Seminar microbiology presentation

1. RT AND GIT SPECIMEN
PROCESSING
PRESENTER: BMLS GROUP 3
MUHAS, 2023
MICRO SPECIMEN PROCESSING

2. The respiratory and gastrointestinal tracts are important parts of the human
body that play vital roles in our overall health and well-being.
The respiratory tract consists of the organs and tissues involved in breathing,
such as the nose, throat, and lungs. It is responsible for the
Exchange of oxygen and carbon dioxide
Defense mechanism against harmful substances, preventing them from
entering the lungs.
Has mucus and tiny hair-like structures, to remove trapped particles and
keep the airways clear.
Infections of the respiratory tract, include the common cold, Sinusitis, flu,
and pneumonia, they can cause symptoms like coughing, sneezing, and
difficulty breathing
Introduction

3. The gastrointestinal tract, often referred to as the digestive system, is
responsible for the
Breakdown and absorption of food and nutrients. It includes organs
such as the mouth, esophagus, stomach, small intestine, and large
intestine.
The gastrointestinal tract processes food through mechanical and
chemical digestion towards absorption.
Gastrointestinal disorders, includes gastroenteritis, irritable bowel
syndrome, and inflammatory bowel disease, can lead to symptoms like
abdominal pain, diarrhea, and constipation.
Introduction..

4. The respiratory tract, includes the nose, throat, and lungs, has its own normal
flora/microbiota. The distribution of normal flora in the respiratory tract
varies depending on the specific location.
Nasal Cavity:
Common site for the colonization of bacteria.
Staphylococcus aureus, including (MRSA).
Other Coagulase-Negative staphylococci (CoNS)
Corynebacterium species and Streptococcus spp. may also be present.
Commonly found in the anterior nares (nostrils).
Respiratory Tract

5. Oropharynx.
The back of the throat.
Streptococcus viridans, is a predominant resident of the oropharynx.
Streptococcus salivarius, Streptococcus pneumoniae.
Haemophilus influenzae, and Neisseria species, may also be present.
Lower Respiratory Tract:
Trachea and lungs, is normally sterile in healthy individuals. In impaired
immunity or underlying lung diseases. Common colonizing pathogens include
Streptococcus pneumoniae, Haemophilus influenzae and
Moraxella Catarrhalis, and Staphylococcus aureus.
Respiratory Tract…

6. Collection
A sample is collected from the respiratory tract.
Sputum,
Throat swab, and nasopharyngeal swab.
Proper collection techniques are followed to minimize contamination.
Sample Preparation
The collected specimen is processed in the laboratory.
Sputum, may be treated with a mucus-dissolving agent to break down
any mucus and make the sample easier to work with.
Other specimen In standard conditions are ready for smear and culture
processing
RT Specimen Processing

7. Culture.
The prepared sample is streaked onto various culture media,
Blood agar, LJ Media
MacConkey agar and Chocolate agar.
These media support the growth of different types of microorganisms.
The plates are then Incubated at appropriate temperatures and atmospheric
conditions to allow bacterial and fungal growth.
RT Specimen Processing…

8. Identification.
Examine the cultured colonies to identify specific microorganisms. Visual
characteristics used.
Colony morphology.
Biochemical tests to identify the bacteria or fungi present in the
specimen.
Susceptibility Testing.
Antimicrobial susceptibility testing may be performed to determine the most
effective antibiotic treatment.
Kirby Bauer
MIC technique
RT Specimen Processing…

9. The gastrointestinal tract: consists of the stomach, small intestine, and large
intestine (colon), harbors a complex and diverse community of
microorganisms known as the gut microbiota.
Stomach.
Has a very low pH due to the presence of hydrochloric acid, which makes it
inhospitable for most microorganisms. A small number of bacteria can survive
in the stomach,
Helicobacter pylori, which is associated with gastric ulcers and other
gastrointestinal disorders.
Gastrointestinal Tract

10. Small Intestine.
Low bacterial load compared to the colon. The upper part called the
duodenum, has a low number of bacteria. Common bacterial species found in
the small intestine include
Lactobacillus, Streptococcus and
Enterococcus
Large Intestine (Colon).
It houses the largest concentration and diversity of gut microbiota. Include
bacteria, fungi, viruses, and other microbes. The predominant bacterial groups
in the colon include
Bacteroidetes, Firmicutes, and Actinobacteria. Various genera and species
are present, such as Bacteroides, Faecalibacterium, Escherichia coli, and
Bifidobacterium.
Gastrointestinal Tract…

11. Collection.
Various gastrointestinal samples can be collected,
Stool, rectal swab and
Gastric aspirate.
Proper collection techniques are followed to maintain sample integrity and
minimize contamination.
Sample Preparation:
The collected specimen undergoes processing in the laboratory. For Stool
samples, series of tests is often performed.
Culture, antigen detection, and
Molecular techniques, depending on the suspected pathogens.
GIT Specimen Processing..

12. Culture
Stool samples are streaked onto specific culture media suitable for the
detection of enteric bacteria, such as Salmonella, Shigella, or Campylobacter.
Selective media and differential tests are used to isolate and differentiate
different microorganisms
GIT Specimen Processing

13. Molecular Testing:
Molecular techniques, such as polymerase chain reaction (PCR), may be
employed to detect specific pathogens, including viruses and parasites.
Identification:
Microbiological examination of the cultured colonies or PCR results to identify
the specific microorganisms present in the specimen.
Biochemical tests or molecular assays are used for further identification,
as needed.
Additional Testing:
Toxin assays, serotyping, Antimicrobial susceptibility.
GIT Specimen Processing…

14. Jawetz, Melnick and Aldelberg Medical microbiology and immunology:
27th edition.
Monica Cheesbrough District Laboratory Practice in Tropical Countries Part 2
Microbiology Manual
Online Resources
REFERENCES