Acanthamoeba strains isolated
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
12
10
Number isolated
LABORATORY
TRENDS
8
Vancouver, BC
6
4
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
February 16, 2012
Year
Laboratory News .................................1
Carbapenemase Resistance ............2
Gastrointestinal Outbreaks .............3
Enteric Surveillance ............................4
Respiratory Outbreaks ......................5
Influenza Surveillance .......................6
Laboratory News
Canadian Tuberculosis Laboratory Technical Network
The Canadian Tuberculosis Laboratory Technical Network
(CTLTN) is a national network made up of a technical
head of each Provincial or Territorial laboratory that
performs Mycobacteriology testing, a representative from
the National Reference Centre for Mycobacteriology,
Public Health Agency of Canada (PHAC), a designee from
the Tuberculosis Prevention and Control, PHAC, and a
designee of the National Microbiology Laboratory.
For BC and the Yukon Territory, the mandate to continue
to improve molecular methods for detection was
accomplished by implementing real-time PCR of M.
tuberculosis complex in 2011. TB PCR is now a daily test
at the PHMRL, improving timeliness of results reporting.
Implementation of the Mycobacterial Interspersed
Repetitive Units - Variable Number of Tandem Repeats
(MIRU-VNTR) fingerprinting method of M. tuberculosis
isolates has also begun. A BioNumerics database has been
built for housing all the fingerprinting data.
Through its pool of expertise from each province/territory,
the CTLTN continues to strive towards goals of:
•
•
•
•
Implementation of biosafety guidelines;
Participation in the national surveillance and
proficiency programs; and,
Exchange of services and information regarding new
technologies.
The main discussion this year was the M. tuberculosis
complex (MTBC) Biosafety Guidelines. A draft document
was disseminated in November, 2011 with the
opportunity for CTLTN members’ review and input. The
other discussion was surrounding the changes to the
recently published CLSI M24-A2, Susceptibility Testing
of Mycobacteria. Members enjoyed another successful
meeting with sights towards next year.
The network recently convened in Vancouver during their
annual meeting to review the previous year’s targets
and to define goals for this year. Dr. Mabel Rodrigues,
TB/Mycobacteriology Section Head, Public Health
Microbiology & Reference Laboratory (PHMRL) attended
as the BC and Yukon Territory representative.
•
In this Issue:
Standardization of methodologies (conventional and
state-of-the-art);
Better biosafety operational practices and physical
requirements;
Toxoplasma PCR: A Supplemental Test for Diagnosing
Active Infection from Unusual Clinical Samples
Toxoplasma gondii is an obligate intracellular protozoan
that infects most species of warm-blooded animals,
including humans. Humans can be infected in many
different ways such as by ingestion of raw or undercooked
meat containing T. gondii cysts, by contaminated water, or
congenitally by placental transmission from the mother
with acute or disseminated infection. Transmission may
also occur through organ transplant or blood transfusion.
A serological test is the most common clinical practice
although histopathology and culture have been
considered as part of the gold standard for the diagnosis
of active disease. For T. gondii specific serology, the
PHMRL offers both IgM and IgG tests, followed by IgG
avidity testing when appropriate.
continued...
Page 1
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
T. gondii may be detected prenatally by PCR testing of amniotic fluid. This test is offered in select cases and done by
very few clinical laboratories in North America. The PHMRL has developed a PCR test for toxoplasmosis targeting the B1
gene and is currently running parallel testing with the reference laboratory. Validation of this test, however, is challenging
since positive cases are rarely seen by PCR. Once this validation is completed, clients may submit a wider range of
suspected samples for toxoplasmosis diagnosis. The PHMRL is always on hand to assist clinicians with suspected cases of
toxoplasmosis.
Carbapenemase Resistant Enterobacteriaceae (CRE)
The latest counts for cases of carbapenemase resistance in BC can be
found in Table 1 (updated from our December 2011 issue). Fourteen
cases with the New Delhi Metallo-β-lactamase gene (NDM) endemic
to South Asia have been detected since this work began in 2010. Two
cases had the Klebsiella pneumoniae carbapenem (KPC) β-lactamase
gene (one case with KPC as well as a Verona integron-encoded
metallo-β-lactamase (VIM) gene) and three cases with only the
VIM gene. One case with the IMP-type β-lactamase has also been
detected.
Table 1. Carbapenem Resistant Enterobacteriaceae
Detected, Bacteriology & Mycology Program, PHMRL.
Type
No. of Cases
NDM
14
Comments
KPC
2
1 case also harboured
the VIM gene
VIM
3
In addition to above
KPC/VIM case
IMP
1
Across Canada, Ontario
and British Columbia
have the highest number
of NDM positive samples
since surveillance
began in 2010. Quebec
leads in the number of
KPC positive samples
followed by Ontario
(Figure 1).
Figure 1 _________________
Enterobacteriaceae
Producing Carbapenemases
in Canada (n=205). Data
is as of January, 2012 and
represents the number of
positive samples. Figure
provided by Dr. M. Mulvey,
National Microbiology
Laboratory, Public Health
Agency of Canada, February
14, 2012.
N=35
20 NDM
5 KPC
1 OXA-48
9 Other
N=3
1 NDM
0 KPC
0 OXA-48
2 Other
N=0
0 NDM
0 KPC
0 OXA-48
0 Other
Page 2
N=2
0 NDM
1 KPC
0 OXA-48
1 Other
N=73
32 NDM
30 KPC
8 OXA-48
3 Other
N=91
2 NDM
83 KPC
2 OXA-48
4 Other
1 NDM
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
Gastrointestinal Outbreaks
In January, there were 63 gastrointestinal (GI) outbreaks investigated at the PHMRL. The number is consistent with the
volumes typically seen at this time in past years (Figure 2). Outbreaks were identified from 26 longterm care facilities, 12
daycare/schools, 19 hospitals, 2 events, 2 restaurants and 2 other locations. Samples for laboratory testing were submitted
for 54 (86%) of these outbreaks. Of these, norovirus was confirmed in 41 (76%) outbreaks.
The data available are from outbreaks in which the PHMRL has been notified. Some acute care microbiology laboratories
are also testing for norovirus in the province and these data do not include outbreaks from Vancouver Island Health
Authority. Given the nature of GI outbreaks, samples are not always available for testing.
Figure 2 __________________________________________________________________
Gastrointestinal outbreaks investigated since January, 2011, Environmental Microbiology,
Bacteriology & Mycology, Parasitology and Virology Programs, PHMRL.
Number of Outbreaks Investigated
GI Outbreak Investigations at the BCCDC Public Health Microbiology & Reference
Laboratory, PHSA
Other
Rest/Food Est
Longterm Care
Event
Daycare/School
Hospital/Acute Care
Average (previous 4 years)
+ 1 STDEV
-1 STDEV
22
20
20
18
16
14
15
12
10
10
8
6
5
4
2
0
0
1 2 3 4 5 6 7 8 9 10111213141516171819202122232425262728293031323334353637383940414243444546474849505152
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
2012
Week
Page 3
SEP
OCT
NOV
DEC
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
Enteric Surveillance
Salmonella Infantis was the fifth most commonly isolated serotype of Salmonella enterica in 2011 at the PHMRL behind,
S. Enteritidis, S. Typhimurium, S. Heidelberg, and S. Typhi (Figure 3). A cluster of S. Infantis has been investigated from
mid-November, 2011 with higher than expected counts from that of previous years (Figure 4). Cases in the cluster had a
common restaurant association.
Figure 3 __________________________________________________________________________________
Top Salmonella Enterica serovars identified from clinical samples, Bacteriology & Mycology Program, PHMRL.
Salmonella Infantis
Salmonella Paratyphi A
80
Salmonella Typhi
Salmonella Heidelberg
70
Number of Positive Samples
Salmonella Typhimurium
Salmonella Enteritidis
60
50
40
30
20
10
0
January
November
October
Salmonella Infantis
December
2011
September
August
July
June
May
April
March
February
January
Salmonella Typhimurium
Salmonella Typhi
2012
Figure 4 ________________________________________________________
Salmonella Infantis isolated in 2011 compared to previous years, Bacteriology
& Mycology Program, PHMRL.
2011
Avg 2008-2010
6
5
4
3
2
1
December
October
November
August
September
July
June
May
April
March
January
0
February
Number of Positive Samples
7
Page 4
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
Respiratory Outbreaks
In January, samples were submitted to the PHMRL for 24 respiratory outbreak investigations from 21 longterm care
facilities, 2 hospitals and 1 from the community (Figure 5). The number of outbreaks investigated was higher in the first
two weeks of the month than this time in previous years; however, the last two weeks of the month saw fewer outbreaks
than the average in previous years. Using PCR and Luminex methods, human metapneumovirus was detected in 8 facilities
including one hospital; influenza A(H3) was detected in 5 facilities, 1 hospital and in 1 community; RSV and parainfluenza
were detected in 2 facilities each; influenza B was detected in 1 facility and coronavirus in another. Figure 4 reflects
respiratory sample results submitted for investigation to the PHMRL and is not representative of respiratory outbreaks in
the entire BC community.
Figure 5 _____________________________________________________________
Respiratory outbreaks investigated by respiratory season, Virology Program, PHMRL.
Respiratory Outbreaks Investigations at the BCCDC Public Health Microbiology &
Reference Laboratory, 2010-2011 Season
Respiratory Virus Types Detected
20
pH1N1
Parainfluenza
Entero/Rhinovirus
RSV
Coronavirus
Influenza B
Influenza A (not typable)
HMPV
H3
H1
No Agent Detected
Avg. Total No. Outbreaks Previous 4 Years
+1 STD
-1 STD
15
10
5
0
35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
SEP
OCT
NOV
DEC
JAN
FEB
MAR
Week
Page 5
APR
MAY
JUN
JUL
AUG
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
Influenza Surveillance
0
100
90
80
70
60
50
40
30
20
10
0
35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
National influenza trends are
2011
2012
seeing low levels of activity with
Week
most of the provinces having
less than 5% positivity. The Prairies have seen slightly increased influenza A positivity rates of 8-9% in the last weeks of
January while the Atlantic Provinces saw influenza B rates climb to nearly 9% in the second week of January and then
decreasing again.
The World Health Organization (WHO) reports that with the exception of Mexico where influenza A(H1N1)pdm09 is the
predominant subtype and China where influenza type B is predominant, the most common subtype circulating in the
temperate, northern hemisphere continues to be influenza A(H3N2) with overall low activity (WHO, 20 Jan 2012 Update).
Table 2 ___________________________________________________________________________________
Positive influenza A and B detections for weeks 1-4 (January 1- January 31, 2012, Virology Program, PHMRL.
(H1N1)pdm09 refers to the 2009 influenza A(H1N1) pandemic virus.
Week 1
Week 2
Week 3
Week 4
Week 5*
Number of Specimens Tested
202
187
162
160
69
Number of Positive Specimens
34 (16.83%)
42 (22.46%)
23 (14.20%)
27 (16.87%)
12 (17.39%)
Influenza A
33 (16..34%)
38 (20.32%)
23 (14.20%)
21 (13.12%)
11 (15.94%)
(H1N1)pdm09
sH3N2
2 (1.23%)
33 (16.34%)
38 (20.32%)
21 (12.96%)
5 (7.25%)
21 (13.12%)
6 (8.70%)
Not typeable
Influenza B
1 (0.49%)
* Week 5 is a partial week from January 29-31.
1 (0.68%)
Page 6
6 (3.75%)
1 (1.45%)
Percent Positivity
Tests
Figure 6 _________________________________________________________________
With the exception of week 1,
volumes for respiratory testing Respiratory testing volumes and influenza percent positivity, Virology Program, PHMRL.
have been consistent or below
Total Tests 2010/11
Total Tests (Current)
% Positive Flu A (Current)
that of the same weeks from the
400
% Positive Flu B (Current)
% Flu A 2010/11
% Flu B 2010/11
380
2010/11 season. In weeks 1-5,
360
influenza positivity rates have
340
varied from 14-22% (Table 2)
320
300
and are below the rates seen
280
in the previous season (Figure
260
6). Influenza A (H3N2) was
240
220
the major virus type detected
200
this period with 119 (15.26%)
180
positive specimens; there
160
were also 7 (0.90%) detections
140
120
of (H1N1)pdm09 (Table 2).
100
Influenza B continues to be
80
detected in very low levels but
60
40
consistent with the previous
20
season’s pattern (Figure 6).
Acanthamoeba strains isolated
12
February 16, 2012
10
Number isolated
LABORATORY
TRENDS
PUBLIC HEALTH MICROBIOLOGY
& REFERENCE LABORATORY
8
6
4
Vancouver, BC
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
Year
A Report of the Public Health Microbiology & Reference Laboratory,
Vancouver, BC
This report may be freely distributed to your colleagues. If you would like more specific information or would like to
include any figures for other reporting purposes, please contact us.
Editor: Yin Chang
Contact: [email protected]
Website: www.phsa.ca/bccdcpublichealthlab
Co-Editors:
Bacteriology & Mycology Program
Program Head and Medical Microbiologist: Dr. Linda
Hoang
Section Head: Ana Paccagnella
Biosafety, Biosecurity, Biohazard Containment
Program
Public Health Lead: Neil Chin
Assistant Biosafety Officer: John Tansey
Molecular Microbiology & Genomics Program
Program Head and Medical Microbiologist: Dr. Patrick Tang
Section Head: Alan McNabb
Parasitology Program
Program Head and Medical Microbiologist: Dr. Judy IsaacRenton
Section Head: Quantine Wong
Pre-Analytical, Central Processing & Receiving
Program
Chief Technologist: Amelia Trinidad
Public Health High Volume Serology Program
Program Head and Medical Microbiologist: Dr. Mel Krajden
Section Head: Annie Mak
Technical Support Program
Chief Technologist: Amelia Trinidad
TB/Mycobacteriology Program
Program Head and Medical Microbiologist: Dr. Patrick Tang
Section Head: Dr. Mabel Rodrigues
Virus Isolation Program
Program Head and Medical Microbiologist: Dr. Mel Krajden
Section Head: Alan McNabb
Water and Food Microbiology Program
Program Head and Medical Microbiologist: Dr. Judy IsaacRenton
Section Head: Joe Fung
Zoonotic Diseases and Emerging Pathogens Program
Program Head and Clinical Microbiologist: Dr. Muhammad
Morshed
Section Head: Quantine Wong