Most Commonly Found Pathogens: Introduction, List of Common Samples and Common Pathogens Found

Introduction of Most Commonly Found Pathogens

Here we are discussing the most commonly found pathogens in our clinical samples. e.g. urine, blood, sputum, etc. The list of common specimens/samples encountered in the Clinical Microbiology Laboratory is given below-

1. Urine
2. Sputum
3. Pus
4. Eye swab
5. Body fluid (CSF, pleural fluid, ascitic fluid, and others)
6. Throat swab
7. Stool
8. HVS, Vaginal Swab, Endocervical swab, and Urethral discharge
9. Ear Swab
10. Blood culture

Urine

Most Commonly Found Pathogens in the Urine sample are-

• Escherichia coli
• Klebsiella pneumoniae
• Staphylococcus saprophyticus
• Enterococcus faecalis
• Group B Streptococci (Streptococcus pyogenes and Streptococcus agalactiae),
• Proteus mirabilis
• Pseudomonas aeruginosa
• Staphylococcus aureus
•  Candida species

Sputum

Most Commonly Found Pathogens in the sputum are-

• Klebsiella pneumoniae
• E. coli
• Acinetobacter baumanii
• Enterobacter cloacae
• Staphylococcus aureus
• Pseudomonas aeruginosa
• Enterobacter freundii
• Proteus mirabilis
• Haemophilus influenzae
• Klebsiella oxytoca

Pus

Most Commonly Found Pathogens in the pus are-

Gram-positive cocci

• Beta Haemolytic Streptococci (Streptococcus pyogenes and Streptococcus agalactiae)
• Enterococci (Enterococcus faecalis)
• Staphylococcus aureus
• Methicillin-Resistant Staphylococcal aureus (MRSA)

Gram-negative aerobic rods

• Pseudomonas aeruginosa

Gram-negative facultative rods

• Enterobacter species
• Escherichia coli
• Klebsiella species
• Proteus species

Anaerobes

• Bacteroides
• Clostridium

Fungi

• Candida
• Aspergillus

Eye swab

Most Commonly Found Pathogens in the ear swab are-

Viral conjunctivitis
Adenovirus (Predominant pathogen)
Herpes simplex( Occasional)
Zoster virus( Occasional)

Bacterial conjunctivitis

• Haemophilus influenzae
• Streptococcus pneumoniae
• Staphylococcus aureus

Gonococcal conjunctivitis

• Neisseria gonorrhoeae

Chlamydial conjunctivitis

Chlamydia species

Rarely

• Fungi
• Acanthamoeba (Protozoa)

Body fluid (CSF, pleural fluid, ascitic fluid, and others)

Most Commonly Found Pathogens in the body fluid are-

Gram-positive

• Streptococcus pneumoniae
• Staphylococcus aureus
• Streptococcus agalactiae

Gram-negative

• Neisseria meningitidis
• Haemophilus influenzae
• Pseudomonas aeruginosa
• Salmonella species
• Other Gram-negative rods/ bacilli

Throat Swab 

• Only for Streptococcus pyogenes

Stool

Gram-negative

1. Salmonella species
2. Shigella species
3. Vibrio cholerae

HVS, Vaginal Swab, Endocervical swab, and Urethral discharge

Gram-positive

• Hemolytic streptococci
• Staphylococcus aureus
• Candida species

Gram-negative

• E. coli
• Klebsiella species
• Neisseria gonorrhoeae
• Other Gram-negative rods/ bacilli

Ear Swab

• P. aeruginosa
• S. aureus
• Proteus spp.
• CoNS
• K. pneumoniae
• E. coli
• S. pneumoniae
• Candida

 Blood Culture 

Gram-positive

• Staphylococcus aureus
• Streptococcus pneumoniae
• Streptococcus pyogenes
• Varidans streptococci

Gram-negative

• Salmonella Typhi
• Salmonella Paratyphi A
• Other Salmonella
• Haemophilus influenzae
• Pseudomonas aeruginosa
• Klebsiella species
• E. coli
• Other Gram-negative Bacilli
• Neisseria meningitidis

 Further Readings on Most Commonly Found Pathogens

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457377/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914753/
3. https://www.aclr.com.es/clinical-research/isolation-of-pathogens-causing-sepsis-pus-and-infected-wounds-from-critical-care-unit-a-retrospective-study.php?aid=8092
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833760/
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003010/