United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 1 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

1. Purpose

To provide a standard procedure for the isolation and identification of Salmonella species from 

commodities analyzed for the USDA/AMS Microbiological Data Program (MDP).

2. Scope

This standard operating procedure (SOP) shall be followed by all laboratories conducting 

microbiological studies for MDP, including support laboratories conducting non-routine 

activities. This SOP represents minimum MDP requirements and is presented as a general 

guideline. Each laboratory shall have written procedures that provide specific details concerning 

how the procedure has been implemented in that laboratory.

3. Principle

Salmonella is isolated on selective media and identified by biochemical tests including 

automated systems such as VITEK®developed by bioMérieux. The reliability and accuracy are a 

result of the use of a panel of biochemical tests that are used to characterize the test organism. 

The resulting profile is compared to known profiles of numerous microorganisms and a 

subsequent identification is made.

4. Outline of Procedures

Equipment and Materials........................6.1

Media and Reagents..............................6.2

Controls............................................6.3

Isolation of Salmonella.......................... 6.4

Selective Enrichment and Plating.............. 6.5

 Identification.......................................6.6

Biochemical Confirmation.......................6.7

Reporting and Shipment..........................6.8
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 2 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

5. References

 BAM Online, 8th edition. 2001. Chapter 5. Salmonella, 

http://www.cfsan.fda.gov/~ebam/bam-5.html (last accessed 11/10/05)

 SOP MDP-DATA-01, Record Keeping and Results Reporting

 SOP MDP-MTH-04, Detection of Salmonella in Fresh Produce by BAXPCR

 SOP MDP-MTH-09, Detection of Salmonella using VIDAS Method

 SOP MDP-SHIP-03, Procedures for Packaging, Shipping, and Archiving 

 Microbiological Cultures

 SOP MDP-QA-03, Quality Assurance (QA) Controls

 VITEK® Users Manual, bioMérieux

6. Procedures

6.1. Equipment and Materials 

 VITEK®System or VITEK®2 Compact System, bioMérieux

 VITEK® GNI+ Card or GN cards, bioMérieux

 Water bath, 42  0.2C

 Incubator, 35  2C

 Vortex mixer

 Serological pipettes, sterile, disposable, various sizes

 Dynal® Automated BeadRetriever or manual Immunomagnetic Separation (IMS)

equipment, Invitrogen 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 3 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

6.2. Media and Reagents

 Optional: SDIX RapidCheck© SELECTTM Salmonella media, XLT4, Brilliant Green Sulfa 

Agar (BGSA), Chromagenic agars

 Rappaport-Vassiliadis (RV) broth: Follow manufacturer’s instructions for preparation. 

Dispense 10-mL aliquots into 16 x 150 mm test tubes before autoclaving.

 Tetrathionate (TT) broth: Follow manufacturer’s instructions for preparation. DO NOT 

AUTOCLAVE. Dispense 10-mL aliquots into sterile 16 x 150 mm test tubes. On day of 

use, add 0.2 mL iodine solution and 0.1 mL Brilliant Green solution per 10 mL tube of 

TT broth. Mix by vortexing.

 M broth: 16 x 150 mm test tubes containing 10 mL aliquots

 Iodine solution for basal TT broth, commercially available.

 Brilliant Green Dye solution for basal TT broth, commercially available.

 Xylose lysine deoxycholate (XLD) agar, commercially available or follow manufacturer’s 

instructions for preparation. 

 Hektoen enteric (HE) agar, commercially available or follow manufacturer’s instructions 

for preparation. 

 Bismuth Sulfite (BS) agar: Follow manufacturer’s instructions for preparation. 

 Triple Sugar Iron (TSI) agar slants, commercially available or follow manufacturer’s 

instructions for preparation.

 Lysine Iron agar (LIA) slants, commercially available or follow manufacturer’s 

instructions for preparation.

 Urea Broth tubes or Urea Agar slants (use Proteus vulgaris ATCC 13315 as positive 

control and E. coli MDP 017 as negative control)

 Nutritive broth such as Tryptic Soy or Brain Heart Infusion, follow manufacturer’s 

instructions for preparation.

 Tryptic Soy agar with 5% Sheep’s Blood, commercially available.
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Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 4 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

 Dynabeads®anti-Salmonella, Invitrogen or Pathatrix®

 Salmonella polyvalent somatic (O) antiserum, Poly A-I and Vi (poly O antiserum): 

Contains agglutinins for at least the following somatic (O) antigens: 

1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,19,22,23,24,25,34, and Vi. They are agglutinins 

for somatic (O) groups: A, B, C1, C2, D, E1, E2, E3, E4, F, G1, G2, H, I and Vi, DIFCO, 

Becton Dickinson.

 Salmonella polyvalent flagellar (H), commercially available rapid test (REMEL) or 

DIFCO Salmonella H Antiserum Poly a-z, Becton Dickinson.

 Formalinized physiological saline solution: Prepare by adding 6-mL formaldehyde 

(HCHO) solution (36-38%) to 1-L of sterile 0.85% w/v saline (NaCl) solution.

 Physiological saline solution, sterile 0.85% w/v saline (NaCl) solution.

6.3. Controls (Specific strains are listed in SOP MDP-QA-03)

6.3.1 Carry all cultural controls from all screening methods previously completed through 

 this entire procedure. Refer to SOP MDP-LABOP-02 for control setup. 

NOTE: Alternatively, it is acceptable for laboratories to set up appropriate media controls (positive, 

negative, and uninoculated) from pure cultures without using the cultural controls from the 

screening methods. Each laboratory shall have written procedures for ensuring the appropriate 

controls are used for this procedure.

 6.3.2 If any of the controls fail to yield a satisfactory result refer to SOP MDP-QA-03.

 6.4 Isolation of Salmonella 

6.4.1 Streak one or more each of HE, XLD, and BS plates (chromogenic agar plates may 

also be used) from the TT broth culture, the RV broth culture and M broth 

cultures that were initiated as per MDP MTH-09 SOP. It is recommended that the 

laboratory streak onto several selective agar plates in order to increase the chances 

of identifying typical colonies. Incubate plates at 35 ± 2oC for 24 ± 2 hours. If no 

typical colonies are present on the BS plates, re-incubate the BS plates at 35 ± 2oC 

for an additional 24 ± 2 hours.
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 5 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

6.4.2 Laboratories may perform IMS in order to enhance isolation of Salmonella. Use 

UPB pre-enriched cultures that tested positive for Salmonella by PCR. Follow 

manufacturer’s instructions for performing IMS. Plate or streak the eluted sample 

on HE, XLD and BS agar plates and incubate plates at 35 ± 2oC for 24 ± 2 hours. If 

colonies are present on the BS plates, pick typical colonies and then re-incubate the 

BS plates at 35 ± 2oC for an additional 24 ± 2 hours.

 6.5 Selective Enrichment and Plating (for BAXpositive samples only).

6.5.1 Transfer 1mL of the pooled and individual (the 3 samples that were positive in the 

pooled culture) UPB preenriched BAXSalmonella-positive culture identified using 

SOP MDP-MTH-04 into 10 mL TT broth and incubate at 42 ± 0.2

oC for 18-24 hours.

6.5.2 In parallel, transfer 0.1 mL of the pooled and individual UPB preenriched BAX

Salmonella-positive culture identified using SOP MDP-MTH-04 into 10 mL of RV 

broth and incubate for 18-24 hours at 42 ± 0.2

oC.

6.5.3 Transfer or set-up all appropriate positive, negative and blank controls to TT and 

RV broths as above.

6.5.4 Streak the TT, RV and M Broth enriched cultures on selective agar plates (XLD, 

HE, BS and chromogenic agar plates) for isolation. Incubate plates at 35 ± 2

oC for 

24 ± 2 hours. If no typical colonies are present on the BS agar plates, re-incubate 

the BS plates at 35 ± 2oC for an additional 24 ± 2 hours.

6.5.5 Examine the agar plates for the presence of typical Salmonella colonies.

Typical colony characteristics of Salmonella Other Organisms 

Medium Colony Characteristics

HE blue/green w/ or w/o black center Yellow, orange

XLD pink w/ or w/o black center Yellow, orange

BS

Brown/gray or black w/ or w/o a

metallic sheen

Chromagenic agar

refer to manufacturer’s user 

guide

refer to manufacturer’s user 

guide
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Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 6 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

 6.6 Identification (If you obtain a pooled BAX®positive result followed by an individual 

BAX®negative with an individual negative VIDAS or a pooled negative VIDAS, you 

can consider this to be a double negative and testing can stop. Otherwise, continue 

with steps listed below.) 

 6.6.1 After examining the plates, pick at least 10 suspect Salmonella colonies (if available) 

from any selective agar plates and inoculate triple sugar iron (TSI) agar slants, lysine 

iron agar (LIA) slants, and Urea agar slants or Urea broth tubes for each colony. (If 

no typical or suspect Salmonella colonies are present, TSI, LIA, Urea slants/tubes

should still be inoculated. Pick at least 10 atypical colonies for this step.) Inoculate 

TSI, LIA, and Urea slants/tubes according to instructions given in FDA BAM, 

chapter 5.

Note: Use professional judgment and experience in deciding the number of plates and 

number of colonies needed for screening which depends on the extent of contamination, 

the background microflora level, the commodity type, post harvest handling and type of 

enrichment used.

 6.6.2 Incubate the TSI, LIA, and Urea agar slants for 18-24 hours at 35  2C. 

 6.6.3 Examine slants. Salmonella typically produce alkaline (red) slant and acid 

(yellow) butt, with or without production of H2S (blackening of agar) in TSI agar. 

In LIA agar, Salmonella typically produce alkaline (purple) slant and butt. Refer 

to FDA BAM, chapter 5 for further instruction and interpretation of 

slant/tube results.

 6.6.4 If typical Salmonella reactions are observed, proceed to confirmation steps 

below. If TSI, LIA, and Urea reactions are atypical of Salmonella, no further 

confirmation is needed as the isolate is not Salmonella.

 6.7 Biochemical Confirmation

 6.7.1 From the TSI or LIA or Urea slants/tubesthat show reactions typical of Salmonella, 

streak onto BA plates to check for fluorescence or manufacturer’s suggested media 

source. 
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Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 7 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

6.7.2 Incubate BA plates 18-24 hours at 35  2C or follow manufacturer’s 

recommended incubation conditions.

6.7.3 Select 3-5 isolated colonies from BA or manufacturer’s suggested media source 

and identify each using VITEK® and/or another standard method of identification, such as 

O/H serology.

NOTE: Laboratories shall notify MPO if other pathogenic bacteria such as Enterobacter 

sakazakii are identified.

6.7.4 Perform serology per manufacturer’s instructions and the internal laboratory 

procedures for Salmonella-specific polyvalent somatic O and flagellar H antigens. As an 

option, an agglutination-based test with antisera specific for major serogroups such as 

serogroups B, C, etc. or combinations of antisera can be used for preliminary serotype 

identification. For agglutination tests, use small amount of growth from single colonies.

 6.8 Reporting and Shipping

6.8.1 IMMEDIATELY following completion of biochemical and serological tests, 

report confirmed results to MP per SOP MDP-DATA-01 on Atch 01, Results Notification 

Form, and prepare (3) isolate slants for shipment to ODA for antimicrobial susceptibility 

testing and, if necessary, PFGE and serotyping.

6.8.2 For archiving and shipping, select one typical isolate that has been identified as 

Salmonella by both biochemical means and serotyping. 

6.8.3 Refer to MDP-SHIP-03 SOP for preparation of cultures for shipment.

Disclaimer: Reference to brand names (kits, equipment, media, reagents, etc.) does not constitute 

endorsement by this agency.
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 8 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

Cultural 

(selective 

agar plates) 

BAX Salmonella positive UPB 

pooled/individual cultures

Re-streak on TSI/LIA/Urea

followed by BA and/or 

manufacturer's suggested

media source

Minimum of 

10 typical

Colonies

Serotyping

3-5 colonies on VITEK 

Select one 

confirmed isolate 

for shipping

TT, RV & M Broth

enrichment

Immediately Report

Confirmed Positive to 

MP

M broth to 

VIDAS

Optional: Salmonella Isolation for BAX Positive Samples Flowchart
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 9 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

Mary Tijerina 7 July 2011

___________________________________________________________

Revised by: Mary Tijerina Date

Microbiologist, Monitoring Programs Division

8609 Sudley Road, Suite 206, Manassas, VA 20110

(703) 330-2300 x111

Maya Achen 6 July 2011

Approved by: Maya Achen Date

Chairperson, MDP Technical Advisory Group

Ohio Department of Agriculture Consumer Analytical Laboratory, Bldg 3

8995 E Main St, Reynoldsburg, OH 43068

(614) 728-2790

Shanker Reddy 6 July 2011

___________________________________________________________

Reviewed by: Shanker Reddy Date

Microbiologist, Monitoring Programs Division

8609 Sudley Road, Suite 206, Manassas, VA 20110

(703) 330-2300 x135

Diana Haynes 7 July 2011

Approved By: Diana Haynes Date

Deputy Director, Monitoring Programs Division

8609 Sudley Road, Suite 206, Manassas, VA 20110

(703) 330-2300

ORIGINAL SIGNATURE PAGE MAINTAINED BY USDA, AMS, SCIENCE & TECHNOLOGY, MONITORING PROGRAMS DIVISION

ELECTRONICALLY REPRODUCED SIGNATURES
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 10 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

Revision 04 June 2011 Monitoring Programs Division

 Deleted “(optional)” from “Dynal® Automated...” sentence, Section 6.1

 Added “Optional: SDIX RapidCheck© SELECTTM Salmonella media, XLT4, Brilliant 

Green Sulfa Agar (BGSA), Chromagenic agars”, Section 6.2

 Deleted “Chromogenic Salmonella agar such as CHROMagar Salmonella (DRG 

International), Salmonella SM ID2 (bioMerieux), or equivalent (optional), Section 6.2

 Added “Urea Broth tubes or Urea Agar slants (use Proteus vulgaris ATCC 13315 as 

positive control and E. coli MDP 017 as negative control)”, Section 6.2

 Revised sentence to read as “Dynabeads®anti-Salmonella, Invitrogen or Pathatrix®” by 

removing catalog number and the word “(optional), Section 6.2

 Deleted bold words and added italicized words “Although not required, laboratories 

may also perform IMS using anti-Salmonella Dynabeads in order to enhance isolation 

of Salmonella using UPB pre-enriched cultures that tested positive for Salmonella by 

PCR. Follow manufacturer’s instructions for performing IMS. Plate or streak the eluted 

sample on HE, XLD and BS agar plates and incubate plates at 35 ± 2oC for 24 ± 2 hours.

If colonies are present on the BS plates, pick typical colonies and then re-incubate the 

BS plates at 35 ± 2oC for an additional 24 ± 2 hours.”, Section 6.4.2

 Deleted “CHROMagar Salmonella” and “SM ID2 (SM2)” from table, Section 6.5.5

 Added “Chromagenic agar” to table, Section 6.5.5

 Deleted bold words and added italicized words “After examining the plates, pick at least 

5-10 suspect Salmonella colonies (if available) from any selective agar plates and 

inoculate triple sugar iron (TSI) agar slants, lysine iron agar (LIA) slants, and Urea agar 

slants or Urea broth tubes for each colony. (If no typical or suspect Salmonella colonies 

are present, TSI, LIA, Urea slants/tubes should still be inoculated. Pick at least 10

atypical colonies for this step.) Inoculate TSI , LIA, and Urea slants/tubes according to 

instructions given in FDA BAM, chapter 5.”, Section 6.6.1

 Added Note, Section 6.6.1

 Added words “...and Urea... Section 6.6.2

 Deleted words “...TSI and LIA...” and added bold word “...slant/tube...”, Section 6.6.3

 Added words “...and Urea...”, Section 6.6.4

 Added words “...or Urea tubes...”, Section 6.7.1

 Deleted bold words and added italicized words “Select 3-5 isolated colonies from BA or 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 11 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

manufacturer’s suggested media source and identify each using VITEK® and/or another 

official standard method of identification, If biochemical assay results are consistent 

with Salmonella profile, proceed with serology such as O/H serology.” , Section 6.7.3

 Updated Flowchart

Revision 03 December 2009 Monitoring Programs Division

 Added Outline of Procedures, Section 4

 Alphabetized and removed numbering in References, Section 5

 Removed numbering in Equipment and Materials, Section 6.1

 Removed numbering in Media and Reagents, Section 6.2

 Added “M broth: 16 x 150 mm test tubes containing 10 mL aliquots”, Section 6.2

 Reworded Section 6.4.1 to “Streak one or more each of HE, XLD, and BS plates 

(Chromogenic agar plates may also be used) from the TT broth culture, the RV broth 

culture and M broth cultures that were initiated as per MDP MTH-09 SOP. It is 

recommended that the laboratory streak onto several selective agar plates in order to 

increase the chances of identifying typical colonies. Incubate plates at 35 ± 2oC for 24 ± 

2 hours. If no typical colonies are present on the BS plates, re-incubate the BS plates at 35 

± 2oC for an additional 24 ± 2 hours.”

 Removed “Note” statements (Once 35±2°C incubation has been completed, in case of 

weekend, holiday, etc., plates may be removed from incubator and allowed to sit at room 

temperature or be refrigerated until next business day. If plates are removed from 

incubator, please insure that information, comments, observations, etc., are recorded as 

part of data packets and/or sample data transmitted to MPO.) from Section 6.4.1

 Added “If no typical colonies are present on the BS agar plates, re-incubate the BS plates 

at 35 ± 2oC for an additional 24 ± 2 hours”, Section 6.5.4

 Added “If you obtain a pooled BAX® positive result followed by an individual BAX®

negative with an individual negative VIDAS or a pooled negative VIDAS, you can 

consider this to be a double negative and testing can stop. Otherwise, continue with steps 

listed below.”, Section 6.6

 Added words “to check for fluorescence or manufacturer’s suggested media source”, 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No: MDP-MTH-10 Page 12 of 12

Title: Isolation and Identification of Salmonella using Cultural Methods 

Revision: 04 Replaces: 1/1/2010 Effective: 9/1/2011

Section 6.7.1

 Added words “or follow manufacturer’s recommended incubation conditions”, Section 

6.7.2

 Added words “or manufacturer’s suggested media source” in Section 6.7.3

 Replaced words “Fillable Reporting” with “Results Notification Form” and added words 

“and prepare (3) isolate slants for shipment to ODA for antimicrobial susceptibility 

testing and, if necessary, PFGE and serotyping.”, Section 6.8.1

 Added “Optional” to Flowchart title

 Added “M Broth” and “M Broth to VIDAS” to Flowchart

 Added “and/or manufacturer’s suggested media source” in Flowchart

Revision 02 September 2009 Monitoring Programs Division

 Updated References, Section 4

 Revised Sections 5.4 through 5.8

 Updated Flowchart

Revision 01 March 2009 Monitoring Programs Division

 Added GN cards to 6.1.2

 Added 6.4.1

 Added, “pooled and individual (the 3 samples that were positive in the pooled culture)” to 

6.4.5.1.

 Added “pooled and individual” to 6.4.5.2.

 Added the note in 6.6.3.

 Revised the flowchart to include pooled and individual UPB enriched samples.