isolation, characerization and antimicrobial susceptibility test of soil microorganisms isolated...
DESCRIPTION
A study carried out at the cassava mill factory to test for the susceptibility of microorganisms found in and around the factory. It was found out that Gentamicin still works effectively well against infection caused by E. coli...TRANSCRIPT
CHAPTER ONE
1.0 INTRODUCTION
Cassava (Manihot esculenta Crantz, synonymous with Manihot utilissima Rhol) belongs to
the family Euphorbiaceae. It is mainly a food crop whose tubers are harvested between 713 months
based on the cultivars planted (Cook, 1985; Taye, 1994). Cassava (Manihot esculenta Crantz) is
primarily grown for its starch containing tuberous roots, which are the major source of dietary energy for
more than 500 million people in the tropics (Lyman, 1993). The ability of cassava to grow and produce
relatively well in marginal environment under low management levels makes it an attractive crop for poor
resource (Bencini, 1991). As a food crop, cassava fits well into the farming systems of the small holder
farmers in Nigeria because it is available year round, thus providing household food security. Cassava
tubers can be kept in the ground prior to harvesting for up to two years, but once harvested, they begin
to deteriorate. To forestall early deterioration, and also due to its bulky nature, cassava is usually traded
in some processed form. The bulky roots contain much moisture (60 – 65%), making their
transportation from rural areas difficult and expensive. Processing the tubers into a dry form reduces
the moisture content and converts it into a more durable and stable product with less volume, which
makes it more transportable (IITA, 1990; Ugwu, 1996). Over the years, cassava has been transformed
into a number of products both for domestic (depending on local customs and preferences) and
industrial uses.
Cassava in the fresh form contains cyanide, which is extremely toxic to humans and animals; there is
therefore a need to process it to reduce the cyanide content to safe levels (Eggelston et al., 1992).
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The poor post harvest storage life of fresh cassava tubers is a major economic constraint in its utilization
(Kehinde, 2006).
Cassava processing generates solid and liquid residues that are hazardous in the environment
(Cumbana et al., 2007; Jyothi et al., 2005). On the average, 2.62 m3 ton1 of residues from washing
and 3.68 m3 ton1 from the water residues of flour production (Horsfall et al., 2006 and Isabirye et
al., 2007). There are two important biological wastes derived from cassava processing which are the
cassava peels and the liquid squeezed out of the fermented parenchyma mash (Oboh, 2006).
Cassava effluents are liquid wastes from the cassava mill which are usually discharged on land or water
in an unplanned manner. The cassava peels derived from its processing are normally discharged as
wastes and allowed to rot in the open with a small portion used as animal feed, thus resulting in health
and environmental hazards.
(Desse and Taye, 2001; Aderiye and Laleye, 2003) the edible tubers are processed into
various forms which include chips, pellets, cakes and flour. The flour could be fried to produce gari or
steeped in water to ferment to produce fufu when cooked (Oyewole and Odunfa, 1992). The
production and consequent consumption of cassava have increased extensively in recent times. This
increased utilization of processed cassava products has equally increased the environmental pollution
associated with the disposal of the effluents (Akani et al., 2006; Adewoye et al., 2005)
In most areas, cassava mills are mainly on small scale basis, owned and managed by individuals
who have no basic knowledge of environmental protection. Though on small scale basis, there are
many of them, which when put together, create enormous impact on the environment.
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Oboh, 2005 identified two important wastes that are generated during the processing of cassava
tubers to include cassava peels and liquid squeezed out of the mash. The bioconversion of the cassava
wastes have been documented (Antia and Mbongo, 1994; Okafor, 1998; Raimbault, 1998;
Twenyongyere and Katongole, 2002; Oboh, 2005). The wastewater contains heavy loads of
microorganisms, lactic acid, lysine, amylase capable of hydrolyzing the glycosides (Raimbault, 1998;
Akindahunsi et al., 1999).
During the processing of cassava tubers in various products, liquid wastewaters generated was
reported to cause serious havoc to vegetation, houses and bring about infection. The liquid squeezed out
can be dried and used as animal feeds (Okafor, 1998; Oboh and Akindahunsi, 2003a).
Microorganisms are very important ‘members’ of the soil ecosystem. They play significant roles
in the various transformations that go on in the soil. An important function of soil organisms is the
decomposition of organic residues. This decomposition process is driven by decomposer organisms
which consist of a community of soil biota including microflora and soil fauna (Swift et al., 1979; Tian et
al., 1995). Fungi and bacteria are responsible for the biochemical processes in the decomposition of
organic residues (Anderson and Ineson, 1983; Dinda, 1978).
Despite their importance in soil, the relative abundance and distribution of these soil organisms is
determined by several environmental factors. The soil is the final recipient of all forms of environmental
pollutants and of recent such pollutants have had significant effects on soil microbial populations
(Ogboghodo et al., 2001). Various studies of the microbiology of hydrocation degradation in soil
indicate the presence of microflora in the soil that is able to degrade a wide variety of hydrocarbons
(Niessen, 1970).
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Soon after the widespread use of antibiotics began in the early 1950’s it became apparent that
strains of bacteria were becoming resistant to specific antibiotics, it was later discovered in Europe that
enterobacteriaceae can transfer multiple resistances from one organism to another and even from one
specie to another by means of an extra chromosomal hereditary factors. The problem of antibiotic
resistance could be attributed to long time use of a particular antibiotic by humans, this then makes
bacteria to adapt very well with whatever challenges the antibiotics might pose and subsequently it will
become resistant to such antibiotics.
1.1 STATEMENT OF THE PROBLEM
Cassava is important to human because they serve as a source of staple food for him and his
animals, it could be employed to produce chips, gari, fufu etc. it is also a source of viable income for
farmers who plant it and also to people involved in turning it into finished product e.g. the gari
producers, the transport drivers. But as beneficial as cassava is to humans, its effluent has always
constituted a source of nuisance as well as the odour emanating from gari processing plants are always
offensive.
Due to effluents produced in the environment, studies have been done to find out the
microorganism that can be either pathogenic or nonpathogenic that are present within the cassava mill
factories
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1.2 AIMS AND OBJECTIVES
To isolate, characterize and carry out antimicrobial susceptibility test on soil microorganisms
present within the cassava mill industry.
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CHAPTER TWO
2.1 LITERATURE REVIEW
Cassava (Manihot esculenta Crantz, synonymous with Manihot utilissima Rhol) belongs to
the family Euphorbiaceae. It is mainly a food crop whose tubers are harvested between 713 months
based on the cultivars planted (Cook, 1985; Taye, 1994). The tubers are quite rich in carbohydrates
(8590%) with very small amount of protein (1.3%) in addition to cyanogenic gloucoside (Linamarin
and Lotaustiallin). (Nwabueze and Odunsi, 2007; Oyewole and Afolami, 2001). This high carbohydrate
content makes cassava a major food item especially for the low income earners in most tropical
countries especially Africa and Asia (Desse and Taye, 2001; Aderiye and Laleye, 2003).
The edible tubers are processed into various forms which include chips, pellets, cakes and flour.
The flour could be fried to produce gari or steeped in water to ferment to produce fufu when cooked
(Oyewole and Odunfa, 1992).
Fermentation is one of the oldest and most important traditional food processing and
preservation techniques. Food fermentations involve the use of microorganisms and enzymes for the
production of foods with distinct quality attributes that are quite different from the original
agricultural raw material. The conversion of cassava (Manihot esculenta, Crantz syn. Manihot
utilissima Pohl) to gari illustrates the importance of traditional fermentations.
Cassava is native to South America but was introduced to West Africa in the late 16th century
where it is now an important staple in Nigeria, Ghana, Ivory Coast, Sierra Leone, Liberia, Guinea,
Senegal and Cameroon. Nigeria is one of the leading producers of cassava in the world with an annual
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production of 3540 million metric tons. Over 40 varieties of cassava are grown in Nigeria and cassava
is the most important dietary staple in the country accounting for over 20% of all food crops consumed
in Nigeria. Cassava tubers are rich in starch (2030%) and, with the possible exception of sugar cane;
cassava is considered the highest producer of carbohydrates among crop plants.
Despite its vast potential, the presence of two cyanogenic glucosides, Linamarin (accounting for 93% of
the total content) and lotaustralin or methyl Linamarin, that on hydrolysis by the enzyme linamarase
release toxic HCN, is the most important problem limiting cassava utilization. Generally cassava
contains 10500 mg HCN/kg of root depending on the variety, although much higher levels, exceeding
1000 mg HCN/kg may be present in unusual cases. Cassava varieties are frequently described as sweet
or bitter. Sweet cassava varieties are low in cyanogens with most of the cyanogens present in the peels.
Bitter cassava varieties are high in cyanogens that tend to be evenly distributed throughout the roots.
Environmental (soil, moisture, temperature) and other factors also influence the cyanide content
of cassava (Bokanga et al; 1994). Low rainfall or drought increases cyanide levels in cassava roots due
to water stress on the plant. Apart from acute toxicity that may result in death, consumption of sublethal
doses of cyanide from cassava products over long periods of time results in chronic cyanide toxicity that
increases the prevalence of goiter and cretinism in iodinedeficient areas. Symptoms of cyanide
poisoning from consumption of cassava with high levels of cyanogens include vomiting, stomach pains,
dizziness, headache, weakness and diarrhea (Akintonwa et al; 1994).
Chronic cyanide toxicity is also associated with several pathological conditions including konzo,
an irreversible paralysis of the legs reported in eastern, central and southern Africa (Howlett and
Konzo, 1994), and tropical ataxic neuropathy, reported in West Africa, characterized by lesions of the
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skin, mucous membranes, optic and auditory nerves, spinal cord and peripheral nerves and other
symptoms (Oshuntokun, 1994). Without the benefits of modern science, a process for detoxifying
cassava roots by converting potentially toxic roots into gari was developed, presumably empirically, in
West Africa. The process involves fermenting cassava pulp from peeled, grated roots in cloth bags and
after dewatering, the mash is sifted and fried.
Microbial fermentations have traditionally played important roles in food processing for
thousands of years. Most marketed cassava products like “gari”, “fufu”, “pupuru”, “apu” etc., in Africa
are obtained through fermentation. The importance of fermentation in cassava processing is based on its
ability to reduce the cyanogenic glucosides to relatively insignificant levels. Unlike alcoholic fermentation,
the biochemistry and microbiology is only superficially understood, but it is believed that some
cyanidrophilic/cyanide tolerant microorganisms effect breakdown of the cyanogenicglucoside. It has
been shown that the higher the retention of starch in grated cassava the better the detoxification process.
This could be attributed to the fermentative substrate provided by the starch. Also, the longer the
fermentation process the lower the residual cyanide content.
Generally, fermented cassava products store better and often are low in residual cyanide
content. (Onabowale, 1988) developed a combined acid hydrolysis and fermentation process at FIIRO
(Federal Institute for Industrial Research, Oshodi, Nigeria) and achieved a 98% (approx.) reduction in
total cyanide after dehydration of the cassava flour for use in the feeding of chickens.
Cassava roots can be industrially applied for obtaining starch and flour. However, cassava industries
generate some undesirable subproducts, such as solid residues and a liquid effluent named manipueira,
which may represent a major disposal problem due to the high organic charge and toxic potential,
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resulting from the presence of cyanoglucosides. Manipueira is rich in potassium, nitrogen,
magnesium, phosphorous, calcium, sulfur and iron, presenting a great potential as an agronomic
fertilizer. It contains cyanoglucosides, which explains the application as nematicide and insecticide
(Palmisano et al., 2001).
Cyanoglucosides are secondary metabolites produced by several plant species (Conn, 1994)
used in animal and human diets, such as: apple, bamboo shoot, cassava, cherry, lima bean,
maize, oat, peach, papaya, sorghum and wheat (Muro, 1989). These compounds are dispersed
throughout the plant organs, mostly in nonedible parts (Jones, 1998), but may become concentrated in
edible roots and leaves, as in the case of cassava. Cassava (Manihot esculenta Crantz) roots and
leaves contain high concentrations of Linamarin (alphahydroxyisobutyronitrilebetaDglucopyranoside)
and Lotaustiallin (methylLinamarin). Linamarin is the most abundant cyanoglucosides present in cassava
cells (Conn, 1973) and may generate the equivalent to 0.2100 mg of HCN per 100 g of fresh cassava
following cellular lyses (Bradbury et al., 1991). The cassava effluent has been found to increase the
number of organisms in the soil ecosystem which may be associated with increase in the soil pH,
organic carbon and total nitrogen (Ogboghodo et al., 2001).
WASTE MANAGEMENT IN CASSAVA STARCH FACTORIES
Waste from cassava processing may be solid or liquid. The brown peel of cassava roots,
known as periderm, varies between 25% of the root total. The solid waste is made up of fibrous root
materials and contains starch that physically could not be extracted. The process of starch extraction
from cassava requires large quantity of water resulting in the release of a significant quantity of effluents
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(Balagopalan and Rajalakshmy, 1998). It is common for factories to discharge the effluents into the
nearby rivers, drainage channels, crop fields or to the land adjacent the factories. These effluents pose a
serious threat to the environment and quality of life in rural areas.
Wide variations were observed in physical and chemical constituents of primary and secondary
effluents from cassava starch factories. (Manilal et al., 1991) observed that the chemical oxidation
demand (COD) ranged between 33,600 & 38,223mgl1 in the primary effluents, whereas in the
secondary effluents, the range was only 38009050mgl1.
The biological oxidation demand (BOD) was in the range of 13,20014,300mgl1 in the primary
effluents. The corresponding figures for the secondary effluents were 3,6007,050mgl1. The acidity of
the effluent ranged between pH 4.5 & 4.7. Nitrogen and phosphorus are the main nutrients contributing
to the stability of organic waste and the analysis revealed low nitrogen content indicating necessity for
the enrichment of the effluent to reduce the BOD and COD (Manilal et al., 1991).
Balagopalan and Rajalakshmy, 1998 observed that the concentration of total cyanoglucosides in the
effluents ranged between 12.9mgl1 & 16.6mgl1 in the case of initial samples, whereas in the case of
final waste samples, the concentration ranged between 10.4mgl1 & 27.4mgl1. A high concentration of
cyanide was observed in the ground water source near the processing factories ranging between
1.2mgl1 & 1.6mgl1. Initial settling, anaerobiosis, filtration through sand & charcoal and aeration can
reduce the pollution load to the desired level (Balagopalan et al., 1994)
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Microorganisms can grow on substrates containing cyanides by anaerobic metabolism, or by
using an aerobic respiration chain as an alternative pathway (Cereda et al., 1991). In both pathways,
HCN is eliminated from the substrate, and converted into a nontoxic product (Jensen et al., 1979).
This enzymatic cyanideremoving property can be exploited for the detoxification of cyaniderich
cassava wastewater and industrial residues. These residues currently cause serious environmental
problems in many cassava flour producing plants in Brazil, the largest producer worldwide, and in many
African, Latin American and Asian countries (Romero et al., 2002), where cassava products are
an important input for human diet.
BACTERIA
Bacteria are singlecell organisms and the most numerous denizens of agriculture, with
populations ranging from 100million to 3billion in a gram. They are capable of very rapid reproduction
by binary fission (dividing into two) in favorable conditions. One bacterium is capable of producing 16
million more in just 24 hours. Most soil bacteria live close to plant roots and are often referred to as
rhizobacteria. Bacteria live in soil water, including the film of moisture surrounding soil particles, and
some are able to swim by means of flagella. The majority of the beneficial soildwelling bacteria need
oxygen (and are thus termed aerobic bacteria), whilst those that do not require air are referred to as
anaerobic, and tend to cause putrefaction of dead organic matter.
Aerobic bacteria are most active in a soil that is moist (but not saturated, as this will deprive aerobic
bacteria of the air that they require), and neutral soil pH, and where there is plenty of food
(carbohydrates and micronutrients from organic matter) available. Hostile conditions will not completely
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kill bacteria; rather, the bacteria will stop growing and get into a dormant stage, and those individuals
with proadaptive mutations may compete better in the new conditions.
FUNGI
Fungi are microscopic cells that usually grow as long threads or strands called hyphae, which
push their way between soil particles, roots, and rocks. Hyphae are usually only several thousandths of
an inch (a few micrometers) in diameter. Single hyphae can span in length from a few cells to many
yards. Hyphae sometimes group into masses called mycelium or thick, cordlike “rhizomorphs” that
look like roots.
Fungi perform important services related to water dynamics, nutrient cycling, and disease suppression.
Along with bacteria, fungi are important as decomposers in the soil food web. They convert
hardtodigest organic material into forms that other organisms can use. Fungal hyphae physically bind
soil particles together, creating stable aggregates that help increase water infiltration and soil water
holding capacity.
Soil fungi can be grouped into three general functional groups based on how they get their energy.
Decomposers – saprophytic fungi – convert dead organic material into fungal biomass, carbon
dioxide (CO2), and small molecules, such as organic acids. These fungi generally use complex
substrates, such as the cellulose and lignin, in wood, and are essential in decomposing the
carbon ring structures in some pollutants. A few fungi are called “sugar fungi” because they use
the same simple substrates as do many bacteria. Like bacteria, fungi are important for
immobilizing, or retaining, nutrients in the soil. In addition, many of the secondary metabolites of
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fungi are organic acids, so they help increase the accumulation of humicacid rich organic matter
that is resistant to degradation and may stay in the soil for hundreds of years.
Mutualists – the mycorrhizal fungi – colonize plant roots. In exchange for carbon from the
plant, mycorrhizal fungi help solubolize phosphorus and bring soil nutrients (phosphorus,
nitrogen, micronutrients, and perhaps water) to the plant. One major group of mycorrhizae, the
ectomycorrhizae (see third photo below), grows on the surface layers of the roots and are
commonly associated with trees. The second major group of mycorrhizae is the
endomycorrhizae that grow within the root cells and are commonly associated with grasses,
row crops, vegetables, and shrubs. Arbuscular mycorrhizal (AM) fungi are a type of
endomycorrhizal fungi (see fourth photo below). Ericoid mycorrhizal fungi can by either ecto or
endomycorrhizal.
The third group of fungi, pathogens or parasites, cause reduced production or death when
they colonize roots and other organisms. Rootpathogenic fungi, such as Verticillium, Pythium,
and Rhizoctonia, cause major economic losses in agriculture each year. Many fungi help control
diseases. For example, nematodetrapping fungi that parasitize diseasecausing nematodes, and
fungi that feed on insects may be useful as biocontrol agents.
2.2 ANTIBIOTICS
The control of microorganism is critical for the prevention and treatment of diseases. Modern
medicine is dependent on chemotherapeutic agents, chemical agents that are used to treat infections.
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Most of these agents are antibiotics, microbial products or their derivative that can kill susceptible
microorganism or inhibit their growth. Some bacteria and fungi are able to naturally produce many of the
commonly employed antibiotics. In contrast, several important chemotherapeutic agents such as
sulfonamides, trimethoprim, chloramphenicol, ciprofloxacin and dapsones are synthetic while increasing
number of antibiotics are semi synthetic.
Antibiotics vary in their effectiveness, many are narrowspectrum drugs—that is they are
effective only against a limited variety of pathogens. Others are broadspectrum drugs—they are able
to attack many different kinds of pathogens.
Drugs may also be classified based on the general microbial group they act against:
antibacterial, antifungal, antiprotozoan, and antiviral. Some antibiotics can be cidal or static in action.
Static agents reversibly inhibit growth, if the agent is removed, the microorganism will recover and grow
again. Although a cidal agent kills the target pathogen, its activity is concentration dependent and the
agent may only be static at low levels.
2.2.1 CLASSIFICATION OF ANTIBIOTICS
There are many classes of antibiotics available to modern medicine today, classification may be
based on route of administration, and mode of action (static or cidal) etc. most commonly used groups
of antibiotics is the: Penicillins, Cephalosporins, Aminoglycosides, Macrolides, Quinolones and
fluoroquinolones etc.
Penicillin
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Penicillin is cidal in its mode of action, a narrowspectrum antibiotic that functions to inhibit
transpeptidization enzyme involved in crosslinking the polysaccharide chains of the bacterial cellwall
peptidoglycan. Penicillin is used to treat skin infections, urinary tract infections; gonorrhea etc. examples
include Penicillin G, V, methicillin.
Cephalosporin
Cephalosporins are a family of antibiotics originally isolated in 1948 from the fungus
Cephalosporium. They contain a βlactan structure that is similar to that of penicillin.
Cephalosporin is also cidal in action, it is a broadspectrum antibiotic that functions to inhibit
transpeptidization enzyme involved in crosslinking the polysaccharide chains of the bacterial cellwall
peptidoglycan. Cephalosporin is used to treat pneumonia, strep throat, staphylococcus infection; various
skin infection etc. examples include Cephalothin, Cefoxitin, Ceftriaxone.
Aminoglycosides
They are also cidal in action, a broadspectrum antibiotic that acts by binding to small ribosomal
subunits (30S) and interfere with protein synthesis by directly inhibiting synthesis and causing misreading
of mRNA. Aminoglycosides are given for a short time periods and are injected intravenously rather than
orally because they are easily broken down in the stomach. Examples include Neomycin, Gentamicin,
and Streptomycin.
Macrolides
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These antibiotics are derived from Streptomycin bacteria. They are bacteriostatic and a
broadspectrum antibiotic, binding to 23S rRNA of large ribosomal subunit (50S) to inhibit peptide
chain elongation during protein synthesis. They are used to treat gastrointestinal upset, respiratory tract
infection etc. examples include Erythromycin, Clindamycin.
Erythromycin is a relatively broadspectrum antibiotic effective against grampositive bacteria,
mycoplasmas and a few gramnegative bacteria.
Trimethoprim
Trimethoprim is a synthetic antibiotic that also interferes with the production of folic acid. It does so by
binding to dihydrofolate reductase (DHFR), the enzyme responsible for converting dihydrofolic acid
to tetrahydrofolic acid, competing against dihydrofolic acid substrate. It is a broadspectrum antibiotic
often used to treat respiratory and middle ear infections, urinary tract infections, and traveler’s diarrhea
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2.3 ANTIBIOTICS RESISTANCE BY MICROORGANISMS
Antibiotics are very important to medicine but it is quite unfortunate that microorganisms have
been able to adapt themselves to cohabiting with antibiotics and subsequently developing resistance to
them (Walsh et al., 2004). When microorganisms are continually exposed to the same antibiotics, they
find ways of adapting themselves to such antibiotic and this renders the drug ineffective against them.
Transfer of resistance gene can be transferred by conjugation, transduction or transformation (Walsh,
2003).
Widespread use of antibiotics both inside and outside medicine is playing a significant role in the
emergence of resistant organism (Furaya and Lowy, 2006). Drugs frequently have been overused in the
past. It has been estimated that over 50% of the antibiotic prescriptions in the hospital are given without
clear evidence of infection or adequate medical indication (Payne et al., 2004). Many physicians have
administered antibacterial drugs to patients with colds, influenza, viral pneumonia, and other viral
diseases.
A recent study showed that over 50% of patients diagnosed with colds and upper respiratory infections
and 66% of those with chest colds (bronchitis) are given antibiotics, even though over 90% of those
cases are caused by viruses (Furaya and Lowy, 2006).
Frequently antibiotics are prescribed without culturing and identifying the pathogen or without
determining bacterial sensitivity to the drug (Harbath et al., 2005). Toxic, broadspectrum drugs are
sometimes given in place of narrowspectrum drugs as a substitute for culture and sensitivity testing, with
the consequent risk of dangerous side effects, opportunistic infections, and the selection of
drugresistant mutants (Payne et al., 2005). The situation is made worse by patients not completing
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their course of medication. When antibiotic treatment is ended too early, drugresistant mutants may
survive. Antibiotics are used often in rearing animals for food and this use among others leads to
creation of resistant strains. In supposedly wellregulated human medicine, the major problem of
emergence of resistant strains is due to misuse and overuse of antibiotics by doctors as well as patients
and it has been discovered that infections caused by resistant microorganism often fail to respond to
standard treatment resulting in prolonged illness and greater risk of death (Walsh et al., 2004).
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CHAPTER THREE
3.0 MATERIALS AND METHODS
3.1 MATERIALS
Various materials were involved in the analysis, these materials include:
Petri dishes commonly used for the holding the agar medium on which the organisms are
to be grown,
Syringes and needles which are employed in dispensing accurate measures of liquids
such as distilled water involved in the analysis,
Measuring cylinder used to measure a precise amount of liquids,
Conical flasks used for holding the prepared medium,
Ethanol which is commonly used to swab the working environment and also to supply
fuel to spirit lamps,
Testtubes for holding distilled water needed for serial dilution,
Cotton wool, aluminium foil, paper tape whose functions ranges from swabbing and
plugging of flasks mouth, wrapping of objects airtightly to labeling,
Wire loop for transferring of organism,
Weighing balance used for taking accurate measurements of medium to be used.
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Agars used include: nutrient agar for culturing bacteria, PDA (potato dextrose agar) for
culturing yeasts and moulds.
3.2 COLLECTION OF SAMPLES
Soil samples from three (3) different spots from Lautech gari processing industry were collected:
The first point or location was the point of discharge of the cassava effluent or wastewater i.e.
where the cassava wastewater drains into and this was labeled ‘Sample A’. Next location was one
hundred meters (100m) away from the point of discharge of the cassava effluent or wastewater i.e.
100m along the part of flow of cassava wastewater and this was labeled as ‘Sample B’ while the last
location was soil sample from a neutral source that has not witnessed any form of cassava effluent
discharge or contamination and this was labeled ‘Sample C’.
Sample A which is the soil sample from the cassava effluent was collected using a sterilized spoon, it
was collected into a sterile glass container, and the same procedure was used for Samples ‘B’ and ‘C’
but with different sterilized glass containers and spoons involved. The samples after collection were
transported into the laboratory in a sterile black polythene bag for subsequent microbial analysis.
3.3 CULTURING OF MICROORGANISMS
Media were prepared according to manufacturers’ instructions printed on the container, and
were sterilized in an autoclave at 1210C for 1hour. The collected soil samples were homogenized using
distilled water. 9mls of sterile distilled water was dispensed into each testtube and subsequent plugging
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with cotton wool and aluminium foil; these tubes were then taken to the autoclave for sterilization at
121oc for 1hour and after sterilization, cooling was done.
Serial dilution was done to thin out microbial population so that numbers of colonies that will be
formed would not overpopulate the plate unto which they will be grown.
Serial dilution was carried out for each sample using sterile distilled water as the diluent and this was
done under aseptic condition. The aseptic condition was achieved by the thorough swabbing of the
working environment with ethanol and cotton wool, the work table was also swabbed clean and lit with
spirit lamps to prevent contamination from atmosphere.
Three dilution factors for each soil sample were picked and used as inoculum for the culturing of the
organisms using pour plate method. Incubation was done at 370c for 24hours for bacteria and 48hours
for fungi.
Observation and recording was done after the completion of the incubation period.
ISOLATION OF ORGANISMS
From the mixed culture, distinct colonies were picked and streaked unto a freshly prepared media under
aseptic condition. Subculturing was done repeatedly to obtain pure isolates which were stored on slants.
IDENTIFICATION OF ISOLATES
The isolates were subjected to various biochemical tests for identification according to
specification of (Starr et al., 1981) in the laboratory
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Figure showing arrays of plates in a lamina flow chamber and an isolate growing on the plate
3.7.2 BIOCHEMICAL TESTS
The following are the biochemical tests performed on the isolates;
3.7.2.1 CATALASE TEST
A slide test was employed, a small quantity of the cultures were put on a glass slide, a
drop or two of hydrogen peroxide is then added to the slide. The presence of bubbles represents a
positive (+ve) test while a negative test is signaled by the absence of bubbles.
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3.7.2.2 HYDROGEN SULPHIDE TEST
Examine each SIM tube for the presence of a black color (nothing needs to be added).
A black color indicates the presence of hydrogen sulphide (H2S) which combines with the peptonized
iron in the SIM medium. The result is ‘FeS’ iron sulphide which causes a blackening of the medium and
this represents a positive test; the absence of a black color is a negative test.
Fig. showing hydrogen sulphide test
3.7.2.3 INDOLE TEST
Use a dropper to place 5drops of Kovac’s reagent onto the top of the SIM agar in
each tube. If the amino acid ‘tryptophan’ has been broken down by the enzyme ‘tryptophanase’ to form
23
indole, the kovac’s reagent will combine with the indole to form a red color at the top of the agar and
this represents a positive test. No color change in the kovac’s reagent represent is a negative test.
Fig. showing indole test (notice the red color on the top of the agar)
3.7.2.4 METHYL RED TEST
Using a Pasteur’s pipette, add 10drops of methyl red pH indicator to each tube, swirl
the tube gently to mix the drops into the broth. Examine each tube for color change. Bacteria that
produce many acids from the breakdown of dextrose (glucose) in the MRVP medium cause the pH to
drop to 4.2. At this pH, methyl red is red. A red color represents a positive test. Bacteria that produce
fewer acids from the breakdown of glucose drop the pH to 6.0. At this pH methyl red is yellow and this
represents a negative test.
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3.7.2.5 OXIDASE TEST
Drop 12 drops of oxidase reagent onto colonies of broth culture, watch out for gradual
color change from pink to light purple and then to dark purple within 1030seconds. Such a color
change indicates the presence of the respiratory enzyme ‘cytochrome C oxidase’ and this represents a
positive test. No color change is a negative test.
3.7.2.6 OXIDATIONFERMENTATION (OF) GLUCOSE TEST
OF glucose medium contains the sugar glucose and pH indicator bromthymol blue.
This indicator is green at the initial pH of 6.8, but turns to yellow at a pH of 6.0. if glucose is utilized,
acids are produced and the pH drops, causing the bromthymol blue to turn from green to yellow. If both
tubes (with or without oil) turn yellow, the test organism is said to be a facultative anaerobe able to use
glucose in the presence or absence of oxygen. If only the tube without oil turns yellow, the test organism
is considered an aerobe able to use glucose only when oxygen is present. No color change in either tube
indicates that the test organism is unable to utilize glucose.
3.8 ANTIBIOTIC SENSITIVITY TESTING
Colonies from the slants were picked and used to inoculate appropriate broth culture (Nutrient
broth for bacteria and Potato dextrose broth for fungi) and then incubated for less than 18hours. Fresh
media were prepared and left overnight for surface moisture to dry up. Picking of colonies from the
25
broth cultures was done using sterile applicator stick and proper swabbing unto the surface of the
prepared plates was done. This was left for 1hour after which antimicrobial discs were applied using a
sterile forceps; the discs were pressed down firmly to prevent falling off of the discs from the plates
during incubation.
For fungi, three concentrations of antifungal stock solution were prepared and sterile perforated
filter papers were dipped into each stock solution using a sterile forceps. Picking and application of the
discs unto the plates was done using a sterile forceps.
Incubation was done and sensitivities were observed at 24hours and 48hours for bacteria while
fungi were incubated for 48hours.
After incubation, the zones of inhibition formed were measured in two perpendicular, planes
with the averages determined. After this the results was interpreted using standard tables to determine if
the bacteria are Sensitive (S), Intermediate (I) or Resistant (R) to the antimicrobial drugs.
26
CHAPTER FOUR
4.0 RESULTS AND DISCUSSION
4.1 ISOLATED ORGANISMS
A total number of twentyfive strains were isolated from all the samples; some
of them are (Bacillus cereus, Bacillus subtilis, Pseudomonas aeruginosa, Listeria
monocytogenes, E.coli etc), while fungal strains include; (Aspergillus niger, Aspergillus
flavus and Rhizopus sp etc)
PLATE COUNT RESULT
Table 1 shows the result from the colony count of each sample from different media.
MacConkey Agar
SAMPLE
S
101 102 104
A TNC 67 36
B TNC 70 39
C TNC 80 19
27
PDA
SAMPLES 101 102 104
A TNC 49 17
B TNC 52 36
C 133 93 42
Nutrient Agar
SAMPLES 101 103 105
A TNC TNC 96
B TNC 94 85
C TNC TNC 86
4.2 IDENTIFICATION OF ORGANISMS
28
Table 2 shows the identified organisms obtained in the samples (bacteria and fungi).
S/
N
Codes Isolates
1 NA A1 Pseudomonas aeruginosa
2 NA A2 1 Bacillus cereus
3 NA A22 Bacillus subtilis
4 NA A31 Bacillus subtilis
5 NA A32 Bacillus subtilis
6 NA A53 Pseudomonas aeruginosa
7 NA A54 Bacillus subtilis
8 NA B11 Listeria monocytogenes
9 NA B12 E. coli
10 NA B31 Listeria monocytogenes
11 NA B32 E. coli
12 NA B52 E. coli
13 NA B53 E. coli
14 NA C31 E. coli
15 NA C42 Bacillus cereus
16 NA C42 Bacillus cereus
17 NA C54 Bacillus subtilis
18 NA C54 E. coli
29
A11 Aspergillus niger
A12 Aspergillus flavus
A21 Aspergillus niger
B11 Rhizopus sp
B12 Aspergillus niger
C2 Aspergillus niger
Mycotene Result in ‘mm’
Fungi 50µg/ml 100µg/ml 200µg/ml
A11 R 18 20
A12 13 15 19
A21 15 30 35
Fungi 50µg/ml 100µg/ml 200µg/ml
B11 R R R
B12 12.5 20 22
30
C2 14.5 19 21
4.3 ANTIBIOTIC SENSITIVITY TESTING
Table 3 shows the sensitivity result for the isolated organisms from samples A, B, and C at 24hours and
48hours respectively.
SENSITIVITY TESTING RESULT (24 HOURS)
SAMPLE A (CASSAVA EFFLUENT)
SAMPLE
S
CAZ CRX GEN CPR OFL AUG NIT AMP ER
Y
CTR CX
C
ve A31 R R 21.0 24.5 21.5 18.0 18.5 11.5
ve A21 R R 19.0 24.0 23.5 13.5 17.0 10.5
+ve A32 R R 15.5 20.0 R 11.5 R R
ve A22 R R 25.0 21.0 13.0 15.0 24.5 11.0
ve A1 R R 17.0 20.5 18.0 13.0 16.5 12.0
+ve A53 R R 16.0 20.0 R 11.5 R R
ve A54 R R 18.0 23.0 20.5 12.0 15.0 11.0
31
SAMPLE B (100m from Cassava effluent)
SAMPLES CAZ CRX GEN CPR OFL AUG NIT AMP ERY CT
R
CX
C
ve B11 R R 16.5 23.5 21.5 12.5 13.5 R
+ve B12 R R 21.5 28.0 R 16.0 R R
+ve B53 R R 16.0 17.0 R 15.5 R R
+ve B31 R R 13.0 20.0 R R R R
ve B32 11.0 16.0 19.0 25.0 20.0 20.0 15.0 10.0
ve B52 R R 18.5 16.0 16.0 12.0 14.0 7.5
SAMPLE C (Normal soil)
32
SAMPLE
S
CAZ CRX GEN CPR OFL AUG NIT AMP ERY CT
R
CX
C
ve C42 20.0 15.5 16.0 17.0 22.0 6.0 13.0 R
+ve C31 R R 14.5 14.5 R 9.0 R R
ve C42 20.0 17.0 17.0 25.0 25.0 8.0 9.0 R
+ve C54 R R 14.0 24.0 R 10.0 R R
ve C54 R R 17.0 20.5 20.0 10.0 14.0 10.5
SENSITIVITY TESTING RESULT AT (48 HOURS)
SAMPLE A (CASSAVA EFFLUENT)
SAMPLE
S
CAZ CRX GEN CPR OFL AUG NIT AMP ER
Y
CTR CX
C
ve A31 R R 23.0 24.5 21.5 18.0 19.0 12.0
ve A21 R R 19.0 24.0 24.0 14.5 17.0 13.0
+ve A32 R R 17.5 20.0 R 12.5 R R
ve A22 R R 25.0 23.0 18.5 15.0 24.5 17.0
ve A1 R R 19.0 21.0 19.0 13.5 18.5 12.0
+ve A53 R R 17.0 21.0 R 12.0 R R
33
ve A54 R R 20.0 27.5 25.0 13.0 17.0 12.0
SAMPLE B (100m from Cassava effluent)
SAMPLES CAZ CRX GEN CPR OFL AUG NIT AMP ERY CT
R
CX
C
ve B11 R R 17.5 24.5 23.0 13.0 14.0 R
+ve B12 R R 28.0 32.0 R 20.5 R R
+ve B53 R R 16.5 20.0 R 18.0 R R
+ve B31 R R 15.5 21.0 R R R R
ve B32 12.5 17.0 21.0 27.0 23.0 21.0 15.0 15.5
ve B52 R R 18.5 16.0 16.0 12.0 14.0 9.0
SAMPLE C (Normal soil)
SAMPLE
S
CAZ CRX GEN CPR OFL AUG NIT AMP ERY CT
R
CX
C
ve C42 22.0 19.0 19.0 20.0 25.0 7.5 15.0 R
+ve C31 R R 16.0 21.0 R 11.0 R R
ve C42 22.5 17.0 19.0 25.0 25.5 8.0 14.0 R
+ve C54 R R 15.0 27.0 R 11.0 R R
ve C54 R R 19.0 26.0 26.0 13.5 16.0 11.0
34
Negative Positive
Caz Ceftazidine 30µg Caz Ceftazidine 30µg
Crx Cefuroxime 30µg Crx Cefuroxime 30µg
Gen Gentamycin 10µg Gen Gentamycin 10µg
Cpr Ciprofloxacin 5µg Ctr Ceftriaxone 300µg
Ofl Ofloxacin 5µg Cxc Cloxacilin 5µg
Aug Augumentin 30µg Aug Augumentin 30µg
Nit Nitrofurantoin 300µg Ofl Ofloxacin 5µg
Amp Ampicillin 10µg Ery Erythromycin 5µg
35
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