CHAPTER ONE: INTRODUCTION
1.1: Historical background of bacteriophages
Bacteriophages or “phages”, most abundant forms of life in the biosphere are viruses that
recognize and infect bacteria specifically. They outnumber bacteria in order of magnitude by
an estimated factor of one (Cobián-Güemes et al., 2016). The history of bacteriophages dates
back in 1896 when a British bacteriologist, Ernest Hanbery Hankin, demonstrated the
presence of a biological principle in the waters from rivers Ganga and Yamuna in India that
destroyed the bacteria and caused cholera infection. Larger microorganisms such as bacteria
would be retained but the substance passed through millipore filters (Summers, 2014).
However, Hankin did not pursue his dream.
In 1915, a British bacteriologist, Fredrick Twort noted that pure culture of bacteria may be
associated with a filter–passing transparent material that may entirely breakdown bacteria of a
culture into granules. The Author described the substance secreted by microbes a transparent
material found to be unable to grow in absence of bacteria as ferment (Summers, 2014). The
results of Fredrick Twort were published but due to shortage of funds and the First World
War, the work was disrupted.
Independently, in 1917 similar experimental findings were described by Felix d’ Herelle.
Through filtering stools that were incubated for 18 hours, the Author isolated ‘anti-Shiga’
microorganism from stools of patients recovering from shigellosis. He was undertaking a
study of patients suffering or recovering from bacillary dysentery. He described his discovery
as a microbe that was ‘veritable’ microbe of immunity and an obligate bacteriophage
(Summers, 2014). It was d’Herelle who coined the term bacteriophage meaning bacteria eater.
In order to ascertain their safety, in 1926 he carried out self-ministration of phage
preparations, gave to his colleagues and family members before ministering the phage
preparations to human patients. He was invited for cholera treatment studies by British
government to the Haffkine Institute, Bombay, India after four patients were treated of
bubonic plague in Egypt, a visit that resulted in establishment of ‘The bacteriophage inquiry’.
Due to deficiency understanding of the phage-host interactions, low quality of some of the
scientific studies, coupled with introduction of antibiotics, there was discontinuation of phage
therapy in the Western world (Summers, 2014). The Eliava Institute was opened in Tbilisi,
Georgia in 1923 for study of phages and development of bacteriophage therapy. The study on
1
,the application of bacteriophages in medical field was nearly wiped out in 1930s when
antibiotics were discovered and found to be effective.
However, production of some bacteriophage based prophylactic and therapeutic preparations
on commercial basis continued in Western Europe, Africa and the United States through the
1950s and 1960s despite introduction of antibiotics (Sulakvelidze & Alavidze, 2001). Phages
self-restraint their numbers at the location of infection by the host bacteria contrary to
antibiotics as they replicate on the undesirable pathogen disintegrating into their protein
subunits when the bacterial host is lysed (Rohde & Wittmann, 2020). Bacteriophages have
reemerged as a promising legitimate alternative to fight this international predicament in the
antibiotic dilemma in which bacterial multi-drug resistance as well as pan-drug resistance is
increased adequately. However, the implication of the discovery is that bacteriophages have
received center of interest for prevalent research afresh. In spite of bacteriophages having
been used for more than a centennial, state-of-the-art bacteriophage research is essential in
addition to the case of systematic clinical trials as well as in all fields of phage administration.
More knowledge on bacteriophage diversity as well as taxonomy, their mode of host
interaction, their structure–function interrelationship and their genotype–phenotype
association will benefit research (Rohde & Wittmann, 2020). While discussing bacteriophage
therapy, sole important point that has to be kept in mind is that bacteriophages complement
their actions and finally strengthen the antibacterial effect on the whole but should not
generally replace antibiotic drugs in therapy (Rohde & Wittmann, 2020).
Phage diversity is huge as already revealed by projects analysing the metagenomes of
different habitats; there is always something new to discover with regard to habitat diversity
and to bacterial species still underrepresented in terms of bacteriophage research.
Bacteriophages have also played a considerably crucial role in the development of molecular
biology on top of their impact on ecology and evolution. In order to find new ways to
efficiently use bacteriophage diversity for different applications and phages as tools, research
is going on. Bacteriophages have served as appreciated model systems and are a success story
of nature, entailing for human disease like for example Alzheimer’s disease, acquired
immunodeficiency syndrome (AIDS) and in the year 2020, the SARS-CoV-2 pandemic
(Rohde & Wittmann, 2020). Apart from anti-bacterial objectives, bacteriophages are once
again in the focus in light of the current Covid -19 pandemic. Automation vaccines producible
in a period of a few weeks are indispensable in a virus pandemic as well as the vaccine
2
,response to unfolding RNA viruses like SARS-CoV-2 might be improved through application
of bacteriophages (Rohde & Wittmann, 2020). According to Serwer (2020), application of
coronavirus-like bacteriophages as pathogen homologs for development of model platforms;
bacteriophages can be evolved which bind to particular antibodies against membrane-covered
RNA viruses.
1.2: Chronology of cholera
In 1817, the first cholera pandemic begun from South East Asia, Bengal region of India,
Calcutta, spreading across India by 1820 thereafter to other parts of the globe. In the course of
the past 200 years, seven cholera pandemics have occurred. Six worldwide cholera pandemics
occurred between 1817 and 1923. The documented or presumed etiological agent of the first
six pandemics was Vibrio cholerae O1, the classical type. The causative agent of the seventh
pandemic that appeared in 1961 in Indonesia since spreading worldwide particularly to South
Asia in 1963, Africa in 1970, Latin America in 1991 and the Caribbean (Haiti) in 2010, Vibrio
cholerae El Tor biotype has been described (Weill et al., 2017). Accordingly, recent high
definition genome documentation and isolated historical records stipulate Bay of Bengal as
the major hub linking the spread of cholera around the globe during the 19th and early 20th
centuries (Moore et al., 2014). There were worldwide outbreaks in the early 1990s in South
and Central America. For more than three years, cholera has persisted in Haiti with seasonal
exacerbation of the epidemic occurring during the rainy season. Historically, the disease had
never been documented previously in the country and the epidemic constitutes the largest
national epidemic of the seventh pandemic. The epidemic strain in Haiti is O1 biotype El Tor
serotype Ogawa, a variant of Vibrio cholerae (Moore et al., 2014). The continent of Africa is
mostly affected by the present seventh cholera pandemic. The first Ogawa strain was
introduced in West Africa in 1970 (Guinea, Sierra Leone, Liberia and Ghana) (Weill et al.,
2017).
1.3: The cholera disease
Acute infectious diarrheal diseases remain among the most frequent causes of childhood
deaths, accounting for 10-12% of the death toll for children under the age of five years and
around 1.4-1.9 million fatalities worldwide (Levy et al., 2016). The disease cholera is
devastating, causing watery diarrhea that can lead to severe dehydration and if untreated,
death. It is mainly caused by O1 and O139 toxigenic Vibrio cholerae serotypes. The disease is
3
, spread through faecal-oral route and hence strongly associated with poverty, poor hygiene,
clean water shortage and lack of adequate sanitation facilities (Deen et al., 2020). Vibrio
cholerae is a motile single flagellated, Gram-negative curved rod-shaped bacterium belonging
to Vibrionaceae family. Naturally, worldwide, Vibrio species inhabit the coastal, estuarine as
well as marine environment (Letchumanan et al., 2015a). Occurrence of this bacterium in the
marine environment is perturbation of human on food safety owing to the potential leading to
cholera outbreaks depending on the surrounding conditions (Ceccarelli et al., 2013).
Worldwide, each year approximately 2.9 million cholera cases occur (Somboonwit et al.,
2017). An estimated 1.8 billion are still at risk for cholera due to lack of potable water,
inadequate sanitation and hygiene (Somboonwit et al., 2017). However, the World Health
Organization (WHO) estimates that only 5–10% of the cases occurring annually are officially
reported (Ali et al., 2012).
In Asia, South America and Africa, cholera is endemic, coincidence of outbreaks usually
corresponding to and/or emerging from conflict and natural catastrophe (Martinez et al.,
2010). Outbreaks, in South America and African countries take place after summer rains or
floods (Emch et al., 2008).
In Africa from 2010, there has been cholera outbreaks and statistics show that the highest
number of cases was in 2017 with 5654 deaths and 1,227,391 cases were revealed in
accordance with the cholera yearly review 2017 (WHO, 2018). According to Cholera Bulletin
(Africa, 2019), roughly, 1,681 cholera / Acute watery disease (AWD) cases including thirteen
deaths were announced in seven arising out of the twenty one countries in Eastern and
Southern Africa Region (ESAR); with 0.8% as an average Case Fatality Rate (CFR), from
the onset of the year 2019. Angola, Burundi, Kenya, Tanzania, Somalia, Uganda and
Zimbabwe are among these countries. Outbreaks from the rest of these countries spilled over
from 2018, apart from Kenya. Out of the total case load recorded in the year, 2019, Kenya
accounted for 51.3 % (863) followed by Somalia at 31.2% (524). In 2019 the highest case
fatality rate was recorded in Zimbabwe (6.2%), followed by Uganda (5.7%) then Tanzania
(2.9%). In many African countries, cholera remains a heavy disease burden and it is mostly
escalated during heavy rains that occur every year when cholera springs up killing many.
Kenyan populace has suffered from cholera outbreaks for the last decade due to heavy rains,
poor sanitation coupled with inadequate availability of decontaminated, potable water for
4
1.1: Historical background of bacteriophages
Bacteriophages or “phages”, most abundant forms of life in the biosphere are viruses that
recognize and infect bacteria specifically. They outnumber bacteria in order of magnitude by
an estimated factor of one (Cobián-Güemes et al., 2016). The history of bacteriophages dates
back in 1896 when a British bacteriologist, Ernest Hanbery Hankin, demonstrated the
presence of a biological principle in the waters from rivers Ganga and Yamuna in India that
destroyed the bacteria and caused cholera infection. Larger microorganisms such as bacteria
would be retained but the substance passed through millipore filters (Summers, 2014).
However, Hankin did not pursue his dream.
In 1915, a British bacteriologist, Fredrick Twort noted that pure culture of bacteria may be
associated with a filter–passing transparent material that may entirely breakdown bacteria of a
culture into granules. The Author described the substance secreted by microbes a transparent
material found to be unable to grow in absence of bacteria as ferment (Summers, 2014). The
results of Fredrick Twort were published but due to shortage of funds and the First World
War, the work was disrupted.
Independently, in 1917 similar experimental findings were described by Felix d’ Herelle.
Through filtering stools that were incubated for 18 hours, the Author isolated ‘anti-Shiga’
microorganism from stools of patients recovering from shigellosis. He was undertaking a
study of patients suffering or recovering from bacillary dysentery. He described his discovery
as a microbe that was ‘veritable’ microbe of immunity and an obligate bacteriophage
(Summers, 2014). It was d’Herelle who coined the term bacteriophage meaning bacteria eater.
In order to ascertain their safety, in 1926 he carried out self-ministration of phage
preparations, gave to his colleagues and family members before ministering the phage
preparations to human patients. He was invited for cholera treatment studies by British
government to the Haffkine Institute, Bombay, India after four patients were treated of
bubonic plague in Egypt, a visit that resulted in establishment of ‘The bacteriophage inquiry’.
Due to deficiency understanding of the phage-host interactions, low quality of some of the
scientific studies, coupled with introduction of antibiotics, there was discontinuation of phage
therapy in the Western world (Summers, 2014). The Eliava Institute was opened in Tbilisi,
Georgia in 1923 for study of phages and development of bacteriophage therapy. The study on
1
,the application of bacteriophages in medical field was nearly wiped out in 1930s when
antibiotics were discovered and found to be effective.
However, production of some bacteriophage based prophylactic and therapeutic preparations
on commercial basis continued in Western Europe, Africa and the United States through the
1950s and 1960s despite introduction of antibiotics (Sulakvelidze & Alavidze, 2001). Phages
self-restraint their numbers at the location of infection by the host bacteria contrary to
antibiotics as they replicate on the undesirable pathogen disintegrating into their protein
subunits when the bacterial host is lysed (Rohde & Wittmann, 2020). Bacteriophages have
reemerged as a promising legitimate alternative to fight this international predicament in the
antibiotic dilemma in which bacterial multi-drug resistance as well as pan-drug resistance is
increased adequately. However, the implication of the discovery is that bacteriophages have
received center of interest for prevalent research afresh. In spite of bacteriophages having
been used for more than a centennial, state-of-the-art bacteriophage research is essential in
addition to the case of systematic clinical trials as well as in all fields of phage administration.
More knowledge on bacteriophage diversity as well as taxonomy, their mode of host
interaction, their structure–function interrelationship and their genotype–phenotype
association will benefit research (Rohde & Wittmann, 2020). While discussing bacteriophage
therapy, sole important point that has to be kept in mind is that bacteriophages complement
their actions and finally strengthen the antibacterial effect on the whole but should not
generally replace antibiotic drugs in therapy (Rohde & Wittmann, 2020).
Phage diversity is huge as already revealed by projects analysing the metagenomes of
different habitats; there is always something new to discover with regard to habitat diversity
and to bacterial species still underrepresented in terms of bacteriophage research.
Bacteriophages have also played a considerably crucial role in the development of molecular
biology on top of their impact on ecology and evolution. In order to find new ways to
efficiently use bacteriophage diversity for different applications and phages as tools, research
is going on. Bacteriophages have served as appreciated model systems and are a success story
of nature, entailing for human disease like for example Alzheimer’s disease, acquired
immunodeficiency syndrome (AIDS) and in the year 2020, the SARS-CoV-2 pandemic
(Rohde & Wittmann, 2020). Apart from anti-bacterial objectives, bacteriophages are once
again in the focus in light of the current Covid -19 pandemic. Automation vaccines producible
in a period of a few weeks are indispensable in a virus pandemic as well as the vaccine
2
,response to unfolding RNA viruses like SARS-CoV-2 might be improved through application
of bacteriophages (Rohde & Wittmann, 2020). According to Serwer (2020), application of
coronavirus-like bacteriophages as pathogen homologs for development of model platforms;
bacteriophages can be evolved which bind to particular antibodies against membrane-covered
RNA viruses.
1.2: Chronology of cholera
In 1817, the first cholera pandemic begun from South East Asia, Bengal region of India,
Calcutta, spreading across India by 1820 thereafter to other parts of the globe. In the course of
the past 200 years, seven cholera pandemics have occurred. Six worldwide cholera pandemics
occurred between 1817 and 1923. The documented or presumed etiological agent of the first
six pandemics was Vibrio cholerae O1, the classical type. The causative agent of the seventh
pandemic that appeared in 1961 in Indonesia since spreading worldwide particularly to South
Asia in 1963, Africa in 1970, Latin America in 1991 and the Caribbean (Haiti) in 2010, Vibrio
cholerae El Tor biotype has been described (Weill et al., 2017). Accordingly, recent high
definition genome documentation and isolated historical records stipulate Bay of Bengal as
the major hub linking the spread of cholera around the globe during the 19th and early 20th
centuries (Moore et al., 2014). There were worldwide outbreaks in the early 1990s in South
and Central America. For more than three years, cholera has persisted in Haiti with seasonal
exacerbation of the epidemic occurring during the rainy season. Historically, the disease had
never been documented previously in the country and the epidemic constitutes the largest
national epidemic of the seventh pandemic. The epidemic strain in Haiti is O1 biotype El Tor
serotype Ogawa, a variant of Vibrio cholerae (Moore et al., 2014). The continent of Africa is
mostly affected by the present seventh cholera pandemic. The first Ogawa strain was
introduced in West Africa in 1970 (Guinea, Sierra Leone, Liberia and Ghana) (Weill et al.,
2017).
1.3: The cholera disease
Acute infectious diarrheal diseases remain among the most frequent causes of childhood
deaths, accounting for 10-12% of the death toll for children under the age of five years and
around 1.4-1.9 million fatalities worldwide (Levy et al., 2016). The disease cholera is
devastating, causing watery diarrhea that can lead to severe dehydration and if untreated,
death. It is mainly caused by O1 and O139 toxigenic Vibrio cholerae serotypes. The disease is
3
, spread through faecal-oral route and hence strongly associated with poverty, poor hygiene,
clean water shortage and lack of adequate sanitation facilities (Deen et al., 2020). Vibrio
cholerae is a motile single flagellated, Gram-negative curved rod-shaped bacterium belonging
to Vibrionaceae family. Naturally, worldwide, Vibrio species inhabit the coastal, estuarine as
well as marine environment (Letchumanan et al., 2015a). Occurrence of this bacterium in the
marine environment is perturbation of human on food safety owing to the potential leading to
cholera outbreaks depending on the surrounding conditions (Ceccarelli et al., 2013).
Worldwide, each year approximately 2.9 million cholera cases occur (Somboonwit et al.,
2017). An estimated 1.8 billion are still at risk for cholera due to lack of potable water,
inadequate sanitation and hygiene (Somboonwit et al., 2017). However, the World Health
Organization (WHO) estimates that only 5–10% of the cases occurring annually are officially
reported (Ali et al., 2012).
In Asia, South America and Africa, cholera is endemic, coincidence of outbreaks usually
corresponding to and/or emerging from conflict and natural catastrophe (Martinez et al.,
2010). Outbreaks, in South America and African countries take place after summer rains or
floods (Emch et al., 2008).
In Africa from 2010, there has been cholera outbreaks and statistics show that the highest
number of cases was in 2017 with 5654 deaths and 1,227,391 cases were revealed in
accordance with the cholera yearly review 2017 (WHO, 2018). According to Cholera Bulletin
(Africa, 2019), roughly, 1,681 cholera / Acute watery disease (AWD) cases including thirteen
deaths were announced in seven arising out of the twenty one countries in Eastern and
Southern Africa Region (ESAR); with 0.8% as an average Case Fatality Rate (CFR), from
the onset of the year 2019. Angola, Burundi, Kenya, Tanzania, Somalia, Uganda and
Zimbabwe are among these countries. Outbreaks from the rest of these countries spilled over
from 2018, apart from Kenya. Out of the total case load recorded in the year, 2019, Kenya
accounted for 51.3 % (863) followed by Somalia at 31.2% (524). In 2019 the highest case
fatality rate was recorded in Zimbabwe (6.2%), followed by Uganda (5.7%) then Tanzania
(2.9%). In many African countries, cholera remains a heavy disease burden and it is mostly
escalated during heavy rains that occur every year when cholera springs up killing many.
Kenyan populace has suffered from cholera outbreaks for the last decade due to heavy rains,
poor sanitation coupled with inadequate availability of decontaminated, potable water for
4
