College of natural and computational sciences

School of biological sciences and biotechnology

Department of biotechnology

Research method and report writing proposal

Title: Investigating the Antimicrobial Resistance Profile of Selected
Enteric Pathogens at Hiwot Fana Hospital, Harar.

Proposal
Authors ID
 Abenezer tesfaye: principal investigator 0163/13
 Malede melaku 4451/13
 Tesfalegn tegegn 2874/12
 Emeway alie 0945/13
 Mulunesh abate 2103/13
 Hassen abate 1397/13

Supervisor : Andarge zelalem (PhD), Assistant Professor, Microbiology)

 SUMMARY

Antimicrobial resistance (AMR) poses a significant global health challenge,

necessitating continuous surveillance efforts. This study conducted at Hiwot Fana
Specialized University Hospital, Harar, Eastern Ethiopia, aimed to investigate the
prevalence and distribution of AMR among patients admitted to various hospital
wards. The primary objective was to assess the prevalence of AMR, identify common
bacterial pathogens, and understand their susceptibility patterns in a hospital setting.
A cross-sectional analysis will be conducted on clinical isolates collected from
patients presenting with enteric infections between Septembers through December,
2024. Bacterial strains, including Escherichia coli, Salmonella spp., and Shigella spp.,
will be isolated from clinical specimens and subjected to susceptibility testing against
a panel of commonly prescribed antibiotics. Preliminary findings are expected to
reveal a concerning level of resistance among the targeted enteric pathogens, raising
alarms about the effectiveness of standard treatment regimens. Notably, resistance
rates will vary among different classes of antibiotics, highlighting the need for
judicious antibiotic use and the development of tailored treatment strategies. This
research will contribute valuable insights into the future landscape of antimicrobial
resistance in enteric pathogens at Hiwot Fana Hospital, providing a foundation for
future interventions aimed at preserving the efficacy of existing antibiotics and
safeguarding public health.

Keyword :Antimicrobial resistance, Hiwot Fana hospital ,haramaya university, Harar,

ethiopia,
 Table of content

Contents Page
1. Introduction……………………………….……………………………………..1

1.1. Background of the study……………………………………………………. 1

1.2. Objectives of the Study…………………………………………………….…3

1.2.1.General objective…………………………………………………………3

1.2.2.Specific objectives.....................................................................................3
2. Literature review………………..…………….…………...………………………4
2.1 Origin of Antibiotic Resistance…………………………………………….4
2.3 Consequence of Antibiotic Resistance……………………………………..4
2.4 Regulatory Issues Related to Antibiotic Resistance………………………..5
2.5 The treatment of antibiotic resistance….………………………………………6
3. Materials and methods……………………………………………………………..7
3.1 Study area description……………………………………………………..7
3.2 Study Setting and Design………………………………………………….7
3.3 Study Population………………………………………………………….7
3.4 Sample Size and Sampling Technique…………………………………….7
3.5 Data and Specimen Collection…………………………………………….8
3.6 Processing of Specimens………………………………………………….8
3.7 Quality Control……………………………………………………………8
3.8 Ethical Consideration……………………………………………………..9
4. Work plan ……………………….……………………………………….11
4.1 Table 1: Time frame for proposal writing at Hiwot Fana hospital Harar………11
5. Budget breakdown…………………………………………………………12
5.1 Table 2: Require financial budgeting for proposal implementing……………12
6. References……….…………………………………………………………..……13
 1. INTRODUCTION

1.1. Background

Antimicrobial resistance refers to the ability of microorganisms, such as bacteria,

viruses, parasites, and fungi, to resist the effects of medications that were previously
effective in treating them. This resistance is a global public health concern because it
can lead to the failure of standard treatments, resulting in prolonged illness, increased
healthcare costs, and a higher risk of spread of infections to others. Antimicrobial
resistance (AMR) is one of the top global public health and development threats. It is
estimated that bacterial AMR was directly responsible for 1.27 million global deaths
in 2019 and contributed to 4.95 million deaths. The misuse and overuse of
antimicrobials in humans, animals and plants are the main drivers in the development
of drug-resistant pathogens. AMR affects countries in all regions and at all income
levels. Its drivers and consequences are exacerbated by poverty and inequality, and
low- and middle-income countries are most affected (WHO, 2023).

The global challenge of antimicrobial resistance (AMR) has emerged as a critical

concern in the 21st century. Projections estimate that by 2050, infections caused by
resistant strains could result in 300 million premature deaths. The resistance of
bacterial strains to antibiotics can occur through natural mechanisms or the
acquisition of resistance determinants. While multiple factors contribute to the
development of resistance, the abusive use of antibiotics is identified as a significant
accelerant in this process. The longevity of AMR as a phenomenon, coupled with its
accelerated evolution, underscores the urgent need for effective strategies to mitigate
its impact. Complicating this challenge is the widespread and boundary less
dissemination of antibiotic resistance genes (ARGs) across diverse environments,
including humans, animals, clinical settings, and the broader environment. Addressing
this complex issue requires concerted efforts to curb the abusive use of antibiotics and
implement comprehensive measures to reduce the threat of AMR (WHO, 2023).

Infectious diseases pose significant challenges to public health and global economies.
Bacteria, accounting for over 54% of global infectious diseases, contribute

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substantially to this burden. Antimicrobials play a pivotal role in medical
interventions against bacteria, viruses, fungi, and parasites, serving as crucial tools for
preventing and treating microbial infections. These antimicrobial agents act by either
eliminating or inhibiting microbial growth, disrupting essential cellular processes such
as DNA, RNA, and protein syntheses, cell wall biosynthesis, and folate metabolism
(majumder et al., 2020 ).

Unfortunately, recent reports highlight a concerning trend—the efficacy of numerous

antimicrobials is increasingly compromised due to the emergence of antimicrobial
resistance (AMR) in pathogens. This resistance phenomenon poses a serious threat to
the effectiveness of existing treatments and raises the urgency for comprehensive
efforts to understand, monitor, and address the growing issue of antimicrobial
resistance (kumar et al., 2017).

Harar, a central town in the Harari Regional State, faces distinct health challenges,
and understanding the dynamics of antimicrobial resistance (AMR) in Hiwot Fana
Hospital is vital for tailoring interventions to address the unique healthcare needs of
this region. Serving as a critical referral center for the eastern parts of Ethiopia, Hiwot
Fana Specialized University Hospital plays a pivotal role in catering to a diverse
patient population. This makes it an ideal setting for studying AMR patterns due to
the potential influx of cases from various geographic and demographic backgrounds.

The emergence of antimicrobial-resistant bacteria, particularly pathogens like

Pseudomonas aeruginosa, Staphylococcus aureus, Enterococci spp., Klebsiella spp.,
and Enterobacter spp., poses a significant public health challenge, adding strain to
contemporary medical care within hospital settings. Of particular concern is
methicillin-resistant Staphylococcus aureus (MRSA), known for causing substantial
morbidity and mortality in hospitalized patients. Infections caused by resistant
bacteria impact outcomes for critically ill patients, diminish treatment probabilities,
prolong hospital stays, escalate healthcare costs, and facilitate the easier spread of
infection, making prevention more challenging(mancuso et ai., 2021 ).

The specific objectives include determining the prevalence of culture-confirmed

AMR, identifying and characterizing common bacterial pathogens, assessing

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antimicrobial susceptibility patterns, exploring infection distribution across hospital
wards, and analyzing the prevalence of multidrug-resistant bacterial strains. The
findings are expected to contribute to the broader understanding of AMR in the
Ethiopian healthcare context, offering a foundation for evidence-based strategies to
combat the emergence and spread of antimicrobial resistance in Eastern Ethiopia
(tolera et al., 2018).

One potential research gap in the context of the study at Hiwot Fana Specialized
University Hospital is the lack of comprehensive data on the prevalence and patterns
of antimicrobial resistance (AMR) specifically among enteric pathogens in the region.
While the study aims to investigate the prevalence and distribution of AMR among
patients admitted to various hospital wards, it focuses on enteric pathogens such as
Escherichia coli, Salmonella spp., and Shigella spp. This research gap suggests that
there may be limited information available on the specific AMR profiles of these
pathogens in the study setting.

1.2 Objective
1.2.1 General objective
 To investigate the prevalence and distribution of antimicrobial resistance (AMR)
among patients admitted to Hiwot Fana Specialized University Hospital in Harar,
Eastern Ethiopia, with a focus on understanding the susceptibility patterns of
bacterial pathogens.

1.2.2 specific objective

 To collect clinical specimens from patients presenting with enteric infections at
Hiwot Fana Hospital.
 To determine susceptibility testing on isolated bacterial strains using a
predetermined panel of commonly prescribed antibiotics.
 To Evaluate and record the resistance patterns of each enteric pathogen against
the selected antibiotics.

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 2. LITERATURE REVIEW

2.1 Origin of Antibiotic Resistance

Antibiotic resistance occurs when a drug loses its ability to inhibit bacterial growth
effectively. Bacteria become 'resistant' and continue to multiply in the presence of
therapeutic levels of antibiotics. When bacteria replicate even in the presence of
antibiotics, they are called resistant bacteria (reygaert et al., 2018).

2.2Development of antimicrobial resistance

The development of antimicrobial resistance (AMR) stems from various factors that
influence the evolution and transmission of resistance genes among microorganisms.
Natural genetic mutations in bacteria, viruses, and other microorganisms can confer
resistance to antimicrobial agents, providing a survival advantage. Selective pressure,
exerted by the widespread and often inappropriate use of antimicrobial drugs,
promotes the proliferation of microbes with resistance traits. Bacteria further
contribute to AMR through horizontal gene transfer mechanisms, allowing rapid
dissemination of resistance genes among different species. Inadequate use of
antimicrobials, incomplete antibiotic courses, and the agricultural use of these agents
for growth promotion contribute to the persistence of resistant strains. Environmental
factors, such as the release of antibiotics into wastewater and global movement of
people and goods, further complicate the challenge, making AMR a global health
concern (julian davies et al., 2011).

2.3 Consequence of Antibiotic Resistance

The consequences of AMR are profound and extend beyond healthcare. Diminished
treatment efficacy results in prolonged illnesses, increased infection severity, and
higher mortality rates. The need for alternative, often more expensive, treatments
raises healthcare costs substantially, impacting both individuals and healthcare
systems. Resistant strains can spread within and across communities, posing a risk of
persistent and difficult-to-control outbreaks. The agricultural and veterinary sectors
are also affected, with resistant bacteria transferring between animals and humans.
AMR undermines infection prevention measures, complicating medical procedures

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and compromising the control of infection spread. Chronic diseases such as diabetes
and cancer face compromised treatment options due to limited availability of effective
antimicrobials. The emergence of drug-resistant pathogens represents a significant
threat to global health security, as these strains can rapidly cross borders, making
infectious diseases more challenging to control on a global scaled (WHO, 2023).

2.4 Regulatory Issues Related to Antibiotic Resistance

The absence of universal standards and regulations for antibiotic use and surveillance
contributes to the inconsistent implementation of measures to combat antibiotic
resistance. Harmonized global regulations are essential to effectively address this
transnational health threat. In many regions, antibiotics are available over the counter
without a prescription, fostering misuse, overuse, and inappropriate dosage that
contribute to the development of antibiotic-resistant strains. Strengthening regulations
on antibiotic sales is crucial to curbing these practices. Gaps in surveillance systems
for antibiotic use and resistance hinder a comprehensive understanding of the scope
and dynamics of the problem.

Establishing and enforcing robust surveillance mechanisms are imperative for

effective regulation. Stringent regulatory pathways for approving new antibiotics can
limit their availability. Creating expedited and flexible regulatory frameworks that
balance safety with timely access to new antibiotics is essential to address emerging
resistance. The use of antibiotics in agriculture for growth promotion and disease
prevention significantly contributes to antibiotic resistance, with regulatory
frameworks often lacking strict oversight in this sector. Global collaboration faces
challenges due to differing regulatory standards and practices across countries,
impeding the development of unified strategies to combat antibiotic resistance.

Limited financial incentives for pharmaceutical companies to invest in research and

development of new antibiotics contribute to a stagnant pipeline, necessitating
regulatory frameworks to include incentives for innovation. Public awareness about
responsible antibiotic use is often insufficient, highlighting the need for regulatory
bodies to implement measures to educate the public, healthcare professionals, and
stakeholders. Even when regulations exist, poor enforcement may be a challenge,
emphasizing the crucial need to strengthen regulatory enforcement mechanisms,

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including penalties for non-compliance. Regulatory frameworks often lack integration
between human health, animal health, and environmental considerations, highlighting
the importance of a comprehensive One Health approach integrated into regulatory
strategies (WHO, 2018).

With an abundance of evidence, there is no scope to ignore global antibiotic

resistance. Antibiotic resistance can be more prevalent where antibiotic consumption
is found to be higher. Lack of regulation and control in using antibiotics is prominent
and needs to be targeted at a global capacity. Developing nations are at the greatest
risk. Low prices of antibiotics, ease of availability, and unnecessary use of antibiotics
are causing more burden in developing countries. Treatments for bacterial infections
are becoming intensified every day. Infections remain as antibiotics gain resistance;
treatment failure is common due to antibiotic resistance and multi-drug resistance, for
example, tuberculosis(zaman et al., 2017).

Newer and effective antibiotics that have no known resistance to bacteria are in high
demand. Alternative treatment procedures are under consideration to fight bacterial
infection. Passive immunization or administration of antibodies to non-immunized
individuals to prevent bacterial infections have been found effective. Another
effective intervention is phage therapy, whereas bacteriophages are used to treat
pathogenic bacterial infections. Many newer classes of antimicrobials to fight
antibiotic resistance are in the pipeline for clinical trials. Intervention strategies are
aimed not only at targets but rather at the biological networks that may help create
new antibacterial therapies. Combination therapies coupling antibiotics with
antibiotic-enhancing phage have demonstrated the potential to be a promising
antimicrobial intervention (zaman et al., 2017).

The treatment of antibiotic resistance necessitates a comprehensive approach

addressing the emergence and dissemination of resistant bacterial strains. This
strategy encompasses several key facets, including the prudent use of antibiotics, the
development of new antimicrobial agents, enhanced surveillance, and global
collaboration. A fundamental aspect of the treatment approach involves the
implementation of antibiotic stewardship programs within healthcare settings. These
programs are designed to promote judicious antibiotic use through the monitoring and

6
regulation of prescriptions, ultimately minimizing the risks of overuse and misuse.
Simultaneously, education initiatives targeting healthcare professionals, patients, and
the general public play a crucial role in fostering responsible antibiotic usage(salam et
al.,2023 ).

Another pivotal component is the enhancement of surveillance and monitoring

mechanisms, involving the strengthening of systems to monitor antibiotic use, the
development of comprehensive databases to share global resistance patterns, and the
implementation of real-time monitoring tools to promptly identify and respond to
emerging resistance trends. Furthermore, establishing universal standards and
regulations for antibiotic use and surveillance, fostering international collaboration for
harmonized approaches, and encouraging global adherence to common guidelines
represent critical steps in the battle against antibiotic resistance. Additionally, research
and development efforts aimed at creating new antibiotics are integral to expanding
our arsenal of effective antimicrobial agents, ensuring continued efficacy in the face
of evolving resistance challenges (CDC, 2023).
]

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 3. MATERIALS AND METHODS

3.1 . Study area description

Eastern Ethiopia, with Harar as its prominent medical hub, faces unique healthcare
challenges. Hiwot Fana Specialized University Hospital, as a referral center, plays a
pivotal role in addressing these challenges. The study aims to investigate the
susceptibility patterns of bacterial pathogens causing infections among patients with
clinical evidence of AMR. By exploring the prevalence and distribution of AMR in
different hospital wards and infection sites, the research seeks to provide valuable
insights that can inform targeted interventions and guide antimicrobial stewardship
initiatives.

3.2. Study Setting and Design

A cross-sectional quantitative study involving bacteriological analysis will be
undertaken at Hiwot Fana Specialized University Hospital, Harar, Eastern Ethiopia.
Harar, situated 525 km from Addis Ababa, Ethiopia, and serving as the political and
administrative town of the Harari Regional State, will be the study location. The
region, comprising six hospitals and eight health centers, will serve as the backdrop
for the investigation. Hiwot Fana Specialized University Hospital, functioning as a
referral hospital for the eastern parts of the country, will be the focal point for health
care services, characterized by the largest client load and an anticipated average bed
occupancy rate of 83%. The hospital, in this upcoming study, will be explored across
its six major wards: Medical, Surgical, Obstetrics, Gynecology, Malnutrition, and
Pediatric wards(hiwot fana, 2016)

3.3 Study Population

Patients who will be admitted to the Medical, Surgical, Obstetrics, Gynecology,

Malnutrition, and Pediatric wards for more than 48 hours and exhibit clinical evidence
of Antimicrobial Resistance (AMR) will be included.

3.4 Sample Size and Sampling Technique

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The study at Hiwot Fana Specialized University Hospital will involve a sample size of
100 patients presenting with enteric infections. A cross-sectional analysis will be
conducted on clinical isolates collected from patients between during September –
December, 2024.The cross-sectional sampling technique aims to provide a snapshot
of the prevalence and distribution of antimicrobial resistance among patients admitted
to various hospital wards during the specified time frame. This approach allows for
the assessment of AMR patterns and susceptibility profiles of bacterial pathogens,
including Escherichia coli, Salmonella spp., and Shigella spp., within the hospital
setting.

3.5 Data and Specimen Collection

In the forthcoming study at Hiwot Fana Specialized University Hospital, data and
specimen collection will be systematically conducted. The inclusion criteria will
involve patients admitted to the Medical, Surgical, Obstetrics, Gynecology,
Malnutrition, and Pediatric wards for more than 48 hours, displaying clinical evidence
of Antimicrobial Resistance (AMR).Trained healthcare personnel will use structured
data collection forms to gather information on patients meeting the inclusion criteria.
Relevant clinical data, including demographic details, medical history, and specific
signs of AMR, will be recorded. The data collection process will adhere to ethical
guidelines and patient privacy regulations. Bacterial isolates will be collected from
eligible patients exhibiting clinical signs of AMR. Specimens, such as blood, urine, or
wound swabs, will be aseptically obtained by trained laboratory technicians. Standard
operating procedures for specimen collection and transportation will be strictly
followed to maintain the integrity of the samples.

3.6 Processing of Specimens

Collected specimens will be promptly transported to the hospital's microbiology
laboratory for processing. Bacteriological analysis will include isolation,
identification, and characterization of bacterial strains. Antimicrobial susceptibility
testing will be performed using standard methods to determine the resistance profiles
of the isolated bacteria.

3.7 Quality Control

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Stringent quality control measures will be implemented throughout the data and
specimen collection process. This includes regular training sessions for personnel,
standardization of data collection procedures, and adherence to aseptic techniques
during specimen collection. Additionally, internal and external quality control checks
will be conducted in the microbiology laboratory to ensure the accuracy and reliability
of the results.

3.8 Ethical Consideration

Ethical approval will be obtained from the relevant institutional review board before
the initiation of data and specimen collection. Informed consent will be obtained from
each study participant, emphasizing the voluntary nature of their participation and the
confidentiality of their information. The study will strictly adhere to ethical principles
outlined in the Declaration of Helsinki and other applicable regulations.

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 4. WORK PLAN

Table 3: Time frame for proposal writing at Hiwot Fana hospital Harar
No Major
activities Duration
Month Jul Au Se O No De Ja Fe M Apr Ma Ju
. g pt ct v c n b ar i y n
1) Title X
selection
2) Reconnais X

2 sance
survey
3) Site X

3 selection
4) Data X

4 collection
5) Data X

5 analysis
6) Data X

6 organizati
on
7) Proposal X

7 writing
8) Paper X

8 submissio -

n
9) Paper X
9 presentation

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 5. BUDGET BREAKDOWN

Table 4: Require financial budgeting for proposal implementing

No. Material (instrument) and Quantit Price Total
Personal expense y Birr Cent Birr Cent

1 Research Personnel 6 500 00 3000 00

2 Training Cost 6 200 00 1200 00

3 Culture Media 200 100 00 20000 00

4 Antimicrobial - 3000 00 3000 00
Susceptibility Testing
Kits
5 Consumables - 1500 00 1500 00

6 Transportation - 2000 00 2000 00

7 Specimen Transportation - 1000 00 1000 00

8 Reference Strains 5000 00 5000 00

9 Equipment Calibration 500 00 500 00

10 Questionnaires - 600 00 600 00

11 Ethical Approval Fees - 2000 00 2000 00

12 Software Licenses - 1500 00 1500 00

13 Unforeseen Expenses - 10000 00 10000 00

Total 51300 00

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 6. REFERENCES

Tebeje, F., Abate, D. (Assist Prof), & Kabew, G. (Ph.D). (2021). Prevalence of
pathogenic enteric bacteria, associated factors, and antimicrobial susceptibility pattern
among diarrheic pediatric patients in Hiwot Fana Specialized University Hospital,
Harar, Eastern Ethiopia. Retrieved from.
Kumar, Mukesh, Tan Zi, John D Albertson (2017): Intercomparing model
configurations with varied erosion, deposition and transport representations for
simulating sediment yield. American Geophysical Union 2017 Fall Meeting, New
Orleans, Louisiana, 11-15 December 2017.
Tolera, M., Abate, D., Dheresa, M., & Marami, D. (2018). Bacterial Nosocomial
Infections and Antimicrobial Susceptibility Pattern among Patients Admitted at Hiwot
Fana Specialized University Hospital, Eastern Ethiopia.
Reygaert, W. C. (2018). An overview of the antimicrobial resistance mechanisms of
bacteria.
Zaman SB, Hussain MA, Nye R, Mehta V, Mamun KT, Hossain N. A Review on
Antibiotic Resistance: Alarm Bells are Ringing. Cureus. 2017 Jun 28;9(6):e1403. doi:
10.7759/cureus.1403. PMID: 28852600; PMCID: PMC5573035.
Fernanda C Lessa, Dawn M Sievert, Antibiotic Resistance: A Global Problem and the
Need to Do More, Clinical Infectious Diseases, Volume 77, Issue Supplement_1, 1
July 2023, Pages S1–S3.
Majumder MAA, Rahman S, Cohall D, Bharatha A, Singh K, Haque M, Gittens-St
Hilaire M. Antimicrobial Stewardship: Fighting Antimicrobial Resistance and
Protecting Global Public Health. Infect Drug Resist. 2020 Dec 29;13:4713-4738. doi:
10.2147/IDR.S290835. PMID: 33402841; PMCID: PMC7778387.
Salam MA, Al-Amin MY, Salam MT, Pawar JS, Akhter N, Rabaan AA, Alqumber
MAA. Antimicrobial Resistance: A Growing Serious Threat for Global Public Health.
Healthcare (Basel). 2023 Jul 5;11(13):1946. doi: 10.3390/healthcare11131946. PMID:
37444780; PMCID: PMC10340576.

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Mancuso G, Midiri A, Gerace E, Biondo C. Bacterial Antibiotic Resistance: The Most
Critical Pathogens. Pathogens. 2021 Oct 12;10(10):1310. doi:
10.3390/pathogens10101310. PMID: 34684258; PMCID: PMC8541462.
Hiwot Fana Specialized University Hospital Annual Report of 2016).

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