Pathogenic Microorganisms

​Diseases/Pathogens Associated with Antimicrobial Resistance​

A growing number of disease-causing organisms, also known as pathogens, are resistant to one or more antimicrobial drugs.  A wide range of pathogens—including the bacteria that cause tuberculosis, the viruses that causes influenza, the parasites that cause malaria, and the fungi that cause yeast infections—are becoming resistant to the antimicrobial agents used for treatment.  This page contains links to further information about some of the organisms and diseases associated with antimicrobial resistance.

Bacteria that flourish in the presence of antibiotics can spread resistance in two ways. One way is simple reproduction. Some species also possess an additional evolutionary advantage. These bacteria share genes with other members of a population, both within and beyond the boundaries of their own species. The gene exchange described in this diagram spreads antibiotic resistance faster than the rate of reproduction.


Acinetobacter [asz−in−ée−toe–back−ter] is a group of bacteria commonly found in soil and water. While there are many types or “species” of Acinetobacter and all can cause human disease, Acinetobacter baumannii [asz−in−ée−toe–back−ter   boe-maa-nee-ie] accounts for about 80% of reported infections.

Outbreaks of Acinetobacter infections typically occur in intensive care units and healthcare settings housing very ill patients. Acinetobacter infections rarely occur outside of healthcare settings.


Anthrax is a serious disease caused by Bacillus anthracis, a bacterium that forms spores. Anthrax most commonly occurs in wild and domestic mammalian species, but it can also occur in humans when they are exposed to infected animals or to tissue from infected animals or when anthrax spores are used as a bioterrorist weapon. Some strains of B. anthracis may be naturally resistant to certain antibiotics and not others. In addition, there may be biologically mutant strains that are engineered to be resistant to various antibiotics.


Gonorrhea is a sexually transmitted disease (STD). Gonorrhea is caused by Neisseria gonorrhoeae, a bacterium that can grow and multiply easily in the warm, moist areas of the reproductive tract. The bacterium can also grow in the mouth, throat, eyes, and anus. Antimicrobial resistance in N. gonorrhoeae remains an important challenge to controlling gonorrhea; gonococcal strains may be resistant to penicillins, tetracyclines, spectinomycin, and fluoroquinolones.

Group B streptococcus

Group B Streptococcus (group B strep) is a type of bacteria that causes illness in newborn babies, the elderly, and adults with other illnesses, such as diabetes or liver disease. Group B strep has shown confirmed resistance to certain antibiotics.

Klebsiella pneumoniae

Klebsiella [kleb−see−ell−uh] is a type of Gram-negative bacteria that can cause different types of healthcare-associated infections, including pneumonia, bloodstream infections, wound or surgical site infections, and meningitis. Increasingly, Klebsiella bacteria have developed antimicrobial resistance, most recently to the class of antibiotics known as carbapenems. Klebsiella bacteria are normally found in the human intestines (where they do not cause disease). They are also found in human stool (feces). In healthcare settings, Klebsiella infections commonly occur among sick patients who are receiving treatment for other conditions. Patients whose care requires devices like ventilators (breathing machines) or intravenous (vein) catheters, and patients who are taking long courses of certain antibiotics are most at risk for Klebsiella infections. Healthy people usually do not get Klebsiella infections.

Methicillin-resistant Staphylococcus aureus (MRSA)

Methicillin-resistant Staphylococcus aureus (MRSA) is a type of bacteria that is resistant to certain antibiotics. These antibiotics include methicillin and other more common antibiotics such as oxacillin, penicillin, and amoxicillin. Serious or life-threatening occurrences of "Staph" infections, including MRSA, occur most frequently among persons in hospitals and healthcare facilities (such as nursing homes and dialysis centers) who have weakened immune systems.

Neisseria meningitidis

One of the leading causes of bacterial meningitis in children and young adults in the United States is the bacterium Neisseria meningitidis. Meningitis caused by this bacterium is known as meningococcal disease. During 2007-2008 the first reported cases of fluoroquinolone-resistant Neisseria meningitides were reported in the United States


Shigellosis is an infectious disease caused by a group of bacteria called Shigella. The Shigella germ is actually a family of bacteria that can cause diarrhea in humans. Persons with mild infections usually recover quickly without antibiotic treatment.  However, appropriate antibiotic treatment kills Shigella bacteria, and may shorten the illness by a few days. Some Shigella bacteria have become resistant to antibiotics. This means some antibiotics might not be effective for treatment.

Streptococcus pneumoniae

Streptococcus pneumoniaeis a leading cause of serious illness among young children worldwide and is the most frequent cause of pneumonia, bacteremia, sinusitis, and acute otitis media (AOM). Widespread overuse of antibiotics contributes to emerging drug resistance.


"TB" is short for tuberculosis. TB disease is caused by a bacterium called Mycobacterium tuberculosis. TB bacteria can become resistant to the medicines used to treat TB disease. Multidrug-resistant TB (MDR TB) is TB that is resistant to at least two of the best anti-TB drugs, isoniazid and rifampicin. Extensively drug-resistant TB (XDR TB) is a relatively rare type of MDR TB. XDR TB is defined as TB that is resistant to isoniazid and rifampin, plus resistant to any fluoroquinolone and at least one of three injectable second-line drugs.

Typhoid Fever

Typhoid fever is a life-threatening illness caused by the bacterium Salmonella Typhi. Typhoid fever can be prevented and can usually be treated with antibiotics. However, increasing resistance to available antimicrobial agents, including fluoroquinolones, presents a challenge for treatment.

Vancomycin-resistant Enterococci (VRE)

Enteroccocci are bacteria that are normally present in the human intestines and in the female genital tract and are often found in the environment. These bacteria can sometimes cause infections. Vancomycin is an antibiotic that is often used to treat infections caused by enterococci. In some instances, enterococci have become resistant to this drug and thus are called vancomycin-resistant enterococci (VRE). Most VRE infections occur in hospitals.

Vancomycin-Intermediate/Resistant Staphylococcus aureus (VISA/VRSA)

VISA and VRSA are specific types of antimicrobial-resistant staph bacteria. While most staph bacteria are susceptible to the antimicrobial agent vancomycin some have developed resistance. VISA and VRSA cannot be successfully treated with vancomycin because these organisms are no longer susceptibile to vancomycin. However, to date, all VISA and VRSA isolates have been susceptible to other Food and Drug Administration (FDA) approved drugs.





Influenza (the flu) is a contagious respiratory illness caused by influenza viruses. In the United States, four antiviral drugs are FDA-approved for use against influenza: amantadine, rimantadine, zanamivir and oseltamivir. Samples of viruses collected from around the United States and worldwide are studied to determine if they are resistant to any of the four FDA-approved influenza antiviral drugs.


Candida is a type of fungal infection that encompasses superficial infection (oral thrush, vaginitis) to systemic and possibly life-threatening diseases that are mostly found in greatly immunocompromised persons, such as cancer, transplant, and AIDs patients. Symptoms may vary. Infection of the vagina or vulva may cause severe itching, burning, soreness, irritation, and discharge. Most ca Candida is a type of fungal infection that encompasses superficial infection (oral thrush, vaginitis) to systemic and possibly life-threatening diseases that are mostly found in greatly immunocompromised persons, such as cancer, transplant, and AIDs patients. Symptoms may vary. Infection of the vagina or vulva may cause severe itching, burning, soreness, irritation, and discharge. Most candidial infections are treatable and result in minimal complications such as redness, itching and discomfort, though complication may be severe or fatal if left untreated in certain populations. Candidiasis is commonly treated with antimycotics—the antifungal drugs commonly used to treat candidiasis are topical clotrimazole, topical nystatin, fluconazole, and topical ketoconazole. Candida may develop resistance to antimycotic drugs, such as fluconazole, one of the drugs that is often used to treat candidiasis. Recurring infections may be treatable with other anti-fungal drugs, but resistance to these drugs may also develop.


Malaria is a mosquito-borne disease caused by a parasite. People with malaria often experience fever, chills, and flu-like symptoms. The development of resistance to drugs poses one of the greatest threats to malaria control and has been linked to recent increases in malaria morbidity and mortality. Antimicrobial resistance has been confirmed in only two of the four human malaria parasite species, Plasmodium falciparum and P. vivax.

Salmonella Serotype Enteritidis

Salmonella serotype Enteritidis infection

Salmonella serotype Enteritidis (SE) is one of the most common serotypes of Salmonella bacteria reported worldwide. During in the 1980s, SE emerged as an important cause of human illness in the United States.  The number of outbreaks of SE rose dramatically during that time, beginning in the northeastern states and then spreading west during the 1990s. SE illness now occurs in most regions of the country. Consumers should be aware of the disease and learn how to minimize the chances of becoming ill.

Eggs have been the most common food source linked to SE infections. SE can be inside perfectly normal-appearing eggs. If eggs contaminated with SE are eaten raw or lightly cooked (runny egg whites or yolks), the bacterium can cause illness. Since the early 2000s, poultry has also been found to be a common food source for SE infections. Multiple other, less frequently identified sources include raw milk, pork, beef, sprouts, and raw almonds. International travel and contact with reptiles have also been associated with SE infection.


A person infected with the Salmonella bacterium usually has fever, abdominal cramps, and diarrhea beginning 12 to 72 hours after consuming a contaminated food or beverage. The illness usually lasts 4 to 7 days, and most persons recover without antibiotic treatment. However, the diarrhea can be severe, and the person may be ill enough to require hospitalization.

The elderly, infants, and those with impaired immune systems may have a more severe illness. In these patients, the infection may spread from the intestines to the blood stream, and then to other body sites and can cause death unless the person is treated promptly with antibiotics.

Egg and chicken contamination

Most types of Salmonella live in the intestinal tracts of animals and birds and are transmitted to humans when feces from animals directly or indirectly contaminate foods that humans eat. For example, if chicken feces get on the outside of the shell of eggs, Salmonella in the feces can contaminate the egg through cracks in the shell.  This used to be a common problem.  However, stringent procedures for cleaning and inspecting eggs were implemented in the 1970s and have made illness from Salmonella caused by chicken feces on the outside of egg shells extremely rare. However, unlike Salmonella infections from eggs in past decades, the epidemic that started in the 1980s and continues to cause illnesses today is due to SE being inside of intact grade A eggs with clean shells. The reason is that SE can silently infect the ovaries of healthy appearing hens and contaminate the inside of eggs before the shells are formed.

SE infection is present in hens in most areas in the United States. An estimated one in 20,000 eggs is internally contaminated. Only a small number of hens might be infected at any given time, and an infected hen can lay many normal eggs while only occasionally laying eggs contaminated with SE.

Chickens raised for meat, called broiler chickens, can also be contaminated with SE. During the period 2000–2005, as eating chicken emerged as a risk factor for SE infection, studies by the US Department of Agriculture’s Food Safety and Inspection Service (USDA-FSIS) found an average of one in eight sampled broiler chickens were contaminated with Salmonella, and of the Salmonella-positive chickens, one in 20 were contaminated with SE.


Who can be infected?

Anyone can get a Salmonella infection, but the elderly, infants, and persons with impaired immune systems are at increased risk for serious illness. In these persons, a relatively small number of Salmonella bacteria can cause severe illness. In outbreaks, most of the deaths caused by SE have occurred among persons in nursing homes and hospitals. Egg-containing dishes prepared for any of these high-risk persons, whether in hospitals, nursing homes, restaurants, or at home, should use pasteurized eggs. Poultry dishes prepared for these high-risk persons should be cooked thoroughly, to a minimum internal temperature of 165º F (74ºC).


What is the risk?


According to estimates from the 1990s, about one in 20,000 eggs is contaminated with SE. With approximately 65 billion eggs produced per year in the United States and 30% sent for pasteurization, an estimated 2.2 million individual eggs remain contaminated with SE. Many dishes made in restaurants or commercial or institutional kitchens, however, are made from pooled eggs, not from eggs prepared individually. One contaminated egg can contaminate an entire batch of pooled eggs. Everyone who eats eggs from that batch is at risk for illness. In individual eggs and pooled eggs that are thoroughly cooked (firm egg whites and yolks), SE will be destroyed and will not make a person sick. A person who eats eggs can lower the risk of SE infection by eating eggs that are thoroughly cooked, or by eating foods that are made from pasteurized eggs.


Based on sampling at processing plants in 2007–2008, USDA-FSIS estimates that SE contaminates about one in 250 broiler chickens (USDA-FSIS communication, October 2010). Eating chicken prepared outside of the home, such as in restaurants, is a risk factor for becoming ill with SE. Lack of hand washing, not separating raw eggs or chicken from produce or other foods during preparation, and other unsafe food handling practices in homes and in commercial food establishments can increase risk of an SE infection.


What you can do to reduce risk

Eggs, poultry, meat, milk, and other foods are safe when handled properly. Shell eggs are safest when stored in the refrigerator, individually and thoroughly cooked, and promptly consumed after cooking. The larger the number of Salmonella bacteria present in the egg, the more likely the egg is to cause illness. Keeping eggs adequately refrigerated prevents any Salmonella present in the eggs from growing to higher numbers, so eggs should be refrigerated until they are needed. Cooking reduces the number of bacteria present in an egg; however, a lightly cooked egg with a runny egg white or yolk still poses a greater risk than a thoroughly cooked egg. Lightly cooked egg whites and yolks have both caused outbreaks of SE infections. Cooked eggs should be consumed promptly and not be held in the temperature range of 40 to 140ºF for more than 2 hours.
Cross-contamination occurs in the kitchen when unwashed hands or food preparation surfaces transfer SE from chicken to other foods. Keeping uncooked meat separate from other foods during storage and preparation can help prevent cross-contamination. Cooking chicken to 165ºF (74ºC) inside (use a thermometer!) kills SE and helps prevent illness. Prompt refrigeration of unused or leftover food prevents growth of bacteria. Dividing large amounts of leftovers into several shallow containers allows for quicker cooling in the refrigerator.


What else is being done?

Government agencies and the egg industry have taken steps to reduce SE outbreaks. These steps include the difficult task of identifying and removing infected hens from flocks that supply eggs and increasing quality assurance and sanitation measures. The US Food and Drug Administration (FDA) issued a rule that went into effect on July 9, 2010 that requires shell egg producers to implement measures on the farm to prevent SE from contaminating eggs. Eggs from commercial flocks that are known to be infected are pasteurized instead of being sold as grade A shell eggs. The rule also includes refrigeration requirements during storage and transportation.

The US Centers for Disease Control and Prevention (CDC) has advised state health departments, hospitals, and nursing homes about specific measures to reduce SE infection in humans. The CDC, FDA, and select laboratories across the country also collaborate to monitor contamination of meats sold in stores and other suppliers by SE and other contaminants.

State agencies and authorized laboratories of the USDA Animal and Plant Health Inspection Service’s National Poultry Improvement Plan, an industry-State-Federal cooperative program, certify participating breeding flocks and hatcheries of chickens that lay eggs as SE clean (“tested free”). USDA-FSIS regulates the safety of egg products, which are eggs removed from their shells for processing. USDA-FSIS also monitors contamination of broiler chickens with SE and other contaminants at all stages of chicken production at processing plants.

Research by these agencies and the egg industry is addressing many unanswered questions about SE, the infections in hens, and contaminated eggs. Informed consumers, food-service establishments, and public and private organizations are working together to reduce, and eventually eliminate, disease caused by this infectious organism.

Centers for Disease Control and Prevention

800-CDC-INFO (800-232-4636) TTY: (888) 232-6348 - Contact CDC–INFO

Salmonella Typhimurium Enteritidis

Until recently the most common cause of food poisoning by Salmonella species was due to S. Typhimurium. As its name suggests, it causes a typhoid-like disease in mice. In humans S. Typhimurium does not cause as severe disease as S. Typhi, and is not normally fatal. The disease is characterized by diarrhea, abdominal cramps, vomiting and nausea, and generally lasts up to 7 days. Unfortunately, in immunocompromized people, that is the elderly, young, or people with depressed immune systems, Salmonella infections are often fatal if they are not treated with antibiotics.


What are Salmonella?

Salmonella are bacteria. The Salmonella consist of a range of very closely related bacteria, many of which cause disease in humans and animals.


What does their name mean?
There is a great deal of confusion over the naming of Salmonella strains (even the people who work on Salmonella are confused!) but in essence, the strains which we will deal with here are generally different serovars of Salmonella enterica.

This means that they all belong to the genus Salmonella, a division that groups similar, though not identical bacteria together. These bacteria are named after the scientist who discovered them, Dr. Daniel Salmon. The majority of the components of these bacteria are identical, and at the DNA level, they are between 95% and 99% identical. (As a comparison E. coli and Salmonella, which are closely related to each other, are about 60-70% identical at the DNA level).

As their name suggests Salmonella enterica are involved in causing diseases of the intestines (enteric means pertaining to the intestine). The three main serovars of Salmonella enterica are Typhimurium, Enteritidis, and Typhi. Each of these is discussed further below. These distinctions are are designed to help scientists distinguish similar bacteria from each other in papers and when discussing the genetics.

To complicate matters, serovars of Salmonella enterica can be subgrouped even further by "phage type". This technique uses the specificity of phage to differentiate between extremely closely related bacteria. Often these bacteria are indistinguishable by other means, and indeed, the reasons for the differences in phage specificity are often not known.

Salmonella enterica serovar Typhi. (Also called Salmonella Typhi or abbreviated to S. Typhi)
This bacterium is the causative agent of typhoid fever. Although typhoid fever is not widespread in the United States, it is very common in under-developed countries, and causes a serious, often fatal disease. The symptoms of typhoid fever include nausea, vomiting, fever and death. Unlike the other Salmonella discussed below, S. Typhi can only infect humans, and no other host has been identified. The main source of S. Typhi infection is from swallowing infected water. Food may also be contaminated with S. Typhi, if it is washed or irrigated with contaminated water.

Salmonella enterica serovar Typhimurium (Also called Salmonella Typhimurium or abbreviated to S. Typhimurium)
Until recently the most common cause of food poisoning by Salmonella species was due to S. Typhimurium. As its name suggests, it causes a typhoid-like disease in mice. In humans S. Typhimurium does not cause as severe disease as S. Typhi, and is not normally fatal. The disease is characterized by diarrhea, abdominal cramps, vomiting and nausea, and generally lasts up to 7 days. Unfortunately, in immunocompromized people, that is the elderly, young, or people with depressed immune systems, Salmonella infections are often fatal if they are not treated with antibiotics.

Salmonella enterica serovar Enteritidis (Also called Salmonella Enteritidis or abbreviated to S. Enteritidis).
In the last 20 years or so, S. Enteritidis has become the single most common cause of food poisoning in the United States. S. Enteritidis causes a disease almost identical to the very closely related S. Typhimurium. S. Enteritidis is particularly adept at infecting chicken flocks without causing visible disease, and spreading from hen to hen rapidly. Many people have blamed the recent increase in the rise of S. Enteritidis infections on the use of mass production chicken farms. When tens or hundreds of thousands of chickens live together, die together, and are processed together a Salmonella infection can rapidly spread throughout the whole food chain. A compounding factor is that chickens from a single farm may be distributed over many cities, and even states, and hence Salmonella infections can be rapidly dispersed through millions of people.


How does Salmonella cause disease?
After Salmonella is eaten it passes through the stomach to the intestine. Here, it binds to the wall of the intestine, and through some special proteins that it makes in response to the particular conditions in the intestine it actually penetrates the barrier between us and the outside. Once it has gained access to our insides, it is taken to the liver or spleen. For most other bacteria, this journey would kill them, however Salmonella has evolved mechanisms to prevent our immune system from doing its job efficiently. In the liver, the Salmonella can grow again, and be released back into the intestine.

Of course, not all of the Salmonella pass through the intestinal wall, and many of them are expelled from the intestine in the diarrhea. In regions with poor sanitation, these bacteria can than survive in the soil or in rivers and infect the next person, cow, chicken or mouse that comes along.

Where do I get Salmonella from?
Well, you can try the Salmonella Genetic Stock Center.

Most infections with Salmonella are traced back to dairy, poultry and meat products, but Salmonella can grow on just about any food. Chickens and eggs are particular high risk foods.

What can I do to prevent Salmonella infections?
The best way of avoiding Salmonella infections is make sure that everything is thoroughly cooked.
Other precautions as suggested by the USDA include:

Wash Hands and Surfaces Often

Wash your hands, cutting boards, dishes etc with hot soapy water before handling food.

Separate raw meat, poultry, and seafood from other foods in your refrigerator.

Cook to Proper Temperatures

Refrigerate Promptly

Staphylococcus aureus bacteria

Almost half of the meat and poultry sold at U.S. supermarkets and grocery stores contains a type of bacteria that is potentially harmful to humans, a new study estimates.
Researchers tested 136 packages of chicken, turkey, pork, and ground beef purchased at 26 grocery stores in five cities around the country, and found that 47 percent contained Staphylococcus aureus (S. aureus), a common cause of infection in people.
What's more, roughly half of the contaminated samples contained strains of the bacteria that were resistant to at least three antibiotics, such as penicillin and tetracycline. Some strains were resistant to a half dozen or more.

Although the high contamination rates may sound alarming, the threat these bacteria pose to humans is still unclear.
"We know that nearly half of our food supply's meat and poultry are contaminated with S. aureus, and more than half of those are multidrug resistant," says Lance B. Price, Ph.D., the senior author of the study, which was published Friday in the journal Clinical Infectious Diseases. "What we don't know [is] how often these transfer to people. We need more studies to quantify the public health impact."

S. aureus, and drug-resistant strains in particular, can cause serious infections and even death in humans. However, simple precautions including cooking meat thoroughly, washing hands after handling meat, and keeping raw meat separate from other foods to prevent cross-contamination are believed to neutralize the risk of infection, according to experts not involved in the research.

"Numerous studies of this type done in other countries...have generally come up with the same findings, that multidrug-resistant S. aureus are present in a variety of animal meats," says Pascal James Imperato, M.D., the dean of the School of Public Health at SUNY--Downstate Medical Center, in Brooklyn. "But, so far, no one has been able to draw a connection between the presence of those bacteria in meats and human illness."
Multidrug-resistant bacteria strains are "always a concern for humans," says M. Gabriela Bowden, Ph.D., a bacteria expert and assistant professor at the Texas A&M Health Science Center, in Houston. "But if you follow the hygiene rules that you would follow for Salmonella or E. coli, there shouldn't be a problem."

The meat, which was sold under 80 different brands, was purchased in Los Angeles; Chicago; Washington, D.C.; Fort Lauderdale; and Flagstaff, Ariz. The variety and number of S. aureus strains found on the samples suggest that the livestock themselves -- rather than contamination during processing and packaging -- are the source of the bacteria, the study notes.

Each year farmers and ranchers give millions of pounds of antibiotics to farm animals, most of them healthy, to make them grow faster and to prevent -- rather than treat -- diseases, says Price, the director of the Center for Food Microbiology and Environmental Health at the Translational Genomics Research Institute, a nonprofit organization in Flagstaff.
The combination of bacteria, antibiotics, and livestock living in close quarters creates the perfect environment for bacteria to thrive and mutate, which may explain the high levels of drug-resistant S. aureus seen in the study, he adds.
Virtually all (96 percent) of the S. aureus strains Price and his colleagues isolated had developed resistance to at least one antibiotic. Strains resistant to three or more antibiotics were found in 79 percent of turkey, 64 percent of pork, 35 percent of beef, and 26 percent of chicken samples. "It's four different meats from four different animals in different geographical areas," Bowden says. "[S. aureus] may be more prevalent than we think."

Methicillin-resistant S. aureus (MRSA), which has been a particular menace to humans in hospitals and communities alike, was found in one package each of beef, turkey, and pork, though not chicken. This sample size wasn't large enough to arrive at an accurate estimate of its prevalence in meat nationwide, according to the study.

The Centers for Disease Control and Prevention, the Food and Drug Administration, and the U.S. Department of Agriculture currently monitor the country's meat supply for evidence of four major types of antibiotic-resistant bacteria (including Salmonella and E. coli). The study findings suggest that S. aureus should be screened for regularly as well, the researchers say.

Copyright Health Magazine 2011

Listeria monocytogenes

Listeria monocytogenes is found in both wild and domestic mammals as well as birds and some species of fish and shellfish. It also can be isolated from soil, silage and other environmental sources.

  • L. monocytogenes is hardy and has been associated with such foods as raw milk, supposedly pasteurized fluid milk, cheeses (particularly soft-ripened varieties), ice cream, raw vegetables, fermented raw-meat sausages, raw and cooked poultry, raw meats (all types), as well as raw and smoked fish.
  • It’s ability to grow at temperatures as low as 3°C permits multiplication in refrigerated foods.

Listeria monocytogenes can be found in both the egg processing plant environment as well as in the egg itself.

Campylobacter jejuni

Campylobacter jejuni (C. jejuni) bacteria are found naturally in the intestines of poultry, cattle, swine, rodents, wild birds and household pets like cats and dogs. The bacteria have also been found in untreated surface water (caused by fecal matter in the environment) and manure.

C. jejuni is the most common type of campylobacter bacteria involved in human illness. People who eat food contaminated by C. jejuni bacteria can become ill with campylobacteriosis. Like other foodborne illnesses, the symptoms of campylobacteriosis can feel like stomach flu, but they can also develop into serious illness with long-lasting effects.

Campylobacter jejuni is one of the most common causes of diarrheal illness in humans. As with Salmonella, FSIS requires poultry establishments to meet Campylobacter performance standards and conducts in-plant testing to verify compliance.

Yersenia pestis

Yersinia pestis (formerly Pasteurella pestis) is a Gram-negative rod-shaped bacterium. It is a facultative anaerobe that can infect humans and other animals.

Human Y. pestis infection takes three main forms: pneumonic, septicemic, and the notorious bubonic plagues. All three forms are widely believed to have been responsible for a number of high-mortality epidemics throughout human history, including the Plague of Justinian in 542 and the Black Death that accounted for the death of at least one-third of the European population between 1347 and 1353.[citation needed] It has now been shown conclusively that these plagues originated in rodent populations in China. More recently, Y. pestis has gained attention as a possible biological warfare agent and the CDC has classified it as a category A pathogen requiring preparation for a possible terrorist attack.

Vibrio cholerae

Vibrio cholerae is a "comma" shaped Gram-negative bacteria with a single, polar flagellum for movement. There are numerous strains of V. cholerae, some of which are pathogenic and some of which are not.

The most wide sweeping pathogenic strain is the Vibrio cholerae serotype O1 El Tor N16961 strain that causes the pandemic disease cholera.2 The latest pathogenic serotype O139 was discovered in 1992. The El Tor strain was active in the seventh and most recent pandemic of cholera from 1960's-1970's, as well as in the early 1990's along with serotype O139, both displaying resistance to multiple drugs.

The bacteria infects the intestine and increases mucous production causing diarrhea and vomiting which result in extreme dehydration and, if not treated, death. It is usually transmitted through the feces of an infected person, often by way of unclean drinking water or contaminated food. Since water treatment and sanitation is more advanced in the United States, cholera is not nearly as high of a public health threat in the US as it is in densely populated, economically reduced areas like India or sub-Saharan Africa where water and sewage treatment technology is low.

It is for this great risk to human health that makes it so worthy of studying and sequencing. And because of the variety of strains, it could be possible to determine the pathogenicity of new strains by comparing their genomes to strains of known pathogenic status.

Corynebacterium diphtheriae

Corynebacterium diphtheriae infects the nasopharynx or skin. Toxigenic strains secrete a potent exotoxin which may cause diphtheria. The symptoms of diphtheria include pharyngitis, fever, swelling of the neck or area surrounding the skin lesion. Diphtheritic lesions are covered by a pseudomembrane. The toxin is distributed to distant organs by the circulatory system and may cause paralysis and congestive heart failure.

Bacillus cereus

Bacillus cereus is a large, 1 x 3-4 µm, Gram-positive, rod-shaped, endospore forming, facultative aerobic bacterium. It was first successfully isolated in 1969 from a case of fatal pneumonia in a male patient and was cultured from the blood and pleural fluid. 16s rRNA comparison reveals Bacillus cereus to be most related to Bacillus anthracis, the cause of anthrax, and Bacillus thuringiensis, an insect pathogen used as pesticide. Although they have similar characteristics, they are distinguishable as B. cereus is most motile, B. thuringiensis produces crystal toxins, and B. anthracis is nonhemolytic.

B. cereus is mesophilic, growing optimally at temperatures between 20°C and 40°C, and is capable of adapting to a wide range of environmental conditions. It is distributed widely in nature and is commonly found in the soil as a saprophytic organism. B. cereus is also a contributor to the microflora of insects, deriving nutrients from its host, and is found in the rhizosphere of some plants.

As a soil bacterium, B. cereus can spread easily to many types of foods such as plants, eggs, meat, and dairy products, and is known for causing 25 % of food-borne intoxications due to its secretion of emetic toxins and enterotoxins. Food poisoning occurs when food is left without refrigeration for several hours before it is served. Remaining spores of contaminated food from heat treatment grow well after cooling and are the source of food poisoning.

In addition, Bacillus cereus is an opportunistic human pathogen and is occasionally associated with infections, causing periodontal diseases and other more serious infections. Immunocompromised patients are susceptible to bacteremia, endocarditis, meningitis, pneumonia, and endophthalmitis. Its potential to cause systemic infections are of current public health and biomedical concerns. Thus, the genome sequence of Bacillus cereus is significant in order to establish genetic background information for future investigations. Sequencing its genome is vital to expand understanding of its pathogenicity for treatment and for the development of antimicrobial drugs. Additionally, since Bacillus cereus strains are so genetically closely related to B. anthracis, genomic comparisons between the two species are important to the study of B. anthracis virulence.

Helicobacter pylori

Helicobacter pylori (H. pylori) is a type of bacteria responsible for widespread infection with more than 50% of the world's population infected, even though 80% of those infected have no symptoms. H. pylori infection is associated with low grade inflammation of the stomach and duodenum (the first part of the small intestine that empties the stomach).

The bacteria has evolved to survive in the acidic environment of the stomach where enzymes digest food. The H. pylori bacteria burrow into the cells of the stomach lining and cause low grade inflammation. H. pylori is the most common cause of gastric ulcers and gastritis (gastro=stomach +itis=inflammation). Ten percent of those infected may develop an ulcer. Also, those infected have an increased risk of stomach cancer and lymphoma.

Bordetella pertussis

Bordetella pertussis is a small, Gram-negative, coccoid bacterium about the size of 0.8 µm by 0.4 µm. It is an encapsulated immotile aerobe that does not make spores. Bordetella pertussis produces a number of virulence factors, including pertussis toxin, adenylate cyclase toxin, filamentous hemagglutinin, and hemolysin. It cannot survive in the environment; it must reside in a host either in small groups or singly. It grows at an optimal temperature of 35-37ºC.

Bordetella pertussis is a strict human pathogen that is the causative agent of pertussis (whooping cough). Its natural habitat is in the human respiratory mucosa. Whooping Cough, or pertussis, is a respiratory infection in which a “whooping” sound is produced when the sufferer breathes. Pertussis kills an estimated 300,000 children annually, most of which occur in developing countries. 

Neisseria gonorrhoeae

The prevalence of gonorrhea (Neisseria gonorrheae) in the United States and abroad, especially under-developed and developing countries, has decreased in the last two decades.  As of recently, though, higher rates of infection have been reported due to the increase of antimicrobial -resistant gonococci (Knapp et al., 1994). Gonorrhea is a very common infectious bacterium, a Gram negative, fastidious,  diplococci, that can grow and rapidly multiply in the mucous membranes, especially the mouth, throat, and anus of males and females, and the cervix, fallopian tubes, and uterus of the female reproductive tract.  Uncomplicated gonorrhea  affects approximately 650,000 persons per year (WebMD, 1999).  This bacteria can be passed through sexual contact (vaginal, oral, or anal), even without ejaculation, or spread from the mother to child at birth.  However, the spread and transmission of gonorrhea, along with other sexually transmitted diseases, can be prevented using condoms and other safe sexual practices.

Clostridium tetani

Clostridium tetani is a bacillus, or rod-shaped, bacterium. It is Gram positive and commonly appears to be shaped like a drumstick or tennis racket when stained. This strange appearance is due to the sporulation that occurs inside the cell. C. tetani is an obligate anaerobe and must rely on fermentation. As an obligate anaerobe, it is not able to tolerate the presence of oxygen. C. tetani is known for causing tetanus. Spores of the bacterium enter the body through open wounds and germinate once inside. C. tetani move around by the use of rotary flagella. The organization of these flagella is peritrichous, which means that there are flagella randomly assorted around the cell. C. tetani are found in many different environments, but most commonly in soil, dust, or sediment. They are also found in human and animal intestinal tracts, where they become pathogenic. (GoldenMap)

Escherichia coli (commonly abbreviated E. coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls due to food contamination.[2][3] The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and by preventing the establishment of pathogenic bacteria within the intestine.

E. coli and related bacteria constitute about 0.1% of gut flora, and fecal–oral transmission is the major route through which pathogenic strains of the bacterium cause disease. Cells are able to survive outside the body for a limited amount of time, which makes them ideal indicator organisms to test environmental samples for fecal contamination. There is, however, a growing body of research that has examined environmentally persistent E. coli which can survive for extended periods outside of the host.

The bacterium can also be grown easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is the most widely studied prokaryotic model organism,[citation needed] and an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA.

 Escherichia coli (E. coli)

Staphylococcus aureus

Staphylococcus aureus [staf I lō-kok is aw ree us] (staph), is a type of bacteria that about 30% of people carry in their noses. Most of the time, staph does not cause any harm; however, sometimes staph causes infections. In healthcare settings, these infections can be serious or fatal, including:

• Bacteremia or sepsis when bacteria spread to the bloodstream.
• Pneumonia, which predominantly affects people with underlying lung disease including those on mechanical ventilators.
• Endocarditis (infection of the heart valves), which can lead to heart failure or stroke.
• Osteomyelitis (bone infection), which can be caused by staph bacteria traveling in the bloodstream or put there by direct contact such as following trauma (puncture wound of foot or intravenous (IV) drug abuse).

Staph bacteria can also become resistant to certain antibiotics. These drug-resistant staph infections include: Methicillin-resistant Staphylococcus aureus (MRSA), Vancomycin-intermediate Staphylococcus aureus (VISA), and Vancomycin-resistant Staphylococcus aureus (VRSA)

Klebsiella pneumoniae

K. pneumoniae is a gram negative bacterium. It is facultative anaerobic. It is rod-shaped and measures 2 µm by 0.5 µm. In 1882, Friedlander C. Uber first discovered Klebsiella to be a pathogen that caused pneumonia. Many hospital cases around the world have been linked to K. pneumoniae. Therefore, more studies of the strains were important and performed. The bacterium was isolated and sequenced from a patient in 2004. K. pneumoniae is commonly found in the gastrointestinal tract and hands of hospital personnel. The reason for its pathogenicity is the thick capsule layer surrounding the bacterium. It is 160 nm thick of fine fibers that protrudes out from the outer membrane at right angles. Another site on the human body that this bacteria can be found is the nasopharynx. Its habitat is not limited to humans but is ubiquitous to the ecological environment. This includes surface water, sewage, and soil.

Clostridium botulinum

Clostridium botulinum is a rod-shaped microorganism. It is an obligate anaerobe, meaning that oxygen is poisonous to the cells. However, C. botulinum tolerates traces of oxygen due to the enzyme superoxide dismutase (SOD) which is an important antioxidant defense in nearly all cells exposed to oxygen. C. botulinum is only able to produce the neurotoxin during sporulation, which can only happen in an anaerobic environment. Other bacterial species produce spores in an unfavorable growth environment to preserve the organism's viability and permit survival in a dormant state until the spores are exposed to favorable conditions.

In the laboratory Clostridium botulinum is usually isolated in tryptose sulfite cycloserine (TSC) growth media in an anaerobic environment with less than 2% of oxygen. This can be achieved by several commercial kits that use a chemical reaction to replace O2 with CO2 (E.J. GasPak System). C. botulinum is a lipase positive microorganism that grows between pH of 4.8 and 7 and it can't use lactose as a primary carbon source, characteristics important during a biochemical identification.

Streptococcus pyogenes

Streptococcus pyogenes is one of the gram-positive cocci in chains overlap. The cell walls of streptococcal cells has some interesting features. The high content of peptidoglycan (murein layer) of carbohydrate (C polysaccharide) gives the cells a very strong structure. The C-polysaccharide antigen is effective. It is in some species, especially beta-hemolytic streptococci, species-specific and is then called a group antigen. By the American microbiologist Rebecca Lancefield established classification of streptococci and enterococci D in the serological groups A, B, C, etc. based on these antigenic. Streptococci of serological group A belong to the species Streptococcus pyogenes. As a further antigen in Streptococcus pyogenes has the M-protein. This feature allows the subdivision into serovars. The typing relies today mostly on the sequencing of the genes of the M proteins (emm genes). Currently more than 150 different emm-types are known. The M protein has an antiphagocytic effect.

Treponema pallidum

Treponema pallidum is a Gram-negative bacteria which is spiral in shape. It is an obligate internal parasite which causes syphilis, a chronic human disease. Syphilis is a sexually transmitted disease but transmission can also occur between mother and child in utero; this is called congenital syphilis. Syphilis was first discovered in Europe near the end of the fifteenth century. The virulent strain of T. pallidum was first isolated 1912 from a neurosyphilitic patient by Hideyo Noguchi, a Japanese bacteriologist. Although for the past decades treatment has been available, syphilis remains a health problem throughout the world. The WHO (world health organization) “estimates that 12 million new cases of syphilis occur each year.” This is a major problem in developing countries where prenatal testing and antibiotics are not available. In such cases syphilis can be passed from mother to unborn child. In a recent study, congenital syphilis was reported as the cause of 50% of all stillbirths in Tanzania. Another major complication of syphilis is its ability to increase the likelihood of transmission of HIV.

T. pallidum is an important organism because of its ability to cause disease in humans and in efforts to better understand it, its genome was sequenced in July of 1998. T. pallidum cannot be cultured in the lab and therefore cannot be investigated using conventional lab techniques. By sequencing its genome, scientists are able to better understand T. pallidum, however many things remain a mystery, most notably what exactly is the virulence factor of this bacteria.

Streptococcus pneumoniae, or pneumococcus, is a Gram-positive, alpha-hemolytic, aerotolerant anaerobic member of the genus Streptococcus. A significant human pathogenic bacterium, S. pneumoniae was recognized as a major cause of pneumonia in the late 19th century, and is the subject of many humoral immunity studies.

Despite the name, the organism causes many types of pneumococcal infections other than pneumonia. These invasive pneumococcal diseases include acute sinusitis, otitis media, meningitis, bacteremia, sepsis, osteomyelitis, septic arthritis, endocarditis, peritonitis, pericarditis, cellulitis, and brain abscess.

S. pneumoniae is one of the most common causes of bacterial meningitis in adults and young adults, along with Neisseria meningitidis, and is the leading cause of bacterial meningitis in adults in the USA. It is also one of the top two isolates found in ear infection, otitis media. Pneumococcal pneumonia is more common in the very young and the very old.

S. pneumoniae can be differentiated from Streptococcus viridans, some of which are also alpha-hemolytic, using an optochin test, as S. pneumoniae is optochin-sensitive. S. pneumoniae can also be distinguished based on its sensitivity to lysis by bile (the so-called "bile solubility test.") The encapsulated, Gram-positive coccoid bacteria have a distinctive morphology on Gram stain, the so-called, "lancet-shaped" diplococci. They have a polysaccharide capsule that acts as a virulence factor for the organism; more than 90 different serotypes are known, and these types differ in virulence, prevalence, and extent of drug resistance.

Streptococcus pneumoniae

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