Professional Documents
Culture Documents
Drug-resistant bacteria — also known as superbugs — are on the rise globally, and they're now killing
more people each year than either HIV/AIDS or malaria. And low- and middle-income countries are being hit the hardest by the rise in antibiotic-resistant
infections. "That resistance out there is actually now one of the leading causes of death in the world," says Dr. Chris Murray, the director of the Institute for Health Metrics and Evaluation.
people and played a role in 5 million more deaths worldwide. Murray and his colleagues set out to
quantify how much of a problem antibiotic resistance is globally, and they found that bacteria are
mutating to evade antibiotics at a pace far faster than many researchers had previously forecast. These deadly new
strains of bacteria are causing untreatable blood infections, fatal pneumonia, relentless urinary tract infections, gangrenous wounds and terminal cases of sepsis, among other conditions. The
conventional wisdom used to be that the failure of antibiotics was a "First World" problem. But Murray says this new study shows it happening all over the world. "In the past, we all thought that
you had to be rich enough to use a lot of antibiotics inappropriately to have this problem," he says. "But that's not the case." The researchers calculate that deaths caused directly by antibiotic
resistance are the highest in sub-Saharan Africa, causing 24 deaths per 100,000 population annually, compared with an average fatality rate of 13 per 100,000 in high-income countries. Australia
has the lowest mortality rate globally from antibiotic resistance, at 6 deaths per 100,000. Latin America is right in the middle. But Fiorella Krapp Lopez, an infectious disease physician in Lima,
Peru, says being in the middle is still quite bad. "We do have a very high frequency of resistance to different types of antibiotics, first line and second line [antibiotics]," Krapp says. "And the
problem has been increasing in the last years." She says antibiotic resistance is affecting every level of health care in Peru. "Unfortunately, I think it's everywhere. We are seeing it in the
community with infections that used to be very simple to treat, like urinary infections," she says. Physicians are seeing minor wounds that in the past may have needed only a bandage but now are
turning into multidrug-resistant infections. "And we also see it in very sick patients with bloodstream infections or very severe pneumonia. So unfortunately, it's across the full spectrum of
bacterial infectious diseases right now in Peru," she says. Krapp was one of dozens of researchers around the world who contributed to the new Lancet report. She provided data specifically on
available to
drug resistance in Peru. She says there are many reasons that this problem is harder to address in low- and middle-income countries. First, antibiotics are often readily
anyone without a prescription. Misuse and overuse of these drugs fuels mutations in bacteria, leading to
more resistance. Second, the systems to flag and test for potentially drug-resistant infections are not as robust as in some wealthier countries. Third, low- and middle-income countries in general report higher rates of
infections in hospitals than high-income countries do, and those infections are more likely to be drug resistant. Fourth, while some new, more powerful antibiotics are being developed, lower-income countries are still dependent on
older, cheaper, less-effective drugs. Krapp says the COVID-19 crisis exacerbated all of these problems in Peru. And while it's too early to tell, she worries that the coronavirus pandemic has led
to a significant increase in drug resistance. "First, there was a lot of antibiotic use during the pandemic," she says. As the COVID-19 crisis pounded Peru,
many people who contracted the virus did not want to go anywhere near the overcrowded hospitals, so they self-medicated at home. "It is still very easy to get antibiotics in the local pharmacy
without a prescription," Krapp notes. "Unfortunately, more than 70, 80% of [COVID-19] patients that arrived to the hospital were already using antibiotics at home." They believed the drugs
would aid in their recovery. But antibiotics target bacteria and wouldn't be of much help against a coronavirus. This scenario may be one of the reasons that Peru has had the world's highest per
capita death rate from COVID-19. At times, hospitals and clinics were barely able to function as they were inundated with patients. "We believe that a lot of the high COVID mortality that we
had in Peru was due to secondary infections acquired in the hospitals rather than just by COVID-19," Krapp says. Whether or not that happened is hard to say. Monitoring for antibacterial
resistance in Peru — and in many other lower-income countries — is limited during the best of times but especially unlikely when hospitals are overflowing with COVID-19 patients. "During the
pandemic, the hospitals were overloaded. A lot of patients went into ICUs that were understaffed. That was just the perfect storm to have a very high transmission of these [drug-resistant]
pathogens," she says. It's unclear if that was happening because as health care workers were simply trying to keep COVID-19 patients breathing, testing bacterial samples for resistance fell low
on the priority list. Krapp says that overall she's very concerned that are evolving and learning how to evade what had been some of the world's most powerful drugs. "We are in a race, and
bacteria
bacteria are moving faster than we are," she says. "They are becoming resistant much faster than we humans are able to
these
create new antibiotics and make those antibiotics accessible to the most vulnerable populations."
Phage therapy—using specific viruses to fight difficult bacterial infections—shows great promise as a
tool for solving the problem of antibiotic-resistant bacteria (also called superbugs). Here at Yale
Medicine, the experimental treatment has already been used to benefit some patients—good news given
that antibiotic-resistant bacteria are now considered one of the most alarming public health problems. A
recent report from the Centers for Disease Control and Prevention (CDC) blames the problem for a death
every 15 minutes here in the U.S. Since the discovery of penicillin, doctors have used antibiotics to cure
people of once lethal bacterial infections. But now we know that, over time, bacteria have the ability to
protect themselves by evolving and becoming stronger and more complex (called antibiotic resistance).
Researchers have found that viruses can be a powerful tool that can be used against them. Specifically, a
type of friendly virus called bacteriophage (sometimes referred to as just phage) can be weaponized to
fight even the most difficult bacterial infections. This works because, unlike viruses that make us sick, phages can only infect
bacteria—and they are even selective about which bacteria they target. These phages are not rare; phages come from nature and are found nearly
everywhere in the world. This gives them the power to become, potentially, superheroes in our battle against resistant superbugs. This video
explains how Yale research scientist Benjamin Chan, PhD, collaborates with Yale Medicine doctors like Jonathan Koff, MD, to not only develop
phage therapy, but to use them to treat people who are especially vulnerable to infection (for instance, patients with cystic fibrosis). The goal is to
develop a library of effective treatments for specific types of bacteria and make these treatments available to patients with antibiotic-resistant
infections when other options are exhausted. “It’s definitely the dream,” says Chan. “It’s fantastic to go from doing basic research and then
bringing it to a patient in the clinic.”
Need for a Phage-Based Regulatory Framework and Future Perspectives. The current regulatory framework worldwide is not allowing the use of
phage therapy in Western Europe and the United States (Parracho et al., 2012). Hence, the phage community calls for new and specific standards
to implement phage therapy. The
phage therapy-based regulatory framework should include providing
well-characterized phages, including isolation and purification, defining host range, sequencing, and
storage in phage banks. These will provide an available well-defined collection ready-to-use for clinical care. Importantly, patients
should be informed of the phage therapy and given the option to decide to try it. It is also worth mentioning that it is recommended by the FDA to
follow phage manufacturing under Good Manufacturing Practice (GMP) guidelines and infrastructure. However,
the implementation
of GMP is considered for a large phage production whereas phage-specific patients are produced for a
limited number of phages, thus, a simpler GMP system is recommended. Phage banks are already
increasing, and some of them are located in Belgium, Republic of Georgia, Russia, Germany, Switzerland,
Finland, and Canada (Moelling et al., 2018). In addition, Phage Directory, an online database of phage
laboratories, phages, and bacterial hosts, in which phage researchers, regulators, and biotech companies
are communicated, is an interesting example of a network to implement the use of phages in clinics. This
huge phage database provides an opportunity to continue working on research to form therapeutic phages,
even as a form of individualized medicine. Political authorities, stakeholders, academics, and researchers
around the world must be aware of the need for urgency to treat a high number of people suffering from
MDR infections, which are predicted to be much higher as a primary and as a secondary infection during
the current pandemics, being a major global health threat. This can be achieved by the establishment of a
phage therapy-related regulation to allow for phage therapy research development and to increase
incentives in order to increase basic research and translate it to proper clinical trials.
Drug-resistant bacteria — also known as superbugs — are on the rise globally, and they're now killing
more people each year than either HIV/AIDS or malaria. And low- and middle-income countries are
being hit the hardest by the rise in antibiotic-resistant infections. "That resistance out there is actually now
one of the leading causes of death in the world," says Dr. Chris Murray, the director of the Institute for
Health Metrics and Evaluation. Murray is one of the authors of a new study, published in the medical
journal The Lancet, that finds that in 2019, drug-resistant infections directly killed 1.2 million people and
played a role in 5 million more deaths worldwide. Murray and his colleagues set out to quantify how
much of a problem antibiotic resistance is globally, and they found that bacteria are mutating to evade
antibiotics at a pace far faster than many researchers had previously forecast. These deadly new strains of
bacteria are causing untreatable blood infections, fatal pneumonia, relentless urinary tract infections,
gangrenous wounds and terminal cases of sepsis, among other conditions. The conventional wisdom used to be that
the failure of antibiotics was a "First World" problem. But Murray says this new study shows it happening all over the world. "In the past, we all
thought that you had to be rich enough to use a lot of antibiotics inappropriately to have this problem," he says. "But that's not the case." The
researchers calculate that deaths caused directly by antibiotic resistance are the highest in sub-Saharan Africa, causing 24 deaths per 100,000
population annually, compared with an average fatality rate of 13 per 100,000 in high-income countries. Australia has the lowest mortality rate
globally from antibiotic resistance, at 6 deaths per 100,000. Latin America is right in the middle. But Fiorella Krapp Lopez, an infectious disease
physician in Lima, Peru, says being in the middle is still quite bad. "We do have a very high frequency of resistance to different types of
antibiotics, first line and second line [antibiotics]," Krapp says. "And the problem has been increasing in the last years." She
says antibiotic resistance is affecting every level of health care in Peru. "Unfortunately, I think it's everywhere. We are seeing it in the community
with infections that used to be very simple to treat, like urinary infections," she says. Physicians are seeing minor wounds that in the past may
have needed only a bandage but now are turning into multidrug-resistant infections. "And we also see it in very sick patients with bloodstream
infections or very severe pneumonia. So unfortunately, it's across the full spectrum of bacterial infectious diseases right now in Peru," she says.
Krapp was one of dozens of researchers around the world who contributed to the new Lancet report. She provided data specifically on drug
resistance in Peru. She says there are many reasons that this problem is harder to address in low- and middle-income countries. First, antibiotics
are often readily available to anyone without a prescription. Misuse and overuse of these drugs fuels mutations in bacteria, leading to more
resistance. Second, the systems to flag and test for potentially drug-resistant infections are not as robust as in some wealthier countries. Third,
low- and middle-income countries in general report higher rates of infections in hospitals than high-income countries do, and those infections are
more likely to be drug resistant. Fourth, while some new, more powerful antibiotics are being developed, lower-income countries are still
dependent on older, cheaper, less-effective drugs. Krapp says the COVID-19 crisis exacerbated all of these problems in Peru. And while it's too
early to tell, she worries that the coronavirus pandemic has led to a significant increase in drug resistance. "First, there was a lot of antibiotic use
during the pandemic," she says. As the COVID-19 crisis pounded Peru, many people who contracted the virus did not want to go anywhere near
the overcrowded hospitals, so they self-medicated at home. "It is still very easy to get antibiotics in the local pharmacy without a prescription,"
Krapp notes. "Unfortunately, more than 70, 80% of [COVID-19] patients that arrived to the hospital were already using antibiotics at home."
They believed the drugs would aid in their recovery. But antibiotics target bacteria and wouldn't be of much help against a coronavirus. This
scenario may be one of the reasons that Peru has had the world's highest per capita death rate from COVID-19. At times, hospitals and clinics
were barely able to function as they were inundated with patients. "We believe that a lot of the high COVID mortality that we had in Peru was due
to secondary infections acquired in the hospitals rather than just by COVID-19," Krapp says. Whether or not that happened is hard to say.
Monitoring for antibacterial resistance in Peru — and in many other lower-income countries — is limited during the best of times but especially
unlikely when hospitals are overflowing with COVID-19 patients. "During the pandemic, the hospitals were overloaded. A lot of patients went
into ICUs that were understaffed. That was just the perfect storm to have a very high transmission of these [drug-resistant] pathogens," she says.
It's unclear if that was happening because as health care workers were simply trying to keep COVID-19 patients breathing, testing bacterial
samples for resistance fell low on the priority list. Krapp says that overall she's very concerned that bacteria are evolving and learning how to
evade what had been some of the world's most powerful drugs. "We are in a race, and these bacteria are moving faster than we
are," she says. "They are becoming resistant much faster than we humans are able to create new
antibiotics and make those antibiotics accessible to the most vulnerable populations."
In 2019, England’s Chief Medical Officer warned that antimicrobial resistance might cause the death of
around 10 million people every year. This is a threat that may overtake climate change in causing
humanity’s extinction. What are antibiotics? Antibiotics are drugs that are designed to either destroy bacteria or slow down their growth.
They can cost billions of euros and take years to develop. Unfortunately, they don’t work against fungal or viral infections which means there’s no
point in taking them for coughs, colds or influenza. The problem is that resistance to these drugs is growing rapidly. Professor Dame Sally Davies
noted that the number of bugs immune to antibiotics is on the rise, with a variety of causes being cited, including: The high volume of people
carrying harmful bacteria Overuse of antibiotics Non-adherence to prescribed hygiene practice These are also the primary reasons why numerous
large infection outbreaks occur in hospital. In this setting, many patients are susceptible due to their weak immune systems. When a particular
bacteria strain becomes resistant to antibiotics, treatment is often difficult or even impossible. There are also cases where these resistant bacteria
will pass their genes to other strains. Antibiotic resistance in farming and the environment The farming industry also uses antibiotics to protect
livestock from bacterial infection. However, in some countries, farmers administer these drugs in low doses as a preventive measure or even to
promote growth. Unfortunately, both the drug and the anti-resistant bacteria can escape farms and contaminate the local food chain and
environment. Nurses.co.uk published an article in which Dame Sally proposed that, in order to protect the British public, the UK should stop
importing beef and other meats from countries that misuse antibiotics. Why do humans need antibiotics? Every day, you can encounter bacteria
that could potentially be harmful to your health. For instance: Due to injury, even if it’s just a small scratch When you have been exposed to a
contaminated environment After undergoing a medical procedure (ranging from dental work to cancer therapy) Doctors administer antibiotics to
people with a bacterial infection, a condition where the uncontrolled growth of harmful bacteria can cause cell damage. These bacteria also
excrete toxins that are harmful to the human body. Usually, people’s immune systems can fight off the bacteria. However, if the infection is too
strong, they will need antibiotics to help the body recover. Currently, around 46,000 people die from sepsis in the UK every year, it is a severe
condition where harmful bacteria invade an individual’s bloodstream or tissues. The primary treatment for sepsis is antibiotics. Otherwise, the
infection could lead to organ failure, shock and ultimately death. The UK’s response By 2014, the UK had reduced antibiotic use by almost 10%
and by around 40% in livestock. However, drug-resistant
infections still increased by more than 30% between 2013
and 2017. Dame Sally laments the apparent lack of concern for the potential doomsday disaster. In her
view, despite the vital importance of this subject, not enough is being done in terms of research.
Conclusion If the current antibiotics being used are no longer effective, then even minor infections such
as a skin wound could cause death. There is a need to reduce the usage of antibiotics in both humans and
agriculture. It is pointless continuing to manufacture powerful drugs if bacteria can develop resistance to
them in a short period of time. Antibiotics should only be used when necessary. Furthermore, medical
researchers should find safer alternatives that can overcome resistant bacteria and therefore treat people
and animals successfully.
Poverty and conflict are widely understood to be closely interconnected; with poverty making countries
more prone to civil war, and armed conflict weakening governance and economic performance, thus
increasing the risk of conflict relapse (Goodhand 2001). The selected readings in this pack move beyond
reductive and harmful assumptions about ‘pathologies’ of poverty to examine the latest research into the
poverty-conflict nexus. Earlier studies identified macro-level factors that made countries more likely to
experience armed conflict. For example, low per capita income and large populations correlate with civil
war, whereas ethnic and religious diversity does not make countries more prone to conflict (Fearon &
Laitin 2003). Newer research examines the processes and mechanisms that precipitate and shape violence
on the ground. At the state level, poverty can lower resilience to conflict by weakening government
institutions, stripping capacity for public goods provision, and limiting the projection of power and
authority, whether soft or coercive. Poverty also compounds vulnerability to insurgency at the individual
and community level by lowering the opportunity cost of mobilising for violence. High rates of
unemployment and inequality, combined with low levels of education and development, are thought to
soften the ground for recruitment and provide motives to fight (Humphreys & Weinstein 2008).1 These
individual correlates of poverty often follow systematic patterns that lead to ‘horizontal inequalities’.
Horizontal inequalities occur when members of ethnic, religious, or other identity groups have unequal
access to public goods, opportunities and resources. Group-level inequalities can generate social and
economic polarisation that increases the risk of violent conflict (Østby 2008; Stewart 2009). Of course,
these dynamics alone do not start wars. Political grievances and conflict proneness are most likely to lead
to violence—from terrorism to civil war—when poverty and inequality combine with repression,
particularly in anocracies, regimes that are neither strongly democratic, nor wholly autocratic (Abadie
2004; Mousseau et al. 2003). Yet, governance can also mitigate the link between poverty and conflict.
Resource governance plays a key role in shaping countries’ economic and structural vulnerability to
conflict (Ross 2004; Thies 2010). While social welfare spending, particularly on education and
healthcare, and stable aid flows reduce the risk of war, aid shocks and excessive military spending
increase its likelihood (De Ree & Nillesen 2009; Nielsen et al. 2011; Savun & Tirone 2011; Taydas &
Peksen 2012). Similarly, economic shocks, such as the 2008 spike in global food prices, can spark social
unrest that escalates into armed conflict in vulnerable political settings (Blattman & Miguel 2010; Lagi et
al. 2011). Once conflict breaks out, it hits the poor the hardest: social welfare is depleted as goods and
services are diverted to the war effort; rural infrastructure is destroyed in contested territory; and justice
and security provision retracts into urban areas and elite enclaves. Conflict causes and compounds
poverty. First depleting labour and human capital, then destroying productive assets and financial capital, and finally, eroding the social capital
of trust and cooperation upon which strong political and economic systems depend (Mercier et al. 2016). The war economies and institutions that
are created in conflict are overwhelmingly extractive, and tend to warp local political economies through their reliance on smuggling and
coercion (Keen 1997). These practices can become conflict drivers in their own right, and can perpetuate conflict-related violence and inequality
even after war has officially ended (Justino 2013). Our understanding of the effects of conflict over time is still nascent. Evidence from Burundi
suggests that households exposed to violence at the local level are more likely to face long-term poverty and deprivation than those who were
spared. Exposure to violence also hurts those who participate in armed groups, as they have to overcome an education deficit, social stigma, and
psychological distress that can leave them economically alienated and socially marginalised (Annan et al. 2011). At the country-level, this leads
to what some call the ‘conflict trap’ (Hegre et al. 2011). The strongest predictor of civil war onset is whether a country has recently experienced
vicious
civil war, with harmful ‘neighbourhood effects’ making surrounding countries similarly vulnerable to conflict spillover. However,
cycles of conflict that exacerbate poverty, slow economic growth, destabilise weak institutions and lead to
violent relapse are not inevitable. The international response to post-conflict reconstruction can support a
potential ‘phoenix effect’ of strengthened economic growth, where infrastructure development, debt relief
and foreign aid, and currency stabilisation help to generate private investment (Addison et al. 2001; Kang
& Meernik 2005). More importantly, local communities have proven remarkably resilient in rebuilding
trust, social cohesion and civic engagement after war ends (Bellows & Miguel 2009; Blattman 2009;
Gilligan et al. 2014; Voors et al. 2012).
Food is the primary route of transmission for more than 200 known diseases. The leading bacterial
food-borne pathogens of concern are Salmonella, Campylobacter, Shiga toxin-producing E. coli, and
Listeria monocytogenes [32]. Each of them can be associated with serious gastrointestinal infections.
Food-borne diseases remain a major cause of hospitalization and death worldwide, despite many advances
in modern technologies including food sanitation techniques and pathogen surveillance. As estimated by
the World Health Organization (WHO), 600 million—almost one in 10 people in the world—fall ill after
eating contaminated food and 420 000 die every year [33]. Several approaches are used to improve the
safety of our foods, but food-borne outbreaks occur relatively frequently. A new multihurdle approach
identified to prevent the food-borne bacterial pathogens from reaching the consumers is the use of lytic
bacteriophages for targeting specific food-borne bacteria in foods, without deleteriously impacting their
normal—and often beneficial—microflora. This approach is termed ‘bacteriophage or phage biocontrol’
[34]. Table 1 summarizes the list of studies on bacteriophage biocontrol of the more important food-borne
pathogens. Since the regulatory acceptance of the first phage-based product, ListShield™ (approved in
2006 as ‘generally recognized as safe’), for use in the control of L. monocytogenes in meat and poultry
products, the attempts to develop new phage-based technologies for pathogen control in postharvest foods have increased [3],[35]. The main
organizations approving bacteriophage cocktails for use in agri-food sector are the European Food Safety Authority (EFSA) and the US Food and
Drug Administration (FDA).The production of commercially available bacteriophage cocktails should be carried out according to the good
manufacturing practices. Bacteriophages used in phage-based products should be strictly lytic (use of lysogenic phages for phage therapy is
undesirable due to horizontal gene transfer) and effective against the highest possible number of strains belonging to the target bacterium [8]. It is
recommended to use cocktails consisting of a mixture of bacteriophages to achieve improved efficiency and avoid the formation of strains
resistant to bacteriophages [3],[36]. Changes in the composition of phage cocktails should be made systematically; however, this may be
associated with additional difficulties in the production of these cocktails. For example, according to the EU regulations (1107/2009 EC), changes
in the composition of plant protection products based on bacteriophages may require a new registration [8]. Campylobacter infections are among
the most frequently encountered food-borne bacterial infections around the world. Handling and consumption of raw or
undercooked poultry products have been identified to be the main route of transmission of these
infections. Studies have analyzed the use of phages to target the Campylobacter bacteria growing on the surface of chicken carcasses, raw
chicken meat, and raw and cooked beef [37]–[39]. The Shiga toxin-producing E. coli serotype O157:H7 can invade the human gastrointestinal
tract and trigger disease, with symptoms including abdominal cramping and hemorrhagic diarrhea. Recent work has demonstrated that E.
coli-specific phage preparation was effective in inhibiting this serotype [41]–[46]. Listeria monocytogenes is a major food-borne pathogen of
public health concern associated with a high mortality rate in individuals at risk such as pregnant women, neonates, immunocompromised
individuals, and the elderly [61]. It is therefore critically important to ensure the safety of the food chain, especially in the case of ready-to-eat
(RTE) foods. The
application of bacteriophages to assorted foods has been shown to be effective at reducing
contamination with L. monocytogenes (Table 1). Food-borne Salmonella infections are a major public health concern worldwide. All
Salmonella phages reported so far have been able to decrease the number of viable cells present in raw meats, processed and RTE foods, and fresh
products but not on apple slices. This indicates that the acidic pH of the apples may have inactivated the phages [17]. The concept of hurdle
technology has been applied in the food industry following the observations that the rate of microorganism survival decreases greatly when the
organisms are confronted with multiple antimicrobial factors or hurdles [62]. Several studies demonstrated the synergistic effect of using a
bacteriophage with another food-grade antimicrobial such as nisin [57] and trans-cinnamaldehyde oil [46]. The antibacterial effect was also
reported to be improved when phages were combined with a protective culture or modified atmosphere packaging [45],[49]. The Listeria-specific
phage was effective against L. monocytogenes when used alone, and additionally, enhanced the effectiveness of other antimicrobials such as
sodium diacetate and potassium lactate when used together [51],[52]. In recent years, an
increasing number of phage products
have been commercially used for pathogen control, as shown in Table 2.
Studies prove phage cocktails are effective against food borne diseases
Picozzi et. al 21, Picozzi Claudia, Garcia Pilar and Vives Martha. Editorial: Bacteriophages to Fight
Food-Borne Pathogens/Phages Struggling for Food Safety.” Frontiers, 23 September 2021,
https://www.frontiersin.org/articles/10.3389/fmicb.2021.741387/full
In recent years, the application of phage therapy for the control of pathogenic bacteria has been experiencing a new renaissance driven by the emergence of multidrug-resistant bacteria (Gordillo Altamirano and Barr, 2019).
Bacteriophages are natural predators of bacteria, presenting several benefits, the main ones related to their high specificity and their harmlessness to humans, animals, and plants. The interactions between phages and their hosts play an
important role in the evolutionary ecology mechanisms of bacterial resistance and phage infectivity (“antagonistic coevolution”). Some failures in the application of phage therapy are indeed due to bacterial mutations that led to
resistance (Buckling and Rainey, 2002). To be considered as excellent candidates as biocontrol agents in foods, phages should be strictly lytic and possibly have a broad host range. To overcome this limitation, formulations with more
than one phage (phage cocktails) can be used. But how many and which isolates should compose these cocktails? The optimum formulation should provide a compromise between achieving a high reduction on the bacterial load and
minimizing the side effects (cost of production, dysbiosis, risk of horizontal transfer of toxins, antibiotic resistance, or virulence genes) of an increasing cocktail complexity. Molina et al. tackled these challenging questions proposing a
new pipeline for designing phage cocktails. Their analysis started with the building of a phage-bacteria infection network (PBIN) from host range matrices using two different algorithms, a genetic and a heuristic one. The first one led
to the lower temperature, i.e., increased nestedness, simplifying the identification of phages with the broadest host range. They performed a meta-analysis of 35 host range matrices and proposed a new metric (Φ) for estimating phage
cocktail size. At the end they applied an agglomerative hierarchical clustering on their data, developing a cocktail that was able to reduce bacterial counts of cheese-isolated Escherichia coli of five orders of magnitude. To further
validate these results, Molina et al. submitted another work where they characterized coliphages isolated from ewe feces and E. coli strains isolated from goat and sheep raw milk cheeses. Several phages showed a broad host range,
making them good candidates for E. coli biocontrol. However, they highlighted that phage virulence decreased as bacterial susceptibility range increased, until reaching a plateau, revealing a local gene-for-gene coevolution between
hosts and phages that explained the ability of the phages they isolated to propagate on host strains from different niches. They concluded that, when devising long-term and short-term biocontrol strategies, different phage cocktail
The formulation of a
formulations might be required. Their results affirm the importance of knowing the specific interactions between phages and bacteria to develop successful phage applications.
cocktail is also the basis of the work of Mangieri et al. which shows the relevance of this particular step in
any phage therapy endeavor. The aim of the authors was to formulate a cocktail able to reduce the counts
of pathogenic E. coli (Shiga toxin-producing E. coli-STEC) in food. They analyzed 20 different
bacteriophages isolated from feces, sewage, and bedding material for their lytic ability toward a
population of STEC strains belonging to different serogroups and with different antibiotic-resistance
profiles. Three of these phages were selected, also taking into account their RAPD (Random
Amplification of Polymorphic DNA) profile and the absence of antibiotic-resistance genes and
virulence-encoding genes. This cocktail was then tested directly on a food matrix (cucumber) at different
temperatures resulting in a 2-log reduction of E. coli cells after 24 h both at 4 and 25°C, suggesting
possible application in biocontrol of different STEC serogroup on raw products and RTE foods.
Considering that foodborne diseases were estimated to cause 600 million illnesses resulting in 420,000
deaths (Havelaar et al., 2015), the possibility to use bacteriophages and their derivatives to prevent or kill
food pathogens is extremely crucial. This work shows the potential of using phages in fresh vegetables
and opens new possibilities for upcoming studies on its applications. Another important benefit of
bacteriophages is that they will not cause any problem in consumers nor affect the taste, color, smell, and
texture of the food products. Starting from this assumption, Ahmadi et al. investigated the effectiveness of using
bacteriophages added as an ingredient in a cooked meat product to control the growth of Listeria monocytogenes. They
elaborated different scenarios for bacteriophage application and pathogen contamination where phage and sensitive strain were
introduced inside or on the surface of the cooked meat stored at 4°C. Only when phage was applied directly on top of L.
monocytogenes inoculated on the surface of cooked meat was there a reduction in cell number below the detection limit. As
concerning other applications where phage and bacteria were mixed and inoculated in meat or when only the bacteriophage was
inoculated in meat and L. monocytogenes spread on the surfaces, or vice versa, they were not able to obtain any reduction in cell
numbers. The main reason is probably the immobilization of phages and bacteria inoculated in a solid food matrix that limits
bacteriophage-host interactions. Therefore, more studies are needed to increase the access of phages to their hosts in complex
matrixes, and integration of fields such as food technology, nanomaterials, active compound-controlled delivery, and food
compatible bio-emulsifiers. Overall, bacteriophages undoubtedly have a great potential in a food safety context. Since more
research is necessary to achieve a suitable cocktail or phage-derived product to cover the current industrial sector needs, this
emerging and exciting area is an open field for interdisciplinary research and innovations.
Plan
The United States federal government should substantially increase its security
cooperation with the North Atlantic Treaty Organization in the area of
biotechnology by partnering with NATO through the Science for Peace and Security
program to work on developing phage therapy.
Solvency
NATO key for existing SPS framework to connect scientists
Funds for NGOs 5-31
“CFPs: NATO Science for Peace and Security Program.” fundsforNGOs, 31 May 2022,
https://www2.fundsforngos.org/information-technology/cfps-nato-science-for-peace-and-security-progra
m/. Accessed 6 September 2022.
The North Atlantic Treaty Organization Science for Peace and Security (SPS) Programme is accepting
proposals for Multi-Year Projects and Events (Advanced Research Workshops, Advanced Training
Courses and Advanced Study Institutes). The SPS Programme enhances civil science and technology to
address emerging security challenges and their impact on international security. It connects scientists,
experts and officials from NATO and partner nations to work together to address these challenges, by
supporting security-relevant activities in the form of four established grant mechanisms, which are:
Multi-Year research and development Projects (MYP)
Events, in the following formats:
Advanced Research Workshops (ARW)
Advanced Training Courses (ATC)
Advanced Study Institutes (ASI)
Through the SPS Programme, NATO has demonstrated its longstanding commitment to science,
innovation and practical cooperation with partners. The SPS Programme offers funding, expert advice and
support to tailor-made, civil security-relevant activities that respond to NATO’s strategic objectives.
Participation in the SPS Programme enables experts and scientists to develop innovative solutions to
today’s security challenges, and to build partnerships with their peers in NATO and partner nations.
Themes
Proposals focusing on the convergence and integration of different technologies and disciplines with the
purpose of serving a common goal (i.e. integration of engineering, biotechnologies, physical sciences, data
science, computation, life sciences, social sciences, etc.) can also be accepted.
Topics In preparation to the upcoming 2022 NATO Summit and in line with the NATO 2030 agenda, proposals addressing the topics below are especially encouraged.
Security-related advanced technology
Climate change and security
Defence against CBRN agents
Resilience
Eligibility Criteria
Applications for funding must be developed jointly by a NATO country Co-Director (NPD) and a Partner country Co-Director (PPD). To be deemed eligible for funding, proposals submitted to
the SPS Programme must:
Contribute towards NATO’s Strategic Objectives and have a clear link to security;
Address at least one of the SPS Key Priorities;
Be led by a co-director who is a national of, resident and employed in a NATO member country, and a co-director who is a national of, resident and employed in a partner nation;
Be developed and implemented by co-directors affiliated with a government, academic, or other non-profit institutions. For-profit private companies are not eligible for SPS funding;
Include realistic plans and budgets;
Be developed and managed in alignment with rules and regulations outlined in the SPS handbooks, which are regularly updated and made available at the time of publication of new calls for
proposals.
NATO Countries: Albania, Belgium, Bulgaria, Canada, Croatia, Czech Republic, Denmark, Estonia, France, Germany, Greece, Hungary, Iceland, Italy, Latvia, Lithuania, Luxembourg,
Montenegro, Netherlands, the Republic of North Macedonia, Norway, Poland, Portugal, Romania, Slovakia, Slovenia, Spain, Turkey, United Kingdom, United States.
NATO Partners: Afghanistan, Algeria, Armenia, Australia, Austria, Azerbaijan, Bahrain, Belarus, Bosnia and Herzegovina, Colombia, Egypt, Finland, Georgia, Iraq, Ireland, Israel, Japan,
Some of the major human phage therapy studies performed in Poland and the former Soviet Union
Reference(s) Infection(s) Etiologic agent(s) Comments
Babalova et al. (7) Bacterial dysentery Shigella Shigella phages were successfully used for prophylaxis of bacterial dysentery.
Bogovazova et al. Infections of skin K. ozaenae, K. Adapted phages were reported to be effective in treating Klebsiella infections in all of the 109 patients.
(11) and nasal mucosa rhinoscleromatis,
and K. pneumoniae
Cislo et al. (17) Suppurative skin Pseudomonas, Thirty-one patients having chronically infected skin ulcers were treated orally and locally with phages. The
infections Staphylococcus, success rate was 74%.
Klebsiella, Proteus,
and E. coli
Ioseliani et al. (22) Lung and pleural Staphylococcus, Phages were successfully used together with antibiotics to treat lung and pleural infections in 45 patients.
infections Streptococcus, E.
coli, and Proteus
Kochetkova et al. Postoperative Staphylococcus and A total of 131 cancer patients having postsurgical wound infections participated in the study. Of these, 65 patients
(25) wound infections in Pseudomonas received phages and the rest received antibiotics. Phage treatment was successful in 82% of the cases, and
cancer patients antibiotic treatment was successful in 61% of the cases.
Kucharewicz-Kruko Various infections Staphylococcus, Immunogenicity of therapeutic phages was analyzed in 57 patients. The authors concluded that the phages'
wska and Slopek (27) Klebsiella, E. coli, immunogenicity did not impede therapy.
Pseudomonas, and
Proteus
Kwarcinski et al. (29) Recurrent E. coli Recurrent subphrenic abscess (after stomach resection) caused by an antibiotic-resistant strain of E. coli was
subphrenic abscess successfully treated with phages.
Litvinova et al. (32) Intestinal E. coli and Proteus Phages were successfully used together with bifidobacteria to treat antibiotic-associated dysbacteriosis in 500
dysbacteriosis low-birth-weight infants.
Meladze et al. (33) Lung and pleural Staphylococcus Phages were used to treat 223 patients having lung and pleural infections, and the results were compared to 117
infections cases where antibiotics were used. Full recovery was observed in 82% of the patients in the phage-treated group,
as opposed to 64% of the patients in the antibiotic-treated group.
Miliutina and Bacterial dysentery Shigella and The effectiveness of treating salmonellosis using phages and a combination of phages and antibiotics was
Vorotyntseva (35) and salmonellosis Salmonella examined. The combination of phages and antibiotics was reported to be effective in treating cases where
antibiotics alone were ineffective.
Perepanova et al. (40) Inflammatory Staphylococcus, E. Adapted phages were used to treat acute and chronic urogenital inflammation in 46 patients. The efficacy of
urologic diseases coli, and Proteus phage treatment was 92% (marked clinical improvements) and 84% (bacteriological clearance).
Sakandelidze and Peritonitis, Staphylococcus, Phages administered subcutaneously or through surgical drains in 236 patients having antibiotic-resistant
Meipariani (45) osteomyelitis, lung Streptococcus, and infections eliminated the infections in 92% of the patients.
abscesses, and Proteus
postsurgical wound
infections
Sakandelidze (46) Infectious Staphylococcus, A total of 1,380 patients having infectious allergoses were treated with phages (360 patients), antibiotics (404
allergoses (rhinitis, Streptococcus, E. patients), or a combination of phages and antibiotics (576 patients). Clinical improvement was observed in 86, 48
pharyngitis, coli, Proteus, and 83% of the cases, respectively.
dermatitis, and enterococci, and P.
conjunctivitis) aeruginosa
Slopek et al. (52–58) Gastrointestinal Staphylococcus, A total of 550 patients were treated with phages. The overall success rate of phage treatment was 92%.
tract, skin, head, Pseudomonas, E.
and neck infections coli, Klebsiella, and
Salmonella
Stroj et al. (67) Cerebrospinal K. pneumoniae Orally administered phages were used successfully to treat meningitis in a newborn (after antibiotic therapy
meningitis failed).
Tolkacheva et al. (69) Bacterial dysentery E. coli and Proteus Phages were used together with bifidobacteria to treat bacterial dysentery in 59 immunosuppressed leukemia
patients. The superiority of treatment with phage-bifidobacteria over antibiotics was reported.
Weber-Dabrowska et Suppurative Staphylococcus and Orally administered phages were used to successfully treat 56 patients, and the phages were found to reach the
al. (74) infections various patients' blood and urine.
gram-negative
bacteria
Zhukov-Verezhnikov Suppurative Staphylococcus, The superiority of adapted phages (phages selected against bacterial strains isolated from individual patients)
et al. (77) surgical infections Streptococcus, E. over commercial phage preparations was reported in treating 60 patients having suppurative infections.
coli, and Proteus
Polish papers. The most detailed English language reports on phage therapy in humans were by Slopek et al., who published a series of six papers (52–57) on the effectiveness of phages against infections caused by several bacterial pathogens, including multidrug-resistant mutants. Their seventh paper (58) summarized the results of all these studies, and it is discussed in some detail here. Five hundred fifty patients having bacterial septicemia and ranging in age from 1 week to 86 years were treated at a total of 10
clinical departments and hospitals located in three different cities. Antibiotic treatment (no information was given about the specific antibiotics used) was reported to be ineffective in 518 of the patients, leading to the decision to use phage therapy. The etiologic agents in the studies of Slopek et al. (52–58) were staphylococci, Pseudomonas, Escherichia, Klebsiella, and Salmonella, and treatment was initiated after isolating the etiologic agents and selecting specific, highly potent phages from a collection of more than
al cavities; and (iii) by applying a few drops of phage suspension to the eye,
250 lytic phages. Phages were administered as follows: (i) orally, three times a day before eating and after neutralizing gastric acid by oral administration of baking soda or bicarbonated mineral water a few minutes prior to phage administration; (ii) locally, by applying moist, phage-containing dressings directly on wounds and/or pleural and peritone
middle ear, or nasal mucosa. During the course of phage treatment, the etiologic agents were continuously monitored for phage susceptibility, and if phage resistance developed, phages were replaced with different bacteriophages lytic
The results
patients in group A (223 individuals) received phages, and the patients in group B (117 individuals) received antibiotics. Also, this clinical trial is one of the few studies using i.v. phage administration (48 patients in group A received phages by i.v. injection).
were evaluated based on the following criteria: general condition of the patients, X-ray examination,
reduction of purulence, and microbiological analysis of blood and sputum. No side effects were observed
in any of the patients, including those who received phages intravenously. Overall, complete recovery was
observed in 82% of the patients in the phage-treated group as opposed to 64% of the patients in the
antibiotic-treated group. Interestingly, the percent recovery in the group receiving phages intravenously
was even higher (95%) than the 82% recovery rate observed with all 223 phage-treated patients.
TABLE 2
Very specific (i.e., usually affect only the Antibiotics target both pathogenic High specificity may be considered to be a
targeted bacterial species); therefore, microorganisms and normal microflora. disadvantage of phages because the
dysbiosis and chances of developing This affects the microbial balance in the disease-causing bacterium must be
secondary infections are avoided (15). patient, which may lead to serious identified before phage therapy can be
secondary infections. successfully initiated. Antibiotics have a
higher probability of being effective than
phages when the identity of the etiologic
agent has not been determined.
Replicate at the site of infection and are They are metabolized and eliminated from The “exponential growth” of phages at the
thus available where they are most the body and do not necessarily concentrate site of infection may require less frequent
needed (59). at the site of infection. phage administration in order to achieve
the optimal therapeutic effect.
No serious side effects have been Multiple side effects, including intestinal A few minor side effects reported (17, 58)
described. disorders, allergies, and secondary for therapeutic phages may have been due
infections (e.g., yeast infections) have been to the liberation of endotoxins from
reported (76). bacteria lysed in vivo by the phages. Such
effects also may be observed when
antibiotics are used (42).
Phage-resistant bacteria remain Resistance to antibiotics is not limited to Because of their more broad-spectrum
susceptible to other phages having a targeted bacteria. activity, antibiotics select for many
similar target range. resistant bacterial species, not just for
resistant mutants of the targeted bacteria
(47).
Selecting new phages (e.g., against Developing a new antibiotic (e.g., against Evolutionary arguments support the idea
phage-resistant bacteria) is a relatively antibiotic-resistant bacteria) is a that active phages can be selected against
rapid process that can frequently be time-consuming process and may take every antibiotic-resistant or
accomplished in days or weeks. several years (16, 51). phage-resistant bacterium by the
ever-ongoing process of natural selection.
Phage cocktails speed up process
Barron 8-31-22
Barron, Madeline. “Phage Therapy: Past, Present and Future.” American Society for Microbiology, 31
August 2022, https://asm.org/Articles/2022/August/Phage-Therapy-Past,-Present-and-Future. Accessed 7
September 2022.
Nevertheless, while phage therapy is no longer on the back burner of medicine in the U.S., it’s not at the forefront either. “One of the biggest reasons why phage therapy is not mainstream in the
West right now is because the clinical trials haven't been done to show that it's efficacious,” Strathdee explained. She noted that clinical trials form the backbone of therapeutic development in the
U.S.—anecdotal evidence and/or case studies are not enough. Finding the Right Phages Can Take Time There are 2 types of phages: lytic and temperate. Strictly lytic phages infect their host cell
and cause it to burst, thus killing the bacterium. Temperate, or lysogenic, phages don’t kill their bacterial prey outright—they integrate their genome (which may harbor AMR or toxin genes) into
the host cell. The phage may eventually lyse the cell, but this does little to immediately thwart bacterial infection, and may contribute to the spread of AMR and other virulence genes. As such, it
is critical to ensure strictly lytic phages are used for phage therapies. With that in mind, the process for identifying phages to treat an infection can be lengthy. It often involves testing phages from
existing libraries to find those that kill a patient’s bacterial isolate. “It’s like [having] a million keys and you’re trying to sort through a million locks to figure out which key matches the lock,”
Strathdee said. One study reported a range of 28 to 386 days between the time of request for phage therapy and actual administration to the patient. However, there are products being developed
a company that develops engineered phage biotherapeutics,
with a broader target range. For example, Locus Biosciences,
manufactures phage cocktail drug products for each of 4 different pathogens (Escherichia coli, Klebsiella
pneumoniae, Pseudomonas aeruginosa and Staphyloccocus aureaus) that target >95% of clinical strains.
This approach does not require culturing a patient’s isolate and screening a library for the right phages, and thus may streamline the process. Manufacturing and
Administrating Phage Therapeutics Isn't Straightforward Unlike antibiotics, where concentrations of the drug decrease within the body over time, phages multiply. This means that the dose of a
phage cocktail that a patient is administered is not necessarily the dose they receive. How this self-replicating feature of phage therapies influences treatment efficacy, and potential for adverse
effects, is still unknown. “[We need] pharmacokinetic and pharmacodynamic studies to try to figure out, ‘okay, [if] you deliver this amount of phage, but through this particular route, what
happens to the phage?’” Strathdee said. Similarly, researchers must confirm “that [the phages] perform in the matrix they’re expected to perform [in],” said Dr. Nick Conley, Vice President of
Technology at Locus Biosciences. For example, if phages are used to treat a urinary tract infection (UTI), they need to be active in urine. There are also important considerations from a
manufacturing standpoint. For instance, to create phage preparations, the phages are amplified in bacterial hosts—they infect the bacteria, the bacteria lyse and release more phages to create a
high-titer phage soup. However, upon lysis, “all of the guts of the bacteria get spilled out,” Conley explained. This includes toxins and DNA, among other cell components, which must be
removed before the phage could be, for example, injected into someone’s bloodstream. Potential for Bacterial Phage Resistance Patients generally receive mixtures (cocktails) of phages that
target bacteria in different ways. The chances of the bacteria evolving resistance to multiple phages is lower than for a single phage—lower, but not impossible. Patients receiving phage therapy
must be continuously monitored to ensure the phages are still effective against their infection. If not, researchers must find a new set of phages that can combat the pathogen. Still, the
In some cases, the modifications to the bacteria that promote phage
development of resistance is not always a bad thing.
resistance increase their susceptibility to antibiotics, and thus work synergistically with the antibiotics to
promote their efficacy.
and matched to a patient’s specific bacterial infection and purified within a matter of days, making
personalized phage therapy-on-demand a potential reality in the future.