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Preparing SOP For Microbiology Laboratory: A Short Guideline
Preparing SOP For Microbiology Laboratory: A Short Guideline
Preparing SOP For Microbiology Laboratory: A Short Guideline
Review article
1Department of Microbiology, Ibrahim Medical College, Shahbag, Dhaka, 2Department of Microbiology, Holy Family Red
Crescent Medical College, Dhaka, 3 Department of Microbiology and Infection Control, Square Hospital, Dhaka
Infections frequently challenge the physician's diagnostic A written set of instructions must be available for every test,
skill and must be considered in the differential diagnoses of process or procedure to set the minimum acceptable standard.
syndromes affecting every organ system. For that reason, These instructions are now termed as standard operating
diagnostic microbiology has obviously become an integral procedures or SOPs.4 Every laboratory must have SOP also
and inseparable component of modern medicine and public referred to as the 'laboratory procedure manual, hand book or
health. Microbiology laboratories play a decisive role in the local laboratory bench manual'.
diagnosis, treatment, prognosis and monitoring of
communicable diseases. Therefore, reliable, reproducible and The difficulty in preparing the SOP for microbiology
rapid laboratory services, organized in a cost-effective laboratory is that written methods of how to do tests are not
manner, is very much essential for providing quality health enough. Microbiologists also require documentation relating
services. Accurate detection of microbes and quality to : (a) what to look for, (b) when and what to report, (c) what
assurance in laboratory services, aimed at improving sensitivities to test, (d) which, if any, to report, (e) the level of
reliability, efficiency and facilitating inter-laboratory identification required, and (f) the need for confirmatory test
comparability in testing, is the backbone of quality healthcare in-house or referral to a reference laboratory, etc.
delivery. The use of standard operating procedure (SOP) in
clinical microbiology laboratory is one of the most crucial It is obviously very difficult to cover every eventuality, but
factors in achieving quality health services.2 comprehensive criteria for processing, secondary testing and
reporting of all routine specimens must be covered. The
Standard operating procedure (SOP) manual should lay down the policy of the laboratory for the
Microbiology investigations are important in the diagnosis, kinds and sequence of examinations to be made on each of
treatment, and surveillance of infectious diseases and policies the different kinds of specimen, the criteria for determining
regarding the selection and use of antimicrobial drugs. It is, the content of specimen, and the standardized wording of
therefore, essential that test reports are relevant, reliable, and reports.4
timely and interpreted correctly. The primary goal of the
3
25
Preparing SOP for Microbiology Laboratory: A Short Guideline Jilani et al
Need of SOP s in laboratory work like (i) cholera, (ii) enteric fever, (iii) diphtheria, (iv)
Standard operating procedures in a microbiology laboratory meningitis, (v) dysentery, (vi) sexually transmitted diseases,
are needed for following reasons: 3
(vii) UTI, (viii) tuberculosis, (ix) malaria, (x) parasitological
• To improve and maintain the quality of laboratory service examination of stool, (xi) mycological techniques, (xii) water
to patients and identify problems associated with poor bacteriology, etc.
work performance;
• To provide laboratory staff with written instructions on how There must be a guideline regarding collection and
to perform test consistently to an "acceptable standard" in transportation of clinical materials (like bacterial food
the laboratory; poisoning, viral diseases such as AIDS, viral hepatitis,
• To provide written standardized techniques for use in the
poliomyelitis, dengue etc) to referral laboratories.
training of laboratory personnel;
• To facilitate the preparation of a list of essential reagents,
Stages of SOP
chemicals and equipments;
Total activities performed by laboratory personnel in order to
• To promote safe laboratory practice.
provide accurate diagnosis from a clinical specimen can be
divided into three stages. These are :
Important features of SOP
• Pre-Analytical stage- primarily deals with the general
An individual SOPs must be:5
concepts for specimen collection and handling
• Applicable and achievable in the laboratory in which they
• Analytical stage- deals with testing the specimens, and
will be used;
• Post-Analytical stage- comprises of reporting and
• Clearly written and easy to understand and follow; and
• Kept up-to-date using appropriate technologies. interpreting test results.
Request form : format. The guidelines must emphasize two important aspects:10
Accurate information must be obtained on the request form to (i) Collection of the specimen before the administration of
ensure unequivocal identification of the patient and the antimicrobial agent;
requesting physicians. Each specimen must be accompanied (ii) Prevention of contamination of the specimen with
by a request form which includes: externally present organism or normal flora of the body.
1. Patient name, sex, date of birth, address and telephone
number, and record number for outpatient and hospital World Health Organization had formulated general rules for
inpatient; collection and transportation of specimens which is modified
2. Printed name, practice address and telephone number of and summarized as below:
the requesting physician; • Strict aseptic techniques must be applied throughout the
3. Space should be provided for a description of the specimen procedure;
(e.g., clotted blood, stool, rectal swab etc), the date of • Hands of the phlebotomist should be washed before and
request, date and time of collection; after the collection;
4. The form should be so designed that the submitting • Specimen should be collected from the site representative
clinician gives all of the information needed by the of the infectious process (e.g., sputum is the specimen for
laboratory staff to determine the natures and range of test pneumonia not the saliva and cervical not vaginal swab for
to be done; Neisseria gonorrhoeae isolation). Even careful collection
5. Clinical note summarizing the patient's illness, the date of methods will produce a little clinical value if it is not
onset of illness and the provisional diagnosis; obtained from a site where the infection is active;
6. The request form should specifically seeks details of the • Specimen should be obtained at the appropriate phase of
type of examination requested, with notes on the patients disease (e.g., acute phase of illness, and before antibiotics
occupation, history of recent foreign travel, relevant are administered);
immunization and any antibacterial therapy or • Specimen should be placed in an appropriate sterile
prophylaxis. container;
• Clean and uncontaminated outside of the container should
Carelessness in submitting specimens with inadequate be ensured;
information would markedly reduce value of the report in • Specimen should be collected in adequate volume,
many cases.8 insufficient material may yield false negative result;
• Specimen container should be leak-proof and closed tightly
Collection of clinical specimens: so that its contents do not leak during transportation;
The diagnosis of an infectious disease begins with the
• Specimen should be labeled with the patient's name,
collection and transportation of a clinical specimen for
identifying number and date. Enough information must be
examination in the laboratory.
provided on the specimen label so that the specimen can be
matched up with the requisition when it is received in the
It is a critical consideration because any result, the laboratory
laboratory;
generates, is limited by the quality of the specimen and its
• Specimen containing dangerous pathogens should be
selection on arrival in the laboratory.9 In order to obtain the
labeled HIGH RISK and if possible a warning symbol (i.e.,
appropriate diagnosis, the specimen must be-
red dot, star or triangle) should be attached.11
• the right one,
• collected at the right time,
• transported in the right way, and Note: As because of any specimen may contain infectious
• submitted to the right laboratory. pathogens, it is important for laboratory personnel to handle all
specimens with adequate safety precautions and to wash their
Guidelines for collection and transportation of the specimens hands after handling specimens.
should be made available to clinicians in a lucidly written
Collection procedure of different specimens: • In case of discharge, 1-2 ml sample in a sterile vial is
The clinical state of the patient will not be reflected in the preferable;
result of laboratory investigation (despite the correct • Two swabs in sterile containers should be sent - one for
performance) unless the specimen is collected under optimal microscopic examination and another for culture. A third
conditions required for the analysis. Few examples of the swab dipped in suitable transport media is preferable in
important specimens and their proper collection and special situation like, urethral or HVS swab;
transportation methods are described below in order to ensure • Vaginal swab should be high vaginal swab and should not
quality.15,17 touch the sides of the vaginal wall;
• Two throat swabs should be taken in the morning before
Blood: mouth washing. Swabs should be collected under direct
• Whole blood is required for bacteriological examination; visualization without touching the tongue or buccal
• Skin antisepsis is extremely important and performed by mucosa;
using tincture of iodine (1-2%), povidone iodine (10%), • Conjunctival swab should be collected in the morning
and chlorohexidine (0-5%) in 70% alcohol;13 before washing of the face and eyes.
• Blood should be collected during the acute and early stages
of disease and during paroxysms of fever (since the number CSF and other sterile body fluids:
of bacteria is higher during this period); • Should be colleted under aseptic condition (preferably by
• In the absence of antibiotic administration, 99% culture attending physician) and transported immediately to the
positivity can be seen with three- samples blood culture; laboratory;
• Small children usually have higher number of bacteria in • They should not be refrigerated, if delay in transport is
their blood as compared to adults and hence less quantity expected, than should be kept at room temperature.12
of blood is required from them; and
• If immediate transportation to the laboratory is not possible, Analytic stage
specimen should be inoculated into liquid media and kept The microbiology laboratory should have a carefully
in the incubator. If not available, should be kept at room considered and clearly designed policy for accurate detection
temperature but never be refrigerated.15 of etiological agent. They should formulate a sequence of
laboratory tests, like gross examination of specimen,
Urine: microscopy, culture procedures, biochemical tests, serological
• Best collected soon after patient wakes up in the morning; test and antibiotic sensitivity tests. This sequence will be
• Mid-stream urine is collected after giving proper used in the examination of most of the specimens and
instructions to the patient, such as: (a) genitalia should be microbial isolation.
cleaned properly, (b) mid-stream, clean catch urine
collected in a sterile container; Gross examination of specimen:
• In case of catheterized patients, urine should be collected All processing should begin with a macroscopic or physical
from an area over the collecting tubes after cleaning and the examination of specimen. Areas with blood or mucus should
sample is collected by puncturing with a sterile needle and be located and sampled for direct microscopy and culture.
syringe;
• Urine should be transported immediately to the laboratory. Direct microscopic examination:
If delay is more than half an hour, sample should be All appropriate specimens should have a direct microscopic
o
refrigerated at 4 C. examination. The direct examination serves several purposes:
• First, the quality of the specimen can be assessed, for
Pus, Discharge and Swabs: example, sputum can be rejected that represent saliva by
• The site of collection (i.e., wound) should be cleaned with quantitation of WBCS and squamous epithelial cells
normal saline and antiseptics, and should not be applied (should be 10: 1);
before collection; • Infection can be assumed by observing plenty of pus cells
• Safe disposal of specimen and cultures; policy for the wording of reports and all staff should adhere to
the policy.18
• Cleaning of glasswares, plasticwares, etc and
• Sterilization procedures and their control.
Reporting policy:
The laboratory policy for reports should specify not only the
Control of stains and reagents:
wording of interpretative comments, but also the
• All stains and reagents must be clearly labeled, dated and
circumstances in which the different comments are to be
stored correctly;
made. It should, for instance,
• These should not be used by their expiry dates or when they
• Lay down the circumstances in which the finding of
show signs of deterioration, such as, abnormal turbidity and
coagulase-negative Staphylococci in a blood culture to be
decoloration;
reported with the comment 'probably a contamination from
• At regular intervals and whenever a new stain is prepared
the skin', and without giving its antibiotic sensitivity report.
control smear should be stained;
• In different circumstances as, in a compromised patient
• Control smear for gram stain can be prepared from mixed
when the finding is to be reported as 'possibly of clinical
culture of reference strain of Staphylococci and
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