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GRDI-AMR.ris
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TY - JOUR
TI - MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
AU - Robertson, James
AU - Nash, John H. E.
T2 - Microbial Genomics
AB - Large-scale bacterial population genetics studies are now routine due to cost-effective Illumina short-read sequencing. However, analysing plasmid content remains difficult due to incomplete assembly of plasmids. Bacterial isolates can contain any number of plasmids and assembly remains complicated due to the presence of repetitive elements. Numerous tools have been developed to analyse plasmids but the performance and functionality of the tools are variable. The MOB-suite was developed as a set of modular tools for reconstruction and typing of plasmids from draft assembly data to facilitate characterization of plasmids. Using a set of closed genomes with publicly available Illumina data, the MOB-suite identified contigs of plasmid origin with both high sensitivity and specificity (95 and 88 %, respectively). In comparison, plasmidfinder demonstrated high specificity (99 %) but limited sensitivity (50 %). Using the same dataset of 377 known plasmids, MOB-recon accurately reconstructed 207 plasmids so that they were assigned to a single grouping without other plasmid or chromosomal sequences, whereas plasmidSPAdes was only able to accurately reconstruct 102 plasmids. In general, plasmidSPAdes has a tendency to merge different plasmids together, with 208 plasmids undergoing merge events. The MOB-suite reduces the number of errors but produces more hybrid plasmids, with 84 plasmids undergoing both splits and merges. The MOB-suite also provides replicon typing similar to plasmidfinder but with the inclusion of relaxase typing and prediction of conjugation potential. The MOB-suite is written in Python 3 and is available from https://github.com/phac-nml/mob-suite.
DA - 2018/08/01/
PY - 2018
DO - 10.1099/mgen.0.000206
DP - DOI.org (Crossref)
VL - 4
IS - 8
LA - en
SN - 2057-5858
ST - MOB-suite
UR - https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000206
Y2 - 2020/04/23/14:23:37
ER -
TY - ELEC
TI - iAM.AMR project documentation
AU - The iAM.AMR Team
T2 - The iAM.AMR project documentation
DA - 2023///
PY - 2023
UR - https://docs.iam.amr.pub/
ER -
TY - JOUR
TI - Organic cranberry pomace and its ethanolic extractives as feed supplement in broiler: impacts on serum Ig titers, liver and bursal immunity
AU - Das, Quail
AU - Tang, Joshua
AU - Yin, Xianhua
AU - Ross, Kelly
AU - Warriner, Keith
AU - Marcone, Massimo F.
AU - Diarra, Moussa S.
T2 - Poultry Science
AB - ABSTRACT With the pressure to reduce antibiotics use in poultry production, cost-effective alternative products need to be developed to enhance the bird’s immunity. The present study evaluated the efficacy of cranberry fruit by-products to modulate immunity in broiler chickens. Broiler Cobb 500 chicks were fed a control basal diet, basal diet supplemented with bacitracin (BACI, 55 ppm), cranberry pomace at 1% and 2% (CP2), or cranberry pomace ethanolic extract at 150 and 300 ppm (COH300) for 30 d. Blood sera were analyzed at days 21 and 28 of age for Ig levels by ELISA. The innate and adaptive immune-related gene expression levels in the liver and bursa of Fabricius were investigated at 21 d of age by quantitative polymerase chain reaction arrays. At day 21, the highest IgY level was found in the blood serum of the CP2-fed birds. In the liver, 13 of the 22 differentially expressed genes were downregulated across all treatments compared with the control. Expression of genes belonging to innate immunity such as caspase 1 apoptosis–related cysteine peptidase, chemokine receptor 5, interferon gamma, myeloid differentiation primary response gene 88, and Toll-like receptor 3 were significantly downregulated mainly in BACI- and COH300-fed birds. In the bursa, 5 of 9 genes associated with the innate immunity were differentially expressed. The expression of anti-inflammatory IL-10 gene was upregulated in all treatment groups in bursa compared with the control. The expression of transferrin gene was significantly upregulated in livers of birds fed COH300 and in bursa of birds fed BACI, indicating feeding practices and organdependant modulation of this gene in broiler. Overall results of this study showed that cranberry product feed supplementation modulated the innate immune and suppressed proinflammatory cytokines in broilers, providing a platform for future investigations to develop berry products in poultry feeding.
DA - 2021/02//
PY - 2021
DO - 10.1016/j.psj.2020.09.044
DP - DOI.org (Crossref)
VL - 100
IS - 2
SP - 517
EP - 526
J2 - Poultry Science
LA - en
SN - 00325791
ST - Organic cranberry pomace and its ethanolic extractives as feed supplement in broiler
UR - https://linkinghub.elsevier.com/retrieve/pii/S0032579120306969
Y2 - 2024/06/14/12:09:50
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Research Note: Effects of supplementing cranberry and blueberry pomaces on meat quality and antioxidative capacity in broilers
AU - Xu, Qi
AU - Si, Wei
AU - Mba, Ogan Iheanacho
AU - Sienkiewicz, Olimpia
AU - Ngadi, Michael
AU - Ross, Kelly
AU - Kithama, Munene
AU - Kiarie, Elijah G.
AU - Kennes, Yan-Martel
AU - Diarra, Moussa S.
AU - Zhao, Xin
T2 - Poultry Science
AB - ABSTRACT Cranberry and blueberry pomaces are rich in antimicrobial and antioxidant compounds. They have been identified as potential antibiotic alternatives in animal feed, but their antioxidative capacity for maintaining or improving the meat quality in broilers is not well documented. This study was to determine whether cranberry and wild blueberry pomaces in diets could positively influence the broiler meat quality. A total of 3,150 broilers were randomly allotted to 10 dietary treatments with bacitracin methylene disalicylate, wild cranberry pomace (CRP) (0.5 and 1% of the basal diet), and wild blueberry pomace (BLP) (0.5 and 1% of the basal diet) alone or in combination with a mixture of feed enzymes. The results showed that supplementation with the CRP or BLP did not affect meat lightness and yellowness, while the deeper red meat (higher a* values) was observed in the birds receiving the diet containing 0.5% BLP against those in CRP treatments (P 5 0.015). In addition, inclusion of CRP or BLP in the diet did not change meat texture and proximate composition (moisture, protein, fat, ash) irrespective of pomace concentrations. Although there were no obvious effects of CRP or BLP supplementation on meat antioxidant capacity and the incidence of myopathies (P . 0.05), the upward trend of antioxidant capacity and less severity of woody breast were observed in birds fed with 0.5% CRP. Furthermore, supplementation of 0.5 or 1.0% CRP without the enzyme resulted in higher mRNA levers of Nrf, Gpx2, and HO-1 (P , 0.05). Taken together, 0.5% CRP supplementation without the enzyme could potentially maintain meat quality and attenuate the severity of woody breast.
DA - 2021/03//
PY - 2021
DO - 10.1016/j.psj.2020.11.069
DP - DOI.org (Crossref)
VL - 100
IS - 3
SP - 100900
J2 - Poultry Science
LA - en
SN - 00325791
ST - Research Note
UR - https://linkinghub.elsevier.com/retrieve/pii/S0032579120309512
Y2 - 2024/06/14/12:09:51
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants
AU - Marano, Roberto B.M.
AU - Fernandes, Telma
AU - Manaia, Célia M.
AU - Nunes, Olga
AU - Morrison, Donald
AU - Berendonk, Thomas U.
AU - Kreuzinger, Norbert
AU - Tenson, Tanel
AU - Corno, Gianluca
AU - Fatta-Kassinos, Despo
AU - Merlin, Christophe
AU - Topp, Edward
AU - Jurkevitch, Edouard
AU - Henn, Leonie
AU - Scott, Andrew
AU - Heß, Stefanie
AU - Slipko, Katarzyna
AU - Laht, Mailis
AU - Kisand, Veljo
AU - Di Cesare, Andrea
AU - Karaolia, Popi
AU - Michael, Stella G.
AU - Petre, Alice L.
AU - Rosal, Roberto
AU - Pruden, Amy
AU - Riquelme, Virginia
AU - Agüera, Ana
AU - Esteban, Belen
AU - Luczkiewicz, Aneta
AU - Kalinowska, Agnieszka
AU - Leonard, Anne
AU - Gaze, William H.
AU - Adegoke, Anthony A.
AU - Stenstrom, Thor A.
AU - Pollice, Alfieri
AU - Salerno, Carlo
AU - Schwermer, Carsten U.
AU - Krzeminski, Pawel
AU - Guilloteau, Hélène
AU - Donner, Erica
AU - Drigo, Barbara
AU - Libralato, Giovanni
AU - Guida, Marco
AU - Bürgmann, Helmut
AU - Beck, Karin
AU - Garelick, Hemda
AU - Tacão, Marta
AU - Henriques, Isabel
AU - Martínez-Alcalá, Isabel
AU - Guillén-Navarro, Jose M.
AU - Popowska, Magdalena
AU - Piotrowska, Marta
AU - Quintela-Baluja, Marcos
AU - Bunce, Joshua T.
AU - Polo-López, Maria I.
AU - Nahim–Granados, Samira
AU - Pons, Marie-Noëlle
AU - Milakovic, Milena
AU - Udikovic-Kolic, Nikolina
AU - Ory, Jérôme
AU - Ousmane, Traore
AU - Caballero, Pilar
AU - Oliver, Antoni
AU - Rodriguez-Mozaz, Sara
AU - Balcazar, Jose L.
AU - Jäger, Thomas
AU - Schwartz, Thomas
AU - Yang, Ying
AU - Zou, Shichun
AU - Lee, Yunho
AU - Yoon, Younggun
AU - Herzog, Bastian
AU - Mayrhofer, Heidrun
AU - Prakash, Om
AU - Nimonkar, Yogesh
AU - Heath, Ester
AU - Baraniak, Anna
AU - Abreu-Silva, Joana
AU - Choudhury, Manika
AU - Munoz, Leonardo P.
AU - Krizanovic, Stela
AU - Brunetti, Gianluca
AU - Maile-Moskowitz, Ayella
AU - Brown, Connor
AU - Cytryn, Eddie
T2 - Environment International
AB - The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the en vironment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantifi cation methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with ex tended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (< 0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater anti biotic resistance status.
DA - 2020/11//
PY - 2020
DO - 10.1016/j.envint.2020.106035
DP - DOI.org (Crossref)
VL - 144
SP - 106035
J2 - Environment International
LA - en
SN - 01604120
UR - https://linkinghub.elsevier.com/retrieve/pii/S0160412020319905
Y2 - 2024/06/14/12:09:53
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - A within-flock model of Salmonella Heidelberg transmission in broiler chickens
AU - Collineau, Lucie
AU - Phillips, Charly
AU - Chapman, Brennan
AU - Agunos, Agnes
AU - Carson, Carolee
AU - Fazil, Aamir
AU - Reid-Smith, Richard J.
AU - Smith, Ben A.
T2 - Preventive Veterinary Medicine
AB - As part of the development of a quantitative microbial risk assessment (QMRA) model of third-generation cephalosporins (3GC)-resistant Salmonella Heidelberg, a compartmental (SEIR) model for S. Heidelberg transmission within a typical Canadian commercial broiler chicken flock was developed. The model was constructed to estimate the within-flock prevalence and the bacterial concentration in the barn environment at pre-harvest, and to assess the effect of selected control measures.
DA - 2020/01//
PY - 2020
DO - 10.1016/j.prevetmed.2019.104823
DP - DOI.org (Crossref)
VL - 174
SP - 104823
J2 - Preventive Veterinary Medicine
LA - en
SN - 01675877
UR - https://linkinghub.elsevier.com/retrieve/pii/S0167587719302740
Y2 - 2024/06/14/12:09:55
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - A farm-to-fork quantitative risk assessment model for Salmonella Heidelberg resistant to third-generation cephalosporins in broiler chickens in Canada
AU - Collineau, Lucie
AU - Chapman, Brennan
AU - Bao, Xu
AU - Sivapathasundaram, Branavan
AU - Carson, Carolee A.
AU - Fazil, Aamir
AU - Reid-Smith, Richard J.
AU - Smith, Ben A.
T2 - International Journal of Food Microbiology
AB - Salmonella Heidelberg resistant to ceftiofur (a third-generation cephalosporin antimicrobial agent) in broiler chicken products pose a risk to public health in Canada. The objective of this study was to assess the extent of that risk and to evaluate the effect of intervention measures along the agri-food chain. A stochastic farm-to-fork quantitative microbial risk assessment model was developed following the Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance. Different scenarios were analyzed to assess the individual relative effects of 18 possible interventions in comparison to a baseline scenario. The baseline scenario represented the first year of on-farm antimicrobial use surveillance in the Canadian broiler industry and the year before an industry-imposed ban on the preventive use of antimicrobials of very high importance to human health (2013), where 31.3% of broiler flocks consisted of birds to which ceftiofur was administered.
DA - 2020/10//
PY - 2020
DO - 10.1016/j.ijfoodmicro.2020.108559
DP - DOI.org (Crossref)
VL - 330
SP - 108559
J2 - International Journal of Food Microbiology
LA - en
SN - 01681605
UR - https://linkinghub.elsevier.com/retrieve/pii/S0168160520300532
Y2 - 2024/06/14/12:09:57
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Dietary organic cranberry pomace influences multiple blood biochemical parameters and cecal microbiota in pasture-raised broiler chickens
AU - Islam, Md. Rashedul
AU - Hassan, Yousef I.
AU - Das, Quail
AU - Lepp, Dion
AU - Hernandez, Marta
AU - Godfrey, David V.
AU - Orban, Steve
AU - Ross, Kelly
AU - Delaquis, Pascal
AU - Diarra, Moussa S.
T2 - Journal of Functional Foods
AB - Cranberry processing by-products/pomace can be an excellent source of functionally bioactive molecules such as polyphenolics, complex carbohydrates, fibers, and nutritive minerals. While there are currently few applications for such processing-residues in poultry nutrition, there are many potential opportunities for the development of sustainable and value-added products. The aim of the current work was to investigate the effect(s) of four consecutive weeks of cranberry pomace (CBP) feeding on blood serum metabolic profiles and the cecal microbiota of pasture-raised broiler chickens. Six hundred day-old Cobb 500 broiler chicks were divided into three groups: one group receiving the basal diet, and two groups each receiving the basal diet supplemented with either 1 or 2% of CBP. Blood and cecal samples were collected from the birds before, during, and after the treatment over a period of 64 days for biochemical and 16S rRNA gene sequencing analysis, respectively. The detailed analysis of CBP (and formulated final feed) indicated its content in essential amino- and fatty acids in addition to its richness in dietary fibers. Incorporating the pomace in feed induced a dichotomous response in broilers, with short-term improvements in blood-serum iron and cholesterol levels coupled with long-term modulation of cecal microbiota characterized by an increase in beneficial bacterial taxa (including Bifidobacterium, unclassified_Rikenellaceae, and Faecalibacterium) while decreasing the presence of undesirable ones (unclassified_Synergistaceae and Desulfovibrio, and unclassified_Fusobacteriaceae). Overall, the outcome of this study suggests the possibility of using organic CBP as a feed supplement with potential ability to positively influence blood metabolites and gut microbial community composition in pasture-raised broiler chickens.
DA - 2020/09//
PY - 2020
DO - 10.1016/j.jff.2020.104053
DP - DOI.org (Crossref)
VL - 72
SP - 104053
J2 - Journal of Functional Foods
LA - en
SN - 17564646
UR - https://linkinghub.elsevier.com/retrieve/pii/S1756464620302772
Y2 - 2024/06/14/12:09:59
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing
AU - Petrillo, Mauro
AU - Fabbri, Marco
AU - Kagkli, Dafni Maria
AU - Querci, Maddalena
AU - Van Den Eede, Guy
AU - Alm, Erik
AU - Aytan-Aktug, Derya
AU - Capella-Gutierrez, Salvador
AU - Carrillo, Catherine
AU - Cestaro, Alessandro
AU - Chan, Kok-Gan
AU - Coque, Teresa
AU - Endrullat, Christoph
AU - Gut, Ivo
AU - Hammer, Paul
AU - Kay, Gemma L.
AU - Madec, Jean-Yves
AU - Mather, Alison E.
AU - McHardy, Alice Carolyn
AU - Naas, Thierry
AU - Paracchini, Valentina
AU - Peter, Silke
AU - Pightling, Arthur
AU - Raffael, Barbara
AU - Rossen, John
AU - Ruppé, Etienne
AU - Schlaberg, Robert
AU - Vanneste, Kevin
AU - Weber, Lukas M.
AU - Westh, Henrik
AU - Angers-Loustau, Alexandre
T2 - F1000Research
AB - Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
DA - 2021/02/08/
PY - 2021
DO - 10.12688/f1000research.39214.1
DP - DOI.org (Crossref)
VL - 10
SP - 80
J2 - F1000Res
LA - en
SN - 2046-1402
UR - https://f1000research.com/articles/10-80/v1
Y2 - 2024/06/14/12:10:01
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario
AU - Cooper, Ashley L.
AU - Carter, Cassandra
AU - McLeod, Hana
AU - Wright, Marie
AU - Sritharan, Prithika
AU - Tamber, Sandeep
AU - Wong, Alex
AU - Carrillo, Catherine D.
AU - Blais, Burton W.
T2 - FACETS
A2 - Ivanova, Elena P.
AB - Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.
DA - 2021/01/01/
PY - 2021
DO - 10.1139/facets-2020-0101
DP - DOI.org (Crossref)
VL - 6
IS - 1
SP - 569
EP - 591
J2 - FACETS
LA - en
SN - 2371-1671
UR - https://facetsjournal.com/doi/10.1139/facets-2020-0101
Y2 - 2024/06/14/12:10:02
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - From farm management to bacteriophage therapy: strategies to reduce antibiotic use in animal agriculture
AU - Kahn, Laura H.
AU - Bergeron, Gilles
AU - Bourassa, Megan W.
AU - De Vegt, Bert
AU - Gill, Jason
AU - Gomes, Filomena
AU - Malouin, François
AU - Opengart, Ken
AU - Ritter, G. Donald
AU - Singer, Randall S.
AU - Storrs, Carina
AU - Topp, Edward
T2 - Annals of the New York Academy of Sciences
AB - Abstract
To reduce the use of antibiotics in animal agriculture, a number of effective or commercially viable alternatives have been implemented by food animal producers or are under development. Perhaps the most well‐established strategies are flock and herd management practices to mitigate disease introduction and spread, and, subsequently, reduce the need for antibiotic use. While vaccines in food animal production have been used to prevent both bacterial and viral diseases, but historically, most vaccines have targeted viral diseases. Though vaccines against viral diseases can help reduce the need for antibiotic use by controlling the spread of secondary bacterial infections, more recent vaccines under development specifically target bacteria. New developments in selecting and potentially tailoring bacteriophages provide a promising avenue for controlling pathogenic bacteria without the need for traditional small‐molecule antibiotics. In this article we discuss these established and emerging strategies, which are anticipated to reduce the reliance on antibiotics in food animal production and should reduce the prevalence and transmission to humans of antimicrobial resistant bacteria from these systems.
DA - 2019/04//
PY - 2019
DO - 10.1111/nyas.14034
DP - DOI.org (Crossref)
VL - 1441
IS - 1
SP - 31
EP - 39
J2 - Annals of the New York Academy of Sciences
LA - en
SN - 0077-8923, 1749-6632
ST - From farm management to bacteriophage therapy
UR - https://nyaspubs.onlinelibrary.wiley.com/doi/10.1111/nyas.14034
Y2 - 2024/06/14/12:10:04
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment
AU - Taggar, Gurleen
AU - Attiq Rehman, Muhammad
AU - Boerlin, Patrick
AU - Diarra, Moussa
T2 - Antibiotics
AB - The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (blaKPC), class B (blaIMP, blaVIM, blaNDM), and class D (blaOXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.
DA - 2020/10/13/
PY - 2020
DO - 10.3390/antibiotics9100693
DP - DOI.org (Crossref)
VL - 9
IS - 10
SP - 693
J2 - Antibiotics
LA - en
SN - 2079-6382
UR - https://www.mdpi.com/2079-6382/9/10/693
Y2 - 2024/06/14/12:10:06
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape
AU - Ma, Yvonne
AU - Chen, Jessica
AU - Fong, Karen
AU - Nadya, Stephanie
AU - Allen, Kevin
AU - Laing, Chad
AU - Ziebell, Kim
AU - Topp, Ed
AU - Carroll, Laura M.
AU - Wiedmann, Martin
AU - Delaquis, Pascal
AU - Wang, Siyun
T2 - Antibiotics
AB - Antibiotic resistance (AR) phenotypes and acquired resistance determinants (ARDs) detected by in silico analysis of genome sequences were examined in 55 Shiga toxin-producing Escherichia coli (STEC) isolates representing diverse serotypes recovered from surfaces waters and sediments in a mixed use urban/agricultural landscape in British Columbia, Canada. The isolates displayed decreased susceptibility to florfenicol (65.5%), chloramphenicol (7.3%), tetracycline (52.7%), ampicillin (49.1%), streptomycin (34.5%), kanamycin (20.0%), gentamycin (10.9%), amikacin (1.8%), amoxicillin/clavulanic acid (21.8%), ceftiofur (18.2%), ceftriaxone (3.6%), trimethoprimsulfamethoxazole (12.7%), and cefoxitin (3.6%). All surface water and sediment isolates were susceptible to ciprofloxacin, nalidixic acid, ertapenem, imipenem and meropenem. Eight isolates (14.6%) were multidrug resistant. ARDs conferring resistance to phenicols (floR), trimethoprim (dfrA), sulfonamides (sul1/2), tetracyclines (tetA/B), and aminoglycosides (aadA and aph) were detected. Additionally, narrow-spectrum β-lactamase blaTEM-1b and extended-spectrum AmpC β-lactamase (cephalosporinase) blaCMY-2 were detected in the genomes, as were replicons from plasmid incompatibility groups IncFII, IncB/O/K/Z, IncQ1, IncX1, IncY and Col156. A comparison with surveillance data revealed that AR phenotypes and ARDs were comparable to those reported in generic E. coli from food animals. Aquatic environments in the region are potential reservoirs for the maintenance and transmission of antibiotic resistant STEC, associated ARDs and their plasmids.
DA - 2021/02/26/
PY - 2021
DO - 10.3390/antibiotics10030237
DP - DOI.org (Crossref)
VL - 10
IS - 3
SP - 237
J2 - Antibiotics
LA - en
SN - 2079-6382
UR - https://www.mdpi.com/2079-6382/10/3/237
Y2 - 2024/06/14/12:10:07
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 2; peer review: 1 approved, 2 approved with reservations]
AU - Petrillo, Mauro
AU - Fabbri, Marco
AU - Kagkli, Dafni Maria
AU - Querci, Maddalena
DA - 2022///
PY - 2022
DP - Zotero
LA - en
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Application of artificial intelligence to the in silico assessment of antimicrobial resistance and risks to human and animal health presented by priority enteric bacterial pathogens
AU - Steinkey, Rylan
AU - Moat, Janice
AU - Gannon, Victor
AU - Zovoilis, Athanasios
AU - Laing, Chad
T2 - Canada Communicable Disease Report
DA - 2020/06/04/
PY - 2020
DO - 10.14745/ccdr.v46i06a05
DP - DOI.org (Crossref)
SP - 180
EP - 185
J2 - CCDR
LA - en
SN - 14818531
UR - https://www.canada.ca/content/dam/phac-aspc/documents/services/reports-publications/canada-communicable-disease-report-ccdr/monthly-issue/2020-46/issue-6-june-4-2020/ccdrv46i06a05-eng.pdf
Y2 - 2024/06/14/12:10:11
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Ceftiofur-resistant <i>Salmonella enterica</i> serovar Heidelberg of poultry origin – a risk profile using the Codex framework
AU - Carson, Carolee
AU - Li, Xian-Zhi
AU - Agunos, Agnes
AU - Loest, Daleen
AU - Chapman, Brennan
AU - Finley, Rita
AU - Mehrotra, Manisha
AU - Sherk, Lauren M.
AU - Gaumond, Réjean
AU - Irwin, Rebecca
T2 - Epidemiology and Infection
AB - Codex published the ‘Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance’ to standardise the approach for evaluating risk posed by foodborne antimicrobial-resistant bacteria. One of the first steps in the guidelines is to compile a risk profile, which provides the current state of knowledge regarding a food safety issue, describes risk management options and recommends next steps. In Canada, ceftiofur/ceftriaxone-resistant Salmonella enterica subsp. enterica serovar Heidelberg from poultry was identified as an antimicrobial resistance (AMR) food safety issue. The first objective of this article was to contextualise this food safety issue, using the risk profile format of the Codex Guidelines. A second objective was to evaluate the applicability of the Codex Guidelines. This risk profile indicated that ceftiofur/ceftriaxoneresistant S. Heidelberg (CSH) was commonly isolated from poultry and was associated with severe disease in humans. Ceftiofur use in poultry hatcheries temporally mirrored the prevalence of CSH from poultry meat at retail and from people with salmonellosis. The evidence was sufficient to indicate the need for risk management options, such as restricting the use of ceftiofur in poultry. The Codex Guidelines provided a useful approach to summarise data for decision-makers to evaluate an AMR food safety issue.
DA - 2019///
PY - 2019
DO - 10.1017/S0950268819001778
DP - DOI.org (Crossref)
VL - 147
SP - e296
J2 - Epidemiol. Infect.
LA - en
SN - 0950-2688, 1469-4409
UR - https://www.cambridge.org/core/product/identifier/S0950268819001778/type/journal_article
Y2 - 2024/06/14/12:10:13
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing <i>Acinetobacter</i> spp. in Canadian hospitals, 2010–16
AU - Boyd, David A
AU - Mataseje, Laura F
AU - Pelude, Linda
AU - Mitchell, Robyn
AU - Bryce, Elizabeth
AU - Roscoe, Diane
AU - Embree, Joanne
AU - Katz, Kevin
AU - Kibsey, Pamela
AU - Lavallee, Christian
AU - Simor, Andrew E
AU - Taylor, Geoffrey
AU - Turgeon, Nathalie
AU - Langley, Joanne M
AU - Amaratunga, Kanchana
AU - Mulvey, Michael R
AU - Canadian Nosocomial Infection Surveillance Program
AU - Wong, Alice
AU - McGeer, Allison
AU - Simor, Andrew
AU - Lee, Bonita
AU - Frenette, Charles
AU - Ellis, Chelsea
AU - Lavallee, Christian
AU - Mertz, Dominik
AU - Bryce, Elizabeth
AU - Henderson, Elizabeth
AU - Taylor, Geoffrey
AU - German, Gregory
AU - Davis, Ian
AU - De Heer, Janice
AU - Minion, Jessica
AU - Embree, Joanne
AU - Langley, Joanne
AU - Srigley, Jocelyn
AU - Embil, John
AU - Vayalumkal, Joseph
AU - Suh, Kathryn
AU - Katz, Kevin
AU - Johnston, Lynn
AU - Lefebvre, Marie-Astrid
AU - John, Michael
AU - Blackburn, Michael Missy
AU - Bridger, Natalie
AU - Turgeon, Nathalie
AU - Thampi, Nisha
AU - Kibsey, Pamela
AU - Stagg, Paula
AU - Richardson, Susan
AU - Hota, Susy
AU - Pelletier, Suzanne
AU - Longtin, Yves
T2 - Journal of Antimicrobial Chemotherapy
AB - Objectives: Globally there is an increased prevalence of carbapenem-resistant Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs) in the hospital setting. This increase prompted the Canadian Nosocomial Infection Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and infections identified from patients in CNISP-participating hospitals between 2010 and 2016.
Methods: Participating acute care facilities across Canada submitted CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from medical records using a standardized questionnaire. WGS was conducted on all CRAs and data underwent single nucleotide variant analysis, resistance gene detection and MLST.
Results: The 7 year incidence rate of CRA was 0.02 per 10 000 patient days and 0.015 per 1000 admissions, with no significant increase observed over the surveillance period (P . 0.73). Ninety-four CRA isolates were collected from 58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%) was the most common due to two separate clusters, followed by the OXA-23 group (41.9%). Patients with a travel history were associated with 38.8% of CRA cases. The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA cases. Colistin was the most active antimicrobial agent (95.8% susceptibility).
Conclusions: CRA remains uncommon in Canadian hospitals and the incidence did not increase from 2010 to 2016. Almost half of the cases were from two clusters harbouring OXA-235-group enzymes. Previous medical treatment during travel outside of Canada was common.
DA - 2019/02/01/
PY - 2019
DO - 10.1093/jac/dky416
DP - DOI.org (Crossref)
VL - 74
IS - 2
SP - 315
EP - 320
LA - en
SN - 0305-7453, 1460-2091
UR - https://academic.oup.com/jac/article/74/2/315/5127718
Y2 - 2024/06/14/12:10:15
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Identification of a novel metallo-β-lactamase, CAM-1, in clinical Pseudomonas aeruginosa isolates from Canada
AU - Boyd, David A
AU - Lisboa, Luiz F
AU - Rennie, Robert
AU - Zhanel, George G
AU - Dingle, Tanis C
AU - Mulvey, Michael R
T2 - Journal of Antimicrobial Chemotherapy
AB - Objectives: To identify the b-lactamase responsible for the positive detection of carbapenemase production in four clinical isolates of Pseudomonas aeruginosa that were negative by PCR for KPC, OXA-48, NDM, VIM, IMP, GES and NMC/IMI carbapenemase genes.
Methods: WGS using short-read and long-read methods was used to characterize the isolates. Bioinformatic analysis was used to identify the potential gene encoding a carbapenemase. Cloning, antimicrobial susceptibility testing and biochemical and phenotypic characterization were used to determine metallo-enzyme activity. Single-nucleotide variant (SNV) typing was used to determine strain relatedness. Conjugation experiments were used to determine transmissibility of the novel carbapenemase-encoding gene.
Results: WGS analysis revealed a novel class B b-lactamase gene, blaCAM-1 (Central Alberta Metallo-b-lactamase), located in a 73 kb integrative element, named IMEPaCAM-1, in the chromosome of four clinical isolates of P. aeruginosa. The cloned blaCAM-1 gene conferred carbapenem resistance to Escherichia coli TOP10. The four isolates, which were all closely related, were from three patients, all of whom spent time in the same hospital in 2008 and/or 2009. IMEPaCAM-1 could not be transferred by conjugation.
Conclusions: A novel metallo-enzyme, CAM-1, is encoded on an integrative element, IMEPaCAM-1, located in the chromosome of clinical isolates of P. aeruginosa. No additional isolates harbouring CAM-1 have been identified in Alberta since 2007.
DA - 2019/06/01/
PY - 2019
DO - 10.1093/jac/dkz066
DP - DOI.org (Crossref)
VL - 74
IS - 6
SP - 1563
EP - 1567
LA - en
SN - 0305-7453, 1460-2091
UR - https://academic.oup.com/jac/article/74/6/1563/5353165
Y2 - 2024/06/14/12:10:16
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Enterobacter sp. N18-03635 harbouring blaFRI-6 class A carbapenemase, Canada
AU - Boyd, David A
AU - Lefebvre, Brigitte
AU - Mataseje, Laura F
AU - Gagnon, Simon
AU - Roger, Michel
AU - Savard, Patrice
AU - Longtin, Jean
AU - Mulvey, Michael R
T2 - Journal of Antimicrobial Chemotherapy
DA - 2020/02/01/
PY - 2020
DO - 10.1093/jac/dkz438
DP - DOI.org (Crossref)
VL - 75
IS - 2
SP - 486
EP - 488
LA - en
SN - 0305-7453, 1460-2091
UR - https://academic.oup.com/jac/article/75/2/486/5625686
Y2 - 2024/06/14/12:10:18
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Measures used to assess the burden of ESBL-producing <i>Escherichia coli</i> infections in humans: a scoping review
AU - McDonald, Kathryn L
AU - Garland, Sarah
AU - Carson, Carolee A
AU - Gibbens, Kimberly
AU - Parmley, E Jane
AU - Finley, Rita
AU - MacKinnon, Melissa C
T2 - JAC-Antimicrobial Resistance
AB - Background: ESBL-producing bacteria pose a serious challenge to both clinical care and public health. There is no standard measure of the burden of illness (BOI) of ESBL-producing Escherichia coli (ESBL-EC) in the published literature, indicating a need to synthesize available BOI data to provide an overall understanding of the impact of ESBL-EC infections on human health.
Objectives: To summarize the characteristics of BOI reporting in the ESBL-EC literature to (i) describe how BOI associated with antimicrobial resistance (AMR) is measured and reported; (ii) summarize differences in other aspects of reporting between studies; and (iii) highlight the common themes in research objectives and their relation to ESBL-EC BOI.
Methods and results: Two literature searches, run in 2013 and 2018, were conducted to capture published studies evaluating the BOI associated with ESBL-EC infections in humans. These searches identified 1723 potentially relevant titles and abstracts. After relevance screening of titles and abstracts and review of full texts, 27 studies were included for qualitative data synthesis. This review identified variability in the reporting and use of BOI measures, study characteristics, definitions and laboratory methods for identifying ESBL-EC infections.
Conclusions: Decision makers often require BOI data to make science-based decisions for the implementation of surveillance activities or risk reduction policies. Similarly, AMR BOI measures are important components of risk analyses and economic evaluations of AMR. This review highlights many limitations to current ESBL-EC BOI reporting, which, if improved upon, will ensure data accessibility and usefulness for ESBL-EC BOI researchers, decision makers and clinicians.
DA - 2021/01/18/
PY - 2021
DO - 10.1093/jacamr/dlaa104
DP - DOI.org (Crossref)
VL - 3
IS - 1
SP - dlaa104
LA - en
SN - 2632-1823
ST - Measures used to assess the burden of ESBL-producing <i>Escherichia coli</i> infections in humans
UR - https://academic.oup.com/jacamr/article/doi/10.1093/jacamr/dlaa104/6134944
Y2 - 2024/06/14/12:10:19
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace
AU - Das, Quail
AU - Lepp, Dion
AU - Yin, Xianhua
AU - Ross, Kelly
AU - McCallum, Jason L.
AU - Warriner, Keith
AU - Marcone, Massimo F.
AU - Diarra, Moussa S.
T2 - PLOS ONE
A2 - Johnson, Timothy J.
DA - 2019/07/03/
PY - 2019
DO - 10.1371/journal.pone.0219163
DP - DOI.org (Crossref)
VL - 14
IS - 7
SP - e0219163
J2 - PLoS ONE
LA - en
SN - 1932-6203
UR - https://dx.plos.org/10.1371/journal.pone.0219163
Y2 - 2024/06/14/12:10:21
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Importation of Extensively Drug-Resistant Salmonella enterica Serovar Typhi Cases in Ontario, Canada
AU - Eshaghi, Alireza
AU - Zittermann, Sandra
AU - Bharat, Amrita
AU - Mulvey, Michael R.
AU - Allen, Vanessa G.
AU - Patel, Samir N.
T2 - Antimicrobial Agents and Chemotherapy
AB - A strain of extensively drug-resistant (XDR) Salmonella enterica serovar Typhi has caused a large ongoing outbreak in Pakistan since 2016. In Ontario, Canada, 10 cases of mainly bloodstream infections (n ϭ 9) were identified in patients who traveled to Pakistan. Whole-genome sequencing showed that Canadian cases were genetically related to the Pakistan outbreak strain. The appearance of XDR typhoid cases in Ontario prompted a provincial wide alert to physicians to recommend treatment with carbapenems or azithromycin in suspected typhoid cases with travel history to Pakistan.
DA - 2020/04/21/
PY - 2020
DO - 10.1128/AAC.02581-19
DP - DOI.org (Crossref)
VL - 64
IS - 5
SP - e02581
EP - 19
J2 - Antimicrob Agents Chemother
LA - en
SN - 0066-4804, 1098-6596
UR - https://journals.asm.org/doi/10.1128/AAC.02581-19
Y2 - 2024/06/14/12:10:22
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Editorial: The Environmental Dimension of Antibiotic Resistance
AU - Zhang, Tong
AU - Fukuda, Keiji
AU - Topp, Edward
AU - Zhu, Yong-Guan
AU - Smalla, Kornelia
AU - Tiedje, James M
AU - Larsson, D G Joakim
T2 - FEMS Microbiology Ecology
DA - 2020/08/01/
PY - 2020
DO - 10.1093/femsec/fiaa130
DP - DOI.org (Crossref)
VL - 96
IS - 8
SP - fiaa130
LA - en
SN - 0168-6496, 1574-6941
ST - Editorial
UR - https://academic.oup.com/femsec/article/doi/10.1093/femsec/fiaa130/5871492
Y2 - 2024/06/14/12:10:23
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges
AU - Collineau, Lucie
AU - Boerlin, Patrick
AU - Carson, Carolee A.
AU - Chapman, Brennan
AU - Fazil, Aamir
AU - Hetman, Benjamin
AU - McEwen, Scott A.
AU - Parmley, E. Jane
AU - Reid-Smith, Richard J.
AU - Taboada, Eduardo N.
AU - Smith, Ben A.
T2 - Frontiers in Microbiology
DA - 2019/05/21/
PY - 2019
DO - 10.3389/fmicb.2019.01107
DP - DOI.org (Crossref)
VL - 10
SP - 1107
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
ST - Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance
UR - https://www.frontiersin.org/article/10.3389/fmicb.2019.01107/full
Y2 - 2024/06/14/12:10:25
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance
AU - Cooper, Ashley L.
AU - Low, Andrew J.
AU - Koziol, Adam G.
AU - Thomas, Matthew C.
AU - Leclair, Daniel
AU - Tamber, Sandeep
AU - Wong, Alex
AU - Blais, Burton W.
AU - Carrillo, Catherine D.
T2 - Frontiers in Microbiology
AB - Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results of traditional phenotyping assays. A total of 111 S. enterica isolates recovered from a Canadian baseline study on broiler chicken conducted in 20122013 were selected based on phenotypic resistance to 15 different antibiotics and isolates were subjected to WGS. Both SeqSero2 and SISTR accurately determined S. enterica serotypes, with full matches to laboratory results for 87.4 and 89.2% of isolates, respectively, and partial matches for the remaining isolates. Antimicrobial resistance genes (ARGs) were identified using several bioinformatics tools including the Comprehensive Antibiotic Resistance Database – Resistance Gene Identifier (CARDRGI), Center for Genomic Epidemiology (CGE) ResFinder web tool, Short Read Sequence Typing for Bacterial Pathogens (SRST2 v 0.2.0), and k-mer alignment method (KMA v 1.17). All ARG identification tools had ≥ 99% accuracy for predicting resistance to all antibiotics tested except streptomycin (accuracy 94.6%). Evaluation of ARG detection in assembled versus raw-read WGS data found minimal observable differences that were gene- and coverage- dependent. Where initial phenotypic results indicated isolates were sensitive, yet ARGs were detected, repeat AMR testing corrected discrepancies. All tools failed to find resistance-determining genes for one gentamicinand two streptomycin-resistant isolates. Further investigation found a single nucleotide polymorphism (SNP) in the nuoF coding region of one of the isolates which may be responsible for the observed streptomycin-resistant phenotype. Overall, WGS-based predictions of AMR and serotype were highly concordant with phenotype determination regardless of computational approach used.
DA - 2020/04/03/
PY - 2020
DO - 10.3389/fmicb.2020.00549
DP - DOI.org (Crossref)
VL - 11
SP - 549
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/article/10.3389/fmicb.2020.00549/full
Y2 - 2024/06/14/12:10:27
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood
AU - Liu, Xiaoji
AU - Teixeira, Januana S.
AU - Ner, Saurabh
AU - Ma, Kassandra V.
AU - Petronella, Nicholas
AU - Banerjee, Swapan
AU - Ronholm, Jennifer
T2 - Frontiers in Microbiology
AB - Geographic food fraud – misrepresenting the geographic origin of a food item, is very difficult to detect, and therefore this type of fraud tends to go undetected. This potentially negatively impacts the health of Canadians and economic success of our seafood industry. Surveillance studies have shown that up to a significant portion of commercially sold seafood items in Canada are mislabeled or otherwise misrepresented in some way. The current study aimed to determine if the microbiome of fresh shellfish could be used as an accurate marker of harvest location. Total DNA was extracted from the homogenate of 25 batches of fresh soft-shell clams (Mya arenaria) harvested in 2015 and 2018 from two locations on the East Coast of Canada and the microbiome of each homogenate was characterized using 16S rRNA targeted amplicon sequencing. Clams harvested from Nova Scotia in both years had a higher abundance of Proteobacteria and Acidobacteria (p < 0.05), but a lower abundance of Actinobacteria (p < 0.05) than those from Quebec. Alpha-diversity also differed significantly between sites. Samples harvested from Nova Scotia had greater diversity (p < 0.0001) than those from Quebec. Beta-diversity analysis showed that the microbial community composition was significantly different between the samples from Nova Scotia and Quebec and indicated that 16S rRNA targeted amplicon sequencing might be an effective tool for elucidating the geographic origin of unprocessed shellfish. To evaluate if the microbiome of shellfish experiences a loss of microbial diversity during processing and storage –which would limit the ability of this technique to link retail samples to geographic origin, 10 batches of retail clams purchased from grocery stores were also examined. Microbial diversity and species richness was significantly lower in retail clams, and heavily dominated by Proteobacteria, a typical spoilage organism for fresh seafood, this may make determining the geographic origin of seafood items more difficult in retail clams than in freshly harvested clams.
DA - 2020/04/17/
PY - 2020
DO - 10.3389/fmicb.2020.00696
DP - DOI.org (Crossref)
VL - 11
SP - 696
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/article/10.3389/fmicb.2020.00696/full
Y2 - 2024/06/14/12:10:28
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012
AU - Yousfi, Khadidja
AU - Usongo, Valentine
AU - Berry, Chrystal
AU - Khan, Rufaida H.
AU - Tremblay, Denise M.
AU - Moineau, Sylvain
AU - Mulvey, Michael R.
AU - Doualla-Bell, Florence
AU - Fournier, Eric
AU - Nadon, Celine
AU - Goodridge, Lawrence
AU - Bekal, Sadjia
T2 - Frontiers in Microbiology
DA - 2020/06/17/
PY - 2020
DO - 10.3389/fmicb.2020.01317
DP - DOI.org (Crossref)
VL - 11
SP - 1317
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/article/10.3389/fmicb.2020.01317/full
Y2 - 2024/06/14/12:10:30
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model
AU - Laskey, Alexander
AU - Ottenbrite, Marie
AU - Devenish, John
AU - Kang, Mingsong
AU - Savic, Mirjana
AU - Nadin-Davis, Susan
AU - Chmara, John
AU - Lin, Min
AU - Robertson, James
AU - Bessonov, Kyrylo
AU - Gurnik, Simone
AU - Liu, Kira
AU - Nash, John H. E.
AU - Scott, Andrew
AU - Topp, Edward
AU - Guan, Jiewen
T2 - Frontiers in Microbiology
AB - Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to the dissemination of antibiotic-resistance genes in the gut microbiota and the development of antibiotic-resistant bacterial infection, a significant threat to animal and public health. Food or water may be contaminated with multiple resistant bacteria, but animal models on gene transfer were mainly based on single-strain infections. In this study, we investigated the mobility of β-lactam resistance following infection with singleversus multi-strain of resistant bacteria under ampicillin treatment. We characterized three bacterial strains isolated from food-animal production systems, Escherichia coli O80:H26 and Salmonella enterica serovars Bredeney and Heidelberg. Each strain carries at least one conjugative plasmid that encodes a β-lactamase. We orally infected mice with each or all three bacterial strain(s) in the presence or absence of ampicillin treatment. We assessed plasmid transfer from the three donor bacteria to an introduced E. coli CV601gfp recipient in the mouse gut, and evaluated the impacts of the bacterial infection on gut microbiota and gut health. In the absence of ampicillin treatment, none of the donor or recipient bacteria established in the normal gut microbiota and plasmid transfer was not detected. In contrast, the ampicillin treatment disrupted the gut microbiota and enabled S. Bredeney and Heidelberg to colonize and transfer their plasmids to the E. coli CV601gfp recipient. E. coli O80:H26 on its own failed to colonize the mouse gut. However, during co-infection with the two Salmonella strains, E. coli O80:H26 colonized and transferred its plasmid to the E. coli CV601gfp recipient and a residential E. coli O2:H6 strain. The co-infection significantly increased plasmid transfer frequency, enhanced Proteobacteria expansion and resulted in inflammation in the mouse gut. Our findings suggest that single-strain infection models for evaluating in vivo gene transfer may underrepresent the consequences of multi-strain infections following the consumption of heavily contaminated food or water.
DA - 2020/07/07/
PY - 2020
DO - 10.3389/fmicb.2020.01591
DP - DOI.org (Crossref)
VL - 11
SP - 1591
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/article/10.3389/fmicb.2020.01591/full
Y2 - 2024/06/14/12:10:31
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Inhibitory Activity of Natural Synergetic Antimicrobial Consortia Against Salmonella enterica on Broiler Chicken Carcasses
AU - Zhang, Liya
AU - Ben Said, Laila
AU - Diarra, Moussa Sory
AU - Fliss, Ismail
T2 - Frontiers in Microbiology
AB - The currently most utilized antimicrobial agent in poultry processing facilities is peracetic acid, a chemical increasingly recognized as hazardous to human health. We evaluated the efficacy of mixtures of natural antimicrobial compounds, namely reuterin, microcin J25, and lactic acid, for reducing the viability of Salmonella enterica and total aerobes on broiler chicken carcasses. The compounds were compared singly and in combination with water and 0.1% peracetic acid. The minimum inhibitory concentrations of reuterin, lactic acid, and microcin J25 against S. enterica serovar Enteritidis were respectively 2 mM, 0.31%, and 0.03 μM. In vitro, the combinations of reuterin + lactic acid and reuterin + microcin J25 were synergic, making these compounds effective at four times lower concentrations than those used alone. Salmonella viable counts fell to zero within 10 min of contact with reuterin + lactic acid at 10 times the concentrations used in combination, compared to 18 h in the case of reuterin + microcin J25. Sprayed onto chilled chicken carcasses, this reuterin + lactic acid mixture reduced Salmonella spp. counts by 2.02 Log CFU/g, whereas reuterin + microcin J25 and peracetic acid reduced them by respectively 0.83 and 1.13 Log CFU/g. The synergy of reuterin with lactic acid or microcin J25 as inhibitors of bacterial growth was significant. Applied as post-chill spray, these mixtures could contribute to food safety by decreasing Salmonella counts on chicken carcasses.
DA - 2021/04/29/
PY - 2021
DO - 10.3389/fmicb.2021.656956
DP - DOI.org (Crossref)
VL - 12
SP - 656956
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2021.656956/full
Y2 - 2024/06/14/12:10:33
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum
AU - Zaidi, Sani-e-Zehra
AU - Zaheer, Rahat
AU - Barbieri, Ruth
AU - Cook, Shaun R.
AU - Hannon, Sherry J.
AU - Booker, Calvin W.
AU - Church, Deirdre
AU - Van Domselaar, Gary
AU - Zovoilis, Athanasios
AU - McAllister, Tim A.
T2 - Frontiers in Microbiology
AB - Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.
DA - 2022/06/27/
PY - 2022
DO - 10.3389/fmicb.2022.859990
DP - DOI.org (Crossref)
VL - 13
SP - 859990
J2 - Front. Microbiol.
LA - en
SN - 1664-302X
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2022.859990/full
Y2 - 2024/06/14/12:10:34
KW - grdi-amr-1
KW - open-access
KW - official-index
ER -
TY - JOUR
TI - Gut Microbiota, Blood Metabolites, and Spleen Immunity in Broiler Chickens Fed Berry Pomaces and Phenolic-Enriched Extractives
AU - Das, Quail
AU - Islam, Md. Rashedul
AU - Lepp, Dion
AU - Tang, Joshua
AU - Yin, Xianhua
AU - Mats, Lili
AU - Liu, Huaizhi
AU - Ross, Kelly
AU - Kennes, Yan Martel
AU - Yacini, Hassina
AU - Warriner, Keith
AU - Marcone, Massimo F.
AU - Diarra, Moussa S.