MMSC438 Specimen Processing

Divisions within Microbio Lab

aerobic

anaerobic

mycobacteriology

mycology

parasitology

biology

molecular diagnostics

Aerobic microbiology

Study of microscopic organisms such as bacteria and that need O2 to grow and survive.

Anaerobic microbiology

Study of microscopic organisms, like bacteria, that grow/live without O2.

Mycobacteriology

acid-fast bacilli

Mycology

fungal genetics, biochem, taxonomy and ecological uses

Parasitology

study of parasites, their hosts, and relationship between the two

Molecular diagnostics

NAATs, MALDI-TOF MS

replacing serologic testing and conventional organism identification

rapid tests and point of care of tests

Roles of clinical microbio lab

primary concern is the patient (HIPAA)

accurate and timely testing

communication with other healthcare professionals

approaches to assist optimum disease management of patients

epidemiologists and infection control officers role in relation to clinical microbiology labs?

surveillance

pharmacists role in relation to clinical microbiology labs?

antimicrobian formulary

infectious disease clinicians role in relation to clinical microbiology labs?

advice

Pre-analytical phase of microbiology lab?

patient prep communication with “collectors”

sample collection

sample transport to lab

Analytical phase of microbiology lab?

direct testing

plating, ID

antimicrobial susceptibility testing

Post-analytical phase of microbiology lab?

record keeping

review

reporting

Most common lab acquired infections?

Mycobacterium tuberculosis

Brucella spp.

Salmonella spp.

Shigella spp.

Neisseria meningitidis

Hepatitis B virus

Hepatitis C virus

How should you handle all human body fluids?

as potentially infectious

HEPA filtration

high-efficiency particulate air

filters air and traps small particles

Ultraviolet irradiation

disinfection of pathogenic organisms

kills or inactivates by disrupting nucleic acids

Negative pressure room

prevents aerosolized particles from escaping room

Purpose of specimen collection?

to detect pathogens

Whenever possible when is the best time to collect specimens?

before antimicrobial therapy has begun

how to disinfect site of collection?

70% alcohol 2% tincture of iodine

if there is a large amount of resident biota how would you instead obtain specimen?

needle aspiration

Collection times depend on what?

the type of infectious disease

What is significant about first morning sputum and urine samples?

they are most concentrated

Can you accept a 24 hour specimen for culture?

no

When would you draw blood for specimen collection?

microfilariae

Specimen container labeling requirements

must be sterile except feces

patient name

hospital ID number

location (room #/outpatient)

physician

culture site (source of specimen)

date/time of collection

Requisition slip specimen labeling?

patient name & unique identifier

patient age/sex

patient room #/address

physician name

specific anatomic culture site

clinical diagnosis and relevant patient history

tests requested

notify lab if unusual pathogens/agents of bioterrorism suspected

date/hour of specimen collection

date/time specimen received by lab

name of individual transcribing orders

antimicrobial agents (if any) patient is recieving

specimen transport is dependent on what?

the viability of the agent: bacterial, fungal, parasite, virus

What if specimen is received in an inappropriate container or transport medium or after prolonged delay?

Contact physician immediately

Request another specimen

Provide information regarding appropriate collection and transport

Improper or no label could mean what transport error?

Excessive delay between collection and receipt of specimen in the laboratory

Container identification and request form IDs differ could mean what transport error?

Inappropriate transport medium

Request form with insufficient information could mean what transport error?

Transported at improper temperature

Process all specimens ASAP after arrival in the laboratory preferable within ____ of collection.

1-2 hours

The gram stain is?

he single most efficient and cost-effective test for rapid early diagnosis of bacterial infection

Categorize specimens STAT?

gram stain

Categorize specimens urgently?

Normally sterile body fluids: blood, CSF, pericardial fluid, amniotic fluid also transtracheal aspirates, eye specimens

Specimens potentially containing N. gonorrhoeae ( non molecular testing)

Preliminary information within 30 min - 1 hr (i.e., Gram stain result)

Categorize specimens routinely?

Throat, pleural fluid, burn specimens, surgical specimens, preserved specimens

Specimens from patients suspected of having pneumonia, peritonitis

Specimen Priority issues

one specimen per day per site (except blood cultures)

handling and reporting stat or urgent specimens req by CLSI

reporting resulting of STAT/urgent specimens (telephone results, LIS)

Notations from the macroscopic observation should include

Swab or aspirate

Stool consistency (formed or liquid)

Blood or mucus present

Volume of specimen

Fluid: clear or cloudy

Microscopic Observation

Determines quality of specimen

Can give microbiologist and physician an indication of the infectious process

involved

Can be useful in initial treatment

Helpful for media selection

May provide presumptive identification

Can guide the culture workup

Can dictate the need for non-routine or additional testing

Nonselective culture media

Support growth of most nonfastidious organisms

Standard media used: sheep blood agar or Chocolate agar

Selective culture media

Support growth of one type of organism but inhibit growth of others

Example: Columbia nalidixic acid (CNA) agar, MacConkey Agar

Differential culture media

Allows grouping of microbes based on demonstrated characteristics on the media

Examples: SBA, MacConkey agar

Enriched culture media

medium for fastidious organisms for normally sterile body fluids or sites in which fastidious organisms are expected: Chocolate agar

Sheep Blood Agar

no selective agents

5% sheep blood (intact erythrocytes)

fastidious/non-fastidious pathogens

MacConkey Agar

bile salts, crystal violet (inhibits gram+)

lactose (carbohydrate) neutral red (pH indicator)

gram negative rods (enterbacteriaceae like E.coli)

Columbia CNA Agar

colistin, nalidixic acid (inhibits gram -)

5% sheep blood (intact erythrocytes)

gram positive organisms

Chocolate Agar

highly enriched (non-selective)

no selective agents

fastidious species (haemophilus influenzae, pathogenic neisseria)

no hemolysis (brown agar base)

Sabouraud Dextrose Agar (SDA)

selective (non-differential)

fungi (yeasts like C. albicans, molds like aspergillus)

Most bacteria cultures grow between what temps?

35C and 37C

Time required for most bacteria cultures?

48 to 72 hours

some 5-7 days

Role of the laboratory

Provide accurate and timely information to health care professionals

preliminary results as they are available.

Laboratory scientists cannot tell the primary care provider what to do or how to treat

the patient. They can only what?

present facts, e.g., a blood culture smear shows Gram-positive cocci in clusters.

Panic” or Critical Values

1. Positive smears from sterile body sites

2. Health care-associated (nosocomial) infections

3. Positive cultures from sterile body sites

• Blood, CSF, pleural fluid, pericardial fluid

WASP Automated Specimen Processing

Walk Away Specimen Processor

Plating and streaking

Broth inoculation

Gram stain slide prep

Cost 1 -2 million