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Archive for the ‘Microbiology’ Category

New Tetanus Cases Reported. What to Do About This Deadly Infection?


Tetanus is an infectious disease caused by the pathogenic bacteria Clostridium tetani
Image: 3D illustration of Clostridium tetani, the agent of Tetanus


written by Chandana Balasubramanian

There’s an urban legend about Tetanus shots. Many people feel you need them only when you step on a rusty nail or if a splinter pokes you. Like any good myth, there is a tiny bit of truth attached to it. Yes, stepping on a nail is a good reason to get a Tetanus shot – but not because of the rust. Once your skin barrier is ruptured, Tetanus bacterial spores from contaminated items can easily enter your body.

The truth is there are many ways to get Tetanus. Spores of the bacteria that cause Tetanus, Clostridium tetani, are commonly found in the soil, dust, and intestines, and feces of several household animals and herbivores, and even humans. However, it does not spread from one person to another. The best way to control Tetanus infections is to prevent them from occurring entirely.


Tetanus Epidemiology: Recent and Older Outbreaks

Worldwide, Tetanus cases have declined rapidly due to mass immunization drives by various governments and public health agencies. However, Russia recently reported its first case of Tetanus in nearly two decades in September 2021 [1]. In India, a 12-year-old boy recently survived a severe case of Tetanus [2]. He had not been vaccinated against it. In Northern Kazakhstan, a 53-year-old man died due to Tetanus, and it is not known if he was vaccinated [3].

One potential reason for these new reports of this highly preventable infection is COVID-19.  In July 2020, WHO and UNICEF warned of disruptions to life-saving immunization services across the world due to the pandemic. Healthcare workers and social workers have been unable to follow standard vaccination schedules for many reasons, including:

  • Lockdowns and social distancing,
  • Disruption to transportation,
  • Fear or reluctance to visit hospitals or clinics for non-urgent health services,
  • More healthcare workers diverted towards COVID-19 and emergency services, and
  • A lower number of available auxiliary nursing midwives (ANMs) to drive regional vaccination for children.

Before the pandemic, two notable Tetanus outbreaks occurred in Indonesia during the devastating tsunami in 2005 and an earthquake in 2006. People hurt in disasters are, in general, at a much higher risk of getting infected with Tetanus. In certain parts of Indonesia, a lack of adequate transportation, access to health facilities, and awareness about Tetanus protocols led to many people dying from Tetanus. Another instance of a Tetanus outbreak was after the 2005 earthquake that struck Pakistan [4].


Tetanus worldwide cases and rates
Image: Worldwide Tetanus cases and rates, 1980 to 2020. Copyright © GIDEON Informatics, Inc.


What Causes Tetanus? What are the Symptoms of Tetanus?

Tetanus is one of the deadliest microbial toxins. It is caused by the bacteria Clostridium tetani and has a high fatality rate. Approximately 10-20% of cases are fatal.

Tetanus is also commonly known as lockjaw. Spores of the bacterium, Clostridium tetani, enter our bodies and spread all over the central nervous system. The spores produce a toxin called tetanospasmin that blocks nerve signals from the spinal cord to the rest of the muscles. The condition is also commonly known as lockjaw because it often causes muscle spasms in the jaw and neck, though it may spread to the rest of the body.

Other symptoms are fever, sweats, a rise in blood pressure, and an elevated heart rate. A common complication of Tetanus is when vocal cords begin to spasm, causing breathing difficulties. Infected individuals can also break their bones or spines based on the severity and frequency of convulsions caused by Tetanus [5].


About Clostridium Tetani

Tetanus spores cannot be killed easily. They are found everywhere and can resist extreme conditions like high heat and strong disinfectants. They can remain inactive but infectious for more than 40 years.

Clostridium tetani is an anaerobic bacterium; it does not live or grow in the presence of oxygen. As a result, there is a higher risk of infection with injury sites that do not receive a strong oxygen supply. This includes deep wounds, burns, needle punctures, and surgical procedures performed without adequate hygiene protocols.

While a Tetanus infection can have serious effects, it is now rare in most developed countries. The United States reports an average of 20 cases per year, mostly in unvaccinated individuals. Though most cases are found in developing countries, many of them now maintain rigorous vaccination programs and made great strides in eliminating or minimizing the incidence of Tetanus. Anyone can get infected, but children and newborns are the most susceptible.


Image: Clostridium tetani. Anatomy of the cell with terminal spore, and vegetative cell. Structure of the terminal spore: core, cortex, and spore coat.
Image: Clostridium tetani. Anatomy of the cell with terminal spore, and vegetative cell. Structure of the terminal spore: core, cortex, and spore coat.


What is the Incubation Period for Tetanus?

The incubation period for Tetanus is anywhere from three to twenty-one days, with an average of ten days. The incubation period varies based on how far the injury site is from the central nervous system. Symptoms can last for weeks and even months. They are higher in unvaccinated individuals and older people for whom immunity is lowered.

Is there a Cure for Tetanus?

There is no cure for Tetanus, but the Tetanus vaccine is highly effective in preventing infection. Once infected, however, symptoms are managed until the effects of the toxin diminish. Chances of survival are lower if muscle spasms develop within five days of getting infected.

There are no blood or laboratory tests to diagnose Tetanus. The most common initial symptom is ‘trismus’ or lockjaw due to facial muscle spasms.

Tetanus can be confused with certain other conditions, which makes it more important to educate frontline clinicians about confirming their own initial assessments either with experts or a platform like GIDEON that factors epidemiology data into differential diagnosis.

How to Treat Tetanus?

Tetanus is considered a medical emergency, and hospital care is required. Treatment is often medication called Tetanus Immune Globulin (TIG), also known as Tetanus antitoxin. It is usually administered as a preventive measure for high-risk wounds and injuries. It is also part of the treatment protocol, together with muscle relaxants and antibiotics like penicillin. When required, proper wound cleaning and debridement are also essential to minimize the risk of Tetanus infections. Patients with difficulty swallowing may also need a breathing tube or ventilator [6].

Preventing the Rise of Tetanus Infections

The best prevention is to ensure newborns, children, and adults receive their Tetanus vaccine doses according to the recommended schedule.

Vaccines for Tetanus are often combined with those for other diseases:

  • DT Vaccines: Diphtheria and Tetanus
  • DTaP or DTP Vaccine: Diphtheria, Tetanus, and Pertussis (whooping cough)
  • Td Vaccine: Tetanus and Diphtheria
  • Tetanus Immune Globulin (TIG)

It is important to note that Tetanus vaccines do not offer lifetime immunity. Many people may need booster shots to continue receiving protection against Clostridium tetani. Additionally, building awareness about improved infection control measures for childbirth, surgery, and other medical protocols in developing and under-resourced nations can make a difference.


WHO-UNICEF estimated vaccine coverage of Tetanus
Image: WHO-UNICEF estimated vaccine coverage of Tetanus graph, 1980 – 2019. Copyright © GIDEON Informatics, Inc.



[1] Outbreak News Today, “Russia: First Tetanus case reported in Sverdlovsk in nearly two decades,” 19 09 2021. [Online]. Available: [Accessed 29 09 2021].
[2] Times of India, “12-yr-old with rare Tetanus survives at GMCH after 37 days on ventilator,” 17 09 2021. [Online]. Available: [Accessed 29 09 2021].
[3] Outbreak News Today, “Tetanus death reported in Northern Kazakhstan,” 4 09 2021. [Online]. Available: [Accessed 09 29 2021].
[4] New York Times, “Twenty-two Tetanus deaths reported in Pakistan quake zone,” NY Times, 27 10 2005. [Online]. Available: [Accessed 29 09 2021].
[5] H. Bjørnar, “Tetanus: pathophysiology, treatment, and the possibility of using botulinum toxin against Tetanus-induced rigidity and spasms.,” Toxins (Basel), vol. 5, no. 1, pp. 73-83, 2013.
[6] Centers for Disease Control and Prevention, “Tetanus for Clinicians,” CDC, [Online]. Available: [Accessed 29 09 2021].



Busy Microbiology Labs Can Detect Infectious Diseases And Biological Threats Faster. Here’s How.

Person in a hazmat suit working in a laboratory setting
Photo by Satheesh Sankaran on Unsplash


written by Chandana Balasubramanian


Could your patient have kissed a camel recently? A new patient may have fallen ill after indulging in a little ‘tari’ (fermented date palm sap) in Southeast Asia. Or could your hospital be in the midst of a Candida Auris outbreak – the multi-drug resistant, severe-illness causing, and often-misidentified yeast?  

When you need to identify an unknown pathogen or biothreat agent, as the title song of the movie ‘Ghostbusters’ goes, “Who you gonna call?” If you’re in Maryland, Sheryl Stuckey and her clinical microbiology lab at the Holy Cross Hospital, Silver Spring, may be the help you need.


The system has been helpful in preparing continuing education for my team.  It helps us with unusual organisms and steering us toward possibilities when people have traveled or reside in other countries.”

Sheryl Stuckey, Manager, Microbiology Lab
Holy Cross Hospital, Silver Spring, Maryland, USA


Accuracy and Efficiency: Challenges of a Busy Clinical Microbiology Lab 

Running a Full-Fledged Lab 

Led by Sheryl Stuckey, the Microbiology lab at the Holy Cross Hospital, Silver Spring, Maryland, has to run with a high level of efficiency. It is usually abuzz with energy from handling a wide range of tasks for the hospital and external agencies. Although the hospital is a community hospital with 450+ beds, it serves patients from all over the world. Even the staff is diverse and represents over 80 countries. But that’s not all. 

Expert in Infectious Diseases and Pathogens 

Sheryl faces an added layer of responsibility – she is the lab tech for clinical microbiology in her hospital, and no one else in her chain of command knows this diagnostic area. Hospitalists (physicians who specialize in treating hospitalized patients) often reach out to Sheryl for help with identifying or confirming a pathogen diagnosis. 

For example, she recently helped a hospitalist identify MERS (Middle East Respiratory Syndrome, also known as ‘camel flu’). While the physician suspected something else, the microbiology lab suggested checking for the patient’s travel history. Says Sheryl, “He hadn’t thought to ask, and when he did, he learned that she had traveled to the Middle East and kissed a camel. Crazy, right?”


Image: GIDEON database MERS worldwide distribution notes. Copyright © GIDEON Informatics, Inc
Image: GIDEON database MERS worldwide distribution notes. Copyright © GIDEON Informatics, Inc


Sentinel Clinical Lab for Biothreat Agents 

The Holy Cross Hospital microbiology lab is also a certified Sentinel Clinical lab to assess suspected agents of bioterrorism, special pathogens, and emerging infectious diseases for their county [1]. The lab packages and ships potential and actual biothreat specimens to the Maryland State Laboratory for special pathogens, surveillance organisms (like COVID-19, Auris, CREs, and more). The lab offers guidance on what specimens to collect and how to collect them safely. The CDC states that Sentinel Laboratories “play a key role in the early detection of biological agents.”  

Partners with Automated Laboratory Team 

The lab is also PPE buddies for their Automated Laboratory Partners for routine testing for potentially infectious pathogens and Person Under Investigation (PUI) for a special pathogen. The PPE buddy system ensures that lab members look out for each other and follow all recommended safety protocols when dealing with infectious (or potentially infectious) pathogens. 

There is little room for error when dealing with infectious diseases, special pathogens, and potential biological threats. Early and accurate detection is critical to prevent or mitigate outbreaks and more widespread devastation.


Using GIDEON for Accurate and Timely Detection of Infectious Diseases and Biological Threats


“I rely on this program because it has everything I need in a pinch.” 

– Sheryl Stuckey


For Microbiology Labs

The Holy Cross Hospital Microbiology Lab appreciates the vast resources that GIDEON offers. GIDEON – the Global Infectious Diseases and Epidemiology Online Network – is a preferred partner for microbiology labs worldwide. 

About GIDEON, Sheryl states, “My favorite features are the organism identification function, information about diseases, comparison of organisms, and now the flowchart function.” She adds, “The system has been helpful in preparing continuing education for my team.  It helps us with unusual organisms and steering us toward possibilities when people have traveled or reside in other countries.”

Designed together with microbiology experts, GIDEON’s lab resources can help:

  • Identify 2000+ pathogens with a few clicks,
  • Generate a ranked pathogen probability list based on Bayesian analysis-based differential analysis,
  • View detailed pathogen outbreak maps, and
  • Elevate training to include dynamic step-by-step decision trees for unknown bacteria projects.


Image: GIDEON microbiology lab diagnosis probability engine and unknown pathogen decision tree. Copyright © GIDEON Informatics, Inc
Image: GIDEON microbiology lab diagnosis probability engine and unknown pathogen decision tree. Copyright © GIDEON Informatics, Inc


For Physicians and Researchers 

An added bonus for hospitals, research hospitals, and teaching institutions is that GIDEON is the most comprehensive database of historical and current infectious disease outbreaks worldwide. Healthcare professionals and researchers can save a lot of time by using the GIDEON one-stop resource for infectious disease and epidemiology research



The GIDEON infectious disease database empowers microbiology labs, hospitals, physicians, and researchers to identify and detect pathogens early and more accurately. 

The platform hosts a wide variety of tools to help busy microbiology labs compare pathogens, analyze the epidemiological impact of patients’ travel histories, use probability engines and decision trees for pathogens and unknown bacteria, mycobacteria, and yeasts.


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[1]  ASM (American Society for Microbiology), “Laboratory Response Network (LRN) Sentinel Level Clinical Laboratory Protocols,” 20 11 2013. [Online]. Available: [Accessed 2021 08 16].

Recent Anthrax Infections: All You Need to Know About the Deadly Bacillus Anthracis


Image: Bacillus anthracis, a gram-positive spore-forming bacteria that causes Anthrax
Image: Bacillus anthracis, a gram-positive spore-forming bacteria that causes Anthrax


written by Chandana Balasubramanian

Trends from past decades can be delightful when they return to inspire today’s music, fashion, and art. However, recently, a dangerous blast from the past reared its ugly head. In early August 2021, China reported a case of the deadly Anthrax pneumonia – its first case after ten years [1]. A few weeks later, local health authorities in another Chinese province discovered nine suspected cases of Anthrax [2]. Around the same time, Russia confirmed a case of Anthrax with a cutaneous infection in a patient involved in butchering cattle meat [3]. 

It’s time to pay more attention to these small outbreaks. 


Anthrax Infections Can Be Serious

While these reported incidents seem to have been related to interactions with domesticated animals, Anthrax has been used as a deadly weapon for more than a hundred years. 

One of the most well-known instances of Anthrax used as a biothreat was in the United States, right after the 9/11 attacks of 2001. Five Americans died, and 17 were severely infected when contaminated letters lined with Anthrax were mailed through the U.S. postal service to senators and members of the media. In response, the Federal Bureau of Investigation or FBI launched ‘Amerithrax’- one of the biggest and most complicated investigations in U.S. history. After conducting more than 10,000 interviews on many continents and collecting over 5,730 environmental samples, they found their suspect. 

Understanding the epidemiology, cross-border transmissions, and the history of this zoonotic pathogen is essential to help encourage safe practices when handling livestock and avert potential threats.


Bacillus Anthracis Infections Are Not Contagious but Serious

Anthrax is caused by the gram-positive bacteria Bacillus Anthracis. The infection is not spread rapidly from person to person through the air like the flu or cold. It can, however, cause severe illness in domestic animals and humans if they interact with infected animals or contaminated animal products. 

The most common natural way people get a Bacillus Anthracis infection is cutaneous, after skin contact with contaminated meat, wool, or leather from infected animals. Cutaneous Anthrax infection can be transferred from one person to another through open lesions. Another form of infection is gastrointestinal Anthrax which is contracted when raw or undercooked contaminated meat is ingested. The most harmful method of Anthrax infection is through inhalation, by breathing in bacterial spores in the air. It is fatal unless treated immediately. 

Inhalation of Bacillus Anthracis spores is not common in nature. Still, this method has been exploited throughout history for bioterrorism purposes. Bacillus Anthracis infections have affected almost every corner of the globe.  

Image: World map of Bacillus Anthracis outbreaks, 1770-2021. Copyright © GIDEON Informatics, Inc.
Image: World map of Bacillus Anthracis outbreaks, 1770-2021. Copyright © GIDEON Informatics, Inc.


Bacillus Anthracis: A Dark History of Bioterrorism

Bacillus Anthracis is effective as a weapon primarily because of its spores. In nature, an infected host sheds the spores on the ground, which then multiply on contact with air. These spores can stay dormant for years, even decades, in the soil waiting for another host [4]. The infection cycle then continues. However, when these microscopic spores can be aerosolized as sprays or powders, they can be released silently and escape detection. Even a small number of spores released in the air can infect massive numbers of people.  

In the United States, the Centers for Disease Control and Prevention (CDC) considers Anthrax as Category A – a Bioterrorism Agent. And indeed, the Bacillus Anthracis has been cultivated and used for bioterrorism from as early as 1915. 

A review of the GIDEON Bioterrorism note for Anthrax shows a long murky past of the pathogen being released by countries during the war, by terrorists to spread fear and destruction, or by accident. 


Image: Snippet of Bacillus Anthracis Bioterrorism Note from GIDEON database. Copyright © GIDEON Informatics, Inc.
Image: Snippet of Bacillus Anthracis Bioterrorism Note from GIDEON database. Copyright © GIDEON Informatics, Inc.


The 2001 U.S. Anthrax incident was more recent. A much larger Anthrax outbreak was an accidental 1979 Anthrax leak. Bacillus Anthracis spores were released from a secret Soviet military research center in Sverdlovsk, Russia. The story has all the intrigue and devastation that is characteristic of the Cold War. 60-70 people are estimated to have died from the accident, now termed the ‘Biological Chernobyl.’ The entire incident and related deaths were covered up and blamed on contaminated meat. It was only almost thirteen years later that a team of expert molecular biologists from Harvard University could investigate the spread of the spores on behalf of the CIA [5]. The team confirmed that aerosolized spores spread through the air and caused the outbreak, not meat. 

WATCH/LISTEN TO PODCAST: Dr. Berger discusses Anthrax infections and the associated bioterrorism history with ‘Outbreaks News’

Symptoms of Bacillus Anthracis Infections

Cutaneous Anthrax Infections

  • Itchy blisters or bumps
  • Painless skin sores that are black in the middle develop after the blisters or bumps 

Gastrointestinal Anthrax Infections

  • Fever and chills
  • Swelling of glands in the neck
  • Sore throat and trouble swallowing
  • Nausea and bloody vomit
  • Headaches
  • Diarrhea 
  • Stomach pain, and more

Inhalation Anthrax or Pulmonary Anthrax Infections

The most deadly but rare form of human anthrax infections. 

  • Fever and chills
  • Difficulty breathing
  • Cough
  • Dizziness 
  • Extreme fatigue
  • Sweats, and more.


This image depicts a man, whose left forearm exhibited a large cutaneous lesion, which had been diagnosed as a case of cutaneous anthrax, caused by the bacterium, Bacillus anthracis. Note the characteristic dark-brown to black-colored eschar that covered the lesion, from which the bacterium derives its name, being that the color resembles that of anthracite coal. The photographed had been captured by Georgian Field Epidemiology Training Program (FETP) resident, Archil Navdarashvili, while at Rustavi Hospital, in the country of Georgia, on August 25, 2012.
Image: This image depicts a man, whose left forearm exhibited a large cutaneous lesion, which had been diagnosed as a case of cutaneous anthrax, caused by the bacterium, Bacillus anthracis. Note the characteristic dark-brown to black-colored eschar that covered the lesion, from which the bacterium derives its name, being that the color resembles that of anthracite coal. The photograph was taken by Georgian Field Epidemiology Training Program (FETP) resident, Archil Navdarashvili, while at Rustavi Hospital, in the country of Georgia, on August 25, 2012.


Mitigating Bacillus Anthracis Infections

Cutaneous anthrax infections comprise the majority of anthrax infections worldwide. They are spread through contact with contaminated animals or animal products. The United States, the U.K., E.U., and many other countries worldwide have implemented better tests and protocols around the way animals are handled. With these processes in place, cutaneous anthrax infections have significantly decreased. 

However, it is extremely easy for anyone to carry an infectious disease endemic to one country and spread it to others. National public health agencies, frontline clinicians, infectious disease specialists, and microbiologists will have to work together to mitigate the effects of dangerous pathogens like the Bacillus Anthracis. Taking epidemiological data into account when diagnosing diseases in Point-of-Care settings can be a great first step towards containing emerging infections. 


Prefer your information in a video format? Here’s a recording of Dr. Berger discussing Anthrax on the ‘Outbreak News’ podcast:


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[1] “China Reports First Human Case of Pulmonary Anthrax in 10 Years,” [Online]. Available: [Accessed: 26-Aug-2021].

[2] Global Times, “Shanxi Province reports 9 suspected anthrax cases, treatment underway,” [Online]. Available: [Accessed: 26-Aug-2021].

[3] Press Release, “Human anthrax case reported in Karabudakhkent region, Russia,”, 10-Aug-2021. [Online]. Available: [Accessed: 26-Aug-2021].

[4] A. Chateau, S. Van der Verren, H. Remaut and A. Fioravanti, “The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance”, Microorganisms, vol. 8, no. 12, p. 1864, 2020. Available: 10.3390/microorganisms8121864 [Accessed 26 August 2021].

[5] “Anthrax at Sverdlovsk, 1979”,, 2017. [Online]. Available: [Accessed: 26- Aug- 2021].

Bacterial Unknown Project: Hundreds of Easy Dichotomous Keys for Microbiology Courses

Bacterial Unknown Project - question mark and bacteria photo in the background
Bacterial Unknown Project. Original Photo by CDC on Unsplash


written by Chandana Balasubramanian

Fast, Online Flowcharts for Bacterial Unknown Projects

GIDEON’s Bacterial Unknown Project allows microbiology professors to make and print dynamic dichotomous keys online. Using hundreds of decision trees, you can help your students identify over 2,000 pathogens with a few clicks of your mouse. That’s right. No more drawing elaborate dichotomous key flowcharts by hand or using a clunky word processing program.

GIDEON (Global Infectious Diseases and Epidemiology Online Network) is one of the most well-known reference databases for infectious diseases and a trusted partner for clinicians and microbiologists worldwide. Together with microbiology professors, GIDEON designed an interactive decision tree tool to help identify bacteria, mycobacteria, and yeasts.

Sample screenshot of GIDEON Bacterial Unknown Project decision tree.
Sample screenshots of GIDEON Bacterial Unknown Project, decision tree.


A review from a satisfied customer:

“I was given 2 weeks to prepare the syllabus for two courses I needed to run in the fall semester, one in Public Health and the other in Pathogenic Microbiology. GIDEON was the perfect tool to build activities and learning around it made my job much easier!”

University of South Florida, Dr. Johnny El-Rady, Instructor (Microbiology and Genetics)


Microbiology professors agree that bacterial unknown projects are the ultimate test of a student’s understanding of pathogens in the classroom. Testing microbiology students with “mystery” bacteria allows them to combine their knowledge of pathogen molecular structures and biochemistry with essential laboratory techniques required to identify them.

However, these professors are also unanimous in accepting that preparing dichotomous keys for each class and semester can take time. As a result, students may attempt these active learning tests to identify microbes only once or twice in a semester.


Why Do Students Need to Identify Unknown Bacteria?

Learning through the Bacterial Unknown Project is a great way for microbiology students to get ready for the real world. After all, professionals in the laboratory are counted upon to identify or confirm the presence of pathogens. This expertise is essential whether in a hospital, clinic, or academic research lab. Working knowledge of fundamental laboratory techniques, conducting aseptic transfers, preparing media, and following a systematic flowchart to perform differential testing are invaluable skills.

For example, studying pathogens for further research involves isolating and developing pure colonies to study. This step is critical to make sure the result of further testing is accurate, but new students may find this step difficult and need to practice. This is relevant even though labs are getting more automated than before. To be a professional writer, you have to know the basics of grammar and not rely entirely on auto-correct. Professional musicians need to understand how music notes work together in harmony, even if the software is available to help create music.

Knowing how to perform laboratory techniques correctly will help students identify pathogens in imperfect situations and troubleshoot when things go wrong. Bacterial Unknown Projects are also significant learning assignments because students learn to record and organize their data appropriately, work with their peers, and present their reasoning in written reports. These skills are priceless in a professional setting, private or academic, where we are often asked to defend or explain our work to other teams.

However, since 2020, the learning environment across the globe has changed considerably. Microbiology professors have been facing challenges when it comes to administering Bacterial Unknown Projects online.


How to Conduct Bacterial Unknown Projects Online?

The COVID-19 pandemic inserted a bit of a nonsense mutation in the lives of many microbiology professors. With so much uncertainty, lockdowns, and other restrictions, academic instruction went online. Didactic courses were easier to convert into an online format, but how do bacterial unknown projects translate to remote learning? After all, the very point of a bacterial unknown activity is to train students in a hands-on setting for wet lab techniques.

The Department of Molecular Biosciences at the University of Kansas at Lawrence published their experience in the Journal of Microbiology and Biology Education, March 2021. After administering a test to identify an unknown microbe for about 50 students, they conducted a survey and collected anonymous responses. 80% of students surveyed reported the online bacterial unknown project successful in increasing their skills. The project took over three weeks, with the last week to prepare for oral presentations.

Evaluations focused more on effective student collaborations, arriving at the correct result by asking for the right virtual “tests,” peer evaluations, and communicating their findings in an oral presentation instead of a written report. The entire project was done using images of bacterial stains. The paper discusses how delivering bacterial unknown projects online is not a substitute for wet lab experiences but a complementary teaching method.

Tighter budgets for lab equipment and resources means often having to test students on a limited range of bacteria for in-person wet-lab testing. Creating dynamic dichotomous keys online can help students identify pathogens that are important to learn about but may not be possible to administer in a teaching laboratory.


Using GIDEON’s Bacterial Unknown Decision Trees for Laboratory and Remote Learning

GIDEON’s decision trees for bacterial unknown projects are designed with busy microbiology professors in mind.

Create a dichotomous key in just 3 steps:

Step 1: Specify whether you want to identify a bacteria, mycobacteria, or yeast.

Step 2: If identifying bacteria, select the gram reaction, bacterial shape, respiration, and other laboratory tests by following the intuitive flowchart.

Step 3: Print your key, or export and share with your peers. It’s that simple.

The example below shows the flowchart for Bacillus Subtilis. On the right, you also get a list of the most probable bacteria based on your selections.


Dichotomous key for Bacillus Subtilis. Screenshot from GIDEON's Bacterial Unknown Decision Tree.
Dichotomous key for Bacillus Subtilis. Screenshot from GIDEON’s Bacterial Unknown Decision Tree.



Bacterial Unknown Project is considered to be one of the most effective ways to learn microbiology. Students apply their theoretical knowledge of molecular structure, biochemistry, and lab techniques in a practical wet lab setting. However, the process of preparing dichotomous keys for each test is cumbersome. Microbiology professors who are pressed for time find it challenging to draw decision trees by hand or use a word processing program.

Additionally, when the COVID-19 pandemic began, remote learning became the new normal. While adapting all courses to an online format can be hard, making Bacterial Unknown Project applicable for remote learning is much trickier. Dynamic, online flowcharts and decision trees can help microbiology professors teach their students more effectively in online and wet laboratory settings.


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Misdiagnosing Legionellosis or Legionnaires’ Disease Can Be Fatal. But Why Is It Still Common?

Yellow water is poured from the tap into the glass: standard Legionellosis testing procedure

by Chandana Balasubramanian

Pathogen of the month: Legionella

Doubt strikes fear into the hearts of many. But it is a powerful tool in the hands of medical professionals and researchers. Being uncertain is the impetus that drives truth-seeking peer-to-peer verification and differential diagnoses that can help save lives.

Take Legionnaires’ disease. It is one of the leading causes of pneumonia worldwide [1]. If left untreated without the right antibiotics, it can be fatal. In the United States alone, the economic burden of just one year of Legionnaires’ disease cases can be over 800 million US dollars [2].

Surprisingly, it is often overlooked. So much so that even the World Health Organization or WHO states, “Since many countries lack appropriate methods of diagnosing the infection or sufficient surveillance systems, the rate of occurrence is unknown. In Europe, Australia, and the USA, there are about 10–15 cases detected per million population per year [1].”

A great place to begin addressing these challenges is if clinicians are willing to embrace doubt when faced with diagnosing pneumonia-like symptoms.

What causes Legionnaires’ Disease or Legionellosis?

There were many historical events in 1976. NASA unveiled their first space shuttle, Apple Computers was born, and the first Rocky movie was released. Unfortunately, it was also the year a tragic event led to the discovery of Legionnaires’ disease.

On July 21st, 1976, 4000 delegates from the American Legion, America’s largest veterans’ service organization, traveled to Philadelphia for a convention. Within a few weeks, almost 200 got sick with an upper respiratory illness, and 29 died. It took nearly five months of investigations to identify the pathogen – Legionella – as the cause [3].

Legionnaires’ disease or Legionellosis is caused by the bacteria Legionella. It lives in water and soil and can cause health issues when it grows in showerheads and faucets, hot tubs, and in stagnant water and air conditioning systems in large buildings. We are susceptible to infection by Legionella when we inhale water droplets with the bacteria in it or come in contact with contaminated soil. Legionellosis is not spread through direct human-to-human transmission. It has an incubation period of 2 to 10 days.

Legionella is widely found in warm water environments, so most cases of Legionnaires’ occur in the summer and early autumn. Legionnaires’ is a public health issue. Cassell et al. caution that utmost care must be taken when COVID-19 restrictions are lifted worldwide. Going back to work or school in buildings left unoccupied or unused during lockdowns is a risk factor for Legionellosis [4]. 

Paterna, Valencia, Spain: 03.05.2020; The legionella training
Paterna, Valencia, Spain, 2020; The Legionella training


Why is Legionnaires’ Disease often misdiagnosed or overlooked?

According to Reller et al. [5], a wrong Legionellosis diagnosis is often due to:

  1.     The inability to distinguish Legionnaires’ disease from other types of pneumonia, clinically and radiographically,
  2.     Failure to order diagnostic tests for Legionella infection, and
  3.     Inadequacies in current diagnostic tests and protocols.

The majority of Legionnaires’ disease cases each year remain undiagnosed; the world still awaits better diagnostic tests and protocols for Legionellosis. But the issue of “failure to order diagnostic tests for Legionella infections” can be fixed. The Urine Antigen Test (UAT) and sputum tests prescribed for Legionella are inexpensive, so cost is not the issue.

The solution lies in training medical professionals to embrace doubt and challenge their confirmation biases. Clinicians who take a few minutes to input a patient’s pneumonia and accompanying symptoms on a robust, clinical decision support tool like GIDEON (Global Infectious Diseases and Epidemiology Network) can better understand how to proceed

For example, when the COVID-19 pandemic hit, experts cautioned clinicians to be on the alert for Legionellosis as well. The concern was that clinicians might repeatedly be testing community-acquired pneumonia patients for COVID-19 but not Legionellosis – which would delay diagnosis and treatment. Since initial clinical presentations for the two are similar, clinical decision tools can be extremely useful.

GIDEON, for example, has a built-in feature to help clinicians challenge their confirmation biases. A ‘Why Not?’ feature helps clinicians understand why a specific diagnosis does not show up on the list of probable causes of a patient’s symptoms.

Legionnaires’ disease, misdiagnosed as Malaria, can be fatal because malarial drugs do not work against Legionella. It is even more critical to get the right diagnosis early. 


Legionellosis Misdiagnosed as Malaria

Take the example of the agricultural expert from Israel wrongly diagnosed with malaria instead of Legionellosis. He had traveled to India to work on a farming project in 2005. A week later, when he returned to Israel, he developed fever, headache, vomiting, and muscle pain. In two days, he felt better, but the symptoms reappeared but with cough, shortness of breath, and rigors in tow. The patient was highly lethargic, hypotensive, and blood tests showed elevated bilirubin and creatinine levels.

Because of his recent travel to India, doctors thought it was Malaria. He was started on malarial medication while laboratory tests were being processed. But when blood smears proved negative for Malaria, his doctors wondered if it was Dengue.

Luckily for him, his doctors decided to challenge their cognitive biases and conducted a differential diagnosis. They entered the patient’s symptoms in the popular DDx or differential diagnosis tool, GIDEON. To their surprise, neither Malaria nor Dengue showed up as possibilities. But given the symptoms and the incubation period, Legionellosis turned out to be the prime (and accurate) suspect. This saved his life because standard malarial therapy does not work against Legionellosis.

Legionellosis diagnosis on GIDEON application - two devices


Misdiagnosing Legionnaires’ disease can be fatal, lead to a public health crisis, and add hundreds of millions to an already astronomically high healthcare burden. One of the main reasons it is often overlooked is that clinicians may not think about testing for Legionellosis when treating a patient with pneumonia.

Equipping clinicians with the right clinical diagnosis tools can help them validate their assumptions. Not only that, using a tool like GIDEON, clinicians can also challenge their confirmation biases and learn why a diagnosis does not apply to a specific set of symptoms.

Getting to the correct answer starts with harboring and encouraging healthy doubt in initial diagnoses. As the famous philosopher, Voltaire said, “Doubt is not a pleasant condition, but certainty is absurd.”


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[1] WHO, World Health Organization, “Fact Sheet: Legionellosis,” WHO, February 16th, 2018. [Online]. Available: [Accessed 08 07 2021].
[2] K. R. C. E. a. S. C. M. Baker-Goering, “Economic Burden of Legionnaires’ Disease, United States, 2014,” Emerg Infect Dis., vol. 27, no. 1, pp. 255-257, 2021.
[3] J. E. M. e. al., “Legionnaires’ disease: Isolation of a bacterium and demonstration of its role in other respiratory diseases,” N. Engl. J. Med., vol. 297, no. 22, pp. 1197-1203, 1977.
[4] K. Cassell, “Legionnaires’ disease in the time of COVID-19,” Pneumonia, vol. 13, 2021.
[5] L. R. e. al., “Diagnosis of Legionella Infection,” Clinical Infectious Diseases, vol. 36, no. 1, pp. 64-69, 2003.

Pathogen of the month: Mycobacterium tuberculosis

Mycobacterium tuberculosis (M. tuberculosis), a non-motile, obligately aerobic, intracellular bacterium known to cause Tuberculosis (TB), was discovered by Robert Koch in 1882 [1]. TB primarily affects the lungs along with the abdomen, bones, nervous system, reproductive system, liver, and lymph glands [2].

Pulmonary Tuberculosis ( TB ) : Chest x-ray show alveolar infiltration at both lung due to mycobacterium tuberculosis infectio
Pulmonary Tuberculosis ( TB ): Chest x-ray shows alveolar infiltration at both lungs due to Mycobacterium tuberculosis infection


Global Burden of Tuberculosis

The World Health Organization (WHO) has reported a 22% decrease in TB-related mortality between 2000-2015, with a gradual 1.5% decrease in the annual rate. However, despite this trend and successful control of disease transmission, TB continues to have a significantly higher rate of morbidity. In 2015, six countries (China, India, Nigeria, Pakistan, Indonesia, and South Africa) accounted for 60% of TB-related deaths [3].


Global cases of Tuberculosis between 1965-2019

Worldwide Tuberculosis cases and rates, 1965 - today


Pathogenicity of Mycobacterium tuberculosis

Mycobacterium tuberculosis is transmitted in the form of droplet nuclei exhaled by individuals affected with laryngeal/pulmonary TB. It enters the body via the nasal cavity/mouth and travels to the alveoli of the lungs, where it recruits macrophages to the lung surface, in turn transporting the bacteria to the deeper tissues [4]. Another round of macrophage recruitment to the originally infected locus forms an organized aggregate of differentiated macrophages and immune cells called a granuloma. The infected granuloma undergoes necrosis, promoting bacterial growth and transmission to the next host [5].

Diagnosis of TB

Some patients with TB may present with non-specific findings such as anemia, weight loss, fever of unknown origin, and fatigue; while others may be asymptomatic and show no abnormalities on physical examination [6]. Thus, the physician should collect body fluids/tissues for Acid-Fast bacilli (AFB) smear and culture.  Only a positive culture can confirm the diagnosis of TB.

Confirmatory and diagnostic tests for TB:

– Culture, followed by Ziehl-Neelsen (AFB) staining

– A Chest X-ray to confirm the diagnosis in case of positive culture, indicating active disease

– Gene-based tests and nuclear amplification to identify the bacterial strains using DNA-based molecular techniques, such as GeneXpert [7].


Ziehl-Neelsen staining

AFB staining is the traditional method of TB diagnosis, as it is inexpensive and provides rapid results [8]. Mycobacterium species retain dyes when heated and treated with acidified organic compounds. The most common acid-fast staining method for M. tuberculosis is the Ziehl-Neelsen stain method, in which a specimen is fixed, stained with carbol-fuchsin dye, and decolorized with an acid-alcohol mixture. After counter-staining the smear with methylene blue or a similar dye, AFB appear red against a contrasting blue background [9].  In general, a sputum sample must contain at least 10,000 organisms/mL to visualize these bacteria at 100x magnification. 

Symptoms and ways of infection of tuberculosis. Medical vector infographics, poster

Latent TB vs. Active TB

Latent TB represents the condition where the body’s immune system restricts the growth of M. tuberculosis bacterium, making the individual appear asymptomatic [10].

An individual with latent TB infection shows

– no symptoms.

– is not infectious (cannot spread TB).

– tests positive for TB blood/skin tests.

– may eventually develop active TB if the immune system weakens.

Active TB represents a condition where the body’s immune system is unable to restrict the growth of M. tuberculosis, rendering patients both ill and contagious. 

The symptoms of TB depend on the affected area.

a. General symptoms include:

  1. Night sweats
  2. Weight loss
  3. Prolonged fever
  4. Loss of appetite
  5. Fatigue

b. Symptoms of Pulmonary TB (infected lungs):

  1. Shortness of breath, which progressively worsens
  2. A persistent cough that produces phlegm and sometimes blood, persisting  > 3 weeks. 

c. Symptoms in the case when other areas of the body are infected:

  1. Swellings in the neck or other regions
  2. Pain in a joint or affected bone
  3. Abdominal pain
  4. Headache
  5. Confusion
  6. Seizures



According to the World Health Organization (WHO), first-line treatment for TB may include combinations of five essential drugs: Rifampicin (R), Isoniazid (H), Pyrazinamide (Z), Ethambutol (E), and Streptomycin (S) [11].  Patients with TB undergo a standardized treatment for 6 to 9 months, including an initial two-month course of Rifampicin, Isoniazid, Pyrazinamide, and Ethambutol, followed by another 4-month course of Isoniazid and Rifampicin [12].

For patients with Multi Drug-Resistant Tuberculosis (MDR-TB), directly-observed therapy (DOT) is used. In DOT, drugs are administered at least six days/week under the direct observation of the physician [13, 14]

BCG vaccine

Bacillus Calmette-Guerin (BCG), a vaccine for TB, was introduced in 1921 to control tuberculosis in humans. It is administered at birth, primarily in regions with a high disease burden, such as India, South Africa, and Pakistan [15]. Widespread immunization using BCG vaccine has facilitated a reduction in TB cases globally [16].


Risk factors

Five-to-ten percent of people with latent TB who do not receive appropriate treatment will eventually develop active TB disease [17]

Individuals at a higher risk of contracting TB include:

– Those who have traveled to or are living in a country with a high prevalence of TB. 

– Those living in crowded conditions

– Those who have been in close contact with a person infected with TB

– Children ages <= 5 years who have tested positive for TB

– People who reside or work with persons at high risk for TB, such as those in hospitals, correctional facilities, homeless shelters, residential homes for HIV-infected individuals, and nursing homes

Additionally, immune dysfunction associated with diabetes mellitus, HIV infection, cancer chemotherapy, malnutrition, and advanced age is associated with an increased risk of contracting TB. 

Additional conditions associated with high risk for tuberculosis include silicosis, substance abuse, malignancy, organ transplantation, corticosteroid therapy, Crohn’s disease, and rheumatoid arthritis.

Tuberculosis and HIV

Co-infection by TB and HIV places a diagnostic and therapeutic burden on the health care system. HIV infection has been shown to increase the risk of reactivation of latent TB by 20-fold. [18].


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  1.     K. R, Die Aetiologie der Tuberculose [The aetiology of Tuberculosis.], Berlin: Berliner Klinische Wochenschrift, 1882.
  2. F. K. Dye C, Disease Control Priorities in Developing Countries, New York:: Oxford University Press, 2006.
  3. Z. J. B. Q. H. H. B. L. Y. J. L. Q. L. J. Pan Z, “The Gap Between Global Tuberculosis Incidence and the First Milestone of the WHO End Tuberculosis Strategy: An Analysis Based on the Global Burden of Disease 2017 Database.,” 2020.
  4. CDC, How TB Spreads, CDC, 2016.
  5. G. M. J. Jr., “Microbial pathogenesis of Mycobacterium Tuberculosis: dawn of a discipline,” Cell, no. 104, pp. 477-485, 2001.
  6. J. D. E, Mycobacterial diseases of the lung and bronchial tree: Clinical and laboratory aspects of Tuberculosis, Boston: Brown and Company, 1974.
  7. [Online]. Available:
  8. B. J. R. Elizabeth A. Talbot, Molecular Medical Microbiology, 2015.
  9. R. l. Kradin, Diagnostic Pathology of Infectious Disease, 2018.
  10. World Health Organization, Guidelines on the management of latent Tuberculosis infection, Geneva: WHO, 2015.
  11. World Health Organization, Implementing the WHO Stop TB Strategy: A Handbook for National Tuberculosis Control Programmes.
  12. Gideononline, “,” Gideon, 2021. [Online]. Available:
  13. A. F. Z. L. F. E. Terracciano E, [Tuberculosis: an ever present disease but difficult to prevent], Ig Sanita, 2020.
  14. M.-R. K. R. R. C. R. Chaulk CP, Eleven years of community-based directly observed therapy for Tuberculosis, JAMA, 1995.
  15. “,” [Online]. Available:
  16. Z. a. Lancione, “Using data science to improve knowledge around a century old vaccine,” The BCG Atlas, 2020.
  17. CDC. [Online]. Available:
  18. G. C. G. R. N. P. Getahun H, “HIV infection-associated Tuberculosis: the epidemiology and the response,” Pubmed, 2010.

Pathogen of the Month: Vibrio cholerae, the Causative Agent of Cholera

Vibrio cholerae
This blog was written by Dr. Jaclynn Moskow


Vibrio cholerae (V. cholerae) is a species of Gram-negative facultatively anaerobic bacteria of curved rod-shaped with single polar flagella. V. Cholerae has been classified into approximately 200 serogroups. Strains belonging to serogroups O1 and O139 cause the vast majority of cholera cases (1).

Vibrio cholerae is found naturally in brackish riverine, estuarine, and coastal waters. Recognized hosts of the organism include algae, shellfish, chironomid egg masses, fish, waterfowl, amebae, and copepods (2). V. cholerae colonies can form biofilms on both biotic and abiotic surfaces – including on shells, zooplankton, macroalgae, ship hulls, and plastic pollution (3-5). 


Cholera Transmission and Disease Severity 

Cholera is primarily transmitted through the consumption of fecally contaminated water and food. Foodborne outbreaks are most frequently linked to fish, shellfish, crabs, oysters, clams, rice, millet gruel, and vegetables (6).

Most V. cholerae infections are asymptomatic or mild in nature. Individuals with asymptomatic infections may still shed bacteria in their feces and infect others (7). Approximately 10% of V. cholerae infections will progress to severe disease (8). In endemic settings, the most severe infections occur in children, while in epidemic settings, severe disease occurs in adults as frequently as it does in children (9). 

Individuals with blood type O are more likely to suffer from severe V. cholerae infection (10). The use of drugs that reduce stomach acid, such as antacids, histamine receptor blockers, and proton pump inhibitors, also increases the risk of severe infection (11). 


Vibrio cholerae bacteria on agar
Vibrio cholerae isolated from feces obtained from a patient with profuse diarrhea who had traveled to India. Photo courtesy of Nathan Reading



Signs and Symptoms of Cholera

Cholera has an average incubation period of 1-5 days. Patients will experience a sudden onset of painless, watery diarrhea that may be accompanied by vomiting. The diarrhea is often characterized as having a “rice water” appearance and fishy odor. Fever is uncommon in adults, but often present in children (12).

In severe cases, dehydration may lead to the rapid progression to acidosis and electrolyte imbalance. Coma may occur. Without the replacement of fluids and electrolytes, hypovolemic shock and death ensue (12).

If left untreated, cholera has a 25-50% mortality rate. Proper treatment reduces the mortality rate to less than 1% (13).

Cholera vector illustration. Labeled infection structure and symptoms scheme. Educational infographic with unsafe water and food vibrio microorganism that causes diarrhea, vomiting and dehydration.

Diagnosis and Treatment of Cholera

Cholera is diagnosed via stool culture. When a case is suspected, healthcare and medical laboratory personnel should follow stool precautions.

Mild and moderate cases of cholera can be successfully treated with oral rehydration salts, while severe cases require rehydration with intravenous fluids (14). The World Health Organization (WHO) recommends reserving antibiotics as a treatment for severe cases only, as antibiotic use has no proven effect on controlling the spread of the disease and may contribute to antimicrobial resistance (15). In severe cases, tetracycline, doxycycline, azithromycin, erythromycin, or ciprofloxacin may be used (12). Most people who recover from V. cholerae infection incur long-lasting immunity (16).


Cholera Prevalence

Cholera originated in India and spread across the world during the 19th century (17). Since that time, there have been seven cholera pandemics, including one that is ongoing today (18). 

Currently, approximately 1.3 billion people are at risk for cholera in endemic countries. An estimated 2.86 million cholera cases occur annually, resulting in an estimated 95,000 deaths (19).

Over the last decade, the countries reporting the most cases of cholera have included Yemen, Somalia, the Democratic Republic of Congo, Mozambique, Bangladesh, and Haiti. If you have a GIDEON account, click here to explore the Cholera outbreak map. Cholera is exceedingly rare in Europe and the United States.


Cholera cases by region, 1953 – 2018



Cholera Prevention

Cholera cases by region, 1953 - 2018

When traveling to an area where cholera is endemic, precautions should include adherence to proper hand hygiene, drinking only bottled water, and avoiding uncooked food.

Ongoing worldwide efforts to end the current cholera pandemic center on increasing access to clean water and sanitation and expanding accessibility to existing cholera vaccines.


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(1) Morris, “Infections due to non-O1/O139 Vibrio cholerae”,, 2019. [Online]. Available:

(2) “Cholera: Environmental Reservoirs and Impact on Disease Transmission”, One Health, pp. 149-165, 2014. Available: 10.1128/microbiolspec.oh-0003-2012

(3) B. Wucher, T. Bartlett, M. Hoyos, K. Papenfort, A. Persat and C. Nadell, “Vibrio cholerae filamentation promotes chitin surface attachment at the expense of competition in biofilms”, Proceedings of the National Academy of Sciences, vol. 116, no. 28, pp. 14216-14221, 2019. Available: 10.1073/pnas.1819016116

(4) C. Lutz, M. Erken, P. Noorian, S. Sun and D. McDougald, “Environmental reservoirs and mechanisms of persistence of Vibrio cholerae”, Frontiers in Microbiology, vol. 4, 2013. Available: 10.3389/fmicb.2013.00375 

(5) J. Moskow, “What Do Plastics Have To Do With Infectious Diseases and the Immune System?”, GIDEON Informatics, Inc, 2021. [Online]. Available: 

(6) G. Rabbani, W. Greenough. “Food as a vehicle of transmission of cholera”, J Diarrhoeal Dis Res, vol. 17, no. 1, pp. 1-9, 1999

(7) J. Lewnard, M. Antillón, G. Gonsalves, A. Miller, A. Ko and V. Pitzer, “Strategies to Prevent Cholera Introduction during International Personnel Deployments: A Computational Modeling Analysis Based on the 2010 Haiti Outbreak”, PLOS Medicine, vol. 13, no. 1, p. e1001947, 2016. Available: 10.1371/journal.pmed.1001947

(8) Cholera – Vibrio cholerae infection: General Information”, Centers for Disease Control and Prevention (CDC0, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Division of Foodborne, Waterborne, and Environmental Diseases (DFWED), 2020. [Online] Available:

(9) J. Harris, R. LaRocque, F. Qadri, E. Ryan and S. Calderwood, “Cholera”, The Lancet, vol. 379, no. 9835, pp. 2466-2476, 2012. Available: 10.1016/s0140-6736(12)60436-x

(10) J. Harris and R. LaRocque, “Cholera and ABO Blood Group: Understanding an Ancient Association”, The American Journal of Tropical Medicine and Hygiene, vol. 95, no. 2, pp. 263-264, 2016. Available: 10.4269/ajtmh.16-0440

(11) S. Handa, “Which classes of medications increase the risk of cholera infection?”,, 2018. [Online]. Available: 

(12) “Cholera”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(13) J. Fournier and M. Quilici, “Choléra”, La Presse Médicale, vol. 36, no. 4, pp. 727-739, 2007. Available: 10.1016/j.lpm.2006.11.029 

(14) “WHO | WHO position paper on Oral Rehydration Salts to reduce mortality from cholera”,, 2021. [Online]. Available:

(15) “Cholera”,, 2021. [Online]. Available: 

(16) J. Harris, “Cholera: Immunity and Prospects in Vaccine Development”, The Journal of Infectious Diseases, vol. 218, no. 3, pp. S141-S146, 2018. Available: 10.1093/infdis/jiy414

(17) D. Lippi, E. Gotuzzo and S. Caini, “Cholera”, Paleomicrobiology of Humans, pp. 173-180, 2016. Available: 10.1128/microbiolspec.poh-0012-2015 

(18) S. Handa, “What are the 7 pandemics of cholera”,, 2018. [Online]. Available:

(19) M. Ali, A. Nelson, A. Lopez and D. Sack, “Updated Global Burden of Cholera in Endemic Countries”, PLOS Neglected Tropical Diseases, vol. 9, no. 6, p. e0003832, 2015. Available: 10.1371/journal.pntd.0003832

Pathogen of the month: Staphylococcus aureus

by Dr. Jaclynn Moskow

Staphylococcus aureus, 20,000X magnification
Staphylococcus aureus, 20,000X magnification. Courtesy of Frank DeLeo, NIAID


Staphylococcus aureus (S. aureus) is a facultative anaerobic, gram-positive coccus. S. aureus is part of the normal flora of the body, found in the skin, upper respiratory tract, gut, and genitourinary tract – and most commonly in the anterior nares. Twenty percent of individuals are persistent nasal carriers of S. aureus, and an additional thirty percent are intermittent carriers (1).

Under certain conditions, S. aureus can be pathogenic, causing a variety of infections, including skin conditions, pneumonia, gastroenteritis, endocarditis, osteomyelitis, septic arthritis, meningitis, bacteremia, and sepsis. Individuals at increased risk include patients with diabetes, cancer, HIV/AIDS, and other conditions that compromise the immune system. Intravenous drug users may introduce the bacteria into various tissues and/or the bloodstream. Hospitalization is in itself a risk factor for S. aureus infection.


Staphylococcus Aureus Skin infections

S. aureus can cause a diverse array of skin infections, including folliculitis, impetigo, furuncles, carbuncles, cellulitis, and abscesses. S. aureus is the most common cause of skin infection in individuals with eczema, and many presumed cases of “eczema” are, in fact, inflammatory reactions to colonization by S. aureus (2). 

S. aureus is the most common agent of surgical site infections (3), and a common cause of infection in burn patients. Animal bites, including bites from dogs and cats, can also lead to S. aureus skin infections.

Staphylococcal scalded skin syndrome, also known as “Ritter’s disease”, is caused by exotoxin-producing strains of S. aureus – and is characterized by diffuse erythematous cellulitis followed by extensive skin exfoliation (4). Fever is common, and patients are most often neonates, children, immunocompromised individuals, and individuals with severe renal disease. It is thought that the latter are at an increased risk due to a decreased ability to excrete the exotoxins in urine (5). Healthy adults rarely develop the syndrome, as a result of having antibodies to the exotoxins. Staphylococcal scalded skin syndrome is intraepidermal. Necrosis of the full epidermal layer may also occur as a result of S. aureus infection and is known as toxic epidermal necrolysis – a more severe form of the disease.

Various topical and systemic antibiotics can be used to treat S. aureus skin infections including beta-lactams, macrolides, and aminoglycosides. Treatment may be complicated by antibiotic resistance.


Staphylococcus Aureus Pneumonia 

S. aureus is identified in three percent of community-acquired bacterial pneumonias (6), and 18% of hospital-acquired pneumonias (7). S. aureus is a cause of secondary bacterial pneumonia associated with influenza, and influenza has been shown to increase the adherence of S. aureus to host cells (8). One study showed that 33% of children admitted to the PICU during the 2009 H1N1 pandemic had a secondary bacterial coinfection, with S. aureus being the most common pathogen (9). S. aureus is also frequently isolated from the respiratory tract of children with cystic fibrosis (10).


Doctor examining a lung radiography
Staphylococcus aureus is one of the etiological agents of bacterial pneumonia


S.aureus can cause necrotizing pneumonia, characterized by necrosis, liquefaction, and cavitation of the lung parenchyma (11) – often accompanied by empyema and bronchopleural fistulae. Necrotizing pneumonia caused by community-acquired methicillin-resistant S. aureus (MRSA) strains which produce Panton valentine leukocidin (PVL) toxin has a mortality rate of 60% (12).

Treatment of pneumonia caused by S. aureus is based on testing for antibiotic susceptibility. Nafcillin, oxacillin, and cefazolin are often used to treat methicillin-sensitive S. aureus (MSSA), while vancomycin or linezolid is often used to treat MRSA (13).


Food Poisoning From Staphylococcus Aureus 

S.aureus is one of the most common causes of food-borne disease worldwide (14). Illness is characterized by a short incubation period (2h-4h), nausea, vomiting, intestinal cramping, and profuse watery, non-bloody diarrhea (15). The condition is generally self-limited, and symptoms typically resolve within 12 to 24 hours.


Staphylococcal food poisoning, outbreak-related cases and rates in the United States, 1952 – 2010

Toxic Shock Syndrome From Staphylococcus Aureus

S.aureus is the most common cause of toxic shock syndrome, a life-threatening syndrome resulting from staphylococcal toxin-1 (TSST-1). It is characterized by fever, hypotension, myalgia, macular erythema, desquamation (particularly of the palms and soles), and acute vomiting or diarrhea (16). Most cases are associated with the use of “super absorbent” tampons or staphylococcal wound infection. Case fatality rates of 5 to 10% are reported. The condition is generally treated with vancomycin in combination with clindamycin.


Staphylococcus Aureus Endocarditis

S.aureus is the leading cause of acute bacterial endocarditis. Of infections caused by S. aureus, endocarditis accounts for the highest mortality rates (17). Populations at high risk include IV drug users and patients with implanted medical devices such as prosthetic heart valves, grafts, pacemakers, and hemodialysis catheters (18). Treatment varies and depends on several factors, including antibiotic susceptibility, site of infection (left side versus right side), IV drug abuse status, and if a prosthetic valve is present (19).


Other Infections Caused By Staphylococcus Aureus

Staphylococcus aureus can also cause mastitis, urinary tract infections, osteomyelitis, meningitis, septic arthritis, and many infections associated with medical devices and implants.


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(1) Wertheim HF, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, Nouwen JL. The role of nasal carriage in Staphylococcus aureus infections. Lancet Infect Dis. 2005 Dec;5(12):751-62. doi: 10.1016/S1473-3099(05)70295-4.

(2) Nakamura Y, Oscherwitz J, Cease KB, Chan SM, Muñoz-Planillo R, Hasegawa M, Villaruz AE, Cheung GY, McGavin MJ, Travers JB, Otto M, Inohara N, Núñez G. Staphylococcus δ-toxin induces allergic skin disease by activating mast cells. Nature. 2013 Nov 21;503(7476):397-401. doi: 10.1038/nature12655. 

(3) Mellinghoff SC, Vehreschild JJ, Liss BJ, Cornely OA. Epidemiology of Surgical Site Infections With Staphylococcus aureus in Europe: Protocol for a Retrospective, Multicenter Study. JMIR Res Protoc. 2018 Mar 12;7(3):e63. doi: 10.2196/resprot.8177.

(4) “Staphylococcal scalded skin syndrome”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(5) Ross A, Shoff HW. Staphylococcal Scalded Skin Syndrome. 2020 Oct 27. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan–. 

(6) Hageman JC, Uyeki TM, Francis JS, Jernigan DB, Wheeler JG, Bridges CB, Barenkamp SJ, Sievert DM, Srinivasan A, Doherty MC, McDougal LK, Killgore GE, Lopatin UA, Coffman R, MacDonald JK, McAllister SK, Fosheim GE, Patel JB, McDonald LC. Severe community-acquired pneumonia due to Staphylococcus aureus, 2003-04 influenza season. Emerg Infect Dis. 2006 Jun;12(6):894-9. doi: 10.3201/eid1206.051141.

(7) Kollef MH, Micek ST. Staphylococcus aureus pneumonia: a “superbug” infection in community and hospital settings. Chest. 2005 Sep;128(3):1093-7. doi: 10.1378/chest.128.3.1093.

(8) Morris DE, Cleary DW, Clarke SC. Secondary Bacterial Infections Associated with Influenza Pandemics. Front Microbiol. 2017 Jun 23;8:1041. doi: 10.3389/fmicb.2017.01041.

(9) Randolph AG, Vaughn F, Sullivan R, Rubinson L, Thompson BT, Yoon G, Smoot E, Rice TW, Loftis LL, Helfaer M, Doctor A, Paden M, Flori H, Babbitt C, Graciano AL, Gedeit R, Sanders RC, Giuliano JS, Zimmerman J, Uyeki TM; Pediatric Acute Lung Injury and Sepsis Investigator’s Network and the National Heart, Lung, and Blood Institute ARDS Clinical Trials Network. Critically ill children during the 2009-2010 influenza pandemic in the United States. Pediatrics. 2011 Dec;128(6):e1450-8. doi: 10.1542/peds.2011-0774.

(10) Hurley MN. Staphylococcus aureus in cystic fibrosis: problem bug or an innocent bystander? Breathe (Sheff). 2018 Jun;14(2):87-90. doi: 10.1183/20734735.014718.

(11) Nicolaou EV, Bartlett AH. Necrotizing Pneumonia. Pediatr Ann. 2017 Feb 1;46(2):e65-e68. doi: 10.3928/19382359-20170120-02.

(12) Gillet Y, Vanhems P, Lina G, Bes M, Vandenesch F, Floret D, Etienne J. Factors predicting mortality in necrotizing community-acquired pneumonia caused by Staphylococcus aureus containing Panton-Valentine leukocidin. Clin Infect Dis. 2007 Aug 1;45(3):315-21. doi: 10.1086/519263.

(13) Clark SB, Hicks MA. Staphylococcal Pneumonia. 2020 Oct 1. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan–. 

(14) Kadariya J, Smith TC, Thapaliya D. Staphylococcus aureus and staphylococcal food-borne disease: an ongoing challenge in public health. Biomed Res Int. 2014;2014:827965. doi: 10.1155/2014/827965.

(15) “Staphylococcal food poisoning”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(16) “Toxic shock syndrome”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(17) Fernández Guerrero ML, González López JJ, Goyenechea A, Fraile J, de Górgolas M. Endocarditis caused by Staphylococcus aureus: A reappraisal of the epidemiologic, clinical, and pathologic manifestations with analysis of factors determining outcome. Medicine (Baltimore). 2009 Jan;88(1):1-22. doi: 10.1097/MD.0b013e318194da65.

(18) Fowler VG Jr, Miro JM, Hoen B, Cabell CH, Abrutyn E, Rubinstein E, Corey GR, Spelman D, Bradley SF, Barsic B, Pappas PA, Anstrom KJ, Wray D, Fortes CQ, Anguera I, Athan E, Jones P, van der Meer JT, Elliott TS, Levine DP, Bayer AS; ICE Investigators. Staphylococcus aureus endocarditis: a consequence of medical progress. JAMA. 2005 Jun 22;293(24):3012-21. doi: 10.1001/jama.293.24.3012. 

(19) Bille J. Medical treatment of staphylococcal infective endocarditis. Eur Heart J. 1995 Apr;16 Suppl B:80-3. doi: 10.1093/eurheartj/16.suppl_b.80.

What Do Plastics Have To Do With Infectious Diseases and the Immune System?

by Dr. Jaclynn Moskow

Plastic bottles and microplastics floating in the open ocean


Most people are aware that plastics are harmful to the environment. They pollute soil, air, and water and disrupt our ecosystems. Few people, however, are aware of the influence plastics may have on the spread of infectious diseases and on the function of our immune systems.

In recognition of Earth Day 2021, we will examine the ways in which polluting our planet with plastics may affect human health.


Plastics as a Breeding Ground for Pathogens

Microbes struggle to survive on certain surfaces, and thrive on others. Copper, for example, has anti-microbial properties (1); while plastic keeps some microbes alive longer than other common materials.

Influenza A and B viruses survive for longer periods on plastic surfaces than on cloth or paper (2). SARS-CoV-2 has been shown to survive longer on plastic than on glass, stainless steel, pigskin, cardboard, banknotes, cotton, wood, paper, tissue, or copper (3). Indeed, bacteria – and not only viruses – favor plastic. Methicillin-resistant Staphylococcus aureus (MRSA), for example, survives longer on plastic than on wood, glass, or cloth (4). There is thus concern for plastics serving as fomites, especially in high-risk settings such as hospitals.

But what about the plastics polluting our oceans? Are these free from pathogens? There are actually such complex microbial communities found on the plastics in our ocean that the term “plastisphere” was coined (5). A 2019 study examined the plastisphere of plastic nurdles from five European beaches (6). Escherichia coli (E. coli) and Vibrio spp. were found colonizing nurdles from all beaches examined. Vibrio spp. occur naturally in seawater, and researchers have speculated that fecally-contaminated water was likely the original source of the E. coli.


Environment pollution - plastic floating in the water
Plastisphere is a breeding ground for pathogens


A subsequent study conducted in 2020 analyzed biofilms found on plastic substrates in estuarine tributaries of Lower Chesapeake Bay (7). Vibrio spp. – specifically V. cholerae, V. parahaemolyticus, and V. vulnificus – were identified… all three of which can be pathogenic to humans. Concerningly, the authors noted that, “the concentration of putative Vibrio spp. on microplastics was much greater than in corresponding water samples.” They also found a high rate of antibiotic resistance amongst isolates, noting that “the potential for plastic in aqueous environments to serve as a vector for pathogenic organisms is compounded by the possibility for its dissemination of antibiotic-resistance genes.”

Several additional studies have confirmed the presence of Vibrio spp. on marine plastics found in various bodies of water across the world – and it is only a matter of time before additional pathogens will be identified as common residents of the plastisphere. 


Plastics and the Immune System

In addition to polluting our oceans, plastics are polluting our bodies. A team examined 47 liver- and adipose-tissue specimens from donated cadavers, and detected plastic micro- and nanoparticles in 100% of samples (8). Microplastics have been found in human placentas (9), and animal models indicate that nanoplastics can cross the blood-brain barrier (10). There is also evidence that when plastics accumulate in the body, they may be harmful to the immune system. 

Recent work has examined how immune cells behave in the presence of microplastics. Microplastics coated in blood plasma were placed in culture dishes containing immune cells. Within 24 hours, 60% of immune cells were destroyed. Under the same culture conditions, but in the absence of microplastics, only 20% of immune cells were destroyed (11).

Microplastics may also alter the immune system at the level of gene expression. When adult zebrafish were exposed to microplastics, alterations in the expression of 41 genes encoding proteins attributed to immune processes were observed (12).

The toxic effects of plastic do not appear to be limited to the immune system. In animal models, plastics are found to be potentially harmful to just about every cell type and organ system. Micro- and nanoplastics appear to be pro-inflammatory (13), are known to irritate the respiratory tract (14), can act as endocrine disrupters (15), may be neurotoxic (16), and appear to alter the gut microbiome (17). Such effects are observed even in the absence of controversial additives such as bisphenol A (BPA) and phthalates.


Ocean microplastics pollution cycle
Ocean microplastics pollution cycle


So What Can We Do?

Unfortunately, plastics are now ubiquitous. They are used in packaging materials, construction, textile manufacturing, automobiles, furniture, electronics, toys, medical devices, makeup, and even chewing gum. As a result, micro and nanoplasitics have contaminated our food chain and have been detected in cows milk (18), seafood (19), fruit and vegetables (20), honey and sugar (21), table salt (22), and tap water (23).

In 1960, an estimated half a million metric tons of plastic were produced each year, increasing to 348 million tons in 2017 (24). This compounding problem warrants immediate attention.

Some have suggested the use of fungi, bacteria, or worms to help dissolve plastic. Although the introduction of such organisms into the ecosystem is itself risky, solutions of this type may still be worth exploring.

Many investigators have been directing their efforts at designing biodegradable and compostable plastics and plastic alternatives. The assumption is that such materials would be less harmful to the environment and human health than traditional plastics – but there are many unknowns. One study concluded that the chemical processing required to create some existing bioplastics resulted in a greater amount of pollutants than the chemical processing used to create traditional plastics (25). Beyond this, there is no data on the interaction of biodegradable plastics with the human body.

A woman chooses a paper bag with food and refuses to use plastic on the background of the kitchen. The concept of environmental protection and the abandonment of plastic
Small everyday decisions count


While the “big-picture” solution remains elusive, there are easy steps that we can take to reduce our individual plastic footprints and lessen the potential for harm to our own bodies. We can avoid drinking and eating from plastic containers, abstain from using plastic bags, switch to wire hangers, wooden toys, etc. 

We only get one Earth, and we only get one body… and we must take great care of both. 

Happy Earth Day!


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(1) G. Grass, C. Rensing and M. Solioz, “Metallic Copper as an Antimicrobial Surface”, Applied and Environmental Microbiology, vol. 77, no. 5, pp. 1541-1547, 2010. Available: 10.1128/aem.02766-10 

(2) B. Bean, B. Moore, B. Sterner, L. Peterson, D. Gerding and H. Balfour, “Survival of Influenza Viruses on Environmental Surfaces”, Journal of Infectious Diseases, vol. 146, no. 1, pp. 47-51, 1982. Available: 10.1093/infdis/146.1.47

(3) D. Corpet, “Why does SARS-CoV-2 survive longer on plastic than on paper?”, Medical Hypotheses, vol. 146, p. 110429, 2021. Available: 10.1016/j.mehy.2020.110429

(4) C. Coughenour, V. Stevens and L. Stetzenbach, “An Evaluation of Methicillin-Resistant Staphylococcus aureus Survival on Five Environmental Surfaces”, Microbial Drug Resistance, vol. 17, no. 3, pp. 457-461, 2011. Available: 10.1089/mdr.2011.0007 

(5)E. Zettler, T. Mincer and L. Amaral-Zettler, “Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris”, Environmental Science & Technology, vol. 47, no. 13, pp. 7137-7146, 2013. Available: 10.1021/es401288x

(6) A. Rodrigues, D. Oliver, A. McCarron and R. Quilliam, “Colonisation of plastic pellets (nurdles) by E. coli at public bathing beaches”, Marine Pollution Bulletin, vol. 139, pp. 376-380, 2019. Available: 10.1016/j.marpolbul.2019.01.011

(7) A. Laverty, S. Primpke, C. Lorenz, G. Gerdts and F. Dobbs, “Bacterial biofilms colonizing plastics in estuarine waters, with an emphasis on Vibrio spp. and their antibacterial resistance”, PLOS ONE, vol. 15, no. 8, p. e0237704, 2020. Available: 10.1371/journal.pone.0237704

(8) “Methods for microplastics, nanoplastics and plastic monomer detection and reporting in human tissues – American Chemical Society”, American Chemical Society, 2021. [Online]. Available:

(9) A. Ragusa et al., “Plasticenta: First evidence of microplastics in human placenta”, Environment International, vol. 146, p. 106274, 2021. Available: 10.1016/j.envint.2020.106274

(10) M. Prüst, J. Meijer and R. Westerink, “The plastic brain: neurotoxicity of micro- and nanoplastics”, Particle and Fibre Toxicology, vol. 17, no. 1, 2020. Available: 10.1186/s12989-020-00358-y

(11) “Nienke Vrisekoop on microplastic’s impact on human immune cells | Plastic Health Summit 2019 – YouTube” Available:

(12) G. Limonta et al., “Microplastics induce transcriptional changes, immune response and behavioral alterations in adult zebrafish”, Scientific Reports, vol. 9, no. 1, 2019. Available: 10.1038/s41598-019-52292-5

(13) R. Lehner, C. Weder, A. Petri-Fink and B. Rothen-Rutishauser, “Emergence of Nanoplastic in the Environment and Possible Impact on Human Health”, Environmental Science & Technology, vol. 53, no. 4, pp. 1748-1765, 2019. Available: 10.1021/acs.est.8b05512

(14) A. Banerjee and W. Shelver, “Micro- and nanoplastic induced cellular toxicity in mammals: A review”, Science of The Total Environment, vol. 755, p. 142518, 2021. Available: 10.1016/j.scitotenv.2020.142518 

(15) F. Amereh, M. Babaei, A. Eslami, S. Fazelipour and M. Rafiee, “The emerging risk of exposure to nano(micro)plastics on endocrine disturbance and reproductive toxicity: From a hypothetical scenario to a global public health challenge”, Environmental Pollution, vol. 261, p. 114158, 2020. Available: 10.1016/j.envpol.2020.114158 

(16) M. Prüst, J. Meijer and R. Westerink, “The plastic brain: neurotoxicity of micro- and nanoplastics”, Particle and Fibre Toxicology, vol. 17, no. 1, 2020. Available: 10.1186/s12989-020-00358-y

(17) N. Hirt and M. Body-Malapel, “Immunotoxicity and intestinal effects of nano- and microplastics: a review of the literature”, Particle and Fibre Toxicology, vol. 17, no. 1, 2020. Available: 10.1186/s12989-020-00387-7

(18) G. Kutralam-Muniasamy, F. Pérez-Guevara, I. Elizalde-Martínez and V. Shruti, “Branded milks – Are they immune from microplastics contamination?”, Science of The Total Environment, vol. 714, p. 136823, 2020. Available: 10.1016/j.scitotenv.2020.136823

(19) M. Smith, D. Love, C. Rochman and R. Neff, “Microplastics in Seafood and the Implications for Human Health”, Current Environmental Health Reports, vol. 5, no. 3, pp. 375-386, 2018. Available: 10.1007/s40572-018-0206-z

(20) D. Yang, H. Shi, L. Li, J. Li, K. Jabeen and P. Kolandhasamy, “Microplastic Pollution in Table Salts from China”, Environmental Science & Technology, vol. 49, no. 22, pp. 13622-13627, 2015. Available: 10.1021/acs.est.5b03163 

(21) G. Liebezeit and E. Liebezeit, “Non-pollen particulates in honey and sugar”, Food Additives & Contaminants: Part A, vol. 30, no. 12, pp. 2136-2140, 2013. Available: 10.1080/19440049.2013.843025 

(22) D. Yang, H. Shi, L. Li, J. Li, K. Jabeen and P. Kolandhasamy, “Microplastic Pollution in Table Salts from China”, Environmental Science & Technology, vol. 49, no. 22, pp. 13622-13627, 2015. Available: 10.1021/acs.est.5b03163 

(23) H. Tong, Q. Jiang, X. Hu and X. Zhong, “Occurrence and identification of microplastics in tap water from China”, Chemosphere, vol. 252, p. 126493, 2020. Available: 10.1016/j.chemosphere.2020.126493 

(24) P. Wu et al., “Environmental occurrences, fate, and impacts of microplastics”, Ecotoxicology and Environmental Safety, vol. 184, p. 109612, 2019. Available: 10.1016/j.ecoenv.2019.109612 

(25) M. Tabone, J. Cregg, E. Beckman and A. Landis, “Sustainability Metrics: Life Cycle Assessment and Green Design in Polymers”, Environmental Science & Technology, vol. 44, no. 21, pp. 8264-8269, 2010. Available: 10.1021/es101640n

Occupational Infectious Diseases

by Dr. Jaclynn Moskow

Occupational health: Manufacturer working at storage tanks in brewery


In recognition of World Health Day 2021, which falls on April 7, the WHO points out that “some people are able to live healthier lives and have better access to health services than others – entirely due to the conditions in which they are born, grow, live, work, and age.”

Many of us spend a significant portion of our lives engaged in work. Unfortunately, certain working conditions put us at increased risk of poor health. For example, some occupations involve repeated exposure to respiratory irritants and carcinogens, while others are associated with musculoskeletal injury or hearing loss. Many professions put workers at risk of contracting an infectious disease.

Textbook of Occupational Medicine Practice (1) outlines five primary modes of transmission for occupational infections:

  1. Contact with animals and animal products (zoonoses)
  2. Exposure to vectors 
  3. Care of patients 
  4. Environmental sources, exposure to soils 
  5. Occupational skin infections


Occupational Zoonoses

Farmer with cow

Individuals who work with animals and animal products are at risk of contracting zoonotic diseases. Such occupations include farmworkers, ranch workers, butchers, veterinary workers, and zoo workers. There are currently over 200 recognized zoonoses (2).

Brucellosis is a zoonotic infectious disease caused by Brucella spp. Reservoirs for Brucella include pigs, cattle, sheep, goats, dogs, coyotes, and caribou. Brucellosis can be acquired via direct contact with these animals, or by processing their meat. Symptoms include prolonged fever, hepatosplenomegaly, lymphadenopathy, arthritis, and osteomyelitis (3). A study of occupationally acquired Brucella in Russia found that factors increasing the risk of infection include lack of awareness amongst workers regarding the disease and absence of regular inspections of working conditions (4).

Individuals who work with cats are at increased risk of acquiring bartonellosis, also known as “cat scratch disease.” As the name implies, the disease is caused by species of Bartonella and transmitted via cat scratches. Clinical manifestations include tender suppurative regional adenopathy and fever. Occasionally, systemic infection occurs involving such sites as the liver, brain, endocardium, and bones (5). A recent study of veterinary personnel detected Bartonella in 28% of subjects, compared to 0% of a control group (6).

A review of the incidences of campylobacteriosis and cryptosporidiosis in Nebraska between 2005-2015 identified occupational animal exposure as the cause in 16.6% and 8.7% of cases, respectively (7). Most of these cases were acquired by farmers, ranchers, and those working in animal slaughter and processing facilities; and the most common animal source was determined to be cattle. Additional occupational zoonotic infectious diseases include salmonellosis, Escherichia coli O157 infection, and Q-fever.


Occupational Infections Acquired Via Exposure to Vectors

Woman digging hole with shovel to plant saplings in forest. Forester planting new small trees in deforested area. Vector-borne diseases are occupational hazards for forestry workers.

Individuals working in areas infested with ticks, fleas, and mites are at an increased risk for infectious diseases carried by these arthropods. Occupations at risk include agricultural workers, forestry workers, military personnel, veterinary workers, and pest control workers.

Diseases that may be spread to workers via tick bites include Lyme disease, babesiosis, ehrlichiosis, Colorado tick fever, Rocky Mountain spotted fever, tularemia, and Powassan virus encephalitis. In the United States, Lyme disease is the most common tick-borne illness. It is caused by Borrelia spp. and characterized by the presence of erythema migrans, neurological, musculoskeletal, and cardiac manifestations.

Individuals working around fleas may acquire flea-borne (murine) typhus, caused by Rickettsia typhi, or Plague caused by Yersinia pestis. Additionally, exposure to mites could lead to the development of rickettsialpox, caused by Rickettsia akari, or scrub typhus, caused by Orientia spp.


Occupational Infections Acquired Via Care of Patients

Female nurse tying surgical mask in operation theater


Caring for patients while working in hospitals, ambulatory clinics, diagnostic laboratories, nursing homes, and the home carries an increased risk for several infectious diseases.

Each year, healthcare workers experience approximately 600,000–800,000 exposures to HIV, hepatitis B, and hepatitis C (8). Exposures may occur via needle-stick injury or via blood and other bodily fluids which accidentally contact mucous membranes. Healthcare workers can decrease their risk of contracting bloodborne pathogens by adhering to universal precautions.

Airborne pathogens are also of concern to healthcare workers. Respiratory diseases that can be acquired while caring for patients include tuberculosis, influenza, and COVID-19. Healthcare workers are also at increased risk of contracting methicillin-resistant Staphylococcus aureus (MRSA). Approximately 4.6% of healthcare workers carry MRSA (9), compared to 1% of the general population (10).

Vaccinations recommended to healthcare workers to help prevent occupationally acquired infections include hepatitis B, MMR, and influenza. 


Occupational Infections Acquired Via Exposure to Soils

Close-up low section of woman standing with fork on dirt

Individuals engaged in plowing, digging, and excavating soil at work may be exposed to a variety of infections. Such occupations include construction and demolition work, oil and gas extraction, agriculture workers, landscaping, and archaeology.

Workers exposed to soils are at an increased risk of endemic mycoses, including histoplasmosis, coccidioidomycosis, paracoccidioidomycosis, and blastomycosis. These infections are generally acquired by inhaling fungal spores that become airborne as the soil is disrupted. An example of this occurred between 2011 and 2014 when an outbreak of coccidioidomycosis occurred among workers constructing solar power-generating facilities in San Luis Obispo County, California. A total of 44 cases were documented, including nine hospitalizations (11). 

The paradigm disease associated with soil contact is tetanus, caused by Clostridium tetani. Tetanus is acquired when bacterial spores found in soil are introduced to the body via a breach in the skin. Clinical manifestations of tetanus include trismus (lockjaw), facial spasm, opisthotonos, recurrent tonic spasms of skeletal muscle, and tachycardia. Tetanus has a case fatality rate of 10 to 40% (12). Tetanus cases can be prevented through vaccination…and the CDC reports that the efficacy of the tetanus vaccine is nearly 100% (13).


Occupational Skin Infections

Butchers may catch occupational skin infections by exposure to raw meat

There are a wide variety of professions in which occupational exposure to skin infections may occur. These include farmers, fisherman, butchers, veterinary workers, aquarium workers, swimming pool cleaners, healthcare workers, and salon workers. 

Many occupational skin infections result from exposure to animals and animal tissue. For example, farmers and butchers are at an increased risk of contracting cutaneous anthrax, caused by Bacillus anthracis. Cutaneous anthrax usually begins with pruritus at the affected site and is followed by a small, painless papule that progresses to a vesicle. The lesion erodes and becomes necrotic, and secondary vesicles are sometimes observed. Lymphadenopathy, fever, and headache may also occur. When left untreated, approximately 20% of cases are fatal (14).

Erysipeloid, caused by Erysipelothrix rhusiopathiae, can also occur when working with animals and animal tissues. The infection is characterized by rash, local pain, swelling, and occasionally fever. One report described an outbreak of erysipeloid amongst workers at a shoe factory (15). The source of the bacteria was determined to be raw leather.

Exposure to water is another common source of occupational skin infections. Fish tank granuloma, an infection caused by Mycobacterium marinum, is often acquired by aquarium workers. Fishermen are at risk of contracting Vibrio vulnificus infection through contact with contaminated ocean water or fish.

Other infections of the skin that can be acquired at work are caused by fungi. Examples include candidiasis, dermatophytosis, chromomycosis, and sporotrichosis. Scabies, a parasitic skin infestation caused by a mite, is often reported among healthcare workers, daycare workers, and correctional facility employees.


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(2) “Other Neglected Zoonotic Diseases”, World Health Organization, 2021. [Online]. Available:

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(4) A. Tarkhov,  et al., “The Working Conditions At Animal Farm Complexes of Workers With Occupational Brucellosis”, Med Tr Prom Ekol, vol. 5, pp. 5-9, 2012.

(5) “Bartonellosis – Cat Borne”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(6) P. Lantos et al., “Detection of Bartonella Species in the Blood of Veterinarians and Veterinary Technicians: A Newly Recognized Occupational Hazard?”, Vector-Borne and Zoonotic Diseases, vol. 14, no. 8, pp. 563-570, 2014. Available: 10.1089/vbz.2013.1512

(7) C. Su, D. Stover, B. Buss, A. Carlson and S. Luckhaupt, “Occupational Animal Exposure Among Persons with Campylobacteriosis and Cryptosporidiosis — Nebraska, 2005–2015”, MMWR. Morbidity and Mortality Weekly Report, vol. 66, no. 36, pp. 955-958, 2017. Available: 10.15585/mmwr.mm6636a4

(8) N. Swanson, C. Ross and K. Fennelly, “Healthcare-related Infectious Diseases1”, Emerging Infectious Diseases, vol. 10, no. 11, pp. e3-e3, 2004. Available: 10.3201/eid1011.040622_03

(9) W. Albrich and S. Harbarth, “Health-care workers: source, vector, or victim of MRSA?”, The Lancet Infectious Diseases, vol. 8, no. 5, pp. 289-301, 2008. Available: 10.1016/s1473-3099(08)70097-5

(10) “MRSA and the Workplace”, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 2015. [Online]. Available:

(11) G. Sondermeyer Cooksey et al., “Dust Exposure and Coccidioidomycosis Prevention Among Solar Power Farm Construction Workers in California”, American Journal of Public Health, vol. 107, no. 8, pp. 1296-1303, 2017. Available: 10.2105/ajph.2017.303820

(12) “Tetanus”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(13) “Tetanus”, Centers for Disease Control and Prevention, Epidemiology and Prevention of Vaccine-Preventable Diseases, 2008. Available:

(14) “Anthrax”, GIDEON Informatics, Inc, 2021. [Online]. Available:

(15) V Popugaĭlo VM, et al., “Erysipeloid as an occupational disease of workers in shoe enterprises”, Zh Mikrobiol Epidemiol Immunobiol, vol. 10, pp. 46-9, 1983.