required for survival & embryogenesis (sterility) of macrofilariae Ivermectin (DOC) : effective for killing larvae (microfilariae), but NOT adult worm (macrofilariae) Doxycycline: effective for killing Wolbachia required for survival of macrofilariae (not effective against larvae) — b- Dirofilaria immitis (heartworm disease in dogs) — Sterile Insect Technique (SIT) for controlling Aedes aegypti mosquitoes : Aedes aegypti mosquitoes do not naturally carry Wolbachia bacteria. Wolbachia-infected eggs are developed in the lab, producing sterile male and female mosquitoes. Lab-bred sterile males are released into the wild They mate with wild females, producing non-viable eggs that do not hatch. This reduces the mosquito population over time. Wolbachia is passed down maternally (all offsprings would be infected with it effectively) 4- Termites (small insects) : — Eat but cannot digest wood. — Intestinal protozoa break down large wood molecules into smaller cellulose molecule 5- Lichen : — Colored patches grown on tree trunks & rocks. — Composed of : Fungus: hyphal cell wall’s chitin (alga protection from desiccation) Alga : photosynthesis (CHOs & energy for both) D- Parasitism : Beneficial to one symbiont (parasite) & detrimental (harmful) to the other symbiont (host) : Nonpathogenic : only dumb parasites kill their hosts Pathogenic : — Disease causing or may be fatal — Trypanosoma gambiense (flagellated protozoan) : causing African sleeping sickness 2 Change or shift of symbiotic relationships : Many of microflora are opportunistic pathogens Change commensalistic or mutualistic between humans & their indigenous microflora into parasitic : Healthy IS↑: change of anatomical site habitat → blood, urinary bladder, lungs & others. Weakness of the immune system Burns, lacerations, wounds, & surgery. Human Indigenous Microflora Microorganisms that naturally live in our body with No harm 1- Resident microbiota : All microbes (bacteria, fungi, protozoa, & viruses) that reside on or within body. They are 10 times more than the total number of different human body cells (10 trillion cells → 100 trillion microbes) We humans are actually only 10% “human” & 90% bacteria !! There are 500-1000 different bacterial spp. in human body Body fluids (Blood, Lymph & CSF) ,CNS , (Bone / Joints) are STERILE Destruction of resident microflora → SUPERINFECTION 2- Transient microbiota : From external environment taking residence on or within body only temporary ,due to : Washing by bathing Flushing away by body excretions & secretions (urine, tears, & sweat) Failure to survive in acidic or alkaline pH Killing by toxins of resident Microflora of Skin ,Ears & Eyes Microflora of Skin : Resident microflora in skin are anaerobes (more than aerobes !!) Anaerobes in deeper skin layers, hair follicles, sweat, & sebaceous glands Most common bacteria: Staph (S. epidermidis & other CONS) Corynebacterium (Diphtheroids) Propionibacterium (Acne). Most common fungus: Candida albicans. Hand washing → reduce hospital acquired infections (HAI) Burns, lacerations, wounds, & surgery → skin infections Microflora of ears : Outer ear & auditory canal → flora similar to those of skin. Middle & inner ear → sterile Microflora of eyes (conjunctiva): Staph & Strep Corynebacterium (Diphtheroids) Moraxella catarrhalis. 3  Microflora of Respiratory Tract Lower RT (larynx, trachea, bronchi, bronchioles & lungs) with effective defense mechanisms → usually sterile. Upper RT (nose & throat (pharynx)) with moist warm mucus membrane : 1- Harmless: Diphtheroids, Lactobacilli & Micrococci. 2- Opportunistic: Strep, Staph, Neisseria & Corynebacterium. Healthy asymptomatic carriers : A- Normal Flora : Nasal / skin: Staph aureus. Nasopharyngeal: diphtheriae, pertussis, meningitis, & pneumonia Hands: Klebsiella, Pseudomonas, Staphylococcus. B- Incubatory, convalescent & chronic carrier: EBV, Flu, Covid-19, Poliomyelitis, HBV, & HIV. TB & C. difficile. S. typhi (Mary Mallon / Typhoid Mary) Microflora of mouth Microflora of Oral Cavity : Anaerobic (gum margins, crevices between teeth, & tonsils’ deep folds (crypts)) & aerobic bacteria. Low Dental hygiene → Dental caries, gingivitis & more severe periodontal disease Bacteria : GPC : Staph & Strep GPB : Corynebacterium, Lactobacillus, Actinomyces & Propionibacterium GNC: Neisseria & Veillonella GNB: Hemophilus, Fusobacterium, Porphyromonas, Prevotella, Bacteroides Spirochetes: Treponema & Borrelia α-hemolytic strep (Strep viridans) : The most common microflora in the oral cavity Streptococcus mutans most often implicated in plaque formation Leading contributor to cavities & tooth decay. Growth is suppressed by catechins in Green Tea Microflora of GIT Stomach acidic (low pH = 1.5) → No flora EXCEPT Helicobacter pylori : Gram negative bacteria Causes peptic ulcers in Achlorohydria & partial gastrectomy. Small intestine → Bile in duodenum is preventive BUT jejunum & ileum : Staph, Lactobacillus & Streptobacillus Veillonella & C. perfringens. Colon (large intestine) : largest number & variety of MOs of any colonized anatomical site of human body Note : Opportunistic on changing habitat → Indicators of water fecal contamination 4  Microflora of UGT Urinary system: Healthy kidney, ureters, & urinary bladder : sterile Acidic pH urine mechanical flush → distal urethra & its external meatus : bacteria, yeasts & viruses. Anatomical (ureteric stricture) or physiological (reflux) abnormalities → persistent recurrent UTIs. Most frequent causes of urethritis: Chlamydia trachomatis Gonococcus Mycoplasmas. Note : Cranberry juice could be protective against UTIs Reproductive systems : Usually sterile EXCEPT vagina : During puberty & after menopause (alkaline ,high pH). During Childbearing years (acid ,low pH 4-5) → Lactobacilli. Certain oral contraceptives → high pH→ decrease in Lactobacilli & their inhibitory metabolic product (lactic acid) → increase susceptibility to infections : 1- Bacterial Vaginosis : — Watery non-inflammatory discharge lacking WBCs — Caused by synergistic infection: — Gardnerella vaginalis & Mobiluncus — Bacteroides & anaerobic cocci — Note : Bacterial Vaginitis (inflammation with WBCs). 2- Yeast vaginitis : Candida albicans Beneficial Role of microflora 1- Production of Vitamins by intestinal flora as: Vitamin K (fat soluble vitamin) B2 (Riboflavin). B9 (folic acid) B7 (biotin) B12 (cyanocobalamin) B6 (pyridoxine). B1 (Thiamine) B5 (pantothenic acid).. 2- Constant source of Ags stimulating IS. 3- Microbial Antagonism : Prevention of opportunistic pathogens’ overgrowth & colonization Competing for nutrients and colonization sites & Production of bacteriocins. 5 Probiotics (Biotherapeutic MOs) Harmless MOs provide health benefits to the host 1- Oral ingested in Probiotic (Fermented foods) : Bacteria : Lactobacillus cultures in yogurt Bifidobacterium Non-pathogenic Enterococcus Yeast : Saccharomyces Improve Gut Health : Increase in microbial diversity in the gut Reestablish & stabilize intestinal microbial balance by replacing potentially pathogenic MOs → Reducing Inflammation Prebiotics (Non-digestible food ingredients) : Trans-galacto oligosaccharide Fructo-oligo-saccharide Lactulose Inulin & beta-glucan Stimulate growth & activity of intestinal resident bacteria to improve health. 2- Nasal inhaled in spray : Treatment of Otitis media : Harmless Strep sanguinis Complete or significant recovery Prevention of Meningitis : Harmless Neisseria lactamica ↓ incidence of potentially pathogenic Neisseria meningitidis (from 24 to 7%) 3- Fecal Microbiota Transplantation (FMT) : Transfer of intestinal bacteria (FDA approved) Stool from donor with saline to the GIT (colon) of recipient via colonoscopy (most frequently) Processed stool (food removed, & bacteria separated & cleaned) Treatment of : Recurrent C. difficile infections (twice as effective as Abx) Ulcerative Colitis (IBS). Prevention of : Listeriosis (mainly 4 different Clostridia spp) Cholera (Lactococcus lactis) Harmful Role of microflora Opportunistic potential pathogens (opportunists) 1- Change of anatomical site habitat : In healthy normal immune system Intestinal E coli → serious infections in Urinary bladder (cystitis), blood stream, lungs & wounds 6 2- Prolonged use of broad-spectrum Antibiotics : Reduction of indigenous microflora → SUPERINFECTION A- Clostridium difficile (C. difficile) in colon → Antibiotic-associated diarrhea (AAD) Pseudomembranous colitis (PMC) B- Candida albicans (C. albicans) → candidiasis (moniliasis) : In mouth: Oral thrush In vagina: yeast vaginitis 3- increase vaginal pH: Candida albicans → vaginitis. 4- weakening in Immune Response: due to disease (DM) or chemotherapy. 5- Other conditions : burns, lacerations, wounds, & surgical procedures. Biofilm Complex microbial community (aggregates of assorted bacteria) Embedded in tenacious abundant matrix of hydrated extracellular polymeric substance (EPS) Primarily composed of bacterial secreted polysaccharides, proteins, NAs & lipids. Bacteria grow in tiny clusters (Microcolonies) : Separated by network of water channels Supplying dissolved nutrients Removing waste products. Co-operative organization : Production of surfactants & structural components Matrix production, group motility, & nutrient degradation Biofilm is resistant to Abx & disinfectants: 1- Extensive layers & inherent hydrophobicity : ↓ penetration & diffusion of antimicrobials → ineffective Rx. 2- Bacterial cells localized deep inside 3- Typically divide at very slow rate : resistant to Abx targeting rapidly-dividing cells (Penicillin) 4- Penicillinase production by some protects others At risk groups : 1- Hospital instruments (catheters & endotracheal tubes of ventilated patients) 2- Surgical wounds, burns, bones or extended hospital stays. MOs can easily detach from biofilm → tissues & body fluids → Diseases : Periodontal disease Middle ear infections & Endocarditis Arthritis & Cystic Fibrosis Kidney stones & Prostate infection Prevention of biofilms: Cinnamaldehyde in cinnamon) Active in disrupting of persistent biofilms 7  Synergism (synergistic relationship) More than 2 different MOs in synergistic relationship together produce disease that neither could cause by itself (alone) Causing Synergistic, mixed or polymicrobial infection 1- Acute necrotizing ulcerative gingivitis (ANUG) ,Trench mouth ,Vincent’s angina : Bacterial spp of normal oral flora : Spirochetes (Borrelia vincentii) Anaerobes (Fusobacterium & others as Prevotella & Actinomyces) Spread to oral MMs (Vincent’s stomatitis/ Trench mouth) Spread to pharynx & palatine tonsils (Vincent's angina, ulcero-membranous pharyngitis & tonsillitis) Predisposing factors: Poor oral & dental hygiene. Vitamin deficiency. Poor tooth alignment (malocclusion) Smoking or chewing tobacco Faulty dentures & Severe malnutrition Extreme stress or lack of sleep Weakness in Immune response (DM ,elderly) Treatment : debridement & bactericidal Abx 2- Ludwig’s angina : Bacterial spp of normal oral flora : Staph (aureus & CONS), Strep (Streptococcus viridans) Anaerobes (Peptostrep, Prevotella, Porphyromonas, Fusobacterium) Life-threatening acute progressive painful bilateral cellulitis of floor of mouth Predisposing factors: Most cases often post dental infections Poor oral & dental hygiene Dental extraction Gingival infection & oral injury Lingual frenulum piercing Weakness in Immune response (DM ,elderly) Treatment: Emergency tracheostomy ,Surgical debridement & IV antibiotics 3- Bacterial vaginosis → bacterial spp of normal vaginal flora : Gardnerella vaginalis & Mobiluncus spp Bacteroides & Anaerobic cocci Agricultural Microbiology Soil MOs : Bacteria (cyanobacteria) , Fungi (primarily molds) ,Algae, protozoa, viruses, & viroids. Pathogens in soil : 1- Clostridium spp: C. tetani → tetanus C. botulinum → botulism Other Clostridium spp → gas gangrene. 2- Bacillus anthracis → anthrax. 3- Yeasts (Cryptococcus neoformans), &fungal spores Infectious diseases of farm animals : Pathogens: bacteria, viruses, fungi, protozoa, & helminths. Impact: 1- Zoonoses. 2- Economic burden. 8