WHO list of bacteria for which antibiotics are urgently needed     NYC Public Health testing laboratory manual (good resource for types of viral and bacterial diseases and tests used to identify them)

Vaccine Adverse Even Reporting System

Companies: Entasis Therapeutics

Bacteria are a significant cause of disease. Most critical are the multidrug resistant bacteria which cause problems in hospitals, nursing homes and among patietns using devices such as ventilators and blood catheters. Such drug resistant bacterial include acientobacter, Pseudomonas, and various enterobacteriaceae (including Klebsiella, Escherichia coli, Serratia and Proteus). They can cause severe and often deadly lung and bloostream infections.  Other increasingly drug resistant bacteria that cause more common disease such as gonorrhoea and food poisoning.

One estimate puts some 13.7 million infection related deaths in 2019 of which 7.7 million deaths were assocaited with 33 bacterial pathogens. Five leading pathogens -Staphyloccous aureus, Escherichia coli, Streptococcus pneumoniae, Klebsiella pneumoniae and Pseudomonas aeruginosa were responsible for 54.9% of deaths among the investigated bacterial The age-standardised motality rate assocaited with these bacterial pthogens was highest in the sub-Saharan Afica super-region with 230 deaths per 100k population and lowest in the high incoe super-region with 52.5 deaths per 100k population. S. aureus was the leading bacterial cause of death in 135 countires and was also associated with the most deaths in individuals older than 15, globally. (“Global mortality associated with 33 bacterail pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019, GBD, 2013)

Affecting the Cardiovascular and Lymphatic System

Anaplasmosis: Anaplasma is a small inracellular bacterium that shares lifestyle characteristics with Ehrichia (below) and casues nearly identical clinical manifestations. But the two bacteria differ in geographic distributions and are carried by two different species of ticks. Treatmnet of anaplasmosis is by doxycycline.

Bruceliosis: is a bacterial genus that contains tiny, aerobic, gram-negative coccobacilli. Several species can cause the disease in humans: B. melitensis, B. abortus and B. suis. Brucellosis often casues severe outbreaks of placental infection in levestock, which results in devasting economic impacts. The potential economic impact is one reason the CDC lists it as a possible bioterrorism agent.

Cat-Scratch disease: is one of a group of diseases caused by different species of the small gram-negative rod Bartonella. Bartonella species are considered to be emrging pathogens. They are fastidious but not obligate intracellular parasites, so they will grwo on blood agar. B. henseelae is the agent of cat scratch disease, an infection connected with being clawed or bitten by a cat. It is transmitted among cats by fleas. The pathogen is present in over 40% of cats, especially kittens. Tehre are aobut 25,000 cases per year in the U.S., 80% of them in children of 2-14. The symptoms start after 1-2 weeks, with a cluster of small papules at the site of inoculation. Mmost infections remain localized and resolve in a few weeks, but drugs such as azithromycin, erythromycin and rifampin can be effective therapies. The disease can be prevented by flea control and by through antiseptic cleansing of a cat bite or scratch.

Endocarditis: 

Endocarditis is an inflammation of the endocardium, or inner lining of the heart. Endocarditis is divided into “acute” and “subacute”.

—signs and symptoms: are similar for both acute and subacute endocarditis except that in the subactue condition they develop more slowly.  Symptoms include fever, fatigue, joint pain, endema (swelling of feet, legs and abdomen), weakness, anemia, abormal hearthbeat and soemtimes symptoms similar to myocardial infarction.

–causes:  The acute form of endocarditis is most often casued by Staphyloccoccus aureus. Other agents includes Sreptococcus pyogenes, Sreptococcus pneumononiae and Neisseria gonorrheoeae, as well as a host of ther bacterial.  Most commonly, subactue endocarditis is caused by bacterial of low pathogenicity often originating int he oral cavity. Alpha-hemolytic streptococci, such as Streptococcus sanguis, S. oralis and S. mutans are most often responsible, although normal biota form the skin and other bacteria can also colonize abnormal valvues and lead to this condition.

–Transmission: Minor disruptions in the skin or mucous membranes, such as those induced by overly vigorous toothbrushing, dental procedures, or relatively minor cuts and lacerations can introduce bacteria into the blood stream and lead to valve colonization.

–Prevention: the practice of prophylactic antbiotic therapy in advance of surgical and dental procedures on patients with underlying valve irregularities has decreased the inidicne of this infection.

Ehrichiosis: Ehrlichia is a small intracellular bacterium with a strict aprasitic existence and associated with ticks (Ixodes species). The species of tick varies with the geographic location. The signs and symptoms include an acute febril state resulting in headache, muscle pain, and rigors. Most patients recover rapidly with no lasting effects, but about 5% of older, chronically ill patients can die. Rapid diagnosis is done through PCR tests and indirect fluorescent antibody tests. It cn be critical to differentiae coinfection with Lyme disease Borrelia, which is carried by the same tick. Doxyclycline will clear up most infections within 7-10 days.

Septicemia (Sepsis):

Septicemia occurs when organisms are actively multiplyng in the blood.

–signs and symptoms: include fever, altered mental state, shakin, chills and gastrointestinal symptoms. Often an increased breathing rate is exhibited, accompanied by respitratory alkalosis (increased tissue pH due to breathing disorder). Low blood pressure is a hallmark of this condition and is caseud by the inflammatory response to infectious agents in the blood, which leads to a loss of fluid from the vasculature.

–causes: in the vast majority of cases are by bacteria. MRSA is a very common cause. About 10% of cases are caused by fungal infections. Polymicrobial bloodstream infections increasinly are being identified in which more than one microorganisms is causing the infection.

–pathogenesis and virulence factos: Gram-negative bacteria multipolying in the blood release large amounts of endotoxin sitmulating a massive immune response mediated by a host of cytokines. This response invariabley leads to a drastic drop in blood pressure, a condition called “endotoxic shock”. Gram-postive bacteria can instigate a similar cascade of events when fragments of their cell walls are released into the blood.

–Transmission: in many cases is due to parenteral introduction of the microorganisms via intravenous lines or surgical procedures. Other infetions may arise from serious urinary tract infections or from renal, prostatic, pancreatic, or gallbladder abscesses. Patietns with underlying spleen malfunction may be predisposed to multiplication of microbes in the blood stream. Meningitis, osteomyelitis (bione infections) and pneumonia can all lead to spesis. At least 200,000 cases occur in year in the U.S. resulting in more than 100,000 deaths.

–Diagnosis: is by a blood culture.

–prevention and treatment: empiric therapy, which is begun immediately after blood cultures are taken, often begins with a broad spectrum antibiotic. Once the organisms is identified, and its antbitoic susceptibility is known, treatment can be adjusted. In spesis, the capillaries become leaky, cuasing fluid volume to leave the blood vessels and move to the interstitial space. With depleted plasma volume, the pateint experiences low blood pressure. The rapid adminsitration of intravenous fluid volume is often necessary to resuscitate a patient with sepsis. Medications may also be started to help support the patient’s blood pressue.

Lyme Disease: 

–cause: Borrelia burgdorferi is considered the casue of Lyme disease. They are unusual spirochetes.

–pathogenesis and virulence factors: The bacterium is a master of immune evasion. It changes its surface antigens while it is int he tick and again after it has been transmitted to a mammalian host. It provokes a strong humoral and cellular immune response, but this repsonse is mainly ineffective, perhaps becasue of the bacterium’s abiliyt to switch its antigens.

–transmission and epidemiology: B. burgdorferi is transmitted priarmily by hard ticks of the genus Ixodes, in the northern part of the U.S. Ixodes scapularis (the black legged deer tick) passes through a complex 2 year cycle that involves two principal hosts. In California, the transmission cycle involves Ixodes pacificus, another black legged tick, and the dusky fotted woodrat as reservoir. The greatest concentrations of Lyme disease are found in areas having large populations of obth the intermediate and efinitive hosts.

–diagnosis: culture is not useful. Diagnosis inthe early stages if the rash is present, is usually accomplished based on symptoms and history of possible exposureto ticks. In alte stages, ELISA and/or Wetern blots can be used to detect antiboides in the blood. It is important to consider coinfection with Anaplasma or Babesia since these organisms are transmitted by the same kind of ticks.

–prevention and treatment. Anyone invovled in otudoor activites whould wear protective clothing, boots, leggins and insect repellent containing DEET. One should also inspect their bodies for ticks and remove ticks gently wihtout crusing, preferably with forcepts or fingers protected with gloves, becasue it is possible to become infected by tick feces or boidy fluids. Early, prolonged (2 weeks) treatment with doxycyline or amoxicillin is effective and other antbiotics such as centriaxone and penicillin are used in late Lyme disease therapy.

Plague:

Pneumonic plague is a resptirotry disease. However, bubonic plague enteres the lmph nodes and is filtered by a local lymph node.

–cause: The cause of bubonic plague is a tiny gram-ngeative rod, Yersinia pestis, a member of the family Enterobacteriaceae. Y. pestis displays unusual bipolar staining that makes it look like a safety pin.

–Pathogenesis and virulence factors: the number of bacteria required to initiate a plague infection is small, perhaps only 3-50 cells.

–Transmission and epidemiology: The plague bacterium residues in over 200 species of mammalian hosts. Some of these, such as mice and voles, serve as long term endemic reservoirs, which are not affected by the disease. Other psecies, including rats and rabbits, are amplifying reservoirs, which get sick and tend to be closely connected to outbreaks of plague in humans. The principal agents in the transmission of the plague bacterium are fleas.  After a flea ingests a blood meal from an infected animal, the bacteria multiply in its gut. The bacterium promotes its spread by causing coagulation and blockage of the flea’sesophagus. Being unable to feed properly, the ravenous flea jumps from animal to animal in a futile attempt to get nourishment. Regurgitated infectious material then is inoculated into the bite wound. The distribution of plague is extensive. Although the diase has been reduced in the devleoped world., it has been increasing in Afical and other parts of the world. In the US sporadic cases (usually 1020 per year0 occur as a result of contact with wild and domestic animals. It is considered endemic in US western and southwestern states. Persons most ar risk are veterinatrians and people living and working near woodlands and forests. Dogs and cats can be infected with the plague, often from contact with infected wild aimals such as prairie dogs.

–-signs and symptoms: infection: infection causes inflammation and necrosis of the node, resulting in a swollen lesion called a bubo, usually in the groin or axilla. The incubation period lasts 2-8 days, ending abruptly with the onset of fever, chills, headache, nausea, weakness and tenderness of the bubo. Mortaility rates, even with treatment, can reach up to 15%.

Treatment: is streptomycin or gentamicin.

Rocky Mountain Spotted Fever: is casued by a bacterium called Rickettsia rickettsii that is transmitted by hard ticks such as the wood tick, the American dog tick and the Lone Star tick. After 2-4 days of incubation, the first symptoms are sustained fever, chills, headache and muscular pain. A distinctive spotted rash usually comes on within 2-4 days after the prodome which usually appers first on the wrists, forearms and ankles before spreading. Early lesions are slightly mottled like measles, but later ones can change shape to look like other types of rashes. In the most severe untreated cases, the enlarged lesions merge and can become necrotic, predisposing to gangrene of the toes or fingertips. The most serious manifestations are cardiovascular disruption, including hypotension, thrombosis and hemorrhage. Conditions of restlessness, delirium, convulsions, tremor and coma can occur in about 20% of untreated cases and 5-10% of treated cases.

Tularemia (rabit fever): 

–cause: is a facultative intracellular gram-negative bacterium called Francisella tularensis: It is a zoonotic disease of assorted mammals endemic to the Northern Hemisphere. Becasue it has been associated with outbreaks in wild rabits, it is sometimes celld rabbit fever. It is on a Category A bioterrorism list.

–signs and symptoms: after an incubation from a few days to 3 weeks, acute symptoms of headache, backache, fever, chills, coughing and weakness appear.

–Epidemiology:

During 2011–2022, a total of 47 states reported 2,462 tularemia cases, but four central states (Arkansas, Kansas, Missouri, and Oklahoma) accounted for 50% of all reported cases. Incidence was highest among children aged 5–9 years (0.083 per 100,000 population) and adult males aged 65–84 years (range = 0.133–0.161). Incidence among American Indian or Alaska Native persons (0.260) was approximately five times that among White persons (0.057). See CDC

–transmission and epidemiology:

Although rabbits and rodents (muskrats and ground squirrels) are the chief reservoirs, other wild animals (skunks, beavers, foxes, opossum) and some domestic animals are implicated as well. The main route of transmission has been through the activity of skinning rabbits, but now transmission via tick bites is more common. Mites and mosquitos cna also transmit it. With an estimated infective dose of 10-50 organisms, F. tularensis is often considered one of the most infectious of all bacteria. Cases have appeared in people who have accidnetally run over rabbits while lawn mowing, presumably form inhaling aerosolized bacteria. There are several hundred cases in the U.S. per year and itnernationally 500,000 cases.

–prevention and treatment: antimicrobial therapy must not be discontinued prematurely becasue F. tularensis can lead to relpases. Posexposure proplylaxis with doxycycline or ciprofloxacin can prevent the disease in lab workers or thers who may have been exposed. Laboratroy workers must wear gloves, masks and eyewear.  The eath rate in the most serious forms of disease is 30%, but proper treatment with gentamicin or streptomycin reduce mortality to almost zero.

Q Fever:

The name of this diease arose from not being able to identify its cause; Q standing for “query”. Its cause however is the bacterium Coxiella burnetti. Clinical manifestations of acute Q fever are abrupt onselt of fever, chills, head and muscle ache, and, occasionally, a rash. These disease is soemtimes compolicated by pneumonitis (30% of cases), hepatits, and endocarditis. C. burnetii is a very small pleomorphic (variously shaped) gram-negative bacterium. It is apparently harbored by a wide assortment of vertebrates and athropods, specially ticks. However, ticks do not directly transmit the disease to humans. Humans aquire infection largely by means of environmental contaimination and airbone spread. Soruces of infection include urine, feces, milk and airbone particles form infected aiamsls. The primary protals of entry are the lungs, skin conjunctiva and gastroinestinal tract. People at highest risk are farm workers, meat cutters, veterinarians, laboratory technicians and consumers of raw milk products.

Affect the skin (Also see Bacteria)

Cellulitis: is a condition caused by a fast spreading infection in the dermis and in the subcutaneous tissue below it. It causes pain, tenderness, swelling and warmth. Fever and swelling of the lymph nodes draining the area may also occur. Fequently, red lines leading away from the area are visicle. Most common causes of the condition in healthy people are Staphylococcus aureus and Streptococcus pyogenes, although almost any bacterium and some fungi can cause the condition in an immuncompromised patients. In infants, group B streptococci are a frequent cause. The mild cellulitis responds well to oral antibiotics chosen to be be effective against S. aureus and S. pyogenes. Keep in mind that if it is caused by S. aureus, it usually of the methicillin resistant variety (MRSA). More involved infections in immunocompomised people require intravenous antibiotics.  If there is extensive areas of tissue damage, surgical debridement is warranted.

Conjunctivities: is relatively common. It can be caused by specific microorganisms that have a prediliection for eye tissues, by contaminants that proliferate due to the presence of a contact lens or an eye injury, or by accidental inoculation of the eye by a traumatic event. Cases of neonatal eye infection with Neiseeeria gonorrhaeae or Chlamydia trachomatis are usually transmitted vertically from a genital tract infection in the mother. Bacterial conjunctivities in other age groups is monst commonly casued by Stpahylococcus epidermidis, Streptococcus pyogenes or Streptococcus pneumoniae, although Haemophilus influenzae and Moraxella species are also frequent causes. No. gonorrhaeae and C. trachomatis can also cause conjunctivitis in adults. These infections may result from autoinoculation from a genital infection or from sexual activity, although No.gonorrhaeae can be part of the normal biota in the respiratory tract. A wide variety of bacteria, fungi and protozoa can contaminate contact lenses and lens cases and then be transferred to the eye, resulting in diasease that may be very serious. Newborn children in the U.S. are administered antimicrobials in their eyes after delivery to prevent neonatal conjunctivitis from either N. gonorrhaeae or C. trachomatis.

Cutaneous Anthrax: This form of antrax is the most common and least dangerous version of infection with Bacillus anthracis. It is caused by endospores entering the skin through small cuts or abrasions. Germination and growth of the pathogen in the skin are marked by the production of a papule that becomes increasingly necrotic and later ruptures to form a painless balck eschar. In the fall of 2001, 11 caes of cutaneous anthrax occured in the U.S. as a result of bioterrorism. Mail workers and others contracted the infection when endospores were sent rhough the mail. Left untreated, even the cutaneous form of antrax is fatal about 20% of the time. A vaccine exists but is recommended only for high risk persons and the military.

Impetigo: is a superficial bacterial infection that causes the skin to flake or peal off. It is not a serious disease but it is highly contagious and children are the primary victims. It can be casued by either S. aureus of S. pyogenes and some cases are probably casued by a mixture of the two. Impetigo is highly contageious and transmitted through direct contact but also via fomites and mechanical vector transmission. The peak incidence is in the summer and fall. The only current rpeention is good hygiene. The lesion of impetigo looks variously like peeling skin, crusty and flaky sabs or honey colored crusts. Lisions are most often found around the mouth, face and extremities, although they can occur anywhere on the skin. It is very superficial and it itches.

Keratitis: is a serious eye condition that can lead to complete corneal destruction. Any microrganism can cause this condition, especially after trauma to the eye, but miscellaneous bacteria cause 80% of the infectious keratitis cases.

Staphylococcus aureus, often referred to as “staph”, is a common type of bacteria that is found in about 25 to 30 percent of healthy people, primarily on the skin or in the nose. Most of these individuals are colonized by the staph bacteria, meaning that the bacteria are present but are not causing disease. Some people become infected with staph bacteria indicating that the bacteria are present and cause disease. Although staph bacteria do not usually cause infection, they can bring about disease if they penetrate through a break in the skin or through mucous membranes. Staph bacteria are one of the most common causes of skin infections and sometimes produce relatively minor skin infections such as pimples and boils. However, they can cause more serious illnesses such as surgical wound infections, bloodstream infections, bone infections, and pneumonia. In the past few decades, a more dangerous form of staph has emerged. This form is known as methicillin-resistant Staphylococcus aureus and is usually referred to by the acronym MRSA.

–MRSA infections: of the skin tend to be raised, red tender, localized lsions often featuring pus and feeling hot to touch. They occur easily in breaks in the skin casued by injury, hsaving or even just abrasion. They may localize around a hair follicle. Fever is a common feature. MRSA is a common containinant of all kinds of surfaces you touch, especially those not sanitized. Gym equipment, airplane tray tables, electronic devices, razors are all sources.

MRSA is categorized by the setting in which it is acquired. The first type, healthcare-acquired MRSA (HA-MRSA), has been recognized since the 1960s. Strains of staph were identified in patients in hospital and healthcare facilities that were resistant to methicillin (resistance to penicillin had occurred even earlier). The incidence of this infection has been increasing over time, with patients who have had surgery, medical devices implanted, or weakened immune systems being particularly at risk. Of greater concern is a second type of MRSA which appeared in the 1990s and is known as community-acquired MRSA (CA-MRSA). CA-MRSA occurs outside of hospital settings and usually manifests itself as a skin infection in an otherwise healthy individual. CA-MRSA can develop into a more serious, life-threatening illness. CA-MRSA tends to occur under conditions where people are in prolonged physical proximity, such as in childcare and long-term care facilities, and in soldiers, prisoners, athletes involved in skin-to-skin contact sports such as wrestling, and in individuals sharing personal items such as towels. Unlike HA-MRSA, the source of infection for CA-MRSA is often difficult to identify.  See Baylor College of Medecine

CA-MRSA usually enters the body though a cut or scrape. The first sign of infection is commonly described as resembling a spider bite – a spot on the skin that is red, swollen, and painful. The site may produce pus. Infrequently, CA-MRSA infection can progress to a more serious disease, such as bloodstream infection or pneumonia. CA-MRSA can, in rare cases, lead to death. Highly publicized accounts of the deaths of at least three students from CA-MRSA in late 2007 prompted concern among students, parents, and school officials. The best defense against MRSA is to maintain good hygiene, including frequent and thorough hand washing, and to avoid the sharing of personal care items.

Scientists are working to understand the genetic changes in MRSA that allow the bacterium to cause serious illness in otherwise healthy individuals. To begin to answer this question, MVM scientists and others at Baylor College of Medicine initiated a project to obtain the DNA sequence of a strain of CA-MRSA called USA300. They chose the USA300 strain, one of two strains that cause the majority of CA-MRSA cases, because it has emerged as the predominant strain causing skin infections, as well as more serious infections, in both pediatric and adult patients in many states. Before 2000 this strain was rarely found in the community; today it accounts for 70 percent of CA-MRSA patients at Texas Children’s Hospital. Another reason for the interest in the USA300 strain is that it appears to be more virulent than other strains. The scientists concluded that the USA300 strain that they sequenced was very similar to other staph strains. This suggests that the increased virulence of the USA300 strain is due to subtle genetic changes within its genome. One intriguing finding of their study is that the bacterium has picked up a plasmid that contains a gene that confers resistance to bacitracin, an antibiotic commonly found in over-the-counter skin ointments. See Baylor College of Medecine

All pathogenic S. aureus strains typically produce coagulase, an enzyme that coagulates plassma. Because 97% of all human isolates of S. aureus produce this enzyme, its presence is consdiered a diagnostic characteristic. PCR is routinely used to diagnose MRSA. Alternatively, cultivation on blood agar is useful.

Treatment often starts with incision of the lesion and drainage of the pus. Antimicrobial treatment should include more than one antibiotic. Current recommendations in the U.S. are for teh use of vancomycin. Manuka honey is currently used as a wound treatment and suggested to be effective in Methicilin-resistant Staphylococcus aureus (MRSA) elimination. Manuka honey comes from New Zealand and Australia. It is harvested by European honeybees (Apis mellifera) that have pollinated and collected nectar primarily fomr the Manuka tree. (Frydman “Manuka honey microneedles for enhanced wound healing and the prevention and/or treatment of Methicilin-resistant Staphylococcus aureus (MRSA) surgical stie infection” Scientific Reports, 10, 2020).

Mycobacterium abscessus (also called M. abscessus): is a bacterium distantly related to the ones that cause tuberculosis.  It is part of a group of environmental mycobacteria and is found in water, soil, and dust. It has been known to contaminate medications and products, including medical devices. M. abscessus can cause a variety of infections. Healthcare-associated infections due to this bacterium are usually of the skin and the soft tissues under the skin. It is also a cause of serious lung infections in persons with various chronic lung diseases, such as cystic fibrosis. People with open wounds or who receive injections without appropriate skin disinfection may be at risk for infection by M. abscessus.  Rarely, individuals with underlying respiratory conditions or impaired immune systems are at risk of lung infection. See CDC

Afficting the Urinary Tract (UTIs)

Generally:

The urinary tract is responsible for removing substances form the blood, regulating certain body processes and forming urine and transporting it out of the body. The urinary tract includes the kidneys, ureters, bladder and the urethra. Urine in addition to being acidic, aso contains the antibacterial proteins, lysozyme and lactoferrin. Lactoferrin is an iron binding protein that inhibits bacterail growth. Lysozyme is an enzyme that breaks down peptidoglycan. The urine also contains secretory IgA.

–Transmission:

UTIs acquired in health care facilities are almost always a result of catheterization. Community acquired UTIs are nearly always transmitted not from one person to another but from one organ system to anotehr, namely from the GI tract to the urinary system. In 95% of UTIs, the cause is bacteria that are normal biota in the gastrointestinal tract with E coli being the most common. They are more common in women than in men because of the nearness of the female urethral opening to the anus.

–Symptoms: Common symptoms of UTIs include burning sensations during urination, feverish conditions, constant, strong urge to urinate, pain the the rectal region for mails and pain in the pelvis in females, intense passing out of small amounts of urine, urine with appearance of blood and/or foul odor and pain around the hips, abdomen, or lower back region.

–Treatment: Sulfa drugs such as trimethoprim-sulfamethoxzole are most often used for UTIs of various etiologies. Often another nonantibiotic drug called phenazopyridine (Pyridium) is adminsitered simultaneously. This drug relieves the uncomfortable symptoms of burning and urgency. A large percentage of E coli strains are resistant to penicillin derivatives, so these should be avoided.

Clostridium perfringes: is a Gram-positive, rod-shapped, anaerobic, spore-forming pathogenic bacterium of the genus Clostridium. C. perfringes is ever-present in nature and can be found as a normal component of decaying vegentation, marine sediment, the intestinal tract of humans and other vertebrates, insects, and soil. Its densopores are able to survive long periods of exposure to air and other adverse environmental conditions. It is wone of the most common causes of food borne illnesses.

E. coli: Urinary tract infections (UTIs) are very common infections in humans, and Escherichia coli (E. coli) is the main cause of UTIs. Escherichia coli and urinary tract infections are often discussed together as E. coli (uropathogenic E. coli, UPEC) and is often indicated as the major cause of UTIs.

E. coli as a Gram-negative bacillus belongs to the Enterobacteriaceae family. Treating infections caused by E. coli is challenging due to antibiotic resistant strains. The generation of extended spectrum
beta-lactamas (ESBL) in E. coli causes its resistance against several antibiotics. Beta lactamases can be
generated by Gram-negative bacteria and are present in the Enterobacteriaceae family. ESBL-producing bacteria are resistant to cephalosporins, penicillin, tazobactam/piperacillin and other antibiotics such as co-trimoxazole, fluoroquinolones, and tetracycline. Also, the ESBL-coding plasmid easy transfer is an important threat to hospitalized patients. See Farzinpoor

Leptospirosis: 

Leptospirosis is a zoonotic bacterial disease spread through the urine of infected animals; the typical incubation period is 5–14 days. In approximately 90% of human cases, illness is asymptomatic or mild, characterized by fever, chills, myalgia, nausea, vomiting, diarrhea, headache, calf pain, and conjunctival suffusion, but severe illness can progress to multiorgan dysfunction and death. See CDC

–signs and symptoms: during the early phase, the pathogen appears in the blood and crebrospinal fluid. Symptoms include sudden high fever, chills, head-ache, muslce aches, conjunctivitis and vomiting. During the second phase, the blood infection is cleared and symptoms include milder fever, headache due to leptospiral meningitis and in rare cases, Weil’s syndome, a cluster of syptoms characterized by kidney invasion, hepatic disease, jaundice, anemia and nuerological distrubances. Long term disability and even death can result from damage to the kidneys and liver, but they occur primarily with the most virulent strains in the elderly persons.

–-causative agent: Leptospires are typical spirochete bacterai marked by tight, regular, individual coils with a bend or hook at one or both ends.

–Transmission: infection occurs almost entirely through contact of skin abrasions or mucous membranes with animal urine or some environmental source containing urine. In 1998, dozens of ahtletes competing in the swimming phase of a triathlon in Illinois contactred leptospirosis form water. It is a common pathogen in areas of Latin America and Asia.

–Treatment: early treatment with doxycycline, peniccilin G, or ceftriazone rapidly reduces symptoms and shortens the course of disease, but delayed therapy is less effective.

Affecting the Genitourinary System

The genital system has reproduciton as its major function. The male reproductive system produces, maintains and transports sperm cells and is the source of male sex homrones. It consists of the testes, which produces sperm cells and hormones and the epididymides, which are coild tubes leading out of the testes. Each epididymis terminates in a vas deferns, which combines with the seminal vesicle and terminates in the ejaculatory duct. The contents of the ejaculatory duct empty into the urethra during ejaculation. The prostate gland is a walnut shapped structure at the base of the urethra. It also contribues to the released semen.

The female reproductive system consists of the uretru, the fallopian tubes and vagina. It also includes the cervix, which is at the lower one third of the uterus and the part that connects to the vagina.

Chancroid:

–Cause: Chancroid is caused by a pleomorphic gram-negative rod called Haemophilus ducreyi.

–Symptoms: this ulcerative disease usually beings as a soft apule, or bump, at the point of contact and develops into a “soft chancre” (in contrast to the hard symphilis chancre), which is very painful in men but may be unnoticed in women. Inguinal lymph nodes can become very swollen and tender.

–Epidemiology: Chancroid is very common in the tropics and subtropics and is becoming more common in the U.S.

–Transmission: Chancroid is transmitted exclusively through direct contact, especially sexually. The disease is associated with sex workers and poor hygiene. Uncircumcised men seem to be more commonly infected than those who have been circumcised. People may carry this bacgerium asymptomatically.

Chlamydai: is the most common reportable infectious diasese in the U.S. Annually, more than 1 million cases are reported, but the actual infection rate may be 5-7 times more. Chlamydia trachomatis affects mostly young women, but it can occur in both men and women and in all age groups. It’s not difficult to treat, but if left untreated it can lead to more-serious health problems.  See Mayo Clinic

The sequences of bothChlamydia trachomatisandChlamydiapneumoniaehave been determined with the hope that a comparison between the two genomes will significantly enhance the understanding of both pathogens. 

–signs and symptoms:

Chlamydia doesn’t usually cause any symptoms. So you may not realize that you have it. People with chlamydia who have no symptoms can still pass the disease to others. If you do have symptoms, they may not appear until several weeks after you have sex with an infected partner. See MedlinePlus

In males, the bacterium can cuase an inflmmation of the urethra. The symptoms mimic gonorrhea; discharge and painful urination. Females who experince symptoms have cervicitis, a discharge, and often sapingitis.

Certain strains of C. trachatis can invade the lymphatic tissues, resulting in alymphogramuloma venereum. The condition is accompannied by headache, fever, and muscle aches. The lymph nodes near the lesion begin to fill with granuloma cells and become enlarged and tender. These “nodes” can cause long term lymphatic obstruction that leads to chronic, deforming edema of the genitalia or anus. The disease is endemic to South America, Afica and Asia, but occasionally occurs in other parts of the wrold.

Babis born to mothers with chlamydia can develop eye infections and also pneumonia if they become infected.

–causative agent: C. trachamatis is a very small gram negative bacterium. It lives inside host cells as an ogligate intracellular parasite.

–transmission: The microbe shows an astoundingly borad distribution within the population and incidence is rising. Adolescent women are more likely than older women to harbor the bacterium because it prefers to infect cells that are prevalent on the adoslescent cervix. It is transmitted sexually.

–Immune Response: The first and most important immune response to Chlamydia infection is a local one, whereby immune cells such as leukocytes are recruited to the site of infections, and subsequently secrete pro-inflammatory cytokines and chemokines such as interferon gamma. Immune cells also work to initiate and potentiate chronic inflammation through the production of reactive oxygen species (ROS), and the release of molecules with degradative properties including defensins, elastase, collagenase, cathespins, and lysozyme. This long-term inflammation can lead to cell proliferation (a possible precursor to cancer), tissue remodeling, and scarring, as well as being linked to the onset of autoimmune responses in genetically disposed individuals. See RedGrove

–Detection: is with PCR or ELISA.

–Prevention: avoiding contact with infected tissues and secretions or barrier protection is the only means of prevention.

–Treatment: Chlamydia is treated with antibiotics. The recommended antibiotic treatment is doxycycline taken twice a day for seven days or azrithromycin taken in one single dose. Other alternative medications may be used but are not as effective as azrithromycin and doxycycline. Persons being treated for chlamydia should not have sexual intercourse for seven days after single dose therapy (azrithromycin) or until completion of all seven days of antibiotics (doxycycline). Patients can be re-infected if their sex partners are not treated. See NY State Dept Health

Gonorrhea: has been known as an STD since ancient times.

–signs and symptoms: In the male, infection of the urethra elicity urethritis, painful urination, and a yellowish discharge, although a relatively large number of ases are symptomatic. In ost cases, infection is limited to the distal uronetical tract, but it can occasionally spread from teh urethra to the prostate gland and epididymis.  See WebMD.

In the female, it is likely that both the urinary and genital tracts will be infected during sexual intercourse. A mucopurlent (containing mucos and pus) or bloody vaginal discharge occurs in a minortiy of the cases, along with painful urination if the urethra is affected.

–Causative agent: N. gonorrhaeae is a pyogenic (pus forming) gram-negative diplococcus. It apepars as paris of kidney bean shaped bacterial, with their flat sides touching.

Transmission: gonorrhea is a strictly human infection that ranks among the most common STDs.

–Diagnosis: Specific microbiologic diagnosis of N. gonorrhoeae infection should be performed for all persons at risk for or suspected of having gonorrhea; a specific diagnosis can potentially reduce complications, reinfections, and transmission. Culture, NAAT, and POC NAAT, such as GeneXpert (Cepheid), are available for detecting genitourinary infection with N. gonorrhoeae; culture requires endocervical (women) or urethral (men) swab specimens. Culture is also available for detecting rectal, oropharyngeal, and conjunctival gonococcal infection. NAATs and POC NAATs allow for the widest variety of FDA-cleared specimen types, including endocervical and vaginal swabs and urine for women, urethral swabs and urine for men, and rectal swabs and pharyngeal swabs for men and women. See CDC

–Prevention/screening: no vaccine is available. Using condoms is an effective way to avoid transmission.

Annual screening for N. gonorrhoeae infection is recommended for all sexually active women aged <25 years and for older women at increased risk for infection (e.g., those aged ≥25 years who have a new sex partner, more than one sex partner, a sex partner with concurrent partners, or a sex partner who has an STI) (149). Additional risk factors for gonorrhea include inconsistent condom use among persons who are not in mutually monogamous relationships, previous or coexisting STIs, and exchanging sex for money or drugs. Clinicians should consider the communities they serve and consult local public health authorities for guidance regarding identifying groups at increased risk. Gonococcal infection, in particular, is concentrated in specific geographic locations and communities. MSM at high risk for gonococcal infection (e.g., those with multiple anonymous partners or substance abuse) or those at risk for HIV acquisition should be screened at all anatomic sites of exposure every 3–6 months (see Men Who Have Sex with Men). At least annual screening is recommended for all MSM. Screening for gonorrhea among heterosexual men and women aged >25 years who are at low risk for infection is not recommended (149). A recent travel history with sexual contacts outside the United States should be part of any gonorrhea evaluation. See CDC

—-NGoXIM is a prophylactic vaccine against gonorrhea which has gained funding from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH). NGoXIM candidates uses Intravacc’s outer-membrane vesicle (OMV) platform technology and Therapyx GneX12 sustained-release microspheres to deliver recombinant human IL-12 intranassaly. OMVs are speherical buddings that are rleased spontaneously on the oter membrane of many Gram-negative bacteria during growth. Such vesicles present surface antigens in a native conformation and have natural properites such as immunogenicity, self-adjuvation and uptake by immune cells. Those features make OMVs a good basis for vaccines against pathoglenic bacteria. The OMVs for the gonorrhea vaccine are dervied form genetically modified Neisseria gonorrhaeae. An intranasal vaccine also causes an immune response in other mucosal tissues such as the genital tract, thus hleping to endure induction of an immune resonse at the site of potential infection as with gonorrhea.

–Symptoms: Urethral infections caused by N. gonorrhoeae can produce symptoms among men that cause them to seek curative treatment soon enough to prevent sequelae, but often not soon enough to prevent transmission to others. Among women, gonococcal infections are commonly asymptomatic or might not produce recognizable symptoms until complications (e.g., PID) have occurred. PID can result in tubal scarring that can lead to infertility or ectopic pregnancy. See CDC

–Treatment: treatemnt includes treating chlamydia also since N. gonorrhaeae is freqeuntly coinfected with Chlamydia. CDC recommends a single dose of 500 mg of intramuscular ceftriaxone. Alternative regimens are available when ceftriaxone cannot be used to treat urogenital or rectal gonorrhea. Although medication will stop the infection, it will not repair any permanent damage done by the disease. The CDC has this bacterium in its Urgent Trheat category for antibiotic resistance.  See CDC

Syphilis: 

–cause: Treonema pallidum which is a spirochete, regularly coiled cell with a gram-negative cell wall. See CDC

–Symptoms: Untreated symphilis is marked by distinct clinical stages designated as primary, secondary and tertiary symphilis. The disease also has latent periods of varying duration during which it is quiescent. The primary stage is marked by the appearance of a hard chancre at the site of entry of the pathogen. Because these culcers tend to be pianless, they may escape notice, especially when they are on internal surfaces. The chancre heals spontaneously without scarring in 3-6 weeks. About 3-6 weeks after the chancre heals, the secondary stage appears. By then, many systems of the body ahve been invaded and simptoms include fever, ehadache and sore throat, followed by lymphadenopathy and peculiar red or brown rash that breaks out on all skin surfaces including the palms of the hands and soles of the feet. A person’s hair often falls out. Like the chancre, the lesions contain viable spirochetes and disappear spontaneously in a few weeks. The major complications at this stage occur in the bones, hair follicles, joints, liver, yes and brain.  See Web MD

–Transmission: Human appear to be the sole natural hosts and source of T. pallidum. The bacterium is extremely fastidious and sensitive and cannot survive for long oustide the host, being rapidly destroyed by heat, drying, disinfectants, soap, hogh oxygen tension and pH changes. It survives a few minutes to hours when protected by body secretions and about 36 hours in sotred blood. The risk of infection from an infected sexual partner is 12-20% per encounter.

–Prevention: People identified as being at risk fo syphilis are given immediate prophylactive penicilline in a single long acting dose. The barrier effect of a condom provides excellent proteciton during the primary phase. Protective immunity apparently does arise in humans, allowing the prospect of an effective immunization program in the future, although no vaccine exists currently.

–Treatment: Syphillis can have very serious consequences if left untreated. Current recommendations are for ciprofloxacin or levofloxacin. See Mayo Clinic.   See Drugs.com.  History of treatment

–Diagnosis: There is a rapid plasmin reagin (RPR) test which is coupled with an immunoassay specific for treponemal antigens.

Vaginosis: also known as BV or bacterial vaginosis

–cause: Bacteria Vaginosis (BV) is an infection that is associated with a group of pathogenic anaerobic microorganisms rather than a specific pathogen. It is a very common manifestation among the women population. Although the exact causative pathogen has not been figured out, it has been observed that there is a corresponding decrease in the population of the lactobacilli species. This results in the increase in the pH of the vaginal lumen due to the reduction in the lactic acid production. Apart from the lactic acid, the production of lactocin and H2O2 also receives a setback. In general, the lactobacilli is replaced with the increased population of pathogenic gram-negative anaerobic bacteria such as E. coli, Gardnerella vaginalis, Mycoplasma hominis, and Mycoplasma curtisii.bacterium Garderella. Vaginosis is most likely a result of a shift from a predominance of good bacteria (lactobacilli) to the vagina to a predominance of bad bacteria such as Gardnerrela vaginalis. The genus of bacteria is a facultative anaerobe and gram-positive, although in a Gram stain it usually appears gram-negative. Some texts refer to it as gram-variable fo this reason. Probably a mixed infections leads to the condition. See Kumar

–symptoms, pathogenesis: vaginal discharge which often ahs a fishy order. Itching is also common. Many women have no noticeable symptoms. Vaginosis can lead to complications such as pelvic inflmmatory disease, infertility and more rarely ectopic pregnancies.

–transmission and epidemiology: 30% of women between 15-44 in the US are estimated to have bacterial vaginosis. Rates are greater in non-whte women.

–Treatment: A lot of antimicrobial agents (e.g., ampicillin, penicillin, and metronidazole) have been used in the treatment of bacterial vaginitis. Metronidazole have evolved as a drug of choice for the treatment of BV and is the widely prescribed drug. It is a nitroimidazole derivative having activity against anaerobic microbes and protozoans. It has been administered either orally or locally. Tablets of metronidazole are easily available for oral administration. Formulations for the local administration of the drug include gels and suppositories. See Kumar

Affecting the Gastrointestinal Tract

Acute Diarrhea: In the U.S., up to a third of all acute diarrhea is transmitted by contaminated food. The most common agents are Salmonella, norovirus, Campylobacter, E. coli STEC strains and Clostridium perfingens. The bacterial agents are described here. Although most diarrhea epidoses are self-limited, other such as E. coli 0157:H7 can have serious effects. In most diarrheal illneses, antimicrobial treatment is contraindicted but some such as Dhigellosis call for quick treatment with antibiotics. Thus it is important to know which agents are causing diarrhea.

–E coli: is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine. Most E. oli strains are harmless, but some serotpyes can casue serious food poisoning in humans. The harmless strains are part of the normal floa of the gut, and can benefit their hosts by producing vitamin K2, and by preventing the establishment of pathogenic bacteria within the intestine. Certain strains such as O157:H7 produce potentially lethal toxins. Food poisoning casued by e. coli can result from eating unwashed vegetables or undercooked meat.

In sub-Saharan Africa, with deteriorating environments attributed to high levels of open defecation, drinking water sources remain vulnerable to faecal contamination. See Gwimbi

–Norovirus:

Norovirus is the leading cause of acute gastroenteritis in the United States. In 2012, CDC established the Norovirus Sentinel Testing and Tracking Network (NoroSTAT) to improve timeliness and completeness of surveillance for norovirus outbreaks that occur in the United States. NoroSTAT is a collaboration between CDC and 12 state health departments. See CDC

Noroviruses are divided into 10 genogroups; viruses in genogroups GI, GII, GIV, GVIII, and GIX cause illness in humans. Norovirus GIX was first identified in fecal samples collected in 1990 from US troops deployed to Saudi Arabia. On March 31, 2021, the Utah County Health Department and Utah Department of Health were notified of an outbreak of gastrointestinal illness at LTCF A. The outbreak was believed to have originated from 2 residents on March 28 and 29. One resident vomited in a well-trafficked, carpeted hallway, which likely contaminated the environment. By mid-April, 4 other LTCFs (B–E) within 20 miles of facility A reported similar outbreaks. Nucleic acids were extracted from fecal specimens using the NucliSENS easyMAG instrument (bioMérieux), and genotyped norovirus-positive samples by using conventional reverse transcription PCR. Purified PCR products were submitted to Sequetech for Sanger sequencing and genotyped by using the human calicivirus typing tool. Norovirus-positive samples were analyzed by performing next-generation sequencing (NGS) of complete genomes using the Illumina MiSeq platform and a GIX-specific forward oligonucleotide primer (5′-ATGGCGTCGARTGACGTCGYTACTGCCYTTGGC-3′). Sequences were analyzed by using the Viral NGS Analysis Pipeline and Data Management tool. norovirus phylogenetic trees for complete RNA-dependent RNA polymerase (RdRp) (1,430 nt) and major capsid (1,668 nt) genes by using MEGA11 software. See Osborn, CDC

–Salmonella: The genus Slmonella causes a variety of illnesses in the GI tract CDC estimates that Salmonella casues about 1.4 million infections a year in the U.S. It has a high infectious dose meaning a lot of organisms ahve to be ingested in order for disease to result. Animal products such as meat and milk can be readily contaminted with Salmonella during slaughter, collection and processing. Salmonella bacteria are normal intestinal biota in cattle, pultry, rodents and reptiles nad each has been a documented source of infeciton and disease in humans. The only prevention for salmonellosis is avoding contact wiht the bacterium. Uncomplicated cases of Salmonellosis are treated with fluid and electrolyte replacment. If a patient is immunocompromised or the disease is severe, trimethoprim-sulfamethoxazole is recommneded.

–Shigella: Shigella bacteria are gram-negative rods, nonmotile and non-endospore-forming. They do not product urease or hydrogen sulfide, which aids in their identification. The symptoms of shigellosis include frequent, watery stools, fever and often intense abdominal pain. Nausea and vomiting are common. Stools often contain blood (diarrhea containing blood is also called dysentery). Transmission can be by direct person to person contact because only a small ID is required, in addition to the usual oral route. Prevention as with most diarrheal diseases is good hygiene. Unlike toher acute diarrhea, all cases of shigellosis should be treated with antibiotics: trimethoprim/sulfamethoxazole if it is sensitive to it, and ciprofloxacin in resistant cases of shigellosis.

–Shiga-Toxin-Producing E. coli (STEC): Dozens of different strains of E. coli exist, most of which cause no disease at all. A handful cause various degrees of intestinal symptoms. Some also cause urinary tract infections. E. coli 0157:H7 caused an outbreak originating in a chain of Jack-in-the-Box restaurants in the Pacific Northwest. Shiga toxin producing E. coli is the agent of a spectrum of conditions, ranging form mild gastroenteritis with fever to blood diarrhea. A minority of patients will develop hemolytic uremic symdrom (HUS) which is a several hemolytic anemai that can cause kidney damage and failure. Neurological symptoms such as blindness, seizure, and strok are also possible. Siga toxin interrups protein synthesis in its target cells and appears responsbile for the systemic effects of this infection. The most common mode of transmission is the ingestion of contaminated and undercooked beef, alhtough other foods and beverages can be contaminated. In 2015, the Chipotle chain of restaurants was the source of two distinct E. coli O26 outbreaks in the u.S. In 2016, there was a multistate outbreak of two STEC strains, E. coli O12 and E. coli 026, which were traced to flour manufactured by General Mills. The CDC reminds consumers not to consume raw dough or even to taste batters before they are cooked. The best prevention is good food hygiene. Antiotics may be contraindicated as they may incdrease the pathology by releasing more toxin, leading to HUS. Supportive therapy, including plasma transfusion to dilute toxin in the bood is a good option.

–Campylobacter: is one of the most common bacterial causes of diarrhea in the U.S. The symptoms of campylobacteriosis are frequent watery stools, fever, vomiting, headaches and abdnominal pain. The symptoms may last longer than most acute diarrheal episodes, sometimes extending beyond 2 weeks. They may subside and then recure over a period of weeks. Campylobacter jeuni is the most common cause alhtough there are other pathogenic Campylobacter species. Campylobacters are slender, curved, or spiral gram-ngeative bacteria propelled by polar flagella at one or both pools, often appearing in S-shaped or gull-winged pairs. These bacterai tend to be microaerophilic inhabitants of the intestinal tract, genitourinary tract and oral caivity of humans and animals. Transmission is via the ingestion of contaminated beverages and food, expecially water, milk, meat and chicken. Once ingested, C. jejuni cells reach the mucosa at the last segment of the small intestine (ileum) near its junciton with the colon. They adhere, burrow through the mucus and multiply. Symptoms commence after an incubation period of 1-7 days. The mechansism of patholoy appears to involve a heat labil enterotoxin that stimulates a secretory diarrhea like that of cholera. In a small number of cases, infection can sead to Guillain Barre syndrome, a serious neuromuscular paralysis. GBS is the leading cause of acute paralysis in the U.S. since the eradication of polio. However, many patients recover completely form the paralysis. The disease appears to be an autoimmune reaciton that can be brought on by infection with viruses and bacteria and by vaccination in rare cases and even by surgery. The single most common precipitating event for the onset of GBS is Capylobacter infection.

–Clostridioides difficile: is formerly known as Clostridium difficile and often called C. difficile or C. diff. C. diff is a germ (bacterium) that causes severe diarrhea and colitis (an inflammation of the colon). Most cases of C. diff infection occur while you’re taking antibiotics or not long after you’ve finished taking antibiotics.C. diff can be life-threatening. See CDC

Rebyota is a rectally delivered product developed by Ferring Pharmaceuticals that secured FDA approval in 2022 for treating C. difficile. Another poduct Vowst is an orally devliered product devloped by Seres Therapeutics that securted FDA approval in 2023. Both products are derived form donor supplied materials. Whereas Rebyota is a fecal microbiota suspendsion, Vowst contains purified bacterial spores.

—-Etiology/Transmission/Prevention:

Clostridium difficile is a gram positive endospore forming rod found as noraml biota in the intestine. In most cases, the infeciton seems to be precipitated by therapy with broad spectrum antibiotics such as ampicillin, clindamycin or cephalosporins. although, C. difficile is relatively noninvasive, it is able to superinfect the large intestine when drugs have disrupted the normal biota. It produced two enterotoxins, toxins A nad B, that casue areas of necrosis in the wall of the intestine. More severe cases exhibit abdominal cramps, fever and leukocytosis. The colon is inflammed and gradually soughs off loose, membrane like patches. If the condition is not stopped performation of the cecum and death can result. C. diff releases endospores whcih contaminate the environment. Hospitalized patients must be put in isolation and constant attention to disinfection is required. If a patient is receiving clindamycin, ceftriaxone, or a fluoroquinolone for a different infection and displays C. diff symptoms, the frist step is to withdraw the offending antibiotic. In mild C. Diff infections, metronidazole should be administered. In severe cases, vancomycine is the drug of choice.

High rates of metronidazole resistance have been observed for C. difficile isolates carrying the 7-kb plasmid pCD-METRO, in particular for isolates belonging to PCR ribotype (RT) 010 and RT020 (clade 1) and the epidemic strain RT027 (clade 2). This plasmid has been reported in C. difficile isolates from countries in Europe. Since the discovery of pCD-METRO, we have implemented PCR that uses primers oBH-1 (5′-CCTCGTAGAATCCGGTGCAA-3′) and oBH-2 (5′-TATTTCCTTGCCGCTGAGGT-3′) for national sentinel surveillance and diagnostics of C. difficile infections in the Netherlands. The primers are specific for open reading frame (ORF) 6 of pCD-METRO. In conclusion, the plasmid pCD-METRO confers metronidazole resistance in Clostridioides difficile. We showed high sequence similarity among pCD-METRO plasmids from different isolates and identified pCD-METRO and associated metronidazole-resistant isolates in clinical and veterinary reservoirs in the Americas. We recommend using PCR or genomic assays to detect pCD-METRO in metronidazole-resistant C. difficile. See Kuijiper CDC

The incidences of C. difficile infection (CDI) in developed countries have become increasingly high which may be attributed to the emergence of newer epidemic strains, extensive use of antibiotics, and limited alternative therapies.  The uses of antibiotics usually modify the intestinal microbiome and permit propagation of C. difficile. It has been noticed that hospitalized patients are the prime target of CDI, although C. difficile also present as a colonizer in 2-3% of healthy individuals and 70% in healthy children. C. difficile produces heat-resistant spores that can persist in the environment for several months, thus providing the basis for nosocomial outbreaks even after extensive cleaning measures. The diagnosis of C. difficile colitis should be suspected in any patient with diarrhea, who has been under antibiotics treatment over the previous 3 months or has been recently hospitalized. Having a confirmed CDI, it is crucial that proper infection control measures are in place to avoid further spread of the infection within the same ward or hospital. To avoid spreading of Clostridium spores, hands need to be washed, patients should kept in isolation, and importantly, gloves and protective clothing must be worn by all staff along with continuous hand hygiene after each patient contact. See Arijallila

—–Diagnosis:

Example: Sequence librarires for C. difficile were generated using Twist Library Preparation EF 2.0 kit and Twist UDI Primer (Twist Bioscience). Geneomic DNA was extracted by using the chemagic 360 extraction instrument and chemagic DNA Tissue Kit (boht PerkinElmer). Quantity of DNA in the libraries was assessed using Qubit 3.0 and Qubit dsDNA HS Assay kit (ThermoFisher Scientific) and assesed quality by using the 4200 TapeStation and DNA1000ScrenTap (Agilent). The quantified final library products were quantified for cluster eneration and performed next generation sequencing on an Illumina NovaSeq 6000 sequencer system (Illumina) in 300 bp paired end format according to the Illumina paired-end sequencing protocol. De novo assembly of sequences was performed by using Unicycler version 0.48 and analyzed core genomic multilocus sequence typing using EnteroBase. Statitistical analysis was performed and graphs created by suing both SPSS Statistics 26.0 (IBM Corp) and R verion 4.2.2 (the R Project for Statistical Computting) with a significance level set at 0.05. (Kim, “Identifying contact time required for secondary transmission of Clostridioides difficile Infections by using real-time locating system” Emerging Infectious Diseases, 30(5), 2024).

—-Treatment:

A procedure some might consider unconventional has proven to be an effective treatment for a serious and chronic type of bowel disorder. Fecal Microbiotal Transplantation, or FMT, calls for the transplantation of healthy fecal material into the colon of a person infected with Clostridium difficile, also called C. difficile or CDI. The procedure restores compromised stool and stops the recurrence of CDI. See Michigan medecine

–Vibriosis: The genus Vibrio consists of 103 species. Of these, only ten species have been implicated to cause gastrointestinal and extra-intestinal diseases in human beings. Vibrio species are generally inhabited in marine niches. In humans, Vibrio species has been isolated from stool, vomitus, blood, or wound infections and also from environmental niches such as seawater, sediments, plankton, shellfish (oysters, clams and crabs). Vibrio species which have great medical implications include: V. alginolyticus, V. carchariae, V. cholerae, V. cincinnatiensis, V. fluvialis, V. furnissii, V. metschnikovii, V. mimicus, V. parahaemolyticus, and V. vulnificus.

Vibriosis causes an estimated 80,000 illnesses and 100 deaths in the United States every year. People with vibriosis become infected by consuming raw or undercooked seafood or exposing a wound to seawater. Most infections occur from May through October when water temperatures are warmer.  See CDC

—-Vibrio cholerae: has been a devasting disease for centuries. These bacteria are rods with a single polar flagellum. They belong to the family Vibrionaceae. There are many serogroups of V. cholerae, but only two – O1 and O139 – cause outbreaks. V. cholerae O1 has caused all recent outbreaks. V. cholerae O139 – first identified in Bangladesh in 1992 – caused outbreaks in the past, but recently has only been identified in sporadic cases. It has never been identified outside Asia. There is no difference in the illness caused by the two serogroups. SEE WHO

After an inucubation period of a few hours to a few days, symptoms begin abruptly with vomiting, followed by copious watery feces. If cholera is left untreated death can occur in less than 48 hours and the mortality rate is between 55-70%. V. cholerae has a relatively high infections dose (106 cells). The bacteria survive in water sources for long peridos of time. Prevention is contingent on proper sewage treatment and water purificaiton. Vaccines are available for traverls and people living in endemic regions. For adults traveling from the United States to areas affected by cholera, a vaccine called Vaxchora is available in the United States. It is a liquid dose taken by mouth at least 10 days before travel. See Mayo Clinic

The key to treatment is prompt replacement of water and electrolytes. Oral rehydration therapy is very simply and astonishingly effective. This simple treatment consists of a mixture of the electroytes sodium chloride, sodium bicarbonate, potassium chloride and glucose or sucrose dissolved in water. When admisntiered early in amounts ranging from 100-400 milliliters per hour, the solution can restore patients in 4 hours.

—-Vibrio mimicus: named because of its close metabolic and genetic similarity to V. cholerae, is recognized globally as a cause of foodborne and waterborne diarrheal disease. In June 2019, the Florida Department of Health in Alachua County (DOH-Alachua; Gainesville, FL, USA) received reports of multiple cases of diarrheal illnesses associated with eating at a local seafood restaurant. Six case-patients were subsequently identified who met the case definition of having eaten seafood at the implicated restaurant within a 2-day time window and who experienced acute onset of diarrhea within 96 hours of the reported meal or had a clinical diagnosis of vibriosis. DOH-Alachua determined that the foods most commonly consumed by case-patients were steamed blue crab (5 case-patients), steamed snow crab (5 case-patients), and steamed shrimp (4 case-patients). Only 1 case-patient reported eating oysters. A joint environmental health assessment by DOH-Alachua, the Florida DOH regional environmental epidemiologist, and the Florida Department of Business and Professional Regulation documented multiple food safety violations (i.e., substantive overall sanitation issues, thawing frozen shrimp overnight at room temperature, returning cooked crabs to crates that previously held live crabs), and a lack of required state-approved employee education. Fecal samples from the patients hospitalized at UFHealth were initially screened by using a culture-independent diagnostic PCR technique (BioFire FilmArray GI Panel; BioFire Diagnostics. See CDC

Food Poisoning; should be expected if a patient presents with severe nausea and fequent vomiting accompanied by diarrhea and reprots that companions with whom she shared a recent meal (within the last 1-6 hours) are suffering the same fate. Food poisoning refers to symptoms in the gut that are caused by a preformed toxin of some sort. In many cases, the toxin comes from Staphylococcus aureus. In others, the source of the toxin is Bacillus cereus or Clostridium perfringens.

Chronic Diarrhea: is definted as lasting longer than 14 days. It can have infectious causes or can reflect noninfectious conditions. A person’s HIV status should be considered if she presetns with chronic diarrhea. One type of E. coli, enteroaggregative E. coli is particularly assocaited with chronic disease, especially in children.

Tooth Decay: Dental caries involve the dissolution of solid tooth surface due to the metabolic action of acteria. In the presence of sucrose and to a lesser extent, other carbohydrates, S. mutans and other streptococci produce sticky polymers of glucose called fructans and glucans. These adhesives help bind them to the smooth enamel surfaces and contribute to teh sticky bulk of the plaque biofilm. If mature plaque is not removed form sites that readily trap food, it can result in a carious lesion. This is due to the action of the streptococci and other bacteria that produce acid as they ferment the carbohydrates. If the acid is immediately flushed form the plaque and diluted in the mouth, it has little effect. however, if the denser regions of plaque, the acid can accumulate in direct contact with the enamel surface and low the pH to blow 5, which is acidic enough to begin to dissolve the calcium phosphate of the enamel in the spot. This intial lesion can remain localized in the enamel and can be repaired with various inert materials (fillings). Once the deterioration has reached the level of the dentin, tooth dstruction speeds up and the tooth can be rapdily destroyed. The best way to prevent dental caries is thorugh dietary restriction of sucrose and other refined carbohydrates. Regular brushing and flossing to remove plaque are also important. Most municpal communities in the U.S. add trace amounts of fluoride to drinking water because fluoride when incorporated into the tooth structure, can increase tooth hardness. The CDC estimates that the rate of tooth decay is decdreased by 25% by the addition of fluoride to drinking water.

Periodontal diseases: is so common that 97-100% of the population ahs some manifestation by age 45. Most kinds are due to bacterial colonization and varying degress of inflammation that occur in response to gingival damage. The initial stage of periodontal disease is gingivitis, the signs of which are swelling, loss of normal contour, patches of redness and increased bleeding of the gums (gingiva). Spaces or pockets of varying depth also devlop between the tooth and the gingiva. If this condition persists, a more serious diasese called periodontitis results. The deeper invovlement increases the size of the pockets and can cause bone resorption severe enough to loosen the tooth in its socket. Data fromt eh Human Microbiome Proejct revel that the composition of the microbial community, rather than single organisms is the casue of dental caries or periodontitis. Most periodontal disease is treated by removal of calculus and plaque and maintenance of good oral hygine. Often, surgery to reduce the depth of periodontal pickets is required. Antibiotic therpay, either systemic or applied in periodontal packings, may also be utilized.

Gastritis and Gastric Ulcers: Gastritis is experience as sharp or buring pain emanating from the abdomen. Gastric or peptic ulcers are actual lesions in the mucosa of the stomach (gastric ulcers) or in the uppermost porition of the small intestine (duodenal ulcers). Severe ulcers can be accompanied by bloody stools, vomoting or both. The symptoms are often worse at night, after eating, or under conditions of psychological stress. The curved cells of Helicobacter were first detected by J. Robin Warren in 1979 in stomach biopsies from ulcer palteints. The fifth most common cancer in the world is stomach cancer and ample evidence suggest that long term infection with Helicobacter pylori is a major contributing factor. Helicobacter pylori is a curved fram-ngegative rode. H. pylori si probably transmitted form person to person by the oral-oral or fecal-oral rotue. It seems to be acquired ealry in life and carried asymptomatically unless its activities because to damage the digestive mucosa. This bacterium has also been found in water sources suggesting that perhpas proper sanitation may reduce transmission. The best treatment is a course of antibiotic augmented by acid suppressors. The antibiotics most prescirbed are clarithromycin or metronidazole.

Affecting the Nervous System

Botulism: is casued by clostridium botulinum, which like Clostridium tetani below, is an endospore-forming anaerobe that does its damage through the relaese of an exotoxin. C. botulinum commonly inhabits soil and water and occasionally the intestinal tract of animals. It is distributed world wide, most often in the Northern Hemisphere. The CDC maintains a supply of antitoxin, which, when adminsitered soon after diagnosis, can preent the worst outcomes of the disease.

Foodborne botulism outbreaks occur in home processed foods, including anned vegetables, msoked meats adn cheese spreads. Endospores can be present on teh vegetables or meat at the time of gathering and are difficult to remove completely. When contaminated food is put in jars an steamed in a pressure cooker that does not reach reliable pressure and temperature, some endospores survive.

Botulinum neurotoxins, causative agents of botulism in humans, are produced by Clostridium botulinum, an anaerobic spore-former Gram-positive bacillus. Botulinum neurotoxin poses a major bioweapon threat because of its extreme potency and lethality; its ease of production, transport, and misuse; and the need for prolonged intensive care among affected persons. See Dutta

Meningitis: is an inflammation of the meninges. Many different microorganisms can casue an infection of the meninges, adn they produce a similar set of symptoms. The more serious forms of acute meningitis are casued by bacteria, but it is thought that their entrance to the CNS is often facilitated by coinfection or previous infection with respiratory viruses. Whenever meningitis is uspected lumba puncture (spinal tap) is perforemd to botain CSF, which is then examined by Gram stain and/or culture. Most physicians will begin treatment with a broad-spectrum antibiotic immediately and shift treatment if necessary after a diagnosis has been confirmed.

–Meningococcal disease is caused by bacteria called Neisseria meningitidis. People with meningococcal disease spread the bacteria to others through close personal contact such as living together or kissing. A person with meningococcal disease needs immediate medical attention. Neisseria meningitidis appears as gram-negative diplococci (round cells occurring in joined pairs) and is commonly known as the meningococcus. This organisms causes the most serious form of acute meningitis and accounts for 15-20% of all meningitis cases. Most cases occur in young children because vaccination of otherwise healthy children against the disease is not recommended until age 11. Although 12 different strains with different capsular antigens exist, serotypes B, C and Y are responsible for most cases in the U.S. In Afica other serotypes are prominent. The bacteria enters the body via the upper respiratory trace, moves into the blood, rapidly penetrates the menignes and produces symptoms of meningitis. The disease has a sudden onset, marked by fever higher than 40C or 104F, sore throat, chills, delirium, severe widespread areas of bleeding under the skin, shock and coma. Because meningococci do not survive long in the environment, these bacteria are usually aquired through close contact (e.g., living in close quarters such as college dormitories and military barracks) with secretions or droplets. Meningococcal meningitis has a sporadic or epidemic incidence in the late winter or early spring. The continuing reservoir of infection is humans who harbor the pathogen in the nasopharynx.

The highest risk groups are young children (6-36 months old) and older children and young adults (10-20 years old). Cases peak in January and Febraury in the U.S. Suspicion of bacterial meningitis constitutes a medical emergency and differential diagnosis must be done with great haste and accuracy. It is improtant to confirm (or rule out) meningococcal meningitis becasue it can be rapidly fatal. Treatment is usually started until it can be ruled out. Crerebrospinal fluid, blood or nasopharyngeal samples are stained and observed directly for the typical gram-negative diplococci. Cultivation is the preferred method of diagnosis because it also enable a quick assessment of antimicrobial resistance. Specimens are streaked on modified thayer-martin medium (MTM) or chocolate agar and incubated in a high CO2 atmosphere. Presumptive identification of the genus is obtaind by Gram stain and oxidase testing on isoalted colonies. Specific rapid tests are also avaialble for detecting the capsular polysaccharide or the cells directly from specimens without culturing. When family members, medical personnel or children in day care or school have come in close contact with infected people, they should recive a vaccination. Preventive therapy with rifampin or tetracyline may also be warranted.

In the US immunization begins at the age of 11, followed by a booster dose. Vaccines are also available for younger children and for adults over the age of 55 who are high risk for infection. Routine immunizaiton is with one of two meningococcal vaccines that protect against serotypes A, C, W and Y. At about the time a booster is need (16 years) the CDC recommends additionally the first dose of the new vaccine effective against seroptye B.  See CDC. Two meningococcal serogroup B vaccines are icensed for use in the US. MenB-4C (Bexsero GSK), one of two licensed meningococcal serogroup B vaccines, protects agasint serogroup B N. meningitidis and is licensed for persons aged 10-25 years. On October 24, 2024, the Advisory Committee on Immunization Practices (ACIP) voted to update its recommendations for teh MenB-4C dosing interval and schedule ot align with the new FDA label. ACIP recommends extending the itnerval for the 2 dose series of MenB-4C from 0 up to 1 month to 1 and 6 months for healthy adolescents and young adults aged 16-23 years based on shared clinical decision making and has added a recommendation for a 3 dose series with doeses administered at 1, 1-2 and 6 months for person age 10 or more at increased risk. Two manufactuers provide three MenB vaccine products that are licensed and available for use in the US. MenB vaccines from different manufctuers are not interchangeable; all doses in a series, as well as booster doses, should be form the same manufacturer.

–Steptococcus pneumoniae (pneumococcus): causes the majority of bacterial pneumonias. However, meningitis is also casued by this bacterium. It is the most frequent cause of community acquired menidngitis and is also very severe. It does not cause the petechiae (pinpoint round spots that appear on the skin due to bleeding) as with meningococcal meningitis and that difference is sueful diagnostically. As many as 25% of pneumococcal meningitis patients will also have pneumococcal pneumonia. Pneumococcal meningitis is most likley to occur in patients with underlying susceptibility, such as alcoholic patients and patients with sick-cell disease or those with defective spleen function. This bacterium is also a respiratory disease (see below). The bacterium is a small gram-positive flattened cocus that appears in end-to-end pairs. It has a distinctive appearance in a Gram stain of cerebrospinal fluid. Stianing or culturing the nasopharynx is not useful becasue it is often normal biota there. Many strains are resitant to the first line antibiotic, penicillin. In pneumococcal meningitis initial treatment with vancomycin and ceftriazone is recommended. If the isolate comes back as penicillin sensitive (the crebrospinal fluid must be cultured before beginning antibotic treamtent), then treatment can be switched.

Two vaccine are available for S. pneumoniae: a thirteen-valent conjugated vaccine (Prevnar) which is recommended as part of the hcildhoold immunizaiton schedule, and a 23-valent polysaccharide vaccine (Pneumovax 23), which is available for adults. Current recommendations fo runvaccinated adults call for initial vaccination with Prevnar, follwed by Pneumovax 6-12 months latter.

–Haemophilus influenzae: the meningitis casued by this bacterium is severe. Before the vaccine was introduced in 1988, it was a very common casue of severe meningitis and death. In the course of the alst 13 years, meningitis casued by this bacterium is much less common in the U.S., a situation that can always change if a lower percentage of people get the vaccine and herd immunity is compromised. Cases that occur in the U.S. are now mostly casued by nosertopye B strains. Globally, it is still common, and is an improtant casue of the disease in children under the age of 5.

–Listeria monocytogenes: is a gram positive bacterium that ranges in morphology from coccobacilli to long filaments in palisades formation. Listeria is not fasitdious and is resistant to cold, heat, salt, pH extremes and bile. It grows inside host cells and can move directly from an infected host cell to an adjacent healthy cell. Listeriosis in healthy adults is often a mild or subclinical infection with nonspecific symptoms of feverl, diarrhea, and sore throat. However, in elderly or immuncomplromised patients, fetuses adn neonates, it usually affects the brain and menignes and results in speticemia. Some strains target the heart. The deat rate is about 20%. The primary reservoir is apaprently soil and water and animals, plants and food are secondary sources of infection. Most cases of listeriosis are associated with ingesting contaminated dairy products, pultry, and meat. The pathogen ahs been isoalted in 10-15 of ground beef and in 25-30% of chicken and turkey carcasesses and is also present in 5-10% of luncheon meats, hot dogs and cheeses.

–Tetanus: is a nueromuscular disease whose alternate name, lockjaw, refers to an early effect of the disease on the jaw muslce. C. tetani releases a pwoerful exotoxin that is a nuerotoxin, tetanospasmin, that binds to target sites on periopheral motor nuerons, spinal cord and brain, and in the sympathetic nervous system. The toxin acts by blocking the inhibition of muscle contraction. Without inhibition of contraction, the muscles contract uncontrollably, resulting in spastic paralysis. The first symtpoms are clenching of the jaw, followed in succession by extreme arching of the back, flexion of the arms, and extension of the legs. A pateint with a clinical appearance suggestive of tetanus should immediately receive antitoxin therapy with human tetanus immune gloublin (TIG) adn Pnicillin G.

The etiologic agent, Clostridium tetrani, is a gram-positve, spore-forming rod.

The recommended vaccination series for 1-3 month old babies conssits of three injections of DTap (diphtheria, tetanus, and acellular pertussin) given 2 months apart, followed by booster doses aobut 1-4 years later. Alternativley, they may be vaccinated with a vaccine called “DT” which protects only agaisnt diptheria and tetanus. Chidlren thus immunized probably have protection for 10 eyrs. At that point and every 10 years thereafter, they should recive a dose of TD, tetanus-diptheria vaccine.

Affecting the Respiratory System

Acinetobacter: is a group of bacteria (germs) commonly found in the environment, like in soil and water. While there are many types, the most common cause of infections is Acinetobacter baumannii, which accounts for most Acinetobacter infections in humans. Acinetobacter infections typically occur in people in healthcare settings.Acinetobacter can live for long periods of time on environmental surfaces and shared equipment if they are not properly cleaned. The germs can spread from one person to another through contact with these contaminated surfaces or equipment or though person to person spread, often via contaminated hands. Acinetobacter infections are generally treated with antibiotics. To identify the best antibiotic to treat a specific infection, healthcare providers will send a specimen (often called a culture) to the laboratory and test any bacteria that grow against a set of antibiotics to determine which are active against the germ. The provider will then select an antibiotic based on the activity of the antibiotic and other factors, like potential side effects or interactions with other drugs. See CDC

–Acinetobacter baumannii can cause infections in the blood, urinary tract, and lungs (pneumonia), or in wounds in other parts of the body. It can also “colonize” or live in a patient without causing infections or symptoms, especially in respiratory secretions (sputum) or open wounds.  Acinetobacter baumannii is a bacterium that can cause a range of diseases. It typically infects people inside a healthcare facility — doctors refer to these as “nosocomial” infections. There are many different species of Acinetobacter that can cause disease, but A. baumannii accounts for about 80 percent of reported Acinetobacter infections in the United States, according to the Centers for Disease Control and Prevention (CDC).

Symptoms of A. baumannii infections are often clinically indistinguishable from those of infections caused by other opportunistic bacteria, such as Klebsiella pneumoniae and Streptococcus pneumoniae. Bloodstream infections often initially cause symptoms like fever and chills, rash, and confusion or other altered mental states, and are often associated with an elevated lactic acid level that’s found with severe sepsis. UTIs typically cause various urinary symptoms, including pain or burning sensations while urinating, foul smelling urine that may be cloudy or bloody, and a strong urge to urinate frequently. Meningitis may cause a number of flu-like symptoms ncluding fever, headache, confusion, sensitivity to bright light, and nausea (with or without vomiting). The CDC considers Acinetobacter, including A. baumannii, a serious public health threat because it’s often resistant to multiple antibiotics. 63 percent of Acinetobacter strains are multi-drug resistant, the CDC notes. Before the 1970s, A. baumannii infections could be treated with a range of different antibiotics, such as aminoglycosides, β-lactams, and tetracyclines, according to a report in the journal Clinical Microbiology Reviews. Today, however, some strains of A. baumannii are resistant to most antibiotics, including first-line antibiotics and carbapenems, which are often used only as a last resort. Treating an A. baumannii infection generally requires drug susceptibility tests, which check for antibiotics that are still effective against the particular strain of bacteria. In some cases, sulbactam and polymyxin antimicrobial drugs still work against A. baumannii when other antibiotics fail. See Everyday Health

AB is remarkable in that it is ubiquitous, exists in diverse habitats (e.g., human skin), can survive for long periods of time on dry inanimate surfaces (e.g., hospital bed rails) and as already mentioned can acquire antimicrobial resistance extremely rapidly. These factors combined, especially the latter two, greatly facilitate MDR-AB outbreaks in the ICU, in physical therapy wound clinics and even multi-facility outbreaks. See Buckle

Bordetella pertussis causes whooping cough (pertussis), an acute respiratory infection marked by severe, spasmodic coughing episodes during the paroxysmal phase. Leukocytosis with lymphocytosis is also common during this phase of the illness. Dangerous complications are bronchopneumonia and acute encephalopathy. Bordetella parapertussis can cause a milder form of pertussis. The bordetellae are small, Gram-negative, aerobic coccobacilli. Bordetella pertussis produces a number of virulence factors, including pertussis toxin, adenylate cyclase toxin, filamentous hemagglutinin, and hemolysin. Agglutinogens and other outer membrane proteins are important antigens. The genus Bordetella contains the species B pertussis and B parapertussis, which cause pertussis in humans. Other members of the genus are B bronchiseptica, causing respiratory disease in various animals and occasionally in humans, and B avium as well as B hinzii, which cause respiratory disease in poultry and are very rarely found in humans. See Medical Microbiology

Pertussis, a respiratory illness commonly known as whooping cough, is a very contagious disease caused by a type of bacteria called Bordetella pertussis. These bacteria attach to the cilia (tiny, hair-like extensions) that line part of the upper respiratory system. The bacteria release toxins (poisons), which damage the cilia and cause airways to swell. See CDC

Diphtheria is a highly contagious bacterial infection of the nose and throat. Thanks to routine immunization, diphtheria is a disease of the past in most parts of the world. There have only been five cases of the bacterial infection in the United States in the last 10 years. Diphtheria can infect the respiratory tract (parts of the body involved in breathing) and skin. In the respiratory tract, it causes a thick, gray coating to build up in the throat or nose. This coating can make it hard to breathe and swallow. Diphtheria skin infections can cause open sores or shallow ulcers. See CDC

Sinusitis: is one of the most common health complaints leading to a physician visit in the United States, as well as one of the leading causes of antibiotic prescriptions. In 1 year, there were up to 73 million restricted activity days in patients with sinusitis and total direct medical costs of almost $2.4 billion (not including surgery or radiographic imaging). In addition, up to 14.7% of people in one National Health Interview Survey had sinusitis the preceding year. Causes are a combination of environmental and host factors. Acute sinusitis is most commonly due to viruses and is usually self-limiting. Approximately 90% of patients with colds have an element of viral sinusitis. Those with atopy commonly get sinusitis. It can be caused by allergens, irritants, viruses, fungi, and bacteria. Popular irritants are animal dander, polluted air, smoke, and dust. No laboratory tests are indicated in the emergency department for acute uncomplicated sinusitis because the diagnosis is usually clinical. Humidification, nasal wash, decongestants (topical or systemic) such as pseudoephedrine. Remember that oxymetazoline cannot be used for more than 3 days due to rebound congestion and that oral decongestants should be used with caution in hypertensive patients.  Antihistamines have not been shown to be useful and can lead to impaired drainage. They are only of benefit in early allergic sinusitis.  Topical steroids are used to diminish nasal mucosal edema but are more efficacious in chronic and allergic sinusitis. Only start antibiotics if you strongly suspect bacterial disease. See Battistti

Stenotrophomonas maltophiliais an environmental global emerging Gram-negative MDRO that is most commonly associated with respiratory infections in humans. S. maltophiliais not a highly virulent pathogen, but it has emerged as an important nosocomial pathogen associated with crude mortality rates ranging from 14 to 69% in patients with bacteremia. see Brooke

Pneumonia (Pneumococcal disease): Pneumonia is a common infection of the lungs affecting millions of people worldwide. There are over 30 micro-organisms that cause pneumonia, including several types of bacteria, viruses, and fungi. Pneumonia is most often caused by the bacteria Streptococcus pneumonia, but infection can also be due to a number of viruses, fungi, and mycoplasmas. Pneumonia infection is classified based on how it is acquired and can be categorized into community-acquired, hospital-acquired, healthcare acquired, or aspiration pneumonia. Hospital-acquired pneumonia is a lung infection obtained during a hospital stay. This form of pneumonia can be serious because often times the patient, by nature of being in the hospital in the first place, is in an immune-weakened state due to illness or traumatic injury and thus is more susceptible to infection. The bacteria responsible for this type of pneumonia are often resistant to first-line antibiotics, further complicating treatment regimens. Ventilator tubes or other tubes that open a patient’s throat provide a direct point of access for airborne bacteria and viruses to enter the lungs.

“Pneumococcal disease” is a name for any infection caused by bacteria called Streptococcus pneumoniae or pneumococcus. Bacteria called Streptococcus pneumoniae, or pneumococcus, can cause many types of infections. Some of these infections like pneumonia below can be life threatening. See outline under “streptococcus pneumonaie”.

Community-acquired pneumonia (CAP) is the seventh leading cause of death in the United States, and the cost of these hospitalizations is estimated to cost up to $9 billion in the United States (US) dollars each year. Thirty-day hospital mortality associated with CAP has been estimated to be as high as 22% and is the leading cause of death amongst all infectious diseases.

–Streptococcus pneumoniae is the bacterium that has historically been the most common pathogen to cause CAP worldwide. In the era before antibiotics, S. pneumoniae was estimated to be the cause of 95% of all cases of pneumonia. Currently, however, S. pneumoniae accounts for up to 15% of pneumonia cases in the United States and 27% of cases worldwide today. Blood cultures are positive in only 20% to 25% of all pneumonia cases that are caused by S. pneumonia making it a challenging diagnosis for the clinician. See Dion

Although most commonly a commensal of the human respiratory tract, Streptococcus pneumoniae (the pneumococcus) remains a cause of infectious diseases, including otitis media, community-acquired pneumonia, sepsis, and meningitis. The organism’s thick layer of capsular polysaccharide (CPS) enhances its ability to colonize its host and is required for invasive infection. See Weiser

Tuberculosis (TB) is an infectious disease that usually attacks the lungs but can affect almost any part of the body. Though tuberculosis is spread from person to person through the air, it is not easy to become infected. TB can be fatal if it’s not treated, but taking medicine as directed can almost always cure TB. TB is caused by the bacterium M. tuberculosis. It spreads person to person when an infected individual coughs or sneezes out the bacteria, spreading it through the air to be breathed in by others. It takes prolonged exposure to become infected with TB, so you would typically get sick from a close family member or co-worker, not a casual acquaintance. Once you have inhaled the bacterium, the bacterium lodges in the lung tissue. Healthy individuals may contract latent TB, but the disease may not become active until months or years later, at a time when the immune system becomes weak for some reason. However, people with weakened immune systems are at a greater risk for developing active TB right away. When they breathe in the bacterium, it settles in their lungs and starts growing because their immune systems cannot fight the infection. In these instances, TB disease may develop within days or weeks after the infection. Your doctor will start by collecting a patient history to determine if you may have been exposed. During a physical exam, they will use a stethoscope to listen to your lungs and check the lymph nodes in your neck for swelling. If you have become infected with TB, but do not have the active TB disease you should get preventive therapy. This treatment kills germs that could cause problems if the disease becomes active. The most common preventive therapy is a daily dose of the antibiotic isoniazid (INH) taken as a single daily pill for six to nine months. You are not contagious if you have latent TB. If you have an active TB disease you will probably be treated with a combination of antibacterial medications for a period of six to 12 months. The most common treatment for active TB is isoniazid INH in combination with three other drugs—rifampin, pyrazinamide and ethambutol. You may begin to feel better only a few weeks after starting to take the drugs but treating TB takes much longer than other bacterial infections. You must continue taking your medication as prescribed for the entire time your doctor indicates or you could get sick again, have a harder time fighting the disease in the future and spread the disease to others. Not completing your entire course of medication could also contribute to drug-resistant TB. See American Lung Association. See CDC