Whole Genome Sequencing Research Articles

Full Genomic Sequence of the HLA-DQB1*06:304N Allele Identified by Next Generation Sequencing.

The full-length sequence of HLA-DQB1*06:304N covers the 5'-untranslated region (UTR), all introns and exons, and the 3' UTR.

Comprehensive genomic analysis and selection signature detection in endangered Beigang pigs using whole-genome sequencing data.

The Beigang pig was recently identified as one of the endangered breeds during a Chinese indigenous pig genetic resource survey. The Beigang breed is notable for its remarkable roughage tolerance and high reproductive capacity according to historical records. Morphologically, the Beigang pig resembles many indigenous pigs in eastern China, especially in its large ears. This makes the Beigang pig a valuable reference for studying the genetic mechanisms on large ear size in pigs. However, there is currently a lack of clear understanding regarding the genetic structure and inbreeding levels of the Beigang pig population. This study used whole-genome sequencing data from Beigang pig (N = 145 pigs) and integrated genetic information from commercial pigs and indigenous pigs in eastern China to conduct a comprehensive analysis of the Beigang pig's genetic structure. Three selection signal detection methods-runs of homozygosity, fixation index, and integrated haplotype score-were employed to explore the differences in genomic selection signatures between Beigang pig and other pig populations. Additionally, we used a public project for regulatory variants discovery and molecular phenotype prediction in farm animal species called FarmGtex to explore the expression of three genes (WIF1, LEMD3, and MSRB3) related to ear size in Beigang pig. This research identified five homozygous variant sites in the WIF1 gene as important candidate loci potentially influencing ear size in Beigang pig. The results indicate that the Beigang pig holds a unique status among Chinese indigenous pigs, characterized by high genetic diversity and low levels of inbreeding. The study also revealed that WIF1 may play a significant role in influencing ear size in this breed. These findings contribute to a deeper understanding of the population structure and genetic characteristics of Beigang pig.

NDM-5-plasmid diversity in multiple international high-risk Escherichia coli clones associated with canine and feline extraintestinal infections.

NDM-5-producing Escherichia coli are the predominant carbapenemase producers of medical and public health importance. The global spread of blaNDM-5-containing plasmids in high-risk E. coli clones has been primarily documented in humans and increasingly reported in animals and the environment. Here, we used whole-genome sequence analysis to describe the genetic diversity of 16 high-risk NDM-5-producing E. coli strains, with a variety of NDM-5 plasmids, isolated from dogs and cats with extraintestinal infections in Thailand between 2017 and 2021. The strains belonged to sequence type (ST) 410 (n = 8), ST354 (n = 3), ST648 (n = 2), ST361 (n = 1), ST617 (n = 1), and ST641 (n = 1). The ST641 strain carried blaNDM-5 on an IncX3 plasmid, while blaNDM-5 was localized on single-replicon or multi-replicon IncF plasmids in other STs. Non-conjugative F1:A1:B49 NDM-5 plasmids were limited to ST410 strains. They contained blaNDM-5 associated with the IS26-bounded complex class 1 integron (Int1) with dfrA17-aadA5-qacEΔ1-sul1 cassette array that shared similarities to nearly identical structures with the plasmids of ST410 strains from humans in Thailand and Myanmar. Conjugative IncFII (F2:A-:B-) NDM-5 plasmids containing Int1 with dfrA12-aadA2-qacEΔ1-sul1 cassette array were present in ST354 and ST648, and heterogeneous plasmid STs of conjugative multi-replicon IncF NDM-5 plasmids were found in ST361, ST410, ST617, and ST648. The blaNDM-5 elements mobilized by IS26 were shared among various IncF plasmids in high-risk E. coli clones but were conserved within the endemic E. coli ST410, representing the predominant lineage in Southeast Asian countries. Dogs and cats can develop infections with NDM-5-producing E. coli, posing the risk of further disseminating carbapenemase in veterinary settings and the community. This emphasizes the need to implement infection control and antimicrobial resistance surveillance programs in veterinary settings.

Multiple mechanisms mediate aztreonam-avibactam resistance in Klebsiella pneumoniae: Driven by KPC-2 and OmpK36 mutations.

Aztreonam-avibactam (ATM-AVI) is a promising β-lactam/β-lactamase inhibitor combination with an antimicrobial spectrum covering serine carbapenemase- or metallo-β-lactamase-producing Enterobacterales. Although ATM-AVI has not been widely used in clinical practice, resistance to it in Escherichia coli has been widely reported. In this study, we investigated an ATM-AVI-resistant Klebsiella pneumoniae strain, designated as 1705R, derived from K. pneumoniae ATCC BAA-1705 by induction, with a minimal inhibitory concentration of 128 µg/mL. The 1705R strain contained two copies of the blaKPC-2 variant, which encodes for a K. pneumoniae carbapenemase (KPC) variant with a Ser109Pro substitution, as well as a premature termination in OmpK36 and OmpK35 porins. This KPC variant decreased susceptibility to ATM-AVI by four-fold and demonstrated a reduced affinity for ATM and AVI in molecular docking analysis. In porin-deficient strains harbouring this KPC variant, ATM-AVI susceptibility was further diminished, exhibiting a 32-fold reduction. Whole-genome sequencing revealed that the transposition of Tn4401 carrying blaKPC from the IncFIB/FIIK plasmid into the ColRNAI plasmid produced a second copy of blaKPC. Quantitative polymerase chain reaction revealed that the copy number of blaKPC and its carrier plasmid increased, which significantly up-regulated their mRNA expression. Overexpression of the AcrAB-TolC efflux pump may also be associated with high levels of ATM-AVI resistance. Furthermore, collateral susceptibility and costs of growth and biofilm formation developed after the acquisition of ATM-AVI resistance. This study demonstrates that multiple molecular mechanisms collectively contribute to ATM-AVI resistance in K. pneumoniae 1705R strain, which may represent a mode of resistance to ATM-AVI.

Plasma shallow whole-genome sequencing profiling in patients with RAS WT metastatic colorectal cancer (mCRC) undergoing first-line anti-EGFR therapy.

214 Background: Acquired resistance (AR) to first-line (1L) chemotherapy (CT) + anti-EGFR inhibitors is a major challenge in the management of RAS WT mCRC patients (pts). While AR in later lines has been explained with point mutations in the EGFR pathway, its real mechanisms in 1L remain poorly understood. Tumor molecular biology can be dynamically studied through circulating tumor DNA (ctDNA) analysis, a real-time, non-invasive approach to detect AR. In this context, we conducted the multicenter prospective PLATFORM-B study, which enrolled 100 RAS WT mCRC pts receiving 1L CT + cetuximab across 15 Spanish Medical Oncology Departments, alongside 30 RAS MUT pts (control) treated with 1L CT + bevacizumab. Peripheral blood samples have been collected at baseline (BL), week 8, and disease progression (PD). Next-generation sequencing analysis (Ion S5 system) of ctDNA at PD revealed AR mutations in only 10% of pts, suggesting that alterations in the EGFR pathway may only partially explain AR in 1L. Therefore, we conducted shallow whole-genome sequencing (shWGS) to further characterize genomic profiles possibly related with novel mechanisms of AR. Methods: Baseline and PD samples with sufficient remaining plasma were considered for this analysis. shWGS was performed with a coverage ranging 0.5X to 2.0X and analyzed using ichorCNA pipeline to evaluate various genomic characteristics such as copy number alterations (CNA), tumor fraction (TF), subclonal fraction (SF), and ploidy. Molecular results were correlated to clinical-pathological features and outcomes. Results: Overall, 35 mCRC pts (27 RAS WT and 8 RAS MUT ) were included in the study. At BL ( N = 26), median TF (mTF) was 0.19, median ploidy 2, median SC fraction 0.5, median SC genome fraction 0.21, and median subclonal CNA fraction 0.41. At PD ( N = 33), mTF was 0.08, median ploidy 2, median SC fraction 0.5, median SC genome fraction 0.17, and median subclonal CNA fraction 0.38. Of all the features analyzed, only the TF showed potential prognostic value. At BL, pts with TF levels above the median had poorer overall survival (OS) compared to those with lower levels, approaching statistical significance ( P = .055). At PD, higher TF levels were statistically significantly associated with worse OS ( P = .02). No meaningful differences between the RAS WT and RAS MUT groups were observed. Specific variations in CNA, TF, SF, or ploidy under treatment are being correlated to clinical data to seek for predictive value. Conclusions: This preliminary analysis of the PLATFORM-B using shWGS showed the prognostic value of TF. Further analyses are undergoing to better understand the molecular landscape of acquired resistance to 1L anti-EGFR-based therapy in RAS WT mCRC pts.

Emergence of a blaNDM-5-carrying extensively drug-resistant Enterobacter cloacae ST1718 in Saudi Arabia: Insights from comprehensive genome analysis.

Patients with severe COVID-19 may require intensive care unit (ICU) admission to manage life-threatening complications. However, ICU admission is associated with an increased risk of acquiring nosocomial infections caused by multidrug-resistant (MDR) bacteria, particularly carbapenem-resistant Enterobacterale (CRE). Enterobacter cloacae complex (ECC), a group of closely related species including Enterobacter cloacae, is a common cause of healthcare-associated infections (HAIs). The study conducted a comprehensive genomic analysis of an extensively drug-resistant (XDR) E. cloacae strain (ECloa-JZ71) isolated from the blood of a critically ill COVID-19 patient in Jazan, Saudi Arabia. ECloa-JZ71 exhibited resistance to multiple antimicrobial agents, except for amikacin, gentamycin, and fosfomycin. Whole-genome sequencing revealed that ECloa-JZ71 had a rarely reported sequence type, ST1718. Resistance to β-lactam antibiotics was primarily mediated by the genes blaCMH-3, blaTEM-1B, blaLAP-2, and blaNDM-5. The strain was found to harbor IncFIB(pECLA) and IncX3 plasmid replicons, with the latter encoding the blaNDM-5 gene. The IncX3 plasmid was identified as a significant contributor to the dissemination of the blaNDM-5 gene among Enterobacterale species The coexistence of blaNDM-5 and other carbapenem-hydrolyzing enzymes explains the reduced efficacy of β-lactam drugs in ECloa-JZ71. The coexistence of blaNDM-5 and other carbapenem-hydrolyzing enzymes explains the reduced efficacy of β-lactam drugs in ECloa-JZ71. The presence of specific virulence factors along with carbapenem resistance in ECloa-JZ71 may enhance its pathogenesis, complicating treatment and control efforts. The findings highlight the need for monitoring the spread of multidrug-resistant clones, conducting molecular epidemiological studies, and implementing effective infection control measures to prevent the dissemination of antimicrobial resistance in healthcare settings.

Acute Vestibular Syndrome Unmasking an RFC1-Spectrum Disorder.

Since the discovery of biallelic pentanucleotide expansions in RFC1 as the cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome, a wide and growing clinical spectrum has emerged. In this article, we report a man with acute vestibular syndrome that likely unmasked a RFC1-spectrum disorder. Detailed clinical evaluation, neuroimaging, nerve conduction studies, evaluation of vestibular function, and short-read whole-genome sequencing and targeted long-read adaptive sequencing were performed. Clinical follow-up after acute vestibular syndrome revealed bilateral vestibular areflexia and a gait abnormality with the Scale for the Assessment and Rating of Ataxia score of 5. Brain MRI was normal while 2 electroneurography tests did not show neuropathy. However, severe cough spells raised the suspicion of a RFC1-spectrum disorder. WGS screening detected a recessive intronic pentanucleotide expansion in RFC1, which was verified and sized using long-read adaptive sequencing. This is an unusual presentation; oscillopsia after an acute vestibular syndrome and cough spells should alert clinicians about a RFC1-spectrum disorder, even in the absence of neuropathy and neuroradiologic abnormalities.

Severe acute respiratory syndrome coronavirus 2 variants in patients with coronavirus disease 2019 and environmental sampling from the hospital and market during the coronavirus disease 2019 pandemic in Thailand

Limited genomic surveillance data is available for SARS-CoV-2 in Thailand during the second and third wave outbreaks, including both patient and environmental samples. This study investigated the presence of SARS-CoV-2 RNA in patient samples, on frequently touched surfaces, and in environmental swab samples (EVSs) collected from urban markets in Bangkok between April 2021 and August 2022. A total of 78,159 nasopharyngeal swab samples from patients and 327 environmental swab samples from hospital and market settings were collected. SARS-CoV-2 RNA was detected in 3,706 of 78,159 patient samples and one of 327 environmental samples using real-time RT-PCR. In total, 54 patient samples and an environmental sample were subjected to whole-genome sequencing and mass array genotyping, respectively. Only 46 samples passed the quality assessment based on the analysis criteria. The lineages detected included B.1.1.529 (2 samples), B.1.1.7 (15 samples), B.1.351 (3 samples), B.1.36.16(6 samples), B.1.617.2 (1 sample), AY.102 (1 sample), AY.4 (11 samples), AY.25 (1 sample), BA.1 (1 sample), BA.1.1 (3 samples), and BA.2 (2 samples). The phylogenetic analysis of the viral genome sequences revealed similar lineages during this study period.

A Chromosome-Level Genome Sequence Reveals Regulation of Salt Stress Response in Mesembryanthemum crystallinum.

Salt stress disturbs plant growth and photosynthesis due to its toxicity. The ice plant Mesembryanthemum crystallinum is a highly salt-tolerant facultative crassulacean acid metabolism (CAM) plant. However, the genetic basis of the salt tolerance mechanisms in ice plants remains unclear. In this study, we constructed a chromosome-level whole-genome sequence of the ice plant and performed transcriptome analysis of the effects of salt treatment on the leaves. After 24-hour 500 mM NaCl treatment to the roots, 1100 and 1394 genes, including CAM pathway, glycolysis, and inositol metabolism, were up- and down-regulated in the leaves, respectively. Salt treatment also influenced the abscisic acid (ABA) signaling components, including genes from the PYRABACTIN RESISTANCE1 (PYR1) family and the PROTEIN PHOSPHATASE 2CA (PP2CA) family. We detected the induction of the genes encoding various ion transporters after salt treatment. The expression of most v-ATPase subunits is induced, leading to vacuolar acidification, which facilitates sodium ion sequestration in the vacuoles. Additionally, some genes encoding metal ion transporters, including the genes from the ZIP family and NRAMP family, were induced by salt treatment, accompanied by the accumulation of iron, zinc, and copper ions in the leaves. Cis-motif enrichment analysis revealed that ABRE-like motifs and MYB-binding-like motifs were enriched in the upstream sequences of genes that were either up-regulated or down-regulated by salt. In conclusion, this study highlights how salt treatment induces drastic and rapid transcriptomic changes and unveils the ice plant's genomic foundation. Our resources provide further insights into the regulation of salt tolerance in the ice plants.

Chapter 5: The roles of genetics in primary hyperparathyroidism.

Around 10% of cases of primary hyperparathyroidism are thought to be genetic in origin, some of which are part of a syndromic form such as multiple endocrine neoplasia types 1, 2A or 4 or hyperparathyroidism-jaw tumor syndrome, while the remainder are cases of isolated familial primary hyperparathyroidism. Recognition of these genetic forms is important to ensure appropriate management according to the gene and type of variant involved, but screening for a genetic cause is not justified in all patients presenting primary hyperparathyroidism. The indications for genetic analysis have made it possible to propose a decision tree that takes into account whether the presentation is familial or sporadic, syndromic or isolated, patient age, and histopathological type of parathyroid lesion. Thus, the first consensus recommendation is to propose genetic screening to any patient with a familial form of primary hyperparathyroidism (≥2 1st or 2nd degree relatives) or in syndromic presentation or a sporadic isolated presentation if the patient is under 50 years of age, or over 50 with a recurrent or multi-glandular form, carcinoma, atypical parathyroid tumor and/or loss of parafibromin expression. The panel of genes currently recommended for first-line treatment comprises MEN1, CDKN1B, CDC73, CASR, GNA11, AP2S1 and GCM2. Other genes may also be involved in familial primary hyperparathyroidism, but in a much more rarely and less consistently. The second recommendation is to propose genetic screening, up to and including whole-genome sequencing in the event of inconclusive panel analysis, to patients with proven familial primary hyperparathyroidism and/or pediatric onset. The role of the genetic practitioner is to interpret the sequencing data by categorizing the variants into 5 classes of pathogenicity. The aim of genetic analysis is to identify the genetic variant involved in the patient's phenotype, in order to make or refute a diagnosis of hereditary primary hyperparathyroidism, and to adapt management and monitoring. Appropriate genetic counseling should then be provided for patient and family.

Improvement of the accuracy of breeding value prediction for egg production traits in Muscovy duck using low-coverage whole-genome sequence data

Improvement of the accuracy of breeding value prediction for egg production traits in Muscovy duck using low-coverage whole-genome sequence data

A STUDY OF IMPACT OF CBNAAT IN THE DIAGNOSIS OF TUBERCULOSIS AT A RURAL BASED TERTIARY CARE TEACHING CENTRE IN INDIA

Introduction: India has the highest number of TB cases in the world and it kills more adults than any other infectious disease. The Whole genome sequencing (WGS) and its utility product the GeneXpert MTB/RIF was adopted as integral part of NTEP for quick diagnosis of MTB with resistance to rifampine. Aim & Objective: To assess the impact of CBNAAT on the other modalities i.e. smear microscopy and conventional culture and sensitivity. Material Method: This is a prospective observational, cohort study conducted at RDGMC Ujjain, MP with an enrollment of 200 cases (150 PTB and 50 EPTB) that underwent all the three investigations to fulfill inclusion criteria after a prior approval of the ethic committee and patients consent. Result: Most the cases were in productive age group of and about 66% cases had low BMI and required nutritional support. The Microscopic sensitivity and specificity were 43% and 100% as against 97% and 90% that of CBNAAT. Discussion: The yield of CBNAAT is superior and promising in smear negative, EPTB and immuno-compromised cases being of pauci bacilli status. A meticulous investigation is required for those cases that are smear positive but CBNAAT negative cases for the presence of NTM infection. A CBNAAT reporting that of very low and indeterminate is to be repeated and supportive/ or additional clinical and or radiologic findings should be incorporated. Conclusion: CBNAAT should be mandatory for the entire suspect TB cases especially for EPTB, children and immune-compromised individuals. CBNAAT has certain limitations i.e. it cannot detect drug resistance other than rifampin and non tubercular mycobacterium (NTM). The best approach for diagnosis of EPTB is to combined CBNAAT, histopathology and AFB culture. However the conventional culture and sensitivity with LJ media is gold standard cannot be over looked.

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia

Epigenetic state and gene expression remain stable after CRISPR/Cas-mediated chromosomal inversions.

The epigenetic state of chromatin, gene activity and chromosomal positions are interrelated in plants. In Arabidopsis thaliana, chromosome arms are DNA-hypomethylated and enriched with the euchromatin-specific histone mark H3K4me3, while pericentromeric regions are DNA-hypermethylated and enriched with the heterochromatin-specific mark H3K9me2. We aimed to investigate how the chromosomal location affects epigenetic stability and gene expression by chromosome engineering. Two chromosomal inversions of different sizes were induced using CRISPR/Cas9 to move heterochromatic, pericentric sequences into euchromatic regions. The epigenetic status of these lines was investigated using whole-genome bisulfite sequencing and chromatin immunoprecipitation. Gene expression changes following the induction of the chromosomal inversions were studied via transcriptome analysis. Both inversions had a minimal impact on the global distribution of histone marks and DNA methylation patterns, although minor epigenetic changes were observed across the genome. Notably, the inverted chromosomal regions and their borders retained their original epigenetic profiles. Gene expression analysis showed that only 0.5-1% of genes were differentially expressed genome-wide following the induction of the inversions. CRISPR/Cas-induced chromosomal inversions minimally affect epigenetic landscape and gene expression, preserving their profiles in subsequent generations.

Complete genome sequence of Bradyrhizobium lupini LLZ14, a nitrogen-fixing and plant growth-promoting bacterium.

In this study, we present the complete genome of Bradyrhizobium lupini LLZ14, a nodule-forming bacterium isolated from Lupinus luteus root nodules with high plant growth-promoting abilities. This genome contains genes predicted to be involved in plant stress tolerance and growth promotion, including auxin production, phosphatase, and 1-aminocyclopropane-1-carboxylate deaminase.

Genome sequence of Providencia rettgeri ZAPR22R, isolated from calla lily in China.

Here, we present the complete genome sequence of Providencia rettgeri strain ZAPR22R, isolated from the petiole and tuber of calla lily (Zantedeschia hybrida), infected with soft rot. The genome consists of a single chromosome (4,528,722 bp) with a G+C content of 41.1%.

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata).

Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (FST) and absolute divergence (dXY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.

A TTPA deletion is associated with Retinopathy with Vitamin E Deficiency (RVED) in the English Cocker Spaniel Dog.

Retinopathy with Vitamin E Deficiency (RVED) is a familial disease in the English Cocker Spaniel (ECS) dog breed. Ophthalmic abnormalities observed in RVED-affected ECS include lipofuscin granule deposition within the tapetal fundus and subsequent retinal degeneration resulting in visual deficits. Affected dogs may also exhibit neurological signs that include ataxia and hindlimb proprioceptive deficit. In all cases, circulating plasma concentrations of α-tocopherol are low. This study sought to investigate the genetic basis of RVED in the ECS breed. We undertook a genome-wide association study comprising 30 ECS with normal fundic examinations aged 6 years or older (controls) and 20 diagnosed with RVED (cases) and identified a statistically associated signal on chromosome 29 (Praw = 1.909×10-17). Whole genome sequencing (WGS) of two cases identified a 102bp deletion in exon 1 of the Alpha Tocopherol Transfer Protein gene (TTPA), truncating the protein by 34 amino acids. The c.23_124del variant segregated with RVED in a total of 30 cases and 43 controls. Variants in TTPA are causal for Ataxia with Vitamin E Deficiency (AVED) in humans which is a phenotypically similar disease to RVED. The identification of the canine variant is extremely significant as the availability of a DNA test will allow for identification of presymptomatic dogs and early therapeutic intervention which may prevent development of retinopathy and improve neurological signs. Breeders can also use the DNA test to efficiently eradicate the disease from this breed.

Molecular epidemiology of chicken and turkey parvovirus in Turkiye: high risk, genetic recombination signals, and first complete genome analysis.

The aim of this study was to detect chicken parvovirus (ChPV) and turkey parvovirus (TuPV) on Turkish poultry farms and examine the molecular epidemiology of these viruses. In 2023, a total of 1,060 fecal samples were collected from 76 broiler farms and 30 turkey farms across various regions of Turkiye. The overall positivity rate was 72.3% (55/76) in broiler flocks and 70% (21/30) in turkey flocks. Among these, the positivity rate was 35% (7/20) in birds showing no signs of enteritis. The findings of this study suggest that, depending on the genetic variability of regional strains or the viral load, nested-PCR-based methods may prove more effective than single-step PCR for detecting ChPV and TuPV cases. Therefore, it is recommended to incorporate nested PCR in molecular epidemiological studies to minimize the risk of overlooking positive cases. Phylogenetic analysis of the VP1, VP2, and complete genome sequences of TUR/2023/ChPV and TR/2023/TuPV revealed that both strains clustered with American strains in distinct lineages. Analysis using the recombination detection programs RDP4.0 and SimPlot 3.5.1 strongly suggested that TUR/2023/ChPV may be a recombinant of strains from China and Brazil. Despite the observed genetic variability in the VP2 protein, an examination of B-cell epitopes showed a high degree of similarity between ChPV and TuPV strains. This study represents the first documentation of the emergence and prevalence of TuPVs in Turkiye, providing complete genome sequences for both ChPV and TuPV. Given the high prevalence and genetic diversity of these viruses and their presence in clinically asymptomatic birds, it is crucial for stakeholders in the poultry industry to implement regular flock screenings for these and similar viral pathogens. Proactive measures like these are essential for mitigating the economic impact of these important pathogens and developing effective preventive strategies.

Genetic diversity and virulence of Bacillus cereus group isolates from bloodstream infections.

Bacillus cereus catheter-related bloodstream infections (CRBSIs) are an increasing concern in Japanese hospitals. Although their clinical characteristics have been explored, the genetic relationships and virulence profiles of B. cereus isolates from CRBSIs remain understudied. Here, using advanced genomic techniques, we investigated the genetic diversity, phylogenetic relationships, and virulence profiles of B. cereus isolates from patients with bloodstream infections. We analyzed 28 B. cereus group strains isolated from blood samples at the University of Tokyo Hospital between 2005 and 2017 using whole-genome sequencing, core-genome single-nucleotide polymorphism (SNP) typing, and virulence gene profiling. Core-genome SNP analysis revealed significant genetic diversity among the isolates, suggesting multiple independent sources of infection. The isolates predominantly belonged to panC clades III and IV, with distinct virulence gene profiles. All panC clade III isolates contained hbl operon genes, whereas four isolates from clade IV harbored cereulide synthetase genes (cesABCD). One isolate possessed a capsule gene operon (capBCADE), a rare finding among clinical B. cereus strains. Biofilm formation ability was observed in 50% of catheter-related isolates, although this ability was not significantly different from that of the noncatheter-related isolates.IMPORTANCEThis study provides novel insights into the genetic diversity and virulence potential of B. cereus strains causing bloodstream infections in a Japanese hospital setting. These findings suggest diverse infection pathways and highlight the importance of continuous molecular epidemiological surveillance for effective infection control.