scholarly journals Quaternary ammonium compound resistance as a persistence marker for L. monocytogenes

2020 ◽  
Author(s):  
Ashley L Cooper ◽  
Catherine D Carrillo ◽  
Mylène Deschênes ◽  
Burton Blais
Keyword(s):  
Quaternary Ammonium ◽  
Gene Cassette ◽  
Whole Genome Sequence ◽  
Ammonium Compound ◽  
Whole Genome ◽  
Food Manufacturing ◽  
Risk Managers ◽  
Manufacturing Environments ◽  
Contamination Events

Persistent contamination of food manufacturing environments by Listeria monocytogenes is an important public health risk because such contamination events defy standard sanitization protocols, for example, the application of quaternary ammonium compounds such as benzalkonium chloride (BC), providing a source for prolonged dissemination of the bacteria in food products. We performed whole-genome sequence (WGS) analyses of 1279 well-characterized L. monocytogenes isolates from a variety of foods and food manufacturing environments and identified the bcrABC gene cassette associated with BC resistance in 41.5% of isolates. Of particular interest was the finding that all but one of 177 clonal complex (CC) 321 isolates, representing one of the most commonly occurring CCs found in foods and food-production environments, harbored the intact bcrABC cassette. Thirty-nine (38.6) percent of isolates recovered from foods representing 67 different CCs, and 59.2% of strains from food-manufacturing environmental samples representing 26 different CCs, were found to harbor the intact bcrABC cassette. A representative set of 69 isolates with and without bcrABC was assayed for the ability to grow in the presence of BC, and 34 of 35 isolates harboring the bcrABC cassette were resistant to BC. Determination of bcrABC in colony isolates could be achieved using both polymerase chain reaction and whole genome sequencing techniques, providing food testing laboratories with options for the characterization of isolates. The ability to detect bcrABC provides risk managers with a valuable tool to assess the potential for persistent contamination of the food manufacturing environment, which in turn may indicate the need for more targeted surveillance to ensure the efficacy of mitigation actions.

scholarly journals Determination of whole-genome sequence of Salmonella Abortusequi

2016 ◽  
Vol 39 ◽  
pp. S59 ◽  
Author(s):  
H. Niwa ◽  
M. Akiba ◽  
T. Sekizuka ◽  
M. Kuroda ◽  
Y. Kinoshita ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

scholarly journals Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments

2018 ◽  
Vol 6 (15) ◽  
pp. e00223-18 ◽  
Author(s):  
Hyein Jang ◽  
Nicole Addy ◽  
Laura Ewing ◽  
Junia Jean-Gilles Beaubrun ◽  
YouYoung Lee ◽  
...  
Keyword(s):  
Draft Genome ◽  
Whole Genome ◽  
Cronobacter Sakazakii ◽  
Plant Origin ◽  
Genome Sequences ◽  
Food Manufacturing ◽  
Coding Sequences ◽  
Content Type ◽  
Gene Coding ◽  
Manufacturing Environments

ABSTRACT Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from foods of plant origin and dried-food manufacturing facilities. Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb and 3,977 to 4,256 gene-coding sequences with G+C contents of ∼57.0%.

scholarly journals Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

2016 ◽  
Vol 54 (8) ◽  
pp. 1975-1983 ◽  
Author(s):  
Marc W. Allard ◽  
Errol Strain ◽  
David Melka ◽  
Kelly Bunning ◽  
Steven M. Musser ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Foodborne Illnesses ◽  
Foodborne Outbreak ◽  
Public Health Response ◽  
Food Manufacturing ◽  
Health Response ◽  
Effective Public Health ◽  
Manufacturing Environments

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks.

scholarly journals Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

2016 ◽  
Vol 54 (8) ◽  
pp. 2135-2148 ◽  
Author(s):  
Sophia David ◽  
Massimo Mentasti ◽  
Rediat Tewolde ◽  
Martin Aslett ◽  
Simon R. Harris ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Gold Standard ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Typing Method ◽  
Content Type ◽  
Typing Scheme ◽  
Full Profile

Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current “gold standard” typing method for investigation of legionellosis outbreaks caused byLegionella pneumophila. However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method.L. pneumophilaserogroup 1 isolates (n= 106) from the standard “typing panel,” previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method forL. pneumophila.

Comparative Evaluation of Genomic and Laboratory Approaches for Determination of Shiga Toxin Subtypes in Escherichia coli

2016 ◽  
Vol 79 (12) ◽  
pp. 2078-2085 ◽  
Author(s):  
CATHERINE D. CARRILLO ◽  
ADAM G. KOZIOL ◽  
AMIT MATHEWS ◽  
NORIKO GOJI ◽  
DOMINIC LAMBERT ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Shiga Toxin ◽  
In Silico ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Pcr Method ◽  
In Silico Pcr

ABSTRACT The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition. The choice of technique will depend on the performance characteristics of the method and an individual laboratory's access to specialized equipment or personnel. We developed two whole genome sequence–based ST subtyping tools: (i) an in silico PCR algorithm requiring genome assembly to replicate a reference PCR-based method developed by the Statens Serum Institut (SSI) and (ii) an assembly-independent routine in which raw sequencing results are mapped to a database of known ST subtype sequence variants (V-Typer). These tools were evaluated alongside the SSI reference PCR method and a recently described PCR-based pyrosequencing technique. The V-Typer method results corresponded closely with the reference method in the analysis of 67 STEC cultures obtained from a World Health Organization National Reference Laboratory. In contrast, the in silico PCR method failed to detect ST subtypes in several cases, a result which we attribute to assembly-induced errors typically encountered with repetitive gene sequences. The V-Typer can be readily integrated into bioinformatics protocols used in the identification and characterization of foodborne STEC isolates.

scholarly journals Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nipa Chokesajjawatee ◽  
Pannita Santiyanont ◽  
Kanittha Chantarasakha ◽  
Kanokarn Kocharin ◽  
Chinae Thammarongtham ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Genome Analysis ◽  
Safety Assessment ◽  
Starter Culture ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Microbial Cultures

Abstract The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have been suggested, no methodological detail nor procedural guideline have been published. Herein, we propose a detailed protocol on microbial strain safety assessment via whole-genome sequence analysis. A starter culture employed in traditional fermented pork production, nham, namely Lactobacillus plantarum BCC9546, was used as an example. The strain’s whole-genome was sequenced through several next-generation sequencing techniques. Incomplete plasmid information from the PacBio sequencing platform and shorter chromosome size from the hybrid Oxford Nanopore-Illumina platform were noted. The methods for 1) unambiguous species identification using 16S rRNA gene and average nucleotide identity, 2) determination of virulence factors and undesirable genes, 3) determination of antimicrobial resistance properties and their possibility of transfer, and 4) determination of antimicrobial drug production capability of the strain were provided in detail. Applicability of the search tools and limitations of databases were discussed. Finally, a procedural guideline for the safety assessment of microbial strains via whole-genome analysis was proposed.

Determination of the quaternary ammonium compound trospium in human plasma by LC–MS/MS: Application to a pharmacokinetic study

2010 ◽  
Vol 878 (13-14) ◽  
pp. 981-986 ◽  
Author(s):  
Kishore Kumar Hotha ◽  
D. Vijaya Bharathi ◽  
Sanagapati Sirish Kumar ◽  
Y. Narasimha Reddy ◽  
Pankaj K. Chatki ◽  
...  
Keyword(s):  
Human Plasma ◽  
Pharmacokinetic Study ◽  
Quaternary Ammonium ◽  
Quaternary Ammonium Compound ◽  
Ammonium Compound

scholarly journals High Contiguity Whole Genome Sequence and Gene Annotation Resource for Two Venturia nashicola Isolates

2019 ◽  
Vol 32 (9) ◽  
pp. 1091-1094 ◽  
Author(s):  
Maxim Prokchorchik ◽  
Kyungho Won ◽  
Yoonyoung Lee ◽  
Eu Ddeum Choi ◽  
Cécile Segonzac ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Data ◽  
Asian Pear ◽  
Venturia Nashicola ◽  
Host Range Determination ◽  
Range Determination ◽  
Northeast Asian

Venturia nashicola is a fungal pathogen that causes Asian pear scab disease. This pathogen is of particular importance in Northeast Asian countries, where Asian pears are grown industrially. Scab disease in Asian pear is currently controlled by fungicide spraying and this situation calls for developing scab resistant cultivars. High-quality genome data are therefore required for in-depth comparative genome analysis of different isolates of V. nashicola and V. pyrina, a closely related species, which only infects European pear plants. Here, we report the high-contiguity whole genome assembly of two V. nashicola isolates, which is expected to enable genome comparisons for identification of the genes involved in host range determination of V. nashicola.

Sign in / Sign up

Export Citation Format

Share Document