scholarly journals Use of an Ecosystem-Based Approach to Shed Light on the Heterogeneity of the Contamination Pattern of Listeria monocytogenes on Conveyor Belt Surfaces in a Swine Slaughterhouse in the Province of Quebec, Canada

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1368
Author(s):  
Fanie Shedleur-Bourguignon ◽  
William P. Thériault ◽  
Jessie Longpré ◽  
Alexandre Thibodeau ◽  
Philippe Fravalo
Keyword(s):  
Listeria Monocytogenes ◽  
Meat Products ◽  
Illumina Miseq ◽  
Conveyor Belt ◽  
Production Lines ◽  
Low Genetic Diversity ◽  
Bacterial Indicator ◽  
16S Rna ◽  
Biomarker Analysis ◽  
Miseq Platform

The role of the accompanying microbiota in the presence of Listeria monocytogenes on meat processing surfaces is not yet understood, especially in industrial production conditions. In this study, 300 conveyor belt samples from the cutting room of a swine slaughterhouse were collected during production. The samples were subjected to the detection of L. monocytogenes. Recovered strains were characterized by serogrouping-PCR, InlA Sanger sequencing and for their ability to form biofilm. A selection of isolates was compared with core genome multi-locus sequence typing analysis (cgMLST). The sequencing of the V4 region of the 16S RNA gene of the microorganisms harvested from each sample was carried out in parallel using the Illumina MiSeq platform. Diversity analyses were performed and MaAsLin analysis was used to assess the link between L. monocytogenes detection and the surrounding bacteria. The 72 isolates collected showed a low genetic diversity and important persistence characteristics. L monocytogenes isolates were not stochastically distributed on the surfaces: the isolates were detected on three out of six production lines, each associated with a specific meat cut: the half carcasses, the bostons and the picnics. MaAsLin biomarker analysis identified the taxa Veillonella (p ≤ 0.0397) as a bacterial determinant of the presence of L. monocytogenes on processing surfaces. The results of this study revealed a heterogenous contamination pattern of the processing surfaces by L. monocytogenes and targeted a bacterial indicator of the presence of the pathogen. These results could lead to a better risk assessment of the contamination of meat products.

scholarly journals Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

2019 ◽  
Author(s):  
Andrea Ottesen ◽  
Padmini Ramachandran ◽  
Yi Chen ◽  
Eric Brown ◽  
Elizabeth Reed ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Pathogen Detection ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Ice Cream ◽  
Illumina Miseq ◽  
Source Tracking ◽  
Public Health Response ◽  
Health Response ◽  
Miseq Platform

Abstract Background The more quickly bacterial pathogens responsible for foodborne illness outbreaks can be traced to their source, the more illnesses can be prevented and the less unnecessary destruction of food will occur. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichment (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate.Methods Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes.Results Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture). Conclusions The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and additionally, reduce the unnecessary waste of food that has been detained for investigation and due to lengthy response time, could not be deemed safe before spoilage.

scholarly journals Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

2020 ◽  
Author(s):  
Andrea Ottesen ◽  
Padmini Ramachandran ◽  
Yi Chen ◽  
Eric Brown ◽  
Elizabeth Reed ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Pathogen Detection ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Ice Cream ◽  
Illumina Miseq ◽  
Source Tracking ◽  
Public Health Response ◽  
Health Response ◽  
Miseq Platform

Abstract Background The more quickly bacterial pathogens can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food. Methods Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes . Results Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture). Conclusions The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.

Prepackage Surface Pasteurization of Ready-to-Eat Meats with a Radiant Heat Oven for Reduction of Listeria monocytogenes

2003 ◽  
Vol 66 (9) ◽  
pp. 1623-1630 ◽  
Author(s):  
NANDITHA GANDE ◽  
PETER MURIANA
Keyword(s):  
Listeria Monocytogenes ◽  
Treatment Time ◽  
Meat Products ◽  
Radiant Heat ◽  
Conveyor Belt ◽  
Treatment Temperature ◽  
Heat Processing ◽  
Processed Meat ◽  
Air Temperatures ◽  
Roast Beef

In this paper, a thermal process for the surface pasteurization of ready-to-eat (RTE) meat products for the reduction of Listeria monocytogenes on such products (turkey bologna, roast beef, corned beef, and ham) is described. The process involves the passage of products through a “tunnel” of heated coils on a stainless steel conveyor belt at various treatment times relevant to the manufacture of processed meat for the surface pasteurization of RTE meat products. Two inoculation procedures, dip and contact inoculation, were examined with the use of a four-strain cocktail of L. monocytogenes prior to heat processing. With the use of radiant heat prepackage surface pasteurization, 1.25 to 3.5-log reductions of L. monocytogenes were achieved with treatment times of 60 to 120 s and air temperatures of 475 to 750°F (246 to 399°C) for these various RTE meats. Reduction levels differed depending on the type of inoculation method used, the type of product used, the treatment temperature, and the treatment time. Prepackage pasteurization (60 s) was also combined with postpackage submerged water pasteurization for formed ham (60 or 90 s), turkey bologna (45 or 60 s), and roast beef (60 or 90 s), resulting in reductions of 3.2 to 3.9, 2.7 to 4.3, and 2.0 to 3.75 log cycles, respectively. These findings demonstrate that prepackage pasteurization, either alone or in combination with postpackage pasteurization, is an effective tool for controlling L. monocytogenes surface contamination that may result from in-house handling.

Listeria monocytogenes Contamination of Turkey Franks: Evaluation of a Production Facility

1990 ◽  
Vol 53 (12) ◽  
pp. 1015-1019 ◽  
Author(s):  
JAY D. WENGER ◽  
BALA SWAMINATHAN ◽  
PEGGY S. HAYES ◽  
STANLEY S. GREEN ◽  
MARK PRATT ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Food Processing ◽  
Environmental Samples ◽  
Meat Products ◽  
Conveyor Belt ◽  
Most Probable Number ◽  
Retail Outlet ◽  
Probable Number ◽  
Processing Plants ◽  
Production Stages

A facility which produced turkey franks that had been microbiologically linked to a case of human listeriosis was evaluated to establish prevalence of contamination and identify potential points for intervention. Listeria monocytogenes was isolated from only two of 41 environmental samples obtained in the plant. Among production line product samples analyzed by the Centers for Disease Control, 0 to 8% of samples from the production stages before the peeler-conveyor belt apparatus were positive for the case strain of L. monocytogenes, whereas 12 of 14 (86%) samples collected from this apparatus were positive (p <0.001). The most probable number (MPN) of L. monocytogenes in finished product purchased from a retail outlet was less than 0.3 per gram; however, the opened package of franks from the case patient's refrigerator had an MPN of >1100 per gram. These data suggest that systematic culturing and analysis of products and production facilities may help identify appropriate interventions to reduce L. monocytogenes contamination in food processing plants and contribute to control of L. monocytogenes in ready-to-eat meat products.

scholarly journals Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Yini Dang ◽  
Xintong Zhang ◽  
Yu Zheng ◽  
Binbin Yu ◽  
Dijia Pan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Target Selection ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Control Group ◽  
Characteristic Analysis ◽  
Microbial Composition ◽  
16S Rna ◽  
Miseq Platform

Objectives. Functional prognosis is potentially correlated with gut microbiota alterations following the dysregulation of the gut-microbiota-brain axis after stroke. This study was designed to explore the poststroke alterations of gut microbiota and potential correlations between gut microbiota and global functions. Methods. A total of thirty-eight patients with stroke and thirty-five healthy demographics-matched controls were recruited. Their fecal DNAs were extracted, and the V3-V4 regions of the conserved bacterial 16S RNA were amplified and sequenced on the Illumina MiSeq platform. Microbial composition, diversity indices, and species cooccurrence were compared between groups. Random forest and receiver operating characteristic analysis were used to identify potential diagnostic biomarkers. Relationships between discriminant bacteria and poststroke functional outcomes were estimated. Results. Higher alpha diversity of gut microbiota was observed in poststroke patients as compared to the healthy controls ( p < 0.05 ). Beta diversity showed that microbiota composition in the poststroke group was significantly different from that in the control group. Relative abundance of nine genera increased significantly in poststroke patients, while 82 genera significantly decreased ( p < 0.05 ). The accuracy, specificity, and susceptibility of the optimal model consisted of the top 10 discriminant species were 93%, 100%, and 86%, respectively. Subgroup analysis showed that bacterial taxa abundant between subacute and chronic stroke patients were overall different ( p < 0.05 ). The modified Rankin scale (mRS) ( r = − 0.370 , p < 0.05 ), Fugl-Meyer assessment (FMA) score ( r = 0.364 , p < 0.05 ), water swallow test (WST) ( r = 0.340 , p < 0.05 ), and Barthel index (BI) ( r = 0.349 , p < 0.05 ) were significantly associated with alterations of distinctive gut microbiota. Conclusions. The gut microbiota in patients with stroke was significantly changed in terms of richness and composition. Significant associations were detected between alterations of distinctive gut microbiota and global functional prognosis. It would facilitate novel treatment target selection in the context of stroke while the causal relationships between distinctive gut microbiota alterations and functional variations need to be further verified with well-designed studies.

scholarly journals Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

2020 ◽  
Author(s):  
Andrea Ottesen ◽  
Padmini Ramachandran ◽  
Yi Chen ◽  
Eric Brown ◽  
Elizabeth Reed ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Pathogen Detection ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Ice Cream ◽  
Illumina Miseq ◽  
Source Tracking ◽  
Public Health Response ◽  
Health Response ◽  
Miseq Platform

Abstract Background The more quickly bacterial pathogens can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food. Methods Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes . Results Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture). Conclusions The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.

scholarly journals Complete Genome Sequence of Listeria monocytogenes DFPST0073, Isolated from Imported Mexican Soft Cheese

2018 ◽  
Vol 6 (23) ◽  
Author(s):  
Joelle K. Salazar ◽  
Lauren J. Gonsalves ◽  
Kristin M. Schill ◽  
Maria Sanchez Leon ◽  
Nathan Anderson ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Prokaryotic Genome ◽  
Illumina Miseq ◽  
Annotation Pipeline ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Soft Cheese ◽  
Miseq Platform

ABSTRACT The genome of Listeria monocytogenes strain DFPST0073, isolated from imported fresh Mexican soft cheese in 2003, was sequenced using the Illumina MiSeq platform. Reads were assembled using SPAdes, and genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline.

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

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