Role of microbiology laboratory in IP&C. Objectives 1.Describe the basic properties of microorganisms, including their natural habitat and mode of transmission.

Role of microbiology laboratory in IP&C

Objectives

1. Describe the basic properties of microorganisms, including their natural habitat and mode of transmission.

2. List the most important "alert" microorganisms causing HAIs.

3. Explain the role of microbiology laboratory in managing patients with infections.

4. Explain the four roles of the microbiology laboratory in the prevention and control of HAIs.

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Time involved

• 60 minutes

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Basic microbiology• Microorganisms are agents of infectious diseases• They are ubiquitous in nature and in/on human

body• Most microorganisms harmless for humans

• Some can cause disease• Microorganisms are divided into

• Bacteria• Fungi• Viruses• Prions• Parasites

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Pathogenesis of infection• When microbes find a new host and start to

multiply – called colonisation• A balance can develop between colonised

microbes and humans – will lead to ‘so called’ normal flora

• If microbe causes disease – called an infection • If source of microbe is patient’s own flora –called

an endogenous infection• If source of microbe is flora from outside the

patient’s body – called exogenous infection

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Microorganism Transmission• Spread to a new host from another human,

animal or environment• Transmission direct or indirect• Pathways of transmission could be

• Contact • hands• surgical instruments

• Contaminated surfaces or items (indirect contact)• Air• Water• Food• Live vectors, e.g., mosquitos

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Bacteria

• Smallest microorganisms with all functions of life• Multiply by simple division

• Form visible „colonies” on a solid surface

• Genetic material transferred vertically and horizontally between different bacteria

• Some can form spores • The most resistant form of life

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Bacteria Acinetobacter baumannii

Bordetella pertussis

Campylobacter jejuni, C. coli

Clostridium difficile

Habitat Moist skin, GI tract

NP mucosa GI tract GI tract

Survival on dry surfaces

3 days – 5 months

3-5 days Up to 6 days Spores – 5 months

Spread in HC Contact Droplets Faecal-oral, water, food

Faecal-oral; contact

HAIs UTI, sepsis, meningitis, pneumonia

Pertussis Diarrhoea CDI

Specimens Urine, blood, CSF, sputum, aspirates

NP swab Stool Stool

Prevention Clean environment, instruments, hands

Isolation Safe food and water, clean hands

Clean environment,, hands, use of antibiotics

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Bacteria Clostridium tetani

Coagulase negative staphylococci (CNS)

C. diphtheriae Enterococcus species

Habitat Environment Skin, mucous membranes

NP GI tract, GU tract

Survival on dry surfaces

7 days – 6 months

5 days – 4 months

Spread in HC Entering umbilical cord

Contact Droplet, contact

Contact, endogenous

HAIs Tetanus Various Diphtheria UTI, sepsis

Specimens Various NP swab Urine, blood

Prevention Sterilisation of instruments

Clean environment, instruments, hands

Isolation, vaccination

Clean environment, hands, use of cephalosporins

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Bacteria Enterobacter species

Escherichia coli Helicobacter pylori

Klebsiella pneumoniae

Habitat Environment, GI tract

GI, GU tract Gastric mucosa

Environment, GI tract

Survival on dry surfaces

5-49 days 1.5 hours – 16 months

Less than 90 minutes

2 hours – more than 30 months

Spread in HC Contact, food Faecal-oral, contact, endogenous

GI endoscopes

Contact, endogenous

HAIs UTI, sepsis, wound infection

UTI, sepsis, neonatal meningitis

Gastritis UTI, sepsis, pneumonia

Specimens Various Various Various Various

Prevention Clean environment, equipment, hands

Clean hands, use of cephalosporins

Properly disinfected GI endoscopes

Clean hands, use of cephalosporins

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Bacteria Legionella pneumophila

Listeria monocytogenes

M. tuberculosis

Neisseria meningitidis

Habitat Water GI tract, soil Respiratory tract

NP

Survival on dry surfaces

1 day - months 1 day – 4 months

Spread in HC

Aerosols Contaminated food/equipment ; perinatal

Airborne Droplets

HAIs Legionnaire’s disease

Meningitis, bacteremia

Tuberculosis Meningitis

Specimens Sputum, blood for serology

Blood, CSF Sputum CSF

Prevention Hyperchlorination of water or heating to at least 55°C

Safe food, clean equipment in nurseries

Isolation Isolation, vaccination

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Bacteria Proteus species Pseudomonas aeruginosa

Salmonella species

Salmonella typhi

Habitat GI tract GI tract, humid areas

GI tract GI tract

Survival on dry surfaces

1-2 days 6 hours to 16 months

1 day 10 months – 4.2 years

Spread in HC

Contact, endogenous

Contact Faecal-oral Faecal-oral

HAIs UTI, sepsis Various Diarrhoea, sepsis

Typhoid fever

Specimens Urine, blood Various Stool, blood Stool, blood

Prevention Clean environment, equipment, hands

Clean, dry environment, disinfected/sterilised equipment; clean hands, use of antibiotics

Safe food, water, clean hands

Safe food, water, clean hands

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Bacteria Salmonella typhimurium

Serratia marcescens

Shigella species

S. aureus

Habitat GI tract GI tract, humid areas

GI tract Skin, mucous membranes

Survival on dry surfaces

10 months – 4.2 years

3 days – 2 months

2 days – 5 months

7 days - 7 months

Spread in HC

Faecal-oral Contact, IV fluids Faecal-oral Contact, droplets, equipment, endogenous

HAIs Diarrhoea, sepsis

Sepsis, wound infection

Diarrhoea Various

Specimens Stool, blood Blood, wound exudate

Stool Various

Prevention Safe food, water, clean hands

Clean environment, equipment, hands

Safe food, water, clean hands

Clean hands, environment; use of antibiotics

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Bacteria S. agalactiae (Group B streptococcus)

S. pyogenes (Group A streptococcus)

Vibrio cholerae

Yersinia enterocolitica

Habitat Birth canal Oropharyngeal mucosa

GI tract GI tract

Survival on dry surfaces

3 days-6.5 months

1 – 7 days

Spread in HC

Contact, Intrapartum

Droplet, contact, endogenous

Faecal-oral Blood transfusion

HAIs Sepsis and meningitis of newborn

Pharyngitis, surgical wound infection

Cholera Bacteremia

Specimens Blood, CSF Oropharyngeal swab, wound exudate

Stool Blood, stool

Prevention Antibiotic prophylaxis during delivery; clean hands

Clean hands, masks in operating room

Safe water and food

Safe blood products

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Fungi

• Unicellular (yeasts) or multicellular (moulds)• Reproduce asexually (conidia) and sexually

(spores*)• Ubiquitous in nature

• some are parts of human normal flora

• Most opportunistic pathogens• Cause severe infections in immunocompromised host

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15* Fungal spores are not resistant to environmental factors like bacterial spores!

Fungi Candida albicans (yeast)

Candida glabrata (yeast)

Candida parapsilosis (yeast)

Habitat Environment, mucosa

Environment, mucosa

Environment, mucosa

Survival on dry surfaces

1-120 days 120-150 days 14 days

Spread in HC

Contact, endogenous

Contact, endogenous

Contact, endogenous

HAIs Various Various Various

Specimens Various Various Various

Prevention Clean hands, equipment

Clean hands, equipment

Clean hands, equipment

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Fungi Aspergillus species (mould)

Mucor (mould) Rhizopus (mould)

Habitat Environment, air Environment Environment

Survival on dry surfaces

Conidia and spores are resistant

Conidia and spores are resistant

Conidia and spores are resistant

Spread in HC

Inhalation, (contact)

Inhalation Inhalation

HAIs Various Various Various

Specimens Various Various Various

Prevention Safe water, air, reverse/protective isolation

Safe food,reverse/protective isolation

Safe food,reverse/protective isolation

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Viruses - 1• Smallest infectious agents• Require living cell for reproduction

• bacterial, plant or animal

• Consist of either DNA or RNA and a protein coat• Some have also an outside lipid envelope

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Viruses - 2• Entering the cell,

virus makes the cell synthesise its nucleic acid and proteins• The cell is severely

damaged or destroyed and infectious disease develops

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Virus Adenovirus Coronavirus, including SARS

Coxackie B virus

Cytomegalovirus

Habitat Water, fomites, environment

Humans Humans Humans

Survival on dry surfaces

7 days – 3 months

3 hoursSARS virus: 72-96 hours

>2 weeks 8 hours

Spread in HC

Contact Droplet Faecal-oral; contact

Blood products, tissue and organs

HAIs Eye, respiratory infections

Respiratory infections

Generalised disease of newborn

Various

Specimens Serum sample Serum sample Serum sample Serum sample

Prevention Individual eye drops

Isolation, clean hands, environment

Clean hands, environment

Safe blood products, tissues/ organs for transplantation

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Virus Human immunodeficiency virus

Influenza virus

Norovirus Respiratory syncytial virus

Habitat Humans Humans Humans Humans

Survival on dry surfaces

>7 days 1-2 days 8 hours – 7 days

Up to 6 hours

Spread in HC

Blood, body fluids, tissue, organs for transplant

Droplets, contact

Faecal-oral, contact

Droplets, contact

HAIs Acquired immune deficiency syndrome

Influenza Diarrhoea Acute respiratory infections

Specimens Serum sample Serum sample

Serum sample NP exudate

Prevention Safe blood products and tissues/organs for transplant

Isolation, vaccination

Clean hands, environment, safe food

Isolation, clean hands, environment

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Virus Rotavirus Rubula virus (mumps)

Rubivirus (rubella)

Habitat Humans Humans Humans

Survival on dry surfaces

6-60 days

Spread in HC Faecal-oral, contact

Droplets Droplets

HAIs Diarrhoea Mumps (parotitis)

Rubella (German measles)

Specimens Stool Serum sample Serum sample

Prevention Clean hands, environment

Isolation, vaccination

Isolation, vaccination

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Virus Morbillivirus (measles) Varicella-zoster virus

Habitat Humans Humans

Survival on dry surfacesSpread in HC Droplets Droplets, close contact

HAIs Measles Varicella

Specimens Serum sample Serum sample

Prevention Isolation, vaccination Isolation, vaccination

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Prions• Prions are proteinaceous particles

• Do not contain any nucleic acid

• Connected to several severe neurologic diseases• Highly resistant to usual disinfection and

sterilisation methods• Possibility of iatrogenic transmission

• Through transplantation• Through instruments contaminated with brain tissue,

dura or cerebrospinal fluid of infected person

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Parasites• Include protozoa

• Unicellular microorganisms • Live in nature or in human or animal host • Some of them cause infections

• Multicellular parasites • Worms, that can also cause infections (often called

infestations)

• Cause frequent diseases in humans, especially in warm climates (e.g., malaria, shistosomiasis)

• Not often the cause of HAI

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Parasite Cryptosporidium (protozoa)

Plasmodium species (protozoa)

Trichomonas vaginalis (protozoa)

Enterobius vermicularis (helminth)

Habitat Liver, erythrocytes

Vaginal mucosa Intestinal tract

Survival on dry surfaces

2 hours on dry surface

Several hours in humid environment

Eggs: at least 1 year

Spread in HC

Mosquito-borne; infected blood

Contaminated equipment in gynaecology

Faecal-oral

HAIs Malaria Vaginal infection Enterobiasis

Specimens Blood Vaginal discharge Perianal tape

Prevention Safe blood products

Disinfected/sterilised equipment in gynaecology

Clean environment, clean hands

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Role of microbiology laboratory: Introduction

The diagnosis of infections performed by the laboratory has two important functions

• Clinical • Diagnosis of infection in an individual patient for everyday

management of infections

• Epidemiological • Support for infection prevention and control in searching

for source and route of transmission of HAI

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Minimal requirements for microbiology services - 11. Set up inside the facility

• If not possible, negotiate a contract for diagnostic microbiology with the nearest laboratory

2. Available every day, including Sundays and holidays

• Ideally on a 24-hour basis3. Able to examine blood, cerebrospinal fluid,

urine, stool, wound exudate or swab, respiratory secretions, and perform basic serological tests (HIV, HBV, HCV)

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Minimal Requirements for microbiology services - 24. Identify common bacteria and fungi to species

level 5. Perform susceptibility testing using disc-

diffusion methodology 6. Perform basic phenotyping

• Serotyping• Salmonellae, Shigellae, P. aeruginosa, N. meningitidis

• Biotyping • S. typhi

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Clinical role: Diagnosis of infectionDiagnosis should be rapid and accurate to the species level wherever possible

• Classical bacteriological methods• Direct smear• Culture• Antigen detection

• Sensitivity testing• Antibody detection

• Not very useful in the early stages of infection

• Molecular methods• Rarely used in routine work for the diagnosis of bacterial HAI

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Role in prevention and control of healthcare associated infections • Outbreak investigation• Surveillance of HAIs• Alert microorganisms reports• Designing antibiotic policy

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Outbreak Investigation

• 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

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Additional tests during an outbreak• Sometimes the IP&C Team requires additional

data to clarify endemic or epidemic situations• Microbiological tests may be required

• Blood products• Environmental surfaces• Disinfectants and antiseptics • Air• Water• Hands of personnel• Anterior nares of personnel

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HAI surveillance

• The microbiology laboratory should produce routine reports of bacterial isolates • Allows the IPC& Team to make graphs for specific

pathogens, wards, and groups of patients

• 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

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Alert organism reports

• Identify possible agreed ‘alert’ microorganisms• 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

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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

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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 & sensitivity

• Active surveillance/ awareness• Screening for carriage of resistant bacteria• Molecular detection and typing

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Interpretation of Microbiology 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

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Role in education

• Infection prevention staff• how to interpret microbiological reports/charts

• Other healthcare workers• specimen collection and transport, interpretation of

reports and sensitivity tests

• Students (medical and nursing)• basic microbiology

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Key points - 1

• Microbes are infectious agents not visible to the naked eye• Widespread in nature and some cause human disease

• Diagnosis of infection by the microbiology laboratory has two important functions• Clinical• Epidemiological

• The laboratory should determine the most frequent microbes causing infections, including HAI pathogens

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Key points - 2

• The laboratory should perform basic typing of microorganisms

• The laboratory should produce routine reports for IP&C personnel • To make incidence graphs for specific pathogens,

wards, and groups of patients

• Medical microbiologists interpret microbiological findings for IP&C personnel and act together with clinical and nursing colleagues in prevention of HAI

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References• Diekema DJ, et al. Infection Control Epidemiology and

Microbiology Laboratory. In Manual of Clinical Microbiology, 8th Ed., Murray PR, Editor in Chief, ASM Press, Washington, DC, 2003:129-138

• Peterson LR, et al. Role of clinical microbiology laboratory in the management and control of infectious diseases and the delivery of health care. Clin Infect Dis 2001; 32:605-611

• Gill VJ, et al. The clinician and the Microbiology Laboratory. In: Mandell, Douglas and Bennett’s Principles and Practice of Infectious Diseases, 6th ed., Mandell GL, Bennett JE, Dolin R, Editors, Elsevier, Philadelphia, 2005:203-241

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References• Stratton CW IV, Greene JN. Role of the Microbiology

Laboratory in Hospital Epidemiology and Infection Control. In: Hospital Epidemiology and Infection Control, 3rd Ed., Mayhall CG, Editor, Lippincott, Williams & Wilkins, Philadelphia, 2004:1809-1825

• Poutanen SM, Tompkins LS. Molecular Methods in Nosocomial Epidemiology. In: Prevention and Control of Nosocomial Infections, 4th Ed., Wenzel RP, Editor, Lippincott, Williams & Wilkins, Philadelphia, 2003: 481-499

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Quiz1. Microorganisms that can cause disease in humans

cannot live in the inanimate environment. T/F2. Genetic material in bacteria can be transmitted not

only vertically, but also horizontally. T/F3. For the role of microbiology laboratory in HAI

surveillance, which of the following laboratory characteristics is not necessary:

a. Produce routine periodic reports of isolated microbesb. Make „baseline incidence” graphsc. Have a physician as a microbiologist d. Have a vigorous quality assurance program

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International Federation of Infection Control• IFIC’s mission is to facilitate international networking in

order to improve the prevention and control of healthcare associated infections worldwide. It is an umbrella organisation of societies and associations of healthcare professionals in infection control and related fields across the globe .

• The goal of IFIC is to minimise the risk of infection within healthcare settings through development of a network of infection control organisations for communication, consensus building, education and sharing expertise.

• For more information go to http://theific.org/

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