Browsing by Subject "CONTAMINATION"

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  • Vilar, M. J.; Ranta, J.; Virtanen, S.; Korkeala, H. (2015)
    Bayesian analysis was used to estimate the pig's and herd's true prevalence of enteropathogenic Yersinia in serum samples collected from Finnish pig farms. The sensitivity and specificity of the diagnostic test were also estimated for the commercially available ELISA which is used for antibody detection against enteropathogenic Yersinia. The Bayesian analysis was performed in two steps; the first step estimated the prior true prevalence of enteropathogenic Yersinia with data obtained from a systematic review of the literature. In the second step, data of the apparent prevalence (cross-sectional study data), prior true prevalence (first step), and estimated sensitivity and specificity of the diagnostic methods were used for building the Bayesian model. The true prevalence of Yersinia in slaughter-age pigs was 67.5% (95% PI 63.2-70.9). The true prevalence of Yersinia in sows was 74.0% (95% PI 57.3-82.4). The estimates of sensitivity and specificity values of the ELISA were 79.5% and 96.9%.
  • Heinonen, Jussi S.; Luttinen, Arto V.; Spera, Frank J.; Bohrson, Wendy A. (2019)
    Karoo continental flood basalt (CFB) province is known for its highly variable trace element and isotopic composition, often attributed to the involvement of continental lithospheric sources. Here, we report oxygen isotopic compositions measured with secondary ion mass spectrometry for hand-picked olivine phenocrysts from similar to 190 to 180 Ma CFBs and intrusive rocks from Vestfjella, western Dronning Maud Land, that form an Antarctic extension of the Karoo province. The Vestfjella lavas exhibit heterogeneous trace element and radiogenic isotope compositions (e.g., epsilon(Nd) from -16 to +2 at 180 Ma) and the involvement of continental lithospheric mantle and/or crust in their petrogenesis has previously been suggested. Importantly, our sample set also includes rare primitive dikes that have been derived from depleted asthenospheric mantle sources (epsilon(Nd) up to + 8 at 180 Ma). The majority of the oxygen isotopic compositions of the olivines from these dike rocks (delta O-18 = 4.4-5.2%; Fo = 78-92 mol%) are also compatible with such sources. The olivine phenocrysts in the lavas, however, are characterized by notably higher delta O-18 (6.2-7.5%; Fo = 70-88 mol%); and one of the dike samples gives intermediate compositions (5.2-6.1%, Fo = 83-87 mol%) between the other dikes and the CFBs. The oxygen isotopic compositions do not correlate with radiogenic isotope compositions susceptible to crustal assimilation (Sr, Nd, and Pb) or with geochemical indicators of pyroxene-rich mantle sources. Instead, delta O-18 correlates positively with enrichments in large-ion lithophile elements (especially K) and Os-187. We suggest that the oxygen isotopic compositions of the Vestfjella CFB olivines primarily record large-scale subduction-related metasomatism of the sub-Gondwanan mantle (base of the lithosphere or deeper) prior to Karoo magmatism. The overall influence of such sources to Karoo magmatism is not known, but, in addition to continental lithosphere, they may be responsible for some of the geochemical heterogeneity observed in the CFBs.
  • Azarbaijani, Babak Asadi; Sheikhi, Mona; Oskam, Irma C.; Nurmio, Mirja; Laine, Tiina; Tinkanen, Helena; Makinen, Sirpa; Tanbo, Tom G.; Hovatta, Outi; Jahnukainen, Kirsi (2015)
    Background Cryopreservation of ovarian tissue has been widely accepted as an option for fertility preservation among cancer patients. Some patients are exposed to chemotherapy prior to ovarian tissue cryopreservation. Consequently, assessment of the developmental capacity of human ovarian tissue after chemotherapy is of primary importance. Materials In order to study the impact of previous chemotherapy on in vitro development and viability of ovarian follicles, quality control samples from 34 female cancer patients at median age of 15 years (range 1-35), cryopreserved for fertility preservation before (n = 14) or after (n = 20) initiation of chemotherapy, were thawed and cultured for 7 days. The morphology and developmental stages of ovarian follicles were studied by light microscopy before and after culture. Possible associations between follicular densities, age and exposure to alkylating agents, expressed as cyclophosphamide equivalent dose (CED) were tested. Results Exposure to chemotherapy significantly impaired the survival and development of ovarian follicles in culture. After seven days, significantly higher densities of intermediary, primary and secondary follicles and lower densities of atretic follicles was detected in the samples collected before chemotherapy. Increasing dose of alkylating agents was identified by multivariate linear regression analysis as an independent predictor of a higher density of atretic follicles, whereas increasing age of the patient predicted a better outcome with less follicle atresia and a higher density of maturing follicles. Conclusion This study provides quantitative in vitro evidence of the impact of chemotherapy on developmental capacity of cryopreserved human ovarian tissue. The results indicate that fertility preservation should be carried out, if possible, before initiation of alkylating agents in order to guarantee better in vitro survival of ovarian follicles. In addition, ovarian samples from younger girls show lower viability and fewer developing follicles in culture.
  • Heinonen, Jussi S.; Luttinen, Arto V.; Bohrson, Wendy A. (2016)
    Continental flood basalts (CFBs) represent large-scale melting events in the Earth’s upper mantle and show considerable geochemical heterogeneity that is typically linked to substantial contribution from underlying continental lithosphere. Large-scale partial melting of the cold subcontinental lithospheric mantle and the large amounts of crustal contamination suggested by traditional binary mixing or assimilation-fractional crystallization models are difficult to reconcile with the thermal and compositional characteristics of continental lithosphere,however. The well-exposed CFBs of Vestfjella, western Dronning Maud Land,Antarctica, belong to the Jurassic Karoo large igneous province and provide a prime locality to quantify mass contributions of lithospheric and sublithospheric sources for two reasons: 1) recently discovered CFB dikes show isotopic characteristics akin to mid-ocean ridge basalts, and thus help to constrain asthenospheric parental melt compositions, and 2) the well-exposed basaltic lavas have been divided into four different geochemical magma types that exhibit considerable trace element and radiogenic isotope heterogeneity (e.g., initial εNd from-16 to +2 at 180 Ma). We simulate the geochemical evolution of Vestfjella CFBs using 1) energy-constrained assimilation-fractional crystallization equations that account for heating and partial melting of crustal wallrock and 2)assimilation-fractional crystallization equations for lithospheric mantle contamination by using highly alkaline continental volcanic rocks (i.e. partial melts of mantle lithosphere) as contaminants. Calculations indicate that the different magma types can be produced by just minor (1–15 wt. %) contamination of asthenospheric parental magmas by melts from variable lithospheric reservoirs. Our models imply that the role of continental lithosphere as a CFB source component or contaminant may have been overestimated in many cases. Thus, CFBs may represent major juvenile crustal growth events rather than just recycling of old lithospheric materials.
  • Heinonen, Jussi S.; Luttinen, Arto V.; Whitehouse, M.J. (2018)
    Karoo continental flood basalt (CFB) province is known for its highly variable trace element and isotopic composition, often attributed to the involvement of continental lithospheric sources. Here, we report oxygen isotopic compositions measured with secondary ion mass spectrometry for hand-picked olivine phenocrysts from similar to 190 to 180 Ma CFBs and intrusive rocks from Vestfjella, western Dronning Maud Land, that form an Antarctic extension of the Karoo province. The Vestfjella lavas exhibit heterogeneous trace element and radiogenic isotope compositions (e.g., epsilon(Nd) from -16 to +2 at 180 Ma) and the involvement of continental lithospheric mantle and/or crust in their petrogenesis has previously been suggested. Importantly, our sample set also includes rare primitive dikes that have been derived from depleted asthenospheric mantle sources (epsilon(Nd) up to + 8 at 180 Ma). The majority of the oxygen isotopic compositions of the olivines from these dike rocks (delta O-18 = 4.4-5.2%; Fo = 78-92 mol%) are also compatible with such sources. The olivine phenocrysts in the lavas, however, are characterized by notably higher delta O-18 (6.2-7.5%; Fo = 70-88 mol%); and one of the dike samples gives intermediate compositions (5.2-6.1%, Fo = 83-87 mol%) between the other dikes and the CFBs. The oxygen isotopic compositions do not correlate with radiogenic isotope compositions susceptible to crustal assimilation (Sr, Nd, and Pb) or with geochemical indicators of pyroxene-rich mantle sources. Instead, delta O-18 correlates positively with enrichments in large-ion lithophile elements (especially K) and Os-187. We suggest that the oxygen isotopic compositions of the Vestfjella CFB olivines primarily record large-scale subduction-related metasomatism of the sub-Gondwanan mantle (base of the lithosphere or deeper) prior to Karoo magmatism. The overall influence of such sources to Karoo magmatism is not known, but, in addition to continental lithosphere, they may be responsible for some of the geochemical heterogeneity observed in the CFBs.
  • Kilpeläinen, Tuomas; Pogodin-Hannolainen, Dimitri; Kemppainen, Kimmo; Talala, Kirsi; Raitanen, Jani; Taari, Kimmo; Kujala, Paula; Tammela, Teuvo L. J.; Auvinen, Anssi (2017)
    Purpose: Screening for prostate cancer remains controversial, although ERSPC (European Randomized Study of Screening for Prostate Cancer) showed a 21% relative reduction in prostate cancer mortality. The Finnish Randomized Study of Screening for Prostate Cancer, which is the largest component of ERSPC, demonstrated a statistically nonsignificant 16% mortality benefit in a separate analysis. The purpose of this study was to estimate the degree of contamination in the control arm of the Finnish trial. Materials and Methods: Altogether 48,295 and 31,872 men were randomized to the control and screening arms, respectively. The screening period was 1996 to 2007. The extent of prostate specific antigen testing was analyzed retrospectively using laboratory databases. The incidence of T1c prostate cancer (impalpable prostate cancer detected by elevated prostate specific antigen) was determined from the national Finnish Cancer Registry. Results: Approximately 1.4% of men had undergone prostate specific antigen testing 1 to 3 years before randomization. By the first 4, 8 and 12 years of follow-up 18.1%, 47.7% and 62.7% of men in the control arm had undergone prostate specific antigen testing at least once and in the screening arm the proportions were 69.8%, 81.1% and 85.2%, respectively. The cumulative incidence of T1c prostate cancer was 6.1% in the screening arm and 4.5% in the control arm (RR 1.21, 95% CI 1.13-1.30). Conclusions: A large proportion of men in the control arm had undergone a prostate specific antigen test during the 15-year followup. Contamination is likely to dilute differences in prostate cancer mortality between the arms in the Finnish screening trial.
  • Nowak, J.; Visnovsky, S. B.; Cruz, C. D.; Fletcher, G. C.; van Vliet, A. H. M.; Hedderley, D.; Butler, R.; Flint, S.; Palmer, J.; Pitman, A. R. (2021)
    Aims To understand the genetics involved in surface attachment and biofilm formation ofListeria monocytogenes. Methods and Results Anin vitroscreen of a Himar1 transposon library ofL. monocytogenesstrain 15G01 identified three transposants that produced significantly different biofilm levels when compared to the wild-type strain; two mutants exhibited enhanced biofilm formation and one produced less biofilm biomass than the wild-type. The mutant 15G01mprF::Himar1, which had a transposon insertion in themprFgene, was selected for further analysis. The mutant produced a more densely populated biofilm on solid surfaces such as stainless steel and polystyrene, as determined using scanning electron and light microscopy. The 15G01mprF::Himar1 mutant remained viable in biofilms, but showed an increase in sensitivity to the cationic antimicrobial gallidermin. The mutant also displayed reduced invasiveness in CaCo-2 intestinal cells, suggesting virulence properties are compromised by the inactivation ofmprF. Conclusions Biofilm formation and gallidermin resistance ofL. monocytogenesis influenced bymprF, but this trait is associated with a compromise in invasiveness. Significance and Impact of the Study The presence of pathogenic microorganisms in the food processing environment can cause a significant problem, especially when these microorganisms are established as biofilms. This study shows that the inactivation of themprFgene results in enhanced biofilm formation and abiotic surface attachment ofL. monocytogenes.
  • Grönthal, Thomas; Moodley, Arshnee; Nykäsenoja, Suvi; Junnila, Jouni; Guardabassi, Luca; Thomson, Katariina; Rantala, Merja (2014)
  • Ahmed, Warish; Simpson, Stuart L.; Bertsch, Paul M.; Bibby, Kyle; Bivins, Aaron; Blackall, Linda L.; Bofill-Mas, Silvia; Bosch, Albert; Brandao, Joao; Choi, Phil M.; Ciesielski, Mark; Donner, Erica; D'Souza, Nishita; Farnleitner, Andreas H.; Gerrity, Daniel; Gonzalez, Raul; Griffith, John F.; Gyawali, Pradip; Haas, Charles N.; Hamilton, Kerry A.; Hapuarachchi, Hapuarachchige Chandithal; Harwood, Valerie J.; Haque, Rehnuma; Jackson, Greg; Khan, Stuart J.; Khan, Wesaal; Kitajima, Masaaki; Korajkic, Asja; La Rosa, Giuseppina; Layton, Blythe A.; Lipp, Erin; McLellan, Sandra L.; McMinn, Brian; Medema, Gertjan; Metcalfe, Suzanne; Meijer, Wim G.; Mueller, Jochen F.; Murphy, Heather; Naughton, Coleen C.; Noble, Rachel T.; Payyappat, Sudhi; Petterson, Susan; Pitkänen, Tarja; Rajal, Veronica B.; Reyneke, Brandon; Jr, Fernando A. Roman; Rose, Joan B.; Rusinol, Marta; Sadowsky, Michael J.; Sala-Comorera, Laura; Setoh, Yin Xiang; Sherchan, Samendra P.; Sirikanchana, Kwanrawee; Smith, Wendy; Steele, Joshua A.; Subburg, Rosalie; Symonds, Erin M.; Thai, Phong; Thomas, Kevin; Tynan, Josh; Toze, Simon; Thompson, Janelle; Whiteley, Andy S.; Wong, Judith Chui Ching; Sano, Daisuke; Wuertz, Stefan; Xagoraraki, Irene; Zhang, Qian; Zimmer-Faust, Amity G.; Shanks, Orin C. (2022)
    Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases. Crown Copyright (C) 2021 Published by Elsevier B.V.
  • Kauppinen, Ari; Siponen, Sallamaari; Pitkänen, Tarja; Holmfeldt, Karin; Pursiainen, Anna; Torvinen, Eila; Miettinen, Ilkka T. (2021)
    Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50-55 min) and burst size (124-134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log(10) reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log(10)) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments.
  • Sogacheva, Larisa; Kolmonen, Pekka; Virtanen, Timo H.; Rodriguez, Edith; Saponaro, Giulia; De Leeuw, Gerrit (2017)
    Cloud misclassification is a serious problem in the retrieval of aerosol optical depth (AOD), which might considerably bias the AOD results. On the one hand, residual cloud contamination leads to AOD overestimation, whereas the removal of high-AOD pixels (due to their misclassification as clouds) leads to underestimation. To remove cloudcontaminated areas in AOD retrieved from reflectances measured with the (Advanced) Along Track Scanning Radiometers (ATSR-2 and AATSR), using the ATSR dual-view algorithm (ADV) over land or the ATSR single-view algorithm (ASV) over ocean, a cloud post-processing (CPP) scheme has been developed at the Finnish Meteorological Institute (FMI) as described in Kolmonen et al. (2016). The application of this scheme results in the removal of cloudcontaminated areas, providing spatially smoother AOD maps and favourable comparison with AOD obtained from the ground-based reference measurements from the AERONET sun photometer network. However, closer inspection shows that the CPP also removes areas with elevated AOD not due to cloud contamination, as shown in this paper. We present an improved CPP scheme which better discriminates between cloud-free and cloud-contaminated areas. The CPP thresholds have been further evaluated and adjusted according to the findings. The thresholds for the detection of high-AOD regions (> 60% of the retrieved pixels should be high-AOD (> 0.6) pixels), and cloud contamination criteria for lowAOD regions have been accepted as the default for AOD global post-processing in the improved CPP. Retaining elevated AOD while effectively removing cloud-contaminated pixels affects the resulting global and regional mean AOD values as well as coverage. Effects of the CPP scheme on both spatial and temporal variation for the period 2002-2012 are discussed. With the improved CPP, the AOD coverage increases by 10-15% with respect to the existing scheme. The validation versus AERONET shows an improvement of the correlation coefficient from 0.84 to 0.86 for the global data set for the period 2002-2012. The global aggregated AOD over land for the period 2003-2011 is 0.163 with the improved CPP compared to 0.144 with the existing scheme. The aggregated AOD over ocean and globally (land and ocean together) is 0.164 with the improved CPP scheme (compared to 0.152 and 0.150 with the existing scheme, for ocean and globally respectively). Effects of the improved CPP scheme on the 10-year time series are illustrated and seasonal and temporal changes are discussed. The improved CPP method introduced here is applicable to other aerosol retrieval algorithms. However, the thresholds for detecting the high-AOD regions, which were developed for AATSR, might have to be adjusted to the actual features of the instruments.
  • Törmä, K.; Lunden, J.; Kaukonen, E.; Fredriksson-Ahomaa, M.; Laukkanen-Ninios, R. (2021)
    Meat inspection of broiler chickens (broiler) in the European Union is regulated by common legislation to secure meat safety. However, the legislation is general in nature and proper post-mortem inspection (PMI) of every carcass and visceral organs of broilers is challenging in slaughterhouses (SHs) with a high slaughter line speed. The aim of this study was to investigate the on-site organization and possible differences of the PMI in four Finnish SHs, which slaughter over 99% of broilers in Finland. Our results show that the meat inspector's available inspection time per broiler in the PMI varied between 0.28 and 0.90 s, with the shortest available inspection time in the SH with the highest slaughter line speed and the longest available inspection time in the SH with the slowest line speed. We observed that only part of the total inspection time per broiler could be used for true PMI in most (3/4) SHs, as the meat inspectors also performed other tasks during the PMI. We observed deficiencies in the visual inspection of broiler carcasses; in particular, the proper inspection of all or most of the body cavities was impossible in all SHs during the PMI. Some deficiencies in facilities (e.g. in recording system) were observed. Moreover, lighting properties varied between the SHs and a significant difference between illumination conditions at the first inspection stations in the SHs was observed. This study considered the prerequisites for proper PMI and revealed that the PMI of broilers was not completely uniform in Finland. The results emphasize the need for more precise guidelines and recommendations, especially for inspection time and lighting at inspection stations.
  • Aalto-Araneda, Mariella; Lunden, Janne; Markkula, Annukka; Hakola, Satu; Korkeala, Hannu (2019)
    Listeria monocytogenes causes the foodborne illness listeriosis, which exhibits high fatality among people in risk groups. The incidence of listeriosis has increased in Europe, which raises concerns about L. monocytogenes occurrence in foodstuffs. Ready-to-eat seafood products are considered particularly risky vehicles. Poor hygiene at processing facilities predisposes them to L. monocytogenes contamination, which can be controlled by stringent self-checking system measures. We examined the association of fish-processing plant operational and hygiene practices with the occurrence of L. monocytogenes in vacuum-packaged gravad (cold-salted) and cold-smoked salmon and rainbow trout products. Product sampling of 21 fish-processing plants was carried out, and operational procedures relating to L. monocytogenes control were surveyed using an in-depth risk assessment questionnaire. L. monocytogenes occurred only in sliced and mainly in gravad products of seven fish-processing plants. Shortages in preventive measures were discovered predominantly among the L. monocytogenes positive fish-processing plants. Using generalized linear modeling, we identified the following features associated with L. monocytogenes product contamination: the number of processing machines, deficiencies in the processing environment and machinery sanitation, and staff movement from areas of low toward high hygiene. Furthermore, performing frequent periodic thorough sanitation alongside everyday sanitation practices associated with a decreased risk of product contamination.
  • Stsepetova, Jelena; Baranova, Juliana; Simm, Jaak; Parm, Ulle; Rööp, Tiiu; Sokmann, Sandra; Korrovits, Paul; Jaagura, Madis; Rosenstein, Karin; Salumets, Andres; Mandar, Reet (2020)
    Background Only a few microbial studies have conducted in IVF (in vitro fertilization), showing the high-variety bacterial contamination of IVF culture media to cause damage to or even loss of cultured oocytes and embryos. We aimed to determine the prevalence and counts of bacteria in IVF samples, and to associate them with clinical outcome. Methods The studied samples from 50 infertile couples included: raw (n = 48), processed (n = 49) and incubated (n = 50) sperm samples, and IVF culture media (n = 50). The full microbiome was analyzed by 454 pyrosequencing and quantitative analysis by real-time quantitative PCR. Descriptive statistics, t-, Mann-Whitney tests and Spearman's correlation were used for comparison of studied groups. Results The study involved normozoospermic men. Normal vaginal microbiota was present in 72.0% of female partners, while intermediate microbiota and bacterial vaginosis were diagnosed in 12.0 and 16.0%, respectively. The decreasing bacterial loads were found in raw (35.5%), processed (12.0%) and sperm samples used for oocyte insemination (4.0%), and in 8.0% of IVF culture media. The most abundant genera of bacteria in native semen and IVF culture media were Lactobacillus, while in other samples Alphaproteobacteria prevailed. Staphylococcus sp. was found only in semen from patients with inflammation. Phylum Bacteroidetes was in negative correlation with sperm motility and Alphaproteobacteria with high-quality IVF embryos. Conclusion Our study demonstrates that IVF does not occur in a sterile environment. The prevalent bacteria include classes Bacilli in raw semen and IVF culture media, Clostridia in processed and Bacteroidia in sperm samples used for insemination. The presence of Staphylococcus sp. and Alphaproteobacteria associated with clinical outcomes, like sperm and embryo quality.
  • Husso, Aleksi; Lietaer, Leen; Pessa-Morikawa, Tiina; Grönthal, Thomas; Govaere, Jan; Van Soom, Ann; Iivanainen, Antti; Opsomer, Geert; Niku, Mikael (2021)
    The development of a healthy intestinal immune system requires early microbial exposure. However, it remains unclear whether microbial exposure already begins at the prenatal stage. Analysis of such low microbial biomass environments are challenging due to contamination issues. The aims of the current study were to assess the bacterial load and characterize the bacterial composition of the amniotic fluid and meconium of full-term calves, leading to a better knowledge of prenatal bacterial seeding of the fetal intestine. Amniotic fluid and rectal meconium samples were collected during and immediately after elective cesarean section, performed in 25 Belgian Blue cow-calf couples. The samples were analyzed by qPCR, bacterial culture using GAM agar and 16S rRNA gene amplicon sequencing. To minimize the effects of contaminants, we included multiple technical controls and stringently filtered the 16S rRNA gene sequencing data to exclude putative contaminant sequences. The meconium samples contained a significantly higher amount of bacterial DNA than the negative controls and 5 of 24 samples contained culturable bacteria. In the amniotic fluid, the amount of bacterial DNA was not significantly different from the negative controls and all samples were culture negative. Bacterial sequences were identified in both sample types and were primarily of phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with some individual variation. We conclude that most calves encounter in utero maternal-fetal transmission of bacterial DNA, but the amount of bacterial DNA is low and viable bacteria are rare.
  • Maunula, Leena; Rönnqvist, M.; Åberg, R.; Lunden, J.; Nevas, M. (2017)
    Norovirus (NoV) gastroenteritis outbreaks appear frequently in food service operations (FSOs), such as in restaurants and canteens. In this study the presence of NoV and adenovirus (AdV) genomes was investigated on the surfaces of premises, especially in kitchens, of 30 FSOs where foodborne gastroenteritis outbreaks were suspected. The objective was to establish a possible association between the presence of virus genomes on surfaces and a visual hygienic status of the FSOs. NoV genome was found in 11 and AdV genome in 8 out of 30 FSOs. In total, 291 swabs were taken, of which 8.9% contained NoV and 5.8% AdV genome. The presence of NoV genomes on the surfaces was not found to associate with lower hygiene level of the premises when based on visual inspection; most (7/9) of the FSOs with NoV contamination on surfaces and a completed evaluation form had a good hygiene level (the best category). Restaurants had a significantly lower proportion of NoV-positive swabs compared to other FSOs (canteens, cafeteria, schools etc.) taken together (p = 0.00014). The presence of a designated break room for the workers was found to be significantly more common in AdV-negative kitchens (p = 0.046). Our findings suggest that swabbing is necessary for revealing viral contamination of surfaces and emphasis of hygiene inspections should be on the food handling procedures, and the education of food workers on virus transmission.
  • Mattila, Mirjami; Somervuo, Panu; Korkeala, Hannu; Stephan, Roger; Tasara, Taurai (2020)
    Numerous gene expression and stress adaptation responses in L. monocytogenes are regulated through alternative sigma factors sigma(B) and sigma(L). Stress response phenotypes and transcriptomes were compared between L. monocytogenes EGD-e and its Delta sigB and Delta sigBL mutants. Targeted growth phenotypic analysis revealed that the Delta sigB and Delta sigBL mutants are impaired during growth under cold and organic-acid stress conditions. Phenotypic microarrays revealed increased sensitivity in both mutants to various antimicrobial compounds. Genes de-regulated in these two mutants were identified by genome-wide transcriptome analysis during exponential growth in BHI. The Delta sigB and Delta sigBL strains repressed 198 and 254 genes, respectively, compared to the parent EGD-e strain at 3 degrees C, whereas 86 and 139 genes, respectively, were repressed in these mutants during growth at 37 degrees C. Genes repressed in these mutants are involved in various cellular functions including transcription regulation, energy metabolism and nutrient transport functions, and viral-associated processes. Exposure to cold stress induced a significant increase in sigma(B) and sigma(L) co-dependent genes of L. monocytogenes EGD-e since most (62%) of the down-regulated genes uncovered at 3 degrees C were detected in the Delta sigBL double-deletion mutant but not in Delta sigB or Delta sigL single-deletion mutants. Overall, the current study provides an expanded insight into sigma(B) and sigma(L) phenotypic roles and functional interactions in L. monocytogenes. Besides previously known sigma(B)- and sigma(L)-dependent genes, the transcriptomes defined in Delta sigB and Delta sigBL mutants reveal several new genes that are positively regulated by sigma(B) alone, as well as those co-regulated through sigma(B)- and sigma(L)-dependent mechanisms during L. monocytogenes growth under optimal and cold-stress temperature conditions.
  • Nevalainen, Jaakko; Stenman, Ulf-Hakan; Tammela, Teuvo L.; Roobol, Monique; Carlssone, Sigrid; Talalag, Kirsi; Schroder, Fritz H.; Auvinen, Anssi (2017)
    Background: The European Randomised study of Screening for Prostate Cancer (ERSPC) is a multicentre, randomised screening trial on men aged 55-69 years at baseline without known prostate cancer (PrCa) at randomisation to an intervention arm invited to screening or to a control arm. The ERSPC has shown a significant 21% reduction in PrCa mortality at 13 years of follow-up. The effect of screening appears to vary across centres, for which several explanations are possible. We set to assess if the apparent differences in PrCa mortality reduction between the centres can be explained by differences in screening protocols. Methods: We examined the centre differences by developing a simulation model and estimated how alternative screening protocols would have affected PrCa mortality. Results: Our results showed outcomes similar to those observed, when the results by centres were reproduced by simulating the screening regimens with PSA threshold of 3 versus 4 ng/ml, or screening interval of two versus four years. The findings suggest that the differences are only marginally attributable to the different screening protocols. Conclusion: The small screening impact in Finland was not explained by the differences in the screening protocols. A possible reason for it was the contamination of and the unexpectedly low PrCa mortality in the Finnish control arm. (C) 2016 Elsevier Ltd. All rights reserved.