bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enterobacteria and bacterial food poisoning
Authors: Pennington Hugh 
Published: February 2020

Abstract
Food poisoning denotes gastrointestinal diseases caused by microbes transmitted in food or by microbial toxins preformed there. Food spoilage by microbes also has important consequences for human health because of its impact on food supply. The worldwide impact of food poisoning is very great. Such infections kill many children in the developing world, where diarrhoeal diseases stunt their physical and cognitive development. The number of illnesses is also large elsewhere: in the United Kingdom the most common cause of food poisoning, Campylobacter, accounts for about 500,000 cases every year. The most common bacterial pathogens are Campylobacter and various members of the Enterobacteriaceae, a large family of Gram-negative organisms, of which Escherichia coli, shigella, and salmonella are considered in this chapter.
Bordetella infection
Authors: Grant Cameron C. 
Published: February 2020

Abstract
Bordetella are small Gram-negative coccobacilli, of which Bordetella pertussis is the most important human pathogen. Bordetella pertussis is the cause of whooping cough, which remains one of the 10 leading causes of death among children less than five years old. Transmission of this highly infectious organism is primarily by aerosolized droplets. The preferred diagnostic methods are polymerase chain reaction detection from nasopharyngeal samples and serology (IgG antibodies to pertussis toxin). Macrolide antibiotics are recommended if started within four weeks of illness onset. Preventing severe disease in young children remains the primary goal, hence schedules consist of a three-dose infant series and subsequent booster doses. Acellular vaccines enable immunization schedules to include adolescents and adults. Acellular pertussis vaccine given to pregnant women reduces the risk of pertussis in young infants. Antibiotic prophylaxis is given when there is an infant at risk of exposure.
Other Yersinia infections: Yersiniosis
Authors: Prentice Michael 
Published: February 2020

Abstract
Yersiniosis is caused by the enteropathogenic Gram-negative organisms Yersinia enterocolitica and Yersinia pseudotuberculosis, which are worldwide zoonotic pathogens. Disease is acquired by consumption of contaminated food or water and is commonest in childhood, and in colder climates. Presentation is with diarrhoea, fever, and abdominal pain, which may mimic appendicitis. Late complications include reactive arthritis, erythema nodosum, and erythema multiforme. Systemic infection is more likely with Y. pseudotuberculosis and a subgroup of Y. enterocolitica, and also in patients with diabetes or iron overload. Diagnosis is by culture of the organism or convalescent serology. Most cases of enteritis are self-limiting and antimicrobials are not indicated, but septicaemia or focal infection outside the gastrointestinal tract requires antibiotics (usually cefotaxime, ceftriaxone, or ciprofloxacin). Prevention is by standard food hygiene precautions.
Brucellosis
Authors: Colmenero Juan D. , Morata Pilar 
Published: February 2020

Abstract
Brucellosis is a worldwide zoonotic disease. It remains endemic in the Mediterranean basin, Northern Africa, the Middle East, Western Europe, Central and South America, sub-Saharan Africa, the Indian subcontinent, and Central Asia. There are three species especially pathogens for humans; Brucella melitensis (most commonly associated with goats, sheep, and camels), B. abortus (cattle) and B. suis (pigs). Brucellosis is usually transmitted by direct contact with infected animals, by ingestion of untreated dairy products, and less frequently by inhalation (laboratory workers) or inoculation (veterinary). Symptoms are very non-specific and heterogeneous, hence epidemiological information collected in the clinical history is very important. Definite diagnosis always requires laboratory confirmation, either by isolating the organism from blood, body fluids or tissues, or by demonstration of high titres of specific antibodies or seroconversion.
Botulism, gas gangrene, and clostridial gastrointestinal infections
Authors: Stevens Dennis L. , Aldape Michael J. , Bryant Amy E. 
Published: February 2020

Abstract
Human botulism is caused by seven serological types of C. botulinum, which is ubiquitously distributed in the soil. Poisoning usually results from ingestion of preformed toxin in food, although this is rapidly inactivated at ordinary cooking temperatures, but it can also result from contaminated wounds. C. botulinum toxin binds irreversibly to the neuromuscular junction and is the most lethal known microbial toxin. There are five forms of clinical botulism: food-borne botulism; wound botulism; infant botulism; adult enteric infectious botulism; and inhalational botulism. Clinical presentation is with symptoms suggesting gastrointestinal tract illness, followed by neurological symptoms including diplopia, blurred vision, dizziness, and difficulty with speech or swallowing, leading on to generalized flaccid paralysis. The diagnosis can be confirmed by testing for botulinum toxin in the patient’s serum, urine, or stomach contents, or in the suspect food. Treatment requires supportive care, which may continue for many months.
Tuberculosis
Authors: Chaisson Richard E. , Nachega Jean B. 
Published: February 2020

Abstract
Tuberculosis is caused by organisms of the Mycobacterium tuberculosis complex, including M. tuberculosis (the most important), M. bovis, and M. africanum. It has been present since antiquity and is the leading infectious cause of death ahead of HIV infection. An estimated 2 billion people worldwide carry latent infection, when M. tuberculosis persists within cells and granulomas, with the potential to reactivate to cause disease decades later. Tubercle bacilli are transmitted between people by aerosols generated when an infectious person coughs. Proximity to an infectious person determines the risk of infection. Host immunity and factors affecting it—most importantly HIV infection but also diabetes, cigarette smoking, and alcohol and drug abuse—determine the risk of active disease following infection.
Disease caused by environmental mycobacteria
Authors: van Ingen Jakko 
Published: February 2020

Abstract
There are over 130 species of mycobacteria; species other than M. tuberculosis complex and M. leprae are collectively referred to as the non-tuberculous or environmental mycobacteria. Non-tuberculous mycobacteria are divided into two groups, the slow growers, and the rapid growers. The most common organisms causing human disease are the slow-growing species M. avium complex and M. kansasii and, less commonly, M. marinum, M. xenopi, M. simiae, M. malmoense, and M. ulcerans. The rapid growers that are human pathogens are M. abscessus, M. fortuitum, and M. chelonae. Transmission to humans is though inhalation, ingestion, or traumatic inoculation. The prevalence of non-tuberculous mycobacteria infections is likely to have been underestimated, and appears to be increasing in developed countries.
Buruli ulcer: Mycobacterium ulcerans infection
Authors: de Jong Bouke , Portaels Françoise , Meyers Wayne M. 
Published: February 2020

Abstract
Buruli ulcer is caused by Mycobacterium ulcerans, which secretes a cytotoxic and immunosuppressive toxin, mycolactone. The disease is characterized by necrosis of skin, subcutaneous tissue, and bone, and is re-emerging as a potentially disabling affliction of inhabitants of tropical wetlands. Major foci are in West and Central Africa with an increasing focus in Australia, Mexico, South America, and Southeast Asia. It is not contagious; environmental sources include water, vegetation, and insects, with humans probably becoming infected by traumatic introduction of the bacillus into the skin from the overlying M. ulcerans-contaminated surface in most instances. Clinical presentation may be as a cutaneous nodule, undermined ulcer, plaque, or widely disseminated oedematous lesion. Clinical diagnosis is often accurate by experienced clinicians, and smears for acid-fast bacilli, culture, polymerase chain reaction assays, and histopathology are confirmatory. Treatment was formerly by wide surgical excision and skin grafting, yet antibiotics have now been found effective, including an all-oral regimen.
Actinomycoses
Authors: Schaal Klaus P. 
Published: February 2020

Abstract
Human actinomycoses are always synergistic polymicrobial infections in which fermentative actinomycetes—predominantly Actinomyces israelii, A. gerencseriae, or Propionibacterium propionicum—are the principal pathogens, usually needing the assistance of so-called concomitant microbes to produce disease. Nearly all of the members of the mixed actinomycotic microflora belong to the indigenous microbial community of human mucous membranes, hence actinomycoses present as sporadic endogenous infections which are not transmissible. Antibacterial drugs used for treatment should be active against both the causative actinomycetes and all concomitant bacteria. For cervicofacial actinomycoses, the rare cutaneous processes, and most thoracic forms of the disease, this requirement is best fulfilled by amoxicillin plus clavulanic acid in medium to high doses. The prognosis of cervicofacial and cutaneous actinomycoses is good provided that treatment is adequate; thoracic and abdominal forms are more serious, with grave prognosis without proper treatment.
Rat bite fevers (Streptobacillus moniliformis and Spirillum minus infection)
Authors: Woodhouse Andrew F. 
Published: February 2020

Abstract
Rat bite fever is usually attributable to Streptobacillus moniliformis in the Americas, Europe, and Australasia, and to Spirillum minus in Asia. Bites are increasingly common among children with pet rats, and pet shop and laboratory workers. Both bacteria are commensals of rats, some other rodents, and their predators. After an incubation period less than 1 week, S. moniliformis causes sudden high fever, rigors, myalgia, petechial rash, and migratory reactive or septic polyarthritis with synovial effusions. Complications can include fulminant septicaemia, endocarditis, pneumonia, and metastatic abscesses. S. minus infection (sodoku) has a longer incubation period with similarly high fever but concomitant exacerbation of the bite wound, local lymphadenopathy, papular rash, and arthralgia without effusions. In both diseases, fever subsides after a few days but may relapse repeatedly over months. Prevention is by controlling peri-domestic rats and avoiding bites by pet or laboratory rodents.
Relapsing fevers
Authors: Warrell David A. 
Published: February 2020

Abstract
Louse-borne relapsing fever and tick-borne relapsing fever are characterized by repeated episodes of high fever separated by afebrile periods. They are caused by Borrelia spirochaetes distinct from those responsible for Lyme borrelioses. Untreated patients may suffer as many as five (louse-borne relapsing fever) or ten (tick-borne relapsing fever) febrile relapses of decreasing severity. B. myamotoi is much less likely to relapse.
Humans are the sole reservoir of epidemic louse-borne relapsing fever caused by B. recurrentis and transmitted by body lice (Pediculus humanus corporis). Endemic tick-borne relapsing fevers are caused by at least 17 different Borrelia species and have their own particular species of soft Ornithodoros, or, in the case of B. myamotoi and B. lonestari, hard Ixodes or Ablyomma tick vectors that also act as reservoirs. Transmission transplacentally, or by needlestick, blood transfusion, or laboratory accident is also possible.
Leptospirosis
Authors: Day Nicholas P.J. 
Published: February 2020

Abstract
Leptospirosis, caused by pathogenic spirochetes of the genus Leptospira, is a bacterial zoonosis with a worldwide impact on human and animal health. For human infection rodents are the most important reservoir; infection follows exposure to contaminated water, soil, or urine, the organism entering through skin abrasions or mucosal surfaces.
Subclinical infection is common, but symptomatic disease usually begins with abrupt onset of fever, chills, headache, and myalgia. Most cases are undiagnosed due to the poor availability of diagnostic tests in regions where transmission occurs. Whether treatment of mild leptospirosis with antibiotics prevents more severe disease remains controversial, most experts recommend empirical treatment if leptospirosis is suspected.
Scrub typhus
Authors: Paris Daniel H. , Day Nicholas P.J. 
Published: February 2020

Abstract
Orientia spp. are obligate intracellular Gram-negative bacteria that cause scrub typhus, historically known as ‘tsutsugamushi disease’, a febrile illness characterized by early non-specific ‘flu-like’ symptoms, and sometimes a diffuse, macular, or maculopapular rash and/or a necrotic lesion eschar at the inoculation site. Leptotrombidium mites transmit Orientia spp. to humans via the bite of the larval stage, while all mite stages act as bacterial reservoirs through vertical transovarial and transstadial transmission. Scrub typhus is a leading cause of treatable undifferentiated febrile illness in many regions of Asia, and unfortunately remains an underappreciated neglected disease, mainly due to diagnostic difficulties and lack of awareness among medical staff. Complications include meningo-encephalitis, respiratory and renal failure, and severe multiorgan failure. Scrub typhus can be treated effectively with tetracyclines, macrolides, and chloramphenicol. Humans are dead-end hosts and do not participate in the Orientia life cycle, hence treatment does not affect overall disease incidence.
Bartonella bacilliformis infection
Authors: Llanos-Cuentas A. , Maguiña-Vargas C. 
Published: February 2020

Abstract
Bartonellosis (Carrión´s disease, verruga peruana, Oroya fever, Guaitará fever) is caused by the Gram-negative bacillus Bartonella bacilliformis. It is endemic in the western Andes and inter-Andean valleys of Peru, and is still occasionally reported in Ecuador and Colombia, with infection resulting from the bite of various female sandflies. Infection of red blood cells manifests with non-specific ‘viral-type’ symptoms and haemolytic anaemia in the acute stage of disease. Following an asymptomatic phase, the late ‘eruptive’ stage is characterized by dermal nodules (‘verrugas’) that frequently heal spontaneously. Secondary opportunistic infections are common. Diagnosis in areas where the disease occurs is usually by demonstration of bacteria in the blood film. Mortality is 1.1–2.4% in endemic areas and around 9% in patients admitted to hospital. There is no satisfactory prevention for people living in endemic areas; tourists can take the usual precautions against being bitten by insects.
Mycoplasmas
Authors: Jensen Jørgen Skov , Taylor-Robinson David 
Published: February 2020

Abstract
Mycoplasmas are the smallest self-replicating prokaryotes. They are devoid of cell walls, with the plasticity of their outer membrane favouring pleomorphism, although some have a characteristic flask-shaped appearance. Mycoplasmas recovered from humans belong to the genera Mycoplasma (14 species and one candidatus species) and Ureaplasma (two species). They are predominantly found in the respiratory and genital tracts, but sometimes invade the bloodstream and thus gain access to joints and other organs. Diagnosis is made by nucleic acid amplification tests and/or serology. Culture is slow and of limited value in clinical diagnosis. Apart from supportive care, treatment is usually with tetracyclines or macrolides, although an increasing prevalence of macrolide resistance is seen, primarily in Asia. There is no commercially available effective vaccine.
A checklist of bacteria associated with infection in humans
Authors: Paul John 
Published: February 2020

Abstract
In addition to a relatively small number of well-known pathogenic bacteria that infect otherwise healthy people (e.g. Staphylococcus aureus, Mycobacterium tuberculosis, and Streptococcus pyogenes), there is a steadily growing list of less well-known organisms, many of which cause disease only under special circumstances. Bacteria associated with infections in humans are listed in the table that forms the bulk of this chapter, which has been designed to serve as a single port of call for clinicians who seek concise information on the less well-known clinically significant bacteria. Every name in the table has been checked to see that it has ‘standing in nomenclature’: widely used names that do not have standing in nomenclature (at the time of writing) are included, but written in inverted commas (e.g. ‘Spirillum minus’—one of the causes of rat bite fever).
Fungal infections
Authors: Hay Roderick J. 
Published: February 2020

Abstract
The mycoses are disorders caused by fungi, which are saprophytic or parasitic organisms found in every continent and environment. Many are common commensals in nature, but others cause agricultural disease. The mycoses that are human infections include diseases ranging from those that are worldwide and common, such as dermatophytosis and candida infections, to those that are rare and often potentially life-threatening (e.g. histoplasmosis). In humans, fungi usually adopt one of two morphologies: (1) the yeast form—where individual cells produce daughter cells by a process of budding and subsequently separate; or (2) the hyphal form—where cells do not separate but multiply to produce chains of cells joined end to end.
Pneumocystis jirovecii
Authors: Miller Robert F. , Eades Christopher P. 
Published: February 2020

Abstract
The ascomycete fungus Pneumocystis jirovecii (previously called Pneumocystis carinii) is the cause of pneumocystis pneumonia in humans, which occurs largely among people with impaired CD4+ T-lymphocyte function or numbers (e.g. those infected with HIV, recipients of solid organ or haematopoietic stem cell transplants, and those taking therapeutic immunosuppressive agents). The organism is restricted to humans, and disease is now thought to arise from de novo infection by inhalation from an exogenous source. Aside from supportive care, first-line therapy of pneumocystis pneumonia is sulphamethoxazole–trimethoprim (co-trimoxazole, which has a high rate of treatment-limiting adverse drug reactions), with adjunctive corticosteroids indicated for those with severe disease (i.e. hypoxaemia). In patients whose disease is failing to respond, or those intolerant of co-trimoxazole, the main alternatives are intravenous pentamidine or clindamycin with primaquine. Among HIV-infected patients, early initiation of antiretroviral therapy (i.e. within 14 days of starting antipneumocystis pneumonia therapy) is beneficial.
Talaromyces (Penicillium) marneffei infection
Authors: Chaiwarith Romanee , Supparatpinyo Khuanchai , Sirisanthana Thira 
Published: February 2020

Abstract
Talaromyces (formerly Penicillium) marneffei was first isolated from bamboo rats Rhizomys sinensis in Vietnam in 1956. The fungus is endemic in Southeast Asia, north-east India, south China, Hong Kong, and Taiwan. Fewer than 40 cases of infection with T. marneffei were reported before the HIV epidemic. Since then, the incidence of disseminated T. marneffei infection has increased markedly. Talaromyces marneffei infection is very rare in the immunocompetent but one of the most common opportunistic infections in HIV-infected people in Southeast Asia, north-eastern India, southern China, Hong Kong, and Taiwan. Presentation is usually with fever, chills, lymphadenopathy, hepatomegaly, and splenomegaly, with skin lesions—most commonly papules with central necrotic umbilication—in two-thirds of cases. Diagnosis is made by microscopy of bone marrow aspirate or biopsy specimens. Standard treatment, which is usually effective, is with amphotericin B followed by itraconazole.
Microsporidiosis
Authors: Weiss Louis M. 
Published: February 2020

Abstract
Microsporidia are obligate intracellular eukaryotic pathogens related to the Fungi that can infect both vertebrates and invertebrates. They were first identified about 150 years ago as the cause of pebrine, a disease of silkworms, with the description of Nosema bombycis in these economically important insects. They were first described in mammalian tissue samples about 75 years ago and starting 30 years ago they were recognized as pathogenic organisms responsible for a diarrhoeal syndrome in patients with AIDS. In addition to the gastrointestinal tract, it is now appreciated that microsporidia can infect virtually any organ system. The phylum Microsporidia contains about 1,400 species, distributed in 200 genera, and 15 microsporidian species have been reported in human infections.
Malaria
Authors: White Nicholas J. , Dondorp Arjen M. 
Published: February 2020

Abstract
An estimated 1.1 billion people residing in the tropical world are at high risk for malaria. In 2016, there were an estimated 216 million cases of malaria worldwide causing 445,000 deaths. Africa accounted for 90% of the cases and 91% of deaths; around 70% of the deaths were in children aged less than 5 years. Malaria is transmitted by the female anopheles mosquito and six species of Plasmodium commonly cause malaria in humans: P. falciparum, P. vivax, P. ovale (two species), P. malariae, and P. knowlesi. P. falciparum, the most pathogenic species accounts for 99% of malaria deaths. First line treatment of uncomplicated falciparum malaria is with artemisinin combination therapies (ACTs).
Toxoplasmosis
Authors: Liesenfeld Oliver , Petersen Eskild 
Published: February 2020

Abstract
Toxoplasma gondii is a protozoan parasite with worldwide distribution that infects up to one-third of the world’s population. Human infection is acquired through ingestion in water or food of oocysts shed by cats, or by ingestion of bradyzoites released from cysts contained in uncooked or undercooked meat (e.g. sheep, swine, cattle). Following invasion in the intestine, tachyzoites rapidly disseminate throughout the host. Immune mechanisms mediate the formation of cysts, primarily in the brain, eye, and skeletal and heart muscles, where they persist for the life of the host. Presence of infection can be established by direct detection of the parasite in clinical samples (often by polymerase chain reaction) or by serological techniques.
Cryptosporidium and cryptosporidiosis
Authors: Cacciò Simone M. 
Published: February 2020

Abstract
Parasites within the genus Cryptosporidium infect the mucosal epithelia of a variety of vertebrate hosts, including humans, affecting the health, survival, and economic development of millions of people and animals worldwide. Human infection is mainly caused by two species, Cryptosporidium parvum and C. hominis. The former species is also prevalent in young livestock and has a demonstrated zoonotic potential, whereas the latter species is essentially a human parasite. Direct and indirect (through contaminated water and food) transmission routes exist for both species. Treatment of immunocompetent patients, when necessary, is based on nitazoxanide, a thiazolide drug with broad antiparasitic activities. Nitazoxanide is the only US Food and Drug Administration-approved drug for the treatment of cryptosporidiosis, but it is not licensed in Europe.