FROM THE BENCH
climate conditions. Finally, we tested four
enrichment media for recovery of small
numbers of Salmonella. For all phases, we
used qPCR 5 to confirm the identity of each
suspect-Salmonella colony. By January 2019
we completed all laboratory work and
data analysis.
The Provisional Workflow
Once a stool specimen has been
confirmed as CIDT-positive for Salmonella,
clinical labs should hold the specimen
at room temperature until ready for
shipment to the PHL. When shipped from
the clinical lab, the specimen should be
placed on ice packs. At the PHL, it should
be stored at room temperature until PHL
staff are ready to begin isolation. Then
the specimen should be used to inoculate
both a Hektoen Enteric (HE) Agar and an
enrichment medium (e.g., Selenite Broth,
Tetrathionate Broth or Modified Semi-
Solid Rappaport Vassiliadis Agar) on the
same day; these should be incubated
according to manufacturer’s instructions.
The next day, if a Salmonella isolate
cannot be recovered from the HE Agar, the
enrichment should be used to inoculate a
fresh HE Agar; ideally a Salmonella isolate
will be recovered the following day.
project for CIDT-positive Shiga toxin-
producing Escherichia coli stool specimens;
recommendations will be made after
completion. While it is important to focus
on efficient and cost-effective isolate
recovery workflows, foodborne illness
surveillance is moving towards an isolate-
free future. Currently, PHLs use WGS of
microbial isolates as a primary subtyping
method, so isolate availability is critical
for surveillance.
Culture-independent surveillance
methods such as targeted amplicon
sequencing and shotgun metagenomic
sequencing of whole stool specimens
could greatly reduce the need to isolate
pathogens from stool specimens, thus
decreasing the burden of recovering
an isolate from stool. 4 However, these
technologies are relatively new and
expensive, and they have not yet been
optimized for use in foodborne disease
surveillance. 4 Because of Salmonella’s
public health burden and the lack of
validated direct-from-specimen subtyping
methods, it is essential to maintain isolate
availability.n
What’s Next?
During summer 2019, we asked three PHLs
to pilot this workflow in parallel with their
standard methods on 100 CIDT-positive
Salmonella specimens that they received.
We also started an isolate recovery
Katie Dillon, ORISE Research Fellow
Recently, culture-independent
diagnostic tests (CIDTs) have
emerged as an alternative to culture-
based methods and are proving to be
faster, cheaper, and more sensitive
than culture-based methods
DIGITAL EXTRA:
This article is based upon the Best Poster
Award at APHL 2019. Click here for all
abstracts from the annual conference.
References
1. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M, Roy SL, Jones JL, Griffin PM. Foodborne illness acquired in
the United States. Emerg Infect Dis [Internet]. 2011 Jan [2019 Sep 11];17(1):7-15. Available from: https://www.ncbi.nlm.
nih.gov/pmc/articles/PMC3375761/
2. Huang JY, Henao OL, Griffin PM, Vugia DJ, Cronquist AB, Hurd S, et al. Infection with Pathogens Transmitted Commonly
Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance - Foodborne
Diseases Active Surveillance Network, 10 U.S. Sites, 2012–2015. MMWR Morb Mortal Wkly Rep [Internet]. 2016 Apr 15
[2019 Sep 11];65(14):368-371. Available from: https://www.cdc.gov/mmwr/volumes/65/wr/mm6514a2.htm
3. Langley G, Besser J, Iwamoto M, Lessa FC, Cronquist A, Skoff TH, et al. Effect of Culture-Independent Diagnostic Tests on
Future Emerging Infections Program Surveillance. Emerg Infect Dis [Internet]. 2015 Sep [2019 Sep 11];21(9):1582-1588.
Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550165/
4. Shea S, Kubota KA, Maguire H, Gladbach S, Woron A, Atkinson-Dunn R, et al. Clinical microbiology laboratories’ adoption
of culture-independent diagnostic tests is a threat to foodborne-disease surveillance in the United States. J Clin Microbiol
[Internet]. 2017 Jan [2019 Sep 11];55(1):10-19. Available from: https://jcm.asm.org/content/55/1/10.short
5. Malorny B, Paccassoni E, Fach P, Bunge C, Martin A, Helmuth R. Diagnostic Real-Time PCR for Detection of Salmonella in
Food. Appl Environ Microbiol [Internet]. 12 July 2004 [2019 Sep 18];70(12):7046-7054. Available from: https://aem.asm.
org/content/70/12/7046.short
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