Upload 2 files

infectious_diseases.csv

@@ -0,0 +1,265 @@
+infectious_agent,common_name,diagnosis,treatment
+Acinetobacter baumannii,Acinetobacter infections,Culture,Supportive care
+"Actinomyces israelii, Actinomyces gerencseriae and Propionibacterium propionicus",Actinomycosis,Histologic findings,"Penicillin, doxycycline, and sulfonamides"
+Adenoviridae,Adenovirus infection,"Antigen detection, polymerase chain reaction assay, virus isolation, and serology",Most infections are mild and require no therapy or only symptomatic treatment.
+Trypanosoma brucei,African sleeping sickness (African trypanosomiasis),Identification of trypanosomes in a sample by microscopic examination,Fexinidazole by mouth or pentamidine by injection for T. b. gambiense. Suramin by injection is used for T. b. rhodesiense
+HIV (Human immunodeficiency virus),AIDS (acquired immunodeficiency syndrome),"Antibody test, p24 antigen test, PCR",Treatment is typically a non-nucleoside reverse transcriptase inhibitor (NNRTI) plus two nucleoside analog reverse transcriptase inhibitors (NRTIs)
+Entamoeba histolytica,Amoebiasis,Microscopy,Those with symptoms require treatment with an amoebicidal tissue-active agent and a luminal cysticidal agent. Individuals that are asymptomatic only need a luminal cysticidal agent.
+Anaplasma species,Anaplasmosis,indirect immunofluorescence antibody assay for IgG,"Tetracycline drugs (including tetracycline, chlortetracycline, oxytetracycline, rolitetracycline, doxycycline, and minocycline) and imidocarb"
+Angiostrongylus,Angiostrongyliasis,"Lumbar puncture, brain imaging, serology",Albendazole
+Anisakis,Anisakiasis,"Gastroscopic examination, or histopathologic examination",Albendazole
+Bacillus anthracis,Anthrax,"Culture, PCR","Large doses of intravenous and oral antibiotics, such as fluoroquinolones (ciprofloxacin), doxycycline, erythromycin, vancomycin, or penicillin"
+Arcanobacterium haemolyticum,Arcanobacterium haemolyticum infection,Culture in human blood agar plates,"erythromycin (proposed as the first-line drug), clindamycin, gentamicin, and cephalosporins"
+Junin virus,Argentine hemorrhagic fever,,
+Ascaris lumbricoides,Ascariasis,Fecal smear,"Albendazole, mebendazole, levamisole and pyrantel pamoate"
+Aspergillus species,Aspergillosis,"Chest X-ray and CT, microscopy by silver stains",Voriconazole and liposomal amphotericin B in combination with surgical debridement
+Astroviridae species,Astrovirus infection,"Electron microscopy, enzyme-immunoassay (ELISA), immunofluorescence, and polymerase chain reaction",Supportive care
+Babesia species,Babesiosis,Giemsa-stained thin-film blood smear,"Atovaquone and azithromycin. In life-threatening cases, exchange transfusion is performed."
+Bacillus cereus,Bacillus cereus infection,Culture,Vancomycin
+multiple bacteria,Bacterial meningitis,"Lumbar puncture (contraindicated if there is a mass in the brain or the intracranial pressure is elevated), CT or MRI",Antibiotics
+multiple bacteria,Bacterial pneumonia,"Sputum Gram stain and culture, Chest radiography",Antibiotics
+List of bacterial vaginosis microbiota,Bacterial vaginosis,Gram stain and whiff test,Metronidazole or clindamycin
+Bacteroides species,Bacteroides infection,,
+Balantidium coli,Balantidiasis,"microscopic examination of stools, or colonoscopy or sigmoidoscopy","Tetracycline, metronidazole or iodoquinol"
+Bartonella,Bartonellosis,"microscopy, serology, and PCR",Antibiotics
+Baylisascaris species,Baylisascaris infection,,
+BK virus,BK virus infection,,
+Piedraia hortae,Black piedra,Stain or culture,"Antifungal shampoos such as pyrithione zinc, formaldehyde and salicylic acid"
+Blastocystis species,Blastocystosis,microscopic examination of a chemically preserved stool specimen,Lack of scientific study to support the efficacy of any particular treatment
+Blastomyces dermatitidis,Blastomycosis,"KOH prep, cytology, or histology",Itraconazole or ketoconazole
+Machupo virus,Bolivian hemorrhagic fever,,
+Clostridium botulinum; Note: Botulism is not an infection by Clostridium botulinum but caused by the intake of botulinum toxin.,Botulism (and Infant botulism),"Enzyme-linked immunosorbent assays (ELISAs), electrochemiluminescent (ECL) tests",Botulism antitoxin and supportive care
+Sabiá virus,Brazilian hemorrhagic fever,,
+Brucella species,Brucellosis,Culture,"Tetracyclines, rifampicin, and the aminoglycosides streptomycin and gentamicin"
+Yersinia pestis,Bubonic plague,Culture,"Aminoglycosides such as streptomycin and gentamicin, tetracyclines (especially doxycycline), and the fluoroquinolone ciprofloxacin"
+usually Burkholderia cepacia and other Burkholderia species,Burkholderia infection,,
+Mycobacterium ulcerans,Buruli ulcer,real-time PCR,The most widely used antibiotic regimen is once daily oral rifampicin plus twice daily oral clarithromycin.
+Caliciviridae species,Calicivirus infection (Norovirus and Sapovirus),,
+Campylobacter species,Campylobacteriosis,Stool culture,"Erythromycin can be used in children, and tetracycline in adults."
+usually Candida albicans and other Candida species,Candidiasis (Moniliasis; Thrush),"oral candidiasis, the person's mouth for white patches and irritation. vaginal candidiasis, vaginal itching or soreness, pain during sexual intercourse",Antifungal medications
+"Intestinal disease by Capillaria philippinensis, hepatic disease by Capillaria hepatica and pulmonary disease by Capillaria aerophila",Capillariasis,,
+Streptococcus mutans,Dental caries,,
+Bartonella bacilliformis,Carrion's disease,"Peripheral blood smear with Giemsa stain, Columbia blood agar cultures, immunoblot, indirect immunofluorescence, and PCR",Fluoroquinolones (such as ciprofloxacin) or chloramphenicol in adults and chloramphenicol plus beta-lactams in children
+Bartonella henselae,Cat-scratch disease,Polymerase chain reaction,Azithromycin
+usually Group A Streptococcus and Staphylococcus,Cellulitis,history and physical examination,Penicillinase-resistant semisynthetic penicillin or a first-generation cephalosporin
+Trypanosoma cruzi,Chagas disease (American trypanosomiasis),"Microscopic examination of fresh anticoagulated blood, or its buffy coat, for motile parasites; or by preparation of thin and thick blood smears stained with Giemsa.",Benznidazole and nifurtimox (though benznidazole is the only drug available in most of Latin America)
+Haemophilus ducreyi,Chancroid,Clinical diagnosis,"The CDC recommendation is either a single oral dose (1 gram) of azithromycin, a single IM dose (250 mg) of ceftriaxone, oral (500 mg) of erythromycin three times a day for seven days, or oral (500 mg) of ciprofloxacin twice a day for three days."
+Varicella zoster virus (VZV),Chickenpox,"The diagnosis of chickenpox is primarily based on the signs and symptoms, with typical early symptoms followed by a characteristic rash.",Aciclovir
+Alphavirus,Chikungunya,"Laboratory criteria include a decreased lymphocyte count consistent with viremia. Definitive laboratory diagnosis can be accomplished through viral isolation, RT-PCR, or serological diagnosis.",Supportive care
+Chlamydia trachomatis,Chlamydia,"Nucleic acid amplification tests (NAAT), such as polymerase chain reaction (PCR), transcription mediated amplification (TMA), and the DNA strand displacement amplification (SDA)","azithromycin, doxycycline, erythromycin, levofloxacin or ofloxacin"
+Chlamydophila pneumoniae,Chlamydophila pneumoniae infection (Taiwan acute respiratory agent or TWAR),,
+Vibrio cholerae,Cholera,A rapid dipstick test is available.,oral rehydration therapy (ORT)
+usually Fonsecaea pedrosoi,Chromoblastomycosis,microscopy (KOH scrapings),"Itraconazole, an antifungal azole, is given orally, with or without flucytosine."
+Batrachochytrium dendrabatidis,Chytridiomycosis,,
+Clonorchis sinensis,Clonorchiasis,,
+Clostridium difficile,Clostridium difficile colitis,"Colonoscopy or sigmoidoscopy, cytotoxicity assay, toxin ELISA",Vancomycin or fidaxomicin by mouth
+Coccidioides immitis and Coccidioides posadasii,Coccidioidomycosis,,
+Colorado tick fever virus (CTFV),Colorado tick fever (CTF),,
+usually rhinoviruses and coronaviruses,Common cold (Acute viral rhinopharyngitis; Acute coryza),Based on symptoms,Supportive care
+Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),Coronavirus disease 2019 (COVID-19),,
+Coxsackie B virus,Coxsackie B virus infection,Enterovirus infection is diagnosed mainly via serological tests such as ELISA and from cell culture.,There is no well-accepted treatment for the Coxsackie B group of viruses.
+PRNP,Creutzfeldt–Jakob disease (CJD),,
+Crimean-Congo hemorrhagic fever virus,Crimean-Congo hemorrhagic fever (CCHF),,
+Cryptococcus neoformans,Cryptococcosis,India ink of the cerebrospinal fluid (CSF),Intravenous Amphotericin B combined with flucytosine by mouth
+Cryptosporidium species,Cryptosporidiosis,,
+usually Ancylostoma braziliense; multiple other parasites,Cutaneous larva migrans (CLM),,
+Cyclospora cayetanensis,Cyclosporiasis,,
+Taenia solium,Cysticercosis,,
+Cytomegalovirus,Cytomegalovirus infection,"Blood and urine tests, biopsy","Cidofovir, foscarnet, ganciclovir, valganciclovir"
+"Dengue viruses (DEN-1, DEN-2, DEN-3 and DEN-4) – Flaviviruses",Dengue fever,Clinical diagnosis,Treatment depends on the symptoms.
+Green algae Desmodesmus armatus,Desmodesmus infection,,
+Dientamoeba fragilis,Dientamoebiasis,,
+Corynebacterium diphtheriae,Diphtheria,"Laboratory criteria Isolation of C. diphtheriae culture
+ Histopathologic diagnosis
+ Toxin demonstration 
+ In vivo tests (guinea pig inoculation)
+ In vitro test: Elek's gel precipitation test, PCR, ELISA, ICA
+ Clinical criteria 
+ URT illness with sore throat
+ Low-grade fever
+ An adherent, dense, grey pseudomembrane covering the posterior aspect of the pharynx","Metronidazole, Erythromycin, Procaine penicillin G"
+Diphyllobothrium,Diphyllobothriasis,,
+Dracunculus medinensis,Dracunculiasis,,
+Eastern equine encephalitis virus,Eastern equine encephalitis (EEE),Blood tests,"Corticosteroids, anticonvulsants, and supportive measures (treating symptoms)"
+Ebolavirus (EBOV),Ebola hemorrhagic fever,,
+Echinococcus species,Echinococcosis,"Imaging, Serology test",Surgical removal of the cysts combined with chemotherapy
+Ehrlichia species,Ehrlichiosis,,
+Enterobius vermicularis,Enterobiasis (Pinworm infection),,
+Enterococcus species,Enterococcus infection,,
+Enterovirus species,Enterovirus infection,,
+Rickettsia prowazekii,Epidemic typhus,,
+Parvovirus B19,Erythema infectiosum (Fifth disease),,
+Human herpesvirus 6 (HHV-6) and human herpesvirus 7 (HHV-7),Exanthem subitum (Sixth disease),,
+Fasciola hepatica and Fasciola gigantica,Fasciolasis,,
+Fasciolopsis buski,Fasciolopsiasis,,
+PRNP,Fatal familial insomnia (FFI),,
+Filarioidea superfamily,Filariasis,,
+Clostridium perfringens,Food poisoning by Clostridium perfringens,Stool test,Supportive care
+multiple,Free-living amebic infection,,
+Fusobacterium species,Fusobacterium infection,,
+usually Clostridium perfringens; other Clostridium species,Gas gangrene (Clostridial myonecrosis),,
+Geotrichum candidum,Geotrichosis,,
+PRNP,Gerstmann-Sträussler-Scheinker syndrome (GSS),,
+Giardia lamblia,Giardiasis,Detection of antigens on the surface of organisms in stool,"Treatment is not always necessary. If medications are needed, a nitroimidazole medication is used such as metronidazole, tinidazole, secnidazole or ornidazole."
+Burkholderia mallei,Glanders,,
+Gnathostoma spinigerum and Gnathostoma hispidum,Gnathostomiasis,,
+Neisseria gonorrhoeae,Gonorrhea,Gram stain and culture,Ceftriaxone by injection and azithromycin by mouth
+Klebsiella granulomatis,Granuloma inguinale (Donovanosis),,
+Streptococcus pyogenes,Group A streptococcal infection,Culture,Penicillin
+Streptococcus agalactiae,Group B streptococcal infection,Gram stain,Penicillin and ampicillin
+Haemophilus influenzae,Haemophilus influenzae infection,Gram stain,"In severe cases, cefotaxime and ceftriaxone delivered into the bloodstream, and for the less severe cases, an association of ampicillin and sulbactam, cephalosporins of the second and third generation, or fluoroquinolones are preferred."
+"Enteroviruses, mainly Coxsackie A virus and enterovirus 71 (EV71)","Hand, foot and mouth disease (HFMD)","A diagnosis usually can be made by the presenting signs and symptoms alone. If the diagnosis is unclear, a throat swab or stool specimen may be taken.","Medications are usually not needed as hand, foot, and mouth disease is a viral disease that typically resolves on its own."
+Sin Nombre virus,Hantavirus Pulmonary Syndrome (HPS),,
+Heartland virus,Heartland virus disease,,
+Helicobacter pylori,Helicobacter pylori infection,,
+"Escherichia coli O157:H7, O111 and O104:H4",Hemolytic-uremic syndrome (HUS),"First diagnosis of aHUS is often made in the context of an initial, complement-triggering infection, and Shiga-toxin has also been implicated as a trigger that identifies patients with aHUS.","Treatment involves supportive care and may include dialysis, steroids, blood transfusions, and plasmapheresis."
+Bunyaviridae species,Hemorrhagic fever with renal syndrome (HFRS),HFRS is difficult to diagnose on clinical grounds alone and serological evidence is often needed.,There is no cure for HFRS. Treatment involves supportive therapy including renal dialysis.
+Hendra virus,Hendra virus infection,,
+Hepatitis A virus,Hepatitis A,Blood tests,"Supportive care, liver transplantation"
+Hepatitis B virus,Hepatitis B,Blood tests,"Antiviral medication (tenofovir, interferon), liver transplantation"
+Hepatitis C virus,Hepatitis C,Blood testing for antibodies or viral RNA,"Antivirals (sofosbuvir, simeprevir, others)"
+Hepatitis D Virus,Hepatitis D,Immunoglobulin G,"Antivirals, pegylated interferon alpha"
+Hepatitis E virus,Hepatitis E,Hepatitis E virus (HEV),"Rest, ribavirin (if chronic)"
+Herpes simplex virus 1 and 2 (HSV-1 and HSV-2),Herpes simplex,"Based on symptoms, PCR, viral culture","Aciclovir, valaciclovir, paracetamol (acetaminophen), topical lidocaine"
+Histoplasma capsulatum,Histoplasmosis,"Histoplasmosis can be diagnosed by samples containing the fungus taken from sputum (via bronchoalveolar lavage), blood, or infected organs.","In the majority of immunocompetent individuals, histoplasmosis resolves without any treatment. Typical treatment of severe disease first involves treatment with amphotericin B, followed by oral itraconazole."
+Ancylostoma duodenale and Necator americanus,Hookworm infection,,
+Human bocavirus (HBoV),Human bocavirus infection,,
+Ehrlichia ewingii,Human ewingii ehrlichiosis,The diagnosis can be confirmed by using PCR. A peripheral blood smear can also be examined for intracytoplasmic inclusions called morulae.,Doxycycline
+Anaplasma phagocytophilum,Human granulocytic anaplasmosis (HGA),PCR,Doxycycline
+Human metapneumovirus (hMPV),Human metapneumovirus infection,,
+Ehrlichia chaffeensis,Human monocytic ehrlichiosis,PCR,Doxycycline
+One of the human papillomaviruses,Human papillomavirus (HPV) infection,,
+Human parainfluenza viruses (HPIV),Human parainfluenza virus infection,,
+Human T-lymphotropic virus 1 (HTLV-1),Human T-lymphotropic virus 1 infection,,
+Hymenolepis nana and Hymenolepis diminuta,Hymenolepiasis,Examination of the stool for eggs and parasites,"Praziquantel, niclosamide"
+Epstein–Barr virus (EBV),Epstein–Barr virus infectious mononucleosis (Mono),"Diagnostic modalities for infectious mononucleosis include: Person's age, with highest risk at 10 to 30 years.
+ Medical history, such as close contact with other people with infectious mononucleosis
+ Physical examination, including palpation of any enlarged lymph nodes in the neck, or enlarged spleen.
+ The heterophile antibody test is a screening test that gives results.
+ Serological tests take longer time, but are more accurate.","Infectious mononucleosis is generally self-limiting, so only symptomatic or supportive treatments are used."
+Orthomyxoviridae species,Influenza (flu),"Diagnostic methods that can identify influenza include viral cultures, antibody- and antigen-detecting tests, and nucleic acid-based tests.","Treatment of influenza in cases of mild or moderate illness is supportive and includes anti-fever medications such as acetaminophen and ibuprofen, adequate fluid intake to avoid dehydration, and resting at home."
+Orthomyxoviridae species,Influenza (flu),"Diagnostic methods that can identify influenza include viral cultures, antibody- and antigen-detecting tests, and nucleic acid-based tests.","Treatment of influenza in cases of mild or moderate illness is supportive and includes anti-fever medications such as acetaminophen and ibuprofen, adequate fluid intake to avoid dehydration, and resting at home."
+Isospora belli,Isosporiasis,Microscopic demonstration of the large typically shaped oocysts is the basis for diagnosis.,Trimethoprim-sulfamethoxazole
+Japanese encephalitis virus,Japanese encephalitis,"Available tests detecting JE virus-specific IgM antibodies in serum and/or cerebrospinal fluid, for example by IgM capture ELISA.",Supportive
+unknown; evidence supports that it is infectious,Kawasaki disease,"Based on symptoms, ultrasound of the heart","Aspirin, immunoglobulin"
+multiple,Keratitis,,"Infectious keratitis generally requires urgent antibacterial, antifungal, or antiviral therapy to eliminate the pathogen."
+Kingella kingae,Kingella kingae infection,,
+PRNP,Kuru,Autopsy,None
+Lassa virus,Lassa fever,Laboratory testing,Supportive
+Legionella pneumophila,Legionellosis (Legionnaires' disease),"Urinary antigen test, sputum culture","Effective antibiotics include most macrolides, tetracyclines, ketolides, and quinolones."
+Legionella pneumophila,Pontiac fever,,
+Leishmania species,Leishmaniasis,Hematology laboratory by direct visualization of the amastigotes (Leishman–Donovan bodies).,"For visceral leishmaniasis in India, South America, and the Mediterranean, liposomal amphotericin B is the recommended treatment and is often used as a single dose."
+Mycobacterium leprae and Mycobacterium lepromatosis,Leprosy,"In countries where people are frequently infected, a person is considered to have leprosy if they have one of the following two signs: Skin lesion consistent with leprosy and with definite sensory loss.
+ Positive skin smears.","Rifampicin, dapsone, clofazimine"
+Leptospira species,Leptospirosis,Testing blood for antibodies against the bacterium or its DNA,"Doxycycline, penicillin, ceftriaxone"
+Listeria monocytogenes,Listeriosis,Culture of blood or spinal fluid,"Ampicillin, gentamicin"
+"Borrelia burgdorferi, Borrelia garinii, and Borrelia afzelii",Lyme disease (Lyme borreliosis),"Based on symptoms, tick exposure, blood tests","Doxycycline, amoxicillin, ceftriaxone, cefuroxime"
+Wuchereria bancrofti and Brugia malayi,Lymphatic filariasis (Elephantiasis),Microscopic examination of blood,Albendazole with ivermectin or diethylcarbamazine
+Lymphocytic choriomeningitis virus (LCMV),Lymphocytic choriomeningitis,Blood test,Symptomatic and supportive
+Plasmodium species,Malaria,"Examination of the blood, antigen detection tests",Antimalarial medication
+Marburg virus,Marburg hemorrhagic fever (MHF),Blood test,Supportive
+Measles virus,Measles,"Onset of fever and malaise about 10 days after exposure to the measles virus, followed by the emergence of cough, coryza, and conjunctivitis that worsen in severity over 4 days of appearing. Observation of Koplik's spots is also diagnostic.",Supportive care
+Middle East respiratory syndrome–related coronavirus,Middle East respiratory syndrome (MERS),rRT-PCR testing,Symptomatic and supportive
+Burkholderia pseudomallei,Melioidosis (Whitmore's disease),Growing the bacteria in culture mediums,"Ceftazidime, meropenem, co-trimoxazole"
+multiple,Meningitis,Lumbar puncture,"Antibiotics, antivirals, steroids"
+Neisseria meningitidis,Meningococcal disease,,"Treatment in primary care usually involves intramuscular administration of benzylpenicillin. Once in the hospital, the antibiotics of choice are usually IV broad spectrum 3rd generation cephalosporins."
+usually Metagonimus yokagawai,Metagonimiasis,Metagonimiasis is diagnosed by eggs seen in feces.,Praziquantel
+Microsporidia phylum,Microsporidiosis,PCR,Fumagillin has been used in the treatment. Another agent used is albendazole.
+Molluscum contagiosum virus (MCV),Molluscum contagiosum (MC),Based on appearance,"Cimetidine, podophyllotoxin"
+Monkeypox virus,Mpox,Testing for viral DNA,"Supportive, antivirals, vaccinia immune globulin"
+Mumps virus,Mumps,"Antibody testing, viral cultures, and reverse transcription polymerase chain reaction",Supportive
+Rickettsia typhi,Murine typhus (Endemic typhus),Early diagnosis continued to be based on clinical suspicion.,The most effective antibiotics include tetracycline and chloramphenicol.
+Mycoplasma pneumoniae,Mycoplasma pneumonia,"Chest X-Ray, Chest CT, blood test","Erythromycin, doxycycline"
+Mycoplasma genitalium,Mycoplasma genitalium infection,Nucleic acid amplification test,"Azithromycin, moxifloxacin"
+numerous species of bacteria (Actinomycetoma) and fungi (Eumycetoma),Mycetoma,"Ultrasound, fine needle aspiration",Antibiotics or antifungal medication
+parasitic dipterous fly larvae,Myiasis,Examination and serologic testing,Petroleum jelly over the central punctum
+most commonly Chlamydia trachomatis and Neisseria gonorrhoeae,Neonatal conjunctivitis (Ophthalmia neonatorum),,"Antibiotic ointment (erythromycin, tetracycline, or rarely silver nitrate or Argyrol)"
+Nipah virus,Nipah virus infection,,
+Norovirus,Norovirus,Based on symptoms,Supportive care
+PRNP,"(New) Variant Creutzfeldt–Jakob disease (vCJD, nvCJD)",,
+usually Nocardia asteroides and other Nocardia species,Nocardiosis,"chest x-ray to analyze the lungs, a bronchoscopy, a brain/lung/skin biopsy, or a sputum culture.",trimethoprim/sulfamethoxazole or high doses of sulfonamides
+Onchocerca volvulus,Onchocerciasis (River blindness),,
+Opisthorchis viverrini and Opisthorchis felineus,Opisthorchiasis,,
+Paracoccidioides brasiliensis,Paracoccidioidomycosis (South American blastomycosis),,
+usually Paragonimus westermani and other Paragonimus species,Paragonimiasis,,
+Pasteurella species,Pasteurellosis,,
+Pediculus humanus capitis,Pediculosis capitis (Head lice),,
+Pediculus humanus corporis,Pediculosis corporis (Body lice),,
+Pthirus pubis,"Pediculosis pubis (pubic lice, crab lice)",,
+multiple,Pelvic inflammatory disease (PID),"Based on symptoms, ultrasound, laparoscopic surgery","Typical regimens include cefoxitin or cefotetan plus doxycycline, and clindamycin plus gentamicin."
+Bordetella pertussis,Pertussis (whooping cough),Nasopharyngeal swab,"erythromycin, clarithromycin, or azithromycin"
+Yersinia pestis,Plague,"Finding the bacterium in a lymph node, blood, sputum",Gentamicin and a fluoroquinolone
+Streptococcus pneumoniae,Pneumococcal infection,Culture,"cephalosporins, and fluoroquinolones such as levofloxacin and moxifloxacin"
+Pneumocystis jirovecii,Pneumocystis pneumonia (PCP),chest X-ray and an arterial oxygen level,trimethoprim/sulfamethoxazole
+multiple,Pneumonia,"Based on symptoms, chest X-ray","Antibiotics, antivirals, oxygen therapy"
+Poliovirus,Poliomyelitis,Finding the virus in the feces or antibodies in the blood,supportive care
+Prevotella species,Prevotella infection,,
+usually Naegleria fowleri,Primary amoebic meningoencephalitis (PAM),flagellation test,"Miltefosine, fluconazole, amphotericin B, posaconazole, voriconazole, targeted temperature management"
+JC virus,Progressive multifocal leukoencephalopathy,"finding JC virus DNA in spinal fluid, brain CT",
+Chlamydophila psittaci,Psittacosis,Culture,tetracyclines and chloramphenicol
+Coxiella burnetii,Q fever,Based on serology,"doxycycline, tetracycline, chloramphenicol, ciprofloxacin, and ofloxacin"
+Rabies virus,Rabies,fluorescent antibody test (FAT),Supportive care
+"Borrelia hermsii, Borrelia recurrentis, and other Borrelia species",Relapsing fever,blood smear,Tetracycline-class antibiotics
+Respiratory syncytial virus (RSV),Respiratory syncytial virus infection,A variety of laboratory tests,Treatment for RSV infection is focused primarily on supportive care.
+Rhinosporidium seeberi,Rhinosporidiosis,,
+Rhinovirus,Rhinovirus infection,,
+Rickettsia species,Rickettsial infection,,
+Rickettsia akari,Rickettsialpox,,
+Rift Valley fever virus,Rift Valley fever (RVF),,
+Rickettsia rickettsii,Rocky Mountain spotted fever (RMSF),,
+Rotavirus,Rotavirus infection,,
+Rubella virus,Rubella,,
+Salmonella species,Salmonellosis,,
+SARS coronavirus,Severe acute respiratory syndrome (SARS),,
+Sarcoptes scabiei,Scabies,,
+Group A Streptococcus species,Scarlet fever,,
+Schistosoma species,Schistosomiasis,,
+multiple,Sepsis,,
+Shigella species,Shigellosis (bacillary dysentery),,
+Varicella zoster virus (VZV),Shingles (Herpes zoster),,
+Variola major or Variola minor,Smallpox (variola),,
+Sporothrix schenckii,Sporotrichosis,,
+Staphylococcus species,Staphylococcal food poisoning,,
+Staphylococcus species,Staphylococcal infection,,
+Strongyloides stercoralis,Strongyloidiasis,,
+Measles virus,Subacute sclerosing panencephalitis,,
+Treponema pallidum,"Bejel, Syphilis, and Yaws",,
+Taenia species,Taeniasis,,
+Clostridium tetani,Tetanus (lockjaw),,
+Tick-borne encephalitis virus (TBEV),Tick-borne encephalitis,,
+usually Trichophyton species,Tinea barbae (barber's itch),,
+usually Trichophyton tonsurans,Tinea capitis (ringworm of the scalp),,
+usually Trichophyton species,Tinea corporis (ringworm of the body),,
+"usually Epidermophyton floccosum, Trichophyton rubrum, and Trichophyton mentagrophytes",Tinea cruris (Jock itch),,
+Trichophyton rubrum,Tinea manum (ringworm of the hand),,
+usually Hortaea werneckii,Tinea nigra,,
+usually Trichophyton species,Tinea pedis (athlete's foot),,
+usually Trichophyton species,Tinea unguium (onychomycosis),,
+Malassezia species,Tinea versicolor (Pityriasis versicolor),,
+Staphylococcus aureus or Streptococcus pyogenes,Toxic shock syndrome (TSS),,
+Toxocara canis or Toxocara cati,Toxocariasis (ocular larva migrans (OLM)),,
+Toxocara canis or Toxocara cati,Toxocariasis (visceral larva migrans (VLM)),,
+Toxoplasma gondii,Toxoplasmosis,,
+Chlamydia trachomatis,Trachoma,,
+Trichinella spiralis,Trichinosis,,
+Trichomonas vaginalis,Trichomoniasis,,
+Trichuris trichiura,Trichuriasis (whipworm infection),,
+usually Mycobacterium tuberculosis,Tuberculosis,,
+Francisella tularensis,Tularemia,,
+"Salmonella enterica subsp. enterica, serovar typhi",Typhoid fever,,
+Rickettsia,Typhus fever,,
+Ureaplasma urealyticum,Ureaplasma urealyticum infection,,
+Coccidioides immitis or Coccidioides posadasii.[41],Valley fever,,
+Venezuelan equine encephalitis virus,Venezuelan equine encephalitis,,
+Guanarito virus,Venezuelan hemorrhagic fever,,
+Vibrio vulnificus,Vibrio vulnificus infection,,
+Vibrio parahaemolyticus,Vibrio parahaemolyticus enteritis,,
+multiple viruses,Viral pneumonia,,
+West Nile virus,West Nile fever,,
+Trichosporon beigelii,White piedra (tinea blanca),,
+Yersinia pseudotuberculosis,Yersinia pseudotuberculosis infection,,
+Yersinia enterocolitica,Yersiniosis,,
+Yellow fever virus,Yellow fever,,
+Zeaspora fungus,Zeaspora,,
+Zika virus,Zika fever,,
+Mucorales order (Mucormycosis) and Entomophthorales order (Entomophthoramycosis),Zygomycosis,,

processed_medical_history.csv

@@ -0,0 +1,27 @@
+Pathogen_Type,Pathogen_Name,Key_Symptoms,Physical_Findings,Lab_Results,Patient_Demographics,Diagnostic_Methods,Treatment,Prevention,Complications,Transmission,Incubation_Period
+Enterobius vermicularis,Enterobius vermicularis,"abdominal pain, distension, vomiting, absolute constipation, progressive abdominal pain","tinkling bowel sounds on auscultation, obvious dilated loops of bowel, numerous white threadworms in the colon",histological analysis demonstrated pseudotumour related to Enterobius vermicularis infection,"60-year-old male, history of surgical intervention, no history of colorectal cancer or inflammatory bowel disease","intravenous Hartmann's solution, intravenous analgesia, antibiotics and piperacillin/tazobactam, intraoperative colonoscopy, diagnostic laparoscopy, histological analysis","intravenous Hartmann's solution, intravenous analgesia, antibiotics and piperacillin/tazobactam, emergency Hartman’s procedure, intraoperative removal of mass","practicing good hygiene and sanitation, prompt medical attention for symptoms","large-bowel obstruction, pseudotumour formation","faecal-oral route, contamination of soil and surfaces with eggs",varies but commonly 2-8 weeks
+SARS-CoV-2,COVID-19,"Fever, cough, pleuritic chest pain",Reduced breath sounds on both lungs with coarse crackles at the left lower zone,"{""FiO2"": ""0.8 with 60 L/min flow"", ""CRP"": ""70.2 mg/L"", ""PCT"": ""0.33 ng/mL"", ""Serum Ferritin"": ""2537 ng/mL"", ""Hemoglobin"": ""153 g/L"", ""Total White Cell Count"": ""12.4 x 10^9/L"", ""Renal Function"": ""Normal"", ""Liver Function"": ""Normal""}","54-year-old man, weight=62 kg, height=1.72 m","HRCT, nasopharyngeal swab for real-time reverse transcription–PCR, blood and sputum culture","Methylprednisolone 1 mg/kg two times per day, Continuous Venous Hemodialysis Filteration (CVVHDF) with oXiris filter",None specified in the text,"Cytokine release syndrome (CRS), superinfected bacterial pneumonia",Close contact with COVID-19 positive son,5 days
+Bartonella,"Bartonella henselae, Bartonella quintana","fever, progressive confusion, mild bilateral pleural effusions, left greater than right pleural effusion, left mid and lower lung zone airspace opacities most consistent with atelectasis","mild bilateral pleural effusions, left greater than right pleural effusion, left mid and lower lung zone airspace opacities","{""Bartonella henselae IgG"": ""1:4096"", ""Bartonella quintana IgG"": ""1:512"", ""Bartonella IgM"": ""positive"", ""PCR testing"": ""not performed"", ""Blood cultures"": ""negative"", ""Complete blood count"": ""mild hyponatremia to 134 meq/L and transaminitis of alanine aminotransferase (ALT) to 51 U/L"", ""Chest X-ray"": ""mild pulmonary oedema and left greater than right effusion""}",60-year-old male,"PCR testing, blood cultures, serological tests","intravenous doxycycline 100 mg two times per day, intravenous rifampin 300 mg two times per day for 4 weeks","adequate antimicrobial therapy for Bartonella, avoidance of cat scratches and bites","pulmonary manifestations, central nervous system involvement","cat scratches and bites, arthropod vectors such as ticks, lice, chiggers and mosquitoes",variable
+Bacteria,Treponema pallidum,"neurological symptoms, limbic encephalitis, altered behavior, impaired awareness","cerebrospinal fluid (CSF) pleocytosis, mesiotemporal lobe hyperintensity","persistently active CSF analysis, positive serum syphilis antibodies",man in his 50s,"MRI brain, CSF analysis","corticosteroid treatment, benzyplencillin therapy",treatment of syphilis,"neuropsychiatric symptoms, cognitive dysfunction",sexually transmitted infection,not specified
+N. meningitidis,Neisseria meningitidis,"fever, headache, neck stiffness, rigors, confusion, purpuric rash","purpuric rash, moderate neck stiffness","positive bacterial PCR for N. meningitidis, positive nasopharyngeal RT-PCR for SARS-CoV-2","22-year-old woman, no medical history, normally working full-time in a supermarket","bacterial PCR, nasopharyngeal RT-PCR",intravenous ceftriaxone,"vaccination against N. meningitidis serogroup C in childhood, not recently vaccinated against SARS-CoV-2",none,"respiratory droplets, nasopharyngeal viral shedding","unknown for SARS-CoV-2, 2 weeks for N. meningitidis"
+SARS-CoV-2,"Legionella pneumophila, Staphylococcus aureus, MRSA","fever, cough, dyspnea, pleuritic chest pain, headache, nausea, sore throat, myalgias","tachypnea, tachycardia, hypotension, crepitation on auscultation, leukocytosis","positive SARS-CoV-2 PCR, positive Legionella urine antigen, positive methicillin-resistant Staphylococcus aureus (MRSA) culture, positive blood culture for MRSA","50-year-old man, no known medical history, recent travel history, work-related exposure","PCR testing, urine antigen testing, blood culture, sputum culture","remdesivir, deamethasone, baricitinib, azithromycin, ceftriaxone, doxycycline","vaccination, social distancing, personal protective equipment, hand hygiene","pneumonia, acute kidney injury, thrombosis","respiratory droplets, fecal-oral route, direct contact","2-14 days for SARS-CoV-2, 2-10 days for Legionella, 2 days for MRSA"
+bacterial,Escherichia coli,"abnormal movements, fever, dysuria, lower abdominal pain","truncal ataxia, multidirectional saccades","elevated inflammatory markers, positive urine culture for E. coli, normal CSF protein",elderly gentleman,"urine analysis, X-ray, contrast-enhanced CT, brain imaging with MRI","intravenous antibiotics, intravenous immunoglobulin, oral prednisolone",treating underlying infections,neurological symptoms lasting over 1 year,bacterial urinary tract infection,not specified
+tick-borne parasitic infection,Babesiosis,"fever, chills, lower abdominal and back pain, sore throat, diarrhea, decreased urine output","anemia, elevated liver enzymes, intravascular hemolysis","haemoglobin 90 g/L, white cell count 5.2×10⁹/L, platelet count 46×10⁹/L, blood urea nitrogen 43 mg/dL, creatinine 4.36 mg/dL, lactate dehydrogenase 1771 U/L, aspartate transaminase 131 U/L,  total bilirubin 0.6 mg/dL","60-year-old Asian woman, medical history of squamous cell carcinomas of the tongue","blood tests, haemoglobinuria, biliuninaemia, proteinuria, ultrasound, chest X-ray, CT abdomen/pelvis, blood cultures, LDH, Coombs test, peripheral blood smear","intravenous volume resucitation, broad-spectrum antibiotics, vasopressors, intravenous haemodialysis, antimicrobial therapy","avoid tick bites, wear protective clothing, use tick repellents","renal failure, intravascular hemolysis, hemolytic uremic syndrome (HUS)","tick bite, intravenous transmission",varying incubation period
+Pneumocystis jirovecii,Pneumocystis jirovecii pneumonia,"Non-productive cough, Generalised weakness, Fever, Dyspnoea, Anorexia, Weight loss, Fatigue","Tachypnoea, Racemic tachycardia, Decreased oxygen saturation","WBC: 2.6x10^9/l, Haemoglobin: 77g/l, Haematocrit: 23.7%, Platelet count: 254x10^9/l, Coccidioides antibody IgM: 1:16, HIV viral load: 1.25x10^6 copies/mL, CD4 count: 7 cells/µL","60-year-old woman, HIV-positive, AIDS-related illness","CT scan, Bronchoscopy, Histological examination, Immunostaining, PCR","Trimethoprim-sulfamethoxazole, Bicillin, Prednisone","Antiretroviral therapy, Pneumocystis prophylaxis, Oral trimethoprim-sulfamethoxazole","Acute respiratory failure, Hypoxemia","Spread from person to person through the air, Immunocompromised individuals are at higher risk","Unknown, but progression can be rapid"
+Histoplasma capsulatum,Histoplasma capsulatum,"cough, fever, weakness, lacups, fever, ulcer","small ulcer measuring 2.5x3.6 cm at the anterior hard palate, bilateral nodules in the lungs with military pattern","elevated protein at 1500 mg/L, histoplasmosis antigen positive at 0.47 ng/mL, serum histoplasma antigen detected at >15 ng/mL, normal CSF fungal culture but weakly positive histoplasma antigen, negative results for other fungal workups, BAL, acid-fast Bacillus culture, and Mycobacterium tuberculosis PCR, normal MRI of the brain","60-year-old man with a history of diabetes mellitus type 2, hypertension, and end-stage renal disease status postrenal transplantation","histoplasmosis antigen test, CT scan, biopsy, PCR, serum cryptococcal antigen, histoplasma antigen, cerebrospinal fluid analysis","amphotericin B therapy, itraconazole 200 mg two times per day for 1 year, secondary prophylaxis for disseminated histoplasmosis infection",prompt diagnosis and treatment of disseminated histoplasmosis for a good clinical outcome,"disseminated histoplasmosis, miliary pulmonary tuberculosis","respiratory route, inhalation of spores from contaminated soil or bird droppings","variable, typically 10-17 days"
+Bacteria,Klebsiella,"weakness, cough, abdominal pain, positive blood cultures, fever, chills","tachycardia, tachypnea, abdominal tenderness, hepatosplenomegaly","positive blood cultures for ESBL Klebsiella, elevated white cell count, negative blood cultures on discharge","woman in her 50s, history of cirrhosis, alcohol use disorder, primary biliary cholangitis, chronic obstructive pulmonary disease","translocation via TIPS, biliary tract origin, abdominal wall cellulitis, Strongyloides serology","intravenous meropenem, ivermectin for Strongyloides","adequate medical therapy for underlying disease, testing and treating for Strongyloides","recurrent bacteremia, hepatosplenomegaly","bloodstream infection, biliary tract infection","unknown for bacteremia, unknown for Strongyloides"
+Fungus,Fusarium falciforme,"Progressive left foot swelling, Nodules, sinuses and pale grain discharge, Painful on walking and standing","Enlarged left foot with multiple pustules and discharging sinuses, Tender on palpation, Yellow gritty sand-like materials on surgical debulking","Histopathological findings: foci of sepitate fungal hyphae, Culture: No growth, Molecular identification: Fusarium falciforme","Middle-aged man, History of recurrent foot injuries from oil palm thorns","Histopathology, Microscopic examination, Molecular sequencing of rDNA ITS1, ITS4 and large subunit regions","Surgical debulking, Oral itraconazole 200 mg twice daily for 9 months","Avoidance of injury and contamination, Proper wound care and treatment","Recurrent infection, Chronic inflammation and tissue damage","Soil contamination, Injury with contaminated materials","Variable, but can present late after initial injury"
+Bacterial,Escherichia coli,"Abnormal movements, Fever, Dysuria, Lower abdominal pain","Tremor, Multidirectional saccades, Truncal ataxia","Elevated inflammatory markers, Positive urine culture for E. coli, Positive CSF for E. coli, Normal EEG",Elderly gentleman,"Clinical examination, Urine analysis, CSF analysis, EEG","Intravenous antibiotics, Intravenous steroids",Early detection and treatment of underlying causes,"Recurrent UTI, Potential long-term neurological issues",Urinary tract infection,Not specified
+Fulminant necrotizing amoebic colitis and COVID-19,Entamoeba histolytica and SARS-CoV-2,"Sudden abdominal pain, Bloody stool, Fever, Dry cough, Malaise, Severe hypoalbuminemia, Hypokalemia, Hypertension","Distended, tender and guarded abdomen, Exaggerated bowel sounds, Grossly distended bowel loops, Extensive gangrenous changes","{""COVID-19"": ""Positive on RT-PCR"", ""Leukocyte count"": ""326.27 mg/L"", ""Procalcitonin"": ""36 \u00b5g/mL"", ""Interleukin-6"": ""1006 pg/mL"", ""LDH"": ""487 U/L"", ""Ferritin"": ""6736.66 ng/mL""}","80s, female","RT-PCR testing, CT scan","Emergency exploratory laparotomy, Packed cell transfusion, Intravenous antibiotics, Intravenous fluids and electrolytes, Total parenteral nutrition, Mechanical compression device for venous thrombosis prevention","Prompt surgical intervention, Appropriate intensive care management","Severe hypoalbuminemia, Hypokalemia, Hypertension, Kidney injury, Deep vein thrombosis","Fecal-oral route, Aerosol transmission (for COVID-19)","Variable, 2-14 days (for COVID-19), Viral shedding up to 33 days"
+Ureaplasma parvum,Ureaplasma parvum,"meningitis, fever, headache, impaired hearing, light sensitivity, headache, lethargic, irritable, acute brain herniation","leukocytosis, increased protein, normal CSF glucose, high CSF lactate, normal CSF leucocytes, abnormal CSF parameters, meningeal biopsy, thrombosis of the superior sagittal sinus, strider","positive CSF PCR for Ureaplasma parvum, negative bacterial cultures, negative PCR for fungal DNA, negative PCR for Ureaplasma urealyticum, positive 16S rRNA PCR for Ureaplasma parvum DNA, negative bacterial DNA PCR","immunocompromised teenager, female, late teens","CT scan, lumbar puncture, cerebral CT, MRI, PCR, 16S rRNA PCR, next-generation sequencing (NGS), cranial CT venography","meropenem, acidovir, dexamethasone, hydrocortisone, liposomal amphotericin B, linezolid, doxycycline, quinolone, metronidazole","macrolides, tetracyclines, chloramphenicol, quinolones","brain herniation, cerebral edema, thrombosis","intracellular bacteria, Ureaplasma species",not specified
+Viral,Kawasaki Disease (KD),"High-grade fever, Maculopapular rash, Conjunctivitis, Strawberry tongue, Erythema of hands and feet, Cervical lymphadenopathy","Enlarged coronary artery, Dilated coronary artery, Mild tricuspid valve regurgitation, Good biventricular function","Elevated inflammatory markers, Positive PCR for human adenovirus, Negative PCR for rickettsia and viral panel, Negative blood culture, Negative throat swab culture","Female siblings, Early and middle childhood, History of autoimmune disease in maternal grandmother, Guillain-Barré syndrome in maternal great-grandmother","Echocardiography, PCR sequencing, Complete blood count, Urine analysis, Rapid antigen detection test","IVIG 2 g/kg, Aspirin 5 mg/kg/day for 8 weeks",Avoidance of triggers and early treatment of infections,"Coronary artery aneurysms, Heart failure, Arrythmias, Haemodynamic instability",Fecal-oral route and respiratory droplets,"Unknown, but symptoms develop within weeks"
+Bacteria,Bartonella henselae,"Fever, Shortness of breath, Intermittent fever, Perspiration, Conjunctivitis","Mild right-sided cervical lymphadenopathy, Tachycardia, Tachypnoea, Mild hypotension","{""CRP"": ""3.9 mg/L"", ""eGFR"": ""90 mL/min/1.73 m\u00b2"", ""Urea"": ""7.1 mmol/L"", ""Creatinine"": ""106 \u00b5mol/L"", ""Alkaline phosphatase"": ""97 U/L"", ""AST"": ""175 U/L"", ""ALT"": ""146 U/L"", ""Bartonella henselae IgM"": ""Positive"", ""HBsAg"": ""Negative"", ""Hepatitis B anti-HBc"": ""Negative"", ""HCV"": ""Negative"", ""HIV"": ""Negative"", ""D-dimer"": ""2.01 mg/mL"", ""hs-TnT"": ""2278 ng/L""}","Mid-30s, Male, Cat owner, No recent travel or contact with stagnant water","Cardiac MRI, Echocardiogram, CT angiography, Blood cultures, PCR analysis","Antibiotics (azithromycin), IV antibiotics (penicillin and gentamicin), Treatments for heart failure","Avoiding cat scratches and bites, Wearing gloves when handling cats","Heart failure, Pulmonary oedema","Cat scratch, Bite or lick from an infected cat","Variable, but typically 1–4 weeks"
+Neonatal nephrotic syndrome,Klebsiella pneumoniae,"Anasarca (severe edema), Generalised swelling over body, Hypoalbuminemia, Nephrotic range proteinuria","Non-specific mild dermatitis, Pale, edematous, and painful abdominal wall, Pleurial effusion and TFE, Tense abdomen and significant weight gain, Maculopapular rash over trunk and extremities","Urine output: 3–4 ml/kg/hour, Urine protein creatinine ratio: 95/0, Urine culture: Klebsiella pneumoniae, Urine protein: 2.16 g/dL, Urine culture: No growth, WBCs: 13.5 x 10^9/L, Hb: 9.1 g/dL, Platelet count: 184 x 10^9/L","Male neonate born at 38 weeks of gestation, Birth weight of 3.1 kg, Appropriate for gestation age","Serum protein electrophoresis, Urine culture, Blood culture, CSF evaluation for meningitis","Broadspectrum antibiotics: Ceftriaxone, Gentamycin, Intravenous immunoglobulin, Suppository support for renal failure, Dynamic fluid management, Enteral feeding: Gradually increased calorie and protein intake","Early diagnosis and treatment of sepsis, Prophylactic antibiotics for neonates with sepsis, Regular monitoring of fluid balance and renal function","Renal failure, Sepsis, Neonatal mortality, Hypoalbuminemia, Pleural effusion","Vertical transmission from mother to neonate, Nosocomial infection",Symptoms onset shortly after birth
+fungal,Histoplasma capsulatum,"fever, chills, productive cough, fatigue, functional decline, anorexia, myalgias, respiratory distress, peripheral oedema, worsening abdominal pain, hepatosplenomegaly","enlarged liver, enlarged spleen, lymphadenopathy, epigastric tenderness, leprosy lesions on arms, legs, and face","anaemia, thrombocytopenia, elevated liver enzymes, elevated LDH, positive histoplasma urine antigen, disseminated histoplasmosis on bone marrow biopsy","63-year-old male, resident of southern Kentucky, of Micronesian descent, long-standing history of lepromatous leprosy, MDT for HD, Addison's disease on corticosteroids, afebrile with tachycardia","CT scans, bone marrow biopsy, laboratory tests for histoplasma, culture and histology of bone marrow","liposomal amphotericin B, itraconazole, high-dose steroids, supportive care including fluids and electrolytes","prophylactic antifungal therapy, regular screening for fungal infections, multidisciplinary team approach","disseminated histoplasmosis, hepatosplenomegaly, pancreatitis, sepsis, multiorgan dysfunction, fatal outcome","haematogenous spread, intravascular haematogenous spread",not specified
+Neurocysticercosis (NCC),Taenia solium,"persistent nausea, vomiting, hiccups","seizures, headache, focal neurodeficits","ring-enhancing lesion in dorsal medulla oblongata, eosinophilic cysts in brain tissue","middle-aged Asian man, unremarkable medical background","MRI of brain, cerebrospinal fluid examination, serological tests for cysticercal antibodies","antibiotics, steroids, antiemetic therapy, anti-helminthic therapy","pork-cysticercus infection control, public health measures to prevent taenia solium transmission","intractable hiccups, refractory seizures, social embarrassment","ingestion of viable cysts of Taenia solium, faeco-oral route","variable, depending on the part of the neuroaxis involved"
+fungal,"Candida albicans, Candida tropicalis","urinary tract obstruction, fungemia, renal failure, bladder rupture","vesical fungal balls, obstructive uropathy, urothelial carcinoma","fungus and fungal spores in urine culture, Candida albicans in urine culture, detachment of epithelial cells and cancer cells in urine","male, type 2 diabetes, history of anthrax and corticosteroid use","cystoscopy, ultrasound, CT scan, histological examination","intravenous empiric antibiotics, nephrostomy, antifungal agents","strict asepsis, sterilisation protocols, controlled diabetes","urinary tract obstruction, urothelial carcinoma","urinary tract infections, catheter use, diabetes mellitus",not specified
+"Bacterial, Fungal","Streptococcus anginosus, S. intermedius, Candida glabrata, P. mirabilis, Bacteroides fragilis, Klebsiella pneumoniae, Proteus mirabilis, Peptostreptococcus asaccharolyticus, Prevotella oris, Fusobacterium spp, Haemophilus influenzae, P. brucea, Chryseobacterium hierrooxidans, Mycobacterium tuberculosis, Stenotrophomonas maltophilia, P. gingivalis, P. stomatis, P. melaninogenica, P. intermedia, Bacteria (not further specified)","Chest pain, Shortness of breath, Fever, Abdominal pain, Nausea, Vomiting, Diarrhea, Haemoptysis, Hematuria, Dysuria, Flank pain, Urethral discharge","Tachycardia, Tachypnea, Hypotension, Decreased breath sounds, Rales, Abnormal heart sounds, Abdominal tenderness, Guaiac-positive stool, Oedema, Jaundice, Fever, Chest discomfort, Leukocytosis, Eosinophilia, Pericardial effusion","Elevated white cell count, Positive blood culture for Streptococcus anginosus, S. intermedius, and Candida glabrata, Positive pericardial fluid culture for P. mirabilis, Positive stool culture for Bacteroides fragilis, Positive urine culture for Klebsiella pneumoniae and Proteus mirabilis, Positive pericardial fluid culture for Peptostreptococcus asaccharolyticus, Prevotella oris, and Fusobacterium spp, Positive blood culture for Haemophilus influenzae, Positive pleural fluid culture for P. brucea, Positive pleural fluid culture for Chryseobacterium hierrooxidans, Positive pericardial fluid culture for Mycobacterium tuberculosis, Positive pericardial fluid culture for Stenotrophomonas maltophilia, Positive blood culture for P. gingivalis, Positive intra-abdominal abscess culture for P. stomatis, Positive blood culture for P. melaninogenica, Positive blood culture for P. intermedia, Positive culture for unspecified bacteria","Age: 34, Sex: Male, Age: 58, Sex: Male, Age: 43, Sex: Male, Age: 49, Sex: Male, Age: 17, Sex: Male, Age: 53, Sex: Male, Age: 62, Sex: Male, Age: 52, Sex: Female, Age: 21, Sex: Female, Age: 55, Sex: Male, Age: 61, Sex: Male, Age: 88, Sex: Female, Age: 63, Sex: Male, Age: 54, Sex: Male","Echocardiogram, Endoscopy, CT scan, Blood culture, Urine culture, Stool culture, Pleural fluid culture, Percardial fluid culture","Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours; ampicillin-sulbactam, 3 g every 6 hours, Antifungals: fluconazole, 400 mg loading dose followed by 200 mg daily, Surgical: pericardial window placement, pericardiectomy, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours, Antibiotics: ceftriaxone, 2 g daily; metronidazole, 500 mg every 6 hours, Antibiotics: ceftriaxone, 2 g daily; ampicillin-sulbactam, 3 g every 6 hours","Maintain sterile technique during invasive procedures, Administer prophylactic antibiotics before dental procedures, Practice good hygiene and handwashing, Avoid immunosuppressive therapy if possible, Monitor for signs of infection post-surgery, Maintain a healthy immune system","Septic shock, Cardiogenic shock, Multiorgan failure, Pericardial effusion, Pneumonia, Septic arthritis, Endocarditis, Abscess formation, Perforation of gastrointestinal tract, Pericardial tamponade, Pleural effusion, Empyema, Cardiac arrest, Death","Direct inoculation during surgical procedures, Hematogenous spread from a distant focus of infection, Contiguous spread from an adjacent organ, Ascending infection from the gastrointestinal tract, Transmission via blood transfusion or organ transplant, Person-to-person contact","Variable, depending on the pathogen and the route of infection, 1-2 days, 24-48 hours, Variable, depending on the pathogen and the route of infection, Immediate, Immediate, Variable, depending on the pathogen and the route of infection, Immediate, Immediate, Variable, depending on the pathogen and the route of infection, Immediate, Immediate, Variable, depending on the pathogen and the route of infection, Immediate, Immediate, Variable, depending on the pathogen and the route of infection, Immediate, Immediate, Variable, depending on the pathogen and the route of infection"
+"bacterial, fungal","Stenotrophomonas, Candida","redness, pain, loss of vision","corneal infiltrate, granulomatous inflammation, stromal keratitis, episcleral congestion","bacterial and fungal culture positive, gram-positive spores on H&E staining","male, age not specified, farmer","culture, histopathological analysis, H&E staining","topical antibiotics, 5% sodium azide eyewashes, exenteration, penetrating keratoplasty","conjunctival scraping or biopsy, early diagnosis and treatment, follow-up","recurrent corneal erosions, episcleral defect",contaminated water or trauma,not specified
+Leishmaniasis,Leishmania donovani,"pleural effusion, cytopenia, bone marrow biopsy, hypoalbuminaemia, shortness of breath, chest pain","pleural effusion, pleural thickening, right-sided chest pain, small segmental pulmonary emboli, tiny deep vein thrombosis","raised D dimer, raised C reactive protein, raised D-dimer, raised C-reactive protein, raised IgG kappa protein bands (18 g/L), raised of liver autoantibodies, anti-liver-kidney microsomal autoantibodies, anti-glycoprotein 210, elevated liver enzymes, raised albumin/globulin ratio","80-year-old female, immunocompetent patient, background of pleuritic chest pains, immunosuppression due to arthritic condition","bone marrow biopsy, pleural fluid analysis, CT scan, PCR testing, liver screen, ultrasound-guided pleural biopsy","intravenous piperacillin-tazobactam, intravenous amoxicillin and clavulanic acid, intravenous ceftriaxone, intravenous amoxicillin and clavulanic acid, liver autoantibodies test, anti-liver-kidney microsomal autoantibodies test, anti-glycoprotein 210 test","avoiding parasitic invasion of the liver, using insecticides, preventing parasitaemia","hypoalbuminaemia, pleural effusion, pitting oedema, recurrence of disease, renal impairment",bite of infected female phlebotomine sandflies,unknown
+Aspergillus,Aspergillus fumigatus,"lesions on inner thigh, erythema, pain, drainage, skin lesions, fever, night sweats, weight loss, bone pain, general malaise","subcutaneous abscess, hyperpigmentation, lymphadenopathy, cutaneous lesions, hepatic abscess, renal and subcutaneous abscesses, asymptomatic, anorexia, fatigue","beta-D glucan assay positive (>300pg/ml), blood cultures negative, serum Aspergillus galactomannan antigen positive (1.32), CT scan demonstrating abscesses and lesions","60-year-old female, history of hypertension, type 2 diabetes","biopsy, CT scan, beta-D glucan assay, serum Aspergillus galactomannan antigen","intravenous voriconazole, surgical incision and drainage, oral posaconazole, antimicrobial therapy","prophylactic antifungal therapy, dermatologic surveillance, prophylactic triazoles","cutaneous abscess, hepatic abscess, renal abscess, lymphadenopathy, skin lesions",inhalation of spores from an environmental source,unknown but typically 1-2 weeks after transplantation
+Ascaris lumbricoides,Ascaris lumbricoides,"Abdominal pain, Nausea, Vomiting, Steady epigastric pain, Passage of worms","Tender abdomen, Pulses full and regular, Normal vital signs, Anorectal disease for 10 years, History of bronchial asthma","Elevated serum lipase, Presence of A. lumbricoides ova, Negative antinuclear antibody test, Negative serum ALT level, Mild acute pancreatitis","22-year-old pregnant female, Second trimester, No known allergies or past surgeries, Occasional alcoholic drinker","MRCP, Ultrasound, Fecal viability study","Conservative management, Pain management, Intravenous hydration and diet progression","Improving sanitation and hygiene, Mass chemotherapy","Local complications, Walled-off necrosis (WON)","Fecal-oral route, Ingestion of food or water contaminated by mature ova",Variable