Utilizing Microbiome and Bioinformatic Tools to Reduce Food Waste in Poultry

ObjectivesIn chicken harvest, the post-harvest chilling process is a crucial step for food safety. Most facilities use either water immersion chilling (WC) or air chilling (AC) to rapidly cool the chicken. A holistic assessment of the consequences of each method to meat quality and shelf life is necessary to determine the impacts of each method. To address this knowledge gap, a multi-faceted project was conducted to determine how the chilling system influenced the microbial ecology and subsequent deterioration of chicken breasts.Materials and MethodsThe study was conducted using a 2 × 2 × 2 factorial design to evaluate the impacts of chilling method (AC vs. WC), fabrication method (bone-in vs. boneless; BI vs. BL), and cold storage period (7 vs. 14 d) on the microbial ecology of chicken breasts. A total of 256 chicken carcasses were used for this study. Carcasses were obtained from a commercial processing plant following dressing and a single antimicrobial treatment. Twenty carcasses were removed for sampling as warm carcasses, and the remaining 236 were divided into eight groups for processing (AC-BI, AC-BL, WC-BI, WC-BL tray-wrapped for 7- and 14-d storage). Collection time-points included: warm, post-chilling, post-fabrication, post-storage, and after 3-d retail display. Microbiome samples were collected at each sampling using a PBS rinsate. Then, samples were further processed for microbiome analysis following standard methods, sequenced for the V4 region of the 16S rRNA gene, and analyzed using the QIIME2 pipeline.ResultsThere were significant differences in microbial diversity between different chilling methods, fabrications methods, and cold storage times. Both chilling methods were different from the warm carcasses based on α diversity metrics, though the two chilling methods were not different from each other. However, there were differences in the β diversity between all three groups. Storage day significantly altered the faith’s phylogenetic α diversity but had no impact on Shannon’s α diversity. By both metrics, the diversity was reduced with increased length of storage, suggesting that a few organisms begin to dominate the product during dark storage. The fabrication methods also resulted in significantly different diversities when phylogenetic metrics (Faith’s, unweighted UniFrac) were used. The products that were sampled prior to dark storage, regardless of chilling method, were dominated by Enterobacteriaceae, while those that were subjected to cold storage were dominated by Pseudomonadaceae. In the stored samples, AC samples tended to have a greater abundance of Moraxellaceae and Enterobacteriaceae than WC.ConclusionThese results suggest that different treatments of chicken breasts, including chilling, fabrication, and storage time, all correspond with changes to the product microbiome. These data will be combined with microbiology, physiochemical, nutritive, and taste and color data as well as a techno-economic analysis to provide a deeper understanding of impacts of processing methods on poultry quality and shelf life.

Fluctuations in the Microbial Community and the Volatile Organic Acids Created During Aerobic Storage of Ground Beef

ObjectivesDegradation due to microbial and chemical mechanisms occurs throughout the storage life of ground beef. These pathways are intertwined and the microbial community and the volatile organic acids (VOCs) that evolve in ground beef are dynamic. Evaluation of microbial growth using traditional culture-dependent techniques can be misleading due to the presence of unculturable organisms. Therefore, utilizing culture-independent techniques allows for a more thorough understanding of the microbial community within a meat matrix during storage life. The objective of this study was to employ 16s rRNA amplicon sequencing and VOC identification using GC–MS to explore diversity and changes of the microbial community and VOC production during shelf-life of ground beef.Materials and MethodsFinely ground beef (80/20) was procured from beef processing facilities in the West (one lot) and Midwest (two lots). The lots were separated into three physically separate replicates. Ground beef lots were transported in chub packaging to Colorado State University (Fort Collins, CO), and the chubs were stored in the dark at 2°C for either 16/17 d or 23/24 d. After dark storage, chubs were reground, and 454 g fluff-packs were placed on polystyrene trays before overwrapping with polyvinyl chloride film. The trays were placed in retail display cases maintained at 2–4°C for 5 d. Samples were collected every day of retail display for evaluation of the microbial community and VOC development. Following standardized extraction, 16S rRNA amplicon sequencing was used to explore microbial communities. Sequencing data were analyzed using the programs in the QIIME2 (version 2018.4) pipeline. Similarly, volatile organic compounds were extracted prior to analysis of targeted VOCs using a GC–MS. The project was designed as a split-plot design and was analyzed using R packages (version 3.4.3), lme4, lmerTest, and emmeans. Least squares means were separated using an α of 0.05.ResultsThe top orders of bacteria found in the meat samples were from Enterobacteriales, Lactobacillales, and Pseudomonadales. No differences (P ≥ 0.05) in Faith’s Phylogenetic Diversity Index, or a measure of diversity of the bacterial species within a sample, were observed between Days 0, 2, and 4 of retail case display. A targeted analysis identified eighteen VOCs associated with ground beef spoilage. In previous studies, the presence of hexanal, acetoin and acetic acid are identified as spoilage indicators. Hexanal, Acetoin and acetic acid increased (P ≤ 0.05) over the 5 d of retail display.ConclusionThe use of 16s rRNA amplicon sequencing technology is a relatively recent tool that has rapidly advanced the study of microbial deterioration during beef storage and shelf-life. Moreover, the combination of 16s rRNA amplicon sequencing and identification of VOCs in this study, afforded an exploration of the relationship between chemical and biological changes which occur during ground beef storage. These analytical technologies, when used in unison, can highlight the dynamic relationships and evolution of chemical and biological constituents in ground beef. Further research in ground beef shelf-life should incorporate such measures.

Microbiological Assay-Trienzyme Procedure for Total Folates in Cereals and Cereal Foods: Collaborative Study

In 1996, U.S. Food and Drug Administration regulations mandated the fortification of enriched cereal-grain products with folic acid, thereby emphasizing the need for validated methods for total folates in foods, particularly cereal products. The AOAC Official Methods (944.12, 960.46) currently used for the analysis of folate in foods for compliance purposes are microbiological methods. When the fortification regulations were finalized, no Official AOAC or Approved AACC methods for folate in cereal-grain products were in place. The AOAC Official Method (992.05) for folic acid in infant formula does not incorporate important improvements in the extraction procedure and was not considered suitable for the analysis of folates in foods in general. Amicrobiological assay protocol using a trienzyme extraction procedure was prepared and submitted for comments to 40 laboratories with recognized experience in folate analysis. On the basis of comments, the method was revised to have the conjugase (gamma-glutamyl-carboxy-peptidase) treatment follow a protease treatment, to include the use of cryoprotected inoculum, and to include the spectroscopic standardization of the standard and optional use of microtiter plates. Thirteen laboratories participated in a collaborative study of 10 required and 10 optional cereal-grain products, including flour, bread, cookies, baking mixes, and ready-to-eat breakfast cereals. The majority of the participating laboratories performed the assay by the standard test tube method; others used the microtiter plate modification for endpoint quantitation with equal success. For the required products, the relative standard deviation between laboratories (RSDR) ranged from 7.4 to 21.6% for 8 fortified (or enriched) products compared with expected (Horwitz equation-based) values of 11–20%. RSDR values were higher (22.7–52.9%) for 2 unfortified cereal-grain products. For the optional products, the RSDR ranged from 1.8 to 11.2% for 8 fortified products. RSDR values were higher (27.9–28.7%) for 2 unfortified cereal-grain products. Based on the results of the collaborative study, the microbiological assay with trienzyme extraction is recommended for adoption as Official First Action.

Evaluation of the VIDAS® Listeria (LIS) Immunoassay for the Detection of Listeria in Foods Using Demi-Fraser and Fraser Enrichment Broths, as Modification of AOAC Official Method 999.06 (AOAC Official Method 2004.06)

A multilaboratory study was conducted to compare the VIDAS® LIS immunoassay with the standard cultural methods for the detection of Listeria in foods using an enrichment modification of AOAC Official Method 999.06. The modified enrichment protocol was implemented to harmonize the VIDAS LIS assay with the VIDAS LMO2 assay. Five food types—brie cheese, vanilla ice cream, frozen green beans, frozen raw tilapia fish, and cooked roast beef—at 3 inoculation levels, were analyzed by each method. A total of 15 laboratories representing government and industry participated. In this study, 1206 test portions were tested, of which 1170 were used in the statistical analysis. There were 433 positive by the VIDAS LIS assay and 396 positive by the standard culture methods. A Chi-square analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting average Chi square analysis, 0.42, indicated that, overall, there are no statistical differences between the VIDAS LIS assay and the standard methods at the 5% level of significance.

Evaluation of the BAX® System for Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® system and the standard cultural methods for detection of Listeria monocytogenes in foods. Six food types (frankfurters, soft cheese, smoked salmon, raw, ground beef, fresh radishes, and frozen peas) were analyzed by each method. For each food type, 3 inoculation levels were tested: high (average of 2 CFU/g), low (average of 0.2 CFU/g) and uninoculated controls. A total of 25 laboratories representing government and industry participated. Of the 2335 samples analyzed, 1109 were positive by the BAX system and 1115 were positive by the standard method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, except radishes, the BAX system performed as well as or better than the standard reference methods based on the Chi square results.

Evaluation of the BAX® System for Detection of Salmonella in Selected Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® System to the standard cultural methods for detection of Salmonella in selected foods. Five food types—frankfurters, raw ground beef, mozzarella cheese, raw frozen tilapia fish, and orange juice—at 3 inoculation levels, were analyzed by each method. A sixth food type, raw ground chicken, was tested using 3 naturally contaminated lots. A total of 16 laboratories representing government and industry participated. In this study, 1386 samples were analyzed, of which 1188 were paired samples and 198 were unpaired samples. Of the 1188 paired samples, 461 were positive by both methods and 404 were negative by both methods. Thirty-seven samples were positive by the BAX System but negative by the standard reference method, and 11 samples were positive by standard cultural method and negative by the BAX System. Of the 198 unpaired samples, 106 were positive by the BAX System and 60 were positive by the standard cultural method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, the BAX System demonstrated results comparable to those of the standard reference methods based on the Chi square results.

Predictors of in-hospital mortality post hip fracture in Ireland 2013-2017

Background

Hip fractures are associated with considerable mortality, morbidity and healthcare expenditure. There are approximately 3,500 hip fractures in Ireland per annum with this figure set to increase considerably over the coming years due to the ageing population. Internationally, mortality following hip fracture is approximately 10% at 1 month and 30% at 1 year, with less than half of survivors regaining their preoperative level of function. The authors aimed to identify the determinants of in-hospital mortality post hip fracture in the Republic of Ireland 2013-2017, with specific reference to the Irish Hip Fracture Standards.

Methods

A secondary analysis of 15,603 patients in the Irish hip fracture database was conducted.

Results

31% (n = 4,769) were male and 69% (n = 10,807) were female. Mean age for males was 75 years (SD 13.5) and 79 years for females (SD 10.5). The largest proportion of hip fractures occurred in the 80-89 age category, with 72.3% (n = 4,600) of these being female. Median in-hospital mortality was 4.7% (n = 711) (Range 2.7-6.2). Univariate logistic regression revealed 11 statistically significant predictors of in-hospital mortality; however, only 4 remained statistically significant on multivariate analysis [mobilised day of/after surgery (OR 1.46, 95% CI 1.25-1.70, p < 0.000), pre-fracture mobility (OR 0.84, 95% CI 0.79-0.89, p < 0.000), gender (OR 0.56, 95% CI 0.41-0.76, p < 0.000) and age (OR 1.05, 95% CI 1.03-1.06, p < 0.000)].

Conclusions

Older males with poor pre-fracture mobility who were not mobilised the day of/after surgery had the highest risk of in-hospital mortality. The ability to be mobilised on the day of/after surgery is a good composite measure of both patient and organisational factors in hip fracture care. This research supports the inclusion of mobilisation on the day of/after surgery as a new formal best practice standard.

Key messages

Patients not mobilised on the day of/after surgery are 46% more likely to die in hospital. In-hospital mortality of 4.7% in Ireland is comparable internationally. None of the IHFSs significantly influenced in-hospital mortality after multivariate analysis, but may well affect other outcomes such as ability to return home.

Cross-sectional study of the prevalence, causes and management of hospital-onset diarrhoea

BACKGROUND

The National Health Service in England advises hospitals collect data on hospital-onset diarrhoea (HOD). Contemporaneous data on HOD are lacking.

AIM

To investigate prevalence, aetiology and management of HOD on medical, surgical and elderly-care wards.

METHODS

A cross-sectional study in a volunteer sample of UK hospitals, which collected data on one winter and one summer day in 2016. Patients admitted ≥72 h were screened for HOD (definition: ≥2 episodes of Bristol Stool Type 5-7 the day before the study, with diarrhoea onset >48 h after admission). Data on HOD aetiology and management were collected prospectively.

FINDINGS

Data were collected on 141 wards in 32 hospitals (16 acute, 16 teaching). Point-prevalence of HOD was 4.5% (230/5142 patients; 95% confidence interval (CI) 3.9-5.0%). Teaching hospital HOD prevalence (5.9%, 95% CI 5.1-6.9%) was twice that of acute hospitals (2.8%, 95% CI 2.1-3.5%; odds ratio 2.2, 95% CI 1.7-3.0). At least one potential cause was identified in 222/230 patients (97%): 107 (47%) had a relevant underlying condition, 125 (54%) were taking antimicrobials, and 195 (85%) other medication known to cause diarrhoea. Nine of 75 tested patients were Clostridium difficile toxin positive (4%). Eighty (35%) patients had a documented medical assessment of diarrhoea. Documentation of HOD in medical notes correlated with testing for C. difficile (78% of those tested vs 38% not tested, P<0.001). One-hundred and forty-four (63%) patients were not isolated following diarrhoea onset.

CONCLUSION

HOD is a prevalent symptom affecting thousands of patients across the UK health system each day. Most patients had multiple potential causes of HOD, mainly iatrogenic, but only a third had medical assessment. Most were not tested for C. difficile and were not isolated.

Water safety plans for water supply utilities in China, Cuba, France, Morocco and Spain: costs, benefits, and enabling environment elements

Water Safety Plans (WSPs) are a management tool to identify and prioritize risks and implement appropriate control measures throughout the water supply chain, from catchment to consumer. WSPs have been implemented in over 90 countries; yet, costs, benefits and the enabling environment elements necessary for WSP implementation are under-studied. To better understand these factors, we conducted interviews with WSP implementation management teams from 20 private urban water utilities in China, Cuba, France, Morocco and Spain in 2014. Collectively, these utilities serve 10.6 million consumers and supply over 2.2 million m3/day of water to consumers. Time for WSP implementation to achieve certification averaged 13 months. The main startup cost was staff time, averaging 16.2 full-time equivalent person-months. Additional costs, averaging €16,777, were for training staff, hiring consultants, purchasing equipment, and certifying WSPs. Benefits commonly reported included improved hazard control, treatment practices, record keeping, and client and health agency confidence.

Delay of transfer from the intensive care unit: a prospective observational analysis on economic effects of delayed in-house transfer

Background

Intensive care unit (ICU) capacity is a scant and precious resource in hospitals. Therefore, an optimal occupancy rate as well as detailed occupation planning is of great importance. Most literature deals with admission to the ICU, while only few discuss discharge from the ICU. Specifically, a delay of transfer from the ICU can cause a shortness of beds, jeopardize urgent patient treatment and lead to a decrease in treatment quality as well as economic downsides. This study examined the incidence, costs and reasons for delayed discharge from the ICU and analyzed the influence of the department the patient was admitted to.

Methods

Over the course of 12 months, the discharges of all 1643 patients of two surgical intensive care units of a large academic medical center were analyzed. Delay in minutes and reasons were recorded and translated into financial figures. A univariate logistic regression model was developed to evaluate the impact of length of stay at the ICU, age, gender, subspecialty and specific ICU on the delay of transfer. In a next step, significant factors of the univariate logistic regression were incorporated into a multivariate regression model.

Results

In 326 out of 1312 patients ready for discharge (24.8%), the transfer to the floor was delayed. Time of delay for all patients added up to a total of 265,691 min in 1 year. The application of the internal cost allocation, in which 1 min corresponds to 0.75 Euro cents, led to costs of 199,268 Euros (~ $240,000) for the study period. In 91.7% of the cases, the reason for the delay was the lack of an available or appropriate bed on the regular ward. Multivariate regression analysis revealed that the type of department the patient is admitted to poses a significantly influencing factor for delayed discharge from the ICU.

Conclusion

Delay in discharge from the ICU is a common problem of economic relevance. The main reason is a lack of appropriate floor beds. Patients from certain specific departments are at a higher risk to be discharged with delay. A solution to this problem lies in the focus on the downstream units. A proper use of the scarce resources is to be pursued because of ethical as well as economic reasons in an increasingly aging population.

Early recognition and management of fetal head trauma with massive subgaleal hemorrhage

Non-obstetrical fetal head injury is an unusual clinical event. While multiple case reports describe motor vehicle collisions resulting in intrauterine fetal skull fractures, management of these injuries has not been emphasized. We report a case of a depressed fetal skull fracture with massive subgaleal and subperiosteal hemorrhage requiring neurosurgical intervention with good clinical outcomes for both mother and infant dyad.