Aditi Shenoy received her B.S. in Biomedical Engineering from The George Washington University in 2014 and is currently pursuing her goal of a graduate degree.
The discovery of bacterial infectious agents in the late 19th century stimulated the search for appropriate preventive and therapeutic measures. Since their discovery, antimicrobials have saved millions of lives and have significantly contributed to the control of infectious diseases that had previously been leading causes of illness and death for most of human history. While there is evidence to suggest that bacteria develop antimicrobial resistance naturally over time due to the long-term persistence of genes conferring resistance to several classes of antibiotics in nature, over the past sixty years there has been a rapid rise in the prevalence of resistant strains of bacterial pathogens.
Since the introduction of antibiotics, millions of metric tons of antibiotics have been produced and employed for more purposes than just human healthcare alone. The results of overuse and underuse of antibiotics are directly related to the development of generations of antibiotic resistant bacterial pathogens and their distribution in microbial populations in the biosphere. A recent database now lists more than 20,000 potential resistance genes evolved in nearly 400 different types of bacteria. Furthermore, many previously non-antimicrobial resistant bacterial pathogens commonly associated with human microbiota and disease have evolved into serious multi-drug resistant (MDR) forms following intensive human antibiotic use in nosocomial bacterial infections, resulting in limited options for treatment and prevention and a rising burden of disease.
In a recent article entitled “A ‘Slow Catastrophe’ Unfolds as the Golden Age of Antibiotics Comes to an End”, the Los Angeles Times describes the case of a patient in the United States who presented with a urinary tract infection caused by Escherichia coli, a microbe normally found in human microbiota. In this patient’s case, physicians were not able to treat her urinary tract infection, despite repeated attempts with a barrage of antibiotics. A preliminary analysis of microbial samples from the patient followed by a more comprehensive genetic analysis confirmed that this bacteria’s DNA contained a gene which made the pathogen impervious to a highly effective antibiotic known as colistin, which is usually used as a last-resort drug to treat serious bacterial infections.
The gene was found to be on a plasmid, a tiny mobile loop of DNA that can be removed and attached to other bacteria (including other species). The spread of the gene to other disease-causing microbes would result in more widespread resistance to colistin, a serious implication for treatment of otherwise treatable diseases. Shortly after the first reported case, a second case of E. coli with the same gene was reported in the United States. Researchers are examining eighteen more samples of antibiotic resistant E. coli from around the world to determine whether these samples contain the same gene. If so, more research will have to go into estimating the current prevalence and distribution of the gene, known as MDR-1. Infectious disease professionals have cautioned of the dangers of a widespread colistin-resistance gene.
Due to a combination of medical and socioeconomic factors, antimicrobial drugs are frequently prescribed by physicians to treat minor infections and injuries, such as sinus pressure, sore throats, and earaches. Bacteria that normally live in the body (known collectively as the microbiome) reproduce, compete with each other, and evolve. With the advent of widespread and indiscriminant antibiotic use, including non-medical applications such as feeding antibiotics to livestock to fatten them up, opportunities emerged as some bacterial strains were able to survive the onslaught of antibiotics and reproduce, passing their resistance genes on to future generations within hours.
It has been noted by many infectious disease epidemiologists that although hospitals are improving their infection control procedures and public health experts are becoming more adept at identifying new pathogenic concerns, there is an overall increase in the incidence of antibiotic resistant infections. Despite the reports of antibiotic resistant pathogens, the connection between antibiotic use in individual patients and the emergence of antibiotic resistance within populations was only recently understood.
Antibiotic resistant infections have resulted in more than 2 million annual cases of patients becoming infected with a bacterium that is no longer able to be treated with their usual drugs, leading to at least 23,000 deaths. Resistant strains of nosocomial bacterial infections are twice as likely to result in mortality as non-resistant strains of the same bacteria. While the regular development of new antimicrobial drugs may theoretically be an effective method of combating the surge in antibiotic resistant pathogens, the economics of drug development raise a significant barrier due to the need for pharmaceutical companies to recompense the cost of drug development from the marketing of the drug. By developing drugs that can be used daily by patients rather than only during a specific infection, pharmaceutical companies are able to reap profits without having to develop novel drugs on a regular basis. Due to these limitations, as well as limitations in the variety of drugs that are available and their increasing obsolescence, antibiotic resistant pathogens continue to propagate virtually unchecked and unnoticed.
Many common bacterial pathogens that are associated with human epidemics have evolved into multidrug-resistant (MDR) forms following antibiotic use in hospital settings. In healthy individuals, pathogens are not able to become opportunistic and result in illness since they are subdued by a healthy immune system. In patients with weaker immune systems, however, opportunistic pathogens such as those found in the microbiome or crawling around hospitals, can produce infections that are normally treated with antibiotics. Mutations, however, have endowed MDR microbes with high levels of resistance to these antibiotics. In some cases, then, these microbes have also mutated into superresistant strains possessing tools for increased virulence and transmissibility.
Some researchers have gone so far as to characterize antimicrobial resistance in itself as a virulence factor. Nosocomial infections with pathogens such as Escherichia coli (which can cause severe anemia or kidney failure, death, urinary tract infections or other infections), Pseudomonas aeruginosa (which can cause bloodstream, pneumonia, and other infections), Acinetobacter baumannii (which can cause pneumonia, meningitis, urinary tract infections, and wound infections), Staphylococcus aureus (which can cause skin and soft tissue infections such as boils, furuncles, and cellulitis, as well as bloodstream infections, pneumonia, or bone and joint infections), and Clostridium difficile (which can cause inflammation of the colon and diarrhea) were previously treatable with antibiotics but have now evolved to become more virulent infections that result in highly enhanced illnesses and death due to multiple mutations in their genomes following widespread use of antibiotics. Collectively, these are known as the ESKAPE pathogens.
E. coli alone has successfully demonstrated the strong correlation between antibiotic and antibiotic resistance. There is a wide variety of resistance genes in E. coli strains common to humans, animals, and food products. Thus, with the exposure to regularly prescribed antibiotics, several strains of E. coli have been able develop resistance to these drugs. As stated in the aforementioned article in the Los Angeles Times, resistance to these antibiotics prompted physicians to use different antibiotics, which in turn were soon rendered ineffective for the same purposes. Fortunately, E. coli is currently still susceptible to a few antibiotic drugs, so all hope is not quite yet lost.
Other nosocomial microbes have evolved to cause more severe infections. P. aeruginosa, for example, has recently become a major nosocomial infection. In the case of this pathogen, antibiotic resistant mechanisms coincidentally evolved with the introduction of new antibiotic treatments that were considered highly effective at the time. This is a major problem in particular for people with cystic fibrosis (CF), since P. aeruginosa infection is common to CF patients. P. aeruginosa resistance is strongly associated with the lengthy antibiotic treatment, another characteristic of CF treatment. A. baumannii and C. difficile are just more pathogens that have become increasingly virulent and equipped with a suite of resistant genes. They are readily transmitted in nosocomial settings and evolve rapidly due to their rapid doubling times. S. aureus, a common nasal microbe in about 30% of the global population, is regarded as the most virulent antibiotic resistant pathogen and has resulted in highly virulent infections and transmissible infections in hospitals, such as methicillin-resistant S. aureus (MRSA). The use of antibiotics has allowed a global increase in the prevalence of the strains of pathogenic nosocomial bacteria that were previously susceptible to antibiotic treatments.
Antibiotic resistant microbes limit and complicate methods of treatment and prevention. Two proposed and emerging methods of treatment and prevention are vaccines aimed at preventing bacterial infections altogether, as well as other methods of killing bacteria, such as bacteriophage therapy (using viruses that infect bacteria to kill pathogenic bacteria). For now, experts argue that the most promising long-term solution to the issue of microbial resistance is to perpetuate the development of new vaccines and improve targeted therapy to limit the use of generic antibiotics. It is not yet not fully clear just how effective these tools will be, although preliminary results from studies involving a conjugate vaccine and bacteriophage therapy for nosocomial infections appear to be promising.
In a study looking at the prevention of antibiotic resistant Streptococcus pneumoniae (a causative agent of pneumonia) it was found that based on an analysis of resistant strains and serotypes, a vaccine reduced the incidence of the disease caused by resistant strains of the pathogen by 81%. However, there was also an increase in drug resistant disease caused by non-vaccine types of the pathogen (referred to as “replacement disease”). Interestingly, though, the magnitude of this effect was relatively small. Despite the slight increase in resistance of some serotypes of the pathogen, the reduction in incidence of the disease is promising and there is potential for this method of treatment to be applied in high resistance settings. In a different study to assess a vaccine for the prevention of S. aureus, a vaccine for two strains of bacteria resulted in partial immunity of subjects for approximately 40 weeks, after which the protection waned. From these studies, it can be concluded that the vaccines were effective against the strains for which they were intended; however, due to limited data regarding vaccines as a method of prevention for antibiotic resistant strains of bacteria, additional assessments of vaccines need to be performed.
Another method of treatment for antibiotic resistant pathogens is to use bacteriophages. Bacteriophages are viruses that exclusively infect bacteria, so they cause no harm to human cells. Bacteriophage therapy was briefly explored in the 1930s for the treatment of pathogens but was quickly discarded when antibiotics, the “Golden Pills,” were discovered. Due to the rise of antibiotic resistant pathogens, bacteriophage therapy has re-emerged, in particular for nosocomial pathogens such as S. aureus and P. aeruginosa, which have high rates of drug resistance.
Recently, a study to assess the effectiveness of six bacteriophages in the treatment of P. aeruginosa found significant improvements in group of subjects treated with bacteriophages but not in the placebo group, with an average duration of treatment of 23.1 days. In addition, there were no reportable side effects of bacteriophage therapy (compared to a long list of side effects for many antibiotics). However, it was noted that bacteriophages have evolved strategies to break down the biofilms of antibiotic resistant pathogens, which would enable pathogens to become more susceptible to common antibiotics. This suggests that an effective method of treatment may be a combination of alternating bacteriophage treatment with antibiotic treatment to maximize effectiveness and minimize antibiotic resistance. Due to the ever-changing nature of bacteria and their population dynamics, it may also be necessary to repeatedly develop new combinations of bacteriophages on a case-by-case basis to enable full, successful elimination of bacteria. This method of treatment is thus far promising, and warrants additional studies.
The widespread and indiscriminate use of antibiotics in the past sixty years has changed the natural evolution of bacteria by selectively reducing or eliminating susceptible pathogenic bacteria and increasing the growth of resistant strains. According to the WHO, antimicrobial resistance is a complex problem that officially affects the entire world. Due to the dependence of society on antibiotics now for treatment of infectious disease, increasing antibiotic resistance of pathogens, particularly in nosocomial infections, presents in a critical global health issue. Alternative methods for treatment and prevention of antibiotic resistant pathogens, such as vaccines and bacteriophages, may be the key to mitigating the current effects of resistant pathogens.
A non-pathogenic virus is studied to improve HIV therapy
Totto Pastime received her M.Sc. from the National Institute of Virology Pune. She is currently completing a project on translational immunology and is eager to understand more about virus-host interactions.
We are all familiar with the severity of HIV. Massive laboratory research efforts to permanently suppress the virus have been underway for years, and current anti-retroviral therapy has vastly improved HIV morbidity and mortality rates. Nonetheless, there is still significant progress to be made on one of humanity’s worst pandemics. Often, when studying diseases, we forget that nature has its own ways of staving off pathogens: according to a few decades of research and a touch of serendipity, there is a mysterious virus that may be able to hinder HIV. Despite this potentially ground-breaking news, the virus has an unremarkable name and is not at all well-known: it is called GBV-C, or GB virus C, also referred to as hepatitis G virus. Here is a glimpse into a tale of Virus vs. Virus, GBV-C vs. HIV.
The GBV class of viruses has been shown to cause hepatitis in New World monkeys known as tamarins. A series of serological and animal experiments since their discovery, though, has found no strong evidence to associate GBVs with any known human disease, including other hepatitis viruses. Our virus of interest today, GBV-C, has genetic similarities with the pathogenic hepatitis C virus (HCV), however, making it an intriguing subject. Researchers over the years have peeled through GBV-C’s morphology and epidemiology in an attempt to compare it with its pathogenic cousin. While screening blood from transplant recipients and patients with hepatitis or other illnesses found no link between the two hepatitides, a surprising correlation was instead found between GBV-C in HIV-positive individuals. In the same year (1998), a Japanese team from Nagoya University School of Medicine and group of scientists at Hannover Medical School in Germany found lower mortality rates and improved clinical outcomes among HIV patients who were co-infected with GBV-C. However, there were flaws in these initial reports – correlations, after all, do not define concrete relationships – and many scientists were not satisfied.
So the race continued. Larger follow-up studies asked whether GBV-C could really slow down HIV progression and, if so, how. Perhaps to show how serious they were, scientists soon abandoned the personal link of the virus’s origin and started calling it Human Pegivirus (HPgV).
A group from Germany published their findings from a 20-year long follow-up of 197 HIV patients with GBV-C viraemia. The term viraemia is derived from the Latin suffix –emia which means blood-related. It simply means that a virus (in this case, GBV-C) is present in a host’s circulatory system. The presence of a pathogen in blood tells us that it has access to the rest of the body. Diana Ernst and her team took to these studies and performed an intensive analysis at the Hannover Medical School on patients who received HIV antirviral therapy (HAART) and HIV patients who did not receive it. They wondered whether the two cohorts would differ in GBV-C co-infection rates. In the end, they wrapped up their report with a sound suspicion towards HAART, arguing that the therapy suppresses the benefits incurred by GBV-C co-infection. Other investigators from the University of Iowa reported similar results. So what’s going on?
By virtue of the fact that GBV-C has been around longer than existing HIV antiviral therapies, there must be a documented number of cases for people with low HIV progression without clinical interventions. And if there are, which ones and how many include a GBV-C/HIV co-infection? Given the research outlined above, it is possible that HAART inadvertently targets GBV-C while targeting HIV, ironically breaking the antagonism between the two. And ultimately, if you can’t have both, which treatment is the better one?
Fortunately, experts are working on elucidating the molecular relationship between the two viruses. When Jinhua Xiang partnered up with Jack Stapleton at the Internal Medicine Center at University of Iowa, both groups were busy running cultures and designing experiments to examine whether GBV-C physiologically inhibits HIV. As they tested GBV-C/HIV co-infection in peripheral blood cultures, they saw a significantly reduced level of HIV particles multiplying in the cells. They discerned this by measuring a specific HIV-associated protein called p24. p24 is a distinctive HIV structural protein, and it is useful for diagnosis.
To explain this inhibitory relationship on a mechanistic level, the researchers found that a protein called NS5A from GBV-C truncates a common “entry gate” that HIV uses to bind to human cells during infection. Gaining from this result, Xiang and Stapleton went on to identify other molecules that can inhibit HIV entry into host cells, and others more that could lead to an inhibitory effect on the virus. And even though direct clinical application might seem unnerving (try explaining to a patient infected with HIV that you would like to infect them with hepatitis), doctors may eventually use GBV-C as immunomodulator to supplement HIV treatment.
In addition to gaining some popularity for being a lethal partner against HIV, this sensational flavivirus has been reported to have additional beneficial effects. Recent reports suggest that Ebola patients have a higher survival rate when co-infected with GBV-C. Ebola, however, is a whole other class of viruses from HIV, and many scientific questions have to be answered before any absolute conclusions are made.
Ready or not, the world needs to accept that not all viruses are bad. In fact, the vast majority of viruses, just like the vast majority of bacteria on Earth, are not actually pathogenic to humans. Viral therapy is a very real possibility for the future of medicine as researchers turn to beneficial viruses to help fight pathogenic ones. In fact, viral therapy has already staked a pretty good claim in the present.
Aditi Shenoy received her B.S. in Biomedical Engineering from The George Washington University in 2014 and is currently pursuing her goal of a graduate degree
Dengue virus causes one of the most severe mosquito-borne illnesses in the world. Previously thought as a sporadic disease, in the past fifty years dengue incidence has increased significantly. Now, the virus is endemic in 112 countries in Southeast Asia, South Asia, Far East regions, South America, and Africa. Around 2.5 to 3 billion people predominantly in urban areas of tropical and subtropical regions are considered to be particularly susceptible to infection.
Dengue belongs to the flaviviridae family of viruses that are typically carried by insects and transmitted to humans. The virus likely originated in monkeys and spilled into humans in Africa or Southeast Asia between 100 and 800 years ago. It then established itself in countries around the world during World War II due to the increased transport of cargo. Insects (namely, mosquitoes) are the key transmitter of the virus, which can cause infection by any one of four distinct but closely related subtypes (known as DENV 1 through 4). What’s more, reinfection can lead to dengue hemorrhagic fever (abbreviated DHF) and an equally severe condition known as dengue shock syndrome (DSS), as well as several clinical sequelae.
The symptoms of dengue infection can range from none to a host of diseases: fever, DHF, or DSS. Different viral subtypes lead to varying clinical and epidemiologic profiles: while DENV 2 and DENV 3 tend to cause more severe disease, DENV 4 typically causes a milder illness. As always, many additional factors ultimately play into the severity of disease including immune system strength and whether one has been previously been infected with the virus.
Once someone has been infected with dengue, the incubation period is 7 to 10 days, and initial symptoms are often overlooked as a standard fever. Dengue-induced fever, however, lasts 2 to 7 days and is often accompanied by flushing on the upper body, a severe headache, abdominal discomfort, joint pain, muscle pain, anorexia, or a flat, red rash on the skin.
Recovery from dengue infection takes longer in adults than in children, during which time DHF may occur. According to the World Health Organization, a person developing DHF starts with a fever, with the additional symptoms of bleeding in various body organs, evidence of plasma leakage, and low platelet count. The first stage of progressed DHF begins with a high fever and generalized symptoms. After this stage, the patient either recovers or progresses to the plasma leakage phase, which is identified by a high heart rate and low blood pressure, and sometimes shock (DSS). During this phase, which lasts from 24 to 48 hours, bleeding may occur from any site in the body, though the most common symptoms include vomiting blood, bleeding from the skin, gums, and nose, and from the vagina in females. After this stage, a patient may begin to recover. However, shock can occur in severe cases, and progression to this stage of disease is associated with a high fatality rate (up to 47%).
Severe dengue viral infections can lead to a variety of clinical sequelae including liver failure, brain disease, inflammation of the heart, acute respiratory distress syndrome (ARDS), amnesia, dementia, and manic psychosis. Liver failure is common in all forms of dengue viral diseases, though the extent of liver damage naturally varies with overall severity of infection. For instance, infection with DENV 3 or DENV 4 subtypes typically results in more frequent liver problems than DENV 1 or DENV 2. Regardless of its origin, severe liver failure can lead to death. Brain disease is furthermore reported in 0.5% of patients with DHF, and has a fatality rate of 22%. Mouse studies have shown that this can be the result of direct viral infection of the brain, which can result in conditions like amnesia, dementia, and manic psychosis. Finally, severe heart inflammation has also been associated with dengue infections.
Despite the high number of people who either contract the virus or are at risk of contracting it, there are currently no specific drugs that are effective against dengue. Treatment, which is often inaccessible for the majority of people who suffer from a dengue infection, usually involves ensuring that a patient is kept well-hydrated in addition to supportive care as symptoms progress (such as anti-inflammatory medications to reduce fevers). Early identification of DHF infection also improves outcomes, since it has been shown that death rates are lower in patients who are admitted to hospitals before the onset of DSS.
There has been a lot of research on development of a safe and effective (against all four serotypes) dengue vaccine. The biggest breakthrough in this endeavor occurred last year with the licensing of Sanofi Pasteur’s new Dengvaxia vaccine. According to the company’s clinical trials, the vaccine is almost 60% effective overall, but varies in specific efficacy across different age groups and viral serotypes. As mentioned previously, dengue has a weird pathology that likely contributed to vaccine design being an especially difficult task: whereas most infectious diseases are milder the second time around because the body has developed an immune response, dengue reinfection causes a more severe disease. Almost paradoxically, then, a vaccine could potentially offer more harm than help, acting as a “first case” of the virus. The WHO thus recommends Dengvaxia only in regions of high-burden dengue, where individuals receiving the vaccine have already been exposed to the virus. But doesn’t this just act as a second infection? Dengvaxia is a heavily contested vaccine, with experts still cautioning that the vaccine has potential to cause more harm than good in most places.
To date, the primary method of protection from dengue fever is still the physical prevention of infection. This includes all sorts of mosquito-targeting efforts like bed nets, and behavioral efforts such as avoiding standing or polluted water (where mosquitos tend to breed), avoiding dark areas indoors (where mosquitos nest), and applying mosquito repellants. It goes without saying that dengue disease, an oft-underestimated virus in populations that have never been exposed to it, poses a critical and devastating public health issue in many parts of the world.