Manual of Clinical Microbiology for Infection Control in Health Services Commemorative Issue for the IX Brazilian Congress on Infection

Control and Hospi tal Epidemiology Salvador, August 30 to September 3, 2004 - Preliminary Version Publisher National Agency for Sanitary Vigilance SEPN 515, Edificio Omega. Bloco B, Brasília (DF), CEP 70770-502 Internet: www.anvisa.gov.br General Management of Technology and Health Services Management Research and Prevention of Infectio ns and Adverse Events Reproduction total of this work, since the source said. 1. ed. 2004. Circulation: 200 copies on CD New edition with changes in content and title, based on the Manual Basic Procedu res in Clinical Microbiology published in 2000. 1. Infection - Control. 2. Infection in Health Services 3. Clinical Microbiology . 4. Health Surveillance of Health Services 5. Microbial resistance. I. Brazil. ANVISA Ministry of Health Project Coordination Adelia Aparecida Marçal dos Santos - Management Investigation and Prevention of Infections and Events / ANVISA / MS Author Carlos Emilio Levy - Microbiology Lab - Centro Infantil Boldrini / Campinas SP Collaborators Angela von Nowakonski - Clinical Microbiology Service, Hospital das Clinicas - U NICAMP / Campinas SP Caio Marcio Figueiredo Mendes - University of São Paulo, La boratório Fleury / São Paulo SP Carlos Emilio Levy - Microbiology Lab - Centro I nfantil Boldrini / Campinas SP Carmen Oplustil - Laboratorio Fleury / São Paulo SP Cássia Maria Zoccoli - Pharmaceutical Biochemistry Cláudia Maria Leite Maffei - Faculty of Medicine of Ribeirao Preto, USP / Ribeirão Preto SP Elza Masae Mam izuka - Faculty of Pharmaceutical Sciences of USP, São Paulo SP Emerson danguy C avassini - Microbiology Lab , Hospital of the EU / Londrina PR Flávia Rossi - Me dical Microbiologist Clinical Igor Mimica - Faculty of Medical Sciences of Santa Casa / São Paulo SP Helena Petridis - Technical Advisor ANVISA Mimica Lycia Mar a Jenne - Faculty of Medical Sciences of Santa Casa / San Paulo SP Marcia de Sou za Carvalho Melhem - Instituto Adolfo Lutz-São Paulo SP Maria Carmen Lopes Gonça lves - Laboratory of Microbiology, Centro Infantil Boldrini / Campinas SP Marine s Dalla Valle Martino - Hospital Israelita Albert Einstein-São Paulo SP Nilton L incopan - Post-Graduate Faculty of Pharmaceutical Sciences - USP Rosangela Apare cida Mendes Silva - Microbiology Laboratory, Centro Infantil Boldrini / Campinas SP Reviewers Claude Andre Solari - Brazilian Society of Microbiology / São Paulo SP Helena Pe tridis - Technical Advisor ANVISA José Carlos Serufo - Brazilian Society of Trop ical Medicine / Faculty of Medicine of Lauro Santos Filho - Department of Pharma ceutical Sciences UFPB / Joao Pessoa PB Maria Rita Elmore - Laboratory of Microb iology, Syrian Lebanese Hospital / São Paulo SP Pedro Bertollini - Retired Profe ssor, School of Dentistry of Piracicaba / USP Silvia Figueiredo Costa - Clinical Hospital of Medical College, USP GENERAL CONTENT Module I 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. Major Infectious Syndromes

Urinary Tract Infections Infections of Bones and Joints Infections of Skin and S ubcutaneous Tissue Infections Intestinal Infections Abdominal Infections Central Nervous System Infections Systemic infections Genital Tract Infections Upper Re spiratory Tract Infection Lower Respiratory References Module V 1. Detection and identification of bacteria of medical importance Staphylococci, streptococci, enterococci and other Gram-positive second. Neisser ia 3. Enterobacteria 4. non-fermenting rods 5. 6 spiral or curved rods. Gram pos itive 7. Fastidious 8. Anaerobic 9. Interpretation of results and reports 10. Re ferences Module II 1. 2. 3. 4. 5. 6. 7. Safety and Quality Control Laboratory of Clinical Microbiology Technical regulation requirements for clinical laboratories for basic microbiolo gy laboratory Classification of laboratories according to level of biosafety lab oratories NB-1, NB-2 and NB-3 precautions regarding contamination in the laborat ory quality control References Module VI 1. 2. 3. 4. 5. 6. 7. Detection and identification of strains of medical importance Introduction Collection of samples Processing of samples for culture isolation o f mycobacteria identification of different species of mycobacteria Attachments R eferences Module III Laboratory Procedures: Request for Examination of Microbiological Analysis 1. 2. 3. 4. 5. 6. 7.€Request microbiological collection, transportation and stor age of sample staining and microscopy seeding in culture media Identification an d Inventory Maintenance Culture Bibliography Module VII 1. 2. 3. 4. 5. 6. Detection and identification of medically important fungi Introduction Collection and transport of samples Sample Identification Process D escription of the main fungal mycosis References Module IV 1. 2. 3. 4. 5. 6. 7. 8. Description of Culture Media Employees in Microbiological Tests Introduction Culture media for transportation and storage media for growth and i solation media for commercial identification tests Formulas and products for pro of of identification means for identifying disks for antimicrobial susceptibilit y testing References INTRODUCTION CLINICAL MICROBIOLOGY LABORATORY The goal of the microbiology laboratory is not just point the responsibility for a specific infectious state, but rather indicate, by monitoring microbial popul ations, the profile of the microorganisms that are interacting with humans. With this information, the health care team is able to determine which microorganism s can be responsible for the patient's condition and thus, suggest a more approp

riate treatment. However, to achieve these goals, microbiology laboratories shou ld have structure that can provide information on the best biological sample, to recognize the normal flora, to recognize the contaminants, to identify microorg anisms which treatment benefits the patient, to identify microorganisms with epi demiological purposes, results quick in emergency cases, rationalize the use of antimicrobials, perform rapid transportation of samples and reporting results an d maintaining a continuing medical education in relation to aspects of hospital infection. The first edition of the Handbook of Basic Procedures in Clinical Microbiology f or Infection Control was proposed to standardize the basic microbiological techn iques considered routine and could give support to the activities of the Commiss ions for Hospital Infection Control. If, on the one hand, virtue was its simplic ity and objectivity in the development of themes, their limitations and the rapi d evolution of knowledge in this area soon claimed his update. We are now faced with the chance to redeem some flaws that first edition, seeking to broaden and deepen themes considered essential, with a select and prestigious editorial boar d and staff. Our expectation is that microbiology laboratories, from the bases o ffered by this Manual, can assimilate and achieve new levels of complexity labor atory, meeting the demands and characteristics of each hospital unit. We had no claim to reach the content and depth of text-books of microbiology traditionally consulted and which will also serve as a reference, but rather to serve as a ma nual bench honored techniques, basic procedures standardized and updated informa tion useful for the hospital . This revised and expanded edition was scheduled i n 10 modules covering the following topics: Module I Module II Module III Module IV Module V Module VI Major infectious synd romes Safety and quality control laboratory in the clinical laboratory procedure s: examination of the request for description of microbiological culture media u sed in microbiological detection and identification of medical bacteria detectio n and identification of medically important mycobacteria Module Module Module VII VIII IX X Module Detection and identification of medically important fungi detection and identifi cation of viruses of medical importance (in production) The main methods of dete cting resistance in the Clinical Laboratory (in production) Laboratory of Microb iology and its interaction with the Committee on Infection Control (in productio n ) We hope to meet the vast majority of microbiologists that outlying do not have a ccess to current information in the field of microbiology and, better trained, c an live up to expectations of Committees of the Hospital Infection Control, prov iding a technical update and more efficient. INTRODUCTION INFECTION HOSPITAL A major concern in health care is the high incidence of nosocomial infections or nosocomial, ie, infection acquired in hospital settings during hospitalization or after discharge the patient, when he was hospitalized and underwent medical p rocedures.€Hospital infection affects the whole world and represents one of the causes of death in hospitalized patients. In Brazil, the Ministry of Health, the average rate of hospital infection is about 15%, while in the U.S. and Europe i s 10%. We should remember, however, that the rate of nosocomial infection varies significantly, as it is directly related to the level of care and complexity of each hospital. Different microorganisms such as bacteria, fungi, and viruses ca using hospital infections. The group of pathogens, however, that stands out is t he bacteria that constitute the human flora and usually do not carry a risk to h ealthy individuals because of their low virulence but can cause infection in ind ividuals with compromised clinical status - so called bacteria opportunists. The second group of medical importance in nosocomial infections are the fungi, Cand ida albicans and Aspergillus pathogens more frequently. Fungi are responsible fo

r about 8% of nosocomial infections. Among the viruses, the hepatitis B and C en teroviruses and viruses associated with nosocomial pneumonia are commonly report ed. The viruses represent about 5% of infections. Usually the sites of nosocomia l infection are most frequently affected the urinary tract, surgical wounds and respiratory tract. The pathogens that lead the ranking of hospital infections ar e described in the table below. Most common agents of nosocomial infections Gram negative pathogen Escherichia coli Proteus Klebsiella Pseudomonas sp sp sp Serratia Enterobacter sp Gram positive Staphylococcus aureus Staphylococcus Stre ptococcus sp epidermitis Fungi Candida albicans other urinary tract, blood, urin ary tract, blood, respiratory tract, urinary tract, respiratory tract, surgical wounds Skin, surgical wounds, blood, skin, surgical wounds, blood, urinary tract , surgical wounds, blood, urinary tract, respiratory tract, urinary tract burns, respiratory tract, surgical wounds urinary tract, surgical wounds urinary tract , respiratory tract, surgical wounds urinary tract, respiratory tract , surgical wounds common sites of isolation of the pathogen The hospital environment is inevitably a large reservoir of virulent pathogens a nd opportunistic, so that nosocomial infections can be acquired not only by pati ents who are most susceptible, but also, although less frequently, for visitors and employees of the hospital. The pathogens implicated in nosocomial infections are transmitted to the individual both endogenous pathway, ie the patient's own flora as by exogenously. The latter includes vehicles such as hands, salivary s ecretion, body fluids, air and contaminated materials, such as equipment and ins truments used in medical procedures. Many of these procedures are invasive, ie, penetrate the protective barriers of the human body in order to increase the ris k of infection (see Table) The main factors influencing the acquisition of an in fection are immune status age (newborns and elderly are more vuneráveis) overuse of antibiotics medical procedures, particularly invasive ones immunosupressão f ailures in infection control procedures Examples of micro flora normal human Skin Propionibacterium Corynebacterium Staphylococcus Micrococcus Streptococcus Malassezia Pityrosporum Respiratory Tract Streptococcus Staphylococcus Corynebac terium Haemophilus Neisseria Branhamella Digestive Tract Bacteroides Lactobacill us Enterococcus Escherichia coli Proteus Klebsiella Enterobacter Citrobacter Bif idobacterium Listened Staphylococcus Corynebacterium Fusobacterium spirochetes E yes Staphylococcus Streptococcus Neisseria Oral cavity Lactobacillus Streptococc us Neisseria Actinomyces Fusobacterium Treponema Urogenital Tract Streptococcus Bacteroides Bacteroides Mycobacterium Neisseria Enterobacter Clostridium Lactoba cillus Candida Trichomonas Common medical procedures associated with nosocomial infections Urinary catheterization procedure Surgery Therapy Intravenous Intubation, Respir atory Disease Cystitis Renal Dialysis wounds, septicemia infection at the inject ion site, sepsis pneumonia, sepsis, pyrogenic reaction Pathogen gram negative ba cilli, enterococci Staphylococcus, gram negative bacilli, Bacteroides Staphyloco ccus, Klebsiella, Serratia, Enterobacter, Pseudomonas Candida , Klebsiella, Serr atia Hepatitis B virus, Staphylococcus aureus, Pseudomonas