No description available.

Listeria monocytogenes is an important foodborne pathogen that can adapt to stress conditions to persist in food processing environments. Our findings show that there was a development of low-level tolerance to quaternary ammonium compound (QAC) and antibiotics ciprofloxacin and trimethoprim in L. monocytogenes after sublethal adaptation to QAC. Using eight L. monocytogenes strains, we determined the changes in MIC, growth rate, and surviving CFU for homologous and heterologous stress-response after sublethal exposure to daily cycles of fixed or gradually increasing concentration of QAC. Three main findings were observed: (1) Short-range MIC of QAC, ciprofloxacin, and trimethoprim increased by 1.6 to 2.3, 1.5 to 2.9, and 1.7 to 2.5 fold against QAC-adapted phenotypes of L. monocytogenes as compared to the non-adapted cells; (2) QAC-adapted phenotypes of L. monocytogenes exhibited a significant increase in growth rate by 2.5 to 7.1, 2.1 to 6.8, or 1.4 to 4.8 fold in the broth model containing QAC, ciprofloxacin, or trimethoprim respectively, as compared to non-adapted cells; and (3) QAC-adapted phenotypes of L. monocytogenes exhibited a significant increase in survival by 1.5 to 4, 2.2 to 4.3, or 1.3 to 3.2 log CFU/ml in the agar model containing QAC, ciprofloxacin, or trimethoprim respectively, as compared to non-adapted cells (P < 0.05). There were strain differences in QAC-adapted phenotypes of L. monocytogenes for both homologous and heterologous stress-response with some strains exhibiting a significant increase in short-range MIC, growth rate, and survival while others exhibiting no changes as compared to non-adapted cells. These findings suggest the potential formation of low-level QAC-tolerant and antibiotic-tolerant phenotypes in some L. monocytogenes strains under residual QAC concentrations (where QAC may be used widely) and such cells if not inactivated may survive longer to increase food safety risk.

Compostos de amônio quaternário (QACs) têm sido amplamente utilizados como desinfetantes e antissépticos, sendo essenciais na prevenção e controle de infecções bacterianas na medicina humana e veterinária. Embora patógenos prioritários multirresistentes têm sido muito bem caracterizados quanto ao perfil de suscetibilidade e contexto genético da resistência aos antibióticos, dados de resistência aos QACs são limitados. Assim, o objetivo do presente estudo foi avaliar a atividade in vitro dos QACs de uso doméstico e hospitalar [cloreto de benzalcônio (BAC), cloreto de cetilpiridinio (CPC) e brometo de cetiltrimetilamônio (CTAB)], contra patógenos prioritários multirresistentes, identificando os principais genes de resistência associados. Foram estudadas 100 cepas multirresistentes previamente sequenciados usando as plataformas Illumina MiSeq e NextSeq representativas de diferentes hospedeiros (humanos e animais) e fontes (ambientes e alimentos). As cepas foram identificadas como Klebsiella pneumoniae (n= 24), Escherichia coli (n= 30); Pseudomonas aeruginosa (n= 10), Enterobacter spp, (n= 8), Acinetobacter baumannii (n= 11) e Salmonella spp. (n= 17). Genes de resistência aos QACs foram identificados in silico através do alinhamento dos contigs obtidos de cada cepa sequenciada com genes de referência obtidos do GenBank, utilizando o programa Geneious versão 8 (Biomatters Ltd). A identidade de cada gene foi analisada utilizando o programa BLASTx, no qual um critério baseado em &#8805;90% identidade resultou na identificação dos genes mdfA (77%), qacE (44%), qacE&#916;1 (43%), sugE(c) (29%), emrE (21%), qacA (19%), sugE(p) (5%), qacF (7%), qacH (7%) e qacL (7%) em 85 cepas; enquanto que 15 cepas não possuíam nenhum gene de resistência aos QACs. A concentração inibitória mínima (CIM) dos QACs para as 100 cepas foi determinada pelo método de microdiluição em caldo. Os resultados sugeriram que a resistência em patógenos prioritários circulando na interface humano-ambiente-animal não é restrita aos antibióticos, uma vez que a elevada ocorrência de genes qacE, qacE&#916;1 e mdfA poderia estar associada com uma redução da suscetibilidade para QACs. Consequentemente, a resistência aos QACs poderia também contribuir para a persistência e adaptação destes patógenos nos seres humanos e outros animais, assim como em ambientes impactados antropogenicamente. / Quaternary ammonium compounds (QACs) have been widely used as disinfectants and antiseptics, being applied as essential compounds in the prevention and control of bacterial infections in human-and veterinary hospital medicine. Although multiresistant priority pathogens have been well characterized with respect to their susceptibility profile and their genetic context of resistance for antibiotics, studies of resistance to QACs are limited. Thus, the objective of the present study was to evaluate the in vitro activity of QACs [(benzalkonium chloride (BAC), cetylpyridinium chloride (CPC) and cetyltrimethylammonium bromide (CTAB)] for household and hospital use against multiresistant priority pathogens, identifying the main resistance genes associated. A hundred multiresistant isolates (previously sequenced using the Illumina MiSeq and NextSeq platforms), representative of different hosts (humans and animals) and sources (environment and food) were studied. Isolates were identified as Klebsiella pneumoniae (n=24), Escherichia coli (n=30), Pseudomonas aeruginosa (n=10), Enterobacter spp. (n=8), Acinetobacter baumannii (n=11) and Salmonella spp. (n=17). In silico analysis for identification of genes conferring resistance to QACs were performed by aligning the contigs obtained from the strains with reference genes deposited in GenBank, using the Geneious version program (Biomatters Ltd). Similarities were analyzed using the BLASTx online program, considering the alignment criteria based on &#8805; 90% identity. The result of these analysis revealed the presence of the following QAC genes: mdfA (77%), qacE (44%), qacE&#916;1 (43%), sugE(c) (29%), emrE (21%), qacA (19%), sugE (p) (5%), qacF (7%), qacH (7%) e qacL (7%); while 15 strains showed no resistance genes for QACs. Determination of QACs minimum inhibitory concentration (MIC) for the 100 isolates, by the broth microdilution method. These results suggest that resistance to QACs in priority pathogens, circulating at the human-environment-animal interface, is not restricted to antibiotics, since the high occurrence of genes qacE, qacE&#916;1 and mdfA were associated with a reduced susceptibility to QACs. Consequently, resistance to QACs could also contribute to the persistence and adaptation of these pathogens in humans and othes animals, as well as in anthropogenically impacted environments.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

No description available.

Dependency parsing can be a useful tool to allow computers to parse text. In 2015, Kuhlmann and Jonsson proposed a logical deduction system that parsed to non-crossing dependency graphs with an asymptotic time complexity of O(n3), where “n” is the length of the sentence to parse. This thesis extends the deduction system by Kuhlmann and Jonsson; the extended deduction system introduces certain crossing edges, while maintaining an asymptotic time complexity of O(n4). In order to extend the deduction system by Kuhlmann and Jonsson, fifteen logical item types are added to the five proposed by Kuhlmann and Jonsson. These item types allow the deduction system to intro-duce crossing edges while acyclicity can be guaranteed. The number of inference rules in the deduction system is increased from the 19 proposed by Kuhlmann and Jonsson to 172, mainly because of the larger number of combinations of the 20 item types. The results are a modest increase in coverage on test data (by roughly 10% absolutely, i.e. approx. from 70% to 80%), and a comparable placement to that of Kuhlmann and Jonsson by the SemEval 2015 task 18 metrics. By the method employed to introduce crossing edges, derivational uniqueness is impossible to maintain. It is hard to defien the graph class to which the extended algorithm, QAC, parses, and it is therefore empirically compared to 1-endpoint crossing and graphs with a page number of two or less, compared to which it achieves lower coverage on test data. The QAC graph class is not limited by page number or crossings. The takeaway of the thesis is that extending a very minimal deduction system is not necessarily the best approach, and that it may be better to start off with a strong idea of to which graph class the extended algorithm should parse. Additionally, several alternative ways of extending Kuhlmann and Jonsson are proposed. / Dependensparsning kan vara ett användbart verktyg för att få datorer att kunna läsa text. Kuhlmann och Jonsson kom 2015 fram till ett logiskt deduktionssystem som kan parsa till ickekorsande grafer med en asymptotisk tidskomplexitet O(n3), där "n" är meningens som parsas längd. Detta arbete utökar Kuhlmann och Jonssons deduktionssystem så att det kan introducera vissa korsande bågar, medan en asymptotisk tidskomplexitet O(n4) uppnås. För att tillåta deduktionssystemet att introducera korsande bågar, introduceras 15 nya logiska delgrafstyper, eller item. Dessa item-typer tillåter deduktionssystemet att introducera korsande bågar på ett sådant sätt att acyklicitet bibehålls. Antalet logiska inferensregler tags från Kuhlmanns och Jonssons 19 till 172, på grund av den större mängden kombinationer av de nu 20 item-typerna. Resultatet är en mindre ökning av täckning på testdata (ungefär 10 procentenheter, d v s från cirka 70% till 80%), och jämförbar placering med Kuhlmann och Jonsson enligt måtten från uppgift 18 från SemEval 2015. Härledningsunikhet kan inte garanteras på grund av hur bågar introduceras i det nya deduktionssystemet. Den utökade algoritmen, QAC, parsar till en svårdefinierad grafklass, som jämförs empiriskt med 1-endpoint-crossing-grafer och grafer med pagenumber 2 eller mindre. QAC:s grafklass har lägre täckning än båda dessa, och har ingen högre gräns i pagenumber eller antal korsningar. Slutsatsen är att det inte nödvändigtvis är optimalt att utöka ett mycket minimalt och specifikt deduktionssystem, och att det kan vara bättre att inleda processen med en specifik grafklass i åtanke. Dessutom föreslås flera alternativa metoder för att utöka Kuhlmann och Jonsson.