Genetic diagnosis: as Polymerase chain reaction (PCR) to amplify a DNA ... infants: 0.5 â 2 ml ..... 4. Detection of Viral Antigens as HBsAg of hepatitis B virus ...
MEDICAL MICROBIOLOGY AND IMMUNOLOGY FOR NURSES
DR Ayman A. Allam Professor of Microbiology and Immunology Faculty of Medicine Zagazig University
To the soul of my father, my mother and my family
2016/2017 رقم االيداع بدار الكتب 2016/4729 حقوف الطبع محفوظة للمؤلف
Contents Bacterial structure-------------------------------------------------2 Bacterial genetics--------------------------------------------------4 Bacterial physiology-----------------------------------------------5 Chain of infection--------------------------------------------------6 Normal Flora------------------------------------------------------11 Specimen collection --------------------------------------------13 Bacterial staining-------------------------------------------------17 Bacterial culture--------------------------------------------------18 Important bacteria----------------------------------------------21 General Mycology-----------------------------------------------23 Important fungi --------------------------------------------------24 Candida-------------------------------------------------------------24 Aspergillus --------------------------------------------------------25 General Virology-------------------------------------------------26 Sterilization -------------------------------------------------------31 Disinfection--------------------------------------------------------34 Antibiotics---------------------------------------------------------37 Antibiotic Resistance--------------------------------------------39 Nosocomial infection ------------------------------------------41 infection control------------------------------------------------- 42 Immunology ------------------------------------------------------45 Antigens------------------------------------------------------------45 Cells of immune response-------------------------------------46 Innate immunity--------------------------------------------------48 Acquired (Adaptive) immunity-------------------------------49 Humeral immunity-----------------------------------------------49 Antibodies (Immunoglobulins)-------------------------------49 Cell mediated immunity----------------------------------------50 Immunization-----------------------------------------------------51 Active immunization schedule in Egypt--------------------52 I
Hypersensitivity --------------------------------------------------53 Food born infection ---------------------------------------------55 Food poisoning ---------------------------------------------------56 Poliovirus ----------------------------------------------------------57 Enteric fever -------------- ---------------------------------------58 Salmonella---------------------------------------------------------58 Bacillary dysentery (shigella)----------------------------------60 Vibrio cholerae----------------------------------------------------61 Hepatitis viruses--------------------------------------------------62 Microorganisms transmitted through skin ----------------68 Human immune deficiency virus-----------------------------68 Microorganisms transmitted through animal bite-------70 Skin and wound infections ------------------------------------71 Staphylococci-----------------------------------------------------72 Pseudomonas aerruginosa------------------------------------73 Bacteroides fragilis----------------------------------------------73 Airborn and droplet infections-------------- -----------------74 Streptococci-------------------------------------------------------75 Pneumococci------------------------------------------------------76 Bodetella pertusis------------------------------------------------76 Mycobacteria-----------------------------------------------------77 Meningitis --------------------------------------------------------78 Neisseria meningitides------------------------------------------79 Viral respiratory diseases--------------------------------------80 Measles virus-----------------------------------------------------80 Mumps virus-------------------------------------------------------80 Rubella virus-------------------------------------------------------81 Influenza virus----------------------------------------------------82 Chicken poxvirus-------------------------------------------------83 Sexually transmitted diseases--------------------------------84 Treponema pallidium-------------------------------------------85 II
Urinary tract infections---------------------------------------86 Zoonosis------------------------------------------------------------88 Brucella Spp-------------------------------------------------------88 Yersinia pestis-----------------------------------------------------89 Vertical transmission--------------------------------------------90 Herpes simplex virus--------------------------------------------90 Cytomegalovirus-------------------------------------------------91
III
INTRODUCTION:
Microbiology is the study of microorganisms, which are tiny organisms that live around us and inside our body. An organismis a living thing that ingests and breaks down food for energy and nutrients, excretes undigested food as waste, and is capable of reproduction.
Microorganisms are the subject of microbiology, which is the branch of science that studies microorganisms.
A microorganism can be one cell or a cluster of cells that can be seen only by using a microscope.
Microorganisms are organized into six fields of study: bacteriology, virology, mycology, phycology, protozoology, and parasitology. General Bacteriology
Eukaryotes & Prokaryotes
Cells have evolved into two different types:
Eukaryotic: Human cells, Fungi, protozoa and helminthes are eukaryotic,
Prokaryotic: Bacteria are prokaryotic.Viruses are not cells and do not have a nucleus.
Bacterial Size: Bacteria range in size from about 0.2 to 5 µm. -1-
Shape of Bacteria: Bacteria are classified by shape into three basic groups: Cocci: round Bacilli: rods Spirochetes:
spiral-
shaped Arrangement: Bacteria are arranged
Shapes of bacteria cell
single Diplococcic
in
pairs
(diplococcic) chains in Streptococci grapelike
clusters
in
Staphylococci The Bacerial Structure
The bacterial cell
The bacteria is formed of essential components and non essential components. The essential components:
The non essential components:
A. The cell wall
A. The plasmid
B. The cytoplasmic membrane
B. The flagella
C. The cytoplasm
C. The pili (fimbria)
D. The nucleus
D. The capsule E. The spore -2-
1-Bacterial Cell Wall: -It is the outer most basic structure of the bacterial cell. 1. Cell Wall of Gram Positive Bacteria Consists of: thick layer of peptidoglycan 50:60% of the cell wall. It is the site of action of penicillins, cephalosporins and lysozyme enzyme. Techoic acid. 2. Cell Wall of Gram Negative Bacteria Consists of: Inner layer ofpeptidoglycan : thin layer (5-10% of the cell wall) Outer membrane (OM): composed of lipopolysaccharide (LPS) containing and lipid A layer (endotoxin). It is the endotoxin causes the fever and hypotension and induce septic shock.
2-Cytoplasmic Membrane: is composed of a phospholipid bilayer. It is generally do not contain sterol (Except the genus Mycoplasma). The membrane has four important functions: -3-
(1) active transport of molecules into the cell (2) energy generation by oxidative phosphorylation, (3) secretion of enzymes and toxins. 3- Cytoplasm An amorphous matrix that contains : 1. Ribosomes: are the site of protein synthesis. 2. Granules: serve as storage areas for nutrients . 3. The Nucleus. 4. The Plasmids 4-The Nucleus: 1. It is formed of DNA. 2. It is single, circular molecule 3. It contains genes. 4. It contains no nuclear membrane, no nucleolus, and no histones whereas eukaryotic DNA does. Plasmid: It is extrachromosomal, double-stranded, circular DNA molecules It can replicates independently of the bacterial chromosome It can be transmitted from cell to cell by conjugation. Plasmids carry the genes for the following functions: 1.Resistance to antibiotics (R plasmid) . 2.Sex Pili (F Factor) responsible for congugation. 3. Exotoxins, 4. Several antibiotics produced by Streptomyces. -4-
5-Capsule The capsule is a gelatinous layer covering the entire bacterium. It is a determinant of virulence of many bacteria since it limits the ability of phagocytes to engulf the bacteria as in pneumococci. Are used as in certain vaccines. 6-Flagella: Flagella are long, whiplikeappendages that move the bacteria (Organ of motility). Responsible for H antigen 7-Pili (Fimbriae) Two types: Ordinary pili mediate the attachment of bacteria to the human cell surface. The sex pilus, forms the attachment between the (donor) and the (recipient) bacteria during conjugation. 7-Spores: 1. These highly resistant structures are formed in response to adverse conditions. 2. Formed by the genus Bacillus, and the genus Clostridium, which. 3. It is resistant to heat, dehydration, radiation, and chemicals. -5-
4. It can be killed by autoclaving. Bacterial Genetics Bacteria are haploid as they have a single chromosome and therefore a single copy of each gene. Eukaryotic cells (such as human cells) are diploid, which means they have a pair of each chromosome and therefore have two copies of each gene. -The Gene: is the basic unit of inheritance formed of a segment of DNA molecule that carries the genetic information for specific biochemical or physiological function. The Nucleic acids are either DNA or RNA. DNA is double stranded molecule formed of complementary double stranded molecule (Adenine-Thymine or Guanine-Cytosine base pairing). It carries the genes. RNA is single stranded molecule. Uracil substitutes thymine of DNA and ribose instead of Deoxy-ribose. It is found in three forms: 1. mRNA( messenger RNA) carries the genetic information from DNA to ribosome. 2. rRNA (Ribosomal RNA) is a constituent of ribosome. It reads the genetic code on mRNA and form protein according to it. -6-
3. tRNA (Transfer RNA): carries the amino acids from cytoplasm to ribosome. The Bactriophage or Phage Is the virus which attack and infect bacteria. It is composed of DNA or RNA genetic material coated by a protein capsid with a tail and attachment fibrils.
-7-
Bacterial physiology Bacterial Reproduction: Bacteria reproduce by binary fission, a process by which one parent cell divides to form two progeny cells. The doubling (generation) time of most bacteria is as little as 20 minutes as Escherichia coli. Oxygen Requirement of Bacteria: 1. Obligate aerobes: require oxygen to grow. 2. Obligateanaerobes: cannot grow in the presence of oxygen as Clostridium tetani. 3. Facultative anaerobes: as E. coli, arethey can grow in the presence or absence of oxygen. 4. MicroaerophilicBacteria: require oxygen in concentration less than its athospheric pressure. Nutritional requirement: 1. Heterotrophs:require preformed organic compounds ( Sugars, amino acids). Most pathologic bacteria are heterotrophs 2. Autotrophs: Can synthesize organic compounds
from
inorganic compounds (chemolithotrophs) or from CO2 and water by the light (photolithotrophs).
-7-
Virulence:
is a quantitative measure of pathogenicity and is
measured by the number of organisms required to cause disease, it is the degree of pathogenicity. Virulence Factors: Certain structures or products that help microorganisms to overcome body defence mechanisms and cause disease. HOW BACTERIA PRODUCE DISEASE? Bacteria produce disease through invasion or toxin production. Invasion is facilitated through capsule and degradative enzymes. Invasive bacteria, on the other hand, grow to large numbers locally and induce an inflammatory response consisting of erythema, edema, warmth, and pain. 1. Capsule: capsulated bacteria as Streptococcus pneumoniae, and Neisseria meningitidis resist phagocytosis. 2. Pili: pili help bacteria to adhere to the surface of host cells as in gonococci. 3. Ezymes : Collagenase and hyaluronidase, which degrade collagen and hyaluronic acid, respectively, thereby allowing the bacteria to spread through subcutaneous tissues in cellulitis caused by Streptococcus pyogenes.
-8-
Coagulase produced by Staphylococcus aureus produce fibrin from
fibrinogen (this clot may protect the bacteria from
phagocytosis by walling off the infected area and by coating the organisms with a layer of fibrin). Immunoglobulin A (lgA) protease, which degrades lgA. Leukocidins, which can destroy leukocytes. 4- Bacterial toxins: There are two types of toxins. exotoxin is a polypeptides secreted by an organism. Exotoxins are very toxic. A very small amount can be fatal to a host organism and even though the immune system can often identify and attack the toxin, the toxin spreads so quickly that the host does not have an opportunity to mount a defense. Endotoxins are lipopolysaccharides (LPS), which form an integral part of the cell wall. Endotoxins occur only in gram-negative rods and cocci cause fever, hypotension, and other generalized symptoms even septic shock. Difference between Exotoxins and Endotoxins Property Exotoxin Endotoxin Source Certain species of Cell wall of gramgram-positive and negative bacteria gram-negative bacteria Secreted Yes No from cell -9-
Chemistry Location of genes Toxicity
Polypeptide Plasmid or bacteriophage High
Clinical Various effects effects Mode of Various modes action Antigenicity Induces high-titer antibodies called antitoxins Vaccines Toxoids used as vaccines Heat Destroyed rapidly stability at 60°C (except staphylococcal enterotoxin) Typical Tetanus, botulism, diseases diphtheria
Lipopolysaccharide Bacterial chromosome Low (fatal dose on the order of hundreds of micrograms) Fever, shock Includes TNF and interleukin-1 Poorly antigenic
No toxoids formed and no vaccine available Stable at 100°C for 1 hour
Meningococcemia, sepsis by gramnegative rods
- 10 -
NORMAL FLORA (1)Normal flora is the term used to describe the various bacteria and fungi that are permanent residents of certain body sites, especially the skin, oropharynx, colon, and vagina. The normal flora organisms are often referred to as commensals. (2)Commensals are organisms that derive benefit from another host but do not damage that host. Resident flora: normally present in the site and reestablish itself after their removal by antiseptics. Transient flora: potentially pathogenic organisms acquired from the environment and don't reestablish itself after its removal by hand washing or antiseptic use. (3)CSF, Blood, urine, serous cavities is sterile sites with no normal flora. Importance of the normal flora: 1. They can cause disease, especially in immunocompromised and debilitated individuals. 2. They constitute a protective host defense mechanism. The flora occupy attachment sites on the skin and mucosa that can interfere with colonization by pathogenic bacteria. 3. They may serve a nutritional function. The intestinal bacteria produce several B vitamins and vitamin K. - 11 -
General lines of Diagnosis of bacterial infection: 1. Specimens: according to the type of lesion; wound swab, pus aspiration, CSF, sputum, stools…etc 2. Direct smear: to show the motility of the organism 3. Stained smear: to show the staining affinity, shape and arrangement of bacteria 1)Gram stain: differentiate bacteria into gram negative or positive organisms. 2)Ziehl-Neelsen stain: show Acid Fast Bacilli. 4. Culture: on the suitable medium usually for 24 h at 37°C aerobically for aerobic organisms anaerobically for anaerobic organisms. The colonies identified by: 1) microscopic examination 2) macroscopic shape of the colony 3) Biochemical reactions as catalase, oxidase..etc 4) serologically 5. Antibiotic sensitivity testing: to know the antibiotics effective for the causative organisms. 6. Serology: to detect specific anti-organism IgM or rising titer of specific anti organism IgG.
- 11 -
7. Genetic diagnosis: as Polymerase chain reaction (PCR) to amplify a DNA sequence unique to the organism to be easily detected.
Specimen collection in Bacteriology: There are three types of specimens: Specimen from normally Sterile site: as CSF, Blood , Pleural effusion. Specimen from flora containing site as stools, sputum, oral cavity, Vagina. Valuable specimen: specimen taken during surgery or taken by painful procedure as surgical biopsy or CSF. Universal precautions for collecting and handling all specimens. 1. Whenever possible, collect all culture specimens prior to administration of any antimicrobial agents. 2. Avoid contamination with indigenous flora. 3. All specimens must be appropriately labeled. The requisition will include the patient name, hospital number, hospital - 12 -
service, date and time of collection, specimen type and tests requested. A requisition needs to accompany each different specimen type. 4. Deliver all specimens to the laboratory as soon as possible after collection. Specimens for bacterial culture should be transported at room temperature. If transport is delayed the following specimens should be refrigerated: urines (within 30 min), stool (within 1 h), respiratory specimens. 5. Specimens should be in tightly sealed, leak proof containers and transported in sealable, leak-proof plastic bags. Specimens for TB should be double bagged. 6. Specimens should not be externally contaminated. Specimens grossly contaminated or compromised may be rejected. 7. You should deal seriously with all specimens as if it is infectious and dangerous. Some Important Bacterial Specimens: 1. Abscess – Tissue or aspirates are always superior to Blood culture bottle
swab specimens. 2. Blood: Venous blood - 13 -
a. Amount: • infants: 0.5 – 2 ml • children: 2 – 5 ml
Blood culture bottle
• adults: 5 – 10 ml b. Cleanse skin with a povidone iodine. applied in concentric circles (start at center). Allow to dry at least 1 min before venipuncture. c. Do not touch site after prep. d. Remove overcaps from blood culture bottles and cleanse each rubber septum with separate 70% alcohol swabs. Allow septum to dry for 1 min before inoculating. e. Draw 20 mL of blood and inoculate each bottle with 10 mL of blood. Do not vent or overfill bottles. Transport time 3 mL) to the Microbiology Laboratory. Transport time 90% of cases About 2% fulminant hepatitis and death About 5% of HBV infections result in a chronic carrier state. Chronic hepatitis, cirrhosis hepatocellular carcinoma Laboratory Diagnosis: by HBV viral markers: There are three important antigens: the surface antigen (HBsAg) - 64 -
the core antigen (HBcAg) not done the e antigen (HBeAg). 5) Three important antibodies appear during infection: Anti-HBsAb Anti-(HBcAb Anti-HBeAb. The most important laboratory test for the detection of early HBV infection is ELISA for surface antigen (HBsAg). HBsAg appears during the incubation period and during the acute disease. Detection of HbsAg for more than 6 months indicates a chronic carrier state. Anti HBs indicates immunity. Prevention: GENERAL MEASURES: Screen Blood donors Using disposable syringes Active Immunization: with recombinant HBV vaccine containing HBs Ag made by recombinant technology. Given in three doses 0, 1 month and 6 months. -It is given to high risk persons as medical and paramedical personnel. -Given compulsory to infants at 0,2 and 6 months of age Hepatitis C Virus It causes Hepatitis C and can lead to hepatocellular carcinoma. HCV is the most prevalent blood-borne pathogen in Egypt. Characteristics: HCV RNA Enveloped - 65 -
HCV has at least six genotypes. Genotype 4 is the most prevalent in Egypt. Pathogenesis Transmission: Most transmission is via blood. Sexual transmission (rare) transmission from mother to child ( rare) Prognosis of HCV: More than 50% of infections result in the chronic carrier state. Chronic hepatitis, cirrhosis hepatocellular carcinoma Laboratory Diagnosis By detecting antibodies to HCV by an ELISA. The test does not distinguish between an acute, chronic, or resolved infection. RT- PCR test detects the presence of viral RNA in the serum to determine whether active disease exists (confirmatory test). Treatment: - oral drugs as sofosbuvir (Sovaldi). Prevention: -Post-transfusion hepatitis can be prevented by detection of antibodies in donated blood.
-There is no vaccine available. Hepatitis D Virus
It is RNA virus. It causes Hepatitis D. Characteristics: Defective virus can replicate only in cells already - 66 -
infected with HBV, i.e., HBV is a helper virus for HDV. Pathogenesis: -Transmitted as HBV by blood, sexually, and from mother to child. -As HBV, Chronic hepatitis and chronic carrier state occur. Prevention: -Prevention of HBV infection by using the HBV vaccine Hepatitis E Virus Similar to hepatitis A virus in the following ways: transmitted by fecal– oral route, no chronic carrier state, no cirrhosis, and no hepatocellular carcinoma. High mortality in pregnant females
No antiviral therapy and no vaccine.
- 67 -
MICROORGANISM TRANSMITTED THROUGH SKIN Microorganisms transmitted through skin can be transmitted through: Blood transfusion and needle stick injury Arthropod bites Wound infection through contact transmission Animal bites
Blood Born Microorganism A blood-borne disease is one that can be spread through contamination by blood and other body fluids. Viruses Hepatitis C Hepatitis B Hepatitis D HIV Cytomegalo virus (CMV) Epstein Barr virus (EBV) Bacteria Treponema pallidum causing syphilis Parasites Malaria
- 68 -
Human Immunodeficiency Virus 1. Disease: Acquired immunodeficiency syndrome (AIDS). 2. RNA virus. The natural host range of HIV is limited to humans Transmission: blood contact sexually transplacental Through breast feeding. Pathogenesis: Target cell of HIV is CD4 cell (Th cell). CD4 cell (Th cell) is the most important immune cell because it produces cytokines that control other immune cells. HIV infects and kills helper T cells, which predisposes to opportunistic infections. Clinically: 1. After exposure to HIV infection flu like symptoms occur that resolve. 2. Then the patient enters in a latent phase in which no clinical manifestation is present but the virus remains and replicates in lymphoid tissues. 3. The duration of latent period is different in different patients and may extend to 10 years or more. 4. AIDS stage: the number of CD4 cells gradually decrease and the immune response fails and the patient enter in the AIDs stage when - 69 -
the number of CD4 is below 200cell/µl. The patient is now exposed to opportunistic infections as: Bacterial as: Salmonellosis and Atypical mycobacteria Viral as Herpes virus. Protozoal infections Malignancy Neurologic manifestations. Laboratory Diagnosis 1. Screenig test:
detecting antibody with ELISA; most will have
seroconverted by 4 weeks. 2. Confirmatory test: PCR. 3. CD4 number by flow cytometry for following treatment. Treatment Highly active antiretroviral therapy (HAART) Prevention Prevention: 1. Screening of blood donor 2. "Safe sex," including the use of condoms 3. Health education
MICROORGANISM TRANSMITTED THROUGH ANIMAL BITES Rabies Virus RNA enveloped virus.
Bullet-shaped.
Pathogenesis: Main reservoir is wild animals such as fox, and bats.
- 70 -
Transmission to humans is usually by rabid animal bite usually dog or cat Replication of virus at the site of the bite, followed by transport up the nerve to the central nervous system. After replicating in the brain, the virus migrates peripherally to the salivary glands, where it enters the saliva. Within the central nervous system, encephalitis develops, with the death of neurons. Infected neurons contain an cytoplasmic inclusion bodies called a Negri bodies. Clinically, It causes Rabies disease. After Incubation Period of 2 weeks to 16 weeks or longer, the patient exhibits nonspecific symptoms such as fever, anorexia, and changes in sensation at the bite site. within a few days, confusion, lethargy, and increased salivation develop. Hydrophobia due to pain on swallowing water. The disease progresses to seizures, paralysis, coma and death. Laboratory Diagnosis In animals:-by detection of inclusion bodies called Negri bodies in brain tissue sections. -The virus can be grown in cell culture. In humans (1) Isolation of the virus from sources such as saliva, spinal fluid, and brain tissue. (2) Serology by a rise in titer of antibody to the virus.
- 71 -
(3) Negri bodies can be demonstrated in corneal scrapings and in autopsy specimens of the brain. Treatment:No antiviral therapy is available. Prevention: Postexposure immunization: After bitting by an animal, The patient should be given : the Rabies vaccine (Human Diploid Cell Vaccine) (on days 0, 3, 7, 14, and 28. human rabies immune globulin (RIG); half of the RIG is given into the bite site, and the remainder is given intramuscularly. Immediate cleaning of the wound. Preexposure prophylaxis : consists of the vaccine only. It is given to high-risk groups, such as veterinarians. Preexposure immunization consists of three doses given on days 0, 7, and 21 or 28.
Skin and Wound infection Organisms causing skin infections Bacteria: 1. Staphaureus causing abscess ( )الخراج 2. Streptococcus group A cause cellulitis ( )االلتهاب الخلوي Wound infection is caused by: 1. Staphaureus 2. MRSA 3. E COLI - 72 -
4. Klebsiella spp 5. Pseudomonas spp 6. Bacteroid spp
Staphylococci: Shape: Gram-positive cocci arranged in clusters. It is positive for catalase test which differentiate it from streptococci which is negative. Catalase test: putting one colony of staphylococci in 1/2 ml of H2O2 leades to bubble formation due production of O2. Staphylococci are divided according to production of coagulase enzyme into: Coagulase positive staphylococci: Staphaureus is the only Coagulase positive Coagulase negative staphylococci: other staph spp as Staph epidermedis.
Staphylococcus aureus (Staphaureus)
Gram-positive cocci
arranged in clusters. Caagulase positive, catalase
positive. Habitat and Transmission: Main habitat is nose;
also
found
on
human
skin.
Transmission is via the hands. Virulence factors and Pathogenesis: -Abscess is the most common lesion it is - 73 -
human
localized lesion due to coagulase production. Coagulase converts fibrinogen into fibrin. Diseases (1)Local: - Abscess
-wound infection
(2) general: endocarditis - hospital-acquired pneumonia . (3) Toxic diseases: gastroenteritis (food poisoning) Staph food poisoning: It is due to eating food containing staph enterotoxin. Incubation period is short 4-6 hours. Vomiting, diarrhea, colic but no fever.
Methicillin Resistant Staphaureus (MRSA)
1. MRSA are Staphaureus that are resistant to penicillinase resistant penicillins as oxacillin, fluxacillin..etc. 2. The resistance due to change in the penicillin binding proteins (PBP) which are the target of penicillins 3. It is an important cause of hospital acquired infections. 4. Hospital acquired MRSA is very resistant to antibiotics
Pseudomonas aeruginosa 1. It is aerobic gram-negative rods 2. It produce Pyocyanin (blue-green) exo-pigment. 3. Oxidase-positive 4. It is very resistant to antibiotics 5. It can grow in improperly used disinfectants. - 74 -
Clinically: Wound infection Urinary Tract Infection Pneumonia One of the most important causes of nosocomial infections, especially in burn patients
Bacteroides fragilis Anaerobic gram-negative rods. Habitat is the human colon as normal flora, where it is the predominant anaerobe. Clinically: peritonitis, and abdominal abscess. Laboratory Diagnosis 1. Specimen: pus or aspirated exudates, usually foul smell 2. anaerobic culture.
- 75 -
AIR BORNE AND DROPLET BORN DISEASES Droplets containing microorganisms can be generated when an infected person coughs, sneezes, or talks. Droplets are too large to and quickly drops to floor within 1 meter. Airborne transmission refers to situations where droplet nuclei dimeter less than 5 µ) or dust particles containing microorganisms can remain suspended in air for long periods of time. Air can carry these nuclei to long distance. Airborne transmission allows organisms to enter the upper and lower respiratory tracts as :
Tuberculosis
Chickenpox
Measles
AIR BORNE AND DROPLET BORN DISEASES includes: Bacteria: 1) Streptococcus group A ()المكورات السبحية 2) Corynebacterium diphtheria ()عصيات الدفتريا 3) Mycobacterium tuberculosis ()عصيات الدرن 4) Bordetella pertusis 5) Bacteria causing pneumonia االلتهاب الرئوي: Pneumococci Mycoplasma Chylamydia M tuberculosis - 76 -
6) Bacteria causing meningitis االلتهاب السحائي: Meningiococci Hemophilus influenza Pneuococci Viruses: Measles Rubella Mumps Chicken pox Influenza Common cold Some bacterial respiratory diseases Streptococci Gram-positive cocci arranged in chains. It is divided according to:-Haemolysis on blood agar: α (Incomplete) haemolysis: greenish colour surrounds colonies as pneumococci and streptococcus viridians. β (Complete) haemolysis: complete clearance around the colonies as streptococcus pyogenes. γ ( No) haemolysis: some strains of enterococci. Streptococcus pyogenes (Group A Streptococcus) Characteristics Gram-positive cocci in chains. β-hemolytic. Catalase-negative. Pathogenesis
Habitat is the human throat and skin. - 77 -
Transmission is via respiratory droplets.
Diseases: A) Local as
1)Tonsillitis
2)pharyngitis
3) scarlet fever 4) cellulitis
B) Generalized disease as Puerperal sepsis C) immunologic diseases: It occurs 3-4 weeks after streptococcus groupB infection due to immunologic response to its antigens -Rrheumatic fever
- Acute glomerulonephritis
-Tonsillitis: The main lesion for Streptococcus pyogenes. Characterized by fever, sore throat, malaise …etc. – Scarlet fever: sore throat, fever, rash due to production of erythrogenic toxin. –puerperal sepsis: infection of the uterus after labour or septic abortion; fever, septicaemia and septic shock. Laboratory Diagnosis: specimen: swab 1)Gram-stained smear: gram positive cocci in chains 2)Culture: β-hemolytic colonies on blood agar. -If rheumatic fever is suspected, Antistreptolysin O (ASO) ESR and CRP are positive. Treatment: Penicillin G (no significant resistance) or macrolide Pneumococcus Characteristics: 1. Gram-stained smear: Gram-positive "lancet-shaped" cocci in pairs (diplococci) 2. Culture. α-hemolytic colonies on blood agar. - 78 -
3. It has prominent polysaccharide capsule. 4. Habitat is the human upper respiratory tract. 5. Transmission is via respiratory droplets. 6. Its polysaccharide capsule resists phagocytosis. 7. The most common diseases are lobar pneumonia meningitis otitis media and sinusitis in children. Bordetella pertussis Small gram-negative small rods. It is the cause of Whooping cough (pertussis): Bouts of severe cough followed by respiratory whoop and vomiting. Prevention: Pertussis vaccine contains the killed bacteria; Usually given to children in combination with diphtheria and tetanus toxoids. DTP vaccine is given to children in age of 2, 4, and 6 months then booster at 18 months and 4 years but it is contraindicated to give the pertussis vaccine after age of 4 years because it cause allergic encephalitis.
Mycobacteria Mycobacterium tuberculosis, the cause of tuberculosis Mycobacterium leprae, the cause of leprosy. It contains High lipid content of cell wall, which prevents dyes used in Gram stain from staining organism. Stained by Ziehl-Neelsen stain (Z-N )stain acid-fast rods. - 79 -
Pulmonary tuberculosis: 1. It is caused by 1) M tuberculosis 2)M bovis 2. Reservoirs are humans for M. tuberculosis and cows for M bovis. 3. Transmission is via air born infection produced by coughing. Extra- pulmonary TB: can occur in any part of the body as kidney, bones, meninges…..etc. Dormant or latent tuberculosis: Deaths of most of the bacilli but few bacilli remain inactive and dormant surrounded by fibrous tissue with no clinical effect. Laboratory Diagnosis of Tuberculosis: Specimen:According to lesion: - Pulmonary TB: 3 morning sputum specimens on 3 subsequent days. - Urinary TB: morning urinary specimen – TB meningitis: CSF Microscopy: Acid-fast rods seen with Ziehl-Neelsen stain Culture: on solid Löwenstein-Jensen medium-----slow-growing (3–6 weeks) colony. Tuberculin Skin Test: to detect Latent TB A) Positive test: indicates that the person has been exposed to TB bacilli but not necessarily that the person has the disease tuberculosis. B) A negative tuberculin test excludes infection in suspected persons. MENINGITIS Causative organisms: Bacteria: most important are: 1) N. meningitides - 80 -
(2)Haemophilus influenza (3)Streptococcus pneumonia In the neonatal period: 1) Group B streptococci 2)Listeria monocytogenes 3) E coli Viruses (aseptic meningitis): - Coxsackie viruses - Echoviruses - Mumps - Herpes simplex virus 1 &2 - Cytomegalovirus(CMV) Fungi: - Cyyptococcus neoformans Lab. diagnosis of meningitis 1. CSF is obtained by lumbar puncture under complete aseptic conditions. 2. Physical examination: In pyogenic meningitis, CSF is turbid and under tension. In viral meningitis, CSF is clear. 3. Chemical examination: In pyogenic meningitis, protein level increases while glucose level decreases. In aseptic (viral) meningitis, glucose level is within normal. 4. Cell examination:
- 81 -
In pyogenic meningitis the number of cells is higher and mainly polymorphs. In tuberculous or viral meningitis, the number of cells is lower and are mainly lymphocytes. 5. Bacteriologic examination : CSF is centrifuged and the deposit examined by : Microscopic examination of direct smear stained by Gram stain Ziehl Neelsen (Z-N stain). Culture: CSF is cultured on blood agar and chocolate agar. PCR for viral or bacterial nucleic acids. Neisseria meningitidis (Meningococcus) It causes acute epidemic cerebro-spinal meningitis. Characteristics: -Gram-negative capsulated "kidneybean shaped" diplococci intra and extracellularly. -Oxidase-positive. -It has large polysaccharide capsule. pathogenesis: Habitat is the human upper respiratory tract; Transmission is via respiratory droplets. After colonizing the upper respiratory tract, the organism reaches the meanings via the bloodstream. Clinically: Fever Headache Stiff neck - 82 -
Vomiting Rash and shock
Laboratory Diagnosis 1. Specimen: CSF by lumber puncture 2. CSF is under Tension and turbid with large number of pus cells >2000/cmm. 3. Gram-stained smear: Gram-negative capsulated "kidney-bean shaped" diplococci intra and extracellularly.. 4. Culture on chocolate agar . 5. Serology to detect capsular Ag in CSF. Prevention: Vaccine contains capsular polysaccharide of important strains . - chemoprophylaxis: Rifampin or ciprofloxacin given to close contacts to decrease oropharyngeal carriage. Some viral respiratory diseases Measles Virus Enveloped RNA virus It has a single serotype. It causes Measles . Pathogenesis: Transmission by respiratory droplets. Initial site of infection is the upper respiratory tract. Virus spreads to local lymph nodes and then via the blood to other organs, including the skin. Clinically Fever Maculopapular rash Koplik’s spots on buccal mucosa. - 83 -
Complications: - encephalitis - pneumonia Prevention: Vaccine contains live, attenuated virus given subcutaneously to children at 15 months of age. Usually given in combination with mumps and rubella vaccines MMR.
Mumps Virus Enveloped RNA virus. It causes mumps Pathogenesis: Transmission by respiratory droplets. The initial site of infection is the upper respiratory tract. The virus spreads to local lymph nodes and then via the bloodstream to other organs, especially the parotid glands, testes, ovaries, meninges, and pancreas. -Clinically: a prodromal stage of fever, malaise, and anorexia is followed by tender swelling of the parotid glands, either unilateral or bilateral. There is a characteristic increase in parotid pain when drinking citrus juices. -Complication: -orchitis (Sterility due to bilateral orchitis is a rare) - meningitis -pancreatitis Prevention:Vaccine contains live, attenuated virus. Usually given in combination with measles and rubella vaccines MMR. Given - 84 -
subcutaneously to children at 15 months of age. The vaccine is effective and long-lasting (at least 10 years) and causes few side effects. Rubella Virus Characteristics: Rubella virus is a RNA Enveloped virus. Pathogenesis:-Transmission by 1) Respiratory droplets 2) across the placenta from mother to fetus - During maternal infection, the virus replicates in the placenta and then spreads to fetal tissue. If infection occurs during the first trimester, a high frequency of congenital malformations occurs.
The virus has
teratogenic properties infecting the fetus where it stops cells from developing or destroys them. Clinically: Rubella (German measles): After an incubation period of 14 to 21 days, a brief prodromal period with fever and malaise. A maculopapular rash, which starts on the face and progresses downward to involve the extremities. The rash typically lasts 3 days. Posterior auricular lymphadenopathy is characteristic. -Congenital
rubella
syndrome
is
characterized
by
congenital
malformations, especially affecting the cardiovascular and central nervous systems, and by prolonged virus excretion. Prevention: Vaccine contains live, attenuated virus. Usually given in combination with measles and mumps vaccine MMR. It is given subcutaneously to children at 15 months of age (usually in combination with measles and mumps vaccine) and to unimmunized young adult women. - 85 -
Influenza Virus Pathogenesis: Enveloped RNA virus and segmented RNA genome. It has two major antigens are the hemagglutinin (HA) and the neuraminidase (NA). Transmission by respiratory droplets. Uncomplicated influenza: Fever (38 - 40 °C) myalgias, headache ocular symptoms photophobia, tears dry cough nasal discharge Pulmonary complications: Croup
(acute laryngotracheobronchitis) in young
Primary
influenza virus pneumonia
Secondary
bacterial infection: This often involves Streptococcus
pneumoniae, Staphylococcus aureus, Hemophilusinfluenzae H1N1 Swine Flu Swine flu variants do sometimes spread to humans and in 2009, a new H1N1 swine flu started to circulate. H5N1 Avian Flu There is concern about a recent outbreak of avian influenza due to a strain of H5N1 influenza A virus . This bird virus seems to be able to infect humans. The case fatality rate is high (~60%) in humans. - 86 -
Treatment: oseltamivir (Tamiflu), is the drug of choice. Prevention:-Vaccines available: The killed vaccine : must be given annually. The vaccine against "standard" influenza contains two A strains (H1N1 and H3N2) and one B strain.
Chicken poxvirus Cause: Varicella-Zoster Virus It causes varicella (chickenpox) in children and zoster (shingles) in adults. Pathogenesis: Transmission: Varicella is transmitted primarily by respiratory droplets. Zoster is not transmitted; it is caused by a reactivation of latent virus, especially in older and immunocompromised individuals. Clinically: Varicella: A papulovesicular rash appears in croups on the trunk and spreads to the head and extremities. Fever and malaise. Shingles (Zoster): occurs in immunocompromised adults. It results from reactivation of latent VZV later in life at times of reduced cell-mediated immunity or local trauma. The virus affects the sensory nerves and ganglia leading to severe pain in the area supplied by these nerves, then crops of vesicles appear over the skin supplied by the affected nerves. The eruptions are unilateral, affecting the trunk and neck. Prevention: Both the varicella vaccine and the zoster vaccine contain live, attenuated varicella-zoster virus.
- 87 -
SEXUALLY TRANSMITTED DISEASES
C. Viral A. Bacterial
Genital herpes (HSV)
Gonorrhea (Neisseria
Genital warts (condyloma
gonorrhoeae)
acuminata) (HPV)
Syphilis
Human immunodeficiency
(Treponemapallidum)
virus (HIV)
Chancroid (Haemophilus
Hepatitis C
ducreyi)
Hepatitis B
Chlamydia
Hepatitis D
(Chlamydiatrachomatis) Non gonococcal urethritis
D. Parasitic
(Ureaplasma urealyticum).
-Pubic lice (Pediculosis
B. Protozoal
pubis)
Trichomoniasis
-Scabies (itch mites)
(Trichomonas vaginalis)
Neisseria gonorrhoeae (Gonococcus) Disease: Gonorrhea. Characteristics:
Gram-negative
"kidney-bean
shaped"
diplococci.
Oxidase-positive. Pathogenesis: Transmission in adults is by sexual contact. Gonorrhea in men is characterized: 1) urethritis accompanied by dysuria and a purulent discharge. - 89 -
2) Epididymitis can occur. In women, infection is located primarily in the endocervix, causing : 1. a purulent vaginal discharge and intermenstrual bleeding (cervicitis). 2. The most frequent complication in women is an ascending infection of the uterine tubes (salpingitis, PID), which can result in sterility or ectopic pregnancy as a result of scarring of the tubes. Laboratory Diagnosis: Specimen: Male; urethral discharge. Females; urthral and cervical discharge. 1. Acute gonorrhea in male:Gram-stained smear of the urethral discharge is diagnostic if it shows Gram-negative "kidney-bean" diplococci intra and extra cellularly. 2. Culture on chocolate agar in 5-10% CO2. 3. Biochemically: Oxidase-positive colonies Prevention: Condoms offer protection. Trace contacts and treat to interrupt transmission. Treponema pallidum It causes syphilis Treponema pallidum is Spirochetes. Not seen on Gram-stained smear because organism is too thin.
Not cultured in vitro.
Pathogenesis: T. pallidum is transmitted by 1) intimate contact 2) Sexually 3)from pregnant women to their fetuses - 90 -
4) by blood transfusions. .Clinically: 1) primary syphilis, the Spirochetes multiply at the site of inoculation and a local, non-tender ulcer (chancre) usually forms in 2 to 10 weeks. 2) secondary syphilis may occur One to three months later, appear as a maculopapular rash, on the palms and soles moist papules on skin and mucous membranes (mucous patches). 3) latent syphilis i.e., no lesions appear, but positive serologic tests indicate continuing infection. 4)Tertiary syphilis may show granulomas (gummas central nervous system involvement (e.g., tabes, paresis) cardiovascular lesions (e.g., aortitis, aneurysm of the ascending aorta). In tertiary lesions, treponemes are rarely seen. 5)T. pallidum also causes congenital syphilis Laboratory Diagnosis Microscopy: Spirochetes are demonstrated in the lesions of primary or secondary syphilis by darkfield microscopy by direct fluorescent antibody (DFA) test. Serology: Nonspecific Serologic Tests: (screening tests) VDRL (Venereal Disease Research Laboratory) RPR (rapid plasma reagin) tests Specific Serologic Tests (confirmatory tests) - TPHA (Treponema Palladium Hem-Agglutination)) assays with - 91 -
URINARY TRACT INFECTIONS (UTI) Causative organisms Bacterial : 1)-Escherichia
Fungal : coli:
the
commonest
1) Candida albicans
urinary pathogen causing 60-90 % of Protozoal: urinary infections
1) T. vaginalis
2)Klebsiella
2) S. haematobium
3) Proteus: associated with renal stones 4)-Pseudomonas: associated with hospital acquired infections 5)S. aureus(upper UTI) 6) S. epidermidis(catheter) 7) S. saprophyticus 8) Enterococci (Strept. faecalis) 9)Mycobacterium tuberculosis
Risk factors: Stone Abnormal urinary tract sexual activity in female chronic disease as diabetes mellitus Clinically: The most common symptoms are 1) Dysuria( burning with urination) - 92 -
2) pelvic pain 3) flank pain 4) fever 5) nausea and vomiting Diagnosis: A ‘mid stream’ urine sample. The urine sample can be obtained by catheterization or suprapubic aspiration. Urine analysis: High number of Pus cells . Urine culture: Significant bacteriurea: Bacterial count > 105CFU/ml is suggestive of UTI.
- 93 -
ZOONOSIS A zoonosis is any infectious disease that can be transmitted (in some instances, by a vector) from animals to humans or from humans to animals (the latter is sometimes called reverse zoonosis or anthroponosis). A. Bacterial
C. Viral
Plague
Yellow fever
Anthrax
Ebola
Brucellosis
H1N1 flu
Bovine tuberculosis
Dengue fever
Escherichia coli O157:H7
Rabies
Psittacosis
Rift Valley fever
Typhus
"mad cow disease"
Francisella tularensis
D. Protozoal Toxoplasmosis
B. Fungal:
Dermatophytes
Brucella Species 1. Brucellae affect animals and human. 2. Small gram-negative rods. 3. It causes brucellosis (undulant fever or Malta fever). Pathogenesis: Reservoir is domestic livestock. Transmission either by ingestion of contaminated milk products or through the skin by direct contact in an occupational setting such as an abattoir. They replicate intracellularly. - 94 -
Clinically: -After an incubation period of 1 to 3 weeks, nonspecific symptoms such as fever, chills, fatigue, malaise, anorexia, and weight loss occur. The onset can be acute or gradual. -The undulating (rising-and-falling) fever pattern that gives the disease its name occurs in a minority of patients. -Enlarged lymph nodes, liver, and spleen are frequently found. - Osteomyelitis is the most frequent complication. Laboratory Diagnosis: During the periods of fever: Blood culture Brucella agglutination test : to detect brucella antibodies. Prevention: Pasteurization of milk Vaccination of cattle. No human vaccine is available.
Yersinia pestis Small gram-negative rods with bipolar ("safety pin") staining. Causes plague الطاعون. Pathogenesis: Reservoir is wild rodents, e.g., rats. Transmission is by flea bite Clinically: The organisms inoculated at the time of the bite spread to the regional lymph nodes, which become swollen and tender. These swollen lymph nodes are the buboes that have led to the name bubonic plague. The organisms can reach high concentrations in the blood (bacteremia) and disseminate to form abscesses in many organs. Death from septicaemia. - 95 -
Prevention: - Control rodent population and avoid contact with dead rodents. - Killed vaccine is available for persons in high-risk occupations. - Close contacts should be given tetracycline. VERTICAL TRANSMISSION This includes Diseases Transmitted From Mother To Fetus Or Newborns. Viruses Bacteria 1. CMV 1) Congenital syphilis (T. 2. Congenital rubella syndrome pallidum) (Rubella virus) 2) Neisseria gonorrheae 3. Parvovirus B19 3) Chlamydia trachomatis 4. HBV 4) Group b streptococci 5. HCV 5) E.coli 6. HSV2 Protozoa 7. HIV 1. Toxoplasmosis (Toxoplasma "Protozoa) HPV
N. B) Diseases Transmitted By breast feeding: 1)CMV 2)HIV 4)Ebola Herpes Simplex Virus Type Characteristics: Enveloped DNA virus . Pathogenesis: HSV-1: Transmission by saliva or direct contact with virus from the vesicle. HSV-2: Sexual contact in adults and during passage through the birth canal in neonates. - 96 -
HSV-1: Initial vesicular lesions occur in the mouth or on the face. Recurrences are induced by fever, sunlight, stress, etc. Clinically: HSV-1: Herpes labialis (fever blisters or cold sores), keratitis, encephalitis. HSV-2: Herpes genitalis, aseptic meningitis, and neonatal infection. There is no vaccine. Cytomegalovirus Transmission: Virus is found in many human body fluids, including blood, saliva, semen, cervical mucus, breast milk, and urine. It is transmitted via contact with these fluids, across the placenta, or by organ transplantation. Pathogenesis: Initial infection usually in the oropharynx. In fetal infections, the virus spreads to many organs, e.g., central nervous system and kidneys. Diseases: 1. It causes cytomegalic inclusion body disease in infants: jaundice, with hepatosplenomegaly, peumonitis and CNS damage. 2. In adults it can cuse Pneumonia and hepatitis in immunocompromised patients. Retinitis and enteritis, especially in AIDS patients. 3. Disseminated infection in immunocompromised patients can result from either a primary infection or reactivation of a latent infection. Laboratory Diagnosis Viral culture "Owl's eye" nuclear inclusions are seen in urinary sediment. CMV IgM No vaccine is available.
- 97 -
References: Abla M. El-Mishad: Manual of Medical Microbiology & Immunology volume I 7th edition, 2008, El-Ahram Press Egypt. Brooks, G.F., Carroll, K.C., Butel, J.S., Morse, S.A. and Mietzner, T.A. (2013:) Medical Microbiology. Jawetz, Melnick and Adelbergs, 26th Edition, McGraw-Hill Companies. Harvey, A. R., Cornelissen C. N.,and Fisher B. D.(2013): Lippincott,s Illustrated Reviews: Microbiology 2nd edition, Lippincott, Williams&Wilkins. Levinson, W. (2014): Review of Medical Microbiology and Immunology, 13th Edition, , McGraw-Hill Companies Wilkpedia, the free encyclopedia, 2012.http://en.wikipedia.org.
The Author: Dr Ayman A. Allam Current Job: Professor of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Egypt Qualifications:
MBBCH with grade very good with honor in Faculty of Medicine, Zagazig University.11,1990. Master degree of Microbiology and Immunology with estimate excellent in Faculty of Medicine, Zagazig University, Session 4/1997. Title of thesis was (Infection control in Zagazig University Surgery Hospital). MD of Microbiology and Immunology in Faculty of Medicine, Zagazig University, Session 11/2001. Title of thesis was (Study of HLA Typing Type II (DRBI) by PCR in Egyptian Rheumatoid Arthritis Patients). Diploma of Internal Medicine with estimate very good, Faculty of Medicine, Al-Azhar University, Session 11/2003.
Fields of Interest (Career Wise):
Infectious diseases Microbiology Allergy and immunology Antimicrobial resistance
Membership of Societies and Associates:
Egyptian Society of Medical Microbiology and Immunology The Egyptian society of Allergy and Clinical Immunology
Registration: In Egyptian Medical Syndicate as 1. Consultant Microbiology 2. Consultant Allergy and Immunology 3. Internal medicine specialist
In Saudi Commission for Health Specialties as 1. Consultant Microbiology and Immunology
