Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

Genetic evaluations for endangered dual-purpose German Black Pied cattle using 50K SNPs, a breed-specific 200K chip, and whole-genome sequencing.

Genetic evaluations of local cattle breeds are hampered due to small reference groups or biased due to the utilization of SNP effects estimated in other large populations. Against this background, there is a lack of studies addressing the possible advantage of whole-genome sequences (WGS) or consideration of specific variants from WGS data in genomic predictions for local breeds with small population size. Consequently, the aim of this study was to compare genetic parameters and accuracies of genomic estimated breeding values (GEBV) for 305-d production traits, fat-to protein ratio (FPR), and somatic cell score (SCS) at the first test date after calving and confirmation traits of the endangered German Black Pied cattle (DSN) breed using 4 different marker panels: (1) the commercial 50K Illumina BovineSNP50 BeadChip, (2) a customized 200K chip designed for DSN (DSN200K) which considers the most important variants for DSN from WGS, (3) randomly generated 200K chips based on WGS data, and (4) a WGS panel. The same number of animals was considered for all marker panel analyses (i.e., 1,811 genotyped or sequenced cows for conformation traits, 2,383 cows for lactation production traits, and 2,420 cows for FPR and SCS). Mixed models for the estimation of genetic parameters directly included the respective genomic relationship matrix from the different marker panels plus the trait-specific fixed effects. For the calculation of GEBV accuracies, we applied repeated random subsampling validation. In the process of separate cross-validations per trait, we created a validation set including 20% of cows with masked phenotypes, and a training set comprising 80% of the cows. The cows were selected randomly in a procedure with 10 replicates considering replacements in the different scenarios. The accuracy was defined as the correlation between the direct GEBV and the phenotypes with subtracted corresponding fixed effects for the cows in the validation set. For FPR and SCS, as well as for lactation production traits, heritabilities were largest based on WGS data, but the increase compared with the 50K or DSN200K applications was quite small in the range from 0.01 to 0.03. Also, for most of the conformation traits, heritabilities were largest based on WGS and DSN200K data, but the increase was in the range of the corresponding standard error. Accordingly, GEBV accuracies for most of the studied traits were highest based on WGS data or when utilizing the DSN200K chip, but the accuracy differences across the marker panels were quite small and nonsignificant. In conclusion, WGS data and the DSN200K chip only contributed to minor improvements in genomic predictions, still justifying the use of the commercial 50K chip. Nevertheless, WGS and the 200KDSN chip harbor breed-specific variants, which are valuable for studying causal genetic mechanisms in the endangered DSN population.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).

BACKGROUND: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement. RESULTS: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. CONCLUSION: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

Bacterial Pneumonia in Brain-Dead Patients: Clinical Features and Impact on Lung Suitability for Donation.

OBJECTIVES: To appraise the epidemiological features of bacterial pneumonia and its impact on lung suitability for donation in brain-dead patients managed with protective ventilatory settings. DESIGN: Retrospective observational study. SETTING: Six ICUs from two university-affiliated hospitals. PATIENTS: Brain-dead adult patients managed in the participating ICUs over a 4-year period. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Among the 231 included patients, 145 (62.8%) were classified as ideal or extended-criteria potential lung donors at ICU admission and the remaining 86 patients having baseline contraindication for donation. Culture-proven aspiration pneumonia and early-onset ventilator-associated pneumonia occurred in 54 patients (23.4%) and 15 patients (6.5%), respectively (overall pneumonia incidence, 29.9%). Staphylococcus aureus and Enterobacterales were the most common pathogens. Using mixed-effects Cox proportional hazard models, age (adjusted hazard ratio, 0.98; 95% CI [0.96-0.99]), anoxic brain injury (3.55 [1.2-10.5]), aspiration (2.29 [1.22-4.29]), and not receiving antimicrobial agents at day 1 (3.56 [1.94-6.53]) were identified as independent predictors of pneumonia occurrence in the whole study population. Analyses restricted to potential lung donors yielded similar results. Pneumonia was associated with a postadmission decrease in the PaO2/FIO2 ratio and lower values at brain death, in the whole study population (estimated marginal mean, 294 [264-323] vs 365 [346-385] mm Hg in uninfected patients; p = 0.0005) as in potential lung donors (299 [248-350] vs 379 [350-408] mm Hg; p = 0.04; linear mixed models). Lungs were eventually retrieved in 31 patients (34.4%) among the 90 potential lung donors with at least one other organ harvested (pneumonia prevalence in lung donors (9.7%) vs nondonors (49.2%); p = 0.0002). CONCLUSIONS: Pneumonia occurs in one-third of brain-dead patients and appears as the main reason for lung nonharvesting in those presenting as potential lung donors. The initiation of antimicrobial prophylaxis upon the first day of the ICU stay in comatose patients with severe brain injury could enlarge the pool of actual lung donors.

Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN).

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log10(p) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (-log10(p) = 11.93, MAF = 0.23, substitution effect of the minor allele (ßMA) = -0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (-log10(p) = 8.47, MAF = 049, ßMA = -0.055%) and the GNG2 region (-log10(p) = 10.48, MAF = 0.34, ßMA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing.

German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.

Surgical strategy for biventricular assist device implantation after previous coronary artery bypass grafting.

In an aging population, numerous patients who underwent previous coronary artery bypass grafting (CABG) are presenting with end-stage ischemic cardiomyopathy. Although redo CABG and cardiological interventions are possible treatment options, orthotopic heart transplantation remains an ultimate option for these patients. However, there is high morbidity and mortality on the waiting list, and mechanical circulatory support is a life-saving concept [Hetzer 2006; Taylor 2009].We developed a simplified and safe technique for implantation of a biventricular assist device as a redo in complex patients after previous CABG and end-stage heart failure.

Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle.

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

Functional outcome after convulsive status epilepticus.

OBJECTIVES: Few outcome data are available about convulsive status epilepticus managed in the intensive care unit. We studied 90-day functional outcomes and their determinants in patients with convulsive status epilepticus. DESIGN: Two hundred forty-eight convulsive status epilepticus patients admitted to 18 intensive care units in 2005-2007 were included in a prospective observational cohort study. The main outcome measure was a Glasgow Outcome Scale score of 5 (good recovery) on day 90. MAIN RESULTS: Convulsive status epilepticus occurred out of hospital in 177 (67%) patients, and all but 15 patients were still seizing at medical team arrival. The median time from convulsive status epilepticus onset to anticonvulsant drug initiation was 40 mins (interquartile range, 5-80). Total seizure duration was 85 mins (interquartile range, 46.5-180). Convulsive status epilepticus was refractory in 49 (20%) patients. The most common causes of convulsive status epilepticus were anticonvulsive agent withdrawal (36.4%) in patients with previous epilepsy and stroke (27.7%) in inaugural convulsive status epilepticus. Mechanical ventilation was needed in 210 (85%) patients. On day 90, 42 (18.8%) patients were dead, 87 (38.8%) had marked functional impairments (Glasgow Outcome Scale score, 2-4), and 95 (42.4%) had a good recovery (Glasgow Outcome Scale score, 5). Factors showing independent positive associations with poor outcome (Glasgow Outcome Scale score, <5) were older age (odds ratio, 1.04/year; 95% confidence interval, 1.02-1.05; p=.0005), cerebral insult (odds ratio, 2.70; 95% confidence interval, 1.37-5.26; p=.007), longer seizure duration (odds ratio, 1.72/120 min; 95% confidence interval, 1.05-2.86; p=.03), on-scene focal neurologic signs (odds ratio, 2.08; 95% confidence interval, 1.03-4.16; p=.04), and refractory convulsive status epilepticus (odds ratio, 2.70; 95% confidence interval, 1.02-7.14; p=.045). CONCLUSIONS: Ninety days after intensive care unit admission for convulsive status epilepticus, half the survivors had severe functional impairments. Longer seizure duration, cerebral insult, and refractory convulsive status epilepticus were strongly associated with poor outcomes, suggesting a role for early neuroprotective strategies.

Interdisciplinary three-step strategy to treat aortic stenosis and coronary artery disease in a patient with end-stage chronic obstructive pulmonary disease.

BACKGROUND: Valvular aortic stenosis is a common disease in the elderly, often in multimorbid patients. It is often associated with coronary artery disease and peripheral artery disease. In this situation, the risk of conventional open-heart surgery is too high, and other treatment strategies have to be evaluated. CASE REPORT: A 79-year-old female patient with severe aortic stenosis, coronary artery disease and end-stage chronic obstructive pulmonary disease suffering from dyspnea at rest and permanently dependent on oxygen was treated in three steps. Firstly, her pulmonary infection was treated with antibiotics for 7 days. Then, the left anterior descending artery was stented (bare-metal stent). In the same session, valvuloplasty of the aortic valve was performed. She was sent to rehabilitation to improve her pulmonary condition and took clopidogrel for 4 weeks. Finally, she underwent transapical aortic valve replacement. She was released to rehabilitation on postoperative day 12. CONCLUSION: A combination of modern interventional and minimally invasive surgical techniques to treat aortic stenosis and coronary heart disease can be a viable option for multimorbid patients with extremely high risk in conventional open-heart surgery.

Dopamine therapy in septic shock: detrimental effect on survival?

OBJECTIVE: The aim of this study is to examine the potential impact of dopamine therapy on 28-day mortality in adult septic shock. METHODS: For 66 months, clinical data, medications taken before admission, doses of catecholamines used, and biological parameters were recorded prospectively in all patients admitted for septic shock. This observational study was followed by (1) post hoc multivariate analyses and (2) risk-adjusted matched cohort study. MEASUREMENTS AND MAIN RESULTS: In 277 patients (65 +/- 14 years; Simplified Acute Physiology Score II = 54 +/- 19, 28-day mortality = 45%; hospital mortality = 53%), 6 factors were linked to 28-day mortality, including Simplified Acute Physiology Score II (P < .0001) and the use of dopamine (P = .043). In a pair-matched cohort of 132 patients, we observed a higher mortality with dopamine (28-day mortality of 62% vs 41%, respectively; P = .006). Dopamine remained linked to day 28 mortality by conditional logistic analysis (odds ratio = 6.2 [1.5-25]). A strong interaction between essential hypertension and dopamine was found, associated to 81% 28-day mortality in patients having both conditions. CONCLUSIONS: In our cohort study, dopamine use was linked to mortality as compared to other vasopressor therapies, particularly in patients with essential hypertension. Future randomized studies attempting to compare dopamine with other therapies in septic shock should pay attention to patients with essential hypertension.

Intrahospital transport of critically ill ventilated patients: a risk factor for ventilator-associated pneumonia--a matched cohort study.

OBJECTIVE: To evaluate the impact of intrahospital transport of critically ill ventilated patients on the acquisition of ventilator-associated pneumonia. DESIGN: An exposed/unexposed matched cohort study. SETTING: An 18-bed adult medical-surgical intensive care unit in a 1,100-bed regional and teaching hospital in France. PATIENTS: From January 1, 2001, to December 31, 2002, 118 of 228 ventilated patients transported out of the intensive care unit (exposed patients) were matched with 118 unexposed patients selected among 295 ventilated patients who did not undergo intrahospital transport. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The matching process was conducted according to six criteria: duration of mechanical ventilation, duration of antibiotherapy, indication for ventilatory support, age, probability of death, and surgical procedures or not during intensive care unit stay. The rates of ventilator-associated pneumonia (as defined by usual clinical and biological criteria plus positive culture of bronchoscopy directed catheter) acquisition between exposed and unexposed patients were compared by univariate analysis and then by multivariate analysis (conditional logistic regression and Cox's proportional-hazards model) to account for potential confounding factors. The ventilator-associated pneumonia rate was 26% in exposed patients compared with 10% in the matched unexposed patients. Using conditional logistic regression, two factors were independently associated with ventilator-associated pneumonia: intrahospital transport (odds ratio, 3.1; 95% confidence interval, 1.4-6.7) and the need for reintubation. Using Cox's model, three independent risk factors were identified: the need for reintubation, enteral nutrition, and intrahospital transport (odds ratio, 2.9; 95% confidence interval, 1.4-5.7). The intensive care unit mortality rate was similar (p > .1) in exposed (35%) and unexposed patients (26%). CONCLUSIONS: Intrahospital transport appears to be a significant risk factor for ventilator-associated pneumonia. However, the respective roles of intrahospital transport and of the cause that leads clinicians to transport patients (mainly for radiographic examinations) are difficult to dissociate even after multiple statistical adjustments. When intrahospital transport is needed, very cautious measures must be taken before and during intrahospital transport to prevent ventilator-associated pneumonia. In addition, in the few days after intrahospital transport, intensive search for ventilator-associated pneumonia is justified.

Obesity-related excess mortality rate in an adult intensive care unit: A risk-adjusted matched cohort study.

OBJECTIVE: To evaluate the obesity-related mortality rate in an intensive care unit. DESIGN: An exposed/unexposed matched cohort study. SETTING: An 18-bed adult medical-surgical intensive care unit in a 1,100-bed regional and teaching hospital in France. PATIENTS: From January 1, 1999, to December 31, 2001, 170 mechanically ventilated exposed patients (obese patients with body mass index of >30 kg/m) were matched with 170 mechanically ventilated unexposed patients (with ideal body mass index of 18.5-24.9 kg/m). INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The matching process was conducted according to eight criteria: cause of admission, indication for ventilatory support, immunologic status, cardiac status, probability of death (+/-5%), age (+/-7 yrs), gender, and acquisition of severe events appearing within 24 hrs before admission (defined as resuscitated cardiac arrest, acute respiratory distress syndrome, or septic shock). The mortality rate between exposed and unexposed patients was compared by univariate analysis and then was adjusted for other possible confounding factors by multivariate analysis, using conditional logistic regression. The matching process was successful for 1,360 of 1,360 criteria. Obesity was significantly associated with intensive care unit mortality (odds ratio, 2.1; 95% confidence interval, 1.2-3.6). Obesity-related excess mortality was verified mainly for the youngest patients (odds ratio, 2.5; 95% confidence interval, 1.6-6.1) and for the patients with a probability of intensive care unit death of 11-50% (odds ratio, 2.6; 95% confidence interval, 1.2-5.5). This excess mortality rate could be explained by the higher risk of intensive care unit acquired complications among obese patients than among the unexposed ones (odds ratio, 4; 95% confidence interval, 1.4-11.8). CONCLUSIONS: Obesity is an independent risk factor for intensive care unit death and should be regarded as a severe comorbidity in such units.