ABSTRACT
The present study aimed at comparing the microbiota of stool of healthy persons and the microbiota of the diarrhoeic stool of patients with gastrointestinal tract infection. A total of 50 stool samples were used for the study, of which 30 were diarrhoeic stool samples of patients being diagnosed of gastroenteritis in Abia State University Teaching Hospital (ABSUTH), Aba while the remaining were 20 formed stool samples collected from healthy individuals in Michael Okpara University of Agriculture Umudike, (MOUAU). All the stool samples were cultured on Salmonella-Shigella agar and the growths were identified using biochemical tests and by Gram staining. The biochemical results and Gram staining results showed that all the isolates from the stool samples were Salmonella and Shigella spp. Out of the 50 stool samples collected 14(28%) were positive for bacteria growth, 13(26%) of the growth were observed in the diarrhoeic stool samples of the patients, of which 9(18%) were Salmonella spp and 4(8%) were Shigella spp while the remaining 1(2%) growth was observed in the formed stool samples and the growth were only Salmonella species. The antimicrobial testing showed that the Salmonella and Shigella isolates were very sensitive to Ciprofloxacin and Ofloxacin with 70% and 100% sensitivity for Ciprofloxacin, and 60% and 75% for Ofloxacin but showed high resistances to Ceftriaxone, Augmentin and Ampicillin wit . The present study indicates that Salmonella spp and Shigella spp are more prevalent in the diarrhoeic stool of patients than in the microbiota of stool of healthy individuals which shows that they are responsible for gastrointestinal tract infection. The study also indicates that Ciprofloxacin and Ofloxacin can be used as first line therapies for Salmonella and Shigella gastroenteritis.
TABLE
OF CONTENTS
Title Page i
Certification ii
Dedication iii
Acknowledgements iv
List of Tables viii
List of Figures ix
Abstract x
CHAPTER ONE:
INTRODUCTION
1.1 Background to the study 1
1.2 Significance of the study 3
1.3 Limitations of the study 3
1.4 Justification of the study 4
1.5 General aim of the study 4
1.5.1 Specific aim of the study 4
CHAPTER TWO:
LITERATURE REVIEW
2.1 General overview of Gastrointestinal tract
infections 5
2.1.1 Pathogens associated with Gastrointestinal tract
infections 6
2.2 Salmonella
as a Gastro enteric pathogen 6
2.2.1 History of Salmonella 6
2.2.2 Taxonomy and Nomenclature of Salmonella 7
2.2.3 Epidemiology of Salmonella 8
2.2.4 Pathogenesis of Salmonella 8
2.2.5 Isolation of Salmonella
from stool samples 11
2.2.6 Sources of Salmonella 12
2.3 Shigella
as a Gastro enteric pathogen 13
2.3.1 History of Shigella
13
2.3.2 Epidemiology of Shigella 13
2.3.3 Pathogenesis of Shigella 15
2.3.4 Isolation of Shigella
from stool samples 17
2.4 Characterization of Salmonella and Shigella spp 17
2.4.1 Cultural characteristics of Salmonella spp 17
2.4.2 Biochemical characteristics of Salmonella 17
2.4.3 Cultural characteristics of Shigella spp 18
2.4.4 Biochemical characteristics of Shigella spp 18
2.5 Antibiogram study of Salmonella and Shigella spp 19
2.5.1 Antibiogram study of Salmonella 19
2.5.2 Antibiogram study of Shigella 19
CHAPTER THREE:
MATERIALS AND METHODS
3.1 Description of study area 20
3.2 Sample collection and study design 20
3.2.1 Study design 20
3.3 Media and Media preparation 21
3.4 Isolation and Identification of bacteria from the
stool of healthy individuals
22
3.4.1 Inoculation and Incubation of stool samples 22
3.5 Isolation and Identification of Bacteria from
diarrheic stool samples of patients
22
3.5.1 Inoculation and incubation of the stool samples 22
3.6 Characterization of Bacteria isolates from the two
groups 23
3.6.1 Gram staining 23
3.6.2 Triple sugar iron test 23
3.6.3 Citrate test 24
3.6.4 Urea test 24
3.6.5 Motility-Indole-Ornithine test 24
3.6.6 Lysine Iron agar test 25
3.6.7 Methyl Red test 25
3.6.8 Voges Proskeaur test 25
3.7 Antimicrobial Susceptibility test 26
CHAPTER FOUR:
RESULT
4.1 Result 27-36
CHAPTER FIVE:
DISCUSSION, CONCLUSION AND RECOMMENDATION
5.1 Discussion 37
5.2 Conclusion
41
5.3 Recommendation
41
References
Appendixes
LIST OF TABLES
Fig no Topic Page no.
4.1 Socio-demographic data of gastrointestinal tract infection
screening of patients in ABSUTH, Aba between May to June 2016 27
4.2 Socio-demographic data of gastrointestinal tract screening
of Healthy individuals in MOUAU between May to June 2016 28
4.3 Results of isolates from diarrheic stool samples of
patients diagnosed of gastrointestinal tract infections in ABSUTH, Aba 31
4.4 Results of Isolates from the formed stool samples of
healthy individuals in MOUAU, Umudike 31
4.5 Summary of the cultural characteristics of bacteria
isolated from stool samples 33
4.6 Biochemical
reaction of the isolates from the stool samples 34
LIST OF FIGURES
4.1 The Percentage of
bacteria growth in the total stool samples 32
4.2 Antibiotic sensitivity
profile of ten (10) Salmonella
isolates 35
4.3 Antibiotic sensitivity
profile of the four (4) Shigella isolates to eight (8) different antibiotics 36
CHAPTER ONE
INTRODUCTION
1.1
BACKGROUND
TO THE STUDY
The
gastrointestinal tract houses a complex and diverse community of microbes. In
recent years, an increased understanding of the importance of intestinal
microbiota of human physiology has been gained. It has been estimated that
trillions of microbes inhabit our gastrointestinal tract (GIT) most of which
reside on the distal intestine where they synthesize essential vitamins and
process indigestible components of our diets such as plant polysaccharides.
Furthermore, these microbes influence both the normal physiology and disease
susceptibilities (Adlerbert et al.,
2000). More than 400 bacterial spp have been identified in the faeces of a
single person and anaerobic bacteria predominate. The upper GIT (the stomach,
jejunum and upper ileum) normally contains a sparse microflora; the bacterial
concentration is less than 104 organisms/ml of intestinal
secretions. In contrast, the large intestine normally contains a luxuriant
microflora with total concentration of 1011 bacterial gram of stool.
Although the stomach constantly receives numerous bacteria from the oral
cavity, the fluid contents of healthy stomach generally contain less than
10bacteria per millilitre because of the bactericidal effect of hydrochloric
acid in the gastric secretion. Various factors tend to remove microorganisms
from the large intestine; the continual movement of intestinal contents through
the channel of the intestine (peristalsis) and also by the desquamation of
surface epithelial cells to which bacteria is attached (Benno et al., 1986). The microflora of the
stomach is mostly anaerobic bacteria and the organisms usually present are bacteriodes (B. Fragilis, B.
Melaninnogenicus, B. Oralis), Bifidobacteria, lactobacillus, and Eubacterium.
The facultative anaerobic species belong to the genera Escherichia, Proteus, Klebsiella and Enterobacter (Benno et al., 1986). The composition of normal
microflora plays significant roles in human physiology, nutrition and
pathological processes.
Gastrointestinal
tract infection is a disease that is pervasive in both the developing and
developed worlds. They are viral, bacterial and parasitic infections that cause
gastroenteritis, an inflammation of the gastrointestinal tract with symptoms
such as diarrhoea, vomiting, and abdominal pain. Bacterial gastrointestinal
infections continue to cause illness and death and contribute to economic loss
in most parts of the world, including high-income countries that have developed
surveillance and control programs (Chan et
al., 2003). The symptoms of acute bacterial intestinal infection are
usually mild to moderate, and spontaneous remission occurs, but in some cases,
the disease can cause rapid deterioration of a patient’s condition. An episode
of acute enteric infection involving extra intestinal organs can also lead to
complications and trigger chronic disease (Chan et al., 2003). Complications include irritable bowel syndrome,
reactive arthritis, haemolytic uremic syndrome (HUS), and Guillain-Barré
syndrome, while for the most part of bacterial gastroenteritis is self
limiting, identification of an etiological agent by bacterial stool culture is
required for the management of patients with severe or prolonged diarrheal,
symptoms consistent with invasive or a history that may predict a cause of
disease (Rabsch et al., 2001). Characterization of bacterial pathogens from
stool cultures in clinical microbiological laboratories is one of the primary
means by which public health officials identify can track outbreaks of
bacterial gastrointestinal tract infections. Some of the enteric pathogens that
commonly cause gastrointestinal tract infections are Vibrio spp, Shigella spp, Salmonella spp, Campylobacter spp, and
certain strains of Escherichia coli (DuPont
1997). The primary mechanisms for bacterial gastroenteritis are (i) excessive
secretion of fluids in the proximal small intestine induced by the action of
luminal toxins expressed by enteropathogens or by minimally invasive bacteria,
(ii) inflammatory or cytotoxic damage of the ileal or colonic mucosa which may
produce blood and pus, or (iii) penetration of the bacterium through the mucosa
to the reticuloendothelial system, as is the case with typhoid fever (Humphries
et al., 2015).
The composition
of the enteric pathogens and normal flora can differ from individual to
individual, by age, environment and also nutrition. The interaction between the
two groups of organisms needs to be balanced for an individual to be healthy
(Majowicz et al., 2010).
1.2
SIGNIFICANCE OF THE STUDY
1.
Characterization of bacterial enteropathogens
from stool cultures is one of the primary means by which public health
officials identify and track outbreaks of bacterial gastrointestinal tract
infections.
2.
Isolates from stool culture are used to carry
out antimicrobial susceptibility testing to know the antimicrobial agents the
pathogens are sensitive and resistant to.
3.
To characterize and compare the organisms
isolated from diarrhoeic stool of patients to isolates from the formed stool of
healthy individuals.
1.3
LIMITATIONS OF THE STUDY
1.
Gastrointestinal tract infections are caused by
bacterial, viral and parasitic agents but this research work is restricted to
only bacteria.
2.
The gastrointestinal tract houses a complex and
diverse community of microbes with different nutrient and mineral requirements.
This study subjects all the stool samples to Salmonella-Shigella agar which has a particular nutrient and
mineral type.
1.4
JUSTIFICATION OF THE STUDY
The
justification of the study is anchored on the fact that millions of pathogens
causing gastrointestinal tract infections are found in stool. This study
highlights this fact and recommends sanitary measures for public health interest.
1.5
GENERAL
AIM AND OBJECTIVE
To compare the
organisms isolated from the microbiota of stool of healthy persons to the
isolates from the stool of patients with gastrointestinal tract infection.
1.5.1
SPECIFIC
AIMS AND OBJECTIVES
1.
To isolate and identify the bacteria isolated
from the stool of healthy persons.
2.
To isolate and identify the bacteria from the
diarrhoeic stool of patients being diagnosed of gastroenteritis.
3.
To characterize the bacteria obtained from the
two groups.
4.
Comparative analysis of data obtained from the
two groups.
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