Jaylin’s Thoughts: Microbiology

First, what is an outbreak? An outbreak occurs when there is a large number of cases above what is normally seen. For example, if 50 people across the US were to contract cholera, we would label this as an outbreak because cholera is, in fact, rare in the United States. It is usually third world countries that are especially susceptible to cholera outbreaks, like the Democratic Republic of the Congo in Africa. The reason for this lies in wealth disparities between the two countries, as resources and capabilities for fighting cholera are drastically different. Not only does this pose a threat to public health in the DRC, but it means that there are totally preventable deaths occurring every day. Now, with the world eyes and efforts on stopping COVID-19, the DRC and other African countries could suffer even more than usual not just from cholera, but from other preventable outbreaks as well.

Vibrio cholera is a Gram-negative bacteria that is transmitted in contaminated water. The bacteria can survive especially well in water because of their ability to form biofilms when they sense that they are present in high numbers (this is achieved through cell signaling). Cholera outbreaks are more common in third world countries because of their lack of sanitation and sewage measures, which comes down to a lack of money and resources. In the DRC alone, there were 31,00 cases of cholera and 540 deaths in 2019, children making up 45% of cases (UNICEF). Boiling water kills V. cholera, and although it sounds simple, it is not plausible for places like the DRC who lack the simplest of resources like electricity. Several communities in the country also have no access to healthcare in the event that they do develop cholera infections, they cannot receive treatment.

Especially with the COVID-19 pandemic, an already sparse and underfunded healthcare system is being overwhelmed, so the DRC is facing a potential rise in cholera cases. UNICEF is now the biggest advocate for making improvements to the healthcare system in the DRC. As of now, less than 6% of the countries budget is allocated towards healthcare, which is not enough in normal conditions, so it is even less adequate during this pandemic (Prinsloo, n.p.) To add to the burden, there is a measles endemic and Ebola outbreak as well. Although the situation is dangerous for the citizens of the DRC now, it is an ongoing problem that requires attention and extensive efforts to combat.

In this post I will be discussing adalimumab, a monoclonal antibody primarily used for treating rheumatoid arthritis. Monoclonal antibodies are antibodies made in vitro using B-cells and cancerous myeloma cells to ensure that all the antibodies produced recognize a single, specific epitope. The goal of this is to produce large numbers of antibodies against a specific epitope that you are looking to target. From there, it can either be “humanized,” or modified to be more human-like as opposed to having animal derived components. Either way, the antibodies are useful for diagnostic tests and medications for several conditions.

The specific mechanism of adalimumab’s therapeutic effect is the blockage of tumor necrosis factor (TNF) alpha by directly binding to it, thus preventing it from interacting with receptors on the surface of cells and causing inflammation in specific tissues (FDA 13). As we learned in microbiology, TNF is a pro-inflammatory cytokine released by macrophages, T-cells, and NK cells. TNF-alpha plays a known role in rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, and there is evidence of increased levels of TNF in psoriasis patients (FDA 13). Taking adalimumab lessens the severity of these conditions and can stop progression in most of these conditions. Just as with any drug, there is a list of side effects that can occur.

The most common side effects are:

• injection site reactions
• upper respiratory tract infections
• headaches
• rash
• nausea/ upset stomach

Other, less common, but still possible side effects include:

• allergic reactions
• Hepatitis B reactivation
• anemia
• development of tuberculosis (TB) infections

All of these symptoms have something in common: they occur because the antibody downregulates you immune system. Although TNF-alpha is the source of the inflammation in these conditions, it is also used elsewhere in the body, so inhibiting it also inhibits beneficial adaptive immune processes that TNF-alpha is involved in. An extensive history is taken for all individuals who are considering the adalimumab in order to determine any risk factors or preexisting conditions that may occur as a result of the drug. If patients have an active or latent TB infection, that is treated before starting adalimumab. Both latent TB and Hepatitis B infections have been shown to reactivate when on adalimumab (FDA 5). These occur because, as I stated before, a major player in your adaptive immune system is being suppressed, so this weakens your defenses against infections.

Although there are still some aspects of the therapy that can be improved, it provides a higher quality of life for individuals suffering from the conditions above. It is important to remember that making changes/improvements is often complicated, but one possible way to improve drugs like adalimumab is to find a way to make the antibodies target only the tissues being affected. The development of monoclonal antibodies was innovative and it just shows how much work and revolutionary thinking goes into developing therapies like these. When you think of the mechanism of these drugs though, the fundamental concept is not difficult to understand, it is just HOW develop these therapies into safe and effective treatments for the human body that is difficult.

This week’s post was somewhat difficult to write because in the search for articles covering meningitis, I mostly ran into articles comparing meningitis and COVID-19 somehow. I had the same problem for tuberculosis and HIV. Although it was annoying, it shows how easily other public health concerns are being pushed to the side amidst efforts to make vaccines and treatments for COVID-19. For those at risk for meningitis, particularly those in the “meningitis belt,” this will be detrimental, as mass vaccine efforts are being put on pause. Knowing that so many people will suffer because of this is concerning, especially as I have some personal “beef,” if you will, with meningitis. One of my cousins living in El Salvador contracted, and passed away, from a bacterial meningitis infection at the young age of 9. He and his family lived in an impoverished part of El Salvador, with the nearest hospital about 2 hours away. His situation is likely very similar to those in the “meningitis belt” of Africa who have little access to medical care and rely on preventative measures like mass vaccination efforts to avoid these life-threatening infections.

Some more “bad news” about meningitis is that it is quickly developing antibiotic resistance, so preventative measures are growing even more important to lowering the death rate for bacterial meningitis infections. There is also good news, though, there are studies being conducted that are showing potential improvements for the Neisseria meningitidis vaccine. The form of meningitis that is caused by this bacteria has a 20% fatality rate, and about 15% of those who survive the infection suffer lifelong impairments (da Silva, et.al, n.p.). The problem with this organism and vaccine effectiveness is that the bacterial protein mutate and change continuously, decreasing the efficacy of vaccines. A group of researchers at the University of Nottingham studied over 2000 isolates and found that 88% of strains made a precursor Factor H binding protein (FHbp), a lipoprotein found in the cell wall of the bacteria (da Silva, et.al, n.p.) Although the FHbp itself undergoes mutations and is constantly changing, this precursor molecule is the same in a majority of strains, so a vaccine targeting this precursor protein is effective regardless of which final version of FHbp the bacterial strain makes. This is the basis of two new meningitis B vaccines, which are major causative agents of meningitis in some countries and lack effective, widely used vaccines.

Another way to decrease meningitis occurrence, specifically in the African “meningitis belt” is to reinforce the medical and laboratory structures dedicated to detecting and monitoring bacterial meningitis cases and outbreaks. This is precisely what is being done. Foundations such as MedAfriNet are placing an emphasis on basic microbiological tests and specimen transport to laboratories to confirm cases as a way to manage meningitis cases in Africa significantly better (Feagins, et.al., n.p.) Another reason that laboratories are being reinforced is because of the changing epidemiology of bacterial meningitis. There are several “groups” and each outbreak is different, so being able to identify the margins and populations being affected by, let’s say, group B meningitis and group W meningitis, is important for combatting and stopping outbreaks (Feagins, et.al., n.p.) Efforts like these are extremely important because they consider the disease and it’s spread from a “big picture” perspective. Similar strategies are used for other diseases such as HIV and TB, and even COVID-19.

Learning so much about COVID-19, at the microscopic level, has been scary, but it has also been helpful. Knowing how viruses spread has also afforded me the knowledge of what steps to take to protect myself and my family. It has also been reassuring to learn about our innate and immune responses and to know that there are cellular processes going on every moment to protect me from invaders. Another thing that we have learned about is antibodies and the role that they play in the immune response, whether it is to SARS-CoV-2 or to the flu. Antibodies are also useful to use because they can be used in diagnostic tests. We can examine things like the presence of antibodies in our blood, as well as their type to determine whether or not we have been infected with SARS-CoV-2 and/or if we have been exposed to it in the past.

The two antibody types that tell us the most about an infection are IgG and IgM. Both of these are eventually synthesized to combat infections, but they are synthesized at distinct stages throughout and after the course of infections. IgM is the first antibody made in response to an infection, whereas IgG is made later in the infection and is long-lived, so it remains in the blood even after recovery. Generally, having just IgM antibodies indicated an active infection, so you are still contagious. Having only IgG antibodies often indicates a past infection, but when present with IgM it can indicate a current infection and that you are still contagious. If you only have IgG, though, this is more likely to mean that you have been infected sometime in the past and that your body has mounted a successful immune response to eliminate the infection.

Now, why would being able to test for antibodies help us understand COVID-19 more clearly? Well, if we were able to determine people who have been infected with and recovered from SARS-CoV-2 infections, we can start piecing things together (Kossakovski, n.p.) For example, are there any risk groups? Are there any groups that have a much higher rate of survival? Is it possible that our bodies can form long lasting immunity against SARS-CoV-2? Not only that but studying and isolating antibodies from people who have recovered from COVID-19 could lead to potential treatments, since they are being taken from a body that has successfully fought off the virus (Kossakovski, n.p.) With so much value in antibody titers, there are several US companies working to get FDA approval for tests they have developed. One test developed by Cellex in RTP has been approved for “emergency use” by the FDA, which is a step towards being the first titer to gain FDA approval (Saplakoglu, n.p.) This “rapid test” takes about 15 to 20 minutes and assesses IgG and IgM in serum (Saplakoglu, n.p.), which is already faster than some current diagnostic methods and gives us a better idea of where in the infection course the person is.

Well, one thing that has changed about COVID-19 is that the virus has officially been named SARS-CoV-2, as the second virus known to cause severe acute respiratory syndrome (SARS). As the number of cases continues to rise in the US and hospitals grow more and more overwhelmed with patients seeking testing and treatment, researchers are working hard to develop a preventative vaccine and/or treatment for the virus. There is bound to be some wait-time for these to be developed, as scientists must first gain a detailed understanding of the pathogenesis of the virus. Not only does SARS-CoV-2 share a name with 2003 SARS-CoV, but the two viruses are believed to share a receptor protein to which they attach, called ACE-2. Studying this protein could be effective against preventing COVID-19 since it offers a possible way to block the virus from entering its target cells.

This is exactly what is being done by an international team led by the University of British Columbia’s (UBC) Dr. Josef Penninger working to develop antivirals against COVID-19. They are focusing on ACE-2 and how they can use this receptor to lessen the viral load in severe cases. They have developed a drug called hrsACE2, or human recombinant soluble angiotensin-converting enzyme 2. Using stem cell-derived models of blood vessels and kidneys, which have both been shown as target cells of the virus, the team at UBC was able to show that SARS-CoV-2 infected these cells at a much lower rate when treated with hrsACE2 (ScienceDaily, n.p.) The mechanism of this drug is basically binding the virus before it can bind to actual ACE2 on target cells and infect them. The team is working on moving towards clinical trials soon, but the study is promising.

As for the vaccine, this is another important key to stopping the epidemic. Moderna, a biotechnology company based in Cambridge, and the National Institute of Health have partnered to find a COVID-19 vaccine and are currently underway with phase 1 human trials and on track to phase 2 around spring or early summer. Their trials are aimed at “hijacking” mRNA to carry a copy of the viruses genome and induce the production of antibodies against the virus (Harbert, n.p.) The company has no approved vaccine to date, but they had been working on a vaccine against MERS, another type of coronavirus, so they had a headstart to developing their vaccine, as MERS is genetically similar to SARS-CoV-2. Even if this sounds good, widespread distribution of the vaccine is still expected to come no sooner than September of 2020, which is why social distancing and taking individual precautions are so important right now during the height of the US pandemic.

When we compare cells from two different people, they are not the same. This is also true about tumor cells, they may share some characteristics, but no two tumors are the same. “Personalized medicine” is based on this exactly because we can sequence and study individuals tumors to customize therapies that are equipped to fight that specific tumor. There are two target cells for these therapies and they are T-cells, which are involved in both marking and killing infected or cancerous cells, as well as dendritic cells, which act as a bridge between innate and adaptive immune responses. If we are able to design treatments that effectively activate and train these cells to target specific diseased cells, the therapeutic benefits would help save millions of lives, ranging from those with cancer to others with autoimmune diseases and even HIV.

Several trials are being conducted to develop new chimeric antigen receptor T-cell (CAR-T) therapies. A study at the Institute for Advanced Medical Research in Japan is working on mice models to test human CAR-T therapies, but they have observed promise in a specific CAR-T therapy in mice with solid tumors with no adverse side effects (Kato, n.p.) Kato and his team have genetically engineered T-cells to target the antigen glycipan-1 (GPC1). This antigen is found in high levels in tumor cells, but not in normal cells, which is why no adverse effects have resulted from this potential cancer treatment. In order to move into human clinical trials, the team is working on developing new models to show both the effectiveness and safety of this CART-therapy.

The most common side effect of these therapies, especially once the CAR-T cells have started to multiply in your body is cytokine release syndrome (CRS), marked by fever and low blood pressure. It is a double-edged sword as CRS takes a toll on the patients themselves, but is a sign that the CAR-T cells have started their work, producing cytokines to activate effector cells to destroy their targets (Thibodeaux, n.p.) This is one example of adverse effects called “on-target/off-tumor toxicity,” which results when CAR-T cells attack normal, healthy cells that are presenting their target antigen (Thibodeaux, n.p.). This is why the study I discussed in the previous paragraph is so impressive because it is increasing the safety of this therapy while still maintaining the therapeutic effect. Aside from these health concerns, another obstacle for these therapies is cost. Two specific therapies, tisagenlecleucel and axicabtagene ciloleucel, are over $373,000, and that is for just one infusion (Locke, Lin, n.p.) “While we know the high list prices of CAR T-cell therapies, we also know that there is a high cost to administering them. Unfortunately, the U.S. medical system appears to have a bureaucratic inability to actually deliver the dollars where they belong (Locke, Lin, n.p.).” Yet again, people who are suffering from life-threatening diseases must choose between dying and going into tremendous amounts of debt to receive a treatment that may or may not work for them. It is a visionary therapy, but it also sheds light on one of the biggest problems of the US health system.

With the COVID-19 pandemic going on, it is hard to focus on other threats to public health, but there are still ongoing pandemics that we cannot ignore. Tuberculosis (TB) is one that I want to focus on for this post. With a quarter of the world suffering from TB infections, it remains the world’s top infectious killer (WHO). For this reason, the World Health Organization has been taking steps towards eliminating TB by 2030. Just recently at the 2020 World TB day conference, WHO emphasized their efforts to provide preventative care around the world. The targets for these increased measures are those who are most at-risk for the infection, including those with HIV, family members of individuals with TB, and people living in crowded communities (WHO). Based on what we know about TB (and COVID-19), controlling the spread of a pandemic is the key to eliminating it.

The biggest distinction between COVID-19 and TB is the type of pandemic that they are. COVID-19 is a new pandemic that has spread rapidly, whereas TB is a slow pandemic that has been around for quite some time. The individuals that are affected also differ, with children being an at-risk group for TB. In 2018, 1.1 million children suffered from TB, of which 200,000 died (Wingfield, p.1). Amidst the COVID-19 crisis, though, it is also important to evaluate how the two interact, as the new pandemic can change the way TB affects some populations (Wingfield, p.1). It is possible that COVID-19 could increase or decreased TB transmission. COVID-19 is overwhelming the nation’s healthcare system, so it could be possible that some people are not receiving treatment for TB as a result. I say all this to emphasize the epidemiological standpoint of the two pandemics, which changes a lot about each.

Now, as we look at TB from a microbiology standpoint, there is still a lot of things that scientists don’t know about Mycobacterium tuberculosis, which is the bacteria that causes TB. There are several studies aimed at learning more about the bacterium, and one at Stanford Linear Accelerator Center (SLAC) has discovered a transport protein in its membrane that may play a role in the disease. The protein was shown to have a “huge interior pocket,” which could allow large molecules to enter the bacterial cell (Collins, n.p.) This particular protein is of interest because the bacteria’s vitamin B12 uptake has been shown to play a vital role in its survival and progression into TB disease (Collins, n.p.) Although it is a new finding, the researchers at SLAC have still found a potentially critical piece to the puzzle that is TB. Future research needs to be conducted to figure out if vitamin B12 is transported using this new protein, but it is still progress being made in favor of developing new treatments and better understanding the bacterium.

The meme for today is in Spanish, but it reads: “when you’re learning about tuberculosis and you hear someone cough.”

First, let me start by saying that it is crazy to think about how much is going to change as a result of COVID-19. The way that we act and react will never be the same. As a college senior, so ready to put on my cap and gown and have my family at my graduation, the crisis has changed my plans for the foreseeable future. A lot of my classmates are likely experiencing similar circumstances, so I thank Dr. Cramer for allowing us to dedicate this blog post to our feelings about COVID-19. So far, during the first week of “self-quarantine,” I have been able to keep up with my work for all my classes, including MICRO. Although it is different, it has actually given me something to occupy myself with. Being at home all day, every day, it can be easy to just watch TV or stay on your phone, but (never thought I would say this) homework is something I look forward to now.

There are a lot of things that this pandemic has revealed about the world, though. First that public health measures and being prepared for events like this are essential. I know that this is beyond what anyone expected, but seeing the course that COVID-19 took in Italy, then comparing it to the US is astounding. The virus spread at a rate quite similar to Italy in the USA but has now surpassed the situation in Italy. I partially believe that this is due to the government response (parts of Italy were shut down at one point, but in all but 1 US state all the liquor stores are still open as “essential businesses”), but what do I know. A lot of the information that I have been getting about COVID-19 has been on twitter, which may not be the most reliable source, but it is interesting to see the pandemic from so many perspectives. There are doctors, retail workers, politicians all weighing in on the pandemic, so it is good to have a well-rounded idea of COVID-19, not just the microbiology side that we have been learning in class.

Lastly, as a student, it is important to evaluate my learning and how this new method is working for me. I have some experience with “flipped” and online classes, so although it isn’t as effective as getting to attend class, I am still able to retain the information I am being given. One of my strategies for studying at home which has particularly helped me alot is making study aids. I have made flashcards, quizlets, diagrams, drawings, etc. Aside from listening to a lecture, I feel this is the most effective method for me in this particular circumstance. Another thing that is really easy to do when in the house all day is eating. Starting Monday, I am going to make an attempt at working out at least 30 minutes a day, but until then enjoy this meme (it summarizes my overall quarantine experience).

Sexually transmitted diseases, or STDs, are not things that most people like to talk about, which is partially the reason that they are becoming increasingly common. The stigma surrounding these diseases/infections have resulted in decreased awareness and discourages people from asking their partners about their sexual health, which ultimately facilitates their spread. One particular STD is listed as an “urgent threat” by the CDC due to increased antibiotic resistance: Neisseria gonorrhoeae. Just as the superbugs that I discussed in last week’s blog post, N. gonorrhoeae has developed resistance to almost all antibiotics that we have for treating the infection. Just by looking at the chart below (Nature, p. 3), you can see how relatively short-lived new treatments for this bacterial infection are, and why it is becoming a huge threat in terms of public health. With such increasing resistance, the best way to combat this bacteria is to prevent it, and there are several ways to do this and I will discuss a few in this blog post. 

Antibiotic resistance is absolutely crazy. Thinking that the source of some of these superbugs are small, random mutations just blows my mind. You don’t usually think of bacteria in terms of natural selection, but it is important to remember when we talk about these microbes, which evolve in response to selective pressures. These small mutations lead to changes that ultimately decrease the effectiveness of antibiotics, thus resulting in resistance. Changes that lead to decreased influx of antibiotics, increasing efflux of antibiotics, decreased affinity of antibiotics to their target on the microbe, and several other changes are why N. gonorrhoeae has been growing resistance since the 1940s, when Penicillin was introduced. In fact, by the 1950s, most strains of N. gonorrhoeae had developed resistance to standard doses of Penicillin G, and by the early 1970s, Penicillin G, even at increased doses was no longer a viable option for most strains of the bacteria (Nature, p. 3). Most concerning is that in 2018, strains were isolated in the UK and Australia that showed resistance to the dual treatment consisting of ceftriaxone and high-level azithromycin (Nature, p. 4), leaving us with an alarmingly small arsenal to combat this STD. 

The reason that this is such a concern is because N. gonorrhoeae can spread beyond just the reproductive organs to the liver, heart, joints, and can lead to complications with pregnancy and infertility. From 2018 to 2019, the number of reported gonorrhea cases in the US increased by 5 percent to 580,000, which is the highest number in over 30 years (Stack, n.p.). If you look at the rate in 2014, gonorrhea has increased by over 63 percent since then (Stack, n.p.). This increase goes back to several things, which include increasing stigma around STDs, decreased use in condoms, and, to an extent, decreasing resources and health centers for sexual health. There are three things that everyone as individuals can do to prevent catching & spreading this STD: abstinence, monogamy, and condoms (AMC). All three of these methods can protect you and others from N. gonorrhoeae. Adding other preventative measures to this AMC method confers even more protection. Some other things you can do is regular STD screening, communicating with your sexual partners, and making changes to your behavioral/sexual tendencies that may be putting you at risk (Nature, 13). Basically, what I want you to take away from this post is that gonorrhea is scary and getting scarier, so you should do everything you can to protect yourself and others.

The first antibiotic, penicillin, was discovered in 1928 and first used to treat bacterial infections in 1941. This was just 80 years ago, so why are we seeing a rise in antibiotic resistance and “superbugs”?  When I say “superbugs,” I am referring to organisms that have developed resistance to almost all known antibiotics. As we discussed in class, a big factor in this rise is the misuse (both intentional and unintentional) of antibiotics in general. Some examples of this would include: using antibiotics for viruses, not taking the entire dosage of antibiotics prescribed, and using antibiotics on crops and for cattle. Using antibiotics for cattle is beneficial, but only to the farmers selling these animals as it alters normal microbiota and promotes growth. This means a bigger check for them, but it puts the community at risk as it gives rise to antibiotic-resistant organisms, which can make their way into crops and spread into the community.  Although there is bound to be antibiotic resistance among populations of bacteria due to random mutations or innate resistance, misusing antibiotics has definitely propelled the development of superbugs. The problems associated with these organisms are that they can spread among communities and are extremely difficult to treat.

THE CDC, WHO, and NIH do year-round tracking and research to identify emerging superbugs as well as how we can try to combat them. As of January 2020, the CDC has five bacteria and fungi listed as urgent threats, eleven as serious threats, two as concerning threats, and three on the CDC watch list (CDC 4). Two of those organisms are new to the list: Candida auris, a yeast, and carbapenem-resistant Acinetobacter, a genus of gram-negative bacteria (Sun, n.p.). The main concern all the superbugs is that they are evolving quickly to resist the effects that antibiotics have on them, while we are making no progress in developing new drugs to combat them. It has been over three decades since a new class of antibiotics has been developed (Sun, n.p.). Another concern is C. difficile infections, which usually arise when people take antibiotics, a double-edged sword that kills good bacteria along with the bad, making us more vulnerable to infection. Superbugs alone are responsible for 2.8 million infections and 35,900 deaths, but when you add C. difficile to the numbers, it puts infections at above 3 million and death at 48,700 (CDC 6). These numbers are just a glimpse of the future to come if we were to completely lose the ability to use antibiotics. The burden it would have on global health would be extremely dangerous and we would see a lot more individuals dying as a result of once manageable infections. 

Now, a bit off-topic, but we’re going to move to Vibrio cholera. A recent study found that this bacterium can “steal” up to 150 genes from neighboring cells (Science Daily, n.p.). What this means for V. cholera is that it can change and adapt quickly. What this study doesn’t mention though, is how mechanisms like this are how antibiotic resistance occurs. Gene transfer is at the center of how organisms are able to “evolve” and dodge our modern medications. I hate to admit it, but bacteria are continuing to outsmart us and we are in dire need of more education and awareness about this issue if we hope to survive this post-antibiotic era. The corporation and actions of physicians, consumers, and government officials that have the power to impose more regulations on these miracle drugs are where we need to look to improve this growing issue. I’d like to end on a funny meme as I usually do, but considering the urgency of this issue, I’ll end with a piece of advice (it’s still funny too).