Bacterial cultures – Aerobic – Reference ID/Confirmation

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Background

This page provides identification/confirmation information for aerobic bacterial cultures at Public Health Ontario (PHO). The causative agent of variety of bacterial infections are aerobic bacteria.

For information regarding other testing options, refer to the following PHO webpage:

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Testing Indications

The accurate identification of bacterial cultures assists in the diagnosis and treatment of patients with bacterial infections. Proper interpretation of culture results is dependent on specimen source and known pathogenicity of the isolated organism.

Acceptance/Rejection Criteria

Primary specimens are not acceptable. Only pure cultures are accepted.
If the source of isolation of the culture is not indicated in the requisition, it will be rejected.
Mixed or non-viable cultures will not be tested. A written report will be issued to indicate that the test has been rejected.
Mis-labelled or un-labelled culture will not be tested. A report will be sent stating “Culture received un-labelled” or “Requisition identification does not match the identification information on the culture received. Please re-submit.”
The submitting laboratory will be contacted regarding isolates or specimens from critical sites (e.g. brain abscess) that are submitted inappropriately (e.g. improper transport conditions or mis-labelled/un-labelled).

Specimen Collection and Handling

Specimen Requirements

Test Requested	Required Requisition(s)	Specimen Type	Minimum Volume	Collection Kit
Bacterial Cultures-Aerobic-Reference ID/Confirmation	Reference Bacteriology Requisition	Pure viable subculture of organism on appropriate media that supports the growth (e.g. Blood Agar) or a swab of a pure subculture in Amies transport medium^2,3

Submission and Collection Notes

Complete all fields of the requisition form, including:

Test(s) requests (includes confirmation and identification) and indications for testing
Patient setting/population/source
- indicate if immunocompromised
Culture information (presumptive identification, gram morphology, catalase, oxidase)
Clinical/ epidemiology information
Date of primary specimen collection
Source of isolation (very important):
- Type of urine specimen(s) (e.g. midstream, indwelling catheter, cystoscopy etc.)
- The site and type of wound swab; be as specific as possible (e.g. animal bite, surgical wound, decubitus ulcer, etc.
- The type of specimen if other than blood culture, urine or wound swab, please provide as much detail as possible
- The number of consecutive blood cultures positive for the submitted isolate when isolates are from blood cultures

Label the culture container(s) with the patient’s first and last name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.

If the bacterial culture submitted for identification confirmation is provided on a swab in Amies charcoal transport media or broth media (instead of on a plate) the turnaround time will be delayed by at least 24 hours.

If the healthcare provider requires susceptibility testing, the submitter must call within 5 days of receiving final results and provide necessary information and justification for susceptibility testing request.

Do not submit multiple isolates from the same specimen/site of infection - for polymicrobic infections, only submit most clinically significant pathogens for testing.

Primary specimens are unacceptable as they should be processed in the originating lab. A report will be issued to indicate that the test has been rejected.

Where full bacterial identification and susceptibility testing is clinically indicated, such as for an immunocompromised patient, please clearly indicate this on the requisition.

Storage and Transport

Place the sealed culture in a biohazard bag and properly seal. Store at 2-8°C while awaiting for shipping. Transport a fresh subculture to ensure viability on receipt. It should be shipped to PHO’s laboratory within 48 hours of isolation. All cultures must be shipped in accordance to the Transportation of Dangerous Good Act.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Aerobic bacteria culture isolates are tested Monday to Friday at PHO’s laboratory, Toronto site.

Turnaround time is 5-7 business days from date of receipt at PHO’s laboratory.

Test Methods

All bacterial culture isolates are identified/confirmed by conventional identification methods:

Gram stain morphologic examination
Biochemical testing
Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)

If the conventional identification methods are not able to provide definitive identification of the isolate being tested, 16S rRNA gene sequencing will be performed on the isolate.

Algorithm

Consistent with principles of appropriate test utilization, the following takes place for the testing of the bacteria listed in Table A cultured from urine, lower respiratory tract specimens (e.g. sputa), wound/drainage:
- Limited bacterial identification will be performed to the extent to which phenotypically similar but medically important organisms can be safely excluded.
- For mid-stream urine, urine from in and out catheterization or urine from indwelling catheters, limited identification and no susceptibility testing will be performed on the organisms listed in Table A.
For blood cultures, the following algorithm is used:
- If only one set of blood culture bottles is positive with an organism listed in Table A within a 24-hour timeframe, limited identification will be performed
- NOTE: The list of organisms in Table A does not apply to neonatal blood cultures or those from individuals identified on the requisition as being immunocompromised
For cultures isolated from critical specimens (e.g. CSFs), surgically collected specimens (e.g. tissues) and other sterile sites specimens (e.g. synovial fluids) full identification testing will be performed.
Other than the scenarios described in Table A, full identification will be performed on sterile site isolates; for all others, identification testing will be performed only on special request by the healthcare provider based on clinical relevance.
Identification will be performed on organisms commonly considered to be contaminants/commensal flora only on special request by the healthcare provider based on clinical relevance. Contact Public Health Ontario’s laboratory Customer Service for these requests.

Table A

Organisms commonly considered to be contaminants/commensal flora for which limited identification will be performed (this is not to be considered a complete list)

Source	Organism
Single Positive Blood Culture^1,3-6	Coagulase- negative Staphylococcus andrelated organisms (e.g. Micrococcus spp, Rothia spp), not including S. lugdunensis “Viridans group Streptococci” Corynebacterium spp and related organisms (e.g. Arthrobacter spp), not including C. diphtheriae Bacillus spp and related organisms (e.g. Paenibacillus spp, Lysinibacillus spp etc), not including B. anthracis Neisseria spp other than N. meningitidis or N. gonorrhoeae Propionibacterium sppand Cutibacterium spp
Urine⁸	Lactobacillus spp Viridans group Streptococcus Coagulase- negative Staphylococcus andrelated organisms (e.g. Micrococcus spp, Rothia spp) Corynebacterium spp and related organisms (e.g. Arthrobacter spp), not including C. urealyticum, C. glucoronolyticum and C. pseudogenitalium Bacillus spp and related organisms (e.g. Paenibacillus spp, Lysinibacillus spp etc.), not including B. anthracis Neisseria spp other than N. meningitidis, N. gonorrhoeae
Lower Respiratory Tract Specimens^2,7,9	Viridans group Streptococcus Neisseria sppincluding N. meningitidis (identification only) Coagulase- negative Staphylococcus andrelated organisms (e.g. Micrococcus spp, Rothia spp), not including S. lugdunensis Corynebacterium spp and related organisms (e.g. Arthrobacter spp), not including C. pseudodiphtheriticum and C. diphtheriae Moraxella sppother than M. catarrhalis Enterococcus spp
Wound swab and Drainage³	Coagulase -negative Staphylococcus, unless isolated from chest/sternum Coagulase -negative Staphylococcus, not including S. lugdunensis “Viridans groupStreptococci” Corynebacterium spp and related organisms (e.g. Arthrobacter spp), not including C. diphtheriae Bacillus spp and related organisms (e.g. Paenibacillus spp, Lysinibacillus spp etc.), not including B. anthracis Micrococcus spp Neisseria spp other than N. meningitidis, N. gonorrhoeae Propionibacterium sppand Cutibacterium spp

Reporting

The Laboratory Test Report will show the identification of the isolate : “ Isolate identified as [Genus species]”

Results are reported to the ordering physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

References

Institute for Quality Management in Healthcare (IQMH): Consensus Practice Recommendations – BACT-Blood Cultures. Revision date: 2017-09-28.
Institute for Quality Management in Healthcare (IQMH): Consensus Practice Recommendations – BACTSputum specimens. 2013-10-07.
Institute for Quality Management in Healthcare (IQMH): Consensus Practice Recommendations – BACT Superficial wound swabs. 2013-12-09.
Miller JM, Binnicker MJ, Campbell S, Carroll KC, et al. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clinical Infectious Diseases, Volume 67, Issue 6, 31 August 2018, Pages e1–e94, doi.org/10.1093/cid/ciy381
Clinical and Laboratory Standards Institute (CLSI). Principles and procedures for blood culture; approved guideline. CLSI document M47-A, Vol. 27, No. 17. Wayne, Pennsylvania, USA. 2007.
Baron EJ, Weinstein MP, Dunne Jr WM, Yagupsky P, Welch DF, Wilson DM. 2005. Cumitech 1C, Blood Cultures IV. Coordinating ed., EJ Baron. ASM Press, Washington DC.
Sharp SE, Robinson A, Saubolle MA, Santa Cruz M, Carroll K, Baselski V. 2004. Cumitech 7B, Lower respiratory tract infections. Coordinating ed., SE Sharp. ASM Press Washington, DC.
McCarter YS, Burd EM, Hall, GS, Zervos M. 2009. Cumitech 2C, Laboratory Diagnosis of Urinary Tract Infections. Coordinating ed. SE Sharp. ASM Press, Washington, DC.
Waites KB, Saubolle MA, Talkinton DF, Moser SA, Baselski V. 2006, Cumiteech 10A, Laboratory Diagnosis of Upper Respiratory Tract Infections. Coordinating ed. SE Sharp. ASM Press, Wahington, DC.