Role of Microbiology Lab Flashcards
1
Q
role of microbiology lab
A
diagnosis of infections performed by the laboratory has two important functions:
- clinical
- epidemiological
Clinical and epidemiological role of the microbiology laboratory are very much connected: knowledge of an infective microbe in a patient helps find its source and route of transmission and prevent the spread to other patients.
2
Q
clinical role of microbiology lab
A
- Diagnosis of infection in an individual patient for everyday management of infections
3
Q
epidemiological role of microbiology lab
A
- Support for infection prevention and control in searching for source and route of transmission of HAI
- Bigger picture – drives infection control and prevention measures
4
Q
6 minimal requirements for microbiology services
A
- set up insider the facility
- available every day, including sundays and holidays
- able to examine different clinical specimens
- identify common bacteria and fungi to species level
- perform susceptibility testing using disc-diffusion methodology/broth microdilution
- perform basic phenotyping
- serotyping
- biotyping
Every microbiology laboratory has to have quality assurance procedures and a microbiologist with good communication skills.
5
Q
if not possible to have microbiology service set up within facility
A
negotiate a contract for diagnostic microbiology with the nearest laboratory
6
Q
operating times of microbiology lab
A
24 hours, every day
7
Q
every microbiology lab MUST
A
have quality assurance procedures and a microbiologist with good communication skills.
8
Q
e.g. clinical samples variety which lab needs to be able to examine
A
blood, cerebrospinal fluid, urine, stool, wound exudate or swab, respiratory secretions, and perform basic serological tests (HIV, HBV, HCV)
9
Q
e.g. organisms ID by serotyping phenotyping
A
- Salmonellae, Shigellae, P. aeruginosa, N. meningitidis
10
Q
e.g. organism ID by biotyping phenotyping
A
S.typhi
11
Q
3 things microbiology lab should be able to determine
A
- what the species is
- what it is senstive to
- any differences between the species
12
Q
how to send sample and grow it
A
- appropriate device (sheath) to microbiology lab*
- Most organisms from clinical samples grow well on blood agar (non-selective)*
- place in incubator (generally 37o), looking for single colonies – take colony and spread over agar dish with antibiotic disc to see if a zone of inhibition forms*
- Obligate anaerobes – grow without oxygen – need to get to lab quickly or they will die*
13
Q
issue with obligate anaerobes
A
grow without oxygen
need to get to lab quickly or they will die
14
Q
what clinical sample would be taken for an abscess
A
pus
- Insert needle into abscess and withdrawing the pus*
- Tends to be anaerobic organisms in pus – need to get specimen to lab quickly as organism may die*
15
Q
diagnosis should be
A
rapid and accurate to the species level wherever possible
16
Q
4 methods of diagnosis
A
classical bacteriological methods
sensitivity testing
antibody detection
molecular methods
17
Q
3 classical bacteriological methods of diagnosis
A
- Direct smear – pseudomembranous candidiasis
- Culture
- Antigen detection
18
Q
sensitivity testing for diganosis helps determine
A
if pt non compliance or organism resistant
19
Q
antibody detection useful
A
in later stages of infection
not very useful in early stages of infection as none developed
e.g. viruses – COVID, hepatitis – indicator of active infection
20
Q
molecular methods use
A
Rarely used in routine work for the diagnosis of bacterial HAI – expense
- Limitation is that culture is important – to enable sensitivity tests for HAIs
21
Q
why do we need to know the aetiology of infection ASAP in HAIs
A
we can give to the patient targeted antimicrobial therapy – in that case patient’s causative agent will be eradicated earlier
so he/she will stop to be a source for other patients earlier than if the therapy would be unsuccessful
22
Q
when is antibody detection useful
A
only in some viral diseases when we can detect IgM
23
Q
who can give advice to ward staff about collection and transport of specimens
A
labratory staff
24
Q
6 stages in simplified scheme for bacterial identification
A
- specimen
- direct examination
- culture
- pure culture and identification of species
- species name established
- typing or fingerprinting for taxonomic or epidemiological purposes
25
specimen collection involves
stating site of origin
collection correctly
transport correctly to labratory
26
direct examination involves
microscopy
* wet film and gram stain
* smell
* gross appearance
* types of bacteria and other cells
27
culture involves
plate culture
* non selective or selective mediu
* gaseous enviroment - aerobic, anaerobic, microaerophillic, CO2
* quantitive or non-quantitive
* enrichment broth culture
28
pure culture and identification to species involves
colonal morphology
* microscopy
* wet film for observation of motility and spores and gram stain for gram reaction and cell morphology
* biochemical (metabolic) tests
* traditional or commercial 'kit'
a.k.a APIs
29
typing or fingerprinting for taxonomic or epidemiologycal purposes involves
serological, phenotypic and genotypic methods
30
2 shapes of bacteria
cocci
rods (bacilli)
31
cocci
round, grape like
32
rods (bacilli)
length of bacteria
33
gram positive bacteria features
thick peptidoglycan wall
34
gram negative bacteria feature
thin peptidoglycan wall
35
gram +ve Vs gram -ve
gram +ve has a thick peptidoglycan wall
gram -ve has a thin peptidoglycan wall with outer membrane
36
gram stain test
* prepare a heat fixed film of bacteria on a glass slide
* stain with crystal violet for 1 mins and rinse with water
* stains everything
* treat with Gram Iodine for 1 mine and rinse with water
* helps fix the crystal violet
* briefuly decolourise with acetone/ethanole (a few secs depening on thickness of film)
* gram -ve will loose crystal violet as thin peptidoglycan
* counter stain with basic fushin or safranin (pink dye) for 1 min and rinse with water
* Gram +ve no effect as purple stained
* gram -ve will go clear to pink
* blot dry and view under oil immersion
37
purpose of gram stain test
allows differentiation
* shape
* structure of cell wall
38
describe this bacteria
*Long strands gram positive streptococci*
39
describe this bacteria
* Short, dumpy rods*
* Pink gram -ve*
40
describe this culture
mixed
41
when would dentist send away a chairside sample
* Unlikely to get quick answer from chairside sample*
* Consider*
* *Do you need this information*
* *Not responding to antimicrobials*
* *Immunosuppressed*
*Help know to Tx effective*
42
why is gram stain test one of the first tests performed
Need to know cell wall composition so can do subsequent down stream testing
43
4 roles of microbiology lab in prevention and control of HAIs
1. Outbreak investigation
2. Surveillance of HAIs
3. Alert microorganisms reports
4. Designing antibiotic policy
## Footnote
*Every health board have different specific microbe concerns for their area*
44
outbreak investigation aims
* To determine the cause of a single-source outbreak the causative agent must be defined
* Then microbiology laboratory determines if two or more isolated strains are same or different
microbial species may contain subspecies and variants, moreover individual bacteria of the same species can differ as much as 30% in their genomes and differ in phenotypes
*genotypes determination more favourable than phenotypes*
45
possible additional tests carried out by IP&C team during outbreak (7)
* Blood products
* Environmental surfaces
* Disinfectants and antiseptics
* Air
* Water
* Hands of personnel
* Anterior nares of personnel
46
benefit of knowing pathogen involved in outbreak
microbiology labs can use special media for culture for rapid and inexpensive identification of the pathogen in environmental specimens.
47
reports made by microbiology labs for HAI surveillance
The microbiology laboratory should produce routine reports of bacterial isolates
* Allows the IP&C team to create statistics (figures/tables) for specific pathogens, wards, and groups of patients
* E.g. amoxicillin for gingivitis – all pts sensitive to – great work, over prescribing see change in trends where Mos associated with gingivitis
* Need to capture data continuously to see change
* A ‘baseline incidence’ can be established
* Any new isolate can then be compared with this incidence
* If the laboratory is computerised, these data can be made readily available
48
key benefit of regular microbiology lab reports
* enable IP&C team to discover an outbreak earlier than it could be discovered from clinical data only
* point to the trends in the specific pathogen occurrence and are very useful in planning preventive measures
* may also report clustering of infections (two related isolates in different patients in the same time frame
49
most reliable data from microbiology lab
isolates from blood culture, urine and infected wounds,
data from respiratory tract infections should be very carefully interpreted in the light of clinical picture.
50
alert organisms reports
wide varierty of agreed alert organisms
The isolation and immediate report of an unusual microorganism (unusually pathogenic or unusually resistant) enables IP&C Team to take appropriate measures and stop it from spreading.
51
e.g. alert organisms
* Methicillin-resistant *Staphylococcus aureus* (MRSA)
* Vancomycin-intermediate *S.aureus* (VISA)
* Vancomycin-resistant enterococci (VRE)
* MDR *Pseudomonas aeruginosa*
* MDR *Acinetobacter baumannii*
* MDR *Mycobacterium tuberculosis*
* ESBL enterobacteria
* *Clostridium difficile*
* *Candida auris*
* COVID-19
52
antibiotic policy
Regular reporting of changing resistance patterns
* Newsletters
* Specialty specific data
Restricted antibiotic reporting
* Routinely only first line antibiotics
* Reserve antibiotics only if pathogen is resistant to first line antibiotics
* Problems arise if reserve used before first line – increase chance of resistant form
53
why is regular reporting in antibiotic resistance patterns important
* Allow to think why – antibiotic over use, coincidence*
* Don’t determine resistance – need to link to reason*
* *Organisms don’t suddenly become resistant – they are driven there*
54
importance of restricted antibiotic reporting in individual pts
important for saving of reserve antibiotics.
55
antibiotic stewardship
* Role of Clinical Microbiologist/ID specialist
* Provide leadership to antimicrobial team
* Antibiotic ward rounds
* Interpretation of patient specific data to optimise treatment
* culture and sensitivity
* Active surveillance/ awareness
* Screening for carriage of resistant bacteria – *programmes, swabs*
* Molecular detection and typing
56
role of clinical mircrobiologist/ ID specialist in antibiotic sterwardship
* Provide leadership to antimicrobial team
* Antibiotic ward rounds
* Interpretation of patient specific data to optimise treatment
* culture and sensitivity
57
active surveillance/awareness in antibiotic stewardship
* Screening for carriage of resistant bacteria – *programmes, swabs*
* Molecular detection and typing
know what is in the communtiy
58
who interpret microbiologucal data
Microbiologists interpret microbiological data for IP&C staff
* Results of isolation, identification, susceptibility tests, typing
Ideally should be medical doctor specialistt
* If this is not possible, then a properly educated scientist is required
59
what to consider when interpreting microbiological data
* nature of isolated organisms (primary or opportunistic pathogen),
* specimen from which the organism was isolated,
* clinical picture of the patient and actual immunological status of the patient.
To interpret microbiology data for epidemiological purposes one should take into account the properties and main habitat of isolated organism, as well as the opportunity to be transmitted to a specific patient.
60
microbiology lab educates (3)
* Infection prevention staff
* Other healthcare workers
* Students (medical and nursing)
61
IP&C staff are educated by microbiology lab on
how to interpret microbiological reports/charts
62
other healthcare workers are educated by microbiology staff on
specimen collection and transport, interpretation of reports and sensitivity tests
63
students are educated by microbiology lab on
basic microbiology
64
3 key transmission routes for dental
* aerosol
* hands
* blood
65
chain of infection
66
how to break chain of infection
* contact tracing
* infectious agent
* isolation
* early treatment
* source
* education/ policy (social distancing)
* environmental sanitation
* disinfection
* exit
* handwashing
* control of aerosols/splatter
* means of transmission
* isolation
* disinfection
* handwashing
* portal of entry
* first aid
* personal hygiene
* handwashing
* susceptible host
* vaccination
* treatment of underlying diseases
antibiotic prophylaxis (e.g. meningitis)
67
airborne transmission examples
*e.g. S.aureus, S.pyogenes, M.tuberculosis, S. pneumoniae, Respiratory viruses, Legionella*
68
direct contact e.g
*e.g. S.aureus, Enterobacteria, psudomonas, vancomycin resisted enterococci (VRE)*
69
solutions to try and break transmission
* hospital/ward design
* isolation facilities
* maintenance of ventilation
* adequate space
* infection control policies
* staff education
* good clinical practice
* sterile supplies, equipment sterilisation or single use items
* disinfection policy
70
5 points of hand hygiene
* before pt contact
* before an aseptic task
* after body fluid exposure risk
* after pt contact
* after contact with pt surroundings
71
microbes prevalence
* infectious agents not visible to the naked eye
* Widespread and ubiquitous in nature and some cause human disease
72
key epidemiological role of microbiology lab
perform basic typing of microorganisms
73
reports from microbiology labs can be used to construct
incidence graphs for specific pathogens, wards, and groups of patients
74
why handhygiene before pt contact
to protect pt against harmful germs carried on your hands
75
why HH before aspectic task
to protect the pt against harmful germs, inc the pts own germs, entering his or her body
76
why HH after body fluid exposure risk
to protect yourself and the health care enviorment from harmful pt germs
77
why HH after pt contact
to protect yourself and the health care enviroment from harmful pt germs
78
why HH after contact with pt surroundings
to protect youself and the health care environment from harmud pt germs
