MICROBIOLOGY INVESTIGATIONS & SAMPLE COLLECTION GUIDELINES DEPARTMENT OF MICROBIOLOGY DR. RAM MANOHAR LOHIA HOSPITAL & POST GRADUATE INSTITUE OF MEDICAL EDUCATION & RESEARCH NEW DELHI-110001 2019
MICROBIOLOGY INVESTIGATIONS
&
SAMPLE COLLECTION GUIDELINES
DEPARTMENT OF MICROBIOLOGY
DR. RAM MANOHAR LOHIA HOSPITAL
&
POST GRADUATE INSTITUE OF MEDICAL EDUCATION & RESEARCH
NEW DELHI-110001
2019
Dr. Ram Mahohar Lohia Hospital
&
Post Graduate Institute of Medical Education & Research
New Delhi
MICROBIOLOGY INVESTIGATIONS
&
SAMPLE COLLECTION GUIDELINES
From the desk of Medical Superintendent
I extend my best wishes to Department of Microbiology for making a vast list of investigations available in our hospital and doing quality reporting on all clinical samples. As you would all agree, Microbiology with its various sections like Bacteriology, Virology, Parasitology, Immunology, Mycology, Molecular testing and Infection control plays a very important role in helping clinicians to arrive at etiological diagnosis which aids in providing appropriate patient management. With emerging infections like Ebola, H1N1, Nipah etc, the role of Microbiology is further enhanced in the diagnosis, prevention and control of these diseases.
The information provided in this booklet would help all clinicians to know the spectrum of tests available and more importantly how to send appropriate samples for getting quality results.
I wish Microbiology department more success in making the department a state-of-art facility for quality work and thus help improve patient care.
Dr. (Prof.) V.K. Tiwari
Director & Medical Superintendent
PGIMER Dr. Ram Manohar Lohia Hosp
From the desk of HOD
On behalf of Microbiology Dept, it is our great privilege to provide all our colleagues with this booklet on “Microbiology investigations and sample collection guidelines” This would help all in knowing the tests available in the department as the spectrum of tests have really increased in various fields of Bacteriology, Virology, Immunology, Parasitology, Mycology, Molecular Testing etc. The importance of sample collection is emphasized here as “ Only good quality samples yield quality reports” thus helping us all work towards our main goal of providing best patient care in such a reputed, tertiary care hospital as ours.
Our Microbiology team comprising of Consultants, Residents, Technical Staff & Group-D workers are all working hard to provide better services with the full support and encouragement of our Medical Superintendent and our administration.
Looking forward for support from all our colleagues.
Dr. (Prof.) Nandini DuggalConsultant & HeadDept of Microbiology
Department of Microbiology
Contents
Page No.
Introduction 1
Location 2
Timings 2
List of Microbiology Investigations 3-7
General Instructions for sample collection 8-9
Sample collection techniques 10-19
Sample collection at a glance 20-22
Introduction
Department of Microbiology is a multidisciplinary unit consisting of Bacteriology (Aerobic & Anaerobic), Mycobacteriology, Mycology, Virology, Serology & Immunology, Parasitology, PCR and Hospital Infection Control Sections.
Diagnostic Services: The department provides diagnostic support to 1447 bedded Dr RML Hospital which also has OPD Department of various specialties and super-specialties. The department is equipped with conventional and advanced automated technology for diagnosis of infectious and immunological disorders. Approximately, 5-6 Lakh tests are performed annually. The department provides various guidelines for hospital infection prevention & control and investigates and monitors nosocomial infections.
Support to Public Health Programmes: The department is the sentinel site for National Vector Borne Disease Control Programme (NVBDCP) for surveillance and diagnosis of Dengue & Chikungunya infections. It provides data to Integrated Disease Surveillance Programme (IDSP), and plays an important role during emerging and re-emerging diseases like H1N1, SARS, Ebola and Nipah Virus Diseases etc.
Post Graduate Teaching: The department is involved in postgraduate teaching (MD Microbiology) with intake of 5 students per year. Quality applied research is undertaken in the department.
This booklet provides information on the currently available investigations in the department and sample collection guidelines.
The information provided in the booklet is also available on the website. In the endeavor to expand the department, newer tests will be added as per the requirement and the same will be uploaded on the website. This booklet will also be revised from time to time. It is pertinent to mention that the tests will be carried as per the availability of kits and reagents.
Microbiology Investigations & Sample Collection Guidelines 1
Location:
Ground Floor Microbiology lab, X Ray Building *th
Microbiology Lab, Academic block, PGIMER, 6 floorrd
*Proposed to be shifted to OPD Block, 3 Floor
Timings :
Microbiology department is open all 365 days.
Routine sample collection timings:
o Monday to Friday - 09:00AM to 11:30AM
o Saturday - 09:00AM to 10:30AM
Emergency / Urgent sample** collection timings :
o Round the clock
** Urgent sample of /HBV/HCV/HIV will be processed.
Note: From 08:00 PM to 08:00 AM samples will be collected / received through Emergency Window.
�
�
�
�
Microbiology Investigations & Sample Collection Guidelines 2
List of the Microbiology Investigations
1. BACTERIOLOGY
1.1 Microscopy & culture1.1.1 Aerobic culture & sensitivity
�PUS (Swab & Aspiration Samples)�Sputum/BAL�Throat Swab�Body fluids & aspirates (Pleural, Pericardial,
Peritoneal, ET, Joints Fluids etc)�CSF�Blood (conventional & automated system)�Urine�Stool�Tissue / Biopsies
1.1.2 Anaerobic culture
�PUS (Deep seated abscesses /Brain abscess etc)�Stool�Tissue Biopsies
1.1.3 Mycobacterium culture, sensitivity & PCR
�ZN stain for mycobacterium�Modified ZN Stain for M. Leprae�Automated Liquid Culture & sensitivity
[Mycobacteria growth Indicator Tube (MGIT)] + DST
�CB-NAAT/Gene xpert
1.2 Serology
1.2.1 Rapid Tests
�Bacterial Antigen detection in CSF(N.meningitidis, S.pneumoniae, H.influenzae,E.coli)
�Salmonella antibody�Scrub Typus antibody
Microbiology Investigations & Sample Collection Guidelines 3
1.2.2 Others
�Widal Test�VDRL & TPHA�ASO Antibody�Brucella Antibody
2. MYCOLOGY
2.1 Microscopy (KOH, Gram Stain, India Ink) & culture�Skin Scrapings / Hair / Nail�Urine�Sputum/BAL�Body Fluids�Corneal scrapings / Aqueous humor/ Vitreous�aspirate�Pus from various sites (Ear/Eye/Nasal/Brain
abscess/ Liver abscess etc)� Tissue Biopsy
2.2 Antifungal Susceptibility testing
� Yeast
2.3 Serology
� Cryptococcus detection in CSF� Galactomannan Antigen detection for invasive
Aspergillosis
3. VIROLOGY
3.1 Serology: Rapid / ELISA
�HIV Antibody�Dengue NS1 Antigen�Dengue IgM Antibody�Chikungunya IgM Antibody�Hepatitis A Virus Antibody
Microbiology Investigations & Sample Collection Guidelines 4
� Hepatitis B Virus Profile
§ Hepatitis B Virus Surface Antigen/Antibody§ Hepatitis B Virus e Antigen§ Hepatitis B Virus e Antibody§ Hepatitis B Virus Core IgM Antibody§ Hepatitis B Virus Core total Antibody
�Hepatitis C Virus Antigen/ Antibody� Hepatitis D Virus Antigen/ Antibody***�Hepatitis E Virus Antibody�Cytomegalovirus IgM Antibody�Herpes Simplex I & II IgM Antibody�Measles IgM Antibody�Mumps IgM Antibody�Japanese Encephalitis (JE) IgM Antibody�Enterovirus Antigen 71***
3.2 Stool
�Rota Virus Antigen
3.3 Rapid Test / Viral Load: PCR Quantitative
�HIV�Hepatitis B Virus�Hepatitis C Virus�Cytomegalovirus�H1N1 (Nasopharangeal swab / Respiratory
Secretions)�BK Virus***
4. PARASITOLOGY
4.1 Microscopy (Wet mounts)
�Stool for Ova / Cyst / Trophozoites etcCorneal Scrapings for acanthamoeba
4.2 Staining
�Modified ZN staining for Cryptosporidium / Microsporidium / Cyclospora /Isospora
***
Microbiology Investigations & Sample Collection Guidelines 5
4.3 Serology
�Malaria Antigen�Filaria Antigen�Toxoplasma IgM Antibody�Leishmania Serology
5. IMMUNOLOGY
�CD 4 counts and percentages�RA factor�Anti CCP�ds DNA�ANA�ANA Profile (ds DNS, Nucleosome, histone,
SmD1, PCNA, PO (RPP), SS-A/Ro60, SS-A/Ro52,SS-B/La,CENP-S,Scl70,U1-smRNP, AMA-M2,Jo-1, PM-Scl, Mi2,Ku)
�Anti Phospholipid Antibody (APLA)
§ â2 Microglobulin IgM Antibody§ â2 Microglobulin IgG Antibody§ Anti Cardioipin IgM Antibody§ Anti Cardiolipin IgG Antibody
� Biomarkers for Sepsis§ CRP§ Procalcitonin
�Complements (C3, C4)�Immunoglobulins (IgA, IgM, IgG, IgE)�Myositis profile (JO-1, PL-7, CL-12, EJ, SRP,
Mi-2, MBA-5, TIF1-4, KU, PM-Scl-100, Scl-70, SSA/Ro52kd)
�Vasculitis profile (PR3, MPO, GBM)***�Auto immune Liver disease Profile (AMA, M2,
SP 100, LKM1, gp120, LC1, SLA)***
Microbiology Investigations & Sample Collection Guidelines 6
6. INFECTION CONTROL SURVEILLANCE
�Air Bacteriology (critical areas-OT, ICU etc)�Samples like blood bags & packed sterile objects
for sterility testing�Water culture�Disinfectant Testing�Biological Indicators for Autoclave sterility
testing�Suspected outbreaks
§ Environmental sampling§ HAI Surveillance (Hand /Nasal swabs etc)
7. Fluorescent microscopy (TB, Immunology)***
*** Tests will be starting soon
The information will be uploaded on the website
Microbiology Investigations & Sample Collection Guidelines 7
General Instructions For Sample Collection
�All samples should be collected in sterile containers only.
�The containers must be adequately labelled and sent with microbiology requisition form duly completely filled, signed and stamped with information in respect of:
a. Name, Age, Sex b. Ward/OPD No. c. Doctor In charge d. Date of admission e. Date of onset of illnessf. Date & time of sample collectiong. Duration of Hospital stay h. Antibiotic historyi. Last change of antibiotic j. Relevant clinical history k. Radiological findings l. Provisional diagnosis.m Associated co-morbities
Collection of sample
1. Routine samples
Samples collected at common collection centre:
�Samples for Virology, Immunology & Serology VDRL, TPHA, Widal, Rheumatoid factor (RF), ASO, CRP, AntiNuclear Antibodies (ANA), Hepatitis Viral markers (HBs Ag, Antibodies for HAV, HEV & HCV)
�Blood samples for Malaria antigen, Filarial antigen & other rapid blood tests.
�Blood culture Samples for OPD patients.
Microbiology Investigations & Sample Collection Guidelines 8
Samples received at Department of Microbiology
�
indoor cases.
�Samples for ELISA, nd th
�ELISA for TORCH – 2 & 4 Monday of the month
�Samples for HIV testing and CD4 /CD8 counts (ICTC Centre).
2. Emergency samples
�Emergency samples: Samples collected intra- operatively, Blood culture, Throat swab for Diphtheria, Stool for V. cholerae, CSF culture, HIV, HBs Ag, HCV, gas gangrene and samples pertaining to any acute infection outbreaks.
�Sample Rejection Criteria
� Sample collected in improper container
�Insufficient quantity of sample
�Haemolysed samples
�Incompletely filled –in forms
�Containers soiled from outside and overflowing samples
�Visibly soiled forms
All tests are performed as per the availability of Kits and Reagents
All microbiology investigation requests from
Microbiology Investigations & Sample Collection Guidelines 9
Sample Collection Techniques.
1. Sputum Culture
�Early morning coughed up sputum (Not Saliva) sample.
�Collect in a sterile wide mouthed container withscrew tight cover.
�For Gram stain request of sputum sample : it is mandatory to mention the organism/ disease being clinically suspected
Without this information Gram stain of sputum sample may not have any clinical significance
2. Throat Swab
�Collect the sample with sterile swab by swabbing tonsillar area, posterior pharyngeal wall or inflamed area of the throat without touching the oral area.
�Try to include the pus or membrane if any.
�Send two swabs, one for culture and other forstaining.
3. Blood Culture
Give details of duration of hospital stay, day of onset of fever, duration of fever, antibiotic therapy, whether sample collected directly or from canula, earlier report of organism isolated & its sensitivity.
Collection procedure: clean the site from inside out in a circular pattern, first with 70% alcohol, let it dry, then clean with povidone iodine & collect venous blood.
Send in BHI broth provided by department of Microbiology.
Amount Adult-5-10 ml Blood in adult culture bottleChildren-1-5 ml Blood in paediatric culture bottle
Microbiology Investigations & Sample Collection Guidelines 10
� Do not open the cap. Clean cap with spirit swab and then inject blood into bottle by needle through hole in the cap.
�Do not refrigerate.
�In case of delay, store in a incubator at 37 °C or at room temperature.
Ideally paired blood cultures should be sent from different sites from non continuous veins (wherever possible) before starting antibiotic therapy
�For blood culture by BACT Alert 3D, (For ICU, NICU, Paediatric cases, Nursery etc)
FA Plus-Adult (Green colored) add 5-10 ml Blood.
PF Plus - Paediatrics (Yellow colored) 0.5 ml – 4 ml
Blood. (Minimum 1 ml)
4. Urine Culture
Duly filled form should include clinical indications, details of antibiotics & diuretics administered H/O catheterization, renal stones, BPH, comorbities & previous culture reports. Mention sample collected from catheter/mid stream/supra pubic aspirate along with timing of collection 'early morning sample or not'.
�Collect clean catch mid stream urine sample in sterile Universal container. Patient should be given instructions for collection of urine
�Transport to the laboratory immediately, if refrigerated till processing.
�In catheterized patients: Catheter is clamped
Microbiology Investigations & Sample Collection Guidelines 11
above the distal end to collect freshly voided urine. Tubing is cleaned vigorously with 70% alcohol (spirit). Under all aseptic precautions, urine is aspirated with needle & syringe. Then, urine is collected in wide mouth sterile container Never collect urine from Uro-bag.
5. Pus Culture & Sensitivity
�Always mention source & site of sample taken
�Aspirated samples are preferred.
�Clean the wound area with sterile normal saline and collect the pus sample on a sterile swab stick (provided by the Microbiology Department) in sterile test tube following all aseptic precautions.
�Pus swabs should be visibly charged with pus. However, expressed pus samples are preferred.
�Send separate swab for staining purpose. Pus sample collected by I&D/FNAC should be directly transferred in a sterile container
�Do not collect PUS from dressing material
�Do not send sample in syringe with needle.
�Send separate form for ZN staining (For AFB).
(Sufficient quantity of sample is a pre-requisite for ZN stain)
6. CSF Culture Sensitivity/CSF Antigen detection (Bacterial and Fungal)
�Give relevant clinical history & details of CSF cytology if available.
�Collect 2-3 ml of CSF in sterile container under all aseptic precautions & transport immediately.
�In case of delay, store in a incubator at 37 °C or at room temperature.
�Do not refrigerate.Microbiology Investigations & Sample Collection Guidelines 12
7. Stool
a) Culture & Sensitivity
�Collect the sample in sterile wide mouth container
�Send only a small amount (2-3 g).
�Sample should not be mixed with urine.
�Rectal swab can be collected in case of infants (Insert swab into the rectum and rotate gently). Swab should be visibly charged.
b) Modified ZN staining:
�For acid fast oocyst.(Cryptosporidium, Isospora, Cyclospora etc)
8. Stool for Cholera
�1-2 ml stool specimen should be preferably sent in alkaline peptone water (transport media) provided by Microbiology department.
�Sample if collected in an ordinary container should be immediately transported to the Lab.
9. Body fluids & Aspirates
Mention date & duration of fever, site of infection, surgical procedure, blood counts, radiological findings & other relevant investigations done.
�Collect in sterile container and transport immediately.
�In case of delay, store in a incubator at 37 °C or at room temperature.
�Do not use unsterile container regardless of investigation.
10. Sputum for AFB Microscopy
�After rinsing mouth with plain water collect early
Microbiology Investigations & Sample Collection Guidelines 13
morning coughed up sputum (not saliva) sample in clean wide mouthed container with screw tight fitting cover.
�A total of two consecutive samples are required to be submitted.
11. Urine for AFB
�Collect first early morning voided whole urine sample in clean, dry and sterile container.
�Send sample for at least three consecutive days.
12. Mycobacterial Culture
�Sputum, gastric aspirate, sterile body fluids, biopsies, pus, endometrial biopsy (pre menstrual) and first voided whole urine in sterile container.
�Blood is not an appropriate sample for mycobacterial culture.
13. CB NAAT for Mycobacterium Tuberculosis
�Sputum, gastric aspirate, sterile body fluids and pus samples should be sent in sterile containers.
�Urine, blood & blood stained samples are not acceptable for CBNAAT.
14. Anaerobic Culture
�Aspirated pus samples in sterile containers.
�Tissue/biopsy in sterile containers.
�Swabs / surface samples / BAL Sputum are not acceptable.
�Samples should be transported to lab immediately after collection to maintain viability of anaerobes present in sample.
�Request forms must specifically mention anaerobic culture.
Microbiology Investigations & Sample Collection Guidelines 14
15. Mycology
Give relevant clinical history including immune status of the patient & any preexisting disease.
�Area should be cleaned with 70% alcohol and let it dry.
�Skin, nail scraping / clipping should be sent in clean paper / sterile container
�Hair should be cut short & epilated with help of forceps along with hair root.
�Sputum: Coughed up, early morning 3 consecutive sputum samples in a sterile container after rinsing the mouth with plain water.
�CSF / Urine should be sent in sterile container.
�Sample should be delivered at the earliest.
�For corneal scraping, sterile Kit should be collected from department and immediately transferred to lab after inoculation.
�Biopsy/tissue specimens should be sent in sterile saline. (NEVER IN FORMALIN)
16. Serology / Immunology
�Samples will not be processed without relevant clinical history .
�Collect 3 ml venous blood (preferably fasting) in plain vial with aseptic technique.
�DO NOT COLLECT BLOOD FROM I.V. CATHETERS. Hemolysed samples will not be processed
16.1 ASO, VDRL, TPHA, WIDAL, Brucella serology & Scrub typhus serology (3ml Blood sample in plain vial for each test)
Microbiology Investigations & Sample Collection Guidelines 15
16.2 CRP, PCT (3ml Blood sample in plain vial)
16.3 C3, C4 (complement levels) / IgG, IgA, IgM, IgE
(Immunoglobulin Profile) (3ml Blood sample in plain vial) Samples for immunoglobulin profile & complement levels should be sent from Monday to Wednesday only.
16.3 For ELISA: Anti CCP, RF, ANA, APLA, dsDNA
Collect 3 ml venous blood in plain vial under aseptic conditions for each of the above test.
16.4 Dengue & Chikungunya Serology
�Dengue (NS1 Ag / MAC ELISA / Rapid IgG,
IgM),Chikungunya (IgM, MAC ELISA)
�Collect 2-3 ml blood in plain vial under aseptic condition.
�Haemolyzed sample shall not be accepted.
�All Dengue & Chikungunya requests to be accompanied by duly filled performa prescribed by NVBDCP (available on RMLH website).
�Platelet counts are must.
16.5 ELISA for Hepatitis markers (HBsAg, Anti HBc IgM, Anti HBc total, HBeAg, Anti HBe, HCV Ag & Anti HCV Ab, Anti HAV, Anti HEV, Anti HBS & HDV Ag / Ab).
�Collect 4-5 ml venous blood in plain vial.
�Separate forms should be filled completely along with clinical details, duly signed and stamped, without which samples will not be accepted.
�Give clinical indication for the test along with LFTprofile, H/o blood transfusion, and immunizationfor hepatitis B, H/o needle stick injury & any otherinjectables.
Microbiology Investigations & Sample Collection Guidelines 16
16.6 ELISA for TORCH nd th
�Collection on 2 & 4 Monday of the month
�Collect 3 ml blood in plain vial.
�Give obstetric history, details of congenital anomalies in child, history of infertility & other clinical indications for the test.
16.7 HIV
�Routine samples are collected in Integrated Counselling and Testing Centre (ICTC Center in the Deptt. of Microbiology) after pre test counseling. Consent form is to be signed prior to the test.
�Collection time: 9.00 am to 11.30 am Monday to Friday, and 9:00 am to 11:00 am on Saturday.
�For voluntary clients and cases of needle stick injuries: 9.00 am to 3.00 pm Monday to Friday, and 9:00 am to 12:00 pm on Saturday.
�Reports are given by counselors after post test counselling (11:30 am to 4:00 pm)
Note: All needle stick injuries to be reported to ICTC centre for counseling and testing.
16.8 (a) Leishmania Serology
�By rapid immunochromatographic test.
�2-3 ml blood in plain/EDTA vial.
16.8 (b) Malaria & Filarial Antigen
�By rapid immunochromatographic test
�Collect 2-3 ml blood in EDTA vial.
17. CD4 Counts and Percentage
�Test is done for only HIV positive patients.
Microbiology Investigations & Sample Collection Guidelines 17
�Samples collected from Monday to Friday (9:00 am to 11:30 am) in Deptt. of Microbiology.
�For indoor patients samples sent in vacutainers (EDTA vial) supplied by the Deptt. along with completely filled form and appropriate clinical details.
18. Molecular Tests (PCR)
�Sample should be accompanied with specific PCR form available in microbiology laboratory.
�The request form must be signed by requesting faculty/consultant along with stamp.
�Request form must be accompanied with payment slip except for CGHS card holders, for thesis cases and in special cases if forwarded by respective head of departments and MS office.
�In case of BPL patients, sample can be requested for free processing from assigned authority.
�PCR for H1N1 is free of cost.
�Samples are to be deposited in microbiology th
laboratory at 6 floor PGIMER
18.1 TB PCR
Following samples are acceptable in a sterile container :
�Sputum 2-5 ml (not saliva), preferably two samples.
�Gastric aspirate (2-5ml).
�Bronchoalveolar lavage BAL (2-5 ml).
�Urine
�CSF/ Aspirated body fluids
�Endometrial biopsy (premenstrual)
�Pus/Tissue/Biopsy/bone marrow
Microbiology Investigations & Sample Collection Guidelines 18
�Lymph node biopsy/Aspirate
�Menstrual blood
18.1 CMV PCR
�Blood in EDTA vial (2-5 ml)
�Urine
18.2 HIV, HCV, HBV PCR
�Blood in EDTA vial (2-5 ml)
18.3 H1N1 PCR
�Swab stick and viral transport media (VTM) are provided by laboratory.
�Collect nasopharyngeal swab and throat swab in VTM
Microbiology Investigations & Sample Collection Guidelines 19
Sam
ple
co
llect
ion
at
a gl
ance
Sa
mp
le
Co
nta
iner
Rem
arks
Inve
stig
atio
ns
Pu
s
Ster
ile c
ont
ain
er
Asp
irat
ed P
us
Mic
rosc
op
y (M
enti
on
susp
ect
orga
nis
m):
Gra
m S
tain
, ZN
Sta
in, W
et m
oun
t,KO
HC
ultu
re: B
acte
rial
, Myc
ob
acte
riu
m, F
ung
alPC
R/C
BN
AAT
for
Myc
obac
teri
um
TB(c
anno
t b
e pe
rfo
rmed
on
pus
swab
sam
ple
s)
Swab
sti
ck in
ste
rile
tu
be
Cha
rge
the
swab
sti
cks
(at
leas
t tw
o-
one
for
cult
ure
and
othe
r fo
r st
aini
ng)
and
put
it in
the
ste
rile
tu
be
No
t su
itab
le f
or
PC
R/C
BN
AA
T
Sput
um
Ste
rile
wid
e m
outh
co
ntai
ner
Ear
ly m
orni
ng c
ough
ed u
p s
pu
tum
(Not
Sal
iva)
sam
ple
In s
peci
fic in
stan
ces
3 co
nse
cuti
ve
days
sam
ple
s h
ave
to b
e su
bm
itte
d
Mic
rosc
op
y (M
enti
on
susp
ect
orga
nis
m):
Gra
m S
tain
, ZN
Sta
in, W
et m
oun
t, K
OH
Cul
ture
: Bac
teri
al, M
yco
bac
teri
um
, Fu
ngal
PCR
/CB
NA
AT f
or M
ycob
acte
riu
m T
B
Thro
at S
wab
Swab
sti
ck in
ste
rile
tu
be
At
leas
t tw
o sw
abs
(one
for
cul
ture
an
d ot
her
for
stai
ning
)
Mic
rosc
op
y (M
enti
on
susp
ect
orga
nis
m):
Gra
m S
tain
,C
ultu
re: B
acte
rial
, Fu
ngal
Nas
oph
aran
geal
sw
abSw
ab s
tick
in s
teri
le
tube
Cul
ture
Swab
sti
ck in
VTM
Ava
ilab
le f
rom
the
lab
PCR
-H
1N1
Bro
chio
alve
ola
r La
vage
(B
AL)
Ste
rile
con
tain
erLa
vage
flu
id 2
-5 m
lM
icro
sco
py
(Men
tio
n su
spec
t or
gan
ism
): G
ram
Sta
in,
ZN S
tain
, KO
HC
ultu
re: B
acte
rial
, Fu
ngal
PCR
/CB
NA
AT f
or M
ycob
acte
riu
m T
B
Bo
dy F
luid
s&
A
spir
ates
Ste
rile
con
tain
er2-
5ml
Plu
ral,
Peri
card
ial,
Peri
tone
al,
Mic
rosc
op
y (M
enti
on
susp
ect
orga
nis
m):
Gra
m S
tain
, ZN
Sta
in, W
et m
oun
t, K
OH
Microbiology Investigations & Sample Collection Guidelines 20
Join
t Fl
uid
etc
Endo
trac
heal
sec
reti
ons
Cul
ture
: Bac
teri
al, M
ycob
acte
riu
m, F
ung
alPC
R/C
BN
AAT
for
Myc
obac
teri
um T
B
CSF
Ster
ile c
onta
iner
2-3
ml.
Tra
nspo
rt im
med
iate
ly to
lab
Do
not
ref
rige
rate
Mic
rosc
opy
(Men
tion
sus
pect
org
anis
m):
Gra
m S
tain
, ZN
Sta
in, W
et m
ount
, KO
HA
ntig
en d
etec
tion
: B
acte
rial
& C
rypt
ococ
cus
Cul
ture
: Bac
teri
al, M
ycob
acte
riu
m, F
ung
alPC
R/C
BN
AAT
for
Myc
obac
teri
um T
B
Uri
ne
Ste
rile
con
tain
er
Mid
-str
eam
cle
an c
atch
Sup
ra-p
ubic
asp
irat
e
Cat
hete
r cl
amp
met
hod
Nev
er c
olle
ct f
rom
th
e b
ag
Wet
Mou
ntC
ultu
re: B
acte
rial
, Fu
ngal
PC
R/C
BN
AAT
for
Myc
obac
teri
um
TBPC
R fo
r CM
V
Fir
st
earl
y m
orni
ng
void
ed
who
le
urin
e sa
mpl
e in
ste
rile
con
tain
er o
n at
leas
t thr
ee c
onse
cuti
ve d
ays.
Mic
rosc
opy:
ZN
Sta
inC
ultu
re: M
ycob
acte
rium
Stoo
l
Ste
rile
wid
e m
outh
co
ntai
ner
2-3
gms
only
Wel
l ch
arge
d R
ecta
l sw
ab
from
in
fant
s: A
t le
ast
two
swab
s (o
ne f
or
cult
ure
and
othe
r fo
r st
aini
ng)
Mic
rosc
opy:
Wet
mou
ntfo
r O
va,
Cys
ts, t
roph
ozoi
tes
etc
Var
iou
s ot
her
stai
ning
(Mod
ified
ZN
etc
)C
ultu
re: B
acte
rial
, Fu
ngal
Ant
igen
det
ecti
on: R
ota
viru
s
In a
lkal
ine
pept
one
wat
er1-
2 m
lsto
olTu
bes
avai
lab
le fr
om t
he la
bIn
sus
pect
ed c
ase
of C
hole
ra
Tiss
ue
Bio
psie
sS
teri
le c
onta
iner
Bio
psy
sam
ple
in s
alin
eN
EV
ER
in f
orm
alin
Cul
ture
: Bac
teri
al, F
unga
l, M
ycob
acte
rium
PCR
for
Myc
obac
teri
um
TB
Microbiology Investigations & Sample Collection Guidelines 21
Blo
odB
ottl
e (A
dult
&
Paed
iatr
ic)
wit
h C
on
ven
tion
alA
dul
ts: 5
-10m
l blo
od
Paed
iatr
ics:
1-5
ml b
lood
BA
CT
aler
tFA
Plu
s-A
dult
(gr
een)
- 5-10
ml
FA p
lus-
Paed
iatr
ic (
yello
w)-
0.5-
4ml
(min
imu
m 1
ml)
Bot
tles
ava
ilabl
e fr
om t
he la
b
Cul
ture
: Bac
teri
al, Y
east
In p
lain
via
l
(Wit
hou
t co
agul
ant)
5m
l
to 1
0 m
l
(dep
end
ing
on n
umbe
r of
tes
ts)
Se
rolo
gica
l tes
ts
Wid
al t
est,
Typh
idot
,
VD
RL
& T
PHA
, Scr
ub T
yphu
sA
b,
HIV
Ab
, Den
gue
Ag
& A
b C
hiku
ngu
nya
Ab,
Hep
atit
is
sero
logy
(H
AV
A
b, H
CV
A
g &
Ab
,
HD
V
HEV
A
b &
Ab,
A
b
& H
BV
(HB
s )
Ag
& A
b, H
Be
Ag
& A
b, H
Bc
IgM
& t
otal
TOR
CH, M
easl
es A
b, M
ump
s A
b, J
E A
bLe
ish
man
ia A
b, G
alac
tom
ann
an A
gIm
mu
no
logi
cal t
ests
A
SO, R
A f
acto
r, A
nti C
CP, A
NA
scr
een
& p
rofi
le, d
s D
NA
, APL
A (
Mic
rogl
obul
in &
car
diol
ipin
ab)
, CR
P,
Proc
alci
toni
n, C
ompl
emen
ts (
C3,
C4)
Imm
unog
lob
ulin
s (I
g A
,M,G
,E),
Myo
siti
s pr
ofile
, Va
scul
itis
Pro
file
, Aut
o im
mun
e Li
ver
dise
ase
prof
ile.
In E
DTA
via
l
5ml
Ant
igen
det
ecti
on: M
alar
ia, F
ilari
alC
D4
test
ing
PCR
-
HIV
, HB
V, H
CV
Skin
scr
apin
gs,
Hai
r, N
ail C
lippi
ngs
Ster
ile C
onta
iner
Cle
an p
aper
-
Mic
rosc
opy
and
cult
ure
for
Fung
us
Cor
neal
scr
app
ings
Ster
ile c
onta
iner
Kit
avai
labl
e fr
om
the
lab
Mic
rosc
opy
and
cult
ure
for
Fung
usM
icro
scop
y fo
r A
cant
ham
oeb
a
Microbiology Investigations & Sample Collection Guidelines 22