UNIVERSITY OF GHANA MEDICAL SCHOOL

COLLEGE OF HEALTH SCIENCES

Topic: Bacterial culture negative and positive with antimicrobial

susceptibility profiles of pediatric patients with sepsis

Student name and index number

Student’s address
Supervisor’s address

A RESEARCH PROPOSAL TO THE ETHICAL AND PROTOCOL REVIEW COMMITTEE

OF THE COLLEGE OF HEALTH SCIENCES, UNIVERSITY OF GHANA

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 DEDICATION

I, Henry Wedoi Awuviri, hereby declare that, I dedicate this work to my parents.

……………………………………….. DATE: ……………

(STUDENT’S NAME)

………………………………………………… DATE: ………………

(SUPERVISOR’S NAME)

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ABSTRACT

Background; Sepsis is a medical emergency that describes the body’s systemic immunological
response to an infectious process that can lead to end-stage organ dysfunction and death. Sepsis
presents a significant healthcare challenge globally with an estimated 30 million cases and 6
million deaths annually worldwide. Culture-negative sepsis is a common but relatively
understudied condition. There has been increased interest in the past decade on the treatment of
culture-negative sepsis. Outcome data comparing culture-negative sepsis with culture-positive
sepsis are mixed and it is unclear if culture-negative sepsis is a distinct entity. Recent
recommendations promoting antibiotic de-escalation in culture-negative sepsis can be difficult to
implement. Recent reports suggest that up to 10 times as much antibiotic is used for culture-
negative sepsis as for culture-proven sepsis. The evidence for unintended harm caused by
prolonged or unnecessary antibiotic exposure continues to mount and includes increased risk for
obesity, atopy, and, for preterm infants. Understanding and finding ways to manage culture-
negative sepsis in pediatric patients is crucial for improving patient care and avoiding harm from
antibiotics. Aim; To determine the incidence of blood infections, antimicrobial resistance
patterns and incidence of culture negative bacterial sepsis in the pediatric population. Methods;
This is a retrospective cross-sectional study that will be conducted at the Korle-bu Teaching
Hospital to assess the epidemiology of clinically suspected sepsis, bacterial culture positive
cases of sepsis and antimicrobial resistance patterns as well as non-bacterial cases of sepsis
using laboratory report data of pediatric patients who are 18 and below. Expected Results; The
study is expected to reveal the distribution of bacterial culture positive and negative cases among
pediatric patients diagnosed with sepsis at Korle-Bu Teaching Hospital. Additionally, it is
expected to identify the bacterial pathogens responsible for sepsis in pediatric patients, including
both culture positive and negative cases. The analysis of antimicrobial susceptibility profiles of
bacterial isolates obtained from pediatric patients with sepsis is expected to reveal the prevalence
of antimicrobial resistance among common pathogens. Overall, the study's findings are expected
to contribute to improve the management of pediatric sepsis by guiding antimicrobial therapy
selection, improving diagnostic strategies, and informing antimicrobial practices to combat
antimicrobial resistance.

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 Chapter 1
Introduction

1.1 Background
Sepsis is a medical emergency that describes the body’s systemic immunological response to an
infectious process that can lead to end-stage organ dysfunction and death. Sepsis remains one of
the major causes of morbidity and mortality in critically ill patients (Kaukonen et al., 2014;
Gyawali et al., 2019). It presents a significant healthcare challenge globally with an estimated 30
million cases and 6 million deaths annually worldwide. Mortality rates vary by region, with
Europe experiencing approximately a 41% mortality rate compared to approximately 28.3% in
the United States according to data from the Surviving Sepsis Campaign 2012 (Torio and
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Andrews, 2013; Levy et al., 2012). Pediatric sepsis remains a major public health problem and
an important cause of morbidity and mortality. Severe sepsis is responsible for more than 8% of
all pediatric intensive care unit (PICU) admissions and causes more than 4.5 million childhood
deaths worldwide per year (Weiss et al., 2020; Fleischmann et al., 2018). A study in Switzerland
from 2011 to 2015 found 444 cases of blood culture-proven sepsis in newborns, with 20%
classified as early-onset, 62% as hospital-acquired late-onset, and 18% as community-acquired
late-onset. The estimated national incidence rates per 1000 livebirths were 0.28 for early-onset,
0.86 for hospital-acquired late-onset, and 0.28 for community-acquired late-onset sepsis.
Mortality rates varied with 18% for early-onset, 12% for hospital-acquired late-onset, and 0% for
community-acquired late-onset, with higher rates seen in preterm infants and those with
complications like septic shock or requiring mechanical ventilation (Giannoni et al., 2018).
The recognition of sepsis in children is challenging and is related to the high prevalence of
common febrile infections, poor specificity of discriminating features, and some capacity of
children’s physiology to compensate until shock is in an advanced stage (Weiss et al., 2020).
Sepsis outcomes in children are strongly dependent on the timeliness of recognition and
treatment. In neonatal sepsis, pathogens responsible for sepsis might be acquired through in utero
infection (Goldenberg et al., 2000), maternal microbiota during delivery, or postnatal hospital or
community environment. A large proportion of sepsis is usually caused by bacteria and as a
result empiric antibiotics based on country specific guidelines are usually administered while
waiting for the results of these tests (Abebe et al., 2021). Antibiotics are then adjusted to fit the
antibiotic sensitivity patterns based on the results of these tests. Enhancement of early detection
methods and the availability and efficacy of antibiotics have played a huge role in the
improvement of outcomes in infections in general and sepsis in particular in recent years.
While bacteria are the most common causative agents of sepsis, cultures only detect pathogens in
about half of cases (Martin et al., 2003). Failure to administer appropriate antibiotics correlates
with increased mortality which emphasizes the importance of early broad-spectrum treatment.
However, the understanding of culture-negative sepsis remains limited, with sensitivity issues in
culture detection being a concern. There's a notable lack of comprehensive information on
patients with culture-negative sepsis in the medical literature (Phua et al., 2013). Despite the
massive advancements in the treatment of sepsis which can be attributed, at least in part to
antibiotics, bacteria are extremely hardy organisms and have developed various mechanisms of
becoming resistant to these drugs. In recent times the drastic increase in antimicrobial resistance
rates has generated a great deal of global concern and has threatened to destroy the strides made
in the management of sepsis. (Laxminarayan et al., 2016) Improvements in antimicrobial
surveillance and stewardship have been proposed as a means of reducing resistance rates and
further reduce sepsis related mortality. (Omenako et al., 2022)

1.2 Problem Statement and Justification

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Culture-negative sepsis is a common but relatively understudied condition (Phua et al., 2013).
There has been increased interest in the past decade on the treatment of culture-negative sepsis.
Outcome data comparing culture-negative sepsis with culture-positive sepsis are mixed and it is
unclear if culture-negative sepsis is a distinct entity. Recent recommendations promoting
antibiotic de-escalation in culture-negative sepsis can be difficult to implement (Thorndike et al.,
2020). Recent reports suggest that up to 10 times as much antibiotic is used for culture-negative
sepsis as for culture-proven sepsis. This practice must stop. The evidence for unintended harm
caused by prolonged or unnecessary antibiotic exposure continues to mount and includes
increased risk for obesity, atopy, and, for preterm infants (Cantey et al 2017). Understanding and
finding ways to manage culture-negative sepsis in pediatric patients is crucial for improving
patient care and avoiding harm from antibiotics.
1.3 Aim
To determine the incidence of blood infections, antimicrobial resistance patterns and incidence
of culture negative bacterial sepsis in the pediatric population.
1.4 Objectives
1. To determine the prevalence of bacterial culture negative and positive cases among
pediatric patients diagnosed with sepsis at Korle-Bu Teaching Hospital.
2. To identify the bacterial pathogens responsible for sepsis in pediatric patients,
focusing on both culture positive and negative cases.
3. To characterize the antimicrobial susceptibility profiles of bacterial isolates obtained
from pediatric patients with sepsis, including both culture positive and negative cases.

Chapter 2

LITERATURE REVIEW

2.1 Overview of Sepsis

For the past two decades, sepsis has garnered substantial global attention as a result of growing
recognition that it is one of the most common and lethal conditions that the world faces
(Kempker & Martin, 2020). In spite of the ever increasing body of knowledge on this complex
disease, mortality from sepsis remains one of the greatest causes of death in children especially
in neonates (Bone et al., 1992). The concept of sepsis is composed of two fundamental parts, a
systemic inflammatory response syndrome (SIRS) and an infection. SIRS includes two or more
of the following; Temperature greater than 38oC or less than 36 ⁰C, a heart rate greater than 90
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beats per minute, tachypnea greater than 20 breaths per minute or PaCO2 less than 32 mm Hg
and a white blood cell (WBC) count greater than 12,000 per cubic millimeter or fewer than 4000
per cubic millimeter, or greater than 10% immature (band) forms. This can lead to organ
dysfunction, hypoperfusion, lactic acidosis and eventually septic shock (Bullock & Benham,
2020). Taking this into consideration sepsis in its most basic form can be defined as a systemic
infection caused by pathogens invading the blood circulation, growing, and reproducing in it, and
producing toxins leading to serious health conditions and neonatal death (Yadav & Kumar
Yadav, 2022).

Sepsis can also be described as a life-threatening organ failure caused by the host’s inappropriate
response to infection. Organ failure is now characterized as a sequential, sepsis-related organ
failure assessment scores. Septic shock is defined as a subtype of sepsis, and is manifested by
circulatory, cellular, and metabolic instability associated with a higher risk of death than sepsis
itself. Septic shock is diagnosed when blood pressure drops, requiring vasopressors to keep it
above 65 mmHg, along with elevated serum lactate levels above 2 mmol/L after addressing
hypovolemia. The updated definition omits "SIRS" criteria, simplifying diagnosis for clinical
use. The previous understanding of septicemia, which focused on a non-specific term requiring a
bloodstream infection and an individual to be unwell, has evolved significantly. The
contemporary concept of sepsis encompasses various pathogens beyond bacteria and emphasizes
the host response as a major contributor to morbidity and mortality. It no longer mandates
confirmed infection, recognizing that many cases are suspected without definitive proof. (Rudd
et al., 2020).

2.1.1 Pathophysiology of Sepsis

There has been a shift in the focus of the pathophysiology of sepsis from the causative organisms
to the abnormal host response to the infection. It must be noted that although grossly classified as
dysregulated, the immune responses at play are generally geared towards host protection and the
elimination of the pathogen. It is the magnitude of the response that is usually exaggerated
leading to the damage of the host’s own tissues (Arina & Singer, 2021). Blood stream infections
trigger a pro-inflammatory immune response. The pro-inflammatory response initially
perpetuates an inflammatory response which is geared towards the eradication of the infection
which in an ideal situation is kept in check by expansive anti-inflammatory mechanisms
comprising of both the humoral and cellular arms of the immune system. The activity of an anti-
inflammatory response leads to a cytokine storm with associated activation of coagulation and
complement pathways (Chousterman et al., 2017). Most of the damage from the inflammation is
as a result of oxidation from reactive oxygen species which overwhelms the antioxidant defenses
of the body. This eventually leads to endothelial dysfunction, systemic vasodilation and shock.
The ensuing shock, together with an associated activation of pro-coagulants with reduced
anticoagulation culminating in disseminated intravascular coagulation and resulting in

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microvascular thrombus formation, collectively lead to tissue hypo perfusion and organ
dysfunction (Rivers et al., 2012, Angus & van der Poll, 2013). In the late stages of sepsis, the
anti-inflammatory mechanisms lead to a depressed immune response culminating in the
occurrence of immunoparalysis and opportunistic infections (Jacobi, 2021).

2.2 Prevalence and Global Burden of Sepsis

The epidemiology of sepsis varies widely across time and space as it is dependent on the
definition which has changed greatly over time. The initial consensus definition on sepsis,
established in 1991, possessed a low level of sensitivity and specificity with a resulting
underestimation of the incidence of sepsis. The definition was modified to improve its sensitivity
and specifity and the current definition (sepsis 3) may be the reason behind an apparent rise in
the prevalence of sepsis. In addition, despite the global burden of sepsis, a lot more data is
available from high income countries as opposed to low and middle income countries. However
the relative increment in the amount of data generated by developing countries coupled with the
ever increasing sensitivity of the definition of sepsis produce a possible ascertainment bias, in
which the inclusion of fewer critically sick individuals in sepsis case counts over time results in a
perceived increase in sepsis incidence and a fall in sepsis fatality rates (Chiu & Legrand, 2021,
Rhee & Klompas, 2020).

In a recent study assessing the global epidemiology of sepsis which was the first to use
multinational individual-level data to produce global sepsis estimates , (Rudd et al., 2020) using
the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) estimates, discovered
that there were an estimated 48·9 million (95% UI 38·9–62·9) incident cases of sepsis and 11·0
million (10·1–12·0) sepsis-related deaths in 2017. This is more than twice the figure quoted by
previous global figures, which is as previously discussed may be due to the inclusion of more
data from low-income and middle-income countries, where data on sepsis was previously under-
represented. Their findings show that about 41·5 million (32·1–54·5) incident sepsis cases in
2017 (85·0% [82·2–87·4] of total) occurred in countries with a low, low-middle, or middle
income countries. If this data is a true reflection of the actual situation on the ground then urgent
action is required (Sakr et al., 2018). Although these findings imply that the global burden of
sepsis is larger than previously appreciated and requires urgent global attention, They have been
received with some skepticism especially with regards to the modalities of coding applied to this
study (Kempker & Martin, 2020). In the breakdown of the data it was found that in children less
than 5 years, the most common causes of sepsis in 2017 were diarrhoeal diseases (5·9 million
[95% UI 2·1–14·2] cases of sepsis [27·9%, 95% UI 12·0–50·8]), neonatal disorders (5·1 million
[2·9–8·9] cases of sepsis [25·7%, 13·7–40·9]), and lower respiratory infections (3·3 million
[1·8–6·3] cases of sepsis [16·5%, 0·1–29·3]. Of the 48.9 million incident cases of sepsis, 20·3
million (95% UI 14·0–29·7) were children younger than 5 years and 4·9 million (3·5–7·0)
occurred in the pediatric population between 5–19 years. This suggests that about half of the

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global cases of sepsis occurred in the pediatric population with a substantial amount occurring in
children under 5, reflecting the need to pay particular attention to patients in this age group
(Rudd et al., 2020). The overall percentage of positive blood culture was 19.1% in Africa(Droz
et al., 2019)

In Sub-Saharan Africa, although many studies have been done in individual countries, they are
largely confined to neonates. The prevalence of early onset neonatal sepsis in a study done in
Ethiopia was f 75.4% (Assemie et al., 2020); whereas in a study done in Sri Lanka blood stream
infections had an incidence of 50.8% (Afolayan et al 2023). In South Africa, the overall
incidence risk of culture-confirmed infections was 6·0 per 1000 livebirths. The incidence risk of
late-onset neonatal sepsis was 4·9 per 1000 livebirths and that of early-onset sepsis was 1·1 per
1000 livebirths in South Africa (Mashau et al., 2022). Blumenröder et al (2023) determined the
prevalence of neonatal sepsis to be 22%. Of these 57% of them had culture-positive bloodstream
infections with Gram-negative bacteria being the most prevalent. In Tanzania 29.8% of the
patients with clinical sepsis were culture-positive (Godfrey et al., 2022).

In Ghana the point prevalence of culture confirmed septicaemia was 70.3% among neonates
clinically diagnosed with sepsis (Kwame Opare-Asamoah et al., 2023). In a study done in Korle
bu the overall incidence of septicaemia was 1.0 per 100 person days (Labi et al., 2021). In 2015
Sub-Saharan Africa (SSA) had the highest mortality rates from sepsis at the sub region level(Liu
et al., 2015). A study done in Sri Lanka had a mortality of 13.2% Mortality of 13.2% was
recorded among children with BSI in Sri Lanka (Afolayan et al 2023) and in Ghana neonatal
mortality caused by Gram-negative bacterial infection was higher than that caused by Gram-
positive bacteria.(Afeke et al., 2021)

2.3 Causes of Sepsis

Sepsis is usually caused by bacterial infections but may be the result of other infections such as
viruses, parasites or fungi (WHO, 2023). However, any infection at all in the body that is severe
enough can lead to sepsis. Infections that are notorious for causing sepsis include pneumonia,
intra-abdominal infections, and urinary tract infections, in order of increasing prevalence (Singer
et al., 2016). Respiratory, gastrointestinal, genitourinary, and skin and soft tissue infections are
the most common sources of sepsis (Gauer et al., 2020). In Africa the common bacterial isolates
are S. aureus (17.8%), Streptococcus pneumoniae (16.8%) and Escherichia coli (10.7%) (Droz et
al., 2019). In sub-Saharan Africa, bacterial culture positive bloodstream infection are the most
common cause of morbidity and mortality (Abebe et al., 2021). In a study undertaken in
Tanzania, the common Gram-positive bacterial isolates were S.aureus (39.7%) Coagulase
Negative Staphylococcus (CoNS) (35.6%) and Gram-negative isolates were E.coli (12.3%),
Klebsiella spp (6.8%) and Pseudomonas aeruginosa (5.5%). Gram-positive bacteria are found to
be predominant cause of sepsis (Godfrey et al., 2022). Blumenröder et al. (2023) found that the
common gram-negative bacterial isolates were Salmonella enterica, Acinetobacter spp. and
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Klebsiella pneumoniae. The common gram-positive isolates were Staphylococcus haemolyticus,
S. aureus and Enterococcus spp. Lochan et al. (2017) determined E. coli, Staphylococcus aureus
and Streptococcus pneumoniae to be the most frequent causes of community acquired blood
stream infection whereas Klebsiella pneumoniae, Acinetobacter baumanii and S.aureus were
most common bacterial isolates in Hospital acquired sepsis in South Africa. Gram-positive
organisms were the commonest isolated pathogens (70.3%) in Sri Lanka (Afolayan et al., 2023).
In Ghana coagulase-negative staphylococcus (CoNS) was the most prevalent isolate, followed by
Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus agalactiae, the Acinetobacter
species, and Escherichia coli in the rest. The commonest coagulase negative staphylococci were,
S. haemolyticus and S. epidermidis were (Afeke et al., 2021).

2.4 Diagnosis of Sepsis

The diagnosis of sepsis is aided by screening tools such as the quick Sepsis-related Organ Failure
Assessment (qSOFA) and the systemic inflammatory response syndrome (SIRS) criteria but still
largely depends on identifying general systemic manifestations like hypotension an a fever,
manifestations of organ dysfunction/failure such as acute respiratory failure and acute kidney
injury and finally, microbiological documentation(Serafim et al., 2018).Prompt diagnosis and
treatment is vital to obtain positive outcomes. However recognizing and diagnosing sepsis in the
pediatric age group presents a significant challenge in as abnormalities in the vital signs and
examination findings are usually not as clear cut as compared to adults. This variability in
clinical presentation is so great that it poses a great challenge in even formulating a precise
definition of sepsisin pediatrics (Garcia et al., 2020). In light of this despite the huge strides
made in diagnosing and understanding sepsis in general, due to the peculiarities of its
manifestation in children sepsis and antibiotic resistance among other reasons, sepsis still
remains a major cause of child mortality.

2.4.1 Clinical features and Complications

Patients with sepsis generally present with clinical manifestations of the systemic response.
These include fever, tachycardia, tachypnea and hypotension (Jacobi, 2021, Khassawneh et al.,
2009). Other features of sepsis are hypothermia, tachypnea as well as clinical evidence of of a
source of the infection (Bone, 1991). Patients may also present with an altered mental
status,jaundice and clinically significant edema as well as reduced capillary refill time (Siqueira-
Batista et al., 2011). The presentation is more variable in neonates but they typically present with
respiratory distress, fever difficultiesin feeding, neonatal jaundice, bulging fontanels and
hypothermia (Jatsho et al., 2020). Eventually the disease progresses to involve other organs
resulting in end organ damage and shock (Jacobi, 2021) This is depicted by either poor or altered
cerebral function, hypoxemia, elevated plasma lactate level, or oliguria (Bone, 1991) This can be
assessed using the sequential organ failure assessment (SOFA) score, a clinical tool which
screens for respiratory, cardiovascular, hepatic, coagulation, renal and neurological dysfunction.
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Acute renal dysfunction affects about half of these patients and is usually one of the earliest
manifestations of multi-organ dysfunction as sepsis progresses (Skube et al., 2018, He et al.,
2022). More than two-thirds of sepsis patients have been found to develop Encephalopathy and
polyneuropathy (Bolton et al., 1993, Schmutzhard & Pfausler, 2017, Chaudhry & Duggal, 2014)
In-hospital sepsis patients are also at risk of myocardial infarctions and stroke (Wu et al., 2019).
Sepsis can also cause hepatic dysfunction with resulting hypoxic hepatitis, sepsis-induced
cholestasis or dysfunction of protein synthesis (Woźnica et al., 2018). Jaundice can also occur
and is a sign of negative outcomes (Kobashi et al., 2012). There can also be associated
pulmonary dysfunction with respiratory alkalosis as well as haematological abnormalities
ranging from coagulopathies to full blown disseminated intravascular coagulopathy. It is
important to note that organ dysfunction closely intertwined of sepsis and multiple organs are
usually affected. (Lelubre & Vincent, 2018).

2.4.2 Investigations

Distinguishing between localised infections and sepsis can be a challenge and requires a high
index of suspicion as well as laboratory testing (Fan et al., 2016). There is no single laboratory
test that can diagnose sepsis and significant emphasis is placed on the clinical assessment of the
patient (Prucha et al., 2015). Haematological, biochemical and microbiological tests are usually
done to diagnose sepsis in addition to imaging tests such as X-rays, CT scans or ultrasounds to
screen for end organ damage. However the advent of novel biomarkers that facilitate the early
diagnosis of sepsis has garnered substantial global attention (Rello et al., 2017). National
Institutes of Health defines a biomarker as “a characteristic that is objectively measured and
evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic
responses to a therapeutic intervention”(Biomarkers Definitions Working Group, 2001).
Pierrakos et al. (2020) identified 258 biomarkers and recent data shows that increased levels of
procalcitonin and presepsin serve as reliable surrogate measures of the host's immune response
to infection(Cervellin et al., 2019). This phenomenon makes procalcitonin an excellent marker
of to assess patient response to treatment to determine when to stop antibiotics(Fan et al., 2016).
It has also been shown to be superior to C-reactive protein and interleukin 6 (Bloos & Reinhart,
2013). Apart from C-reactive protein (CRP) or procalcitonin (PCT), only 26 biomarkers have
been assessed in clinical studies with more than 300 participants and 9 were shown to have a
better diagnostic value for sepsis than either or both of these biomarkers. (Pierrakos et al., 2020).
Serum lactate also as some prognostic value and its presence predicts to a large extent, imminent
organ dysfunction and an associated increase in mortality rate from 35% to 70%(Rello et al.,
2017). The role of the white blood cell count is debatable and while Duncan et al. (2021) argue
that it has a low specificity and sensitivity in the diagnosis of sepsis it still remains of paramount
importance as it is inexpensive, accessible and readily available in all settings and provides a lot
of information(Agnello et al., 2021).

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2.4.3 The role of blood culture in the diagnosis of sepsis

Blood culture has been the gold standard in making a diagnosis of sepsis for many years.
However it's diagnostic value is limited by its low sensitivity especially in patients undergoing
treatment before samples are taking (Rello et al., 2017). In lieu of this samples must be taken
within 45 minutes before the administration of antimicrobial therapy (Esposito et al., 2017). It is
also of little value in diagnosing sepsis from noninfectious causes. It's sensitivity and specificity
are also plagued by technical challenge (Rello et al., 2017). It also has a long processing time
which elongated the diagnostic process (Duncan et al., 2021). In neonates especially, many
issues exists with use of cultures in the diagnosis of sepsis such as the amount of blood obtained
from neonates, the presence of low or intermittent bacteremia, in addition to maternal
intrapartum antimicrobial exposure (Connell et al., 2007). A lot of progress has been made in the
diagnosis of sepsis including but not limited to the development of more sensitive automated
blood culture detection systems and the availability of rapid molecular tests such as the
polymerase chain reaction and Fluorescent in situ hybridization for faster organism identification
and detection of resistance genes. However, most blood cultures in clinical practice do not grow
organisms, (Fabre et al. 2022, Bloos & Reinhart, 2013, Esposito et al., 2017).

2.7 Treatment of sepsis

Current recommendations are that antibiotic treatment should be administered as soon as

possible when there is suspected or proven sepsis or serious bacterial infection and usually after
appropriate blood cultures have been taken. Ensuring responsible antibiotic use is necessary to
ensure effective treatment reduce antimicrobial resistance. Likely causative organisms need to be
considered in order to provide an appropriate antibiotic coverage. (Martínez et al.,
2020)Antimicrobial therapy should be initiated early. Most research indicates that antimicrobial
therapy should be started within three hours of presentation. The latest guidelines recommend
starting antimicrobials within one hour, but this is controversial (Weiss et al., 2020). Fluid
resuscitation is one of the mainstays in the early management of sepsis. It entails administering
an intravenous fluids, either colloids or crystalloid at 30 mL per kg within the first three hours to
in a bid to resolve septic shock (Gavelli et al., 2021). Vasopressor therapy and admission to the
intensive care unit is indicated if hypotension is refractorytothis attempted fluid resuscitation.
(Gauer et al., 2020).

2.9 Antimicrobial resistance

Mortality from sepsis has reduced substantially and access to antibiotics has played a significant
role, particularly in lower-middle-class and low-income nations; however, the rise in bacterial
resistance to antibiotics poses a threat to these gains (Laxminarayan et al., 2016). In light of these
developments, antimicrobial resistance (AMR) in bacteria is globally acknowledged as a global
public health concern. The rise in infections from multi drug resistant bacteria also pose a huge
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threat to the pediatric population, with the greatest mortality burden expected to occur in low-
and middle-income countries(Lester et al., 2019). AMR-attributable neonatal deaths recently
estimated between 140,000 and 214,000 annually (Kowalski et al., 2024), and sub saharan
Africa has been noted to have the highest burden and risk of death from antimicrobial resistance
(Kowalski et al., 2024, Murray, 2022). This combined with the fact that the sub region currently
has the highest incidence and mortality from sepsis is worrying and paints a bleak picture of the
future unless prompt measures are taken to resolve the problem (Lester et al., 2019).

2.9.1 Mechanisms of Antimicrobial resistance

Antibiotic resistance is of major public health concern given that at least some resistance exists
to almost every antibiotics currently in clinical use while few newer drugs are in development. It
as been shown that bacteria utilise both phenotypic and genetic modalities to mount resistance
against antibiotics (Urban-Chmiel et al., 2022). Deciphering the mechanism by which bacteria
develop resistance to antibiotics is essential to understand global patterns of resistance and to
improve antimicrobial stewardship, (Darby et al., 2022) Althogh antimicrobial resistance is an
inevitable occurrence that entails both genetic mutation an the processor natural selection in
bacteria it can be hastened by antibiotic overuse and misuse as it increases the exposure of the
bacteria to the drug unnecessarily(Abushaheen et al., 2020). Many mechanisms of antimicrobial
resistance exist but they fall under the following groups: reduced permeability, active transport
of antibiotics, changes in drug targets, changes to the drug and bypassing the target (Kakoullis et
al., 2021). Some bacteria also utilise a phenomenon referred to as target protection which inolves
the interaction of a resistance protein with the drug taregt in order to protect it (Wilson et al.,
2020). Some bacteria also create biofilms which impede antimicrobial penetration and make it
difficult to eradicate them (Uddin et al., 2021).

2.9.2 Multi Drug Resistance

The ever increasing prevalence of antibiotic-resistant bacterial isolates is of great global

concern(Lim et al., 2016) It is commonly defined as resistance to two or more antimicrobial
agents in at least three categories of antibiotics. These bacteria cause infections that are
associated with a greater length of ime spent in the hospital, worse outcomes, more antimicrobial
use increased financial burden to the patient an health care system (Nathwani et al., 2014). Huge
quantities of antibiotics are no just in treating human diseases but also in agriculture o improve
the health and yield of farm animals like sheep, goat and and even for fish, resulting in the
natural selection of bacteria,mostly commensals that are resistant to multiple drugs (Catalano et
al., 2022). Low an middle income countries are major contributor to this problem.(Laxminarayan
et al., 2016). Many studies are ongoing to formulate new drugs that will be efficacious against
multi drug resistant bacteria an example of which is a synthetic antibiotic consisting of a rigid
oxepanoproline backbone which is combined with the aminooctose residue of clindamycin to
create an antibiotic of exceptional potency and spectrum of activity, which was named
13
iboxamycin (Mitcheltree et al., 2021). Other studies into other drug options are also being
undertaken but from the time being, until any of these efforts are successful, multi drug resistant
bacteria seems likely to remain a global health challenge.

2.9.3 Antimicrobial resistance patterns of bacteria implicated in sepsis

A high degree of resistance to methicillin was generally associated with staphylococcus aureus in
Africa (Droz et al., 2019). Many enterobacterales cultured in the sub-Saharan paediatric
population were found to be resistant to antibiotics like amoxicillin, gentamicin, ciprofloxacin or
cotrimoxazole which are commonly used for empiric treatment (Kowalski et al., 2024). In
Tanzania Gram-positive and Gram-negative bacteria had a high resistance to first and second
line antimicrobials including: ampicillin, gentamycin, and ceftriaxone (Godfrey et al., 2022).
Among neonates in the subregion gram negatives were common and there was a high
prevalence of extended-spectrum β-lactamase-producing organisms. Gram-positive bacteria were
responsible for a high proportion of infections among children beyond the neonatal period, with
high reported prevalence of non-susceptibility to treatment advocated by the WHO therapeutic
guidelines (Williams et al., 2018). In Tanzania resistance to WHO recommended β-lactams was
reported in 614 (68%) of 904 cases and resistance to aminoglycosides in 317 (27%) of 1176
cases (Okomo et al., 2019). Blumenröder et al (2023) found that gram-negative bacteria isolated
from blood cultures of neonates were resistant to ampicillin which is alarming. All bacteria
showed a high resistance to ampicillin (80%- 100%) followed by ceftriaxone (40 - 70%).
(Godfrey et al., 2022) in their study ascertained that Pseudomonas aeruginosa were completely
resistant to ampicillin, gentamycin and ceftriaxone but were sensitive to amikacin. There was
less than 40% resistance to co-amoxiclav, meropenem, ciprofloxacin, amikacin, and
clindamycin. The overall case mortality rate from sepsis was 9.4%. All bacteria showed a high
resistance to ampicillin (80%- 100%) followed by ceftriaxone (40 - 70%). Third generation
cephalosporins and aminoglycosides were the most frequently used in the subregion which may
be the reason behind the overwhelming resistance to these antibiotics (AKINTAN et al., 2022).
In a study conducted in the 31 military hospital, a tertiary hospital in Ghana, Staphylococcus
species and Gram-negative bacteria, mostly from the Enterobacteriaceae family, were common
causes of culture positive late onset neonatal sepsis with coagulase negative staph being the most
common cause. Of the coagulase negative staph infections, 52% were found to be multi drug
resistant. Wuni et al. (2023) in a study undertaken in Upper East Regional Hospital from 2019 to
2020 found that Staphylococcus aureus and Staphylococcus epidermidis were the most common
causes of bacterial positive culture proven sepsis and were also resistant to commonly prescribed
antibiotics namely ampicillin, flucloxacillin, and cefotaxime.

14
 Chapter 3

Methodology

3.1 STUDY DESIGN

15
The study will be a retrospective cross sectional study that will assess the epidemiology of clinically
suspected sepsis, bacterial culture positive cases of sepsis and antimicrobial resistance patterns as well as
non-bacterial cases of sepsis using laboratory report data.

3.2 STUDY SITE

The study will be undertaken in the Pediatric Department of the Korle-Bu Teaching Hospital.
Korle-Bu Teaching Hospital (KBTH) is a public teaching hospital situated in the Ablekuma
South Metropolitan District in Accra, Ghana. It was established on October 9, 1923. It is the only
public tertiary hospital in the southern part of the country. It is the third largest hospital in Africa.
The department is manned by some of the best specialists in Ghana and is affiliated with
University of Ghana medical school. As a result it is the leading national referral centre in Ghana
with a very diversified patient base with a more accurate reflection of demographic patterns of
diseases in the country.

3.3 STUDY POPULATION

The study population consists of pediatric patients under the age of 18 who presented with
clinically suspected sepsis.

3.4 CRITERIA FOR INCLUSION AND EXCLUSION

3.4.1 INCLUSION CRITERIA

1. Pediatric patients (age ≤ 18 years) diagnosed with sepsis at Korle-Bu Teaching Hospital.

2. Patients with positive blood cultures indicating bacterial infection.

3. Patients with negative blood cultures but clinically diagnosed with sepsis based on predefined
criteria, including clinical signs and symptoms such as fever, tachycardia, tachypnea, altered
mental status, and evidence of organ dysfunction.

4. Availability of complete electronic medical records including demographic information,

clinical history, laboratory results, and antimicrobial susceptibility profiles .

3.4.2 EXCLUSION CRITERIA

1. Patients with incomplete electronic medical records lacking essential clinical or laboratory
information.

2. Patients with sepsis of fungal, viral, or parasitic etiology.

16
3. Patients with polymicrobial bloodstream infections.

4. Patients with incomplete or inconclusive blood culture results.

3.5 PARTICIPANT RECRUITMENT

Potential participants meeting the inclusion criteria will be identified through medical records
and clinical consultations at Korle-bu Teaching Hospital.

3.6 DATA COLLECTION

Data from preexisting records from the Paediatric Department at the Korle-bu Teaching Hospital
will be gathered.

3.7 DATA ANALYSIS

Quantitative data collected will be analyzed using appropriate statistical methods. Descriptive
statistics, including means, standard deviations, frequencies, and percentages, will be used to
summarize demographic characteristics. Inferential statistics, such as t-tests or analysis of
variance (ANOVA), may be employed to examine differences in bacterial infections across
demographic subgroups. Regression analysis, such as linear regression or logistic regression, will
be conducted to identify factors associated with variations in bacterial infections among
participants.

3.8 ETHICAL CONSIDERATION

Ethical approval will be obtained from the Ethics and Protocol Review Committee (EPRC) of the
College of Health Sciences (CHS) of the University of Ghana and the Medical Directors of the
selected facilities. To ensure anonymity and confidentiality, the study will employ unique
identification. Participants will be informed that the study is entirely voluntary and that they may
withdraw at any time without penalty.

APPENDIX

Project Plan and Timelines

17
 FEBRUARY MARCH APRIL MAY JUNE

PROPOSAL

SUBMISSION OF
PROPOSAL

ETHICAL

CONSIDERATIO
N

DATA

COLLECTION

DATA ENTRY
AND ANALYSIS

THESIS WRITE
UP

THESIS
SUBMISSION

BUDGET

INTERNET AND COMMUNICATION GHC 200.00

ADMINISTRATIVE COST GHC 300.00

STATISTICIAN COST GHC 800.00

TOTAL GHC 1300.00

18
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