AHL Newsletter, June 2015

For a pdf copy of AHL Newsletter, June 2015 please click here

May 1, 2015, AHL User’s Guide and Fee Schedule

Effective May 1, 2015 we have updated our tests and fees. We’ve added in various new or modified tests over the past year: Porcine coronavirus (PEDV, TGEV, PDCoV), triplex PCR; Orf virus/Papular stomatitis virus, PCR; virus sequencing (Canine distemper virus, Canine parvovirus 2/Feline panleukopenia virus); Feline calicivirus/Felid herpesvirus 1, PCR; fish viral hemorrhagic septicemia virus (VHSV), PCR; fish bacterial identification by MALDI-TOF MS; Batrachochytrium dendrobatidis and B. salamandrivorans, duplex PCR.

We have inactivated many older or less popular tests, such as virus isolation and fluorescent antibody testing, in favor of more suitable PCR tests.

Our complete test list is available in our May 1, 2015 AHL User’s Guide and Fee Schedule recently sent out to our clients. For a searchable test listing and pricing, our clients can visit us at our website at www.ahl.uoguelph.ca   If you do not have client access for fees – please contact  ahlinfo@uoguelph.ca , or call 519 824 4120 ext. 54320 and we will be more than happy to help you with this or anything else you might require.

Once again, we look forward to serving you!   

AHL staffing update

Mike Deane

Liz King

Pauline Smikle

Michael Deane, joins us as our new Communications Assistant in the Ontario Animal Health Network, supporting Dr. Melanie Barham, our OAHN Coordinator, under the Disease Surveillance Program (DSP).

Liz King has assumed the role of Quality Manager for Lab Services Division, following the recent retirement of Nadine Ryan. Liz, with a staff of 4, oversees the ongoing maintenance of the LSD quality program, and the whole range of LSD quality accreditations—ISO/IEC 17025, AAVLD, and OECD GLP.

Pauline Nelson-Smikle is the new Information Technology Manager for Lab Services Division, replacing the retiring Phyllis Few. Pauline, with a staff of 4, ensures the ongoing functionality of all LSD IT infrastructure, including our LIMS (Lab Information Management System, i.e., LabVantage or Sapphire).

“Influenza D” in cattle and swine? Keeping an eye out for new diseases…        

Davor Ojkic, Anna Marom, Murray Hazlett

A novel influenza virus with 50% homology to human influenza C viruses was isolated from a pig during an outbreak of influenza-like illness in Oklahoma, and 9.5% of laboratory submitted porcine serum samples were serologically positive when tested subsequently (1). This virus was later demonstrated via PCR from nasal swabs in 18% of cattle with respiratory disease (45 tested), and was found serologically to be common in most bovine herds (2).

The proposal is to call this orthomyxovirus “influenza D virus”. We did a brief survey of recent respiratory disease submissions looking for involvement of this novel virus. Histology scrolls for PCR testing were prepared from histology blocks – including bovine pneumonic lung (15 blocks), porcine pneumonic lung (15 blocks), and bovine and porcine abortion tissues (5 blocks each – used as controls). In addition, 15 miscellaneous non-fixed bovine samples were tested (7 lung, 3 mucosal swabs, 2 serum samples, and 1 fetal lung/tissue pool.

No “influenza D” virus was identified in any of the samples tested. This was admittedly a very small study, and is part of our ongoing disease surveillance efforts. The test may be periodically requested by pathologists in unusual or suspect cases however it will not be available as a routine test.

OAHN podcasts

Making sense of Salmonella spp. serotyping results

Đurđa Slavić, DVM, MSc, PhD  Updated February 2016

At the Animal Health Laboratory (AHL), all clinical Salmonella isolates are sent for serotyping to Laboratory for Foodborne Zoonoses (LFZ) because of public health concerns.  As a rule of thumb, if Salmonella spp. are isolated from multiple samples from the same farm, their colony morphology is examined.  If they look similar, only one colony is selected for serotyping.  If morphology differs, multiple colonies are sent.  Salmonella isolates are sent to LFZ every Wednesday and it usually takes 4-6 weeks to receive serotyping and phagetyping results back.  It should be noted that phagetyping is done only for Salmonella Enteritidis, Salmonella Typhimurium, and Salmonella Heidelberg.

Salmonella taxonomy underwent a major overhaul in 2005 when Salmonella enterica and Salmonella bongori (formerly group V) were established as the only 2 species of salmonellas.  At the same time, it was recognized that the S. enterica group is comprised of 6 subspecies:

  1. Salmonella enterica subsp. enterica (group I)
  2. Salmonella enterica subsp. salamae (group II)
  3. Salmonella enterica subsp. arizonae (group IIIa)
  4. Salmonella enterica subsp. diarizonae (group IIIb)
  5. Salmonella enterica subsp. houtenae (group IV)
  6. Salmonella enterica subsp. indica (group VI)

Differentiation of Salmonella species and subspecies is relatively straightforward and it can be done biochemically.  However, within each Salmonella subspecies, isolates can be further divided into different serotypes.  Serotyping of salmonellas is based on immunological detection of 2 groups of cell surface antigens: lipopolysaccharides (O antigens) and flagellin proteins (H antigens).  Moreover, H antigens in salmonellas are usually expressed as phase 1 and phase 2 antigens, a feature unique to Salmonella sp.  As a result, each Salmonella enterica serotype has a specific antigenic formula shown as a combination of letters and numbers.  This formula consists of subspecies designation (i.e., I, II, IIIa, IIIb, IV, VI), O antigens (i.e., a number or combination of numbers), phase 1 (i.e., lower case letter), and phase 2 flagellin (i.e., lower case letter or combination of numbers) antigens (Fig. 1).  When all of the antigens are detected for a specific serotype of group I salmonellas, then that serotype is reported by a name.  For example, Salmonella entericasubsp. enterica will be reported as serotype Typhimurium only if the following antigens are detected: S. I 4,5,12:i:1,2 (Fig.1).  If any of these antigens are not detected, then that particular isolate will be reported by its antigenic formula only (e.g., S. I 4,5,12:i:-).  In contrast to group I salmonellas, serotypes belonging to groups II through VI are always reported by their antigenic formulas only (e.g., S. IIIa 51:z4,z23:-). 


Fig. 1.  Antigen designation in Salmonella sp. serotyping scheme. 

To translate this into a practical perspective when you are looking into Salmonella serotyping results - if there is a name reported, it means that this particular serotype belongs to group I and that all antigens defining that serotype were detected.  If there is an antigenic formula only, the first thing that one needs to look at is the subspecies designation.  If there is a subspecies designation from II through VI, the full serotype is reported and there is not much additional information to be inferred from the results.  However, if an antigenic formula for subspecies I is reported, in some cases more information can be gathered including serotype variants.  A variant that we most frequently see in the lab is a monophasic S. Typhimurium with antigenic formula S. I 4,5,12:i:-.  This antigenic formula defines a variant of S. Typhimurium missing a phase 2 H antigen.  Some other variants of S. Typhimurium are shown in Table 1.

Table 1.  Variants of S. Typhimurium and their antigenic formulas.


Antigenic formula


S. I 4,5,12:i:-


S. I 4,5,12:nonmotile

S. I rough:i:1,2