Microbiology

• ILOs:
• Definition of meningitis, Common pathogens causing bacterial
meningitis and diagnosis.
• Definition of pneumonia, common pathogens causing pneumonia and
diagnosis.
• Definition of infectious diarrhea / food poisoning, common pathogens
and diagnosis.
• Definition of urinary tract infection, Common pathogens causing UTIs
and diagnosis.
• Anti-microbial chemotherapy.
Meningitis
• Meningitis is an infection or inflammation of the meninges, which is
the connective tissue covering the central nervous system (CNS).
•Common pathogens causing bacterial
meningitis:
• 1- Streptococcus pneumoniae is the most common cause of
bacterial meningitis for all patients beyond the neonatal period.
• 2- Neisseria meningitidis, spread by respiratory droplets, is the
most common cause of meningitis in adolescents.
• 3- In the past, Haemophilus influenzae was the most common
cause of meningitis in children, but this has markedly decreased with
the Haemophilus type B vaccine.
• 4- Group B Streptococcus (Streptococcus agalactiae) is the most
common cause of meningitis in the neonatal period.
• 5- Listeria monocytogenes is more common in those with immune
system defects.
Diagnosis:

• Patients usually present with fever, photophobia, headache, nuchal

rigidity (neck stiffness, positive Kernig and Brudzinski signs), as well as
nausea and vomiting. Altered mental status is possible.
• A specimen of cerebrospinal fluid (CSF) should be obtained for cell
count and differential, glucose and protein concentration, Gram stain,
and culture. Characteristic findings in bacterial meningitis include
decreased glucose concentration, elevated protein and white blood
cell count in the CSF.
• The most accurate test for bacterial
meningitis on the lumbar puncture is the
culture of the CSF
• The Gram stain has a limited sensitivity
and is positive in 50–70% of patients at
most. When positive, however, the Gram
stain has a high degree of specificity.
Diagnosis:

• Patients usually present with dysuria, urinary frequency, urinary urgency,

and/or suprapubic pains. Pyuria (the production of urine that contains
white blood cells) is commonly found in UTIs. Fever or flank tenderness
could indicate pyelonephritis.
• Best initial test is the urinalysis looking for WBCs, RBCs, protein, and
bacteria; WBCs are the most important.
• Nitrites are indicative of gram-negative infection.
• A count of <5 WBCs is normal.
• A count of 100,000 colonies of bacteria per mL of urine confirmatory but
not always necessary with characteristic symptoms and a positive
urinalysis.
Pneumonia
• Pneumonia is an infection of the lung parenchyma.
• Common pathogens causing pneumonia:
• 1- The most common cause of community-acquired pneumonia in
all groups is S. pneumoniae when an actual cause is identified
(however, viruses are the most common cause in children age <5).
• 2- Hospital-acquired or ventilator-associated pneumonia shows a
predominance of gram-negative bacilli such as E. coli, the other
Enterobacteriaceae, or Pseudomonas, as well as MRSA.
 Frequency of infectious agents causing
pneumonia
“Typical” 40 – 60%

Strep pneumoniae 15 – 35%

Haemophilus 2 – 10%

Moraxella < 5%

“Atypical” 10 – 30%

Legionella 0 – 15%

Mycoplasma 10%

Chlamydia 5 – 10%

Viral 2 - 20%

Unknown 30 – 60%
Diagnosis

• Sputum culture is the most specific diagnostic test for lobar pneumonia,
such as with S. pneumoniae, Staphylococcus, Klebsiella, and Haemophilus.
• Organism-specific diagnostic methods are as follows:
• Mycoplasma—Specific serologic antibody titers. Cold agglutinins have
both limited specificity and sensitivity.
• Legionella—Specialized culture media with charcoal yeast extract,
urine antigen tests, direct fluorescent antibodies, and antibody titers.
• Chlamydia pneumoniae, Coxiella, Coccidioidomycoses, and Chlamydia
psittaci—All of these are diagnosed with specific antibody titers.
 INFECTIOUS
DIARRHEA/FOOD
POISONING
• Most infectious diarrhea is caused by contaminated food and water,
so the overlap between infectious diarrhea and food poisoning is
considerable. There are several types of food poisoning, such as
Bacillus cereus and Staphylococcus aureus, which present
predominantly with vomiting, so the two terms are not entirely
synonymous.
Common pathogens causing

• A wide variety of agents can cause food poisoning.

1- Campylobacter (most common)
2- Salmonella (most commonly associated agent with contaminated
poultry and eggs)
3- E. coli (most common cause of travelers’ diarrhea; produces a
wide spectrum of disease depending on whether it makes toxin or is
invasive)
• E. coli 0157:H7 is associated with undercooked hamburger meat.
• 4- Bacillus cereus is associated with fried rice; the rice becomes
contaminated with bacillus spores, and as it is prepared for serving it
is warmed only at a moderate temperature not hot enough to kill the
spore.
• 5-Viral infections such as rotavirus or Norwalk agents are most
commonly associated with outbreaks in children.
• 6-Clostridia associations are as follows:
• C. difficile with previous antibiotic use
• C. botulinum with ingestion of infected canned foods
• C. perfringens with ingestion of meat contaminated with spores
due to unrefrigeration
Diagnosis:

• When there is no blood present in the stool, determine the etiology

of the diarrhea via a stool test for the presence of WBCs with
methylene blue testing.
• WBCs will indicate that there is an invasive pathogen, but only a
culture will identify the specific type.
• Giardia and Cryptosporidia are detected by direct examination of the
stool for the parasites, as well as for their eggs.
• A special modified acid fast bacilli (AFB) stain is necessary to detect
Cryptosporidia. Stool ELISA is also used for Giardia.
URINARY TRACT
INFECTIONS
• Urinary tract infections (UTIs) most commonly affect either the lower
urinary tract (infection of the urethra or bladder) or, less frequently,
the upper urinary tract (acute pyleonephritis, or infection of the
kidney).
Common causes and classification of pathogens causing UTI:

• 1-Escherichia coli: the most common cause (70-95% of infections) in

young women
• 2-Staphylococcus saprophyticus: second to E. coli, causing (5 to 20%
of infections).
• 3- Klebsiella species
• 4-Proteus species
• 5-Pseudomonas aeruginosa.
Diagnosis

• Patients usually present with dysuria, urinary frequency, urinary urgency,

and/or suprapubic pains. Pyuria (the production of urine that contains
white blood cells) is commonly found in UTIs. Fever or flank tenderness
could indicate pyelonephritis.
• Best initial test is the urinalysis looking for WBCs, RBCs, protein, and
bacteria; WBCs are the most important.
• Nitrites are indicative of gram-negative infection.
• A count of <5 WBCs is normal.
• A count of 100,000 colonies of bacteria per mL of urine confirmatory but
not always necessary with characteristic symptoms and a positive
urinalysis.
 Anti-microbial chemotherapy

• An ideal antimicrobial agent exhibits selective toxicity, this term

implies that a drug is harmful to a pathogen without being harmful to
the host.
• The mechanism of action of most anti-microbial drugs can be
summarized under four headings.
1-Inhibition of cell wall synthesis: examples; bacitracin, penicillins,
cephalosporins, cycloserine, ristocetin, vancomycin.

2- Alteration of cell membrane permeability: examples; amphotericin B,

colistin, imidazoles, nystatin, polymyxins.
3-Inhibition of protein synthesis: examples; chloramphenicol,
Erythromycins, lincomycins, tetracyclines, aminoglycosides (amikacin,
garamycin, gentamycin, neomycin, netlimicin, streptomycin, tobramycin,
kanamycin).

4-Inhibition of nucleic acid synthesis: examples; nalidixic acid, novobiocin,

rifampin, sulfonamides, trimethoprim, pyrimethamine
 Antibiotic Sensitivity Test

Antibiotic sensitivity testing is used to determine the susceptibility of

bacteria to various antibiotics. This standardized test is used to measure the
effectiveness of a variety of antibiotics on a specific organism in order to
prescribe the most suitable antibiotic therapy.
• It includes:
I- Kirby-Bauer test (disk diffusion method)
II-Epsilometer or “E” test
III- Automated methods.
 Dangers of indiscriminate use of antibiotics

1- The drugs may cause hypersensitivity reactions e.g. penicillins and

cephalosporines.
2- Emergence of resistant strains due to inadequate dosage or improper
treatment. The problem is very serious in hospitals because the development of
resistant mutants in a patient can be transmitted to other patients particularly
severely ill and elderly patients.
3- Changes in the normal flora of the body leading to superinfection due to
growth of drug-resistant organisms.
4- Masking serious infection without eradicating it.
5- Direct drug toxicity particularly in prolonged use of antibiotics. Important
examples are aplastic anaemia due to chloramphenicol and renal damage or
auditory nerve damage due to aminoglycosides.
 Precauations to prevent emergence drug resistance

• Antimicrobial drugs intended for bacterial infections should not be taken for viral
infections such as colds, coughs or the flu.

• Raising awareness among healthcare providers not to prescribe antimicrobials for

non-bacterial infection.

• Raising pubic awareness about proper use of antibiotics. very low consumption of
antibiotic lead to the lowest prevalence of resistance.
• Maintain sufficiently high levels of the drug in tissues for full course to inhibit the
emergence of mutations.

• Combination of drugs should be administered in severe infections.

• Avoid exposure of microorganisms to valuable antibiotics in hospitals and should be

restricted to severe infections.

• Restrict the use of antimicrobial drugs in animal feeds and agriculture. The continuous
use of low- level doses of antimicrobials in animal feeds for prophylaxis results in the
development of resistant bacteria that can infect humans.

• Lack of education in developing countries: many patients purchase antibiotics without

visiting health worker first. This is a perfect ground for development of bacterial
resistance.