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