scholarly journals Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

2016 ◽  
Vol 82 (8) ◽  
pp. 2433-2443 ◽  
Author(s):  
Xiang Yang ◽  
Noelle R. Noyes ◽  
Enrique Doster ◽  
Jennifer N. Martin ◽  
Lyndsey M. Linke ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Shotgun Sequencing ◽  
Meat Production ◽  
Global Public Health ◽  
Beef Production ◽  
Sequencing Technology ◽  
Production Chain ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Processing Steps

ABSTRACTFoodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads forSalmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus,Clostridiumspp. (C. botulinumandC. perfringens), andCampylobacterspp. (C. jejuni,C. coli, andC. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts forS. enterica,E. coli, andC. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.

scholarly journals Whole-Genome Sequences of Seven Listeria monocytogenes Strains from Different Stages of a Poultry Meat Production Chain

2019 ◽  
Vol 8 (11) ◽  
Author(s):  
Victoria López-Alonso ◽  
Sagrario Ortiz ◽  
Joaquín V. Martínez-Suárez
Keyword(s):  
Listeria Monocytogenes ◽  
Draft Genome ◽  
Poultry Meat ◽  
Meat Production ◽  
Whole Genome ◽  
Genome Sequences ◽  
Production Chain ◽  
Content Type ◽  
Three Stages

Here, we present the draft genome sequences of seven Listeria monocytogenes strains isolated during three independent studies carried out in three stages of a poultry meat production chain. The genome sequences of these strains obtained from different stages can help to understand the possible transmission of L. monocytogenes.

scholarly journals Antibodies Are Major Drivers of Protection against Lethal Aerosol Infection with Highly Pathogenic Burkholderia spp.

mSphere ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Robert J. Hogan ◽  
Eric R. Lafontaine
Keyword(s):  
Public Health ◽  
Burkholderia Pseudomallei ◽  
Pathogenic Bacteria ◽  
Cross Protection ◽  
Burkholderia Mallei ◽  
Global Public Health ◽  
Highly Pathogenic ◽  
Content Type ◽  
Causative Agents ◽  
Aerosol Infection

ABSTRACT Burkholderia pseudomallei and Burkholderia mallei are the causative agents of melioidosis and glanders, respectively. There is no vaccine to protect against these highly pathogenic bacteria, and there is concern regarding their emergence as global public health (B. pseudomallei) and biosecurity (B. mallei) threats. In this issue of mSphere, an article by Khakhum and colleagues (N. Khakhum, P. Bharaj, J. N. Myers, D. Tapia, et al., mSphere 4:e00570-18, 2019, https://doi.org/10.1128/mSphere.00570-18) describes a novel vaccination platform with excellent potential for cross-protection against both Burkholderia species. The report also highlights the importance of antibodies in immunity against these facultative intracellular organisms.

scholarly journals Forecasting beef production and quality using large-scale integrated data from Brazil

2020 ◽  
Vol 98 (4) ◽  
Author(s):  
Vera Cardoso Ferreira Aiken ◽  
Arthur Francisco Araújo Fernandes ◽  
Tiago Luciano Passafaro ◽  
Juliano Sabella Acedo ◽  
Fábio Guerra Dias ◽  
...  
Keyword(s):  
Linear Regression ◽  
Beef Cattle ◽  
Large Scale ◽  
National Level ◽  
Parameter Tuning ◽  
Absolute Error ◽  
Meat Production ◽  
Beef Production ◽  
Production Chain ◽  
Testing Set

Abstract With agriculture rapidly becoming a data-driven field, it is imperative to extract useful information from large data collections to optimize the production systems. We compared the efficacy of regression (linear regression or generalized linear regression [GLR] for continuous or categorical outcomes, respectively), random forests (RF) and multilayer neural networks (NN) to predict beef carcass weight (CW), age when finished (AS), fat deposition (FD), and carcass quality (CQ). The data analyzed contained information on over 4 million beef cattle from 5,204 farms, corresponding to 4.3% of Brazil’s national production between 2014 and 2016. Explanatory variables were integrated from different data sources and encompassed animal traits, participation in a technical advising program, nutritional products sold to farms, economic variables related to beef production, month when finished, soil fertility, and climate in the location in which animals were raised. The training set was composed of information collected in 2014 and 2015, while the testing set had information recorded in 2016. After parameter tuning for each algorithm, models were used to predict the testing set. The best model to predict CW and AS was RF (CW: predicted root mean square error = 0.65, R2 = 0.61, and mean absolute error = 0.49; AS: accuracy = 28.7%, Cohen’s kappa coefficient [Kappa] = 0.08). While the best approach for FD and CQ was GLR (accuracy = 45.7%, Kappa = 0.05, and accuracy = 58.7%, Kappa = 0.09, respectively). Across all models, there was a tendency for better performance with RF and regression and worse with NN. Animal category, nutritional plan, cattle sales price, participation in a technical advising program, and climate and soil in which animals were raised were deemed important for prediction of meat production and quality with regression and RF. The development of strategies for prediction of livestock production using real-world large-scale data will be core to projecting future trends and optimizing the allocation of resources at all levels of the production chain, rendering animal production more sustainable. Despite beef cattle production being a complex system, this analysis shows that by integrating different sources of data it is possible to forecast meat production and quality at the national level with moderate-high levels of accuracy.

scholarly journals Engineered Reporter Phages for Rapid Bioluminescence-Based Detection and Differentiation of Viable Listeria Cells

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Susanne Meile ◽  
Anne Sarbach ◽  
Jiemin Du ◽  
Markus Schuppler ◽  
Carmen Saez ◽  
...  
Keyword(s):  
Food Production ◽  
Pathogenic Bacteria ◽  
False Negative ◽  
Host Cells ◽  
Target Cells ◽  
Broad Host Range ◽  
Specific Detection ◽  
Production Chain ◽  
Content Type ◽  
Culture Dependent

ABSTRACT The pathogen Listeria monocytogenes causes listeriosis, a severe foodborne disease associated with high mortality. Rapid and sensitive methods are required for specific detection of this pathogen during food production. Bioluminescence-based reporter bacteriophages are genetically engineered viruses that infect their host cells with high specificity and transduce a heterologous luciferase gene whose activity can be detected with high sensitivity to indicate the presence of viable target cells. Here, we use synthetic biology for de novo genome assembly and activation as well as CRISPR-Cas-assisted phage engineering to construct a set of reporter phages for the detection and differentiation of viable Listeria cells. Based on a single phage backbone, we compare the performance of four reporter phages that encode different crustacean, cnidarian, and bacterial luciferases. From this panel of reporter proteins, nanoluciferase (NLuc) was identified as a superior enzyme and was subsequently introduced into the genomes of a broad host range phage (A511) and two serovar 1/2- and serovar 4b/6a-specific Listeria phages (A006 and A500, respectively). The broad-range NLuc-based phage A511::nlucCPS detects one CFU of L. monocytogenes in 25 g of artificially contaminated milk, cold cuts, and lettuce within less than 24 h. In addition, this reporter phage successfully detected Listeria spp. in potentially contaminated natural food samples without producing false-positive or false-negative results. Finally, A006::nluc and A500::nluc enable serovar-specific Listeria diagnostics. In conclusion, these NLuc-based reporter phages enable rapid, ultrasensitive detection and differentiation of viable Listeria cells using a simple protocol that is 72 h faster than culture-dependent approaches. IMPORTANCE Culture-dependent methods are the gold standard for sensitive and specific detection of pathogenic bacteria within the food production chain. In contrast to molecular approaches, these methods detect viable cells, which is a key advantage for foods generated from heat-inactivated source material. However, culture-based diagnostics are typically much slower than molecular or proteomic strategies. Reporter phage assays combine the best of both worlds and allow for near online assessment of microbial safety because phage replication is extremely fast, highly target specific, and restricted to metabolically active host cells. In addition, reporter phage assays are inexpensive and do not require highly trained personnel, facilitating their on-site implementation. The reporter phages presented in this study not only allow for rapid detection but also enable an early estimation of the potential virulence of Listeria isolates from food production and processing sites.

scholarly journals Risk Factors and Control Measures for Bacterial Contamination in the Bovine Meat Chain: A Review on Salmonella and Pathogenic E.coli

2015 ◽  
Vol 4 (5) ◽  
pp. 98 ◽  
Author(s):  
Eugène Niyonzima ◽  
Martin Patrick Ongol ◽  
Anasthase Kimonyo ◽  
Marianne Sindic
Keyword(s):  
Risk Factors ◽  
Pathogenic Bacteria ◽  
Control Measures ◽  
Meat Production ◽  
Cattle Farm ◽  
Faecal Excretion ◽  
Production Chain ◽  
Efficient Management ◽  
Processing Plants ◽  
Food Borne Infections

<em>Salmonella</em> and pathogenic <em>Escherichia coli</em> are known to be the major bacterial agents responsible for human foodborne infections attributable to meat. A review of the specialized literature was carried out to identify the risk factors for bovine meat contamination by these pathogens from the cattle farm to meat consumption. Animal stress during transport to the slaughterhouse and the duration of the lairage period were identified as the key factors influencing the faecal excretion of <em>Salmonella</em> and pathogenic <em>E. coli</em> as well as cattle contamination prior to slaughter. At the abattoir level, hides and visceral contents appear to be the main sources of pathogenic bacteria that contaminate carcasses along the meat production chain. Finally, temperature abuses during distribution and meat contamination by infected handlers were found to be important contributors to the post-slaughter contamination of bovine meat. The findings of this study indicate that efficient management of human food borne infections attributable to bovine meat requires an integrated application of control measures involving all actors along the meat chain, namely slaughterhouses, meat processing plants, distributors and consumers.

scholarly journals Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

2021 ◽  
Vol 87 (8) ◽  
Author(s):  
Leonardo Mancabelli ◽  
Walter Mancino ◽  
Gabriele Andrea Lugli ◽  
Christian Milani ◽  
Alice Viappiani ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Vaginal Microbiota ◽  
Microbial Consortia ◽  
Microbial Composition ◽  
Vaginal Infections ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Lactobacillus Crispatus ◽  
Vaginal Tract

ABSTRACT The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxon composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results, we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated 15 L. crispatus strains from different environments in which this species abounds, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study revealed a genetic adaptation of strains to their respective ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains, together with a synthetic vaginal microbiota, reveal how this species is able to modulate the composition of the vaginal microbial consortia at the strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. IMPORTANCE The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus strains is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genomes of new L. crispatus strains from different environments, and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.

scholarly journals Are Antimicrobial Interventions Associated with Heat-Resistant Escherichia coli on Meat?

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Peipei Zhang ◽  
Frances Tran ◽  
Kim Stanford ◽  
Xianqin Yang
Keyword(s):  
Escherichia Coli ◽  
Heat Resistance ◽  
Ecological Niches ◽  
Beef Production ◽  
Production Chain ◽  
Content Type ◽  
E Coli ◽  
Heat Resistant ◽  
Significant Difference ◽  
Antimicrobial Interventions

ABSTRACT Decontamination practices, which often involve thermal treatments, are routinely performed in beef packing plants and have generally improved the safety of meat in North America. We investigated whether Escherichia coli in the beef production chain is becoming more heat resistant due to those treatments. Cattle isolates (n = 750) included seven serogroups (O157, O103, O111, O121, O145, O26, and O45) which were collected between 2002 and 2017. Beef plant isolates (n = 700) from carcasses, fabrication equipment, and beef products were included. Heat resistance was determined in Luria-Bertani broth at 60°C and by PCR screening for the locus of heat resistance (LHR). The decimal reduction for E. coli at 60°C (D60ºC values) ranged from 0 to 7.54 min, with 97.2% of the values being <2 min. The prevalence of E. coli with D60ºC values of >2 min was not significantly different (P > 0.05) among cattle and meat plant isolates. E. coli from equipment before sanitation (median, 1.03 min) was more heat resistant than that after sanitation (median, 0.9 min). No significant difference in D60ºC values was observed among E. coli isolates from different years, from carcasses before and after antimicrobial interventions, or from before and during carcass chilling. Of all isolates, 1.97% harbored LHR, and the LHR-positive isolates had greater median D60ºC values than the LHR-negative isolates (3.25 versus 0.96 min). No increase in heat resistance in E. coli was observed along the beef production chain or with time. IMPORTANCE The implementation of multiple hurdles in the beef production chain has resulted in substantial improvement in the microbial safety of beef in Canada. In this study, we characterized a large number of Escherichia coli isolates (n = 1,450) from various sources/stages of beef processing to determine whether the commonly used antimicrobial interventions would give rise to heat-resistant E. coli on meat, which in turn may require alternatives to the current control of pathogens and/or modifications to the current cooking recommendations for meat. The findings show that the degree and rate of heat resistance in E. coli did not increase along the production chain or with time. This furthers our understanding of man-made ecological niches that are required for the development of heat resistance in E. coli.

scholarly journals Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink

2017 ◽  
Vol 5 (44) ◽  
Author(s):  
Akhikun Nahar ◽  
Anthony L. Baker ◽  
John P. Bowman ◽  
Margaret L. Britz
Keyword(s):  
Lactobacillus Casei ◽  
Draft Genome ◽  
Cheddar Cheese ◽  
Fermented Milk ◽  
Shotgun Sequencing ◽  
Sequencing Technology ◽  
Genome Sequences ◽  
Content Type ◽  
Gc Contents

ABSTRACT MiSeq Illumina shotgun sequencing technology was used to sequence two Lactobacillus casei strains, designated strains GCRL 163 and MJA 12. The estimated genome sizes for GCRL 163 and MJA 12 were 2.9 Mb and 3.1 Mb, with 46.35% and 46.31% GC contents, respectively.

How should beef be produced? Consumer expectations and views on local beef production in South Tyrol (Italy)

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Sarah Kühl ◽  
Gesa Busch ◽  
Matthias Gauly
Keyword(s):  
Design Methodology ◽  
Meat Production ◽  
Local Production ◽  
Beef Production ◽  
Content Type ◽  
Future Studies ◽  
South Tyrol ◽  
Free Feeding ◽  
Italian Province ◽  
Calf Rearing

PurposeLocal origin of meat acts as a key quality indicator for consumers. How an ideal local meat production should look like is rather unknown. The purpose of this study is to comprehensively analyse how an ideal local beef production should be constituted.Design/methodology/approach432 consumers from a North Italian province (South Tyrol) were questioned online about their views regarding (local) beef production. 12 attributes, from calf rearing to transport times, were presented with different options. Participants selected the most ideal options from their perspective. Further, willingness to pay for local beef and for the ideally produced local beef as well as the importance of local production for different food categories were assessed.FindingsThe results are quite heterogeneous but show that local production is especially of importance for eggs, dairy products and beef. Traceability to the farms, daily access to a paddock and access to pasture during summer, silage-free feeding, low transport times and suckler cow husbandry are aspects that are mostly selected as ideal. A price premium of 35% for locally produced beef and up to 50% for this ideal production seems reasonable for most consumers.Research limitations/implicationsThe study only includes South Tyrolean consumers and thus the validity is limited to this area. Although transferability to other regions can be assumed, future studies are necessary to confirm this assumption.Originality/valueThis is the first study analysing consumers expectations towards local beef production considering several production levels.

0552 - Tracing microbial contamination sources in the meat production chain

2018 ◽  
Author(s):  
Benjamin Zwirzitz ◽  
Stefanie Urimare Wetzels ◽  
Beate Pinior ◽  
Evelyne Mann
Keyword(s):  
Microbial Contamination ◽  
Meat Production ◽  
Production Chain ◽  
Contamination Sources
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