Recent studies have identified Clostridium difficile in food animals and retail meat, and concern has been raised about the potential for food to act as a source of C. difficile infection in humans. ...Previous studies of retail meat have relied on enrichment culture alone, thereby preventing any assessment of the level of contamination in meat. This study evaluated the prevalence of C. difficile contamination of retail ground beef and ground pork in Canada. Ground beef and ground pork were purchased from retail outlets in four Canadian provinces. Quantitative and enrichment culture was performed. Clostridium difficile was isolated from 28/230 (12%) samples overall: 14/115 (12%) ground beef samples and 14/115 (12%) ground pork samples (P = 1.0). For ground beef, 10/14 samples (71%) were positive by enrichment culture only. Of the 4 ground beef samples that were positive by direct culture, 20 spores/g were present in 2 while 120 and 240 spores/g were present in 1 each. For ground pork, 10/14 (71%) samples were positive by enrichment culture only. Of the 4 ground pork samples that were positive by direct culture, 20 spores/g were present in 3 while 60 spores/g were present in 1. Ribotype 078 predominated, consistent with some previous studies of C. difficile in food animals. Ribotype 027/North American pulsotype 1 was also identified in both retail beef and pork. This study has identified relatively common contamination of retail ground beef and pork with C. difficile spores; however, the levels of contamination were very low.
Whole genome sequencing (WGS) of
supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility ...testing (AST) and in silico prediction of AMR from WGS in
(
= 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5-100%), a specificity of 99.7% (98.6-100%), a positive predictive value of 95.4% (68.2-100%), and a negative predictive value of 99.1% (95.6-100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried
, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in
was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.
Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic ...food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012–2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1–7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This study investigated the frequency of Salmonella serovars on pig carcasses at various processing steps in two commercial pork processing plants in Alberta, Canada and characterized phenotypic and ...genotypic antimicrobial resistance (AMR) and PFGE patterns of the Salmonella isolates. Over a one year period, 1000 swab samples were collected from randomly selected pigs at two slaughter plants. Sampling points were: carcass swabs after bleeding (CSAB), carcass swabs after de-hairing (CSAD, plant A) or skinning (CSASk, plant B), carcass swabs after evisceration (CSAE), carcass swabs after pasteurization (CSAP, plant A) or washing (CSAW, plants B) and retail pork (RP). For plant A, 87% of CSAB and 8% of CSAE were positive for Salmonella while at plant B, Salmonella was recovered from 94% of CSAB and 10% of CSAE. Salmonella was not recovered from the RP samples at either plant, indicating that the plants used effective control measures. Salmonella enterica serovar Derby was the most common serotype (23%, 29/127) recovered in plant A and plant B (61%, 76/124). For plant A, 35% (45/127) of isolates were resistant to at least one antimicrobial. Five isolates (3.9%), 4 serovar Ohio strains and one serovar I:Rough-O:I,v:-, strain were simultaneously resistant to antimicrobials of very high (Category I), high (Category II), and medium (Category III) importance to human medicine. The 4 S. Ohio isolates were recovered from 3 different steps of pork processing on the same sampling day and displayed resistance to 5–7 antimicrobials, with all of them displaying resistance to ceftiofur and ceftriaxone (Category I). An I:Rough-O:l,v:- isolate, recovered on a different sampling day, was resistant to 7 antimicrobials that included resistance to ampicillin/clavulanic acid, ceftiofur and ceftriaxone (Category I). Salmonella strains isolated from plant A harbored 12 different AMR genes. The most prevalent genes were sul1, sul2, tet(A), tet(B), aadA, strA/strB, aac(3)IV and aphA1. For Salmonella isolates from plant B, 7 resistance genes were identified alone or in combination where tet(B) was found in 77 (62.3%) of the isolates. For plant A, 19 different PFGE subtypes of Salmonella isolates that displayed phenotypic and/or genotypic resistance were observed while 13 different PFGE subtypes were observed for plant B. The lack of detection of Salmonella on the surfaces of RP suggests that current pork processing practices can dramatically reduce Salmonella. Salmonella isolates from pig carcasses at various steps displayed multidrug resistance, including to those of very high importance in human medicine, which represent a public health concern.
•Salmonella enterica was isolated from ≥87% of pig carcasses after bleeding.•Salmonella strains were carried through the pork processing stages on carcasses.•S. enterica was not detected on retail pork products from the processing plant.•S. enterica serovar Derby was the most common serotype (Plant A, 23%; plant B, 61%).•Resistance to multiple antimicrobials of very high importance to human health
We investigated whether gentamicin resistance (Gen
) in Escherichia coli isolates from human infections was related to Gen
E. coli in chicken and whether resistance may be due to coselection from use ...of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Gen
E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Gen
gene was different in human and chicken sources; however, both sources carried
,
, and
. Forty-one percent of human clinical isolates of Gen
E. coli contained a
extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Gen
isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Gen
and spectinomycin resistance (Spec
) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Gen
and Spec
genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Gen
isolates and plasmids were mostly different in chickens and humans.
During 2005-2010, the Canadian Integrated Program for Antimicrobial Resistance Surveillance identified increased prevalence of ciprofloxacin (a fluororquinolone) resistance among Campylobacter ...isolates from retail chicken in British Columbia (4%-17%) and Saskatchewan (6%-11%), Canada. Fluoroquinolones are critically important to human medicine and are not labeled for use in poultry in Canada.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We previously reported Clostridium difficile in 20% of retail meat in Canada, which raised concerns about potential foodborne transmissibility. Here, we studied the genetic diversity of C. difficile ...in retail meats, using a broad Canadian sampling infrastructure and 3 culture methods. We found 6.1% prevalence and indications of possible seasonality (highest prevalence in winter).
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and ...whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Gen
) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Gen
Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Gen
serovars were Salmonella enterica serovars Heidelberg (
= 93; 31.5%), 4,5,12:i:- (
= 42; 14.2%), Kentucky (
= 37; 12.5%), Infantis (
= 33; 11.2%), and Typhimurium (
= 23; 7.8%). Phylogenomic analysis revealed that for
Heidelberg and
Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by
and
''
, respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.
•The majority of respondents reported adherence to physical distancing guidelines.•Precautionary behaviour increased during the second wave of COVID-19 in Canada.•Controlling for stringency index and ...disease incidence, behaviour did not change.•Support for school closures declined while support for business closures increased.
The long-term dynamics of COVID-19 disease incidence and public health measures may impact individuals’ precautionary behaviours as well as support for measures. The objectives of this study were to assess longitudinal changes in precautionary behaviours and support for public health measures. Survey data were collected online from 1030 Canadians in each of 5 cycles in 2020: June 15-July 13; July 22-Aug 8; Sept 7–15; Oct 14–21; and Nov 12–17. Precautionary behaviour increased over the study period in the context of increasing disease incidence. When controlling for the stringency of public health measures and disease incidence, mixed effects logistic regression models showed these behaviours did not significantly change over time. Odds ratios for avoiding contact with family and friends ranged from 0.84 (95% CI 0.59–1.20) in September to 1.25 (95% CI 0.66–2.37) in November compared with July 2020. Odds ratios for attending an indoor gathering ranged from 0.86 (95% CI 0.62–1.20) in August to 1.71 (95% CI 0.95–3.09) in October compared with July 2020. Support for non-essential business closures increased over time with 2.33 (95% CI 1.14–4.75) times higher odds of support in November compared to July 2020. Support for school closures declined over time with lower odds of support in September (OR 0.66 95% CI 0.45–0.96), October (OR 0.48 95% CI 0.26–0.87), and November (OR 0.39 95% CI 0.19–0.81) compared with July 2020. In summary, respondents’ behaviour mirrored government guidance between July and November 2020 and supported individual precautionary behaviour and limitations on non-essential businesses over school closures.
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