Measurement of SARS-CoV-2 in air and on surfaces in Scottish hospitals.

BACKGROUND: There are still uncertainties in our knowledge of the amount of SARS-CoV-2 virus present in the environment - where it can be found, and potential exposure determinants - limiting our ability to effectively model and compare interventions for risk management. AIM: This study measured SARS-CoV-2 in three hospitals in Scotland on surfaces and in air, alongside ventilation and patient care activities. METHODS: Air sampling at 200 L/min for 20 min and surface sampling were performed in two wards designated to treat COVID-19-positive patients and two non-COVID-19 wards across three hospitals in November and December 2020. FINDINGS: Detectable samples of SARS-CoV-2 were found in COVID-19 treatment wards but not in non-COVID-19 wards. Most samples were below assay detection limits, but maximum concentrations reached 1.7×103 genomic copies/m3 in air and 1.9×104 copies per surface swab (3.2×102 copies/cm2 for surface loading). The estimated geometric mean air concentration (geometric standard deviation) across all hospitals was 0.41 (71) genomic copies/m3 and the corresponding values for surface contamination were 2.9 (29) copies/swab. SARS-CoV-2 RNA was found in non-patient areas (patient/visitor waiting rooms and personal protective equipment changing areas) associated with COVID-19 treatment wards. CONCLUSION: Non-patient areas of the hospital may pose risks for infection transmission and further attention should be paid to these areas. Standardization of sampling methods will improve understanding of levels of environmental contamination. The pandemic has demonstrated a need to review and act upon the challenges of older hospital buildings meeting current ventilation guidance.

Compensatory growth in crossbred Aberdeen Angus and Belgian Blue steers: Effects on the colour, shear force and sensory characteristics of longissimus muscle.

The effect of feed restriction (99days) followed by compensatory growth during a 200day re-alimentation period on the colour and sensory characteristics of meat from Aberdeen Angus×Holstein-Friesian (AN) and Belgian Blue×Holstein-Friesian (BB) steers was examined. Compensatory growth had no effect on muscle pH and temperature decline, chemical composition, drip loss, fat colour, or juiciness, but increased (P=0.009) Warner-Bratzler shear force and decreased tenderness (P=0.08) and overall liking (P=0.09). Compared to meat from BB steers, meat from AN steers had a higher intramuscular fat concentration and was rated similarly for tenderness, but higher for many of the flavour characteristics examined. While adjustment for intramuscular fat concentration removed some of these differences, genotype-specific flavour differences remained. It is concluded that genotype had greater effects on meat quality than the compensatory growth feeding regime imposed in this study.

Polymorphisms in the regulatory region of the porcine MYLPF gene are related to meat quality traits in the Large White breed.

The MYLPF gene encodes fast myosin regulatory light chain, and is a positional and functional candidate gene for meat quality. The aim of this study was to identify associations between SNPs in the promoter region of the porcine MYLPF gene and meat quality traits. A total of 22 SNPs were identified in a population of crossbred animals (n=86) and based on minor allele frequency and proximity to the transcription start site, five SNPs were genotyped in purebred; Large White (n=98), Duroc (n=99) and Pietrain (n=98) pigs. No associations were observed in the Pietrain breed, while the Duroc breed was almost monomorphic for all SNPs. In the Large White breed SNP g-1314A>G and linked SNPS g.-871T>G, g.-566T>C, g.-403C>G were associated with ultimate pH and driploss (P<0.05). This study identified associations between MYLPF and meat quality and highlights the importance of considering the genetic background within gene-assisted selection programmes.

Novel SNPs in the Ankyrin 1 gene and their association with beef quality traits.

Single nucleotide polymorphisms (SNPs) in the promoter region of bovine Ankyrin 1 (ANK1) have been associated with tenderness and intramuscular fat level in beef. The objectives of this study were to characterise novel DNA variants in the coding region of bovine ANK1 and test for association with beef quality traits. A 3kb region of ANK1 cDNA was amplified and sequenced in 32 Charolais cattle using five sets of overlapping primers. Eighteen SNPs were identified and a predicted exon was confirmed. An in silico translation indicated that SNP4 and SNP16 were non-conservative. Three SNPs were genotyped in 158 crossbred cattle (n=158) with associated meat quality data. SNP6 was associated with texture scores while SNP17 was associated with juiciness. Haplotype (cHAP) 1 was associated with lightness, redness, ultimate pH, as well as sarcomere length. Alleles of the ANK1 gene could be potential targets for gene-assisted selection to improve a range of meat quality traits in beef.

Novel variation in the FABP3 promoter and its association with fatness traits in pigs.

This study examines associations between SNPs in the promoter region of the fatty acid binding protein 3 (FABP3) gene and fatness traits in pure bred Large White (n=98), Duroc (n=99) and Pietrain (n=98) populations. In the Large White breed, SNP g.-634 C>A was associated a 27% increase in IMF (%) in the heterozygote (CA) and a 38% increase in the homozygote (CC) relative to the (AA) genotype in the M. semimembranosus (SM) muscle (P=0.02). While the associations observed in this breed were suggestive of significance in both the SM and in the M. longissimus thoracis et lumborum (LTL) (P=0.08), these associations no longer attained significance at thresholds adjusted for multiple testing. In conclusion, SNPs in the FABP3 promoter may contribute to IMF without influencing carcass fatness traits in pigs, however further confirmation of these associations in larger independent populations would be essential before their incorporation into breeding programmes.

Cerebral Scedosporium apiospermum infection presenting with intestinal manifestations.

We present a case of cerebral Scedosporium apiospermum infection presenting with intestinal manifestations in a 64-year-old male patient on immunosuppression for orthotopic liver transplantation. At admission, the patient's chief complaint was chronic watery diarrhea and he was found to have colonic ulcers on endoscopy. His hospital course was complicated by a tonic-clonic seizure caused by a left frontal brain abscess, with the causative agent being identified by culture. He was treated with lobectomy, high-dose intravenous voriconazole, and liposomal amphotericin with clinical, endoscopic, and histologic improvement. To our knowledge, S. apiospermum has not been previously described as a cause of colitis. The septate branching appearance of the Scedosporium species is similar to the more common Aspergillus species. This case of gastrointestinal Scedosporium brings into question previously reported cases of isolated gastrointestinal aspergillosis diagnosed by histopathology. Clinical suspicion for S. apiospermum must be maintained in immunosuppressed patients presenting with neurologic and gastrointestinal symptoms.

Association of polymorphisms in candidate genes with colour, water-holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus.

The objective of this study was to determine the association of single nucleotide polymorphisms (SNP) in selected candidate genes with sensory and technological meat quality traits in commercial cattle. SNP in seven candidate genes were genotyped in 130 crossbred Bos taurus cattle using PCR-RFLP. Reported associations between calpastatin (CAST) and Warner-Bratzler shear force and carboxypeptidase E (CPE) and intra-muscular fat were not confirmed. However, SNP in CAST, amp-activated protein kinase, gamma-3 subunit (PRKAG3), growth hormone receptor (GHR) and stearoyl coA desaturase (SCD) genes were significantly associated with colour traits (p<0.05). The PRKAG3 SNP was additionally associated with cook loss in M. longissimus thoracis et lumborum (p<0.05) and tended towards association in M. semimembranosus (p<0.1). An association with pH was identified for the SCD SNP (p<0.001). The GHR polymorphism was influential on moisture and intra-muscular fat in M. semimembranosus and protein content in both muscles (p<0.05). Only CPE was associated with sensory traits (flavour in M. longissimus, p<0.01).

Association analysis of single nucleotide polymorphisms in DGAT1, TG and FABP4 genes and intramuscular fat in crossbred Bos taurus cattle.

Previous studies have indicated that single nucleotide polymorphisms (SNPs) in the diacylglycerol-O-acyltransferase1 (DGAT1), thyroglobulin (TG) and adipose fatty acid binding protein (FABP4) genes are associated with intramuscular fat (IMF) levels or marbling scores in beef. The objectives were to estimate the frequency of SNPs in these candidate genes in purebred Irish cattle (n=459) and to determine if individual SNPs are associated with IMF values of longissimus thoracis et lumborum (LTL) and semimembranosus (SM) muscle of crossbred animals (n=138). Results indicated no significant association between the SNPs and IMF, despite the power of this study being sufficient to detect an association with SNPs in the DGAT1 and FABP4 genes. The results confirm the lack of an association found by many other studies and suggest that these SNPs are not influential on the divergent IMF levels in the crossbred population tested.

New single nucleotide polymorphisms in the mu-calpain gene in Spanish maternal beef breeds.

Calpains play an important role in the postmortem tenderization process of meat and several SNP in the mu-calpain gene (CAPN1) have been reported to be associated with tenderness in beef cattle. Our objectives were to identify the previously reported CAPN1 331G>C SNP and to detect new polymorphisms in this gene in Spanish maternal beef breeds. A fragment (exon 8 to 10) of the bovine CAPN1 gene was sequenced and genotyped in a sample of the main Spanish maternal beef breeds including Retinta, Morucha, and Avilenã Negra-Ibérica. These breeds are characterized for their high meat quality, their adaptation to adverse environmental conditions, and their good maternal aptitude. This adaptation makes it possible to rear these breeds in the south and west of Spain, where drought and feed shortages occur frequently. Six SNP in the mu-calpain gene were found, five of which (CAPN1 80C>T, 302C>G, 310G>A, 445C>T, 524A>C) have not been reported previously. Sequences obtained for these five newly found SNP were submitted to GenBank (Accessions EU386166 to EU386183).

Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P < 0.001), but there was no relationship with cooking temperature. Quality (A(260)/A(280), i.e., absorbance at 260 and 280 nm) was also affected by cooking (P < 0.001). For all 3 genes, large PCR amplicons (product size >800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (<200 bp) were present for all core temperatures. Cooking meat to high temperatures thus resulted in a reduced overall yield and probable fragmentation of DNA to sizes less than 800 bp. Although nuclear DNA is preferable to mitochondrial DNA for food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.

Lack of an association between single nucleotide polymorphisms in the bovine leptin gene and intramuscular fat in Bos taurus cattle.

Leptin contributes to the regulation of adiposity and metabolism, and single nucleotide polymorphisms (SNPs) in the leptin gene have been associated with intramuscular fat (IMF) levels in beef. Our objectives were to estimate the frequency of four SNPs in the leptin gene in nine purebred cattle (n=430), to test for linkage disequilibrium and infer haplotypes, and to determine if individual genotypes or estimated haplotypes were associated with IMF values in crossbred cattle (n=244). The four SNP loci were found to be in linkage disequilibrium and thus, the frequencies of each of the 16 possible haplotypes were inferred by maximum likelihood. No significant association between any individual SNP and haplotype was found with the divergent IMF values. Our results suggest that these SNPs are not influential on the divergent IMF levels in the crossbred population tested.

Fluid-containing emphysematous bullae: a spectrum of illness.

Fluid-containing emphysematous bullae are an under-reported complication of chronic obstructive pulmonary disease. The roles of bronchoscopy in the work-up and of antibiotics in the treatment are undefined. This study reports the combined results from the analysis of 16 cases treated at the present authors' institution and 36 previously reported cases. The median age at presentation was 58 yrs and the median duration of follow-up was 60 weeks. A third of the patients were asymptomatic, while two-thirds presented with symptoms, including 10% who had evidence of a severe lung infection. Methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa and Bacteroides melaninogenicus were cultured from the bullae fluid in three symptomatic patients. Sputum and blood cultures were uninformative. Bronchoscopy, performed in two-thirds of the cases, added no diagnostic information. Antibiotic treatment did not result in a more rapid resolution of the air fluid level. Percutaneous drainage was safe and effective in four patients. In conclusion, patients with fluid-containing bullae present with a spectrum of illness. Antibiotic treatment does not hasten radiographic resolution and bronchoscopy has no diagnostic or therapeutic role.

Disseminated histoplasmosis manifesting as a soft-tissue chest wall mass in a heart transplant recipient.

Soft-tissue masses are rarely associated with Histoplasma capsulatum infection. We describe a heart transplant patient who presented with a large right-sided chest wall mass as a manifestation of disseminated histoplasmosis. A successful clinical outcome was achieved upon recognition of the fungal pathogen.

Sex and differentiation: population genetic divergence and sexual dimorphism in Mexican goodeid fish.

Genetic differentiation arises due to the interaction between natural and sexual selection, migration and genetic drift. A potential role of sexual selection in speciation has received much interest, although comparative studies are inconsistent in finding supporting evidence. A poorly tested prediction is that species subject to a higher intensity of sexual selection should show greater genetic differentiation amongst populations because females from these populations should be more choosy in mate choice. The Goodeinae is a group of endemic Mexican fishes in which female choice has driven some species to be morphologically sexually dimorphic, whereas others are relatively monomorphic. Here, we measured population divergence, using microsatellite loci, within four goodeid species which show contrasting levels of sexual dimorphism. We found higher levels of differentiation between populations of the more dimorphic species, implying less gene flow between populations. We also found evidence of higher levels of genetic differences between the sexes within populations of the dimorphic species, consistent with greater dispersal in males. Adjusted for geographic distance, the mean F(ST) for the dimorphic species is 0.25 compared with 0.16 for the less dimorphic species. We conclude that population differentiation is accelerated in more sexually dimorphic species, and that comparative phylogeography may provide a more powerful approach to detecting processes, such as an influence of sexual selection on differentiation, than broad-scale comparative studies.

Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L.

Fossil evidence shows that populations of species that currently inhabit arctic and boreal regions were not isolated in refugia during glacial periods, but instead maintained populations across large areas of central Europe. These species commonly display little reduction in genetic diversity in northern areas of their range, in contrast to many temperate species. The mountain hare currently inhabits both temperate and arctic-boreal regions. We used nuclear microsatellite and mtDNA sequence data to examine population structure and alternate phylogeographic hypotheses for the mountain hare, that is, temperate type (lower genetic diversity in northern areas) and arctic-boreal type (high northern genetic diversity). Both data sets revealed concordant patterns. Highest allelic richness, expected heterozygosity and mtDNA haplotype diversity were identified in the most northerly subspecies, indicating that this species more closely maps to phylogeographic patterns observed in arctic-boreal rather than temperate species. With regard to population structure, the Alpine and Fennoscandian subspecies were most genetically similar (F(ST) approximately 0.1). These subspecies also clustered together on the mtDNA tree and were assigned with highest likelihood to a common Bayesian cluster. This is consistent with fossil evidence for intermediate populations in the central European plain, persisting well into the postglacial period. In contrast, the geographically close Scottish and Irish populations occupied separate Bayesian clusters, distinct clades on the mtDNA maximum likelihood tree and were genetically divergent from each other (F(ST) > 0.4) indicating the influence of genetic drift, long isolation (possibly dating from the late glacial era) and/or separate postglacial colonisation routes.

Understanding meat quality through the application of genomic and proteomic approaches.

During the past few decades, advances in molecular genetics have led to the identification of multiple genes or genetic markers associated with genes that affect traits of interest in livestock, including single genes of large effect and QTL (genomic regions that affect quantitative traits). Transcriptomics enables analysis of the complete set of RNA transcripts produced by the genome at a given time and provides a dynamic link between the genome, the proteome and the cellular phenotype. Through a functional genomics approach to understanding the molecular basis of meat quality, we can gain further insight into the complex interplay of gene expression events involved in the development of meat quality. Proteomics permits visualisation of the protein content of the cell under varying conditions, combining powerful separation techniques with highly sensitive analytical mass spectrometry. To date, both the human and bovine genome projects have advanced our understanding of gene expression and helped elucidate the function of large portions of the genome. Advantages from this research have permeated through to a broader spectrum of research including that of meat science. Meat quality is manifested through a complexity of events in the muscle and their interactions with many environmental stimuli in both the live animal and during the post-mortem period. A lot of progress has been made in our understanding of the biological processes that contribute to the delivery of consistent quality meat. Through the application of tools of genomics and proteomics we are gaining a deeper insight into these processes and their interaction with environmental factors. Knowledge gained from these approaches can be beneficial in defining and optimising management systems for quality, providing assurance of meat quality and in tailoring quality to suit market needs.

Influence of condition of surgical margins on local recurrence and disease-specific survival in oral and oropharyngeal cancer.

BACKGROUND: The clearance of surgical margins at the primary site is widely thought to influence the subsequent course of the disease in patients operated on for oral and oropharyngeal carcinoma. In some reports the adverse impact of close or involved margins was not negated by postoperative radiotherapy. These findings, in addition to descriptive histopathological studies, have led some authors to recommend margins of more than a macroscopic clearance of 1cm at certain subsites. We have therefore examined the relation between the condition of surgical margins and local recurrence and disease-specific survival. METHODS: Identical treatment protocols were used to treat two independent groups of patients (Sydney, Australia, n=237; Lanarkshire, n=95) who presented with previously untreated carcinoma of the mouth or oropharynx. All patients were operated on with the primary objective of achieving a macroscopic clearance of 1cm. Postoperative radiotherapy was used according to a protocol. Data about patients were entered into comprehensive computerised databases prospectively. Known clinical and pathological prognostic indicators, in addition to the condition of surgical margins, were analysed to find out if they were predictive of local recurrence and disease-specific survival using the Cox proportional hazard model. RESULTS: Local recurrence was predicted by the presence of perineural invasion at the primary site in both groups. Disease-specific survival was predicted by the presence and extent of regional lymph node metastases in both groups. The condition of surgical margins (clear, close, or involved) did not predict local recurrence, or disease-specific survival on multivariate analysis. CONCLUSIONS: A macroscopic margin of 1cm seems adequate in the surgical management of oral and oropharyngeal carcinoma. For most patients who have close or involved margins the biology of the disease influences the subsequent course irrespective of the width of clearance of tumour.

Trends in antifungal drug susceptibility of Cryptococcus neoformans isolates in the United States: 1992 to 1994 and 1996 to 1998.

The antifungal drug susceptibilities of two collections of Cryptococcus neoformans isolates obtained through active laboratory-based surveillance from 1992 to 1994 (368 isolates) and 1996 to 1998 (364 isolates) were determined. The MICs of fluconazole, itraconazole, and flucytosine were determined by the National Committee for Clinical Laboratory Standards broth microdilution method; amphotericin B MICs were determined by the E-test. Our results showed that the MIC ranges, the MICs at which 50% of isolates are inhibited (MIC(50)s), and the MIC(90)s of these four antifungal agents did not change from 1992 to 1998. In addition, very small numbers of isolates showed elevated MICs suggestive of in vitro resistance. The MICs of amphotericin B were elevated (>or=2 microg/ml) for 2 isolates, and the MICs of flucytosine were elevated (>or=32 microg/ml) for 14 isolates. Among the azoles, the fluconazole MIC was elevated (>or=64 microg/ml) for 8 isolates and the itraconazole MIC (>or=1 microg/ml) was elevated for 45 isolates. Analysis of 172 serial isolates from 71 patients showed little change in the fluconazole MIC over time. For isolates from 58 patients (82% of serial cases) there was either no change or a twofold change in the fluconazole MIC. In contrast, for isolates from seven patients (12% of serial cases) the increase in the MIC was at least fourfold. For isolates from another patient there was a 32-fold decrease in the fluconazole MIC over a 1-month period. We conclude that in vitro resistance to antifungal agents remains uncommon in C. neoformans and has not significantly changed with time during the past decade.

Cryptococcosis in human immunodeficiency virus-negative patients in the era of effective azole therapy.

We conducted a case study of human immunodeficiency virus (HIV)-negative patients with cryptococcosis at 15 United States medical centers from 1990 through 1996 to understand the demographics, therapeutic approach, and factors associated with poor prognosis in this population. Of 306 patients with cryptococcosis, there were 109 with pulmonary involvement, 157 with central nervous system (CNS) involvement, and 40 with involvement at other sites. Seventy-nine percent had a significant underlying condition. Patients with pulmonary disease were usually treated initially with fluconazole (63%); patients with CNS disease generally received amphotericin B (92%). Fluconazole was administered to approximately two-thirds of patients with CNS disease for consolidation therapy. Therapy was successful for 74% of patients. Significant predictors of mortality in multivariate analysis included age > or =60 years, hematologic malignancy, and organ failure. Overall mortality was 30%, and mortality attributable to cryptococcosis was 12%. Cryptococcosis continues to be an important infection in HIV-negative patients and is associated with substantial overall and cause-specific mortality.