Theme 1- core microbiology Flashcards
What are types of gram posive cocci?
Staphylococcus aureus
Streptococcus pyogenes
Streptococcus agalactie
What are types of gram negative cocci?
- Neisseria meningitidis
- Neisseria gonorrhoeae
What are types of gram positive bacilli (aerobes and anaerobes)?
- Bacillus anthracis
- Clostridium difficile
- Listeria monocytogenes
- Corynebacterium diptheriae
What are types of gram negative bacilli?
- Salmonella typhi
- Shigella spp
- Escherichia coli
- Proteus spp
- Yersinia pestis
What are types of gram negative coccobacilli?
- Haemophilus
- Bordetella
- Brucella
- Pasteurella
What are types of spiral bacteria?
Helicobacter
Campylobacter
Borrielia
Leptospira
Treponema pallidum
Do gram positive or negative cells have thick walls? What colour does each stain with?
Gram positive has a thicker cell wall than negative. Gram positive stain stains organism blue/ black is retained. Gram negative- fatty outer cell membrane which doesn’t retain the blue/black, then stained with counter stain that appears red.

Why do certain bacteria cause paticular infections?
- Host factors- Immune system and devices can cause colonisation
- Opportunity- exposure and normal flora
- Bacterial infections- environmental factors, virulence, resistance
Exposure to environmental or animal based pathogens.
Source of the infection is on you and what your normal flora is. Skin surrounding anus is colonisation of E. coli which is close urinary tract which can cause infection.
Where is E. coli found? Where is it able to adhere to?
- Part of normal bowel flora in most humans
- Colonisation of urethral meatus and surrounding area
- Short urethra in females
- Able to adhere to uroepithelial cells/urinary catheter materials
What does E. coli do?
- Triggers host inflammatory response
- Able to develop resistance to antibiotics
- Most common cause of UTIs
Where is S. aureus found?
Nasal carriage in up to 50% of people
Able to adhere to damaged skin
What does S. aureus do?
Produces exoenzymes and toxins that can damage tissues and provoke host response (e.g. pus formation)
What does Staphylococcus aureus cause?
- Causes skin/soft tissue infections – commonest cause, including of surgical site infections
- Bacteraemia/septicaemia
- Osteomyelitis/septic arthritis
- Endocarditis
- Pneumonia
- UTI
- Meningitis

Where is staphylococcus epidermis found?
- Opportunistic pathogen
- Skin commensal
- Most people will carry it on their skin
- One of 20+ species of ‘coagulase negative staphylococci’
What does staphylococcus epidermis adhere to?
Adheres to plastics/metals using glycocalyx (‘slime’), forming biofilms
What does staphylococcus epidermis cause?
Causes infection in association with ‘foreign bodies’ e.g. intravascular catheters, prosthetic joints, prosthetic cardiac valves, etc
What is the commonest cause of a sore throat?
Streptococcus pyogenes- Can also be referred to as ‘Group A Strep’
What does streptococcus pyogenes cause?
- Scarlet Fever
- Necrotising fasciitis (‘flesh eating bug’)
- Other SSTIs
- Invasive infections, such as pneumonia
- Puerperal sepsis- infection of genital tract in mothers that have given birth
- Also associated with secondary immunological presentations, such as glomerulonephritis

What is the commonest cause of bacterial pneumonia and menigitis (except in neonates)?
Streptococcus pnuemoniae
Can also cause other common childhood infections, such as otitis media

What is pneumonia?
Pneumonia is an infection that inflames the air sacs in one or both lungs. The air sacs may fill with fluid or pus (purulent material), causing cough with phlegm or pus, fever, chills, and difficulty breathing. A variety of organisms, including bacteria, viruses and fungi, can cause pneumonia.1
What does streptococcus agalactiae cause?
- Can also be referred to as ‘Group B strep’
- Commonest cause of bacterial meningitis and sepsis in neonates (babies aged under three months)
What is streptococcus milleri complex?
- Three closely related species of pus-forming streptococci
- Associated with abscesses: dental, lung, liver, brain and others

What is Viridans streptococci? Where are they found?
- Collective name for a number of species of α-haemolytic streptococci that inhabit the upper respiratory tract e.g. S. oralis, S. mitis
- Classic cause of sub-acute bacterial endocarditis
If you have heart valve from disease like aortic stenosis/ mitral regurgitation can lead to stasis of blood flow around valves allowing organisms to survive and adhere to the tissues leading to bacterial vegetation leading to bacterial endocarditis.
What is streptococcus gallolyticus? Where is it found?
- Formerly known as Streptococcus bovis
- A type of α- haemolytic streptococcus that forms part of bowel flora
- Bacteraemia with this organism can be associated with colonic malignancies

What is listeria monocytogenes?
Gram positive bacillus
What is listeria monocytogenes from?
- Zoonosis (infectious disease in animals), able to grow at low temperatures
- Associated with consuming cheese made from unpasteurised milk and other foodstuffs
What does listeria monocytogenes cause?
Rare but significant cause of sepsis and meningitis in pregnancy, neonates and immunosuppressed patients
What are corynebacterium species?
Gram positive bacilli
Where are corynebacterium species found?
A number of species are commensals of skin and the upper respiratory tract
Occasional opportunistic infections associated with devices and trauma
What is an exmaple of corynebacterium species?
Corynebacterium diphtheriae

What are the classic symptoms of diptheria?
Classic cause of diphtheria- mainly affects nose and throat
Rarely seen now in the UK because of immunisation
What is propionbacterium acnes?
Gram positive bacillus
Now referred to as Cutibacterium acnes
What does propionibacterium causes?
- Associated with acne
- Can also cause device-associated and post-procedural infections
What are enterobacteriaceae (‘coliforms’)?
A collective term for a number of species of gram negative bacilli found in bowel flora
What are examples of enterobacteriaceae?
- Common species include Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae
- Look like short cocktail sausages

What is the most common cause of UTI’s?
E. coli
What is the most common cause of bacteraemia?
E. coli
What is the most common cause of nosocomial infections (originating from hospitals) e.g. line infections, pneumonia, wound infections?
E. coli
How is severe diarrhoea and haemolytic uraemic syndrome (HUS) caused from E. coli?
Toxigenic strains (e.g. O157) associated with severe diarrhoea and haemolytic uraemic syndrome (HUS)- produce toxins- zoonosis from contact with animals- farms, dairy products not being pasteurised
What is pseudomonas aeruginosa?
Multi-resistant gram negative bacillus
What does pseudomonas aeurginoa cause?
- Can cause respiratory infections, UTIs, soft-tissue and other infections in vulnerable patients
- Often produces characteristic green pigment

What is Neisseria meningitidis?
Gram negative diplococcus
Glass test where you press against rash and rash lesions don’t disappear

What does neisseria meningitidis cause?
Causes meningococcal sepsis and/or meningitis
What does Neisseria meningitidis present as?
Classic presentation is of a purpuric non-blanching rash (sepsis)
What is Neisseria gonorrhoeae?
Gram negative diplococcus
What does Neisseria gonorrhoeae cause?
Cause of gonorrhoea
What is ophthalmia neonatorum?
Ophthalmia neonatorum- born with gonorrhoea from mother
Can Neisseria gonorrhoeae cause invasive infections secondary to primary sexually transmitted infections?
Can rarely cause invasive infections (e.g. septic arthritis) secondary to primary sexually transmitted infection
What is haemophilius influenzae?
Gram negative bacillus
What does Haemophilus influenzae form?
Forms part of normal respiratory tract flora
What can haemophilus influenzae cause?
Can cause respiratory tract infections (e.g. pneumonia, infective exacerbations of COPD)
What are the types of haemophlius influenzae?
Capsulated types (e.g. type b) associated with meningitis and epiglottitis (leads to airway obstruction)
Only type b infections prevented by the HIb vaccine
What are anaerobes?
Bacteria that grow in the absence of oxygen
What does C. difficile, C.perfringens and C. tetani cause?
- Clostridium species. Many are spore-forming organisms- allows to survive more, occurs a lot in hospital and ingested and exposed to antibiotics germinating and forming toxins leading to diarrhoea
- C. difficile – antibiotic-associated diarrhoea/colitis
- C. perfringens – classical cause of gas gangrene
- C. tetani – cause of tetanus
What does C. botulinum cause?
C. botulinum – cause of botulism
What are these bacteria?
Bacteroides species, Fusobacterium species, Prevotella species and many others
Often part of polybacterial infections e.g. dental infections, lung abscesses, colonic abscesses, post-trauma skin/soft tissue infections
Anaerobes
What are mycobacterium species?
Often referred to as ‘Acid Fast Bacilli’ (AFBs)- RHS acid fast bacilli stain
Do NOT stain using conventional gram staining

What does mycobacterium tuberculosis cause?
Mycobacterium tuberculosis – cause of TB
What are other mycobacterium species referred to as? What do they cause?
Other Mycobacterium species are sometimes referred to as ‘Atypical Mycobacteria’ and cause respiratory infections in those with chronic lung disease or opportunistic infections in immuno-compromised patients e.g. AIDS, transplant patients, etc
What are bacteria without a conventional cell wall?
- Chlamydia species
- C. trachomatis – commonest cause of STI
- Mycoplasma species
- M. pneumoniae – common cause of respiratory tract infections
What is a spirochaetes called?
Treponema pallidum- cause syphilis
Leptospirosis- can be from rats
Lyme Disease- associated with tick bites
What does Treponema cause?
This causes syphilis
Which of the following are ‘Gram Negative’ bacteria?
A] Streptococcus pneumoniae
B] Mycobacterium tuberculosis
C] Escherichia coli
D] Listeria monocytogenes
E] Neisseria gonorrhoeae
F] Mycoplasma pneumoniae
A] Streptococcus pneumoniae- gram positive cocci
B] Mycobacterium tuberculosis- acid fast bacilli
C] Escherichia coli
D] Listeria monocytogenes- gram positive bacillus
E] Neisseria gonorrhoeae
F] Mycoplasma pneumoniae – doesn’t have bacterial cell or stain with gram stain
Which of these bacteria is a common cause of skin infection?
A] Klebsiella pneumoniae
B] Streptococcus pneumoniae
C] Haemophilus influenzae
D] Neisseria meningitidis
E] Staphylococcus aureus
F] Clostridium difficile
A] Klebsiella pneumoniae
B] Streptococcus pneumoniae
C] Haemophilus influenzae
D] Neisseria meningitidis
E] Staphylococcus aureus- commonest cause of skin infection
F] Clostridium difficile
Which of the following is the most common sexually transmitted infection?
A] Chlamydia trachomatis
B] Treponema pallidum
C] Corynebacterium diphtheriae
D] Staphylococcus aureus
E] Neisseria gonorrhoeae
F] Viridans streptococci
A] Chlamydia trachomatis
B] Treponema pallidum- cause of syphilis
C] Corynebacterium diphtheriae- not an STI
D] Staphylococcus aureus- not an STI
E] Neisseria gonorrhoeae- not as common as Chlamydia trachomatis
F] Viridans streptococci- not an STI
Which of the following can cause meningitis?
A] Neisseria meningitidis
B] Streptococcus pneumoniae
C] Listeria monocytogenes
D] Streptococcus agalactiae
E] Haemophilus influenzae
F] Staphylococcus aureus
Which of the following can cause meningitis?
A] Neisseria meningitidis- common cause of primary meningitis
B] Streptococcus pneumoniae- commonest cause of primary meningitis
C] Listeria monocytogenes- can cause in pregnant/ immunocompromised and new-born
D] Streptococcus agalactiae- commonest cause in a new born
E] Haemophilus influenzae- not as often due to vaccination
F] Staphylococcus aureus- normally when devices inserted
What are viruses made up of?
- Simple micro-organisms
- Not capable of independent existence
- Need a host cell to survive (e.g. a red blood cell, a respiratory epithelial cell…)
- ‘Steal’ energy, metabolic intermediates and enzymes from host cells to replicate

What is the virus’ life cycle?
Viruses attach, enter, uncoat, reveal genetic material, use host cell machinery to copy genomic material into proteins which are used to assemble new variants which had been released from the host cell.

How do you classify viruses?
Genetic material inside them
- DNA vs. RNA
- single vs. double stranded
- if single, positive vs. negative sense
Presence or absence of an envelope
What is a herpes viruses?
- Double-stranded enveloped DNA viruses
- 9 types known to infect humans
- Once infected characterised by their ability to establish latency and reactivate

What is Herpes simplex 1 also called?
HSV-1, ‘cold sores’

What is the epidemiology of herpes simplex 1?
- Exists worldwide, humans only known reservoir
- 80% of UK population experience HSV-1 in their lives
What is the mode of transmission of herpes simplex 1?
- Direct contact with vesicle fluid from lesions
- Latency in sensory nerve ganglion***
- Periodic reactivations
What are the important clinical syndromes of herpes simplex 1?
- Vesicles / ulcers to skin or mucous membranes – typically mouth (oral sex- can find on genitals) (HSV-1)
- Encephalitis – (brain inflammation) often severe or fatal HSV-1 = commonest cause of viral encephalitis worldwide
What are the other disease names of herpes simplex 2?
HSV-2, ‘genital herpes’, ‘herpes’
What is the epidemiology of herpes simplex 2?
Exists worldwide, humans only known reservoir
HSV-2 ~10-20% population
What is the mode of transmission of herpes simplex 2?
Direct contact with vesicle fluid from lesions
Latency in sensory nerve ganglia***
Periodic reactivations

What are the important clinical syndromes of herpes simplex 2?
- Vesicles / ulcers to skin or mucous membranes – typically genitals/buttocks
- Meningitis – often follows an outbreak of genital lesions
- Neonatal herpes – severe disseminated viraemia (life-threatening)
Vertical transmission from mother’s genital tract after vaginal birth
What are the disease names of Varicella zoster virus?
Primary (first) infection = ‘chicken pox’
Reactivation = ‘herpes zoster’ or ‘shingles’

What is the epidemiology of the varicella zoster virus?
In UK, ~95% have had chicken pox by age 20
In the tropics this decreases to ~50%
What is the mode of transmisson of varicella zoster virus?
Respiratory droplet from person with chicken pox
Direct contact with vesicle fluid from person with chicken pox or shingles
Latency established in dorsal root ganglia of whole CNS- means when have shingles can reactivate down any of the dermatomes
What are the other Epstein Barr virus disease names?
‘Glandular fever’, ‘infectious mononucleosis’
What is the epidemiology of Epstein Barr virus?
90% in the UK are infected by age 25
Of these, 50% infected before age 5yrs
What is the mode of transmisson of the Epstein Barr virus?
Virus is shed in saliva and genital secretions – ‘kissing disease’- requires intimate close contact to be passes on
What are the clinical syndromes of the Epstein Barr virus?
- Infectious mononucleosis (primary infection):
tonsilitis, fever, lymphadenopathy, hepatosplenomegaly
atypical lymphocytes on blood film (look like monocytes – ‘mononucleosis’)***
80% of clinical infectious mononucleosis is caused by EBV- remainder caused by CBV
- Reactivation (from latency in B cells***)
If unwell or immunosuppressed (e.g. solid organ or bone marrow transplant)
Associated with malignant B cell lymphoproliferative disorders- EBV referred to as an oncogenic virus

What is the alternate disease name for the herpes virus cytomegalovirus?
Disease names: ‘CMV’
What is the epidemiology of CMV?
Epidemiology:
In UK, % prevalence = ~ age (e.g. 20% of 20yr olds)
What is the mode of transmisson of the CMV?
Saliva or genital secretions
Donated blood, stem cells or solid organs
Latency in myeloid progenitors / monocytes / dendritic cells
What are the important clinical syndromes of the CMV?
- Infectious mononucleosis (primary infection): see EBV slide
- Congenital CMV infection
In infants born to mothers who have infection during pregnancy
Retinitis, deafness, microcephaly, hepatosplenomegaly in the neonate
- Reactivation in immunosuppressed patients (e.g. transplant patients, advanced HIV)
Reactivation of latent CMV can cause retinitis, colitis, pneumonitis
What are the proportion of respiratory viruses?

What is the disease name for a rhinovirus?
‘Common cold’
‘Rhino’ = ‘nose’
What is the epidemiology of a rhinovirus?
Worldwide distribution
Occur in epidemics in the autumn, winter and spring
What is the mode of transmission of the rhinovirus?
Aerosolised respiratory secretions and droplets from nose and eyes
What are the important clinical syndromes of rhinovirus?
‘Common cold’ – sneezing, nasal obstruction & discharge, sore throat, cough, headache and fever
What is the epidemiology of the coronavirus?
Worldwide distribution
Infect humans and animals
What is the mode of transmission of the coronavirus?
Aerosolised respiratory secretions and droplets from nose and eyes
What are the clinical syndromes of coronavirus?
Alpha coronaviruses- 2- 229E and NL63 causing the common cold. In the Beta coronaviruses in group A- OC43 and HKU1 responsible for the common cold. In group SARS-CoV-1 derived from cat and SARS-CoV-2- cause of the pandemic.
Group C- MERS (Middle East Respiratory Syndrome)

What is the epidemiology of influenza?
Infect humans and animals, can spread between species
Peaks in winter annually
What are the types of influenza?
Virology
3 distinct types: A, B, C
Influenza A mutates regularly, so strains vary yearly
What are the two important surface proteins of influenza?
2 important surface proteins H & N have multiple variants
Used in nomenclature: e.g. H1N1 (swine), H3N2 (seasonal)
What is the mode of transmisson of influenza?
Aerosolised respiratory secretions (coughs and sneezes!)
What are the clinical syndromes of influenza?
- Primary influenza illness: fever, myalgia (muscle aches), then headache, cough, sore throat, nasal discharge
- Post-influenza secondary bacterial lung infection:
with S.pneumoniae, H.influenzae, S.aureus
What is the other disease name for respiratory syntical virus?
Disease names: ‘RSV’
What is the epidemiology of the repsiratory syncytical virus?
Epidemiology:
Worldwide distribution, occurs in epidemics in winter
Commonest in young children***: 70% are infected and 30% have had clinical illness in their first year of life
What is the mode of transmisson of the respiratory syncytical virus?
Aerosolisation of respiratory secretions
What are the important clinical syndromes of respiratory syncytical virus?
Bronchiolitis: affects children under 2 yrs
Inflammation of smallest airways – bronchioles
Causes cough, wheeze, hypoxia and apnoeas

What is HIV?
HIV – Human immunodeficiency virus
What is the clinical course for HIV between 2-6 weeks?
HIV targets helper T lymphocytes (CD4) cells, part of the cell-mediated immune system
2-6 weeks after transmission, patients may develop an acute seroconversion illness (flu-like)
How long can you be asymptomatic to HIV for?
Steady state between virus and immune system, lasts 5-15 years***
What causes AIDS?
AIDS = rise in viral load and fall in CD4 count, patient becomes vulnerable to opportunistic infections
Patients become vulnerable and immune system weakens- leads to AIDS
What are AIDS defining illnesses?
AIDS defining illnesses: e.g. pneumocystis pneumonia, cryptococcal meningitis, Kaposi’s sarcoma
What are the hepatitis viruses?
A and E normally feaco-oral spread.
B and C- blood borne

What is the mode of transmission and clinical syndromes of Hep A and E?

What is the epidemiology, the populations it affecrs and special considerations of Hep A?

What is the epidemiology, symptomatic populations and special considerations of Hep E?

What is Hep B epidemiology?
Epidemiology:
248 million people chronically infected
>500,000 deaths annually
What is the mode of transmisson of Hep B?
Mode of transmission:
Vertical- blood borne
Sexual, parenteral
What is the clinical course of Hep B?
- After transmission, acute clinical hepatitis may occur
but 90% children and 50% young adults are asymptomatic
- Hepatitis B is then cleared, or persists and becomes chronicRisk of chronicity is inversely related to age at infection ***
90% perinatally acquired infection progress to chronic
vs. <5% adult-acquired infections
* Over time, chronic hepatitis → cirrhosis → hepatocellular carcinoma
Risk of becoming chronic is inversely related to age of infection, acquire Hep B at young age, higher chance of it becoming chronic.
What is Hep C epidemiology?
170 million people infected worldwide
Prevalence in developed countries is low, ~0.5-2%
In the UK, 50% of PWIDs (people who inject drugs) have evidence of hepatitis C***
What is the mode of transmission of Hep C?
Sharing needles, needlestick injuries, transfusion of contaminated products
Vertical & sexual transmission is less common
What are the important clinical syndromes of Hep C?
After transmission, approximately 25% develop acute clinical hepatitis
15% will then clear the virus, but 85% will become chronically infected ***
Over time, chronic hepatitis → cirrhosis → hepatocellular carcinoma (HCC)

What is the epidemiology of norovirus?

What is the mode of transmisson and clinical syndrome of norovirus?

What is the epidemiology of the rotavirus?

What is the mode of transmisson and clinical syndromes of the rotavirus?

What are types of enteroviruses?
Group includes poliovirus, echoviruses and Coxsackie A and B
What is the epidemiology of the enteroviruses?

What is the mode of transmisson and pathogenesis of the enteroviruses?

What are the important clinical syndromes of the enteroviruses?
Enterovirus the most common cause of meningitis in the UK.

What is the epidemiology of mumps?
Endemic childhood infection worldwide
Cases peak in temperate climates in winter
What is the mode of transmisson of mumps?
Virus shed in saliva and respiratory secretions
Respiratory droplet transmission
Very infectious
What are the important clinical syndromes of mumps?
- Acute parotitis - unilateral or bilateral
- Orchitis (inflammation of testicles)
Affects 20-30% of males with mumps***
Typically develops 4-5 days after parotitis
- Meningitis
Occurs in up to 15% of mumps cases
Can lead to meningoencephalitis and sensorineural deafness***
Prior to MMR vaccine, mumps was one of the commonest causes of viral meningitis
What is the epidemiology of measles?
Previously endemic in UK with 2-3 yearly epidemics
Now, due to vaccine, occurs in clusters of unvaccinated
What is the mode of transmisson of measles?
Respiratory droplet transmission
Highly infectious – environment still infectious after 2 hours***
What are the clinical syndroms of measles?
- Primary measles
Fever, coryza (inflammation of mucous membrane in nose), cough,conjunctivitis, Koplik’s spots on inside of cheek***
Then maculopapular rash (top right)
- Acute post infectious measles encephalitis (1:1000)
Occurs 7-10 days after acute infection, high mortality rate
Immune-mediated
- Subacute sclerosing pan-encephalitis SSPE (1: 1000000)
7-10 years after natural measles infection
Progressive, degenerative and fatal disease of the CNS

What is the disease name of rubella?
Disease names: ‘German measles’
What is the epidemiology of rubella?
Epidemiology:
Previously common in UK with 6-8 yearly epidemics
Now, due to vaccine, rare
What is the mode of transmisson of rubella?
Droplet transmission from respiratory route
What are the clinical syndromes of rubella?
- Primary rubella
Mild illness, fever and maculopapular rash
Arthralgia (aching without swelling of joints)/ arthritis occurs in 30% adults*
- Congenital rubella
Classic triad: Bilateral cataracts, sensorineural deafness (caused by a lesion or disease of the inner ear or the auditory nerve), cardiac defects
Risk of foetal malformation is highest in first 12 weeks of pregnancy
Parvovirus B19

What is the parvovirus B19 diease name?
‘Slapped cheek syndrome’ or ‘Fifth disease’
What is the epidemiology of parvovirus B19?
Spring time = peak
50% infected by 15yrs, 90% by 90yrs
What is the mode of transmisson of the parvovirus B19?
Respiratory droplet transmission
Infects and kills erythrocyte progenitor cells – causing transient anaemia
What are the clinical syndromes of parvovirus B19?
- Erythema infectiosum = fever, coryza, fiery red rash to cheeks***, ‘lacy’ rash to body
- Transient aplastic crisis
affects those with high erythrocyte turnover e.g. sickle cell, thalassemia ***
- Infection in pregnancy
7-10% fetal loss if maternal parvovirus infection in first 20 weeks
2-3% develop hydrops fetalis: severe fetal anaemia → heart failure → oedema, ascites
What is a prion?
Small infectious particle containing protein, no nucleic acid
What is the mode of transmission of a prion?
→ 1. gene mutation leads to changes in folding pattern of protein
→ 2. prion becomes resistant to protease enzyme due to abnormal folding
→ 3. prion accumulates abnormally in cell
→ 4. promotes other proteins to abnormally fold
What is sporadic Cruetzfeld-Jakob disease (CJD)? What are the clinical syndromes?
Sporadic Creutzfeld-Jakob disease (CJD) = very rare
1 in million
Gene mutation
Progressive ataxia (generative disease of nervous system), depression, dementia then death.
What is nvCJD? What is it associated to?
nvCJD directly linked to BSE (bovine spongiform encephalopathy)
- same structure prion
- nvCJD cases associated with consumption of contaminated beef