UNIVERSITY OF PORT HARCOURT

FACULTY OF SCIENCE
DEPARTMENT OF MICROBIOLOGY

A TECHNICAL REPORT ON A SIX (6) MONTHS STUDENT

INDUSTRIAL WORK EXPERIENCE SCHEME (SIWES)

BY

ONYEMACHI CHINEMEREM JOSEPH

U2018/5555144

IN PARTIAL FULFILMENT FOR THE AWARD OF BACHELOR DEGREE

OF SCIENCE (B.SC) IN MICROBIOLOGY, UNDERTAKEN AT THE
UNIVERSITY OF PORT HARCOURT TEACHING HOSPITAL,
P.M.B 6173
PORT HARCOURT

COURSE CODE: MCB 309.2

COURSE COODINATOR: DR. V.C. WOKEM
INSTITUTIONAL SUPERVISOR:

APRIL, 2023
 DEDICATION
I dedicate this report to God almighty, the maker and giver of life, special dedication to my
supportive family for their relentless encouragement and compassion towards me during the
cause of my six (6) months SIWES training.

I also devote the work of this SIWES report to the respectable and honorable staff of the
University of Port Harcourt Teaching Hospital who taught and supported me in developing
myself to becoming a better person at large.

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 ACKNOWLEDGEMENT
I sincerely appreciate everyone who contributed to the success of this program. I’m grateful to
my family for their support and love. My appreciation goes to the chief medical director of the
University of Port Harcourt Teaching Hospital for the opportunity to undergo my industrial
training in this institution, the H.O.D, the chief resident doctor, Dr. Duru, other resident doctors,
Dr. Princewill and Dr. Valentine, their guidance and tutelage lead me through the program in the
department of microbiology U.P.T.H.
I am grateful to Dr. Benjamin Aleme and Dr. Showers for their love and support. I thank my
colleagues for their cooperation during the program, making it hitch-free and giving me a good
experience. I wish you the best in future endeavors was a pleasure working with you all. I am
also grateful to my S.I.W.E.S supervisor Dr. V.C Wokem for his guidance. I pray the almighty
God blesses you all.

Finally, I appreciate the almighty God for his love, provision and guidance throughout the
program.

Table Of Contents

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Title Page
Dedication Acknowledgement Abstract Table Of Contents Chapter One
Brief History of SIWES
Brief History of University of Port Harcourt Teaching Hospital
Fig 1.0 Organogram of University of Port Harcourt Teaching Hospital Chapter
Two
2.0. The Laboratory
2.0.1. Introduction To The Laboratory
2.0.2. Laboratory Safety
2.0.3. Phases In The Laboratory 2.0.4.
Laboratory Equipments
2.1.0 Media Preparation.
2.1.1. Blood Agar
2.1.2. Nutrient Agar
2.1.3. MacConkey Agar
2.1.4. Cystine Lactose Electrolyte Deficient Agar (Cled)
2.1.5. Chocolate Agar
2.1.6. Bile Esculin Agar (Bea)
2.1.7. Tryptic Soy Agar
2.1.8. Xld Agar
2.1.9. Tryptic Soy Agar
2.1.10. Preparation Of Broth Media.
2.1.10.1. Tryptic Soy Broth (Tsb)
2.1.10.2. Chocolate Agar Slant
2.2. Gram Staining
2.3. Tests
2.3.1. Biochemical Tests
2.3.2. Urine Processing
2.3.3. Laboratory Diagnosis Of Malaria
2.3.4. Blood Culture
2.3.5. Serology
2.3.6. Blood Culture
2.3.7. Intracervical And High Vaginal Swab Processing
Chapter 3
3.0. Challenges Encountered
3.1. Relevance of the SIWES program.
Chapter 4
4.0. Conclusion And General Appraisal of The Program
4.1. Ways Of Improving the Program.
4.2. Advice To Future Participants
CONCLUSION

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 ABSTRACT
This report covers the experience acquired outside the institution as a challenge to be exposed
to industrial sector. This report is based on the student industrial work experience scheme
(SIWES) held at the University of Port Harcourt Teaching Hospital, Port Harcourt.

It provides a brief explanation about the SIWES program such as its history, objective, aim and
while also giving a description of the work done in the University of Port Harcourt Teaching
Hospital.

It further focuses on the exposure gained from the department of Chemical Pathology, UPTH. It
finally gives account to some of the reagents, apparatus and tasks completed during the time
spent in the organization and the far knowledge learnt so far of the stay. It also provides an
insight of some of the challenges faced and gives a few recommendations on how to further
improve the program.

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 BRIEF HISTORY OF SIWES
SIWES was established by ITF in the year 1973 to solve the problem of lack of adequate proper skills
for employment of tertiary institutions graduates by Nigerian Industries. Before this scheme was
established there was a growing concern and trend noticed by industrialists that graduates of higher
institutions lacked sufficient practical background for employment. The scheme, therefore, serves as a
smooth transition from the classroom to the world of work and further helps in the application of
knowledge. It works with professional bodies such as the Nigeria university commission (N.U.C), the
National board for technical education (N.B.T.E), and the National Commission for colleges of education
(N.C.C.E), to ensure it functions effectively across tertiary institutions worldwide thus equipping students
with the necessary skills and technical knowledge to make them highly competitive and professional
individuals in the labor market.
AIM OF SIWES.
1. SIWES provides an avenue for students in institutions of higher learning to acquire industrial
skills and experiences in their course of study.
2. To prepare students for the industrial work situation they are likely to meet after graduation
3. To make the transition from school to the world work easier and enhance student ob contact to
later job placements.
4. To expose students to work methods and techniques in handling equipment and machinery that
may not be available in their institution.
5. It provides students with an opportunity to apply their knowledge in real work situations
thereby bridging the gap between theory and practice.

SCOPE OF SIWES
The scheme is conducted by the industrial training fund (ITF) through their respective units and offices
situated within the various institutions and in major cities or towns in Nigeria with the necessary
industrial rudiments needed to corroborate practice and actualize the required technical knowledge.
The industrial training experience not only puts them in real-life experience but also exposes their
practical knowledge of the course of study, consequently perfecting this knowledge thereby producing
competent and versatile professionals.

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 BRIEF HISTORY OF THE UNIVERSITY OF PORT HARCOURT TEACHING HOSPITAL
University of Port Harcourt Teaching Hospital (U.P.T.H) was established in April 1980 and was officially
commissioned by the federal government in 1985, it is a major tertiary-care teaching and research
facility in Rivers State. It is as a result of the desire of the Federal Government to provide excellent
medical services, manpower training, and research in all the geopolitical zones of the country. The
mandate of the Hospital was derived from Decree 10 of 1985, University Teaching Hospitals
(reconstitution of Board etc) Decree.
In its 38 (thirty-eight) years of existence, it has gone through a remarkable journey in terms of physical
and manpower development. The Hospital started as a small cottage Hospital, the Emohua General
Hospital which had a 60-bed capacity in 1981. However, in September 1983 it was obvious that the
Hospital was too small to serve as a Teaching Hospital. The University of Port Harcourt Teaching Hospital
was consequently relocated to the 180-bed Port Harcourt General Hospital. Between 1983 and the
present day this Hospital has been upgraded to an 800-bed Hospital with tremendous expansion in
physical, equipment, and infrastructure to meet accreditation requirements of the Nigerian Medical and
Dental Council (NMDC) and the two Post-graduate Medical Colleges, National/West Africa for the
training of both graduate and postgraduate Doctors. Thus, presently all the major clinical and pathology
departments of the hospital have been fully accredited and re-accredited.
In 1982 the Federal Government commenced work in the Permanent Site next door to the University of
Port Harcourt. Work was however abandoned in 1984 and later recommenced in 1998, a period
spanning 14 (fourteen) years.

By 2001 the first phase was completed and some services commenced at the Permanent Site, leading to
its commissioning on the 12th of October 2006 by the then President, Chief Olusegun Obasanjo.
Presently, work is still ongoing in order to meet strategic development goals.
The current chief medical director is Professor Henry Arinze Anthony Ugboma.
University of Port Harcourt Teaching Hospital is managed through a three-tier managerial system
consisting - the Board of Management, Hospital Management Committee (HMC) and the
Departments. Nearly 200,000 patients are seen annually in both outpatient and inpatient settings, as
well as over 3000 surgical operations a year. Average bed occupancy rate in 12 months has risen above
80%. Besides offering medical services, the hospital tends to provide clinical education and training to
students, nurses, and other healthcare professionals. Over the years, many research activities and
results from its organized units have appeared on several major national and international medical and
scientific journals.

HIGHLIGHTS OF SOME ACHIEVEMENTS

The UPTH has recorded significant achievements in major areas in the health sector under the watchful
supervision of the parent ministry, the Federal Ministry of Health, and other allied ministries/agencies.
The achievements basically cut across various segments in the hospital ranging from manpower, clinical,
and infrastructural, the establishment of clinical subspecialties, improvement, and increase in service
delivery, Public, Private Partnership (PPP), and collaborations with Non-Government Organizations and
Research.
Vision:
To be a first-rate, world class hospital.

Mission:

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To provide excellent medical services, manpower training, and research, using a well-trained and
wellmotivated workforce and the best affordable modern technology with a culture of courtesy,
humanness, and patient friendliness.
Objective:
Our driving objective at UPTH is to become a world-class teaching hospital, using cutting-edge
technology and highly developed human resources to render excellent medical care/services.

VARIOUS DEPARTMENTS AND FUNCTIONS:

COMMUNITY MEDICINE
It involves the various departments which include: - General Outpatients Department (GOPD); Maternal
and Child Health including Family Planning, Immunization; Pharmacy; Medical Records; Laboratory; and
General Maintenance Department.

ORTHOPAEDICS
The Standard Operative Procedures are aimed at establishing guidelines for departmental operations
with respect to the processes involved in patient management.

DENTAL DEPARTMENTS
The department is concerned with the prevention of oral diseases as well as the diagnosis and
management of the diseases of the supporting structures of the teeth. The Department also provides
training for Resident doctors, Dental students, Nursing students, and Community medicine students.

HAEMATOLOGY & BLOOD BANK

The department of haematology and blood transfusion offers laboratory, blood banking and clinical
services. The laboratory services involve the processing and running of samples for various
haematological research.

MEDICAL MICROBIOLOGY DEPARTMENT

The Department of Microbiology University of Port Harcourt Teaching Hospital is one of the 4 pathology
departments of the hospital that was established to provide timely, reliable, and affordable diagnostic
support to clinicians in the management of patients. The department also serves as a training center for
undergraduate medical students, nursing students, pharmacy students, resident doctors, and other
students undergoing postgraduate training in any field of medicine.

EAR, NOSE, AND THROAT

Ear, Nose, and Throat surgery also known as otorhinolaryngology is a surgical specialty which deals with
diseases of the ear. nose and throat and related structures of the head and neck.

OBSTETRICS AND GYNAECOLOGY

The department offers gynaecological, obstetric, and labor (delivery) services. The latter services are
provided in a fully functional labor ward/theatre.

RADIOLOGY

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The department of Radiology attend to the imaging needs of patients of UPTH who are referred from
the various clinical departments of the hospital. It is a service department.

ACCIDENT & EMERGENCY

The Department of Accident & Emergency is the first port of call for all Surgical, Medical and
Gynaecological emergencies arriving in the hospital. It is therefore the eye of the Hospital and its image.

PAEDIATRICS & CHILD HEALTH DEPARTMENT

The Department of Paediatrics is the main health care providing site for children in the South-South
geopolitical zone of Nigeria which comprises the following states: Rivers, Bayelsa, Akwa Ibom, Abia,
Cross River, and Enugu. It is also a teaching site for Residents and students in Paediatrics and Child
Health and provides opportunities for research.

THE DEPARTMENT OF SURGERY

The Department of Surgery is one of the Clinical Departments of the University of Port Harcourt
Teaching Hospital. It was created with the aim of Equipping the medical graduates of the University of
Port Harcourt with the surgical knowledge and skills they need to take on the challenges of
contemporary medical practice here in Nigeria and abroad Training surgical specialists through its
residency and other associated programs. Providing high-level surgical services for the teeming
population in the sub-region, the rest of Nigeria, and even neighboring countries and for the world at
large. Research with the aim of contributing to the knowledge of surgical conditions especially those
prevalent in our environment.

ACCOUNTS:
They are responsible for billing and collecting payments from patients for services rendered by
healthcare providers. Also, hospital budgets, payroll, legal compliance, financial control, and record
keeping.

ADMINISTRATIVE UNIT:
They are responsible for organizing and overseeing the health services and daily activities of the
hospital.

ANESTHESIOLOGY:
They are also involved in carrying out assessments in critical care units and dealing with emergency
situations.

CATERING:
They provide suitable diets for patients who are hospitalized for long or short periods of time.

CENTRAL STERILIZATION SERVICE DEPARTMENTS (CSSD):

This is a subset in the nursing departments, whose sole function is to ensure that instruments, and
materials, used on patients are free of pathogens.

COMMUNICATION:

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Here all the departments in the hospital are connected and can communicate for any patient-related
work.

COMMUNITY MEDICINE:
They are concerned with the prevention of diseases, the determinants, and the natural history of
diseases in populations.

COMPUTER SCIENCE:
This unit helps connect patients with doctors and to make the job of doctors and nurses more efficient.

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DENTISTRY:(DENTAL UNIT):
They specialize in the diagnosis and treatment of teeth and diagnosing oral diseases and prevention.

EAR, NOSE AND THROAT(ENT):

This unit specializes in the diagnosis and treatment of ear, nose, and throat including head disorders.

GENERAL OUTPATIENT DEPARTMENT:

They render primary medical care to outpatients of the hospital.

INTENSIVE CARE UNIT(ICU):

They provide treatment and monitoring for people who are very ill.

INTERNAL MEDICINE:
They specialize in the diagnosis, treatment, and prevention of diseases in adult patients.

LAUNDRY:
They provide clean material to patients and ensure that hygienic conditions are maintained in the process.

MAINTENANCE:
They carry out corrective repairs of facilities in the hospital.

MEDICAL ILLUSTRATION UNIT:

They create artwork to dissect and explain anatomy and surgical procedures which are meant to teach and
inform.

MEDICAL LABORATORY SERVICES:

(Chemical pathology, hematology and blood bank, medical microbiology and parasitology, anatomical
pathology): This is where tests are done on clinical specimens in order to get information about the health
of the patient pertaining to the diagnosis, treatment, and preparation of the disease.

MEDICAL RECORDS:
They store the medical records or treatment files of patients who are either treated, in the in-patient departments
or emergency unit.

MEDICAL SOCIAL WELFARE:

To prevent, control, and contribute to the solution of social problems associated with patient illnesses or
disabilities.

NEUROPSYCHIATRY:
They treat patients with brain abnormalities.

NUCLEAR MEDICINE:
They provide information on various organs, and how they function, helping the doctor decide on the best
treatment.

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NURSE PRACTICE DEVELOPMENT UNIT:
They facilitate a continuous process of improvement in the delivery of healthcare services.

OBSTETRICS AND GYNAECOLOGY:

Here is the entire scope of clinical pathology involving female reproductive organs and provisions of care for
pregnant women and females in general.

OPHTHALMOLOGY:
This department is responsible for the treatment of diseases and surgery of visual pathways including the
eyes, hairs, and areas surrounding the eyes such as the lachrymal system and eyelids.

ORAL MAXILLOFACIAL:
They are concerned with the diagnosis, investigation, and surgical treatment of oral, jaw, salivary and bony
diseases of the oral cavity, head, and neck.

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Fig 1.0 organizational chart of university of Port Harcourt teaching hospital

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CHAPTER TWO
2.0. THE LABORATORY

2.0.1 INTRODUCTION TO THE LABORATORY

A laboratory is a facility that provides controlled conditions where scientific researches,

experiments, measurements can be performed. Hence the medical laboratory is a laboratory
where clinical specimens are tested in order to get important information about a patient
health.

There are basically four sections in the clinical laboratory, they are; Medical Microbiology section,
Hematology/Serology section, Chemical Pathology section and Anatomical Pathology section. The
overall significance of the laboratory diagnosis is that they guide towards the administration most
effective therapy so as to restore proper health on the patient.

2.0.2 SAFETY RULES IN THE LABORATORY.

Every laboratory should have a code of bio-safety principles and work practice which should be
enforced and strictly adhered to by laboratory staff and visitors. All specimens coming into and
from the laboratory are assumed to be infectious, that is why strict safety measures are put in
place to avoid contamination and laboratory hazard. Below are some laboratory safety rules:

1. Personal protective equipment like laboratory coat, head gears, protective eye glasses, hand gloves,
safety boats should be worn at all times when entering the laboratory.
2. The use of cell phones is strictly prohibited in the laboratory especially when specimens are being
worked on.
3. Eating, drinking, chewing gum and applying cosmetics are prohibited in the laboratory.
4. Appropriate clothing should be worn at all times in the laboratory, closed-toed shoes must be worn
(NO sandals or flip-flops), hair must be cut short, tied properly at the back or a scarf used to cover it,
dangling earing, hand bangles are also prohibited.
5. Foods and beverages for consumption should not be kept in laboratory freezers where specimens
are kept.
6. Never pipette anything by mouth.
7. The work area must be kept clean and uncluttered
8. All chemicals and specimens should be labelled and stored properly.
9. Never conduct unauthorized experiments, immediately report any unsafe behavior to the instructor
10. Pay attention to activities going on in and around the laboratory at all times.
11. Hazards of chemicals should be known (e.g. corrosiveness, flammability, reactivity, stability, and
toxicity).
12. Remove contaminated gloves before touching door knobs, faucets, equipment. Never use a glove
twice, discard any used glove properly before leaving the laboratory.
13. Turn off all electrical appliances before leaving the laboratory.
14. Avoid running in the laboratory.

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2.0.3. PHASES IN THE LABORATORY

There are three phases of laboratory testing: Pre-analytical, Analytical, Post analytical. PRE-

ANALYTICAL PHASE: The following are done in this stage

a. Positive identification
b. Patient preparation
c. Sample collection
d. Sample integrity

ANALYTICAL PHASE: The following are done in this stage

a. Standardization
b. Operating
c. Competence
d. Analysis quality
e. Assurance

POST-ANALYTICAL: The following are done in this stage

a. Result printing
b. Interfacing
c. Reporting
d. Communicating

2.0.4. LABORATORY EQUIPMENT AND THEIR USES

• AUTOCLAVE: This laboratory equipment is used to sterilize liquid substances such as

prepared media and saline (diluents) solutions, to sterilize glassware before use. It has the
same working principle as a domestic pressure cooker. Materials are autoclaved at 121
degrees Celsius, at 15psi for 30minutes.
• MICROSCOPE: This is a very important laboratory equipment as it serves as the eye of
microbiologists. Microorganisms cannot be seen with the ordinary eye there for the need
for microscope invention. It is used to see and study microorganisms. There are two main
types which are: The light microscope and electron microscope.
• REFRIGIRATOR: This serves as a repository for thermo labile chemicals, solutions,
antibiotics, serums, and biochemical reagents at cooler temperatures and even at subzero
temperatures. Stock cultures of bacteria are also stored in-between sub-culturing periods.
It is also used for the storage of sterilized media so as to prevent their dehydration.
• HOT AIR OVEN: This is used for sterilization of glassware such as test tubes, pipettes, petri-
dishes. Such dry sterilization is done for only glassware’s. Liquid substances such as

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 prepared media and saline solutions cannot be sterilized in oven, as they lose water due to
evaporation.
• COLONY COUNTER: This is used to count number of colonies in bacteria samples.
Sometimes, colonies are very small and are too crowded making it difficult to count.
Counting becomes easy when a mechanical hand counter called Quebec colony counter
is used. It divides the plate into several square divisions and the colonies are magnified
1.5 times by a magnifying glass which makes counting easy.
• CENTRIFUGE: This is equipment driven by a motor that spins liquid samples at high speed.
There are various types of centrifuges depending on the size and sample capacity.
Laboratory centrifuges work by the sedimentation principle, where the centripetal
acceleration is used to separate substances of greater and lesser density.
• INCUBATOR: This maintains a constant temperature specifically suitable for the growth of
a specific microbe. The usual temperature of incubation is 37 degrees Celsius. The
incubator has a thermostat that maintains a constant temperature set according to
requirements.
• BUNSEN BURNER: This is used to hold the flame and sterilize materials before inoculation.
• TEST TUBES: These are used to hold cultures in liquid form.
• TEST TUBES HOLDER: This is used to hold test tubes when being passed through flames.
• TEST TUBE RACK: This is used to hold, store and keep test tubes.
• INNOCULATING LOOP: It is used to inoculate organisms into culture media and broth.
• PETRI DISHES: This contains the media (chocolate, blood, MacConkey, nutrient, etc.) which
supports the growth of inoculated organisms.
• GLASS SLIDE: Smears are done on it. It is also used to view specimens under the
microscope.

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Fig 1.1 -laboratory equipments/instruments

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2.1 MEDIA PREPARATION

Culture media also known as growth media is a liquid or gel designed to support the growth of
microorganisms. Louis Pasteur created the first liquid artificial culture medium. Some
importance of culture media is: To obtain a pure culture of microorganisms, to grow and count
microbial cells, and to cultivate and select microorganisms.

CLASSIFICATION OF MEDIA

a. Nutrient agar, multipurpose or a general purpose media: This media is designed to grow most
organisms and do not contain growth inhibitors e.g. blood agar.
b. Differential media: This media allows the growth of different microorganisms at once but
differentiates them based on colors. For example, chocolate agar which is differential for gram-
positive cocci organisms.
c. Selective media: This media allows the growth of a particular organism and inhibits the
growth of others. An example is McConkey agar.

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 COMMON TYPES OF MEDIA

2.1.1. BLOOD AGAR

Materials:
0.5% peptone
0.3% beef extract
1.5% agar
0.5% sodium chloride
Distilled water
5% sheep blood
Ph required (7.2 - 7.6)

Procedure:

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 • The agar medium was prepared as instructed by the manufacturer, sterilized by
autoclaving for 15mins and then transferred to a 50 C water bath
• When the agar is cooled to 50 C and aseptically added in the sterile blood in already
warmed and mixed gently but well to avoid forming bubbles.
• 15ml amount was dispersed aseptically into sterile Petri dishes.
• The medium was dated and given batch number.
• The plates were stored at 2-8 oC preferably in sealed plastic bags to prevent loss of
moisture.

2.1.2. NUTRIENT AGAR

Materials:

Nutrient agar powder

Electric weighing balance

Conical flask

Measuring cylinder

Water Autoclave

Procedure:

• The agar medium was prepared as instructed by the manufacturer, sterilized by autoclaving
for 15minutes.
• 28g of powered nutrient agar is weighed using an electric weighing balance
• 1000 (1 liter) of water is measured using the measuring cylinder.
• The nutrient 28g is soaked and mixed thoroughly in the 1000ml of water and autoclaved for
1hour at 121 oC .
• The agar is allowed to cool for 1hour before pouring a petri dish.

2.1.3. MACCONKAY AGAR

Materials:
MacConkey agar
Electric weighing balance

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 Measuring cylinder
Conical flask
Autoclave Procedure:
• The agar medium was prepared as instructed by the manufacturer, sterilized by
autoclaving for 15 minutes.
• 52g of MacConkey is weighed using an electric weighting balance.
• 1000ml (1 liter) of water is measured using the measuring cylinder.
• The MacConkey (52g) is soaked and mixed thoroughly in 1000ml of water and auto-clave
for 1 hour at 121oC.
• After 1 hour, the Agar is allowed to cool before pouring into the Petri dish.

2.1.4. CYSTINE LACTOSE ELECTROLYTE DEFICIENT AGAR (CLED)

This agar is mainly used in isolating and enumerating bacteria in urine.

Materials:

3.0gram beef extract

0.128gram l-cystine

0.02gram bromothymol blue

10.0gram lactose

4.0gram enzymatic digest of gelatin

4.0gram enzymatic digest of casein

15.0gram agar

Ph 7.3+/-0.2

Distilled water

Procedure:

• The agar medium was prepared as instructed by the manufacturer.

• Suspend 36grams of the medium in 1litre of distilled water.
• Mix well and mix with frequent agitation, boil for one minute until complete to dissolution
• Autoclave at 121Oc for 15minutes
• Cool to 50Oc, mix well and dispense into plates. When the medium is solidified invert to
avoid excess moisture.

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2.1.5. CHOCOLATE AGAR

Chocolate agar is prepared the same way as blood agar, the only difference is blood agar is heated
in a water bath to prepare chocolate agar. Therefore, the same materials are used in preparing
both media.

Procedure:

• Prepare blood agar.

• Add 5-7% v/v of defibrinated blood (horse or sheep blood) and place the media in a water
bath of 75-80 oC and keep swirling gently until the colour changes to dark brown.
• Pour into sterile petri plates under aseptic conditions after the media has cooled to 50 Oc
• Label the plates correctly and store them in an inverted position at 2-8 Oc.
N/B: Other supplements such as isovitalex could be added during preparation.

2.1.6. BILE ESCULIN AGAR (BEA)

Materials:

5.00gram peptic digest of animal tissue

3.00gram beef extract

1.00gram esculin

40.0gram bile salts

0.50gram ferric citrate

15.00 agar

Ph 6.6+/-0.2

Distilled water

Procedure:

• The agar medium was prepared as instructed by the manufacturer.

• Suspend 64.5grams in 1litre distilled water.

• Heat to boiling to dissolve the medium completely.

• Dispense into tubes or flasks.

• Sterilize by autoclaving at 121 Oc for 15minutes.

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 • Allow the tubed medium to solidify and pour into sterile petri dishes.

• Allow the BEA medium warm too room temperature before use.
2.1.7. TRYPTIC SOY AGAR

Materials:

15.0gram pancreatic digest of casein

5.0gram peptic digest of soybean meal

5.0gram sodium chloride

15.0gram agar

Distilled water

Ph 7.3+/-0.2

Procedure:

• The agar medium was prepared as instructed by the manufacturer.

• Suspend 45grams of agar in 1litre distilled water.
• Heat to boiling to dissolve the medium completely
• Sterilize by autoclaving at 121 oC for 15minutes
• Cool to 50-45 Oc
• Mix well and pour into sterile petri dishes • Plates should be warmed to room temperature.

2.1.8. XLD AGAR Materials:

7.5gram lactose

7.5gram sucrose

6.8gram sodium thiosulphate

5.0gram l-lysine

3.75gram xylose
3.0gram yeast extract

2.5gram sodium deoxycholate

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0.8gram ferric ammonium citrate

0.08gram phenol red

15.0gram agar

Ph 7.4+/-0.2

Distilled water

Procedure:

• The agar medium was prepared as instructed by the manufacturer

• Suspend 55grams of dehydrated medium in 1litre distilled water
• Heat with frequent agitation until the medium boils
• DO NOT AUTOCLAVE
• Transfer immediately to a water bath at 50 Oc
• After cooling pour into sterile petri plates

N/B: It is not advisable to prepare large volume which will require prolonged heating and may
produce precipitate.

2.1.9 TRYPTIC SOY AGAR Materials:

10.0gram proteose peptone

75.0gram sodium chloride

10.0gram D-mannitol

1.0gram beef extract

0.025gram phenol red

15.0gram agar

Distilled water
Ph at 7.4+/-0.2

Procedure:

• The agar medium was prepared as instructed by the manufacturer.

• Suspend 15grams of MSA in 1litre of distilled water.
• Boil to dissolve the medium completely

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 • Sterilize by autoclaving at 121 oC for 15minutes
• If desired sterile egg yolk emulsion (E7899) can be added to a final concentration of 5% v/v after
autoclaving
• Pour cooled MSA into sterile petri dishes and allow to cool to room temperature.

2.1.10. PREPARATION OF BROTH MEDIA.

2.1.10.1. TRYPIC SOY BROTH (TSB)

Materials:

15.0gram of pancreatic digest of casein

5.0gram peptic digest of soybean meal

5.0gram sodium chloride

15.0gram agar

Distilled water Procedure:

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 •
Weigh 3gram of TSB powder and dissolve in 100ml distilled water
• Place the bottle on a magnetic stirrer to mix
• Aliquot 10ml of the medium to each 13*100mm glass spiral tubes • After aliquot,
place all tubes into the autoclave at 121 oC for 15 minutes
• Remove the tubes and make sure the cap of the tube is tightly closed.
• Fully cool autoclaved tubes at room temperature before placing stock in 4 oC
refrigerator and avoid light
• Pre-warm to room temperature before use.

2.1.10.2. CHOCOLATE AGAR SLANT

Materials used are the same materials used in preparing blood agar but the only difference is
blood agar is heated in a water bath to prepare chocolate agar slant.

Procedure:

• Dispense the 4ml of the medium into 16x125 screw caps tubes.
• Keep the tubes in slanted position and let them solidify
• Chocolate agar slants appear brown to brownish-red in color. They should be stored at 4
oC when not in use and warmed to room temperature before use.

2.2. GRAM STAINING

Gram Stain is a common technique used to differentiate two large groups of bacteria based on
their different cell wall constituents.
The basic principle of gram staining involves the ability of the bacterial cell wall to retain the
crystal violet dye during solvent treatment. Gram-positive microorganisms have higher
peptidoglycan content while Gram-negative organisms have higher lipid content. A gram stain
is often used to find out if a patient has a bacterial infection.
MATERIALS USED FOR GRAM STAINING
• Primary dye: Crystal violet
• Mordant: Lucose iodine
• Decolorizer: Acetone or alcohol
• Secondary dye or Counter stain: Neutral red or Safranin

PROCEDURE FOR GRAM STAINING

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 •
• Make a smear on a clean glass slide depending on the test to be carried out, example for
wound swab test use the swab stick to make a smear on the slide.
• Heat fix with glass slide to ensure complete dryness.
• Stain the smeared glass slide using the primary stain or dye which is the crystal violet.
Allow it to stay for 30-60 seconds and then rinse under running water for approximately
10 seconds.
• Stain the glass slide again with the mordant which is lucose iodine.
• Leave for 30-60 seconds and then rinse under running water for approximately 10
seconds.
• Decolorize the glass slide using acetone or alcohol, rinse immediately under running
water for approximately 10 seconds.
• Counter stain the smeared slide with neutral red or safranin.
• Leave for 60-120 seconds and rinse under running water for approximately 10 seconds.
• Allow the glass slide to dry completely.
• View the dried glass slide using x100 magnification using immersion oil.

2.3. TESTS

2.3.1 BIOCHEMICAL TESTS

Biochemical tests are the tests used for the identification of bacteria species based on the
differences in the biochemical activities of different bacteria. Bacterial physiology differs
from one type of organism to another

HOW TO PERFORM BIOCHEMICAL TESTS

1. Dilute the organism in a tube of sterile water to obtain a turbidity equivalent to the 0.5
mcfarland test standard.
2. Using a sterile 1ml pipette, place 1ml of organism into the middle of the tube.
3. Cap tightly, do not jostle.
4. Incubate for 24hours at 37 oC

BIOCHEMICAL TESTS USED TO IDENTIFY GRAM POSITIVE BACTERIA.

• Catalase test
• Mannitol salt agar (MSA)
• Blood agar plates (BAP)
• Streak-stab technique
• Taxos A (bacitracin sensitivity testing)

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 •
• Taxos P (optochin sensitivity testing)
• CAMP test
• Bile esculin agar
• Nitrate broth
• Spirit blue agar
• Starch hydrolysis test
• Motility agar
Coagulase test.

BIOCHEMICAL TESTS USED TO IDENTIFY GRAM NEGATIVE BACTERIA.

• Oxidase test
• Sugar (e. g glucose) broth with durham tubes
• Methyl Red/ Vogus Proskaeur (MR/VP)
• Kilger’s iron agar (KIA)
• Nitrate broth
• Motility agar
• MacConkey agar
• Simmons citrate agar
• Urease test
• Sulphur indole motility media (SIM)

• SULPHUR INDOLE MOTILITYMEDIA: This is a differential medium used to determine

whether an organism is equipped with flagella and thus capable of swimming away from
a stab mark. If the entire tube is morbid, this indicates that the bacteria has moved
away from the stab mark i.e the organism is motile but if the stab mark is clearly visible
and the rest of the tube is not turbid, the organism is likely non-motile.
• METHYL RED/VOGUS PROSKAEUR: This test is used to determine which fermentation
pathway is used to utilize glucose.
• COAGULASE TEST: This is an enzyme that clots blood plasma. The test is performed to
identify the coagulase-positive Staphylococcus aureus. The test differentiates
Staphylococcus aureus from other coagulase-negative staphylococcus species.
• OXIDASE TEST: This test is used to identify microorganisms containing the enzyme
cytochrome oxidase. It is commonly used to distinguish between oxidase-negative
Enterobacteriaceae and oxidase-positive pseudomadaceae.
• CATALASE TEST: This test is used to identify organisms that produce the enzyme
catalase. This enzyme detoxifies hydrogen peroxide by breaking it down into water and

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 •
oxygen gas. The bubbles resulting from the production of oxygen gas clearly indicate a
catalase result.

2.3.2. URINE PROCESSING

Urine is a liquid by-product of the body secreted by the kidneys through a process called
urination and excreted through the urethra. The normal chemical composition of urine is
mainly water content but it also includes nitrogenous molecules such as urea as well as
creatinine and other metabolic waste molecules.

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 When a urine sample is collected, macroscopy i.e physical examination of the urine
is carried out, and microscopy, culture, and sensitivity tests are also carried out. Normal
urine should be amber and clear.

TYPES OF URINE SPECIMENS

1. First-morning specimen
2. The single random specimens can be collected to conduct pregnancy tests
3. Timed short-term specimen
4. Timed long-term specimens i.e 12-24 hours are usually collected to conduct
biochemical tests.
5. Catheterized specimen or specimen from an indwelling catheter
6. Double-voided specimens (test for sugar or acetone )
7. Clean catch (midstream) specimen for urine culture and cytological analysis.

URINE SAMPLE COLLECTION

• A sterile screw-top container should be labeled with the patient's name, date
of birth, and date.
• The patient should be told to wash their hands before collecting the urine
• The part of the urine needed for diagnosis should be put into the sterile
bottle i.e first part, mid-stream, or last part urine.
• The container should be closed tightly and sent to the laboratory within
1hour.

N/B: Urine should be stored in a refrigerator or boric acid can be used in the
absence of a refrigerator to prevent the urine

Urine tests are most commonly done to check for:

Infections such as urinary tract infections (UTI) or some sexually transmitted

infections (STI). The first part of a urine sample is collected to check for organisms like
schistomia, Mid-stream urine is collected mainly for culturing because there is a reduced
chance of the midstream urine being infected by bacteria, Last part is collected to check for
organisms like Neisseria gonorrhea. WHAT CAN BE FOUND IN THE SAMPLE?

1. Blood; this is known as HEMATORIA which can be due to trauma, prostate cancer, etc
2. Pus cells; these are more prominent in a cloudy urine sample and can be due to
inflammation and infection.
3. Epithelial cells; can be due to urine contamination
4. Casts and Crystals; can be due to renal and kidney malfunction
5. Red blood cells; can be due to injury, renal stone, or cancer.

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 URINALYSIS

MACROSCOPY (TEST 1)

• Look at the appearance of the urine

• Check for color and turbidity of the urine, and report it e.g clear, amber, or cloudy
red as the case may be.

BIOCHEMICAL (TEST 2): This is also known as the combi-10, multi stick or dipstick test. Here a
urine dipstick is gently placed inside the urine. The following are looked out for; Protein

Blood cells

Glucose

Ph

Bilirubin

Urobilinogen

Ketone bodies

Nitrites

Leukocyte esterase.

The presence of Nitrite, Protein, and Leukocyte esterase indicates possible infections in a
urine sample.

MICROSCOPY (TEST3): This is also known as a wet mouth test

• Centrifuge the urine for 5 minutes at 2500 revolution

• Empty the centrifuged urine
• Place the droplets on a microscopic glass slide
• Place a cover slip over the urine droplets
• View under a microscope using x40 magnification.

CULTURING (TEST 4)

The urine is inoculated on blood agar and is used to check for discrete colonies of organisms.

The most suitable agar used for urine culturing is the Cysteine lactose electrolyte deficient agar
(CLED), it is selective for gram-negative organisms and very suitable for urinary tract pathogens.

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2.3.3. LABORATORY DIAGNOSIS OF MALARIA

Malaria is a disease caused by a plasmodium parasite transmitted by the bite of an infected

female anopheles’ mosquito. The severity of malaria varies based on the species of
plasmodium; a mosquito gets infected when it picks up gametocyte parasite from an
intermediate host (man).

A plasmodium parasite definitive host is the female anopheles’ mosquito and its intermediate
host is man. The lungs are the most affected organs in severe malaria infection. EDTA bottles
are used to collect blood for malaria parasite test to prevent the blood from clotting.

TYPES OF MALARIA PARASITES

• Plasmodium falciparum (P. falciparum)

• Plasmodium malariae ( P. malariae)
• Plasmodium vivax (P.vivax)
• Plasmodium ovale (P. ovale)
• Plasmodium knowlesi (P. knowlesi)

WAYS TO CARRY OUT MALARIA PARASITE TEST

a. Microscopy: This is the World Health Organization (WHO) accepted standard.

b. Rapid diagnostic test kit (RDT): This kit has an antibody embedded in it which binds with
the antigen in the blood and forms a line.
c. Polymerase chain reaction (PCR) test

HOW TO PERFORM MICROSCOPY

• Clean a microscopic glass slide properly to remove grease and dirt.
• Label the slide appropriately.
• Make a thin fame one end of the slide and a thick fame on another end of the slide.
N/B: The quantity of blood used for the thick fame should be more than what is
used for the thin fame. The thick fame shows the quantity of parasite i.e., the
degree of parasitemia, the thin fame shows the actual specie.
• Leave the slide for about 4 hours to dry.
• After drying the blood, fix the thin fame with methanol. Fixing the thin fame helps
the morphology of the red blood cells to be intact.

There are two ways to fix the thin fame;

• Fast stain: This is done with 1ml of gymsa stain and 9ml of buffer water kept for 10-
15 minutes.

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 • Slow stain: This is done with 3ml of gymsa stain and 97ml buffer water kept for 20
minutes.

2.3.4. BLOOD CULTURE

Blood culture is a test of a blood sample to find germs such as bacteria or fungi that can cause
an infection. A blood sample should be collected under aseptic conditions.

A blood sample can be requested for various reasons; bacteriamia is a request for blood
culture for a patient that has malaria, blood culture is also requested for new born, blood
culture is also requested for patients with high fever and for this patient blood should be
collected at the moment the fever begins to rise. 1-3 ml of blood is taken for infants that
require blood culture and 8-10ml is taken for adults that require blood culture.

BLOOD DISORDERS

• Anemia of chronic diseases

• Aplastic anemia
• Erythrocytosis
• Hemochromatosis
• Hyper coagulable disorder
• Immune thrombocytopenic purpura • Iron deficiency anemia
• Leukocytosis.

The most suitable media used for blood culturing is the blood agar. Common organisms like
Haemophilus influenza, Streptococcus pneumoniae and Neisseria species are likely to be found
in the blood and are grown on blood agar. It is also required to detect and differentiate
haemolytic bacteria. Bactec Fx40 machine which is a semi-automated machine detects growth
in a blood sample.

Steps in carrying out blood culturing on blood agar

• A wire loop was heat, allowed to cool and used to take a loopful of the blood sample.
• Make a well in the agar medium, heat the wire loop again and allow to cool.
• Make the first, second, and third streaks accordingly. Close the medium and incubate, to
enable growth.
N/B: Avoid talking while culturing to prevent contamination and wrong results.

2.3.5. SEROLOGY
Serology is the scientific study of serum and other body fluids. The term usually refers
to the diagnostic identification of antibodies in the serum. Serology test is the antibody
test that looks for the presence of antibodies. Its basic principle is the antigen-antibody
reaction, serology tests can be used to identify different organism strains.

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 SEROLOGICAL DISEASES
• Brucellosis caused by bacteria
• Amebiasis caused by a parasite
• Measles caused by a virus
• Rubella caused by a virus
• HIV, Syphilis and other fungal infections.

Serological diagnosis is usually based on either the demonstration of the presence of specific
IgM antibodies or a significant increase in the levels of specific IgG antibodies between two
consecutive samples taken 1-4 weeks apart. Specific kits are used for specific antigens and
antibodies.

SEROLOGICAL TESTS

• Blood analysis
• Syphilis test
• Cephalin-cholesterol flocculation
• Flocculation test
• Complement fixation test
• Wasserman test
• Hemagglutinin inhibition test
• Kahn test

2.3.6 STOOL ANALYSIS

Stool analysis is a series of tests done on a stool (feces) sample to help diagnose certain
conditions affecting the digestive tract. It is also done to see how well the pancreas is
working

TYPES OF STOOL TESTS

Fecal occult blood test: This test helps to check hidden or occult blood in stool.
•
Symptoms;
• Polyps (non-cancerous tissue growth on your mucous membrane).
• Colitis (inflammation of colon)
• Haemorrhoid
• Ulcers
• Colorectal cancer

• Stool DNA tests: Detects abnormal DNA that occurs normally because of colon
polyps or colon cancer.

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 Ova and parasites tests: This is done to check for parasites or ova (egg) in stool
•
sample.
Symptoms;
• Presence of blood or mucus in stool
• Frequent diarrhea
• Fever
• Acute abdominal pain
• Headache
• Vomiting or nausea.

White blood cell tests: This is done to detect leukocytes or white blood cells in
•
stool sample. Leukocytes in stool may indicate a bacterial infection.
Symptoms;
• Mucus or blood in stool
• Fever
• Abdominal pain
• Fatigue
• Watery diarrhea that lasts more than four days

H-Pylori antigen tests: This is used to detect H-Pylori inside the digestive tract,
•
check whether the digestive symptoms are caused by an infection, determine
whether the treatment is working or not.
Symptoms;
• Abdominal pain
• Nausea
• Indigestion
• Frequent vomiting
• Bloated feeling

A normal stool is semi-solid and usually brown in color. There is no fixed timing for a stool
sample collection but a watery stool should get to the laboratory in 15minutes and it can be
collected using a rectal swab that contains a preservative. Various abnormal stool samples can
be an indication of certain infections example blood in stool can be an indication of colon
cancer, a malformed stool is an indication of indigestion.

ILLNESSESS ASSOCIATED WITH STOOL

• Constipation
• Hemorrhoids
• Anal fistula
• Perianal abscesses
• Colitis
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 • Irritable bowel syndrome

STOOL SAMPLE PREPARATION: Stool can be prepared by wet mouth method using
normal saline. The saline wet mouth is used for the initial microscopic examination
of stool. It is employed primarily to demonstrate worm eggs, larvae, protozoan,
trophozoites and cysts. It can also reveal the presence of white and red blood cells.
Common media used for stool culturing are:

• Non-selective medium i.e Sabouraud agar

• Mildly selective medium i.e MacConkey agar
• Moderately selective differential medium i.e Hektoen enteric agar.

2.3.7. INTRACERIVAL AND HIGH VAGINAL SWAB PROCESSING

Swab is a piece of soft material sometimes on the end of a small stick used for applying
medicine, cleaning up wound and collecting sample from a person’s body.

2.3.7.1. HIGH VAGINAL SWAB (HVS).

This is a medical procedure performed in obstetrics and gynaecology to test vaginal

discharge for presence of vaginal thrush, bacterial vaginosis and trichomonas vaginalis. A
swab is used for performing HVS and it is carried out in clean conditions by a health care
professional.

Equipment used:

• Gloves
• Lubricant
• Light source
• Speculum
• Light source
• Paper towels • Cotton wool.

Procedure:

• Personal protective equipment should be worn and hands washed properly

• Make an introduction to the patient and confirm patient details
• Explain the procedure to the patient using a patient friendly language
• Gain consent and ask relevant questions before beginning the procedure
• The patient should lie down straight facing upwards with legs open
• A light source should be in place
• Gently put the speculum inside the vagina

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 • Insert the swab to the top of the vagina and rotate around to obtain a sample of the
discharge
• Gently remove the speculum again
• The sample should be sent to the laboratory for microscopy.

2.3.7.2. ENDOCERVICAL OR INTRACERVICAL SWAB

Here a swab is used to take samples of mucus and cells from the endo cervix. This is the
area around the opening of the uterus. It is a test that checks for abnormal bacteria in or
around the cervix.

Procedure:

The NAAT swab should be performed first and this is used to detect chlamydia and
gonorrhea. The NAAT kit usually contains two swabs, an endocervical and vulvovaginal. The
large tipped white vulvovaginal swab is used to take a sample from the posterior fornix of
the vagina and lower vaginal walls.

• Remove the thin endocervical swab from the packet

• With the speculum in situ pass the tip of the swab through the speculum of the
vaginal OS
• Insert the swab gently into the cervix
• Rotate the swab 10-15 seconds in the endocervix
• Remove thee swab and open the NAAT test tube from the packet • Insert the
swab into the NAAT test tube
• Screw the lid into the NAAT test tube.

CHAPTER 3
3.1. PROBLEMS ENCOUNTERED

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First students were not allowed to work on specimen in the main laboratories. They were made to
watch while the laboratory scientists worked. It took a couple of months before students were allowed
to work on samples.

Secondly, transportation the facility was difficult at some point because of financial constraints.

3.2 RELEVANCE OF THE SIWES PROGRAM

Student internship programs can be highly relevant for a variety of reasons. Some of the main benefits
include:

Hands-on experience: Internships provide students with the opportunity to apply the skills and
knowledge they have learned in the classroom to real-world situations. This can help them to better
understand the practical applications of their education and gain valuable experience in their chosen
field.

Networking opportunities: Internships often provide students with the chance to interact with and learn
from experienced professionals in their field. This can help them to build connections and establish
relationships that can be valuable later on in their careers.

Career exploration: Internships can help students to explore different career paths and gain a better
understanding of the different roles and responsibilities within a particular field. This can help them to
make more informed decisions about their future careers.

Improved employability: Employers often view internships as a sign of initiative and motivation, and may
be more likely to hire candidates who have completed internships in their field.

Overall, internships are a great way for students to gain valuable experience, explore different career
paths, and improve their employability.

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CHAPTER FOUR

4.0 CONCLUSION AND GENERAL APPRAISAL OF PROGRAM

In view of the student industrial work experience scheme(SIWES), I have been

prepared and also given the adequate practical background needed for my course of
study. After my training in the University of Port Harcourt Teaching hospital(UPTH);
i. I can effectively attend to patients in a laboratory and collect blood
samples in any organization I find myself in the nearest future.
ii. I can effectively conduct most tests pertaining to medical Microbiology.
iii. I can make use of most machines found in a laboratory.

I sincerely commend the Federal Government and the National University

Commission (NUC) for the implementation of this scheme and also the industrial
training fund (ITF) for initiating the SIWES program in Nigerian Universities,
preparing students for work experience.

4.1 WAYS OF IMPROVING THE PROGRAM

In order to achieve a greater impact on students through the industrial training, I

recommend that;

• There should be an improvement of allowance and free transportation

for students on attachment to their various organizations.

• There should be a proper placement of the students for such program

by the industrial training department of each institution through creating a
strong alliance with different organizations.

• There should be a proper supervision of the students concerned by

both the ITF and Institution- based supervisors.

4.2 ADVICE FOR FUTURE PARTICIPANTS

To obtain and experience the benefits of a program like this, full participation is required,
therefore I will advise future participants to note the following;

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  Attend SIWES orientation program before going for industrial training attachment.
 They should be sincere in getting a place of training, and not just for monetary gain
but for the relevance of the program and the impact thereafter.
 Take the training serious since it is one of the requirement to obtain the Bachelor of
Science Degree.
 They should be sincere, humble, obedient to instructions, friendly, loyal and
hardworking in their area of attachment as this are some of the hallmark of every Firm
while granting employment.
 Students should be aware of the kind of machinery they are working with and also be
very careful in handling chemical substances as most of them are hazardous to both
human and the environment if carelessly handled.
 Students should keep proper record of their daily activities in the course of training in
their logbooks.
 They should ensure that their reports, materials and logbooks are duly signed by
relevant authorities while rounding-up the program.

CONCLUSION:

SIWES at UPTH exposed me to practical aspects of microbiology, and the role it plays in
diagnosis of diseases and prescription of antibiotics for the treatment of various diseases which
complements the lectures taken in the classroom. The scheme must be applauded for exposing
the students to professionals in the field. I recommend this program to upcoming students.
REFERENCE:

District laboratory practice in tropical countries second edition Monica Cheesbrough Prescott

microbiology https://www.laboratorydeal.com/products/microbiological-lab-equipment-list

https://microbiologie-clinique.com/microbiology-culture-media.html

https://www.otago.ac.nz/oms/education/medlabsci/undergraduate/bmedlabsci/microbiology/

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