Biologic and genomic characterization of a novel virulent Aeromonas hydrophila phage phiA051, with high homology to prophages.

Introduction: Aeromonas hydrophila is particularly harmful to freshwater aquaculture, and the search for phage is an effective biological control method, but reports of possible temperate phages and their mutants are rare in this field. In this study, a virulent phage highly homologous to prophage in the genomes of A. hydrophila was collected and preliminary biological characterization was carried out to understand its nature. Materials and methods: Water samples taken from eel ponds in Fujian, China were combined with the strain. Spot test method and double-layer agar plate assay was used for confirmation and purification. Phage virions were observed using transmission electron microscope. A total of 68 strains of Aeromonas spp. were used to determine the host range. MOI groups of 1,000, 100, 10, 1, 0.1, 0.01, 0.001, 0.0001, 0.00001 were prepared to detect the optimal MOI. The conditions of thermal stability assay were set as 30, 40, 50, 60, 70 and 80°C for 1 h, respectively, and conditions of acid and alkali stability assay were set as 2.0, 4.0, 6.0, 8.0, 10.0 and 12.0 of pH. MOI of 0.01 and 0.1, respectively, are set to determine the inhibitory capacity of phage. Results: A novel virulent A. hydrophila phage designated phiA051 has been isolated from aquaculture water. Electron microscopic observation showed that the phage phiA051 was composed of an icosahedral capsid. The phage phiA051 possesses an optimal multiplicity of infection (MOI) of 0.01, and its burst size was 108 PFU/cell. The phage maintained a high viability at temperatures of 30-50°C or pH 6.0-10.0 for 1 h. Phage phiA051 has certain potentials in rapidly inhibiting the spread of pathogen early in the outbreak, and it has a linear dsDNA with GC content of 60.55% and a total length of 32,212 bp, including 46 ORFs. Discussion: The phage phiA051 behaved as a virulent phage. However, the BLASTN result showed that 23 of the top 25 hits were genomes of Aeromonas strains. It was suggested that phiA051 was probably derived from some prophage in the chromosome of Aeromonas. Further investigation of the mechanism how phage phiA051 transforms from a temperate phage to a virulent phage will provide a unique perspective and idea to explore the potential of prophages.

Identification of copy-number variants in patients with overgrowth disorders.

Overgrowth syndromes (OGS) comprise a heterogeneous group of disorders whose main characteristic is that the weight, height or the head circumference are above the 97th centile or 2-3 standard deviations above the mean for age, gender, and ethnic group. Several copy-number variants (CNVs) have been associated with the development of OGS, such as the 5q35 microdeletion or the duplication of the 15q26.1-qter, among many others. In this study, we have applied 850K SNP-arrays to 112 patients and relatives with OGS from the Spanish OverGrowth Registry Initiative. We have identified CNVs associated with the disorder in nine individuals (8%). Subsequently, whole genome sequencing (WGS) analysis was performed in these nine samples in order to better understand these genomic imbalances. All the CNVs were detected by both techniques, settling that WGS is a useful tool for CNV detection. We have found six patients with genomic abnormalities associated with previously well-established disorders and three patients with CNVs of unknown significance, which may be related to OGS, based on scientific literature. In this report, we describe these findings and comment on genes associated with OGS that are located within the CNV regions.

Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.

BACKGROUND: DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla. RESULTS: Here, we generate base-resolution methylomes for three species with distinct genomic features and phylogenetic positions in Annelida, a major spiralian phylum. All possible 5mC patterns occur in annelids, from typical invertebrate intermediate levels in a mosaic distribution to hypermethylation and methylation loss. GbM is common to annelids with 5mC, and methylation differences across species are explained by taxon-specific transcriptional dynamics or the presence of intronic TEs. Notably, the link between GbM and transcription decays during development, alongside a gradual and global, age-dependent demethylation in adult stages. Additionally, reducing 5mC levels with cytidine analogs during early development impairs normal embryogenesis and reactivates TEs in the annelid Owenia fusiformis. CONCLUSIONS: Our study indicates that global epigenetic erosion during development and aging is an ancestral feature of bilateral animals. However, the tight link between transcription and gene body methylation is likely more important in early embryonic stages, and 5mC-mediated TE silencing probably emerged convergently across animal lineages.

Drug resistance and genetic characteristics of one Eimeria tenella isolate from Xiantao, Hubei Province, China.

Chicken coccidiosis causes retarded growth and low production performance in poultry, resulting in huge economic losses to the poultry industry. In order to prevent and control chicken coccidiosis, great efforts have been made to develop new drugs and vaccines, which require pure isolates of Eimeria spp. In this study, we obtained the Eimeira tenella Xiantao isolate by single oocyst isolation technology and compared its genome with the reference genome GCF_000499545.2_ETH001 of the Houghton strain. The results of the comparative genomic analysis indicated that the genome of this isolate contained 46,888 single nucleotide polymorphisms (SNPs). There were 15,107 small insertion and deletion variations (indels), 1693 structural variations (SV), and 3578 copy number variations (CNV). In addition, 64 broilers were used to determine the resistance profile of Xiantao strain. Drug susceptibility testing revealed that this isolate was completely resistant to monensin, diclazuril, halofuginone, sulfachlorpyrazine sodium, and toltrazuril, but sensitive to decoquinate. These data improve our understanding of drug resistance in avian coccidia.

Genomic analysis of three SARS-CoV-2 waves in west Sumatra: Evolutionary dynamics and variant clustering.

Background: The Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) has been undergoing evolutionary changes to improve its ability to thrive within human hosts, leading to the emergence of specific variants associated with subsequent waves of the coronavirus diseases 2019 (COVID-19) pandemic. Indonesia has grappled with the effects of this pandemic and subsequent waves affecting various regions, including West Sumatra. Although located outside Java island epicenter, West Sumatra experienced significant COVID-19 transmission, especially during the third wave in early 2022. Objective: This study aimed to investigate the genetic evolution and epidemiological dynamics of SARS-CoV-2 variants in West Sumatra throughout the three pandemic waves. Methods: We conducted a genotyping study retrospectively using 278 COVID-19 patient samples from 2020 to 2022. The Real-Time Quantitative Reverse Transcription PCR (RT-qPCR) was used for screening, and whole-genome sequence analysis was conducted through the Illumina MiSeq instrument. Result: The analysis revealed distinct patterns in the prevalence of viral lineages across the waves. The initial wave was predominated by clade 20A (77,4 %) especially lineage B.1.466.2 (50 %). The second wave was marked by a significant emergence of the Delta variant (72,5 %), particularly lineage AY.23 (81,1 %), originating from India, with subsequent local evolution leading to the formation of distinct clusters. We found that about 96,7 % of the third wave variant was dominated by Omicron variants, especially the generation of lineages BA.1 and BA.2, demonstrating widespread global dissemination and local variant development. Phylogenetic analysis indicated a close relatedness of West Sumatra variants to those from Malaysia and other parts of Indonesia, highlighting regional transmission dynamics and potential sources of variant introductions. Conclusion: This study has identified unique variant clusters within each wave, suggesting distinct evolutionary pathways and local adaptations. These findings provide valuable insights into the genomic landscape of SARS-CoV-2 in West Sumatra and emphasize the crucial role of ongoing genomic surveillance in tracking viral changes and guiding public health measures.

Discordance Between Phenotypic and WGS-Based Drug Susceptibility Testing Results for Some Anti-Tuberculosis Drugs: A Snapshot Study of Paired Mycobacterium tuberculosis Isolates with Small Genetic Distance.

Background: Current tuberculosis treatment regimens primarily rely on phenotypic drug susceptibility testing and rapid molecular assays. Although whole-genome sequencing (WGS) offers a promising alternative, disagreements between phenotypic and molecular testing methods remain. In this retrospective study, we compared the phenotypic and WGS-predicted drug resistance profiles of paired Mycobacterium tuberculosis isolates with small genetic distances (≤10 single nucleotide variants) obtained from patients with longitudinal single-episode or recurrent tuberculosis. Additionally, we investigated the distribution of drug-resistance-conferring variants among the identified M. tuberculosis genotypes. Methods: Paired M. tuberculosis isolates from 46 patients with pulmonary tuberculosis (2002-2019) were analyzed. Spoligotyping was performed for all the isolates. WGS data were processed using TB-Profiler software to genotype the strains and detect variants in M. tuberculosis genes associated with drug resistance. The significance of these variants was evaluated using the M. tuberculosis variant catalog developed by the World Health Organization. Phenotypic drug susceptibility test results were obtained from patients' medical records. Results: Among the 46 isolate pairs, 25 (54.3%) harbored drug-resistance-associated variants, with 20 demonstrating identical WGS-predicted drug resistance profiles. Drug-resistant isolate pairs belonged to Lineages 2 and 4, with the most common sub-lineages being 2.2.1 (SIT1 and SIT190 spoligotypes), and 4.3.3 (SIT42). Agreement between phenotypic and WGS-based drug susceptibility testing was highest (>90%) for rifampicin, isoniazid, ethambutol, fluoroquinolones, streptomycin, and amikacin when calculated for M. tuberculosis isolates or isolate pairs. In most discordant cases, isolate pairs harbored variants that could cause low- or moderate-level resistance or were previously associated with variable minimum inhibitory concentrations. Notably, such discrepancies mostly occurred in one isolate from the pair. In addition, differences in resistance-related variant distributions among M. tuberculosis genotypes were observed for most of the analyzed drugs. Conclusion: The simultaneous performance of phenotypic and WGS-based drug susceptibility testing creates the most accurate drug resistance profile for M. tuberculosis isolates and eliminates important limitations of each method.

The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae.

Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.

Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits (Physalis peruviana L.).

Introduction: Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question. Methods: This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes. Results: The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood). Conclusion: Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.

The effects of single and multiple resistance mechanisms on bacterial response to meropenem.

OBJECTIVES: Meropenem is commonly used against Pseudomonas aeruginosa. Traditionally, the time unbound antibiotic concentration exceeds the MIC (fT>MIC) is used to select carbapenem regimens. We aimed to characterize the effects of different baseline resistance mechanisms on bacterial killing and resistance emergence; evaluate whether fT>MIC can predict these effects; and, develop a novel Quantitative and Systems Pharmacology (QSP) model to describe the effects of baseline resistance mechanisms on the time-course of bacterial response. METHODS: Seven isogenic P. aeruginosa strains with a range of resistance mechanisms and MICs were used in 10-day hollow-fiber infection model studies. Meropenem pharmacokinetic profiles were simulated for various regimens (t1/2,meropenem = 1.5 h). All viable counts on drug-free, 3 × MIC, and 5 × MIC meropenem-containing agar across all strains, five regimens, and control (n = 90 profiles) were simultaneously subjected to QSP modeling. Whole genome sequencing was completed for total population samples and emergent resistant colonies at 239 h. RESULTS: Regimens achieving ≥98%fT>1×MIC suppressed resistance emergence of the mexR knockout strain. Even 100%fT>5 × MIC failed to achieve this against the strain with OprD loss and the ampD and mexR double-knockout strain. Baseline resistance mechanisms affected bacterial outcomes, even for strains with the same MIC. Genomic analysis revealed that pre-existing resistant subpopulations drove resistance emergence. During meropenem exposure, mutations in mexR were selected in strains with baseline oprD mutations, and vice versa, confirming these as major mechanisms of resistance emergence. Secondary mutations occurred in lysS or argS, coding for lysyl and arginyl tRNA synthetases, respectively. DISCUSSION: The QSP model well-characterized all bacterial outcomes of the seven strains simultaneously, which fT>MIC could not.

Transition to Whole Genome Sequencing Surveillance: The Impact on National Outbreak Detection and Response for Listeria monocytogenes, Salmonella, Shiga Toxin-Producing Escherichia coli, and Shigella Clusters in Canada, 2015-2021.

Between 2017 and 2019, pulsed-field gel electrophoresis was replaced by whole genome sequencing (WGS) for identifying enteric disease clusters in Canada. The number and characteristics of all clusters of Listeria monocytogenes, Salmonella, Shiga toxin-producing Escherichia coli (STEC), and Shigella spp. between 2015 and 2021 were analyzed. Following the transition to WGS, an increase in the number of Salmonella, STEC, and Shigella clusters was noted, whereas the number of clusters of L. monocytogenes decreased. Unlike previous subtyping methods, WGS provided increased resolution to identify discrete clusters of Salmonella Enteritidis. This led to the identification of a number of outbreaks linked to frozen raw breaded chicken products and ultimately a change in food safety policy to reduce the number of illnesses associated with these products. Other pathogens did not experience a similar increase in the number of outbreaks detected. Although WGS did provide increased confidence in the genetic relatedness of cases and isolates, challenges remained in collecting epidemiological data to link these illnesses to a common source.

Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential.

Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.

Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.

The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g., Interior Alaska and St. Lawrence River have on average 181K and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 kbp and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g., amhby).

Whole genome sequencing enhances molecular diagnosis of primary ciliary dyskinesia.

BACKGROUND: Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia. Most cases are inherited recessively, due to variants in >50 genes that result in abnormal or absent motile cilia. This leads to chronic upper and lower airway disease, subfertility, and laterality defects. Given overlapping clinical features and genetic heterogeneity, diagnosis can be difficult and often occurs late. Of those tested an estimated 30% of genetically screened PCD patients still lack a molecular diagnosis. A molecular diagnosis allows for appropriate clinical management including prediction of phenotypic features correlated to genotype. Here, we aimed to identify how readily a genetic diagnosis could be made using whole genome sequencing (WGS) to facilitate identification of pathogenic variants in known genes as well as novel PCD candidate genes. METHODS: WGS was used to screen for pathogenic variants in eight patients with PCD. RESULTS: 7/8 cases had homozygous or biallelic variants in DNAH5, DNAAF4 or DNAH11 classified as pathogenic or likely pathogenic. Three identified variants were deletions, ranging from 3 to 13 kb, for which WGS identified precise breakpoints, permitting confirmation by Sanger sequencing. WGS yielded identification of a de novo variant in a novel PCD gene TUBB4B. CONCLUSION: Here, WGS uplifted genetic diagnosis of PCD by identifying structural variants and novel modes of inheritance in new candidate genes. WGS could be an important component of the PCD diagnostic toolkit, increasing molecular diagnostic yield from current (70%) levels, and enhancing our understanding of fundamental biology of motile cilia and variants in the noncoding genome.

Whole-genome sequencing identifies novel genes for autism in Chinese trios.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with high genetic heritability but heterogeneity. Fully understanding its genetics requires whole-genome sequencing (WGS), but the ASD studies utilizing WGS data in Chinese population are limited. In this study, we present a WGS study for 334 individuals, including 112 ASD patients and their non-ASD parents. We identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding regions. By integrating these variants with an association model, we identified 33 potential risk genes (P<0.001) enriched in neuron and regulation related biological process. Besides the well-known ASD genes (SCN2A, NF1, SHANK3, CHD8 etc.), several high confidence genes were highlighted by a series of functional analyses, including CTNND1, DGKZ, LRP1, DDN, ZNF483, NR4A2, SMAD6, INTS1, and MRPL12, with more supported evidence from GO enrichment, expression and network analysis. We also integrated RNA-seq data to analyze the effect of the variants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased expression. We further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on phenotype. Regarding variants in non-coding regions, a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence, which were mapped to specific genes or regulatory features. The number of de novo variants found in patient was significantly associated with the parents' ages at the birth of the child, and gender with trend. We also identified small de novo structural variants in ASD trios. The results in this study provided important evidence for understanding the genetic mechanism of ASD.

Whole Genome Sequencing of Epizootic Hemorrhagic Disease Virus.

Next-generation sequencing (NGS) technologies are continuously being developed and are becoming a more cost-effective tool for the characterization of viral genomes. Whole genome sequencing of segmented viruses, such as epizootic hemorrhagic disease virus (EHDV), provides insights into the molecular epidemiology as well as such viral evolutionary mechanisms as genetic reassortment. Here, we present a detailed method for obtaining full genome sequence data for EHDV using Illumina technology. The protocol includes details from RNA extraction and purification, the synthesis of cDNA, sequencing library preparation, to genome assembly.

Imputation strategies for low-coverage whole-genome sequencing data and their effects on genomic prediction and genome-wide association studies in pigs.

The uncertainty resulting from missing genotypes in low-coverage whole-genome sequencing (LCWGS) data complicates genotype imputation. The aim of this study is to find out an optimal strategy for accurately imputing LCWGS data and assess its effectiveness for genomic prediction (GP) and genome-wide association study (GWAS) on economically important traits of Large White pigs. The LCWGS data of 1 423 Large White pigs were imputed using three different strategies: (1) using the high-coverage whole-genome sequencing (HCWGS) of 30 key progenitors as the reference panel (Ref_LG); (2) mixing HCWGS of key progenitors with LCWGS (Mix_HLG) and (3) self-imputation in LCWGS (Within_LG). Additionally, to compare the imputation effects of LCWGS, we also imputed SNP chip data of 1 423 Large White pigs to the whole-genome sequencing level using the reference panel consisting of key progenitors (Ref_SNP). To evaluate effects of the imputed sequencing data, we compared the accuracies of GP and statistical power of GWAS for four reproductive traits based on the chip data, sequencing data imputed from chip data and LCWGS data using an optimal strategy. The average imputation accuracies of the Within_LG, Ref_LG and Mix_HLG were 0.9893, 0.9899 and 0.9875, respectively, which were higher than that of the Ref_SNP (0.8522). Using the imputed sequencing data from LCWGS with the Ref_LG imputation strategy, the accuracies of GP for four traits improved by approximately 0.31-1.04% compared to the chip data, and by 0.7-1.05% compared to the imputed sequencing data from chip data. Furthermore, by using the sequence data imputed from LCWGS with the Ref_LG, 18 candidate genes were identified to be associated with the four reproductive traits of interest in Large White pigs: total number of piglets born - EPC2, MBD5, ORC4 and ACVR2A; number of piglets born healthy - IKBKE; total litter weight of piglets born alive - HSPA13 and CPA1; gestation length - GTF2H5, ITGAV, NFE2L2, CALCRL, ITGA4, STAT1, HOXD10, MSTN, COL5A2 and STAT4. With the exception of EPC2, ORC4, ACVR2A and MSTN, others represent novel candidates. Our findings can provide a reference for the application of LCWGS data in livestock and poultry.

Whole-genome resequencing identifies candidate genes associated with heat adaptation in chickens.

The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.

The mediating role of SARS-CoV-2 variants between income and hospitalisation due to COVID-19: A period-based mediation analysis.

The mechanisms facilitating the relationship between low income and COVID-19 severity have not been partitioned in the presence of SARS-CoV-2 variants of concern (VOC). To address this, we used causal mediation analysis to quantify the possible mediating role infection with VOC has on the relationship between neighbourhood income (exposure) and hospitalisation due to COVID-19 among cases (outcome). A population-based cohort of 65,629 individuals residing in British Columbia, Canada, was divided into three periods of VOC co-circulation in the 2021 calendar year whereby each period included co-circulation of an emerging and an established VOC. Each cohort was subjected to g-formula mediation techniques to decompose the relationship between exposure and outcome into total, direct and indirect effects. In the mediation analysis, the total effects indicated that low income was associated with increased odds of hospitalisation across all periods. Further decomposition of the effects revealed that income is directly and indirectly associated with hospitalisation. The resulting indirect effect through VOC accounted for approximately between 6 and 13% of the total effect of income on hospitalisation. This study underscores, conditional on the analysis, the importance of addressing underlying inequities to mitigate the disproportionate impact on historically marginalised communities by adopting an equity lens as central to pandemic preparedness and response from the onset.

Isolation and characterization of Leptospira licerasiae in Austrian swine - a first-time case report in Europe.

BACKGROUND: Leptospiraceae comprise a diverse family of spirochetal bacteria, of which many are involved in infectious diseases of animals and humans. Local leptospiral diversity in domestic animals is often poorly understood. Here we describe the incidental detection of Leptospira (L.) licerasiae in an Austrian pig. CASE PRESENTATION: During an experiment to characterize the pathogenesis of L. interrogans serovar Icterohaemorrhagiae in pigs, cultivation of a urine sample from a non-challenged contact pig resulted in growth of a spirochetal bacterium that tested negative for pathogenic Leptospira (LipL32 gene). PCR, Sanger sequencing and standard serotyping further confirmed that the recovered isolate was clearly different from the challenge strain L. interrogans serovar Icterohaemorrhagiae used in the animal experiment. Whole genome sequencing revealed that the isolate belongs to the species L. licerasiae, a tropical member of the Leptospiraceae, with no prior record of detection in Europe. CONCLUSIONS: This is the first report describing the occurrence of L. licerasiae in Europe. Since L. licerasiae is considered to have intermediate pathogenicity, it will be important to follow the geographical distribution of this species and its pathogenic and zoonotic potential in more detail.