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Phase 3 > Week 7 - clinical microbiology > Flashcards

Week 7 - clinical microbiology Flashcards

1
Q

Define viral gastroenteritis.

A

inflammation of the stomach and intestines caused by virus(es).

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2
Q

What groups are at higher risk of viral gastroenteritis?

A

Children under 5.
Old age, especially in nursing homes.
Immunocompromised.

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3
Q

Name 5 important viruses that cause gastroenteritis.

A 
Norovirus
Sapovirus
Rotavirus
Adenovirus 40 and 41
Astrovirus
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4
Q

What groups of people are mainly affected by rotavirus/adenovirus/astrovirus?

A

Mainly children under 2, elderly and immunocompromised.

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5
Q

What groups of people can be affected by norovirus/sapovirus (Calciviridae)?

A

Can affect all ages and healthy individuals but most serious in young and elderly.

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6
Q

What are the structural features of the norovirus?

A

Non-enveloped, single stranded RNA virus.

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7
Q

Norovirus is transmitted through a variety of routes. What are these? What is the infectious dose for norovirus?

A

Person-person (i.e. faeco-oral)
Food borne
Water
Very small infectious dose (10-100 virions).

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8
Q

What are the clinical features of norovirus? What is the incubation period? How long after infection can the virus be shed?

A 
Nausea and vomiting 
Diarrhoea 
Abdominal cramps
24-48 hours 
3 weeks
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9
Q

What is the treatment for norovirus?

A

Oral or IV fluids
Antispasmodics
Analgesics
Antipyretics

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10
Q

Can you develop immunity to norovirus? Is there a vaccine?

A

Antibodies are developed to norovirus but immunity only lasts 6-14 weeks.
No.

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11
Q

What infection control measures should be taken to prevent the spread of norovirus?

A 
Isolation or cohorting.
Exclude symptomatic staff for 48 hours until symptom free.
Do not move patients 
Do not admit new patients.
Thorough cleaning surroundings
Hand hygiene - MUST be soap and water.
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12
Q

What is the structure of the rotavirus?

A

Non enveloped double stranded RNA virus.

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13
Q

How is rotavirus mainly spread?

A

Mianly person-to-person i.e. faeco-oral or fomites

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14
Q

What are the symptoms of rotavirus?

A

Watery diarrhoea
Abdominal pain
Vomiting
Dehydration

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15
Q

What are some of the potential complications of rotavirus?

A
  • severe chronic diarrhoea
  • dehydration leading to electrolyte imbalance
  • metabolic acidosis
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16
Q

Re-infection of rotavirus is common in children under 5, which infection is normally the most severe?

A

the 1 st infection

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17
Q

Is there a rotavirus vaccine?

A

Yes

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18
Q

What is the structure of the adenovirus? Which serotypes cause gastroenteritis? What are the symptoms? Is there a vaccine?

A

Double stranded DNA.
Adenovirus 40 and 41
Fever and watery diarrhoea
No vaccine

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19
Q

What is the structure of astrovirus?

A

Single stranded, non enveloped RNA virus.

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20
Q

How is viral gastroenteritis diagnosed?

A

Viruses detected by PCR which detects DNA or RNA in a vomit or stool sample.

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21
Q

What are the potential complications of septic arthritis?

A

Loss of cartilage - osteoarthritis in later life

Severe sepsis/septic shock

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22
Q

What are the clinical features of septic arthritis?

A 
Fever
Single hot joint
Loss of movement 
Pain 
Sometimes polyarticular involvement
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23
Q

What are the key investigations for a septic joint?

A

Blood cultures
Joint aspirate
Bloods - FBC, CRP
Imaging - x-ray

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24
Q

What are some common pathogens that can cause septic arthritis?

A

MSSA or MRSA

Streptococci (s. pyrogenes, group G strep, pneumococcus)

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25
Q

What is the management for septic arthritis?

A

2-3 weeks IV antibiotics followed by three weeks oral.

Monitor response by CRP and clinical features.

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26
Q

Name 5 risk factors for developing a septic joint?

A 
Rheumatoid arthritis 
Diabetes mellitis
Obesity
Concurrent UTI
Steroids 
Malignancy
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27
Q

What two routes of pathogenic spread can cause prosthetic joint infection (PJI)? Which is more common? Which would normally cause an earlier presentation?

A

Local spread
Haematogenic spread
Local spread - 60-80% of PJI
Local spread

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28
Q

Why do bacteria grow more easily on a prosthetic surface than on soft tissue?

A

Avascular surface protects bacteria from circuling immune defences and most antibiotics. Cement can inhibit phagocytosis and lymphocyte/complement function.

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29
Q

What is the clinical presentation of an infected joint?

A 
Pain
Infusion
Warm joint
Fever and systemic symptoms 
If a prosthetic joint may have:
Loosening on x-ray, mechanical dysfunction, discharging sinus.
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30
Q

What are the potential surgical options for a septic joint?

A
  1. DAIR to leave the infected joint in

2. Removal of the infected joint in a one stage or two stage revision).

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31
Q

What is the problem with performing a revision of a joint arthroplasty?

A

Each time a revision is performed the chances of success and cure of infection reduce dramatically and infection becomes harder to suppress making amputation a possibility.

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32
Q

Antibiotics chosen for a septic joint must be able to penetrate bone. Name 5 that could be used.

A

Ciprofloxacin, rifamficin, tazocin, carbapenems, clindamycin

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33
Q

Define osteomyelitis.

A

Progressive infection of bone characterised by death of bone and the formation of sequestra.

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34
Q

What are the potential routes of spread in osteomyelitis?

A

Haematogenous spread or contiguous spread (i.e. from a cellulitic ulcer or trauma)

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35
Q

What is vertebral discitis? What is an important causitive organism?

A

Infection of a disc space and adjacent vertebral end plates.

Tuberculosis

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36
Q

What are the potential complication of vertebral discitis.

A

Deformity, cord compression, paraplegia and disability.

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37
Q

What is the difference in incubation time between GI infections caused by bacterial infection of gut or ingestion of bacterial toxins?

A

Infection - 8-12 hours incubation time pre symptoms

Toxins - much shorter incubation time.

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38
Q

List some of the barriers to GI infection in the mouth, stomach, small intestine and large intestine.

A

Mouth - lysozyme
Stomach - stomach acid
Small intestine - mucous, bile, secretory IgA, lymphoid tissue, epithelial turnover, normal flora.
Large intestine - epithelial turnover, normal flora.

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39
Q

The lowe GI tract has a very rich microbiome. 99% of the flora is what type of organism?

A

Anaerobes

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40
Q

Give 2 examples of zoonotic GI infections.

A

Salmonella carriage in reptiles.

E. Coli 0157 carriage in cattle.

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41
Q

By what route is GI infection transmitted? What 3 F’s are the means which allow this transmission to occur?

A

Faecal-oral

Food - contamination of food.
Fluids - contamination water of juices.
Fingers - poor hand hygiene after toileting and before food handling or consumption.

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42
Q

What are important things to ask about when taking a history of GI infection?

A

Vomiting, abdominal pain, diarrhoea, constipation, frequency and nature of symptoms, travel history, food history, other infected individuals, speed of onset of illness, blood in stools.

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43
Q

How are GI infections treated?

A

Fluids to maintain hydration.

Antibiotic treatment only for severe/prolonged symptoms.

44
Q

What age groups have the highest rates of community acquired pneumonia?

A

Very young and elderly.

45
Q

What 3 typical organisms cause pneumonia?

A

Streptococcus pneumoniae
Haemophilus influenzae
Moraxella catharralis

46
Q

What 3 atypical organisms cause pneumonia?

A

Mycoplasma pneumoniae
Legionella pneumoniae
chlamydia pneumoniae

47
Q

What risk factors make you more susceptible to pneumococcal pneumonia?

A 
Alcohol
Smoking
Influenza infection
Airway disease
Immunosuppression i.e. HIV
48
Q

What are the clinical features of pneumonia?

A

Cough
High fever
Pleuritic chest pain

49
Q

What will be found on examination of a patient with S. pneumoniae?

A

Dull percussion
Course crepitations
Increased vocal resonance

50
Q

What will be seen on an chest x-ray of patient with typical pneumococcal pneumonia?

A

Consolidation

51
Q

How is pneumococcal pneumonia treated?

A

Amoxicillin
If allergy:
- clarithromycin
- doxycycline

52
Q

Haemophilus influenzae commonly colonises the upper respiratory tract. What other conditions can it cause apart from pneumonia?

A

Otitis media

Sinusitis

Conjunctivitis

Meningitis

53
Q

How is haemophilus influenzae pneumonia treated?

A

Amoxicillin or co-amoxiclav

or clarithromycin or doxycycline

54
Q

What is the presentation of mycoplasma pneumoniae?

A 
Non-specific flu like symptoms:
Headache, 
Tiredness,
Muscle aches,
High temperature, 
Cough
55
Q

What clinical effects can happen with mycoplasma outwith the lungs?

A

Guillian barre
Arthritis
Haemolysis

56
Q

How is mycoplasma pneumonia diagnosed?

A

Using PCR or serology because it is very difficult to culture.

57
Q

What are the clinical features of legionella pneumonia?

A 
Flu like illness
Malaise,
Headache,
Myalgia,
Fever,
Respiratory symptoms
58
Q

How is legionella diagnosed?

A

Look for urinary antigen.

59
Q

How is legionella treated?

A

Amoxicillin or co-amoxiclav

or clarithromycin or doxycycline

60
Q

What are important aspects of the history of patients with suspected pneumonia?

A 
Symptoms - fever, cough/sputum, chest pain, insidious/abrupt onset, non-respiratory symptoms.
PMH - lung disease, immunosuppression.
Travel history
Water exposure
Ill contacts
61
Q

The CURB65 score assesses the severity of pneumonia. What risk factors does it measure? What score indicates severe pneumonia?

A 
Confusion
Urea >7
Respiratory rate ≥ 30
Blood pressure diastolic<60 or systolic <90
>65 years

2 or more points = severe pneumonia

62
Q

What features apart from the CURB65 score indicate severe pneumonia?

A

Multilobar consolidation or hypoxia on room air or evidence of sepsis

63
Q

What investigations would be done on a patient with suspected pneumonia?

A

Bloods - FBC, U&E, ABG/oxygen sats
Microbiology - blood culture, sputum culture, throat swab, urine legionella antigen.
Imaging - CXR, ECG

64
Q

What viruses are the main causes of the common cold?

A

Rhinovirus

Coronovirus

65
Q

What viruses commonly cause pharyngitis?

A

Adenovirus, rhinovirus, influenza, parainfluenza.

66
Q

How can you tell if pharyngitis is viral or bacterial?

A

Both - sore throat, red swollen tonsils and throat redness.
Bacterial - swollen uvula, white spots on tonsils.
Viral - nasal symptoms

67
Q

Pharyngitis occurs not only in respiratory viruses. What other viruses can cause pharyngitis?

A
  • Infectious mononucleosis (EBV)
  • HIV seroconversion
  • Herpes simplex
68
Q

What virus mainly causes croup? What is the treatment?

A

Parainfluenza viruses 1-4.

Supportive.

69
Q

Bronchiolitis is a lower respiratory tract infection of young children. What are the clinical features? What virus is responsible for it?

A

Wheezing, tachycardia, persistent cough up to three weeks.

RSV (respiratory syncytial virus)

70
Q

Development of what chronic respiratory condition is associated with bronchiolitis?

A

Asthma

71
Q

What is the treatment of severe RSV infection? What are potential side effects?

A

Ribivirin.

Anaemia, abdominal pain, depression and suicidal thoughts.

72
Q

What prophylactic treatment can be given to children at high risk of hospitalisation from RSV? Which children would be given this?

A

Palivizumab - monthly IM injection

Pre term children under 6 months on oxygen, children under 2 on oxygen, children with chronic lung diseases.

73
Q

What are the symptoms of influenza?

A

Sore throat, headache, fever, myalgia, arthralgia, cough, runny nose, vomiting.

74
Q

What are the common complications of influenza? What are the uncommon complications?

A 
Common:
Acute OM
Sinusitis 
Pneumonia 
Dehydration (infants) 
Uncommon: 
Encephalopathy 
Reye syndrome (children)
Myositis
Myocarditis
Febrile seizures
75
Q

What risk factors are there for developing complicated influenza?

A

Underlying conditions:

  • neurological
  • hepatic
  • pulmonary
  • chronic cardiac
  • DM
  • severe immunosuppression
  • age >65
  • children <6 months
  • pregnancy including up to two weeks post partum
  • morbid obesity
76
Q

What treatments are available for influenza?

A

M2 inhibitors - amantadine and rimantadine (type A only)

Neuraminidase inhibitors - oseltamivir, zanamivir

77
Q

Which type of influenza is only found in humans? Which type can be found in in humans, swine, birds and other animals?

A

TYPE B - humans only

TYPE A - humans and other animals

78
Q

What is an influenza pandemic?

A

Worldwide epidemic of a newly emerged strain of influenza.

79
Q

Type A influenza is characterised by haemagglutinin type and Neuraminidase type. Which haemagglutinins and neuraminidase types are found in bats and which is birds?

A

Haemagluttinin:
H1-H16 in birds
H17 and H18 in bats

Neuraminidase:
N1-N9 in birds
N10-N11 in bats

80
Q

How are viruses diagnosed in a laboratory? How long does it take for the results?

A

Polymerase chain reaction (PCR).

About 5 hours.

81
Q

What is the benefit of molecular testing?

A
  • Improves diagnosis of new pathogens
  • Rapid
  • Reduces unnecessary antibiotics
82
Q

How is TB diagnosed?

A
  • Chest X-ray
  • sputum staining for acid fast bacilli
  • sputum culture
  • MGIT (faster culture method)
83
Q

What is the name of the bacteria that causes TB?

A

Mycobacteria Tuberculosis

84
Q

Which part of the lung are TB changes most likely to be seen in?

A

Apices

85
Q

What is the histological hallmark of TB? What type of necrosis is seen in TB?

A

Granuloma

Caseous necrosis

86
Q

What other organs are commonly affected by TB?

A

CNS, kidneys.

87
Q

Discuss some of the main principles of STI management?

A 
Diagnosis before treatment 
Screen for accompanying STIs
Simple treatment regimens
Follow up after treatment/TOC
Partner notification 
Non-judgemental attitudes
88
Q

What questions do you need to ask when taking a sexual history?

A 
When did you last have sex? (any kind)
Gender of partner?
City or country they had sex in?
What type of sex? (i.e. vaginal, oral, anal)
Was a condom used?
89
Q

How do you get a presumptive and clinical diagnosis of gonorrhoea? What is the gold standard for diagnosis of gonorrhoea?

A

Discharge looked at under microscope - gram negative intracellular diplococci seen.
NAAT test confirmed with a culture.

90
Q

What are the complications of gonorrhoea?

A

PID, cervicitis in women

Disseminated gonorrhoea - skin problems, reactive arthritis, arthalgias.

91
Q

How is a diagnosis of gonorrhoea managed?

A

Single dose of ceftriaxone 500mg IM and
Azithromycin 1g stat
Partner notification

92
Q

What are the complications of untreated chlamydia in women?

A

PID, tubal damage/infertility

93
Q

A NAAT test detects what two conditions?

A

Gonorrhoea and chlamydia

94
Q

What is the treatment for chlamydia? What about for lymphogranuloma verenum (LGV)?

A

Doxycycline 100mg BD for 1 week
LGV - 3 weeks
or
Azithromycin 1g stat and 500mg od 2 days if contraindicated.

95
Q

How does primary, secondary and tertiary syphilis present? How many weeks after exposure would primary and secondary and tertiary syphilis present?

A

Primary - chancre (painless ulcer, could be on lip, anus, genitals) - 3 weeks
Secondary - maculopapular rash - 8-16 weeks
Tertiary - granulomatous lesions in bones and skin and cardiological and neurological manifestations - 10-40 years

96
Q

What is the treatment for syphilis?

A

2 penicillin injections in the buttocks.

97
Q

What is the virus that causes genital warts?

A

Human papilloma virus

98
Q

Molluscum contagiosum present as pearly pink nodules on the groin or anus. What virus is this caused by? How is it treated? If the nodules are extensive or on the face what condition should you test for?

A

Pox virus
Self limiting
HIV

99
Q

What is the treatment for herpes simplex virus?

A

Aciclovir

100
Q

How does HIV cause depletion of CD4 T helper cells? What level of CD4 cells puts a person at risk of opportunistic infections and cancers? Which receptor allows entry of HIV into immune cells?

A 
Direct viral killing of cells
Apoptosis of uninfected 'bystander cells'
CD8 cell killing of infected CD4 cells. 
≤ 200
CD4 receptor
101
Q

What are the 4 different drug types used to treat HIV based on their drug target?

A

Integrase inhibitors
Protease inhibitors
Fusion/R5 inhibitors
NRTI/NNRTI

102
Q

What HIV clinical markers do you test for in people with HIV?

A

CD4 cell count

HIV-1 plasma RNA (viral load test) PCR

103
Q

What number of copies of HIV would be considered low, high and undetectable viral load?

A

Low<10,000
High>100,000
Undetectable<40

104
Q

How do you reduce the risk of drug resistance to HIV?

A

Adherence to HIV medication

105
Q

What is HIV latency?

A

State of reversibly non-productive infection of individual cells.

106
Q

What are the symptoms of an acute HIV infection?

A

Thrush/sores in the mouth, myalgia, liver and spleen enlargement, nausea/vomiting, maculopapular rash, lymphadenopathy, malaise, headache, fever, weight loss.

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