Role of microbiology laboratory in the field

Role of microbiology laboratory in the field

1. Role of microbiology laboratory

2. O bjectives Describe the basic properties of microorganisms, including their natural habitat and mode of transmission. List the most important "alert" microorganisms causing HAIs. Explain the role of microbiology laboratory in managing patients with infections. Explain the four roles of the microbiology laboratory in the prevention and control of HAIs. August 23, 2013 2

3. Time involved 60 minutes August 23, 2013 3

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

5. 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 August 23, 2013 5

6. 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 August 23, 2013 6

7. 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 August 23, 2013 7

8. Bacteria Acinetobacter baumannii Bordetella pertussis Campylobacter jejuni, C. coli Clostridium difficile Habitat M oist skin, GI tract NP mucosa GI tract GI tract Survival on dry surfaces 3 days – 5 months 3-5 days Up to 6 days S pores – 5 months Spread in HC C ontact 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 August 23, 2013 8

9. Bacteria Clostridium tetani Coagulase negative staphylococci (CNS ) C . diphtheriae Enterococcus species Habitat Environment S kin, 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 August 23, 2013 9

10. 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 G astritis 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 August 23, 2013 10

11. 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 M eningitis Specimens Sputum, blood for serology Blood, CSF Sputum CSF Prevention H yperchlorination of water or heating to at least 55°C Safe food, clean equipment in nurseries Isolation Isolation, vaccination August 23, 2013 11

12. 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 August 23, 2013 12

13. 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 August 23, 2013 13

14. Bacteria S . agalactiae (Group B streptococcus) S . pyogenes (Group A streptococcus) Vibrio cholerae Yersinia enterocolitica Habitat Birth canal O ropharyngeal 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 C lean hands , masks in operating room Safe water and food Safe blood products August 23, 2013 14

15. 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 August 23, 2013 15 * Fungal spores are not resistant to environmental factors like bacterial spores!

16. 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 August 23, 2013 16

17. 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 August 23, 2013 17

18. 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 August 23, 2013 18

19. 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 August 23, 2013 19

20. 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 hours SARS 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 August 23, 2013 20

21. 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, cl ean hands, environment August 23, 2013 21

22. 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 August 23, 2013 22

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

24. 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 August 23, 2013 24

25. 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 August 23, 2013 25

26. 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 August 23, 2013 26

27. 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 August 23, 2013 27

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

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

30. Clinical role: Diagnosis of infection D iagnosis 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 August 23, 2013 30

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

32. 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 August 23, 2013 32

33. 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 D isinfectants and antiseptics Air Water H ands of personnel Anterior nares of personnel August 23, 2013 33

34. 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 August 23, 2013 34

35. 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 August 23, 2013 35

36. 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 August 23, 2013 36

37. Antibiotic stewardship R ole of Clinical Microbiologist/ID specialist Provide l eadership 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 August 23, 2013 37

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

39. 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 August 23, 2013 39

40. 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 August 23, 2013 40

41. 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 August 23, 2013 41

42. 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 August 23, 2013 42

43. 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 August 23, 2013 43

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