Ready to eat (RTE) meat products are subject to recontamination after industrial processing, mainly by Listeria monocytogenes, a pathogenic microorganism that can persist for a long time in the environment. A RTE meat product that is contaminated with L. monocytogenes due to cross contamination during some stage after industrial processing, such as weighing, slicing or wrapping, can be an important causer of disease, due to absence of a kill step before consumption. The objective of this project was to measure the transfer of L. monocytogenes during slicing of cooked ham (cross contamination) at retail, simulating in the laboratory the practices in commercial slicing, and to develop a predictive model capable of describing this transfer. It was observed that in the first slices obtained after the experimental contamination of the slicer, the counts and the transfer rates of L. monocytogenes were higher than in the subsequent slices, and the counting curves presented a long tail as the slices were obtained. The data demonstrate that the slicer may be a relevant source of cross contamination of L. monocytogenes for RTE meat products, regardless of the level of contamination of the slicer. With the data obtained, a new transfer model was proposed called 4p-2se, as it contained four parameters (4p) and two environments (2se), and was independent of the quantification of the pathogen transferred to the slicer. The proposed model was compared to two pathogen transfer models previously described, and the predicted data presented lower RMSE (Root Mean Sum of squared errors) values than the other models. The 4p-2se model was able to satisfactorily predict the pathogen transfer data during slicing of cooked ham, which could assist the food retail establishments and regulatory agencies in the evaluation and control of cross contamination of RTE foods and in the design of proper risk management strategies. / Os produtos derivados da carne que são prontos para consumo estão sujeitos à recontaminação após o processamento industrial, principalmente por Listeria monocytogenes, um microrganismo patogênico capaz de persistir por longo tempo no ambiente. Um produto cárneo pronto para consumo que se contamina com L. monocytogenes devido à contaminação cruzada durante alguma etapa após o processamento industrial, tal como pesagem, fatiamento ou acondicionamento, pode ser um importante causador de enfermidade, pois não há uma etapa de eliminação do patógeno antes do consumo. Este projeto teve por objetivo mensurar a transferência de L. monocytogenes durante o fatiamento de presunto cozido (contaminação cruzada), simulando em laboratório práticas adotadas nos estabelecimentos comerciais de fatiamento de produtos prontos para o consumo, e desenvolver um modelo preditivo capaz de descrever esta transferência. Foi observado que nas primeiras fatias obtidas após a contaminação experimental do fatiador, as contagens e as taxas de transferência de L. monocytogenes eram mais altas que nas subsequentes, observando-se que as curvas de contagem apresentavam uma longa cauda ao longo do fatiamento. Os dados demonstram que o fatiador pode ser uma fonte importante de contaminação cruzada de L. monocytogenes para produtos cárneos prontos para o consumo fatiados, independentemente do nível de contaminação do fatiador. Com os dados obtidos, foi possível sugerir um novo modelo de transferência, denominado 4p-2se, formado por uma equação com apenas quatro parâmetros (4p) e dois ambientes (2se,) sendo esse modelo independente da quantificação do patógeno transferido para o fatiador. O modelo sugerido foi comparado a outros dois modelos de transferência previamente descritos, observando os dados preditos no modelo 4p-2se apresentavam valores de RMSE (Root Mean Sum of squared erros) mais baixos que os demais modelos. O modelo proposto mostrou-se capaz de predizer satisfatoriamente os dados de transferência de patógeno durante o fatiamento de presunto cozido, podendo auxiliar os estabelecimentos comerciais de alimentos e as agências reguladoras na avaliação e controle da contaminação cruzada de alimento prontos para consumo e na concepção de estratégias adequadas de gestão de risco.

Today waste management has entered a new stage. Since wastes still contain natural materials and energy that can be extracted, it should be treated in effective ways, for example, for energy recovery or material recycling. Many countries and the municipalities have therefore made waste treatment strategies in accordance with for example, EU directives or governmental regulations. In such circumstances, Envac is one of waste management companies in Sweden, which collects different kinds of waste fractions through an underground pipe system by means of air pressure. In Hammarby sjöstad in Stockholm, currently organic waste, combustible waste, and newspapers are collected by the Envac’s system, however a cross contamination between organic fraction and newspapers has been observed. We therefore performed on-site waste transporting experiments in order to solve this cross contamination and suggest an optimum transporting condition which means that waste bags can be transported with high rate and acceptable condition to the terminal. From the previous study, bag quality and transporting speed were supposed to be the factors that affect the waste purity. Then on-site experiments were designed and carried out based on these factors. In the end, we proposed the optimum condition depending on the bag quality and clarified the causes of the cross contamination.

Contamination is a prevalent issue with reprocessed levered endoscopes. The number of infections caused by resistant enterobacteriaceae in patients due to contaminated endoscopes increased to the point that the United States Food and Drug Administration released a safety alert to health care facilities that perform endoscopic retrograde cholangiopancreatography (ERCP). The purpose of this descriptive project was to evaluate if levered endoscopes used in ERCP procedures met high level disinfection criteria, were properly processed, and were germ free after reprocessing. The project was supported by 2 theories: the middle range theory of patient advocacy and the germ theory. Data (counts and percentages) were collected from testing 150 endoscopes at each of 4 facilities within an organization regarding the effectiveness of the reprocessing of the levered endoscopes. According to the project findings, there was a 7% average germ-free failure rate across the sites after the initial reprocessing. The cleaning process of the levered endoscopes allowed bacteria to remain on the scopes after the manufacturer-recommended cleaning was completed at the sites. Standardization of the organization's cleaning process and improvement in the national protocols were recommended. The project supported protecting the safety of endoscopy patients by identifying that the cleaning process could be improved to prevent introduction of infectious bacteria through a procedure. The results will be informative for laboratory staff who clean levered endoscopes, physicians who use the scopes in patient procedures, patients who undergo the procedures, and nurses who are tasked with improving patient safety in perioperative environments.

Context: Electrodes play an important role in interfacing tissue with electrical stimulation devices. Manufacturers recommend that adhesive metallic mesh cloth electrodes be used no more than 10 times before they are discarded, however, clinically the electrodes are often used up to 30 times. Another concern is sanitation. When electrodes are used on different patients, there is a chance for cross-contamination and bacterial growth on the electrode. Objective: To compare amplitudes of perceived sensation, motor twitch and force produced at specific amplitudes using single-use electrodes that run no risk of cross-contamination, and multiple-use electrodes. Design: Mixed model ANOVA with the subject blocked. Setting: Therapeutic modalities research laboratory. Patients or Other Participants: 20 subjects comprised of 7 males (age 24.7 yrs ± 2.3 yrs, skin fold thickness 5.9 mm ± 2.4 mm) and 13 females (age 21.5 yrs ± 2.3 yrs, skin fold thickness 10.7 mm ± 4.1 mm) recruited by volunteer sample mainly from athletic and athletic training populations. They drew random numbers to determine which group they were assigned to. Interventions: Each subject had electrodes placed on their wrist extensors muscles. Measures were recorded of what intensity it took to achieve perceived sensation, motor twitch, and force produced at a specific intensity. To determine decay, multiple use electrodes were tested initially and on the 10th use. After the multiple use electrodes were tested initially, they were leached out. After eight uses, pretest procedures were repeated (10th use electrode) as the final trial on the subjects. Single use electrodes were tested one time. Main Outcome Measures: The dependent variables were sensation, motor twitch and force production. The experiment was a repeated measures study, using mixed models ANOVA with subjects blocked. Alpha was set at p<0.05. Data was analyzed using a SAS proc mixed 9.1. Results: There was no statistical difference between the measures taken during the initial trial and final trial of the multiple use electrodes for muscle twitch (FMUI MUF muscle twitch= 107.3, p= 0.09) and force production (FMUI MUF force production=28.7, p= 0.11). There was a significant difference between the single use and the multiple use electrodes for the initial and final trial. Average values in mA for perceived sensory were: single use 9.73, multiple use initial 16.70 , multiple use final 21.03; observed muscle twitch: single use 15.87, multiple use initial 29.16, multiple use final 31.78; and force produced: single use 22.8 Newtons, multiple use initial 10.0 Newtons, multiple use final 5.0 Newtons. Conclusion: Single-use electrodes produce more conductive power with fewer milliamps compared to multiple-use electrodes. Single use electrodes are just as, or more efficient as the multiple use electrodes and have the added advantage of eliminating the possibility of cross-contamination of bacteria from patient to patient.

Fresh produce may be contaminated by bacterial pathogens including Listeria monocytogenes during harvesting, packaging, or transporting. Consumers may be at risk of foodborne illness if produce become contaminated. In this project, a cavitation process (formation of bubbles in water) was studied to determine the efficacy of microbubbles at inactivating the pathogen L. monocytogenes on stainless steel and the surface of fresh cucumber and avocado. Stainless steel coupons (1"×2''), cucumber, and avocado surfaces were inoculated with L. monocytogenes (LCDC strain). After 1, 24 or 48 h, loosely attached cells were washed off, and inoculated areas were targeted by microbubbles (~0.5 mm dia.) through an air stone (1.0 L air/min) for 1, 2, 5, or 10 min. After treatment, samples were transferred to sterile containers and serial diluted in peptone water and plated on Oxford agar. Plates were incubated for 48 h at 35℃. For stainless steel, the mean log reduction of L. monocytogenes (48 h drying) peaked at 2.95 after 10 min of microbubbles when compared to a no bubble treatment. After 48 h pathogen drying, cucumbers treated for 10 min resulted in a 1.78 mean log reduction of L. monocytogenes. For avocados, the mean log reduction of L. monocytogenes (24 hr drying) peaked at 1.65 after 10 min of microbubbles. This cavitation treatment (10 mins) reduced over 95% of L. monocytogenes on the surface of stainless steel, cucumber, and avocado. Microbubble applications may be an effective, economical, and environmental-friendly way to remove L. monocytogenes and possibly other bacterial pathogens from food impact surfaces and the surface of whole, intact fresh produce. / Master of Science in Life Sciences / Fresh produce may be contaminated by bacterial pathogens like Listeria monocytogenes during the process of harvesting, packaging, or transport. Consuming contaminated fresh produce without enough and proper decontaminated measures, consumers are in risk of being infected with foodborne illness. A cavitation process (formation of bubbles in water) was conducted to determine the efficacy of microbubbles at inactivating the pathogen Listeria monocytogenes on the impact surface of fresh produce (stainless steel), fresh cucumber, and fresh avocado. Stainless steel coupons (1"×2''), fresh cucumbers, and fresh avocados were inoculated respectively with Listeria monocytogenes (LCDC strain). After removing loosely attached pathogen cells on the surface of inoculated steel coupons, cucumbers, and avocados, their inoculated areas were targeted by microbubbles (~0.5 mm dia.) for 1, 2, or 10 minutes, with a constant air flow rate of 1.0 L/min through an air stone. The L. monocytogenes on stainless steel and cucumber, and avocado surfaces was reduced by 95% to 99%. This study suggests that microbubbles may remove, and possibly inactivate, L. monocytogenes effectively from the surface of fresh produce and their impact surfaces. Microbubbles thus could be an effective, economical, and environmental-friendly tool for minimizing produce contamination.

Understanding potential cross contamination pathways is essential to reducing the risk of food product contamination. The use of a fluorescing abiotic surrogate (GloGermTM) to visualize the potential spread of bacteria may be beneficial to researchers. To quantify cross contamination during experimental trials in a mock retail deli, a rating method for visualization of fluorescence levels using a trained sensory panel was developed. Panelists feedback led to a pre-defined strategy allowing for characterization of contamination seen in photographs and reduced variability within responses. Following validation, GloGermTM was used to visually represent how bacteria may spread through a deli environment. Six origination sites (slicer blade, meat chub, floor drain, preparation table, employee's glove, employee's hands) were evaluated separately and spread was photographed throughout the mock deli. The trained sensory panel then analyzed the photographs. Five of the six contamination origination sites transferred GloGermTM to surfaces throughout the mock deli. Contamination from the floor drain did not spread to any food contact surfaces. To determine the potential of using a GloGermTM/ bacteria mixture to simultaneously track and sample contamination spread; surfaces were co-inoculated with GloGermTM and bacteria to determine if co-inoculation would affect the recoverability of microorganisms from these surfaces. Three common foodborne bacteria (E. coli O157:H7,Salmonella enterica ser. Enteritidis, Listeria monocytogenes, Listeria innocua) were inoculated on 2 by 2 stainless steel coupons alone and with GloGermTM . There was no significant difference found (p > 0.05) between the recovery of bacteria alone and the mixture for all bacteria. Finally, the use of co-inoculation was further explored by inoculating two contamination origination sites with either bacteria alone (L. monocytogenes and L. innocua) or a GloGermTM/bacteria cocktail. Nine recipient sites were sampled after a series of deli procedures were performed. Generally, no significant differences (p>0.05) were seen between the transfer of bacteria inoculated alone and the transfer of bacteria inoculated with GloGermTM to the selected recipient sites, regardless of contamination source or bacteria. These results suggest there may be potential in using L. innocua in combination with GloGermTM to visually track and sample contamination from a known source throughout a retail deli environment. / Ph. D.

No / Aims: To compare an ultra-rapid hand dryer against warm air dryers, with regard to: (A) bacterial transfer after drying and (B) the impact on bacterial numbers of rubbing hands during dryer use. Methods and Results: The Airblade¿ dryer (Dyson Ltd) uses two air `knives¿ to strip water from still hands, whereas conventional dryers use warm air to evaporate moisture whilst hands are rubbed together. These approaches were compared using 14 volunteers; the Airblade¿ and two types of warm air dryer. In study (A), hands were contaminated by handling meat and then washed in a standardized manner. After dryer use, fingers were pressed onto foil and transfer of residual bacteria enumerated. Transfers of 0¿107 CFU per five fingers were observed. For a drying time of 10 s, the Airblade¿ led to significantly less bacterial transfer than the other dryers (P < 0·05; range 0·0003¿0·0015). When the latter were used for 30¿35 s, the trend was for the Airblade to still perform better, but differences were not significant (P > 0·05, range 0·1317¿0·4099). In study (B), drying was performed ± hand rubbing. Contact plates enumerated bacteria transferred from palms, fingers and fingertips before and after drying. When keeping hands still, there was no statistical difference between dryers, and reduction in the numbers released was almost as high as with paper towels. Rubbing when using the warm air dryers inhibited an overall reduction in bacterial numbers on the skin (P < 0·05). Conclusions: Effective hand drying is important for reducing transfer of commensals or remaining contaminants to surfaces. Rubbing hands during warm air drying can counteract the reduction in bacterial numbers accrued during handwashing. Significance and Impact of the Study: The Airblade¿ was superior to the warm air dryers for reducing bacterial transfer. Its short, 10 s drying time should encourage greater compliance with hand drying and thus help reduce the spread of infectious agents via hands. / Dyson Ltd

In this thesis, two algorithms that detect cross-contamination in tumor samples sequenced with next-generation sequencing (NGS) were evaluated. In genomic medicine, NGS is commonly used to sequence tumor DNA to detect disease-associated genetic variants and determine the most suitable treatment option. Targeted NGS panels are often employed to screen for genetic variations in a selection of specific tumor-associated genes. NGS handles samples from multiple patients in parallel, which poses a risk of cross-contamination between samples. Contamination is a significant issue in the interpretation of NGS results, as it can lead to the incorrect identification of genetic variants and, consequently, incorrect treatment. Therefore, contamination detection is a crucial quality control steps in the analysis of NGS data. Numerous algorithms for detection of cross-contamination have been developed, but many of these algorithms are not suited for small, targeted NGS panels, and several are not developed for tumor data. In this thesis, GATK's CalculateContamination and a self-created algorithm called ContaCheck were evaluated on simulated tumor NGS data. NGS samples were generated in silico with a Python script called BAMSynth and mixed to simulate cross-contamination with contamination rates between 1% and 50%. ContaCheck accurately detected contaminations ranging from 3% to 50% and identified the correct contaminant with an accuracy of 94%. CalculateContamination, on the other hand, detected contaminations ranging from 1% to 15% relatively accurately, but consistently failed to detect high level contaminations. The study showed that ContaCheck outperformed CalculateContamination on simulated NGS data, but to determine which algorithm is the best on real data and determine ContaCheck's applicability in a clinical setting, the algorithms need to be further evaluated on real tumor NGS samples.

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No. of bitstreams: 2 Dissertacao_Marina_Ferrasso.pdf: 310156 bytes, checksum: c8d3d7f5990dff92ea8a5bfd6eb9d3a0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-02-24 / Sem bolsa / O consumo de carne suína per capita no Brasil é de 15,1 kg/ano e apesar da sua importância para o consumidor, os produtos suínos, podem ser veículos de patógenos. Uma das Doenças Transmitidas por Alimentos (DTA) mais importantes é a salmonelose, doença causada por bactérias do gênero Salmonella, geralmente contraída através da ingestão de alimentos de origem animal contaminados. O objetivo do trabalho foi rastrear esse micro-organismo durante o fluxograma de abate de suínos, através da comparação de cepas isoladas em diferentes pontos na linha de produção. Durante o período de estudo, foram acompanhados 10 lotes de suínos encaminhados para abate de uma granja no Rio Grande do Sul. Quatro animais de cada lote selecionado foram acompanhados durante o abate e processamento. Foram coletadas amostras de fezes através da introdução de uma zaragatoa no reto do animal, logo após a insensibilização e em três pontos diferentes do fluxograma, imediatamente após a saída dos animais da depiladeira, após a abertura da cavidade abdominal e momentos antes da carcaça entrar na câmara de refrigeração. Também foi realizada coleta de amostra de papada. Amostras da água utilizada no tanque de escaldagem foram coletadas antes de iniciar o abate de cada lote e após a passagem dos animais. Os isolados foram analisados pela técnica de rep-PCR para comparação dos padrões de bandas. A etapa com maior número de isolados teve origem nas amostras coletadas após a insensibilização 35,3%. Nos demais pontos de coleta, após a saída dos animais da depiladeira, após a evisceração, antes da entrada na câmara de refrigeração e papada, foram isolados 17,6%, 17,6%, 23,5% e 5,8%, respectivamente. Através da análise por rep-PCR, comprovou-se que cepas de Salmonella que chegam ao frigorífico em suínos portadores podem não ser eliminadas durante o processamento, sendo possível seu isolamento das carcaças. Também foi observado que cepas introduzidas por animais podem contaminar outros em diferentes etapas do fluxograma de abate, caracterizando contaminação cruzada. Com base nos resultados, recomendam-se cuidados rigorosos na execução de medidas higiênico-sanitárias adotadas durante o abate, de forma a garantir um alimento seguro ao consumidor. / Pork consumption per capita in Brazil is 15.1kg/year and despite its importance for the consumer pork products may be pathogens vehicles. Salmonellosis is one of the most importants foodborne diseases, and it is caused by bacteria of the genus Salmonella, often contracted through the ingestion of contaminated animal products. The objective was to trace this microorganism during the pig slaughter flowchart, by comparing strains isolated at different points on the production line during the study period, were followed 10 lots of pigs from a farm in Rio Grande do Sul sent to slaughter, five lots carriers of Salmonella and five non-carriers. Four animals from each selected lot were followed during slaughter and processing. Stool samples were collected at slaughter and in three different parts of the flowchart, immediately after the animals left from scrap machine, after opening the abdominal cavity and just before the carcass enter the cooling chamber. It was also collected jowl samples. Water samples used in the scalding tank were collected before starting the slaughter process of each lot and after the passage of the animals. The isolates were analyzed by rep-PCR to compare the band patterns. The step with the highest number of isolates originated in the samples collected after stunning 35.3%. In other collection sites, immediately after the animals left from scrap machine, after evisceration, before entering the cooling chamber and jowls were isolated 17.6%, 17.6%, 23.5% and 5.8%, respectively. Through analysis by rep-PCR, it was found that Salmonella strains that reach the fridge in pigs carriers can not be deleted during processing, it is possible isolation of carcasses. It was also observed that animals introduced by strains can infect others in different stages of slaughtering flowchart, featuring cross-contamination. Based on the results, are recommended strict care in the execution of hygiene and sanitary measures taken during slaughter in order to ensure safe food to consumers.

Globally, investigations into food-borne illnesses show that the majority of cases involve poor hand hygiene of the food handler. The challenge of providing safe food therefore requires new strategies for evaluating cross-contamination of pathogenic micro-organisms on the food handler's hands, which might be detrimental or hazardous to the health of the patient Although food-borne diseases may be multifactorial in aetiology, no standards or evaluation systems, such as an occupational health surveillance programme, are available to monitor and ensure that food is free of pathogens. The formulation and implementation of standards may contribute to ensuring that food handlers comply with hand hygiene practices during food handling. Such practices guarantee that food reaching the patient is safe. The objectives in this research project originated from the occupational health practice and gave direction of the empirical research project. The literature was reviewed to discover what is currently known concerning the food handlers' hand hygiene during food handling and food-borne illnesses and the theoretical framework gave direction and guidance to the survey design of the empirical research, which was quantitative, explorative, descriptive and contextual in nature. The food handlers from the food preparation sections of the four major healthcare services in Potchefstroom, in the North West Province, South Africa, were the target population and the sampling method was all-inclusive (n=110). Eighty (75.47%) food handlers participated in the research project. The design entailed three steps. The first was conducted with a questionnaire, to identify the food handlers' compliance with hand hygiene during food handling. The second step involved determining the prevalence of Escherichia coli and Staphylococcus aureus on the food handlers' hands. The results were used for the formulation of standards for the hand hygiene of food handlers. Finally, recommendations for practice, education and research were made. The implementation of these recommendations could contribute knowledge to the body of nursing and promote good hand hygiene practices in the healthcare service. / Thesis (M.Cur.)--North-West University, Potchefstroom Campus, 2009.