Diseases Flashcards
- Bacterial meningitis and diagnosis
- Neonatal (bacterial) meningitis
- Health-care associated, following trauma/surgery
(new)
- ‘PIMALL’:
s.pneumoniae (no1) - capsule (vaccine)
h.influenza - capsule (vaccine)
n.meningititis - capsule (vaccine
s.aureus
Listeria (serous meningitis)
Leptospira (serous, not purulent) - ‘ALE’
s.agalactiae - capsule
listeriosis - can go through placenta
e.coli (k1) - Staphylococcus aureus
- E.coli
- Klebsiella pneumoniae
- Pseudomonas aerguniosa
Diagnosis:
- CSF: elevated WBC, elevated protein, low sugar
- from CSF: microscopy, latex agglutinaton, PCR, cultivation
- Blood cultures
Treatment:
- Empiric: 3rd gen cephalosporin - Ceftriaxone
- prevention with vaccines
Community acquires pneumoniae
- typical
- atypical and diagnosis
- haemorrhagic
- aspiration
Therapy?
- Typical pneumoniae
s.pneumoniae (no1)
H.influenza
s.aureus
Morexella catharralis
Klebsiella
Nocardia - lobar pneumoniae (?)
Symtoms:
- fever, dyspnea, chest pain, coughing, sputum
Diagnosis:
- Sample: sputum, blood culture
- Method: microscopy, cultivation
2. atypical legionella pneumoniae chlamydophilia pneumoniae chlamydia psittaci mycobacterium pneumoniae coxiella burnetti
Symtoms:
- low grade fever, or subfebrility
- dry cough
Diagnosis:
- serology: specific IgM
- PCR from urine, blood and broncho-alveolar lavage
- for legionella: detection from urine, culturing on BCYE.
- hemorrhagic
- yersinia pestis
- b. anthracis
- f.tularencis - aspiration
anaerobes:
- bacteriodaceae
- actinomyces
Other:
- bordetella pertussis
- mycobacterium tuberculosis
- Atypical mycobacterium
- Nocardia
- Actinomyces
Therapy:
- amoxicillin/clavulanic acid +/- macrolide or fluoroquinolones
Hospital acquires pneumoniae/ventilator associated pneumoniae
therapy?
- Pseudomonas aergunisa
- acinetobacter baumanii
- stenotrophomonas maltophilia
- Klebsiella
- e.coli (?)
- s. aureus
Therapy: - for empiric treatment: combination of antibiotics (e.g. piperacillin + tazobactam) vancomycin aminoglycosides etc.
- Nosocomial MDR pathogens
2. other nosocomial pathogens (not MDR)
EsCkAPEe 1. Enterococcus S. aureus C.difficule (k) klebsiella Acinetobacter baumanii Pseudomonas Enterobacter e.coli
2. aeromonas plesimonas proteus stenotrophomonas maltophila
- UTI
2. specimen
E.coli (other pathogenic enterobacteria) - Klebsiella - Serratia - enterobacter - proteus
P.aerginosa
Coagulase - cocci: - s.saphrophyticus - s.haemolyticus - enterococcus acinetobacter baumanii corynebacterium urealyticum
burkholdeira capacia
- specimen:
- clean catch midstream urine or dip-slide techique (uricult).
- culturing
- native microscopic test
- pyuria must be seen
- antibiogram
Storage of specimen: sterile urine: 24h at 4C, or max 2h at room temperature
- STIs
- diagnosis
(new)
1.STDs:
• Ulcer
◦ Haemophilia ducreyi - ‘ulcus molle’ - chancroid
◦ T.pallidum ssp palidum - ‘ulcus durum’ - syphilic Chancroid
◦ Chlamydia trachomatis L1-L3 serotypes (LGV)
◦ Granuloma inguinale/donovaniosis - Klebsiella granulomatis
• Discharge:
- Gonorrhea (N.gonorrhea)
- Non-gonorrheal urethitis: often asymtomatic
- Mycoplasma hominis, M. genitalium
- Ureaplasma urealyticum
- Chlamydia serotype D-K
- diagnosis:
- clinical specimen: genital discharge or cells (for IC pathogens)
- women: collection with cytobrush
- men: first catch urine
- PCR: chlamydia, mycoplasma, ureaplasma
- Gonorrhea: gram stained smear + PCR + culturing + AB testing (inoculation ASAP)
- syphilis:- dark field microscopy from discharge, ulcer
- serology (specific and nonspecific tests)
Serology not used:
- gonorrhea
- mycoplasma
- ureaplasma
- chlamydia
Diarrhea and diagnosis
food poisening: normal diarrhea: by eating toxin-contamonated food and not the bacteria
s. aureus
c. perferinges
b. cereus
Watery diarrhea: v.cholera ETEC EPEC EAEC Bacillus cereus (diarrheal type) Clostidium perferingens and difficile Protozoa: - Cryptosporodium spp - Giardia
Diagnosis:
Stool is tested: culturing and other specific tests (see topics)
When food poisening: usually based on the symtoms and food is tested for pathogen.
c.botulinum: inoculation of mice with patients serum.
Normal flora of the skin (new)
- S. epidermidis
- Other coagulase negative staph.
- Propriobacterium acnes
- Apathogenic corynebacteria
Normal flora of oral cavity (new)
Oral cavity • Streptococci (dominant) viridans, mutans • Lactobacilli (dominant) - Actinomyces - Veillonella - Porphyromonas - Apathogenic Neisseria Apathogenic Corynebacteria • Anaerobes: ◦ Bacteroids ◦ Bifidobacterium
Normal flora of the respiratory tract
Normal flora of the respiratory tract • Nostrils ◦ S.aureus (20-30% of pop) ◦ Cornyebacterium ◦ S. epidermidis ◦ Streptococcus pneumoniae ◦ Neisseria sp ◦ Haemophilus sp
• Upper respiratory tract (nasopharynx) ◦ Streptococci: ‣ Alpha-hemolytic streptococi • Strep. Pneumoniae ‣ Beta-hemolytic: • Strep.pyogenes ‣ Non-hemolytic streptococci ◦ Gram neg cocci: ‣ Neisseria sp = pharyngococci ‣ Neisseria meningitidis ◦ Haemophilus influenza ◦ • Lower respiratiry tract: ◦ Usually sterile :) - by mucociliary elevator
Normal flora of urogenital tract (new)
Vagina:
- Lactobacillus
- Candida
- Gardnerella
- Streptococcus
Normal flora of GI and their role (new)
99% obligate anaerobes Bacteroides fragilis Porphyromonas Fusobacterium Enterococcus E. coli Klebsiella Enterobacter Serratia Proteus Streptococcus Bifidobacterium Lactobacillus Veillonella Prevotella Candida
Anti-tuberculotic drugs
- first phase: intensive replication
‘RIPE’
Rifapmin
Isoniazid (inhibits cell membrane function - blocks mycolic acid )
Pyrazinamide (inhibits cell membrane function - blocks mycolic acid)
Ethambutol (inhibits cell wall synthesis)
2nd line of defense:
- Ethionamide
- Capreomycin
- Cycoserine
- macrolides
- fluoroquinolones
Viral and fungal meningitis and encephalitis
Viral:
- Flavivirus: West nile virus (encephalitis and meningitis)
- Enterovirus (aseptic meningtis)
* Echovirus (aseptic meningitis)
* Poliovirus - HHV7
- LCV (arenavirus)
Fungal:
- Cryptococcous neoformans (meningitis)
- Coccoides immitis (meningitis in disseminated form)
- Histoplasma capsulatum
- Blastomyces dermatitis
Zoonotic infections and their prevention
Zoonotic pathogen: • pasteurella (cat-bite) • salmonella enteriditis (salmonellosis) • Brucella • Bacillus anthracis • Yersinia • Franciella tularensis • Pasteurella • Campylobacter jejuni • Coxellia burnetti • Bartonella • Burkholdeira mallei • Borrelia burgdorferi • Leptospira genus • Chlamydophilia psittaci • Erysipelothrix rhusiopathiae • Clostridium perferingens
Fungal and parasitic lung infections
Fungal:
- Coccoides immitis
- Paracoccoides braziliensis
- Blastyomyces dermatitis
- Histoplasma capsulatum
- Cryptococcus neoformans
- P. jiroveci
- Aspergillus
Protozoa:
- Entamoeba histologyica (lung abscess)
Helminths:
- Paragonius westermanii
Air-borne viral infections
Rhinovirus Paramyxovirus Orthomyxovirus VZV (Pox-virus?) both air-borne and contact Parvovirus Togavirus: rubella
Toxin-mediated
Toxin-mediated infections: • Toxic-shock syndrome ◦ S.aureus • Toxin-shock like infection ◦ S.pyogenes • Dystentery: ◦ Shigella • Gastroenteritis: ◦ S. Aureus ◦ B. Cereus ◦ Shigella ◦ Yersinia ◦ V. Parahemolyticus ◦ Pleisomonas shigellosides ◦ Campylobacter jejuni (most common cause) ◦ Salmonella enteridtis ◦ Listeria • HUS ◦ Shigella ◦ E.coli • Enteral fever ◦ Salmonella typhi • Necrotizing fasciitis ◦ s.pyogenes • Rheumatic fever ◦ S.pyogenes • Rheumatoid artheritis ◦ S.pyogenes • Glomerulonephritis ◦ S.pyogenes
Food-poisoning
- s.aureus
- b.cereus
- c. perferings
- salmonella enterititis
- Listeria
- yersinia enterocolitica
- vibrio parahemolyticus
Impetigo
s. aureus
s. pyogenes
follliculitis
s. aureus
pseudomonas aerginosa
furuncle, carbuncle
s. auerus
cellulitis
s. aureus
s. pyogenes
clostridium perferingens?
fasciitis necrotisans
s. pyogenes
c. perfringens
burn wound
coagulative negative staphylococci
pseudomonas
acinetobacter baumanii
bites
pasteurella multicida s. aureus s. pyogenes streptococcus viridans c. tetani
surgical site infections (SSI)
s. aureus coaguase negative staphylococci e.coli MDR pseudomonas and acinetobacter c. perfringens
chronic wounds, granulomas
mycobacterium leprae
mycobacterium ulcersans
mycobacterium marinum
actinomyces spp
zoonotic wound infections
erysipelptrix rhusiopathie
franciella tularenis
bartonella henselae
bartonella quintana
Intraabdominal infections
Peritonitis and abdominal abcess:
After perforation: e.g. appendicitis, ulcer, diverticulutis, trauma, surgery, colon cancer, PID
Cholecystitis, pancreatitis:
- retrograde bacterial infection from bowel
- Pancreatitis: CMV, Coxsackie B, mumps
Bacterial eye infection:
Viral eye infection:
Bacterial:
- s.aureus (stye)
- s.pyogenes
- pseudomonas aerginosa (contact lens associated)
- chlamydia trachomatis A, B, C
- Neisseria gonorrhea (opthalmoblenorrhea neotatrum)
- Treponema pallidum (interstitial keratitis)
D: Based on the clinical examination: sample collection with swab if necessary
Viral:
- Adenovirus (pink eye) - keratoconjunctivitis
- Herpes, 1 (herpic keratitis)
- Coxsackievirus A: hemorrhagic conjunctivitis
- CMV: chorioretinitis
- Zika: congenital glaucoma
Bacterial upper respiratory tract infections
Tonsillitis:
- S. pyogenes
- S. aureus (but not that frequent)
Sinusitis, otitits media:
- S. pneumoniae (MOPS)
- H. influenza
- Moraxella catarrhalis
- S. aureus
- S. pyogenes
Laryngeal infection:
- C.diphteria
- H. influenza B
- Viruses
D:
- usually based on their clinical symtoms
- if necessary: take sample with cottom swab
- microscopy, cultivation
Childhood infections: xanthemas (rashes)
- Chickenpox (VZV)
- Herpes zoster: shingles (ZVZ)
- Morbili (measles)
- Rubella
- Erythema infectiosum
- Erythema subitum (roseola)
- HSV
- HPV
- Hand, foot- and mouth disease (coxsackie A, enterovirus)
- Molluscum contagiosum
- smallpox - variola
Enterally acquired parasitic infections and their diagnosis
Enteric infections: Protozoa: - Entamoeba histolytica - Giardia lamblia - Cryptosporidium parvum - Balantidum coli
Diagnosis:
- Microscopic examination of stool, ID based on morphology of cysts
Therapy: metronizaole
Helminths:
- Enterobius vermicularis
- trichuris trichuria
- ascaris lumbricoides
- diphyllobotrium lata
- taenia saginata
- taenia solium
Diagnosis:
- Microscopic examination of stool, ID based on morphology of cysts
Therapy: albendazole, mebendazole
Enteric spread, but not enteric symtoms:
Protozoa: toxoplasma gondii
Helminths:
- trichinella spiralis
- taenia solium
- toxocara canis
- fasciola hepatica
- paragonimus westermani
- echinococcus spp
Fungi:
- Aspergillus
Protozoa and helminths causing opthalmic eye infections and their diagnosis
Protozoa:
- Acanthamoeca sp - keratitis
- Toxoplasma gondii - chorioretinitis
Helminths:
- loa loa - chorioretinitis
- Onchocerca volvolus - chorioretinitis
- Toxocara sp - ocular larva migrans
Enteric infections (viral)
Enteric infections:
- Rotavirus
- Calcivirus: norovirus, sapovirus
- Astrovirus
- Coronavirus
- Adenovirus
Enteric spread but not enteric symtoms:
- Hepatitis A, E
- Enterovirus (polio for instance)
* Poliomyelitis virus
* Coxsackie virus
* Echovirus
Anthopode borne infections - viral
Mosquito: Flaviviridae
- yellow fever
- Dengue fever
- West Nile fever
- Zika virus
- Japanese encephalitis virus
- St. Louis encephalitis virus
- Tick borne encephalitis virus
Mosquito: Hantaviridae
- California encephalitis virus
- Toscana virus
- Rift valley virus
- Crimean-Congo haemorrhagic fever (TICK)
Mosquito: togaviridae
- Chikungunya virus
- Eastern-, Western-, Venezuelan- equine encephalitis
Anthopode borne infections - parasites
Protozoa:
- Plasmodium sp: Anopheles mosquito: malaria
- Trypanosoma brucei: tsetse fly: sleeping sickness
- Trypanasoma cruzi: assasin bug: Chagas disease
- Leishmania sp: sandfly: Leishmaniosis
- Bebesia: tick: babesiosis
Helminths:
- Loaloa: deer-fly: loa-loasis
- Onchocerca volvolus: blackfly: oncocerciasis
Anthopode borne infections - bacteria
Rat flea: Yersinia pestis
Flea: Rickettsia typhi
Tick: Rickettsia Rickettsii Borrelia burgdorferi Borrelia garinii Borrelia afzeli Franciella tularensis Coxiella burnetti (spreading amongst other animals)
Body louse:
- Rickettsia prowaczeki
- Borrelia recurrentis
Mite:
- Orentia tsutsugamusi
Enteral spreading bacteria and their diagnosis
Enteric infections:
- Salmonella enteritiits, typhimurium (salmonellosis)
- Helicobacter pylori
- Campylobacter sp
- Shigella sp
- ETEC, EHEC, EAEC, EIEC, EPEC
- Yersinia enterocolitica
- V. cholera
- b.anthrasis
- c. difficile
Enteric spread but not enteric symtoms:
- Salmonella typhi, parayphi
- Listeria monocytogenes
- c.botulinum
- brucella spp
bloody diarrhea
Bloody diarrhea: e.coli: EHEC and EIEC shigella sonnei yersinia enterocolitica campylobacter jejuni aeromonas hydrophila (?) b.anthracis Virus: yellow fever Protozoa: - Entamoeba histolytica - Balantidium coli
Diagnosis:
Stool is tested: culturing and other specific tests (see topics)
When food poisening: usually based on the symtoms and food is tested for pathogen.
c.botulinum: inoculation of mice with patients serum.
most common nosocomial infections
CR-BSI VAP SSI/wound infections CAUTI C.difficule infection (CDI)
Pathogens causing pre-and perinatal infections
Bacterial:
- s.agalactiae: neonatal sepsis, meningitis, pneumonia
- treponema pallidum: congenital sylphilis
- listeria: neonatal sepsis, meningitis
- e.coli K1: neonatal meningitis
- neisseria gonorrhea: opthalmoblenorrhea neonatorum
- chlamydia trachomatis: neonatal eye infections
Viral:
- CMV
- VZV
- parvovirus b19
- zika
- hbv
- hiv
- hsv2
- rubeola
- west nile virus
- HEV
Protozoon:
- toxoplasma gondii
- plasmodium sp
- trypanasoma sp
pathogens of hepatitis
Causative agents of hepatitis
‘Cheetahs Handcuffed Enthusiastic Chihuahuas Ethically Yet Raptors Left Pickled Eggs Fashionably’
- CMV
- HHV-6A, HHV-6B
- EBV
- Coxsackie virus B
- Echovirus 11
- Yellow fever virus
- Rubella virus
- Leptospira sp.
- Plasmodium sp.
- Echinococcus sp.
- Fasciola hepatica
HIV opportunitstic pathogens, and diagnosis
‘Jiroveci har tannlegetime (på) ccc am’
- P.jiroveci
- herpes simplex
- toxoplasma gondii
- CMV
- Cryptococcus
- CMV
- atypical mycobacterium
Diagnosis:
- ELISA (screening test)
- Western blot (confirmation test)
- PCR (when diagnosed): to measure viral load
Diagnosis of sepsis, endocarditis
Lab:
- high or low WBC
- eosinopenia
- thrombocytopenia
- CRP, procalcitonin
- decreased Fe
- hypoalbuminiemia
- blood culture: take before AB are given (if possible) and when the fever is rising
- take from venipuncture, not IV catheters
- 20-30ml from adults, less from kids
- use anaerobic and aerobic bottles: 3 pairs in 24t, at least 20min difference (6 bottles/patient) (directly into the bottle) (enrichment media in bottle)
- put into thermostate or send to lab as fast as possible (no fridge!)
- incubate for at least 7 days
- based on the colour change of the bottom of bottle, ID process starts
For endocarditis:
- blood cultures (3 pairs, so 6 at least) - and imaging
Use of laboratory animals
- Cultivation/maintanance of pathogens (rabbit testis in treponema etc)
- Production of heterologous immunoglobulins (e.g. antitoxins in toxin-mediated diseases)
- Detection of toxins, measurement of toxicity in vivo (eg. measuing toxin in botulism)
- Testing medications (e.g. LAL)
- Testing drugs (before pre-clinical trials)
Rules and reg. of collection, storage and transport
Goal: collect properly, store properly, transport properly.
- Collect: obtain sample before administering AB treatment
- Should be collected in a way that minimizes the contamination by resident flora.
- Should be collected in clean, sterile containers
* cotton swab, dacron swab, syringe or catheter aspiration
* sufficient material for both culture and gram staining
* transport medium (stuart medium)
* transport culture medium (uricult plus) - Transport:
* rapid transport
* all specimens should be labelled
* clinicians should provide the laboratory with diagnostic questions
No refrigeration:
- CSF (in bacterial sampe, viral can be)
- blood culture
- N. gonorrhea
Role of host organism in the pathogenesis
Determinants:
- Age (neonate, children, adult, elderly - get different diseases)
- Immune status (immmunocompetent, immunocompromised)
- Other diseases (diabetes etc - can get candida)
- Medications
- Geographical areas (malaria etc)
- Diet (eating raw fish)
- Malnutrition or obeisity
- Pregnancy
- What is pathogenicity?
2. Determination of virulence?
- the ability of an organism to cause disease.
Depends on:
* species
* the strain of the microbe (e.g. E.coli strains)
* virulence factors
* dose of the microbe needed for infection - Determination of virulence?
Inoculation of the microbe into susceptible host (e.g. guniea pig)
* ID50: Infectious dose at 50: dose of pathogen causing illness in 50% of infected hosts
* LD50: Lethal dose 50: dose of pathogen or toxin killing 50% of inoculated host
Higher dose needed: less virulent is the microbe
What is an:
1. Obligate pathogen?
- Facultative pathogen?
- Opportunistic pathogen?
- Obligate: can cause disease in a host regardless of the host’s resitent microbiota or immune system
(s. aureus, n.meninigititis, s.pyogenes) - Facultative: Normal to have in one site of the body, but if gets elsewhere is causing infection there
- Opportunistic pathogen: can only cause disease in situations that compromise the host’s defenses: e.g. in immunocompromised.
What are Koch’s postulates?
- the microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms
- the microorganisms must be isolated from the diseased organism and grown in pure culture
- the cultures microorganism should cause disease when introduced into a healthy organism
- the microorganism must be reisolated form the inoculated, diseased experimental host and identified as being identical tot he original specific causative agent.
Bacterial typing
- Serotyping
- Phage-typing
- Serotyping:
- Classification based on the cellular antigens (i.e serotypes: O, K, H).
- usually performed with slide/latex agglutination. - Phagetyping:
Looking for bacteriophages: some of these can only infect a single strain of bacteria, so these phages are used to identity different strains of bacteria within a single species.
- a culture of the strain is grown in the agar and dried.
- a grid is drawn on the base of the petri dish to mark out different regions
- Inoculatation of each square of the grid is done by a different phage
- susceptible phase regions will show a circuar clearing where the bacteria has been lysed
Principles of the evaluation of serological tests.
- pair of sera-test
- meaning of titre
Serological tests:
- Demonstration of antibodies in serum:
* ELISA
* Western blot
* Tube agglutination
* Complement fixation - Direct detection of antigen (pathogen)
* real-time PCR
* nucleic acid hybridisation
* immunofluorescent assays
* ELISA
* latex agglutination
Pair of sera-test: two serum samples taken of a patient, usually 2 weeks apart:
the fist is during the acute phase, and the second is in the conalescence.
If there is a 4-fold titer increase: confirms the acute infection!
Molecular examination methods used in microbiology
- pulse-field gel electrophoresis (PFGE)
- multi-locus sequence typing (MLST)
- whole-genome sequencing
- MALDI-TOF
- PCR
What are the persistent virus infections?
- chronic infection (hepatitis, HIV)
- slow infection: prolonged incubation period, followed by progressive disease (acute phase may be lacking)
* Conventional: caused by viruses: HIV –> AIDS dementia, JC –> PML, Measlse –> SSPE
* Nonconventional: prions - latent infections (HSV1,2, VZV)
Obligatory vaccines in hungary
Polio - 2,3,4 and 18 mo MMR - 15 mo, 11 yr Varicella - 18 mo BCG - birth DTaP - 2,3,4 and 18 mo Hep B - birth, 12 yr HPV, 12 yr HiB - 2,3,4 and 18 mo Prevenar-13, 2,3,4 and 18 mo
Non-obligatory vaccines in hungary
Killed vaccine: 'CHIT' Influenza Hep A Cholera Tick-borne encephalitis virus
Live, attentuated: 'RITY' (+MMR, Varicella, BCG) Rotavirus Influenza Typhoid Yellow fever
Subunit:
HPV
Conjugate:
Meningococcal A, C, W, Y
Pneumovax-23
Advantage and disadvantage of killed and attentuated vaccines
Killed:
Advantage: ?
Disadvantage: mostly humoral immunuty, so need boosters
Attentuated:
Advantage: immune response almost identical to natural infection
Disadvantage: not safe for immunocompromised
Pro and con of passive immunisation
Pro:
- rapid protection
- can be used for immunocompromised
- antitoxin for toxin-mediated diseases (tetanus, botulism)
Con:
- temporary effect
- no memory cells
- side effects (if from animals): hypersensitivity
