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      Raw milk cheeses from Beira Baixa, Portugal—A contributive study for the microbiological hygiene and safety assessment

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          Abstract

          Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk cheeses from Beira Baixa, Portugal. Presence and enumeration of Coagulase Positive Staphylococci (CPS), Listeria monocytogenes, Salmonella spp., pathogenic Escherichia coli, and indicator microorganisms (non-pathogenic E. coli and Listeria spp.) was attained. E. coli antimicrobial resistance (AMR) was also evaluated. PCR and/or Whole genome sequencing (WGS) was used to characterize E. coli, Salmonella spp. and L. monocytogenes isolates. Sixteen cheeses (16.3%) were classified as Satisfactory, 59 (60.2%) as Borderline and 23 (23.5%) as Unsatisfactory/Potential Injurious to Health. L. monocytogenes, CPS > 10 4 cfu g −1, Extraintestinal pathogenic E. coli (ExPEC) and Salmonella spp. were detected in 4.1%, 6.1%, 3.1% and 1.0% of the samples, respectively. Listeria innocua (4.1%) and E. coli > 10 4 cfu g −1 (16.3%) were also detected. AMR E. coli was detected in 23/98 (23.5%) of the cheese samples, of which two were multidrug resistant. WGS identified genotypes already associated to human disease and Listeria spp. cluster analysis indicated that cheese contamination might be related with noncompliance with Good Hygiene Practices during cheese production.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s42770-024-01332-y.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

            Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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              Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.

              Many different definitions for multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) bacteria are being used in the medical literature to characterize the different patterns of resistance found in healthcare-associated, antimicrobial-resistant bacteria. A group of international experts came together through a joint initiative by the European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC), to create a standardized international terminology with which to describe acquired resistance profiles in Staphylococcus aureus, Enterococcus spp., Enterobacteriaceae (other than Salmonella and Shigella), Pseudomonas aeruginosa and Acinetobacter spp., all bacteria often responsible for healthcare-associated infections and prone to multidrug resistance. Epidemiologically significant antimicrobial categories were constructed for each bacterium. Lists of antimicrobial categories proposed for antimicrobial susceptibility testing were created using documents and breakpoints from the Clinical Laboratory Standards Institute (CLSI), the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the United States Food and Drug Administration (FDA). MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories, XDR was defined as non-susceptibility to at least one agent in all but two or fewer antimicrobial categories (i.e. bacterial isolates remain susceptible to only one or two categories) and PDR was defined as non-susceptibility to all agents in all antimicrobial categories. To ensure correct application of these definitions, bacterial isolates should be tested against all or nearly all of the antimicrobial agents within the antimicrobial categories and selective reporting and suppression of results should be avoided. © 2011 European Society of Clinical Microbiology and Infectious Diseases. No claim to original US government works.
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                Author and article information

                Contributors
                riitamendonca@gmail.com
                rita.batista@insa.min-saude.pt
                Journal
                Braz J Microbiol
                Braz J Microbiol
                Brazilian Journal of Microbiology
                Springer International Publishing (Cham )
                1517-8382
                1678-4405
                15 April 2024
                15 April 2024
                June 2024
                : 55
                : 2
                : 1759-1772
                Affiliations
                [1 ]Department of Food and Nutrition, National Institute of Health Doutor Ricardo Jorge, ( https://ror.org/03mx8d427) Lisbon, Portugal
                [2 ]Faculty of Sciences, University of Lisbon, ( https://ror.org/01c27hj86) Lisbon, Portugal
                [3 ]Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, ( https://ror.org/03mx8d427) Lisbon, Portugal
                [4 ]NOVA School of Science and Technology, 2829-516 Caparica, Portugal
                [5 ]GRID grid.164242.7, ISNI 0000 0000 8484 6281, Animal and Veterinary Research Center (CECAV), Faculty of Veterinary Medicine, , Lusófona University-Lisbon University Centre, ; Lisbon, Portugal
                Author notes

                Communicated by Responsible Editor: Luis Augusto Nero.

                Author information
                https://orcid.org/0000-0002-8220-6592
                https://orcid.org/0000-0003-3767-2209
                https://orcid.org/0000-0002-2697-2399
                https://orcid.org/0000-0002-9219-4222
                http://orcid.org/0000-0002-2081-682X
                Article
                1332
                10.1007/s42770-024-01332-y
                11153484
                38622468
                800680d9-bbf4-441a-8610-be019e948e7c
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 21 December 2023
                : 3 April 2024
                Funding
                Funded by: Instituto Nacional de Saúde Dr. Ricardo Jorge
                Categories
                Food Safety and Quality - Research Paper
                Custom metadata
                © Sociedade Brasileira de Microbiologia 2024

                raw milk cheese,listeria monocytogenes,escherichia coli,coagulase positive staphylococci,salmonella spp.,whole-genome sequencing (wgs),portugal

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