Mic lab diag and role in ic

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Mic lab diag and role in ic

  1. 1. ByMaha Fathy3/12/2011
  2. 2. Medical Microbiology is the branch of science that is concerned withthe study of microorganisms which produce disease (bacteria, mycoplasma,chlamydiae, rickettsiae, fungi, viruses and parasites), the response of thehost to infection, and the control of infectious disease. Medical Microbiology Laboratory plays an integral role in thepractice of infection control because it defines one of the major componentsof the disease process, which is the agent. Within microbiology laboratorydifferent techniques are used to evaluate agent-host interactions, to evaluatepotential reservoirs within the facility, and to analyze the relatedness ofmicroorganisms for epidemiologic purposes. Medical Microbiology Laboratory DiagnosticsWhen a patient is being evaluated for infection, it usually requires athorough history and physical examination, microbiological assessment, aswell as other diagnostic tests. Microbiologic assessment includes differentmeasurements that may help to diagnose/ identify the infection or to evaluatethe stage of an infectious disease or process.In general there are two methods that are helpful in diagnosing or staginginfections: Direct and indirect methods (see Appendix).Direct methods are used to demonstrate the presence of the causativemicroorganism or one of its components or products (antigens, toxins,nucleic acids) in clinical specimens.Indirect methods depend on detection of the host response to infection;either humoral immune response (antibody detection) or cell mediatedimmune response (e.g. skin tests).I. Specimen Collection and Transport Specimen collection and transport to the laboratory is an essential part of the microbiologic workup. Improperly selected, collected, or transported specimens can generate misleading data that may result in inappropriate patient management. A. Proper Specimen Collection and Transport It is the microbiologist’s responsibility to provide clinicians with the required instructions for optimum collection techniques and transport information. These instructions should include safety considerations, appropriate anatomic collection site, collection, transportation and labeling instructions in addition to any special instructions for specific patient preparation before collection.Maha Fathy 2 3/12/2011
  3. 3. For optimum collection and transport of different specimens the following should be considered: 1. Appropriateness of specimen for suspected pathogen or disease process, or both 2. Sufficient quantity of specimen 3. Appropriate timing: appropriate specimen for disease stage and ideally, collect specimen in acute or early stage of the illness before antimicrobial therapy is initiated 4. Appropriate collection technique (prevent contamination by endogenous) and appropriate container: In general, all specimens should be collected aseptically and placed in sterile containers. 5. Prompt delivery to laboratory is required to prevent death of suspected pathogen or overgrowth by other organism(s). In case of delayed transport, special preservatives or holding media are used to ensure viability of some fastidious agents 6. Appropriate specimen labeling so that the specimen can be matched with the specimen requisition. Many slips in collection can alter the results including:  Inadequate specimen  Inappropriate specimen  Wrong timing  Wrong container  Introduction of contaminants Delay in transport can lead to:  Death of fastidious organisms due to changes in environmental conditions e.g. temperature, pH and oxygen requirements  Overgrowth of pathogens by fast growing commensals  Variation in bacterial count To avoid:  Culture at bed side: In some cases specimens may be placed directly into culture media (e.g., blood cultures, genital cultures).  Use of transport media, preservatives or holding media  Special handling techniques may be necessary for some specimens such as those for anaerobic culture.Maha Fathy 3 3/12/2011
  4. 4.  Adjusting temperature conditions during storage: some specimens may be refrigerated (e.g., urine, stool, sputum) while others should be maintained at 37oC (e.g. CSF). Golden rules for proper specimen collection and transport 1.Ensure adherence to safety precautions  Use the appropriate personal protective equipment (gloves, laboratory coat, and face wear)  Containers should be leak proof, transported in a sealable bag with a separate compartment for paperwork  Avoid transporting syringes with needles attached 2.Instruct patient to overcome fear in painful procedures and to ensure cooperation and participation 3.Consider number of specimens (e.g., blood cultures and acid-fast bacilli smears) 4.Avoid contamination from endogenous flora by means of appropriate site preparation 5.Select collection site properly, consider if fastidious organisms or organisms with special oxygen requirements are expected and if the site has endogenous flora. (e.g., a cervical swab is an unacceptable specimen for anaerobic culture, whereas an endometrial aspirate is acceptable) 6.Collect adequate volume 7.Consider transport media (to protect environmentally sensitive organisms, avoid use of dry swabs) 8.Label specimen properly (patient name, identification number, source, date, and time of collection) and include provisional diagnosis and other reliable clinical data in the specimen requisition 9.Handle and transport specimen properly  Promptly transport to laboratory, preferably within 2 hours  If processing is delayed, store the specimen properly in the appropriate temperature. urine, stool may be refrigerated; never refrigerate genital, eye, or spinal fluid specimens B. Specimen Requisition It is an order form sent to the laboratory along with the specimen in a separate section from the specimen bag. Sometimes this requisition can be sent electronically if the hospital information system offers computerizes orders. A complete requisition should include the following:  Patient nameMaha Fathy 4 3/12/2011
  5. 5.  Hospital identification number  Age  Gender  Collection date and time  Ordering clinician  Exact nature and source of the specimen  Provisional diagnosis  Current antimicrobial history C. Rejection of Specimens Processing improperly selected, collected, or transported specimens can generate misleading data that may result in inappropriate patient management; ideally the specimen should not be processed and should be recollected; examples include: 1. Prolonged transport without proper preservation 2. Improper or leaking container 3. Duplicate specimens on the same day for same request (except blood) 4. Poor-quality clinical specimens (particularly expectorated sputum) 5. Insufficient quantity or the specimen is dried up. 6. Information on specimen label does not match that on requisition form 7. The specimen was sent in a fixative e.g. formalin (it will kill microorganisms) 8. Specimens of questionable medical value e.g. Foley catheter tip. D. Common Clinical SpecimensTable (1) demonstrates the collection, transport and storage of commonclinical specimens submitted to medical microbiology labMaha Fathy 5 3/12/2011
  6. 6. Table (1): Collection, transport and storage of common clinical specimens Patient Transportation to Storage before Type of specimen Container and Special instructions preparation Lab processingAbscess, wound, Wipe area by In deep lesions: Within 24 hours/ 24 hours/ Roomulcer sterile saline (or Aspirate material from wall with sterile Room Temp. Temp. alcohol 70% if syringe and needle or excise tissue and intact skin) transfer aseptically into sterile container with anaerobic transport. Superficial: A swab (preferably moisten with sterile transport medium) is passed deeply into wound bedBurn Wound Removal of debris Biopsy specimen removed from an area Immediately/ Room Process as soon as with saline suggestive of infection, after Temp. received debridement, down to and including viable bleeding tissue in a sterile container (for quantitative culture)Blood culture Disinfect 2 Blood culture bottles (aerobic and Within two hours/ Incubated at 37oC venipuncture site anaerobic) per set Room Temp. on receipt Adults, obtain 10 to 20 ml per set; infant, 1 to 2 ml per set; 2 to 3 sets withdrawn from separate sites within 24 hrs preferably during febrile episode.(for endocarditis, two sets from two sites over 2 hours)IV catheters Disinfect skin Sterile screw-cap container (for Immediately/ Room Process as soon as before removal semiquatitative and quantitative Temp. received cultures)CSF Disinfect skin Aspirate with sterile lumbar puncture Immediately/ Room up to 6 hours/37oC before aspiration needle and aseptically transfer into Temp. (For viruses keep at sterile screw-cap tubes (3 or 4 tubes) 4 oC up to 3 days)
  7. 7. Body fluids (pleural, Disinfect skin Aspirate with sterile aspiration needle Immediately/ Room Process as soon asperitoneal, synovial before aspiration and aseptically transfer into sterile Temp. received screw-cap containerThroat Ordinary throat swab (preferably Immediately/ Room Process as soon as moistened with transport medium) Temp. (avoid received. dryness). 24 hours/ Room Within 24 hours/ Temp. ( if transport Room Temp.( if medium is used) transport medium is used)Nasopharyngeal Pernasal short flexible swab is Immediately/ Room Process as soon asspecimens introduced through nose to the Temp. (avoid received. nasopharynx dryness). 24 hours/ Room Within 24 hours/ Temp. ( if transport Room Temp.( if medium is used) transport medium is used)Lower respiratory Patient rinse or gargle Collected directly into sterile screw-cap Within two hours/ 24 hours/4oCspecimens: with water before container ( patient should cough deeply to Room Temp. expectoration of Sputum produce lower tract specimen) sputum Induced sputum Endotracheal Sterile screw-cap container Within two hours/ 24 hours/4oC aspirate Room Temp. Bronchoalveolar lavage (BAL) Protected specimen brush (PSB)Maha Fathy 7 3/12/2011
  8. 8. Gastric aspirate In the early morning, Sterile screw-cap container Immediately/ Room Must be neutralized with patient still in (For the detection of Mycobacterium Temp. with sodium bed, before tuberculosis in patient who is unable to bicarbonate within eating, introduce produce sputum) nasogastric tube; 1 hour of collection lavage 50 ml sterile water, sampleMid stream urine Clean area Sterile screw-cap container Immediately/ Room 24 hours/4oC thoroughly with soap Temp. and water and rinse Within 24 hours/4oC thoroughly; holding the labia apart (in female) begin voiding; after several ml have passed, collect sample without stopping flowIndwelling catheter Disinfection Aspirate 5-10 ml urine with sterile Immediately/ Room 24 hours/4oC collection port with syringe and needle and transfer Temp. alcohol 70% aseptically into Sterile screw-cap Within 24 hours/4oC containerFeces Clean leak proof container, use transport Immediately/ Room 72 hours/4oC medium if transport will exceed 1 hour Temp.Maha Fathy 8 3/12/2011
  9. 9. II. Microbiological Diagnostic approaches (See appendix) A. Direct Methods 1. Direct detection of infecting organism by microscopy 2. Cultivation, identification and antimicrobial susceptibility testing of infecting organism 3. Direct detection of specific antigens by immunological methods 4. Direct toxin detection assays 5. Direct detection of nucleic acids of infecting agents by molecular techniques B. Indirect Methods 1. Detection of antibodies produced by the patient in response to an infecting organism ( serodiagnosis) 2. Detection of cell mediated immune responseMicroscopyMicroscopic examination of a Gram stained film made directly from theclinical specimen is the most common procedure conducted to directlyexamine a clinical specimen for the presence of microorganisms (i.e.,bacteria or fungus). Acid-fast stains are very useful in identifyingMycobacterium spp. (AFB, or acid-fast bacillus)Why Microscopic Findings are important? • Usually available in the same day or even within hours. • Give an idea about the quality of the specimen. • Can direct primary antibiotic therapy. • Some clinical syndromes can be diagnosed based on results of microscopic examinationCultivation and Identification The specimen is placed into or onto special media to cultivate the organisms in separated colonies (isolation). Once the microbe grows, identification can be made by colonial morphology, microscopic examination of growing organisms and different identification tests depending on some biological characteristics of microorganisms. Sometimes identification of isolated organisms can be made by immunological or molecular techniques. Isolation and identification is the conventional diagnostic approach and is considered the gold standard for diagnosis although it is time consuming and can be problematic in certain situations.
  10. 10. Examples of the common problems facing isolation:‘No Growth’ • Non cultivable organisms • Intermittent discharge of microorganisms‘Pathogen or Colonizer?’ • Quantitative culture: for detection of significant bacterial growth • Ancillary findings including: Abundance of pus cells and Predominance of one bacterial morphologyAntigen detection Several test methods may be used for antigen detection including agglutination tests, immunofluorescence, and enzyme-linked immunosorbent assay (ELISA). Serum, body fluids, and other clinical specimens may be used for antigen testing. Methods are designed to detect the entire agent (e.g., virus) or part of the agent (e.g., bacterial cell wall structures). These tests may be helpful in early diagnosis when cultures are not yet positive or are not possible. Example: detection of antigens causing bacterial meningitis in CSF (Haemophilusinfluenzae, Streptococcus pneumoniae, Neisseria meningitides)Direct Toxin detection assays Example: Detection of Toxin A and/or B in stool for diagnosis of Clostridium difficile associated disease.Molecular techniques Since it is often difficult and sometimes impossible to grow and identify pathogens in culture, identification methods based on molecular diagnosis are widely used. Nucleic acid –based diagnostic procedures become more widely used because (a) nucleic acids can be isolated from infected tissues; (b) can be measured, (c) nucleic acid sequence is unique for each pathogen; and (d) nucleic acid sequence can be amplified to be analyzed. Polymerase chain reaction (PCR): It is a method for copying and amplifying specific DNA sequences up to one million (106) fold.Maha Fathy 10 3/12/2011
  11. 11. It can be used to find very low quantities of an infectious agent present in a clinical sample by increasing the quantity of a specific nucleotide sequence contained within the organism by a process of directed DNA synthesis.Indirect diagnosis Antibody detection (serodiagnosis) Antibody detection is an indirect method of identifying infection by assessment of the humoral host response (antibody production) to the invading microorganism. Results may be reported qualitatively (positive or negative) or quantitatively (titers). A positive antibody titer does not necessarily indicate active infection but may represent a previous infection. For diagnosis of active infection we depend upon the detection of rising titers of IgG antibodies in two consecutive serum samples or the presence of high titers of IgM antibodies. Detection of cell mediated immune response Sometimes we depend upon the detection of cell mediated immune response for diagnosis of infections e.g. positive tuberculin test or detection of in vitro interferon gamma production for diagnosis of Mycobacterium tuberculosis infection.III. Antimicrobial Susceptibility Testing  AST is done to assist in the selection of appropriate antimicrobial therapy.  It should be done by a standard technique (e.g CLSI recommendations). The standardization should include the methodology, selection of tested antimicrobials, interpretation of results and reporting format.  AST has also been used as a simple method to differentiate between 2 isolates of the same speciesMany methods can be used as:  Disc diffusion Method  MIC assay by tube dilution method  E-testChoose of different antibiotics for testing depends on:  Identification of the isolated organismMaha Fathy 11 3/12/2011
  12. 12.  Type of infection whether Community acquired or hospital acquired  Infection site  Age of the patient  Other conditions of the patients The Testing List: should include agents of proven efficacy which have acceptable in vitro test performance taking in consideration minimizing emergence of resistanceReporting:  Reported agents must be pre tested unless reporting based on testing another agent provides a more accurate result  Agents of comparable results need not be duplicated in testing; however the report should include footnotes indicating the agents that usually show comparable interpretive resultsVerification of patient results:  The antimicrobial susceptibility results consistent with the identification.  The results follow established activity rules, e.g. 3rd generation cephalosporins are more active than 1st or 2nd generation cephalosporins against enterobacteriaceae.  The isolate is susceptible to those agents for which resistance has not been documented.Detection of Multi-drug resistant organisms (MDROs) Identification of MDR organisms: depends on either phenotypic or genotypic characteristics: Phenotypic Characteristics: e.g.  Identification of MRSA by detecting resistance to Oxacilline or Cefoxitin disc.  Identification of Penicillin resistant pneumococci and VRE using MIC assays.  Testing Gram-negative bacilli for the production of new β lactamases as ESβLs and Carbapenenemase Genotypic Characteristics: e.g.  Detection of mecA gene that mediate oxacillin resistance in MRSA.  Detection of van (A&B) genes that mediate vancomycin resistance in VRE.Maha Fathy 12 3/12/2011
  13. 13. IV. Typing (Determining organism relatedness) A variety of methods are used to determine the epidemiological relatedness between microorganisms including phenotyping and genotyping methods. 1. Phenotyping methods These methods can differentiate between different strains. They may be based on antigenic structure (serotyping), biologic characteristics (biotyping), susceptibility to antimicrobial agents (antibiogram or resistotyping), bacteriocin (colicin typing) or bacteriophages (phage typing). Some of these methods as serotyping, biotyping and antimicrobial resistance profile are easy to be done and can determine different strains rather than confirming strain relatedness. 2. Genotyping methods: A number of molecular methods have been developed for typing: e.g.  Pulsed- Field gel electrophoresis (PFGE)  Restriction fragment length polymorphism (RFLP)  PCR - based typing methods These genotypic methods have very high typability and discriminatory power and can confirm difference or relatedness between two isolates of the same species. However they require expensive equipment and trained staff.V. Microbiologic Workup, Communication and Reporting The microbiologist should decide what is clinically relevant regarding the specimen workup. He should judge what organisms should look for and report. It is essential to recognize what organisms constitute normal flora and what constitutes a potential pathogen. Indiscriminate reporting of normal flora can lead to unnecessary use of antibiotics and emergence of resistant organisms. In final analysis the results should be compared with the suspected diagnosis. The clinician should supply the microbiologist with all reliable information (e.g. recent travel history, animal exposure, radiographic findings……) so that the microbiologist can use this information to plan the appropriate workup and interpret the analysis results.Maha Fathy 13 3/12/2011
  14. 14. The microbiologist professional obligation necessitates communicating their findings to health care professionals responsible for treating the patient. The microbiologists should avoid confusion and misunderstanding should not use abbreviations. They should provide final reports with clear cut conclusions. Appropriate interpretative findings can be included in the written final report along with the specific result e.g. “suggest contamination at collection”. Certain critical results must be communicated to the clinicians immediately. Each microbiology lab should prepare a list of these critical results in consultation with the medical staff. Common critical results include:  Positive CSF Gram stain or culture  Positive blood culture  Gram stain suggestive of gas gangrene  Positive acid fast stain  Positive blood film for malaria  Detection of a significant pathogen e.g. MDRO, legionella, brucella…Maha Fathy 14 3/12/2011
  15. 15. Appendix Flow Chart for Diagnosis of Infectious Diseases Direct Diagnosis Indirect Diagnosis Patient (suspected infectious disease) Clinical specimen: (e.g. Detection of humoral Detection for Blood, CSF, CSF, feces, immune response i.e cell mediated urine, ….. ) antibody detection immune tissue biopsy, ,... tests response (e.g. (Serological tests e.g. skin tests) ELISA, IF) Direct microscopic examination Immunological direct Molecular direct Inoculation into suitable diagnosis diagnosis culture media (Direct Ag or toxin (Direct nucleic acid detection): detection with or IF, ELISA, particle without amplification): agglutination Nucleic acid Hybridization & Pure culture isolation PCRConventional Identification: Immunological Molecular microscopy, biochemical Identification: Identification: Antibiotic reactions, animal agglutination, hybridization, susceptibility testing inoculation immunofluorescence, PCR …… Conventional Microbiological methods Indirect diagnosis Immunological methods Direct diagnosis Molecular methods Maha Fathy 15 3/12/2011
  16. 16. Role of Microbiology Lab in Infection ControlGoals of Microbiology Laboratory in IC: 1. Microbiological diagnosis of healthcare associated infections. 2. Determining antibiotic susceptibility pattern of isolated strains and detection of MDROs 3. To assist in epidemiological investigations (surveillance): both at endemic level and for outbreak investigations. 4. It helps in situations requiring environmental samplingMicrobiological diagnosis of HCAIs The diagnosis of HCAIs has 2 important functions. The first is clinical- for optimally managing the infected patients. The second is epidemiological – knowledge of the infective agent can lead to finding its source and route of transmission. This allows IPC staff to stop spreading of infection.Microbiological diagnosis of common HCAIs:Urinary tract infections:  Quantitative urine culture is commonly used to differentiate significant bacteriuria from false positive cultures related to contamination during specimen collection.  The value of ≥105 CFU of bacteria /ml of urine in non catheterized patients was chosen because of its high specificity for diagnosis of true infection, even in asymptomatic individuals. In catheterized patients the value of 102-103 is considered significant  Simple and rapid preliminary screening tests can be used to exclude normal samples to avoid such labor work of their further full examination.  Commercially available dipstick tests can be used to predict bacteriuria based on nitrate reduction or peroxidase production by variety of bacteria or by esterase production by leukocytes.Healthcare associated pneumonia  Diagnosis of HAP remains a major challenge.  HAP is suspected based on some clinical criteria  Usually a positive quantitative culture is required to confirm the diagnosis.  It is important to obtain all cultures prior to antibiotic administration.Maha Fathy 16 3/12/2011
  17. 17. In patients with suspected HAP without mechanical ventilation: It is recommended to obtain sputum for Gram stain and culture plus two blood cultures at least 15 minutes apart. A sputum specimen is considered representative of deep respiratory secretions when there is ≥ 25 neutrophils and less than 10 epithelial cells on Gram stained microscopy examination. In mechanically ventilated patients: Endo tracheal aspirate for quantitative culture plus two blood cultures are recommended. The significant threshold for tracheal aspirate quantitative culture is considered 105- 106 cfu/ml. In patients undergoing fiberoptic bronchoscopy, cultures of BAL are considered significant with growth of at least 104 cfu/ml. For specimens obtained via protected brush the significant threshold is considered 103 cfu/ml.Intravascular device infections: The challenge of identifying the source of sepsis, particularly in critically ill patients, makes the clinician point strongly toward an IVD as the source of a septic episode.  If purulence is seen in combination with signs and symptoms of sepsis, it is highly likely the patient has IVDR BSI.  The presence of inflammation or purulence at the catheter insertion site is usually uncommon in patients with IVDR BSI.  Definitions for IVDR colonization, local infection, BSI are based upon microbiologic confirmation. IVD colonization: It is defined by a positive culture (semiquantitative or quantitative) of the implanted portion or portions of the IVD together with absence of signs of local or systemic infection. Local IVD infection: It is defined by a positive culture (semiquantitative or quantitative) of the removed IVD or culture of pus or thrombus from the cannulated vessel together with clinical evidence of infection of the insertion site.Maha Fathy 17 3/12/2011
  18. 18. IVD Related BSI: If the IVD is removed:  positive culture (semiquantitative or quantitative) of the removed IVD or a positive culture of the catheter hub or infusate or culture of pus or thrombus from the cannulated vessel together with one or more positive blood cultures, ideally percutaneously drawn, concordant for the same species. If the IVD is retained:  If quantitative blood cultures are available, cultures drawn both from the IVD and a peripheral vein (or another IVD) are both positive and show a marked step-up in quantitative positivity (≥five-fold) in the IVD-drawn culture.  If automated monitoring of incubating blood cultures is available, blood cultures drawn concomitantly from the IVD and a peripheral vein show both are positive, but the IVD-drawn blood culture turns positive more than 2 hours before the peripherally-drawn cultureSurgical site infections: Identification of SSI is based in most situations on clinical criteria as many SSIs are clear such as when there is purulent drainage and fever or other sign of infection. Yet, in some instances, infections are not quite so obvious and need microbiological workup for identifying infectious agents and its antibiotic susceptibility pattern.II. Antibiotic Susceptibility testing and detection of MDROs In addition to the clinical role of determining antibiotic susceptibility testing, it can also help in planning antibiotic policy and designing the local antibiotic formulary. Resistance patterns should be reported periodically. These reports should be available for clinicians for the design of empirical therapy.III. Surveillance of HCAIs and outbreak investigations The microbiology laboratory plays a pivotal role in both endemic and epidemic epidemiology. It should produce routine reports of bacterial isolates to help IPC staff in surveillance studies as allowing them to make incidence graphs for specific pathogens, hospital units or settings. These graphs enable to identify any new isolates and discover the beginning of an outbreak. Also Microbiology lab can assist in the identification of an outbreak by confirming organism identities and retrieve and reviewMaha Fathy 18 3/12/2011
  19. 19. archival data to determine if an outbreak situation actually exists. Sometimes the IPC staff requires additional tests to clarify endemic or epidemic situations e.g environmental sampling or detection of colonization of patients or HCWs.IV. Microbiologic Environmental Sampling Key concepts:  Microbiologic environmental testing is not generally recommended.  Environmental culturing can be costly and may require special laboratory procedures.  In most cases no standards for comparison exist. Rationale for routine environmental monitoring: In limited situations “routine” environmental sampling may be indicated including:  Biologic monitoring of sterilization processes.  Monthly cultures of water and dialysate in hemodialysis units. Microbiologic air sampling:  There are no recommendations regarding routine microbiologic air sampling.  It can be indicated where there is documented or high potential for healthcare-acquired aspergillosis.  Settling plates should NOT be used.  Volumetric air sampling devices, sampling a constant rate of airflow, can be used for testing. Special Environmental Testing: Environmental testing may be indicated when epidemiological investigation suggests that a source or reservoir of microorganisms may exist. Testing may involve:  personnel,  medical devices  air  water, food  surfaces The type of sampling:  Swab-rinse sampling: uses a template to swab a standardized area.  Rinse-sampling involves direct immersion of an item if it can be totally exposed to a rinse solution.Maha Fathy 19 3/12/2011
  20. 20.  Impression plating is a method where the culture media is placed directly onto the surface being tested.  Liquid or water testing: more difficult than solid surfaces and requires a quantitative culture, agar spread method, membrane filter methodMinimal requirements for microbiology Lab in control ofHCAIs (IIFIC Basic Concepts of Infection Control, 2nd edition- revised 2011) 1. Each health care facility should have a microbiology lab or has access to a nearby one. 2. Should be available every day including holidays, ideally on a 24-hur basis, at least for Gram stain. 3. Should be able to examine most common clinical samples particularly those of utmost of clinical value and those of life threatening infections (blood, CSF, urine, stool, wound exudates, respiratory specimens) and perform serological tests for BBPs. (HIV, HBV, HCV). 4. Should be able to identify common microbial agents causing HCAIs to species level in addition to other agents causing some severe community acquired infections. 5. Should be able to perform antibiotic susceptibility testing by standardized disc diffusion method. 6. Should be able to do basic typing methods (biotyping, serotypin). 7. Should have quality assurance procedures (both internal and external quality control) (national or international). 8. Should have a medical microbiologist with good communication skills with clinical and IPC staff. 9. May have the ability to perform simpler genotyping methods or have access to genotypic methods at central or regional labs for epidemiologic investigations.References: 1. Forbes BA, Sahm DF and Weissfeld AS, Bailey & Scott’s Diagnostic Microbiology, 12th edition, 2007, Mosby Elsevier. 2. Kalenic S, The Role of Microbiology Laboratory, IFIC Basic Concepts of Infection Control, 2nd edition-revised 2011. 3. Keroack MA and Rosen-Kotilainen H, Microbiology/Laboratory Diagnostics, APIC Text of Infection Control 1999, Washington DC. 4. Ritter J, Clinical Microbiology, APIC Text of Infection Control 2005, Washington DC. 5. Ritter J, Laboratory diagnostics, APIC Text of Infection Control 2005, Washington DC.Maha Fathy 20 3/12/2011

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