Role of microbiology laboratory in IPC 1 Describe

Role of microbiology laboratory in IP&C

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. August 23, 2013 Objectives 2

• 60 minutes August 23, 2013 Time involved 3

• Microorganisms are agents of infectious diseases • They are ubiquitous in nature and in/on human body • Most microorganisms harmless for humans August 23, 2013 Basic microbiology • Some can cause disease • Microorganisms are divided into • • • Bacteria Fungi Viruses Prions Parasites 4

• 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 August 23, 2013 Pathogenesis of infection • 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 5

• Spread to a new host from another human, animal or environment • Transmission direct or indirect • Pathways of transmission could be August 23, 2013 Microorganism Transmission • Contact • hands • surgical instruments • • • Contaminated surfaces or items (indirect contact) Air Water Food Live vectors, e. g. , mosquitos 6

• Smallest microorganisms with all functions of life • Multiply by simple division • Form visible „colonies” on a solid surface August 23, 2013 Bacteria • Genetic material transferred vertically and horizontally between different bacteria • Some can form spores • The most resistant form of life 7

Acinetobacter Bordetella baumannii pertussis Campylobacter Clostridium jejuni, C. coli difficile Habitat Moist skin, GI tract NP mucosa 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 Prevention Clean environment, instruments, hands Isolation Safe food and water, clean hands Clean environment, , hands, use of antibiotics August 23, 2013 Bacteria 8

Clostridium tetani Coagulase negative staphylococci (CNS) C. diphtheriae Enterococcus species Habitat Environment Skin, mucous membranes NP GI tract, GU tract 7 days – 6 months 5 days – 4 months Survival on dry surfaces Spread in HC Entering Contact umbilical cord Droplet, contact Contact, endogenous HAIs Tetanus Various Diphtheria UTI, sepsis Various NP swab Urine, blood Isolation, vaccination Clean environment, hands, use of cephalosporins Specimens Prevention Sterilisation of Clean instruments environment, instruments, hands August 23, 2013 Bacteria 9

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 Prevention Clean environment, equipment, hands Clean hands, use of cephalosporins Properly disinfected GI endoscopes Clean hands, use of cephalosporins August 23, 2013 Bacteria 10

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 Airborne food/equipment ; perinatal Droplets HAIs Legionnaire’s disease Meningitis, bacteremia Tuberculosis Meningitis Specimens Sputum, blood for serology Blood, CSF Sputum CSF Prevention Hyperchlorinati on of water or heating to at least 55°C Safe food, clean equipment in nurseries Isolation, vaccination August 23, 2013 Bacteria 11

Proteus species Pseudomonas aeruginosa Salmonella species Salmonella typhi Habitat GI tract, humid areas 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 HAIs UTI, sepsis Various Diarrhoea, sepsis Typhoid fever Specimens Urine, blood Various Stool, blood Prevention Clean environment, equipment, hands Clean, dry Safe food, environment, water, clean disinfected/sterili hands sed equipment; clean hands, use of antibiotics Safe food, water, clean hands August 23, 2013 Bacteria 12

Salmonella typhimurium Serratia marcescens Shigella species S. aureus Habitat GI tract, humid areas GI tract Skin, mucous membranes Survival on dry surfaces 10 months – 4. 2 3 days – 2 years 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 August 23, 2013 Bacteria 13

S. agalactiae (Group B streptococcus) S. pyogenes (Group A streptococcus) Vibrio cholerae Yersinia enterocolitica Habitat Birth canal Oropharyngeal mucosa 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 Safe blood food products August 23, 2013 Bacteria 14

• Unicellular (yeasts) or multicellular (moulds) • Reproduce asexually (conidia) and sexually (spores*) • Ubiquitous in nature August 23, 2013 Fungi • some are parts of human normal flora • Most opportunistic pathogens • Cause severe infections in immunocompromised host * Fungal spores are not resistant to environmental factors like bacterial spores! 15

Candida albicans (yeast) glabrata (yeast) Candida parapsilosis (yeast) Habitat Environment, mucosa Survival on dry surfaces 1 -120 days 120 -150 days 14 days Spread in HC Contact, endogenous HAIs Various Specimens Various Prevention Clean hands, equipment August 23, 2013 Fungi 16

Aspergillus species (mould) Mucor (mould) Rhizopus (mould) Habitat Environment, air Environment Survival on Conidia and spores dry are resistant surfaces Conidia and spores are resistant Spread in HC Inhalation, (contact) Inhalation HAIs Various Specimens Various Safe food, reverse/protective isolation Prevention Safe water, air, reverse/protective isolation August 23, 2013 Fungi 17

• Smallest infectious agents • Require living cell for reproduction • bacterial, plant or animal • Consist of either DNA or RNA and a protein coat August 23, 2013 Viruses - 1 • Some have also an outside lipid envelope 18

• Entering the cell, virus makes the cell synthesise its nucleic acid and proteins August 23, 2013 Viruses - 2 • The cell is severely damaged or destroyed and infectious disease develops 19

Adenovirus Coronavirus, including SARS Coxackie B virus Cytomegalovirus Habitat Water, fomites, environment Humans Survival on dry surfaces 7 days – 3 months 3 hours >2 weeks SARS virus: 7296 hours 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 Prevention Individual eye drops Isolation, clean Clean hands, environment Safe blood products, tissues/ organs for transplantation August 23, 2013 Virus 20

Human immunodeficiency virus Influenza virus Norovirus Respiratory syncytial virus Habitat 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 NP exudate Prevention Safe blood products and tissues/organs for transplant Isolation, vaccination Clean hands, environment, safe food Isolation, clean hands, environment August 23, 2013 Virus 21

Rotavirus Rubula virus (mumps) Rubivirus (rubella) Habitat Humans Survival on dry 6 -60 days surfaces Spread in HC Faecal-oral, contact Droplets HAIs Diarrhoea Mumps (parotitis) Rubella (German measles) Specimens Stool Serum sample Prevention Clean hands, environment Isolation, vaccination August 23, 2013 Virus 22

Morbillivirus (measles) Varicella-zoster virus Habitat Humans Spread in HC Droplets, close contact HAIs Measles Varicella Specimens Serum sample Prevention Isolation, vaccination Survival on dry surfaces August 23, 2013 Virus 23

• 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 August 23, 2013 Prions • Through transplantation • Through instruments contaminated with brain tissue, dura or cerebrospinal fluid of infected person 24

• Include protozoa • Unicellular microorganisms • Live in nature or in human or animal host • Some of them cause infections August 23, 2013 Parasites • 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 25

Cryptosporidium (protozoa) Habitat Survival on dry surfaces Plasmodium Trichomonas species vaginalis (protozoa) Enterobius vermicularis (helminth) Liver, Vaginal mucosa erythrocytes Intestinal tract Several hours in humid environment Eggs: at least 1 year 2 hours on dry surface Spread in HC Mosquitoborne; 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 August 23, 2013 Parasite 26

The diagnosis of infections performed by the laboratory has two important functions • Clinical August 23, 2013 Role of microbiology laboratory: Introduction • 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 27

1. Set up inside the facility • If not possible, negotiate a contract for diagnostic microbiology with the nearest laboratory August 23, 2013 Minimal requirements for microbiology services - 1 2. Available every day, including Sundays and holidays • Ideally on a 24 -hour basis 3. Able to examine blood, cerebrospinal fluid, urine, stool, wound exudate or swab, respiratory secretions, and perform basic serological tests (HIV, HBV, HCV) 28

4. Identify common bacteria and fungi to species level 5. Perform susceptibility testing using discdiffusion methodology 6. Perform basic phenotyping Serotyping • • • August 23, 2013 Minimal Requirements for microbiology services - 2 Salmonellae, Shigellae, P. aeruginosa, N. meningitidis Biotyping • S. typhi 29

Diagnosis should be rapid and accurate to the species level wherever possible • Classical bacteriological methods August 23, 2013 Clinical role: Diagnosis of infection • 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 30

• Outbreak investigation • Surveillance of HAIs • Alert microorganisms reports • Designing antibiotic policy August 23, 2013 Role in prevention and control of healthcare associated infections 31

• 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 August 23, 2013 Outbreak Investigation 32

• 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 August 23, 2013 Additional tests during an outbreak 33

• 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 August 23, 2013 HAI surveillance • 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 34

• 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 August 23, 2013 Alert organism reports 35

• Regular reporting of changing resistance patterns – Newsletters – Specialty specific data August 23, 2013 Antibiotic policy • Restricted antibiotic reporting • Routinely only first line antibiotics • Reserve antibiotics only if pathogen is resistant to first line antibiotics 36

Role of Clinical Microbiologist/ID specialist • Provide leadership to antimicrobial team • Antibiotic ward rounds • Interpretation of patient specific data to optimise treatment August 23, 2013 Antibiotic stewardship • culture & sensitivity • Active surveillance/ awareness • Screening for carriage of resistant bacteria • Molecular detection and typing 37

• Microbiologists interpret microbiological data for IP&C staff • Results of isolation, identification, susceptibility tests, typing August 23, 2013 Interpretation of Microbiology Data • Ideally should be medical doctor specialistt • If this is not possible, then a properly educated scientist is required 38

• Infection prevention staff • how to interpret microbiological reports/charts • Other healthcare workers August 23, 2013 Role in education • specimen collection and transport, interpretation of reports and sensitivity tests • Students (medical and nursing) • basic microbiology 39

• 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 August 23, 2013 Key points - 1 • Clinical • Epidemiological • The laboratory should determine the most frequent microbes causing infections, including HAI pathogens 40

• The laboratory should perform basic typing of microorganisms • The laboratory should produce routine reports for IP&C personnel August 23, 2013 Key points - 2 • 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 41

• • • Diekema DJ, et al. Infection Control Epidemiology and Microbiology Laboratory. In Manual of Clinical Microbiology, 8 th 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, 6 th ed. , Mandell GL, Bennett JE, Dolin R, Editors, Elsevier, Philadelphia, 2005: 203 -241 August 23, 2013 References 42

• Stratton CW IV, Greene JN. Role of the Microbiology Laboratory in Hospital Epidemiology and Infection Control. In: Hospital Epidemiology and Infection Control, 3 rd 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, 4 th Ed. , Wenzel RP, Editor, Lippincott, Williams & Wilkins, Philadelphia, 2003: 481499 August 23, 2013 References 43

1. Microorganisms that can cause disease in humans cannot live in the inanimate environment. T/F 2. Genetic material in bacteria can be transmitted not only vertically, but also horizontally. T/F 3. For the role of microbiology laboratory in HAI surveillance, which of the following laboratory characteristics is not necessary: a. b. c. d. August 23, 2013 Quiz Produce routine periodic reports of isolated microbes Make „baseline incidence” graphs Have a physician as a microbiologist Have a vigorous quality assurance program 44

• 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/ December 1, 2013 International Federation of Infection Control 45