Appendix F Normal and Pathogenic Flora

When do skin/surface would infection often occur

when the skin barrier is broken by trauma

Why do pathogenic bacteria not survive long on skin

an inhibitory acid pH is produced on the skin by the long chain fatty acids found in the sebaceous glands

What do gram pos organisms do to the long chain fatty acids

they convert the fatty acids and lipids to unsaturated fatty acids, which have an inhibitory effect against gram neg bacteria and certain bacteria

What organisms are normal flora to skin

• coagulase negative Staphylococcus

• non-hemolytic Streptococcus

• Viridans group Streptococci

• Anaerobes

• Diphtheroids/coryneforms

• Enterococcus sp

• Bacillus sp (other than B. anthracis)

What organisms are pathogens to skin

• Staphylococcus aureus

• Candida spp

• Arcanobacterium haemolyticum

• Pasteurella spp

• B hemolytic Streptococci

• Pseudomonas aeruginosa

• Corynebacterium diphtheriae

• Staphylococcus intermedius/pseudintermedius

What organisms are potential pathogens to skin

• Enterobacterales

• Anaerobes

• Bacillus cereus

• Enterococcus spp

• Non-fermentative bacilli (other than P. aeruginosa)

boils/furuncles definition

usually caused by S. aureus and often result when a hair follicle or sebaceous gland becomes blocked

carbuncles definition

a more extensive invasion of the skin by S. aureus comprising multiple draining sinuses. They are found frequently on the back and neck, measuring up to several inches in diameter

impetigo definition

a form of pyoderma or purulent skin disease, due either to S. pyogenes or S. aureus and occur almost exlusively in children during warm weather

eysipelas definition

an acute and rapidly spreading inflammation of the superficial layers of the skin caused by S. pyogenes. These lesions are sharply defined

pyoderma definition

a pyogenic (pus-forming) lesion of the skin

What structures are included in the URT

from the larynx and up (mouth/oral, nose/nasal, throat)

What organisms are normal flora to URT

• a and non-hem Streptococci

• Haemophilus spp

• Streptococcus pneumoniae

• Diphtheroids/coryneforms

• Staphylococcus spp

• anaerobes

• Micrococcus spp

• Enterobacterales

What causes more than 80% of acute URT infection in adults

viruses

What % of all resp tract infection can be treated with antibiotics

80%

What organisms are pathogens to mouth

• Candida spp

• Streptococcus pyogenes (if wound present)

thrush definition

candidiasis of the mouth characterized by white or gray patches of exudate lying on an acutely inflamed mucosa

Vinvent’s Angina definition

painful infection of the mouth, throat and tonsils caused by spirochetes and fusiform bacteria. Identified by direct smear (trech mouth)

What organisms are pathogens to nose

• Staphylococcus aureus

• Streptococcus pyogenes (pure or predominant growth)

sinusitis definition

acute inflammatory infection of one or more of the paranasal sinuses

rhinitis definition

nasal catarrh, inflammation of the nasal mucous membranes - usually viral

What organisms are pathogens to throat/pharynx

• Streptococcus pyogenes

• Group C & G Streptococci

• Arcanobacterium haemolyticum

• Corynebacterium diphtheriae (special request)

• Haemophilus influenzae — (epiglottitis)

• Neisseria gonorrhoeae (special request requires charcoal swab)

pharyngitis definition

inflammation of the mucous membrane and underlying parts of the pharynx (‘strep throat’)

How are ocular infections divided

• external structures (eyelids, conjunctiva, sclera and cornea)

• internal sites

What are the major defense mechanisms of the eye

tears and conjuctiva, as well as the mechanical cleansing that occurs with the blinking of the eyelids

How is the internal eye protected from external invasion

primarily by the physical barrier imposed by the sclera and cornea

How can eye infections occur

penetrating injury, ulceration, via blood

What organisms are normal flora to eye

• Non-hemolytic Streptococcus

• Diphtheroids/coryneforms

• Cutibacterium acnes

• Viridans group Streptococci

• Coagulase negative Staphylococcus

• Anaerobic Gram positive cocci

What organisms are pathogens to eye

• Pseudomonas aeruginosa *CRITICAL*

• Bacillus cereus *CRITICAL*

• Neisseria meningitidis *CRITICAL*

• Neisseria gonorrhoeae *CRITICAL*

• Fungus *CRITICAL*

• B hemolytic Streptococci

• Candida spp

• Haemophilus spp

• Moraxella catarrhalis

• Streptococcus pneumoniae

• Staphylococcus aureus

• Enterobacterales (may be colonizers)

• Haemophilus parainfluenzae (may be colonizer)

• Gram neg non-fermentative bacilli (may be colonizers)

blepharitis definition

inflammation of the eyelids

conjuctivitis definition

inflammation of the conjuctiva

keratoconjunctivitis definition

inflammation of the cornea and conjunctiva

ophthalmia neonatorum definition

any hyperacute purulen conjuctivitis occurring during the first ten days of life; usually contracted during birth from infected vaginal discharge of the mother. Most often associated with N. gonorrhoeae

dacryocystitis

inflammation of the lacrimal sac

endophthalmitis definition

infection of the aqueous or vitreous humour. Rare, but often leads to blindness

What areas of the ear should be sterile

middle and inner ear (specimens from behind the tympanic membrane)

How do infections of the ear usually occur

frequently caused by upper respiratory tract organisms, which travel from the nasopharynx to the ear via the Eustachian tube

What organisms are normal flora to ear

• Non-hemolytic Streptococcus

• Diphtheroids/coryneforms

• Non-hemolytic Streptococci

• Bacillus spp (other than B. anthracis)

• Coagulase negative Staphylococcus

• Enterococcus spp (unless recent surgery)

• anaerobes

What organisms are pathogens to ear

• B hemolytic Streptococci

• Pseudomonas aeruginosa

• Candida spp

• Streptococcus pneumoniae

• Haemophilus influenzae

• Staphylococcus aureus

• Moraxella catarrhalis

• Enterobacterales (may be colonizers)

• other non-fermentative bacilli (may be colonizer)

• Haemophilus parainfluenzae (may be colonizer)

• Staphylococcus lugdunensis

• Staphylococcus intermedius/pseudintermedius

otitis media definition

inflammation of the mucosal lining of the middle ear - a common infection of children - frequently secondary to a viral respiratory disease. Streptococcus pneumoniae and Haemophilus influenzae are the agents most often isolated

otitis externa definition

common skin disorder of diverse etiology that affects the external auditory meatus and auricle of the ear - P. aeruginosa (swimmer’s ear) and Streptococcus pyogenes are most often isolated

What structures are included inthe LRT

all structures below the larynx, the trachea, bronchi, bronchioles, and the alveoli

How are LRT specimens not get contaminated with normal flora from throat or mouth

suction or more invasive procedures

Isolation and identification of organisms in the LRT should relate to what

what is seen on the direct smear

What organisms are normal flora to LRT

• Non-hemolytic Streptococcus

• Diphtheroids/coryneforms

• Enterococcus spp

• Micrococcus spp

• Viridans group Streptococci

• Bacillus spp

• Coagulase negative Staphylococcus

• anaerobes

What organisms are pathogens to LRT

• Streptococcus pyogenes

• rare organisms including level III: Bacillus anthracis, Brucella spp, dimorphic fungi, etc

What organisms are potential pathogens to LRT

• Streptococcus pneumoniae

• Moraxella catarrhalis

• B hemolytic Streptococcus (B, C, and G)

• Pseudomonas aeruginosa

• Candida spp

• other non-fermentative bacilli

• Enterobacterales

• Staphylococcus aureus

• Haemophilus influenzae/parainfluenzae

acute infections bronchitis definition

inflammation of the mucous membrane of the bronchial tubes. generally associated with Influenzae or Adenoviruses. may be a secondary complication of bacterial pneumoniae

chronic bronchitis definition

non-specific disease characterized by chronic and recurrent cough with expectoration; usually associated with cigarette smoking, air pollution, and chronic obstructive pulmonary diseases (COPD). found mainly in older people

bronchiolitis definition

inflammation of the smallest bronchial tubes (bronchiles); usually caused by viruses, especially RSV (respiratory synytial virus); in children less than 1 year

pneumoniae (bacterial) definition

inflammation of the lungs characterized by exudation into the alveoli (consolidation)

pneumonia (viral) definition

characterized by high fever, cough and relatively few physical signs - bronchiolitis and interstitial mononuclear and granulocytic infiltration; more insidious onset than bacterial

When is bacterial flora of the GI tract established

within several weeks of birth

What factors prevent disease of the GI tract

acidity of stomach, peristalsi and eosinophils

How does the stomact prevent any significant colonization

acid conditions of the stomach (pH 2-3)

What bacteria is strongly associated with gastric, peptic, and duodenal ulcers

Helicobacter pylori

Is culture performed on Helicobacter pylori for diagnosis

no

The lower part of the small intestine reflects the flora of the colon with what

abundant representatives of the Enterobacterales and anaerobes

What is found 20 to 40% of the time in the small intestine

Candida albicans

When does C. albicans rapidly replace normal flora of the small intestine

when broad-spectrum antibiotics are given

Where is the larest microbial flora of the body

large intestine

The majority of large intestine organisms are what

anaerobes, which outnumber the Enterobacterales 300 to 1

What organisms are normal flora to GI tract

• Enterobacterales

• anaerobes

• Enterococcus sp

• Coagulase negative Staphylococcus

• Diphtheroids/coryneforms

• Candida spp

What organisms are obligate pathogens to GI tract

• Aeromonas spp

• Plesiomonas shigelloides

• Campylobacter jejuni & coli

• Salmonella enterica / spp

• Yersinia enterocolitica

• Vibrio spp

• E. coli 0157 & other shiga-toxin producing organisms

• Shigella spp

What organisms are causes of food poisonings to GI tract

• Staphylococcus aureus

• Bacillus cereus

• Clostridium botulinum

• Clostridium perfringens

Why is culture rarely performed for organisms causing food poisonings

toxin is ingested, organism is not causing infection

dysentery definition

inflammation of the mucosa of the large intestine

cholecystitis definition

inflammation of gall bladder

enteritis definition

inflammation of intestine, chiefly the small intestine

gastritis definition

inflammation of stomach

enterocolitis definition

inflammation on small intestine and colon

gastroenteritis definition

inflammation of stomach and intestinal tract

colitis definition

inflammation of colon

What areas of the urinary tract are bacteria free

kidneys, ureters, and bladder

How are specimens for urine collected

by the “clean catch” or “midstrean urine (MSU)” technique

When are specimens for urine collected

first thing in the morning and if possible, prior to antimicrobial therapy

Side effects of catherization in urine collection

used as an attempt to acoid contamination but occasionally leads to infection itself. indwelling catheters are notoriously related to gram neg bacteriuria and sepsis (patients routinely become “colonized”)

What method is useful for urine collection from babies and is the only technique used for suspected anaerobic infections

suprapubic needle aspiration

What organisms are contaminating flora to urine

• Non-hemolytic Streptococcus

• Diphtheroids/coryneforms

• Coagulase negative Staphylococcus

• Lactobacillus spp

• Viridans group Streptococci

• Neisseria spp

What organisms are pathogens to urine

• Enterobacterales

• Enterococcus spp

• B hemolytic Streptococcus (A and B)

• Staphylococcus aureus

• Pseudomonas aeruginosa

• Staphylococcus saprophyticus

• Haemophilus spp

• Staphylococcus intermedius/pseudintermedius

• Streptococcus pneumoniae

• Aerococcus spp

• Candida spp

• other non-fermentative bacilli

• Group C or G Streptococci

cystitis definition

infmattion of the bladder

dysuria definition

abnormalities in urination including pain, burning, frequency, urgency, dripping and pyuria

glomerulonephritis definition

inflammation of kidney glomeruli. thought to be an allergic or hypersensitivity reaction after infection by S. pyogenes

non-specific urethritis definition

inflammation of the urethra

pyelonephritis definition

inflammation of both the kidney and pelvis of the kidney (parenchyma)

The adult female genital tract has a complex microbial flora that changes with what

the variation of the menstrual cycle

Role of Lactobacillus acidophilus in female vagina

maintains the pH of the vagina at 4.4 to 4.6 by production of lactic acid from glycogen, which in turn is produced by the epithelial cells. this low pH keeps E. coli and other organisms of the GI to not grow

Does the cervix house many normal bacterial flora

no, the cervix is generally sterile or contains only a few bacteria because of its alkaline pH. flora in the upper vagina is similar to that of the cervix

What can be helpful in identification of infection (vaginal, cervical, urtheral) outside of BV

Direct smear results, which can lead to full culture of the specimen for investigation

What clues suspect a bacterial infection

high PMNs and intracellular bacteria

What organisms are normal flora to genital tract

urogenital / genial flora — similar to urine / skin flora

What organisms are pathogens to genital tract

• Gardnerella vaginalis

• Bacteroides spp

• S. pyogenes

• Staphylococcus aureus

• Trichomonas vaginalis

• Candida spp

• Neisseria gonorrhoeae (cervix preferred)

What organisms are possible pathogens to genital tract

• B strep — B, C & G

• Enterobacterales

• Pseudomonas aeruginosa

• L. monocytogenes

• H. influenzae & parainfluenzae

bacterial vaginosis definition

imbalance of normal flora. a decrease in lactobacilli; increase in Gardnerella spp, and anaerobes

cervicitis definition

inflammation of the cervix or the external uterine opening. Often caused by N. gonorrhoeae, anaerobic organisms, Chlamydia or Herpes virus

genital ulcers definition

caused by Treponema pallidum, Haemophilus ducreyi, Chlamydia trachomatis

non-gonococcal urethritis definition

rarely a concern in females. Agents: Chlamydia, Trichomonas, Herpes, Ureaplasma urealyticum

prostatitis definition

inflammation of the prostate glands by extention of gonococcal urethritis or urinary tract infection, mostly in older men — Enterobacterales, P. aeruginosa, Enterococci