Dr Wardak Abdul Qayoum assists the expat microbiologist in supervising the team and carrying out isolation, identification and sensitivity testing of the 3000 bacterial strains expected. He uses a plastic loop to take a colony of bacteria from the culture plate.

Afghanistan 2013 © Vivian Lee/MSF

Antibiotic resistance

Resistance to antibiotics has become a global health crisis, complicating the treatment of bacterial infections and endangering lives around the world.

Putting antibiotic resistance in context

The ability of all types of microbes (bacteria, viruses, parasites, and others) to survive medicines used against them is called antimicrobial resistance. In the case of bacterial pathogens, for which antibiotics are the most important drugs used in treatment, we speak of antibiotic resistance.

Antibiotic resistance (ABR) is increasing at alarming rates in countries with failing health systems and poor sanitation, and especially in regions at war. Without urgent action, simple cuts and many diseases could once again become deadly since today’s medicines will no longer work against them. At Doctors Without Borders/Médecins Sans Frontières (MSF) we are finding more and more ABR infections—in patients ranging from victims of war wounds or burns to severely malnourished children and even newborns—and are expanding our activities to prevent and treat them.

50%

of antibiotics used globally

are prescribed incorrectly

214,000

newborns die each year

from drug-resistant infections

Only 1

new class of antibiotics

was developed in the last 30 years

Facts about antibiotic resistance

Bacteria can become resistant to an antibiotic when they are exposed to it repeatedly, or to incomplete or sub-optimal doses. This can lead to the growth of mutant bacteria which the drug can no longer kill. Resistance occurs in a wide range of disease-causing bacteria and can also be transmitted from one type of bacteria to another.

ABR infections are especially common in settings where off-the-shelf or counterfeit antibiotics are widely available, or where antibiotics are often overused or misused. Without access to proper laboratory diagnostics, health care providers often do not know whether a patient’s symptoms are caused by a bacterial infection, and if so, which type of bacteria is involved. This can lead to unnecessary or incorrect prescriptions for antibiotics. Resistant bacteria can also spread in hospitals with poor sanitation or inadequate infection control, infecting especially vulnerable patients who are already sick or have unhealed wounds.

ABR infections often go unrecognized in their early stages, since they usually cause the same clinical symptoms as antibiotic-sensitive infections. Typically they are identified only after the patient’s symptoms persist despite treatment with appropriate first-line antibiotics.

Prevention of infections is crucial in the fight against ABR. Fewer infections means less antibiotic use, and therefore less chance that bacteria develop resistance or that already-resistant infections spread.

Infection prevention involves many different approaches, such as ensuring widescale population coverage with vaccines against infectious diseases, providing safe water and sanitation in communities, and establishing effective infection control measures in hospitals and health clinics.

When patients seek treatment for illnesses, doctors and health workers must avoid overusing antibiotics, and they need access to microbiology laboratories that can accurately diagnose infections and point doctors to the correct prescription. Patients should be educated about the importance of taking antibiotics only when they are truly necessary, prescribed by a clinician, and provided by a reputable pharmacy, and of taking the prescribed dosage for the prescribed period of time.

Comprehensive infection prevention is challenging since it requires strong commitment and participation by many different stakeholders. Some key steps, such as strengthening laboratory capacity and hospital infection control practices, require investment and good basic infrastructure, while others call for behavioral changes by patients and medical staff alike. And some demand decisive action from policymakers—for example, to end the over-the-counter and black-market antibiotic sale common in many countries.

Antibiotic resistance is often suspected when a patient’s infection fails to improve after a course of what would usually be an appropriate drug. Confirmation of resistance requires laboratory testing of samples from the patient’s blood, bone, tissue, or cerebrospinal fluid; results of these ‘antibiograms’ also provide information on which alternative antibiotics should cure the infection. But antibiograms are usually not done in low-resource settings, since microbiology laboratories and trained clinical staff may be scarce or non-existent.

Without lab support, clinicians may attempt a diagnosis based on available knowledge about the types of bacterial infections and drug resistance patterns prevalent in the region. But even this information is often lacking. In these cases, physicians often prescribe antibiotics that work against a very wide range of bacteria—leading to overuse of, and fueling resistance to, these precious broad-spectrum drugs.

Patients with an ABR infection, especially one resistant to multiple drugs, have fewer antibiotic treatment options, and these options are generally more expensive and used intravenously rather than as oral drugs.

Antibiotics can be categorized as narrow or broad spectrum. Those with a narrow spectrum target only specific bacterial families, while broad-spectrum antibiotics kill many different types of bacteria. To avoid resistance, narrow-spectrum drugs are the best choice when the type of bacteria causing a patient’s infection is known or strongly suspected and is not life-threatening—for example, in cases of chronic infections. But when a patient is very ill and the cause of infection is unclear, doctors often start treatment right away with a broad-spectrum antibiotic and then switch to a narrower one if a bacterial pathogen is identified. For patients with bloodstream or central nervous system infections, immediate antibiotic treatment can mean the difference between life and death.

For many types of highly resistant infections where no current antibiotics are effective, patients may be treated either with old antibiotics that were abandoned due to their potentially dangerous side effects, or with a combination of antibiotics that together might overcome the resistance. When no antibiotics work and the infection is localized to a limb, amputation may be the only hope for saving the patient’s life.

How MSF responds to antibiotic resistance

The rise in ABR infections worldwide, combined with MSF’s increased engagement in Middle Eastern countries at war, has made antibiotic resistance a slow-motion emergency facing many of our teams.

For example, in our reconstructive surgery program in Amman, Jordan, about half of all war-wounded patients from Iraq, Syria and Yemen arrive with serious infections, up to 60% of which are ABR. The same holds true for Yemen, where war has destroyed an already fragile healthcare system, and with it the capacity for proper sterilization, hygiene, and care for patients with open fractures or other severe injuries highly susceptible to infection. Rampant overuse and misuse of antibiotics also helps drive the development and spread of resistant infections in settings like these.

In response, we have developed a comprehensive strategy to detect, treat, and prevent antibiotic-resistant infections. Our strategy focuses on a few key pillars:

Ensuring stringent hygiene in our hospitals and clinics to prevent transmission of infection between patients;
Expanding access to microbiology-based diagnosis;
Providing good quality of care aimed at saving lives and limbs of people with resistant infections, while ensuring that antibiotics are prescribed and used appropriately;
Building local capacity to implement our package of care.

Alongside these core activities, we conduct research on new tools to support these activities. We also engage with global health policymakers on ways to eliminate practices that fuel the spread of antibiotic resistance, and to accelerate the development of urgently-needed new types of antibiotics.

Reinforcing infection prevention and control

While most patients diagnosed with ABR infections developed them before seeking treatment, resistant bacteria can also spread within healthcare facilities. This is a significant problem even in high-income countries, but safeguards against transmission in hospitals and clinics—including basic handwashing and thorough disinfection of all surfaces and medical devices—are more often lacking in under-resourced facilities with high patient loads.

Establishing these safeguards at our projects requires well-planned protocols and trained staff. For example, patients at our specialized burn unit in Drouillard Hospital in Port-au-Prince, Haiti must have their bandages changed every other day until the burns are fully healed. Since these changes can take up to two hours—ample time for bacteria to invade a wound—the procedure must be done in a sterile operating room by staff covered in protective garments. Another less obvious but crucial safeguard is finding space to isolate patients with ABR infections to prevent transmission. These measures can be especially challenging to maintain in emergencies when hospitals receive many wounded or sick patients in a very short time, often requiring a constant and difficult balancing act for our teams.

Improving access to microbiology-based diagnostics

Another crucial part of our strategy is expanding access to laboratories that can accurately diagnose a patient’s infection and test the underlying pathogen for resistance. This is challenging in most settings where we work, where there's often a scarcity of well-equipped microbiology labs with skilled staff who can conduct the necessary tests and correctly interpret the results.

To meet this need, our first step is to look for an existing lab accessible to a given project. If we find one that meets our quality standards and can work with us, we use it, sometimes after helping to build up equipment, supplies, skills, or capacity. In settings without labs and where the need is great, we may build our own and train local staff to run it, and then provide external support as needed. This has succeeded even in some extremely difficult contexts—for example at our trauma hospital in Aden, in war-torn Yemen, a country where the health system is in ruins. As of mid-2019, we have established microbiology labs at six projects, with four more planned in the near future.

Caring for patients with infections while optimizing antibiotic use

Our approach to managing bacterial infections is to use antibiotics that narrowly target the pathogen causing a patient’s illness and that lab tests show will kill it. Only when these tests identify a bacteria showing resistance—or when the patient needs immediate treatment for a life-or-limb-threatening infection, or when microbiological testing is not possible—do we use broader drugs, or even “last-resort” antibiotics for the most resistant infections.

Treatment for ABR infections is typically long. While patients with a simple infection might need only a week's treatment in the hospital, those with resistant infections typically require six weeks of intravenous antibiotics followed by four weeks of oral drugs. During this period, some patients may also need surgeries—for example, for severe burns or orthopedic injuries. To prevent resistant infections from spreading to others, these patients are isolated from other patients, which can take an emotional toll.

Another important part of care is providing psychological support and counseling to patients undergoing these difficult treatments, especially to those in isolation.

Preserving antibiotics through "antibiotic stewardship"

As the number of useful antibiotics shrinks in the face of growing resistance, it’s crucial to preserve the effectiveness of those we still have. Our goal for every patient with a bacterial infection is to use the right antibiotic at the right dose for the right length of time, and by the right route of administration (oral or intravenous). This helps not only to optimize care for each individual but also to avoid using the broadest, “last resort” antibiotics when they’re not needed.

About half of all MSF projects, especially those focused on trauma and surgery, have implemented an “antibiotic stewardship” program to help meet these goals. Our programs bring together a small team of people with relevant expertise—infectious diseases specialist, infection control expert, and pharmacist—to review all antibiotic prescriptions at the hospital or clinic, monitor antibiotic prescribing practices, and investigate suspected outbreaks of antibiotic-resistant infections within the hospital.

Building capacity

Health workers and lab technicians in regions where we work are often unfamiliar with how to recognize and respond to ABR infections. So our ABR response includes working to build this capacity—from hands-on training of lab technicians to perform diagnostic tests and of doctors to interpret the results, to establishing more rigorous handwashing protocols and implementing antibiotic stewardship programs. E-learning tools and a standardized training curriculum are also in development.

One success story is the MSF acute trauma facility in Aden, Yemen, where local staff with no prior microbiology education now run a lab capable of sophisticated, high-quality microbiological testing, including on bone and tissue samples. They also conduct antibiotic stewardship activities to support the project’s intensive care and surgical wards, providing daily feedback about laboratory results and regular audits of prescribing practices and antibiotic consumption.

Much of this training was done by bringing Aden staff to the MSF hospital in Amman, Jordan, a referral center for joint, bone, and tissue injuries, to spend time working and learning alongside counterparts experienced in managing ABR. The Jordan project also provides ongoing remote support to the Aden project.

Developing innovative tools

To help expand microbiology capacity even further in low-resource and emergency settings, MSF is developing a “Mini-Lab” — a simplified, small-scale, “all-in-one,” pre-fabricated clinical bacteriology laboratory, stocked with everything needed to carry out the most important diagnostic tests. MSF designed the Mini-Lab so it can be easily assembled and used by people with limited training. The Mini-Lab is a portable, affordable toolkit that will allow for better diagnosis and treatment of infections, and for surveillance of ABR, even in remote, extremely hot and under-resourced settings.

The first pilot deployment of Mini-Lab was completed in 2020 in Haiti. In 2021 we will pilot implementation at a district hospital in Carnot, Central African Republic, aimed at optimizing use of Mini-Lab in a routine laboratory within a busy clinical environment. The goal is to roll out full deployment in selected MSF projects at the end of 2021.

Another innovative tool in development is a smartphone app designed to help doctors and clinicians in low-resource settings diagnose ABR. ASTapp, as it is called, uses image processing and artificial intelligence technology to guide non-expert microbiologists through interpretation of lab tests that measure resistance to antibiotics. This, in turn, guides clinicians on the best course of treatment and will help ensure that patients receive the most appropriate antibiotics. ASTapp was developed by the MSF Foundation, a specialized unit focused on innovation, through a $1.3 million Google Artificial Intelligence Impact Challenge grant.

A third tool we developed, called MSFeCARE (electronic Clinical Algorithm and Recommendation), helps clinical staff choose an appropriate antibiotic for acutely ill children (from two months to five years old) in regions where diagnostic tests aren't available. Using a tablet, eCARE guides healthcare workers step-by-step through an assessment of the patient’s symptoms and signs. It then provides recommendations and standardized procedures to diagnose and treat the child. We are using eCARE in remote projects, including those in Mali, Niger, Nigeria, Tanzania, Chad, and Central African Republic.

Watch this panel discussion between MSF experts to learn more about how we are fighting ABR.

Four ways we are trying to tackle antibiotic resistance

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