ADAMA SCIENCE AND TECHNOLOGY UNIVERSITY

SCHOOL OF APPLIED NATURAL SCIENCE

DEPARTMENT OF APPLIED BIOLOGY

Report on internship Activity By:

Kalid Jemal: (Ugr 27001/14)
Department advisor name: Dr. Kero Jemal
Supervisor in hosting Organization: Mr. Wake Abebe
Hosting Organization name: Adama Public Health Research and Referral
Laboratory Center
Internship period: Two month (July 1, 2024–August 30, 2024)

Submission Date: -September 28, 2024

Adama, Ethiopia
Executive summary

The internship was carried out in Oromia Regional Healthy Bureau Adama Public
Health Research and Referral Laboratory Center which is found in Adama near
Adama Hospital and Medical College, for Two month from July 1-August 30. The
one-month internship provided with valuable hands-on experience and
knowledge in four key laboratory activities. This are; bacteriology lab, TB lab,
molecular lab and public health laboratory. The principal objective of this
internship is to produce qualified, motivated and practice oriented students with
accompanying report. The Scope of the internship ranges from valuable
information about laboratory activities and its importance. The mission of the
laboratory is to improve health and living condition of peoples of Oromia region.
During my internship at the Adama Public Health Research and Referral
Laboratory Center, I gained valuable hands-on experience in various aspects of
public health research and laboratory operations. I assisted with sample
registration, processing, and analysis, as well as data management and reporting.
I also had the opportunity to observe and learn from experienced professionals in
the field, further enhancing my understanding of public health practices. Overall,
this internship provided me with a comprehensive overview of the important role
that research and laboratory services play in promoting public health and disease
prevention.

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Acknowledgment
Firstly, I thank Adama Science and Technology University for its contribution in
funding, and then I would like to thank the School of Applied Natural Science and
the department of Applied Biology for arrangement of this internship program.
Next, I would like to thanks my department advisor Dr. Kero Jemal, and my
Supervisor in Host Organization Mr. Wake Abebe in Adama Public Health
Research and Referral Laboratory Center.

I would also like to express my deepest gratitude to the staff and management of
the Adama Public Health Research and Referral Laboratory Center for providing
me with the opportunity to complete a two-month internship at their esteemed
institution. I am immensely thankful for their guidance, support, and mentorship
throughout my time there.

Lastly, I would like to thank my family and friends for their unwavering support
and encouragement throughout this internship.

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List of Acronyms

TB- tuberculosis

MTB-micro tuberculosis

EAS- Ethiopian accreditation service

PCR- polymerase chain reaction

TAT- turnaround time

AFB- acid fast bacilli

LAB- laboratory

APHRRLC- Adama Public Health Research and Referral Laboratory Center

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 Table of Content

Contents pages
excutive summary ............................................................................................................ i
Acknoledgment ............................................................................................................... ii
List of Acronyms ............................................................................................................ iii
Table of Content ............................................................................................................ iv
1. Introduction................................................................................................................. 1
2.background of organization ........................................................................................... 2
2.1vision ………………………………………………………………………………,.2
2.2mission of the laboratories …………………………………………………………,.2
2.3 value ………………………………………………………………………………,.3
2. general over view of internship ..................................................................................... 3
3. role and responsibilities ................................................................................................ 4
4. reception room ............................................................................................................. 5
5. bacteriology lab ............................................................................................................ 6
6. TB-lab .......................................................................................................................... 9
7. molecular lab............................................................................................................... 11
8. phl-lab ......................................................................................................................... 14
9. challanged faced ......................................................................................................... 17
10.conclusion .................................................................................................................. 18
11.future recommendation ................................................................................................ 19
12.reference ..................................................................................................................... 20

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1. Introduction
The following report describes the activities carried out during Two month, full-
time internship at Oromia Regional Healthy Bureau Adama Public Health Research
and Referral Laboratory Center. During the Two-month internship at the Adama
Public Health Research and Referral Laboratory Center, hands-on experience is
gained in four distinct laboratory settings: tuberculosis (TB) laboratory, molecular
laboratory, bacteriology laboratory, and the public health laboratory. Each of
these laboratories offers a unique opportunity to delve into different aspects of
public health research and laboratory operations.

The main objective of this text is to reflect upon the experiences collected during
the internship. The activities included in this report are the following; In the TB
laboratory, the importance of early detection and diagnosis of tuberculosis is
learned through various diagnostic tests and procedures. In the molecular
laboratory, viral load and detection is learned in genetic basis of infectious
diseases. In the bacteriology laboratory, skills in culturing and identifying various
bacterial strains are honed, as well as testing their susceptibility to antibiotics.

In the public health laboratory, exposure to the broader scope of public health
research and surveillance activities is gained. From analyzing epidemiological data
to conducting environmental health assessments, a comprehensive
understanding of the multifaceted nature of public health work is developed.
Lastly, time spent in the reception room provides valuable insights into the
administrative and logistical aspects of running a public health laboratory.
Learning about patient registration, sample handling protocols, and quality
control procedures essential for maintaining efficiency and accuracy in laboratory
operations. Detailed definitions and procedures of each topic are also included in
the report.

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2. Background of the Organization
Oromia Regional Healthy Bureau Adama Public Health Research and Referral
Laboratory Center formerly known Adama Regional Laboratory (ARL). It was
established by Oromia Regional Healthy Bureau with the help of CDC-Ethiopia in
1995 EC, in Adama town near Adama Hospital and Medical College. When it
started the services, there were two blocks with two laboratory professionals and
five supporting staffs. Currently the laboratory has G+1Building and has 27
laboratory professionals and 24 supporting staffs.

The laboratory performs its work in the most professional and ethically way
committed to good laboratory and clinical practice as well as to the requirement
of ISO15189:2012. Their laboratory is accredited by Ethiopian accreditation
service (EAS), in the tb-lab it has three accreditation for three lab techniques for
tb diagnosis and others lab also accredited by EAS.

2.1 Vision

To be a leading and innovative laboratory center dedicated to advancing public

health research, diagnostics, and referral services, contributing to the
improvement of healthcare outcomes and population health in the Oromia
region.

2.2 Mission of the laboratory

The mission of Oromia Regional Healthy Bureau Adama Public Health Research
and Referral Laboratory Center is to:

• To improve health and living condition of peoples of Oromia region.

• Perform disease surveillance

• Perform reference testing.

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• To maintain quality management system It provides emergency response
support

• Perform applied research and provide training for laboratory personnel.

2.3 Value

 The company has a passion for the safety

 The member of the company thinks and act like “owners” at all the times

 They work and win in terms of the business

 Accountability is clear and personal

 Safety, quality, the environment, and community are integral to the company's
working lives

3. General overview of internship

At Adama Public Health Research and Referral Laboratory Center, I had the
privilege of gaining hands-on experience in four distinct laboratory settings and
reception room: tuberculosis (TB) laboratory, molecular laboratory, bacteriology
laboratory, and the public health laboratory. Each of these laboratories offered
me a unique opportunity to delve into different aspects of public health research
and laboratory operations.

As ASTU internship rules and regulation I was performed the intern as much as
possible for one month with exception of the weekends due to our program
arrangement in the laboratory.

According to objective of internship I was developed certain skills and knowledge.

The scopes of knowledge and skill I was developed is more mentioned in the next
portion of this laboratory report, but its main points are described here:-

➢ MTB diagnosis by gene expert and AFB microscope

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 ➢ Culture media and its preparation

➢ viral load analyzing and detecting by PCR

➢ Sample registering on inspection log sheet

4. Role and Responsibility

At the Adama Public Health Research and Referral Laboratory Center, I took on
various roles and responsibilities in different laboratory settings. Some of the key
roles and responsibilities I undertook include:

1. Assisting in registering samples in reception room.

2. Performing diagnostic tests for TB detection under the supervision of
experienced professionals.
3. Conducting molecular biology experiments in the molecular laboratory and
analyzing data.
4. Participating in the culturing and identification of bacterial strains in the
bacteriology laboratory.
5. Testing the susceptibility of bacterial strains to antibiotics and recording results.
6. Analyzing epidemiological data and contributing to public health research
projects in the public health laboratory.
9. Learning about patient registration procedures and sample handling protocols in
the reception room.

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5. Reception Room

During my internship, I was involved in the reception department where I

managed the intake of samples from various institutions, including Adama Public
Health and Yoya. Samples were received primarily via postal service, and on one
occasion, we accepted a total of 93 samples at once. My responsibilities included
verifying the assigned numbers on each sample and organizing them in increasing
order. The majority of these samples were blood specimens, accompanied by a
description paper detailing the tests to be conducted. The sample test request
forms were registered online in our laboratory information system, ensuring
accurate tracking and management. After registration, the samples were stored in
a refrigerator until they were ready to be sent to the respective laboratories for
testing. This experience underscored the importance of meticulous sample
handling and documentation in maintaining an efficient work flow. One of the key
components of the reception room is the sample inspection log sheet, where
samples are registered for clinical bacteriology, molecular lab, public health
laboratory (PHL), or tuberculosis testing. This log sheet includes important
information such as the start date of the sample and details about the patient. I
was responsible for accurately recording this information and ensuring that
samples were properly labeled and tracked throughout the testing process.

In addition to sample registration, I learned about the standards for accepting and
rejecting samples. It was essential to follow strict guidelines to maintain the
integrity of the samples and prevent any contamination. I gained valuable
experience in identifying potential issues with samples and communicating
effectively with laboratory staff to address any concerns.

The reception room also housed a refrigerator for storing samples that required
specific temperature conditions. I was responsible for monitoring the refrigerator
temperature regularly and ensuring that samples were stored appropriately to
maintain their integrity.

One of the highlights of my internship was working with the computer system
that facilitated direct information transfer between the reception room and the

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laboratories. This system allowed for seamless communication and tracking of
samples, streamlining the testing process and reducing errors.

Furthermore, I learned about the extensive network of facilities that the

laboratory center is connected to, with direct links to 764 facilities. This network
enables efficient sample transfer and collaboration with other healthcare
providers, enhancing the laboratory's capacity to serve a wide range of patients.

Finally, I gained valuable insights into the concept of Turnaround Time (TAT) for
receiving and processing patient samples. Understanding the importance of
timely testing and reporting results was crucial in ensuring quality patient care
and effective disease management.

6. Bacteriology laboratory
My internship has been an invaluable experience that provided hands-on training
across multiple laboratory disciplines. From sample reception to advanced
molecular techniques, I have gained insights into critical laboratory practices
essential for public health research and disease management. This comprehensive
exposure will significantly contribute to my future career in public health
laboratory science.

Media Preparation in Bacteriology:

Media preparation is a critical aspect of bacteriology laboratory work as it

provides the necessary nutrients for bacterial growth and identification. In the
laboratory, both selective and non-selective media are prepared to support the
growth of different types of bacteria. Selective media contain specific nutrients
that encourage the growth of certain bacteria while inhibiting others, aiding in the
isolation of particular strains. Examples of selective media include MacConkey

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agar, which is used to isolate and differentiate lactose-fermenting Gram-negative
bacteria from non-lactose fermenters. Non-selective media, on the other hand,
support the growth of a wide range of bacteria without any inhibitory
components, allowing for the cultivation of diverse bacterial species.

Steps in Culture Media Preparation:

The preparation of culture media involves several essential steps to ensure the
proper growth and isolation of bacteria. The first step is to weigh and measure
the ingredients required for the specific type of media being prepared. These
ingredients may include peptones, agar, salts, and other nutrients essential for
bacterial growth. The next step involves mixing the ingredients with water and
heating the mixture to dissolve the components completely. Once the media is
prepared, it is sterilized using an autoclave to eliminate any contaminants that
could interfere with bacterial growth. After sterilization, the media is poured into
petri dishes or test tubes and allowed to solidify before use.

Solid and Liquid Media in Bacteriology:

Solid media, such as agar plates, are commonly used in bacteriology laboratories
for isolating and culturing bacteria. Agar is a gel-like substance derived from
seaweed that provides a solid surface for bacterial growth. Solid media allow for
the observation of colony morphology and the isolation of individual bacterial
colonies for further analysis. Examples of solid media include nutrient agar, blood
agar, and MacConkey agar. Liquid media, on the other hand, are used for growing
bacteria in suspension and are often employed in broth cultures for rapid
bacterial growth. Liquid media provide a homogeneous environment for bacterial
growth and are ideal for studying bacterial physiology and metabolism.

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Examples of Solid and Liquid Media:

- Nutrient Agar: A general-purpose medium that supports the growth of a wide

range of bacteria.

- Blood Agar: Enriched medium containing blood cells that promote the growth of
fastidious bacteria.

- MacConkey Agar: Selective and differential medium used to isolate lactose-

fermenting Gram-negative bacteria.

- Broth Culture: Liquid medium used for growing bacteria in suspension, suitable
for rapid bacterial growth and metabolic studies.

Equipment in the Bacteriology Lab:

The bacteriology laboratory at Adama Public Health Research and Referral

Laboratory Center is equipped with essential tools and equipment to support
various microbiology testing procedures. The laboratory features an autoclave for
sterilizing equipment and media, an incubator for maintaining optimal growth
conditions for bacteria, and a biosafety cabinet for handling potentially hazardous
materials safely. Additionally, the laboratory is equipped with microscopes,
centrifuges, and other instruments necessary for conducting microbial analyses.

Bacteria Categorization Based on Harmfulness:

In the bacteriology laboratory, bacteria are categorized based on their

harmfulness to human health. Category A bacteria are highly dangerous
pathogens that require specialized containment facilities and are not handled in
standard laboratory settings. Category B bacteria are moderately harmful and
may be worked with under appropriate safety precautions, such as in a biosafety
cabinet. Category C bacteria are considered non-pathogenic or low-risk organisms
that are commonly studied in laboratory settings for research and educational
purposes.

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Sub-culturing Growth, Gram Staining, and Biochemical Tests:

During my internship, I had the opportunity to perform sub-culturing to observe

bacterial growth on solid media. Sub-culturing involves transferring a small
amount of bacterial culture from one plate to another to obtain isolated colonies
for further analysis. I also conducted Gram staining to differentiate between
Gram-positive and Gram-negative bacteria based on their cell wall characteristics.
Additionally, I performed biochemical tests such as catalase testing to identify
specific enzymes produced by bacteria. A positive catalase test result indicates
the presence of catalase enzyme activity in the bacterial sample.

7. TB-Laboratory

Tuberculosis (TB) is a major global health issue caused by the bacterium

Mycobacterium tuberculosis. It primarily affects the lungs but can also affect
other organs in the body. TB is transmitted through the air when an infected
individual coughs or sneezes, making it highly contagious. The disease can be
latent or active, with symptoms including coughing, chest pain, weight loss, and
fatigue. TB is a significant public health concern due to its high mortality rate and
the emergence of drug-resistant strains.

Laboratory Techniques for TB Diagnosis:

The Adama Public Health Research and Referral Laboratory Center utilizes various
laboratory techniques for the diagnosis of TB. These techniques include
Genexpert, Acid-Fast Bacilli (AFB) microscopy, and culture methods.

1. Genexpert:

Genexpert is a molecular diagnostic technique that detects the presence of

Mycobacterium tuberculosis DNA in clinical samples. The Genexpert system
consists of a four-module system that automates the process of DNA extraction,
amplification, and detection. The test is based on real-time polymerase chain
reaction (PCR) technology, providing rapid and accurate results. Genexpert is

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known for its high sensitivity and specificity in detecting TB and drug resistance
mutations. The technique is particularly useful in diagnosing TB in patients with
HIV co-infection or extrapulmonary TB.

During my internship at the laboratory, I observed the process of sample

preparation, cartridge loading, and result interpretation. The Genexpert assay has
revolutionized TB diagnosis by providing results within hours, compared to
traditional culture methods that can take weeks. However, the cost of the test
may be a limiting factor in resource-limited settings.

2. Acid-Fast Bacilli (AFB) Microscopy:

AFB microscopy is a simple and cost-effective technique used for the direct
detection of acid-fast bacilli in sputum samples. Acid-fast staining differentiates
mycobacteria from other bacteria based on their cell wall composition. The
stained slides are examined under a microscope, and acid-fast bacilli appear as
red, rod-shaped structures. AFB microscopy is commonly used as an initial
screening test for TB due to its rapid turnaround time.

During my internship, I learned about the staining procedure, microscopy

examination, and interpretation of AFB results. While AFB microscopy is less
sensitive than molecular techniques like Genexpert, it remains a valuable tool in
resource-limited settings where sophisticated equipment may not be available.

3. Culture Method:

The culture method involves the growth of Mycobacterium tuberculosis in a

controlled laboratory environment to confirm the presence of the bacteria and
determine drug susceptibility. Liquid media such as Mycobacteria Growth
Indicator Tube (MGIT) and solid media like Lowenstein-Jensen agar are used for
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culturing TB bacteria. Culturing on solid media can take several weeks to yield
results due to the slow growth rate of Mycobacterium tuberculosis.

During my internship, I assisted in inoculating sputum samples onto culture

plates, monitoring growth progression, and performing drug susceptibility testing
using the proportion method. Culturing remains the gold standard for diagnosing
TB and identifying drug-resistant strains. However, the long turnaround time and
technical expertise required for culturing may limit its utility in urgent cases.

8. Molecular laboratory
My internship has been an invaluable experience that provided hands-on training
across multiple laboratory disciplines. From sample reception to advanced
molecular techniques, I have gained insights into critical laboratory practices
essential for public health research and disease management. This comprehensive
exposure will significantly contribute to my future career in public health laboratory
science.

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Abbott RealTime HIV-1 Machine:

The laboratory utilizes the Abbott RealTime HIV-1 PCR machine, which is capable
of processing 96 samples simultaneously. Each run includes three samples: one
for control, one for negative, and one for positive or neutral testing. This machine
plays a crucial role in conducting quantitative viral load tests for various infectious
diseases, including HIV-1.

Molecular Testing and RNA-Based Analysis:

The laboratory conducts molecular tests that involve analyzing RNA-based

samples to detect and quantify viral pathogens. The Abbott RealTime HIV-1
machine specifically targets the RNA of the Human Immunodeficiency Virus Type
1 (HIV-1) to measure the viral load in patient samples. The process involves
extracting RNA from the patient's blood sample and then amplifying and
quantifying it using real-time polymerase chain reaction (PCR) technology.

Laboratory Workflow:

Initially, the laboratory had three separate rooms for reagent preparation,
extraction, and detection. However, to streamline operations, the reagent
preparation and extraction processes were combined into one room, while the
detection process remained in a separate area. This consolidation has improved
efficiency and workflow management within the laboratory.

Workflow Steps:

1. Reagent Preparation: The first step involves preparing five essential reagents:
Microparticles, Lysis buffer, Wash 1 buffer, Wash 2 buffer, and Elution buffer.
These reagents are crucial for extracting and isolating RNA from patient samples.

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2. Extraction: Following reagent preparation, RNA extraction is performed to
isolate viral RNA from the patient's sample.

3. Mastermix Preparation: Once the RNA is extracted, a mastermix is prepared by

combining specific reagents and primers necessary for PCR amplification.

4. Detection: The final step involves running the prepared samples through the
Abbott RealTime HIV-1 machine for detection and quantification of viral RNA. The
machine utilizes real-time PCR technology to amplify and measure the amount of
HIV-1 RNA present in the patient's sample.

Fig.1 Abbott Real Time Systems

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9. Publichealthlaboratory(PHL)
During my internship at the Adama Public Health Research and Referral
Laboratory Center, I had the opportunity to work in the public health laboratory
where various samples from the environment, such as water, food, and soil, were
analyzed. The laboratory primarily focuses on monitoring infectious diseases at
the population level and diagnosing parameters related to physical, chemical, and
biological aspects of the samples.

Sample Analysis:

1. Environmental Sampling: The laboratory collects samples from different

environmental sources, including water, food, and soil. Currently, water samples
are more frequently analyzed due to their crucial role in public health.

2. Infectious Disease Monitoring: The laboratory plays a significant role in

monitoring infectious diseases at the population level through the analysis of
environmental samples.

Parameter Diagnosis:

1. Physical Parameters: Physical parameters of the samples are evaluated using

sensing organs to assess their visual appearance, texture, and other physical
characteristics.

2. Chemical Parameters: Chemical analysis is conducted using techniques such as

atomic absorption spectroscopy and chromatography to determine the chemical
composition of the samples.

3. Biological Parameters: Biological aspects of the samples are assessed to

identifyany microbial or biological contaminants present.

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Instrumentation:

1. Wagtech Instrument: The laboratory utilizes the Wagtech instrument, which

includes a pH meter for measuring conductivity and pH levels in the samples. The
instrument also measures total dissolved solids (TDS) based on conductivity
readings, with a threshold of 1000 indicating no significant issues.

2. Other Instruments: The laboratory also uses a photometer for various tests,
including arsenic detection and turbidity measurements. The photometer can
analyze up to 100 different parameters but currently has only 10 reagents
available, including ammonia, sulfuric acid, nitric acid, nitratest, and fluoride.

Test Procedures:

- Fluoride Test:

1. Prepare the sample for analysis by following standard operating procedures.

2. Use the Wagtech instrument to measure the fluoride levels in the sample.

3. Add the fluoride reagent to the sample according to the prescribed protocol.

4. Utilize the photometer to analyze the sample and determine the fluoride
concentration.

5. Interpret the results based on established guidelines and compare them to

regulatory standards.

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Fig.2 Wagtech palnitest brand

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Challenges Faced:
During my internship at the laboratory, I encountered several challenges that
provided valuable learning opportunities. One of the main challenges was
ensuring the accuracy and reliability of test results. This required meticulous
attention to detail during each step of the testing process to prevent
contamination and ensure correct interpretation of data.

Additionally, maintaining the equipment and ensuring its proper functioning was
another challenge. Regular calibration and maintenance of the Abbott RealTime
HIV-1 machine were essential to obtain accurate results. Any deviations in
temperature, humidity, or machine settings could impact the reliability of test
results.

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 Conclusion
My internship has been an invaluable experience that provided hands-on training
across multiple laboratory disciplines. From sample reception to advanced
molecular techniques, I have gained insights into critical laboratory practices
essential for public health research and disease management. This comprehensive
exposure will significantly contribute to my future career in public health laboratory
science.

Overall, my internship at the laboratory has been a valuable learning experience

that will undoubtedly contribute to my professional growth in the field of public
health research and laboratory practices.

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Future Recommendations:
Based on my internship experience at the Adama Public Health Research and
Referral Laboratory Center, I recommend implementing regular training sessions
for staff members to enhance their knowledge and skills in molecular diagnostics.
Continuous education and training will ensure that all staff members are
proficient in using advanced technologies like the Abbott RealTime HIV-1
machine.

Furthermore, investing in quality control measures and implementing strict

protocols for equipment maintenance will help ensure the accuracy and reliability
of test results. Regular audits and assessments of laboratory practices can also
help identify areas for improvement and enhance overall quality assurance
processes.

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 References:
- Abbott RealTime HIV-1 PCR System Manual

- Laboratory Standard Operating Procedures (SOPs) from Adama Public Health

Research and Referral Laboratory Center

- Personal observations and experiences during internship

- Adama Public Health Research and Referral Laboratory Center. Annual Report
2020. Adama, Ethiopia

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