Micro 2 Flashcards
Campylobacter
Reservoir Poultry & Cattle
Transmission Contaminated food
o NOTE: washing chicken breast sprays the Campylobacter around the area
Clinical Presentation: Diarrhoea, bloating and cramps
Ix: Stool Culture
Mx: Supportive
Salmonella
Gram-ve facultative rod-shaped bacterium
Reservoir: Poultry & Reptiles/amphibians
NB: there are 200 strains of salmonella and only 2 are human pathogens, the rest are zoonoses
Transmission: Contaminated food & Poor hygiene
Clinical Presentation: D&V, fever
Ix: stool culture
Management: SUPPORTIVE
Ciprofloxacin & Azithromycin
Bartonella henselae
Reservoir: Kittens > Cats
Transmission: Scratch, bites, licks of open wounds, fleas
Causes 2 disease:
1. Cat Scratch Disease
PC: Macule at site of inoculation -> Becomes pustular + LNs enlarge. If left untreated you get FLAWS.
Ix: Serology (cheap and easy)
Mx: Erythromycin & Doxycycline
this disease can present fairly similarly to other classical clinical presentations such as TB and lymphoma. So Always consider Bartonella in a young person with fever, weight loss and night sweats who has been in recent contact with a cat.
- Bacilliary Angiomatosis (immunocompromised esp HIV - think freddie mercury)
Angio - blood vessels get eroded and burst
PC: Skin papules, Disseminated multi-organ and vasculature involvement (e.g. hepatitis, in head)
Leads to bursting of blood vessels in various organs and tissues. Can be FATAL
Ix: Histopathology & Serology
Management: Erythromycin, Doxy plus Rifampicin
Toxoplasmosis
Reservoir o Cats o Sheep Transmission o Infected meat o Faecal contamination Presentation o Fever o Adenopathy o Still-birth o Infants with progressive visual, hearing, motor and cognitive issues o Seizures o Neuropathy (immunocompromised, presents as ring enhancements on CT )
Investigations
o Serology
Management o Spiramycin o Pyrimethamine + sulfadiazine [Cause risk taking behaviour in mice, high prevalence in schizophrenics] (DO NOT GET A KITTEN WHEN PREGNANT)
Brucellosis
Reservoir: Cattle & Goats
Transmission
Unpasteurised milk / Undercooked meat
For areas where humans still milk the cows: Mucosal splash into their eyes/mouth/nose and Aerosolisation /inhalation
Presentation
Fever – Classically undulant fever (peaks in eve. normal by morn), malaise, rigors, sweating, myalgia/arthralgia, tiredness (incubation 3-4/52)
Orchitis & Focal abscesses (Psoas, liver)
NB looks a bit like TB
Ix: Blood/pus culture, Serology
IMPORTANT: the lab should be warned that the sample being sent may be brucellosis
Management: Doxycycline AND gentamicin OR rifampicin
Coxiella burnettie
Q fever
Think of the netherlands story
Routes: Goat Sheep and Cattle
Aerolisation /inhalation of goat poop, milk of infected animals, unpasteruised milk
Presentation: Pretty much same as the others, Fever, Flu-like illness, Pneumonia, Hepatitis, Endocarditis Focal abscess (para-vertebral, discitis)
Investigations Serology Management Doxycycline (hydroxychloroquine)
Lyssa Virus
Rabies Lyssa Virus • Reservoir Dogs Cats Bats • Transmission o Bites o Scratches o Contact with infected fluid
Presentation
Seizures, Confusion, ?Rabid dog, Agitation,and Aggression Temperature, Confusion, Headaches, Excess Salivation (SCRATCHES)
Paralysis, Delirum and Death
NOTE: once symptoms start, there is a near 100% mortality. BUT there is a 1-3 month incubation period
• Investigations o Serology o Brain biopsy Management (before sx start) - Immunoglobulin - Vaccine If not vaccinated, 3 doses of vaccination and immunoglobulin within 14 days. If vaccinated, only needs post exposure prophylaxis
Rat related zoonoses.
Reservoir: Rats T: Bites, Contact with infected urine or droppings 1. Rat Bite Fever Presentation o Fevers o Polyarthralgia o Maculopapular progressing to purpuric rash o Can progress to endocarditis • Investigations o Joint fluid microscopy and culture o Blood culture • Management o Penicillins
2. Hentavirus Pulmonary Syndrome Reservoir o Deer mouse - Sin Nombre virus o White footed mouse - Sin Nombre virus o Cotton rat - Black canal virus o Rice rat - Bayou virus Presentation o Fever o Myalgia o Flu-like illness o Respiratory failure (in USA) o Bleeding and renal failure (in SE Asia) • Investigations o Serology o PCR • Management o Supportive
Viral Haemorrhagic Fever
4 different types: (resevoir not confirmed)
o Ebola - Bats?
o Marburg - Bats?
o Lass - Rats
o Crimean-Congo Haemorrhagic Fever - Ticks
Transmission
o Contact with fluids of infected
Presentation o Fever o Myalgia o Flu-like illness o Bleeding
Investigations
o Serology
o PCR
Management
o Supportive
Streptococcus pneumoniae
o Gram-positive diplococci, alpha haemolytic
o 30-50% of CAP
o Acute onset ('rusty coloured sputum')
• Severe pneumonia
• Fever and rigors
• Lobar consolidation
o Almost always penicillin-sensitive
o Penicillin-resistance strains may be imported from Southern EuropeCAP bacterium
Typical:
Strep pneumoniae
Hib (URTI)
Moraxella Catarrhalis (URTI)
Staph - w/ recent viral infection (EMQs: post-INFLUENZA infection) ± cavitation on CXR
Klebsiella Pneumoniae - Alcoholism, elderley. Haemoptysis
Atypical (organisms without a cell wall) Legionella Mycoplasma Coxiella Burnetti Chlamydia Psittaci
CAP organisms by age
0-1 months • Escherichia coli • Group B Streptococcus • Listeria monocytogenes 1-6 months • Chlamydia trachomatis • Staphylococcus aureus • RSV 6 months - 5 years • Mycoplasma pneumoniae • Influenza • Chlamydia pneumoniae
16-30 years
• Mycoplasma pneumoniae
• Streptococcus pneumoniae
How do we know if a pt’s pneumonia is severe
o Confusion o Urea > 7 mmol/L o RR > 30 o BP < 90 systolic, < 60 diastolic o 65+ years Interpretation 2 = consider admitting 2-5 = manage as SEVERE pneumonia, consider ITU
Bronchitis
DEFINITION: inflammation of medium-sized airways Mainly occurs in smokers Presentation o Cough o Fever o Increased sputum production o Increased shortness of breath • CXR is usually NORMAL • Organisms o Viruses o Streptococcus pneumoniae o Haemophilus influenzae o Moraxella catarrhalis • Treatment o Bronchodilation o Physiotherapy o Antibiotics
Causes of cavitation on CXR
o Staphylococcus aureus
o Klebsiella pneumoniae
o TB
Haemophilus Influenzae
- Gram-negative cocco-bacilli “looks like snot on a piece of paper”
- 15-35% of CAP
- More common with pre-existing lung disease
- May produce beta-lactamase
Legionella
T: Aerosol spread & Environmental outbreaks
PC:
• Confusion
• Abdominal pain
• Diarrhoea
o Lymphopaenia
o Hyponatraemia
Can cause multi-organ failure
Ix: urinary antigens, It is grown on a buffered charcoal yeast extract
Mx: Atypical so needs a protein synthesis inhibitor, Sensitive to macrolides and tetracyclines
Atypical pnuemoniae features
- Flu-like Prodrome before fever and pneumonia
- Extra-pulmonary charactersitics hepatitis, hyponatraemia
What should you consider when pts are failing to respond to pneumoniae tx?
• Empyema/abscess (abscesses are walled off and even if the abx can penetrate they are very acidotic and abx will be in@) • Proximal obstruction (tumour) • Resistant organisms (travel is important) • Not receiving/absorbing antibiotics • Immunosuppression • Other diagnosis o Lung cancer o Cryptogenic organising pneumonia
TB
• Must always be considered as a differential
• Clues
o Ethnicity
o Prolonged prodrome
o Fevers
o Weight loss
o Haemoptysis
Ix:
CXR- Classically upper lobe cavitation (but can vary)
Staining- An auramine stain and a Ziehl-Neelsen stain will be done. Red rods are the acid-fast bacilli
HAP
• A pneumonia onset > 48 hours in hospital
• Patients have often had previous antibiotics and maybe even ventilation
• Bronchial lavage is desirable to differentiate upper respiratory from lower respiratory flora
• Aetiology of HAP
o Enterobacteriaciae (e.g. E. coli, K. pneumoniae)
o Staphylococcus aureus
o Pseudomonas spp
o Haemophilus influenzae
o Acinetobacter baumanii
o Fungi (Candida spp)
PCP
Pneumocystic jirovecii pneumonia • Protozoan • Ubiquitous in the environment • Insidious onset Presentation o Dry cough o Weight loss o SOB o Malaise NOTE: the walk test (attaching an oxygen saturation probe and asking the patient to walk) will show desaturation on exertion • CXR - bat wing shadowing • Investigations: bronchoalveolar lavage • Treatment: co-trimoxazole (septrin) • Prophylaxis: co-trimoxazole
Aspergillosis
1. Allergic bronchopulmonary aspergillosis o Chronic wheeze o Eosinophilia o Bronchiectasis 2. Aspergilloma o Fungal ball, often in pre-existing cavity o May cause haemoptysis 3. Invasive aspergillosis o Immunocompromised o Treatment: amphotericin B
Signs: non-specific (interstitial) changes on the CT scan, neutropenia
What organisms can immunosupppressed pts get in lower RTI?
- HIV: PCP, TB , Atypical mycobacteria
- Neutropenic pts: Fungi e.g. Aspergillus spp.
- Bone Marrow Transplant: CMV
- Splenectomy: Encapsulated organisms (S. pneumoniae, H. influenzae, malaria)
Anything can do anything
What test can we get from urine?
o Limited urine antigen tests available for:
• Legionella pneumophila
• Streptococcus pneumoniae
o Send in severe CAP
Other Pneumonia tests
• Antibody Tests
o Only useful on paired serum samples (one when they are acutely unwell and another when they are getting better)
o Usually collected on presentation and 10-14 days later
o Looks for a rise in antibody level over time
o Most useful organisms to send antibody tests for because they are difficult to culture:
• Chlamydia
• Legionella
Immunofluorescence
o Antibody is labelled with fluorescent dye
o Often used in virology
o PCP immunofluorescence is the most commonly used one in microbiology labs
o PCP may also be detected by Silver stain in cytology labs
Abx Guidance for CAP
Mild - Amoxicillin 1st line (macrolide if pen allergic)
Mod/Severe - Amoxicillin + Macrolide (Co-amoxiclav + clari 2-3wks)
S aureus - Fluclox
Legionella - Macrolide + Rifampicin
HAP
1st Line: Ciprofloxacin ± Vancomycin
2nd Line/ pt is from ITU: Piptazobactam + Vancomycin (ITU pts increased risk of resistant bacteria/MRSA)
Pseudomonas - Cipro + Genta or Piptazobactam
MRSA - Vanco
Classification of fungi
Yeats - Candida and Cryptococcus, Histoplasma is diamporphic
Moulds - Aspergillus, Dermatophytes, agents of mucormycosis
Candida
Candida is the most common yeast, it forms individual cells (a bit like bacteria but much bigger), replicate by budding
• It can affect the mouth, perineum, scalp, skin, vagina, nails, lungs and GI tract
• It can become systemic as in septicaemia, endocarditis and meningitis
Candida rf
- Previous abx usage (disrupts flora)
- VLBW infants are more likely to get systemic candida infections (they may require fluconazole and nystatin prophylaxis)
• Immunocompromised patients are also more likely to get invasive candidiasis
• Patients on ITU with lots of lines in (e.g. central lines) are also at risk because Candida is very good at forming biofilms and colonising prosthetic material
Candida species
o Candida albicans (MOST COMMON) o Candida glabrata o Candida krusei o Candida tropicalis o And many others All of them are ubiquitous and occur naturally in humans Candida albicans is sensitive to all the first line antifungals. On the other hand, C. glabrata and C. krusei are resistant to a lot of first-line drugs
Investigation of candidiasis
Candida albicans forms a germ tube whereas the other types will not.
Candida is often outcompeted in cultures because bacteria grow more quickly. This is why an alternative identification system is needed. So, a selective agar plate that is impregnated with antibiotics is usually used (Sabouraud agar). Mannan?
Beta-D Glucan assay (serology) is sometimes used to look for evidence of invasive Candida infection.
Other than cultures, you can test for candida in sites of suspected infection:
Imaging (e.g. for hepatosplenic candidiasis)
Fundoscopy - Candida can affect the eyes causing endophthalmitis
Echo - endocarditis
CT - Upper GI perforation (causes leakage of Candida into the mediastinum which can result in mediastinitis )
Management of candidiasis
2 WEEKS TREATMENT
oEchinicandins are used empirically and for non-albicans Candida infections
oFluconazole is still effective for Candida albicans
oThere are some specific situations in which you need to use a certain type of antifungal because of its pharmacokinetics/pharmacodynamics (e.g. echinicandins don’t penetrate well into the CNS so you have to use Ambisome instead)
amphotericin-B for invasive disease
Cryptococcus
Cryptococcus:
In immunocompromised (particularlyHIV)
▪ Presents as meningitis with insidious onset in HIV, can also cause hydrocephalus (which would invalidate the CSF)
▪ Associated with birds and in particular pigeons!
▪ Dx: Cryptococcal Antigen in serum/CSF (using ELISA)+ india ink staining nolonger used
▪ Rx: 3/52 amphotericin B +/- flucytosine. 2nd line is fluconazoles
(Cryptococcus is resistant to echinicandins)
Has a capsule but the capsule is NOT always present (if the organism is not under any form of stress it will not need the capsule (e.g. in blood cultures))
Aspergillus
A spectrum from intoxication to allergy to invasion
▪ Presents as pneumonia, esp. in immunocompromised. High mortality.
▪ Ix:
1. Serology (look for IgE in allergic aspergillosis,
2. ELISA to detect antigen (galactomannan) use BAL fluid
3. PCR
4. β-Glucan test
5. grows on Czapek dox agar
▪ Mx: voriconazole or amphotericin is the mainstay of treatment (broad-spectrum with good activity against Aspergillus) (At least 6 weeks of therapy)
Dermatophyte Infections
o Ringworm o Tinea o Nail infections Very common (Tricophytonrubrum is a cause in all of the below) Tinea pedis - atheletes foot Tinea cruris - groin area Tinea corporis - on the body Tinea capitis (on the head) Onychomycosis (thickened nails) Pityriasis versicolor (discolourisation of skin) (malassezia furfur)
Mucormycosis
This is a group of moulds that can cause very severe and invasive disease. It affects:
o Immunocompromised patients
o Poorly controlled diabetics
Characterised by cellulitis of the orbit and face which progresses with discharge and black pus from the palate and nose. Black eschars may be seen as the fungus invades and destroys the tissues. Retro-orbital extension produces proptosis, chemosis, ophthalmoplegias and blindness . As the brain is involved, it can cause decreasing levels of consciousness (rhinocerebral mucormycosis)
Mx: SURGICAL EMERGENCY because all the dead and necrotic tissue needs to be debrided
o It requires early referral to ENT
o Antifungal agents may be used: amphotericin (HIGH DOSE), posaconazole
Mucormycosis cellulitis causative agents
o Rhizopum spp.
o Rhizomucor spp.
o Mucor spp.
Antifungals
Cell membrane integrity
Polyene - YEast.
Amphotericin is the main one. It is put into liposomes in a lot of different formulations to try and reduce toxicity and improve penetration. Ambisome has amphotericin within a phospholipid bilayer. It creates transmembrane channels leading to electrolyte leakage. This leads to fungal cell death
Active against most BUT Aspergillus terreus & Scedosporium spp.
S/E: Nephrotoxicity
Cell membrane synthesis
Azole - Yeast e.g. (INTERACT WITH WARFARIN and any other cyp450)
Fluconazole- Candida and Cryptococcus
Itraconazole (useful against dermatophytes)
Posaconazole (has activity against mucor)
Cell membrane
Terbinafine- Mould (vs. dermatophytes)
DNA synthesis
Flucytosine (not really used alone, used in combo with crypto)
Cell wall
Echinocandin e.g. caspofungin, micafungin, anidulafungin- Yeast (less toxic SE and primary therapy for candida) Cyprotcoccus is resistant!!
Candida species (including non-albicans isolates that are resistant to fluconazole) and Aspergillus species only
HAI Epidemiology
Prevalence of HAI in the UK = 8% Most common syndrome of HAI = hospital-acquired PNEUMONIA o 2nd = surgical site infections o 3rd = urinary tract infections o 4th = blood stream infections o 5th = gastrointestinal infections
Hospital Microbiome project
o This tried to figure out where the organisms in the hospital came from
o 1st day (before occupied) - bugs go from the environment onto the patient
o 2+ days - bugs go from the patient outwards
• Surveillance will be useful for reducing infection risk
HAI definition
Onset of infection >48 hours after hospital admission
Common HAI infections
GI: Clostridium difficile diarrhoea.
• Transmission: Spore ingestion.
• Predisposing factor: existing gut flora disturbed by antibiotics, particularly 3Cs:
clindamycin (often used in penicillin allergic patients with cellulitis), cephalosporins,
ciprofloxacin
• Pathology: Toxin. Pseudomembranous colitis.
• Rx: Oral metronidazole.
UTI: E. coli. Resistance: Extended spectrum beta-lactamases
• Risk factor: Catheter
• Other organisms: Klebsiella, Proteus, Pseudomonas
Bacteraemia: Methicillin-resistant Staphylococcus aureus, coag –ve staph, E.Coli, Surgical site infection: MRSA, Coagulase-negative Staphylococcus
Which immune deficiencies make you suspectible to certain viruses?
UNC93B deficiency and TLR3 deficiency -> HSE
HPV/ EVER 1 or EVER2 can predispose to Epidermodysplasia verruciformis
Haemophagocytic lymphohistiocytosis in perforin deficiency, which is associated with incidence of EBV
HHV8 is associated with a STIM1 mutation
How are opportunistic viral infections different?
Occur more frequently in immunocompromised patients (e.g. EBV, CMV)
More severe presentations of normal viral infections (e.g. VZV, measles)
May be an ABSENCE of signs of infection (e.g. afebrile) and a loss of localising signs (e.g. peritonism)
Major Classes of Immunosuppressive Drugs
Glucocorticoid
Calcineurin Inhibitors (Tarcro, Cyclosporine)
Antiproliferative (MMF, Azathioprine, Sirolimus)
Antibody depleting and non-depleting
Co-stimulation blockers
When/how do pts often get viral infections after transplnat?
They do NOT tend to reactive viral infections until over a month after their transplant. Early infections (< 1 month) tend to be those that are transmitted from the donor
Virus can be acquired from graft, rea@from host or novel infection from host.
We can tackle re@ by active monitoring:
looking at the patient’s serostatus, monitoring, prophylaxis and pre-emptive therapy
What viruses do we monitor post transplant?
CMV (most importantly) and EBV
SCT have CMV viral load twie weekly and treat if virus reactivates (pre-emptive therapy)
Organ transplant have valganciclovir (against CMV) prophylaxis for 100d
When is bacteruria significant?
o Asymptomatic bacteriuria is NOT usually relevant
o However, asymptomatic bacteriuria with coliform is significant in PREGNANCY
o It is associated with complications in the pregnancy
o Therefore, it should be treated
What is a complicated UTI?
o Complicated: infection in a urinary tract with functional or structural abnormalities (including indwelling catheters and calculi)
• Groups of patients in which it is regarded a complicated UTI:
• Men
• Pregnant women
• Children
• Patients who are hospitalised or in healthcare-associated settings
UTI (PC, Ix, Mx, Cx, Aet bugs)
Ax: Contamination (eg from rectum). Bacterial adhesion eg:proteus fimbriae;
klebsiella k antigen
Bugs: E. coli, Proteus, Klebsiella, Staphylococcus saprophyticus (frequent causes of Lower UTIs)
Px: Frequency, dysuria, abdo/flank pain (Very young: non-specific; Old: asymptomatic)
Dx: Clinical, Dipstick (nitrite, leucocytes +ve), Bloods - WBCs, Neutrophils, CRP, MSU MC&S (see organism, pyuria)
Rx: Nitrofurantoin is 1st line from NICE or Trimethoprim if low risk of resistance, but check EGFR is >45ml/min if giving Nitrofurantoin”
If pyelonephritis – Broad spec IV Abx eg: Co-amoxiclav ± Gent; Cefuroxime ± Gent.
UTI organisms
1 E coli
2 Proteus mirabilis (g-ve rod)
3 Klebsiella aerogenes (g -ve rod)
4 Enterococcus faecalis (g+ve cocci, strep like)
5 Staphylococcus saprophyticus (G+ve cocci, staph like)
• Coagulase negative
• Associated with infections in young women
• Has virulence factors (P-fimbriae) that allow adherence to the epithelium
6 Staphylococcus epidermidis
• Can cause UTI in the presence of prosthesis (e.g. procedures or long-term indwelling catheter)
What does nitrites on a urine dipstick mean?
Nitrites are very specific because they are produced by coliform bacteria e.g. E. coli or Klebsiella
• So, positive nitrites is suggestive of coliforms being present in the urine
o Nitrite-negative and leucocyte-positive may be a UTI caused by a non-coliform bacterium
UTI Diagnostic criteria
Culture of single organisms > 10^5 colony forming units (CFUs)/mL with urinary symptoms is usually diagnostic of UTI
Lower numbers are used for organisms that are typical of UTI (E. coli and S. saprophyticus)
• The cut-off is > 10^3 CFU/mL
How to interpret urine culture results
> 10^4 represents inflammation
- Pyuria - white cells in urine (often absent in children UTI)
- Squamous epithelail cell in urine - contamination
ie. NOT an MSU, and suggests that the culture has been contaminated by lots of urethral organisms thereby reducing the significant of the culture - Mixed growth reduces the significance of culture (suggests contamination)
- If sterile pyuria (raised WCC but no growth on culture), it might be because abx were given began before the sample but also consider calculi, Chlamydia trachomatis, other vaginal infections and other non-culturable organisms (e.g. TB) or bladder neoplasms
How to treat fungal UTIs?
• Oral fluconazole is NO MORE EFFECTIVE than no therapy
• There is NO BENEFIT in the therapy of asymptomatic infection (so therapy is generally NOT recommended)
• Most Candida UTIs occur in patients with indwelling catheters
• Removal of the catheter may result in cure
Exceptions
o Renal transplant patients
o Patients who are waiting to undergo elective urinary tract surgery
o In these cases, attempts should be made to eliminate or suppress candiduria
Pyelonephritis Mx
• Co-amoxiclav with or without gentamicin
Leptospira
Leptospira interrogens is a gram negative spiral shaped bacterium which causes Leptospirosis. This is charactersied by sudden onset, fever and chills, headache, abdominal pain, pain in lower limb (particularly calf muscle) and pathognomic conjunctival suffusion (conjunctivits without the inflammatory exudate).
BIPHASIC disease - acute/septic phase with flu like symptoms and then immune phase with severe and rare symptoms.
In advanced disease: Jaundice, severe haemopytysis, cardiac arrthymia, acute renal failure and aculopapular rash.
Diagnosed using Faine’s criteria.
Which of the following would not be a contraindication for LP in suspected meningitis :
- loss of sensation along lateral side of the leg
- blurring of optic disc margins seen on fundoscopy
- unkown INR prior to procedure
- Seizures
- Presence of spreading purpuric rash
C
IRIS (immune reconstitution inflammatory syndrome)
A paradoxical clinical worsening of a known condition or the appearance of a new condition after initiating antiretroviral therapy (ART) therapy in HIV-infected patients resulting from restored immunity to specific infectious or non-infectious antigens is defined as immune reconstitution inflammatory syndrome (IRIS).
