Genotype Analysis Research Articles

Clinical, pathological, and genotypic analysis of infectious bronchitis virus in broiler chickens in the Abu Dhabi Emirate, United Arab Emirates

BackgroundInfectious Bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a significant contagious respiratory disease in the poultry industry. The emergence of new variants represents a global challenge for the diagnosis and control of the disease. Despite vaccination efforts in poultry farms in the Abu Dhabi Emirate, United Arab Emirates (UAE), outbreaks continue to occur, raising concerns about the efficacy of vaccination protocols and the potential emergence of new viral strains. This study aims to provide information on clinical, pathological, and genotypes of IBV detected within the Abu Dhabi Emirate, during 2022–2023.MethodsEpidemiological data were collected from twelve suspected IB outbreaks across seven broiler farms located in the Abu Dhabi Emirate. The cases were investigated through clinical and pathological examinations and Forty-six samples, including lung, spleen, kidney tissues, and oro-cloacal swabs, were collected for further analysis. The virus was detected by RT-qPCR assay, genotyping was determined by phylogenetic analysis of the Spike (S)-1 gene, and differentiation between field and vaccine strains was determined by comparing their sequences.ResultsThe age of the affected flocks varies from 2 to 5 weeks. The highest morbidity, mortality and case fatality rates were 36, 33, and 95%, respectively. Necropsy examination revealed characteristic respiratory and renal pathological lesions. Phylogenetic analysis revealed a co-circulation of three lineages of IBV genotype GI-13 or 4/91 serotype (81.8%), GI-1 or Massachusetts serotype (9.1%) and GI-23 or Middle East serotype (9.1%). Approximately 90.9% of the strains classified within GI-1 and G1-13 lineages are 99 to 100% identical to 4/91 and Mass serotypes, respectively, and are considered as vaccine strains. Two strains (9.1%) classified within GI-23 lineage have a < 99% identity to the 4/91 and Mass serotypes vaccine strains and are considered as filed strains.ConclusionCo-circulation of three IBV lineages (GI-13, GI-1, and GI-23) in the Abu Dhabi broiler flocks showing IB symptoms were detected. This complex scenario of different IBV lineages circulation may account for the persistent outbreaks despite vaccination efforts. The results of the study are crucial for optimum IB vaccination and monitoring strategies or designing new vaccines based on local IBV field strains.

Nationwide carrier screening for congenital adrenal hyperplasia: integrated approach of CYP21A2 pathogenic variant genotyping and comprehensive large gene deletion analysis

BackgroundCongenital Adrenal Hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD CAH) is an autosomal recessive disorder resulting from pathogenic variants in the CYP21A2 gene. The disorder exhibits variable clinical severity, with the classical form manifesting as salt-wasting crisis in neonates, while inducing ambiguous genitalia in females and precocious puberty in males through simple virilization. Identifying at-risk couples during the preconception stage holds significance for optimizing reproductive choices. Methods: This study included 204 unrelated preconception individuals undergoing carrier screening. A robust molecular approach was devised for rapid detection of nine prevalent CYP21A2 pathogenic variants, utilizing Amplification-Refractory Mutation System (ARMS) PCR and mass spectrometry (MS) genotyping. Complementary quantitative real-time PCR (qPCR) and PCR-based Restriction Fragment Length Polymorphism (PCR-based RFLP) assays were employed for comprehensive gene deletion analysis. The concordance of pathogenic variant detection between ARMS-PCR and MS, as well as the consistency observed in molecular insights from qPCR and PCR-based RFLP, fortified the accuracy of our methodologies. Results: Our combined method could detect common pathogenic variants and large gene deletions with high concordance between ARMS-PCR, MS genotyping, qPCR, and PCR-based RFLP assays. Remarkably, two carriers exhibited significant large-scale deletions, while another manifested a carrier state due to minor-scale gene conversion. The estimated carrier frequency in our cohort using these methods was approximately 1 in 65 individuals. Conclusions: The methods used for 21-OHD CAH carrier screening offer a reliable, swift, and cost-effective approach for detecting common pathogenic variants and large deletions. Despite some limitations, such as the inability to detect all rare mutations, the techniques provide a practical solution for carrier screening, with an estimated carrier frequency of 1 in 65 in our study population. These findings support the potential adoption of these methods in national carrier screening programs, offering a practical balance between efficiency and affordability.

Association of single nucleotide polymorphisms rs7459185 of the HSPβ1 gene and the risk of hematological toxicity in lung cancer.

Hematological toxicities (HTs) in lung cancer (LCa) may compromise the delivery of Radio-Chemotherapy (RTCT), and consequently affect the control of the disease. The aim of this study is to evaluate the association of Single nucleotide polymorphisms (SNPs) with HT. In this prospective multicentre study, 264 patients with primary LCa treated with RTCT between 2012 and 2018 were included. Genotyping analysis was performed on DNA isolated from peripheral blood samples by real-time polymerase chain reaction (PCR) using TaqMan. HTs were scored using the Common Toxicity Criteria (CTCAE) version 5.0. An increased risk of HT≥grade 2 was observed in patients with the GG genotype of the SNP rs7459185 (HSPβ1) with a hazard ratio (HR) of 1.462 (95%CI 1.054-2.029, p=0.007). Similarly, those patients had an increased risk of overall HT≥grade 3 with a HR of 1.531 (95%CI 1.016-2.30, p=0.007). The patients with the GG genotype experienced an acute lymphopenia≥Grade 3 (HR 1.590 [95%CI 1.004-2.517; p 0.045]) and acute anemia≥Grade 2 (HR 1.886 [95%CI 1.060-3.356; p 0.032]), compared to the GC/CC genotypes. Our findings show a relationship between the functional GG genotypic of the SNP rs7459185 (HSPβ1) and heightened risk the development of HT, including anemia and lymphopenia in patients with LCa. This genetic variant could be utilized as a predictive marker to tailor treatment intensity, contributing to the advancement of individualized therapeutic approaches.

Assessment of Genetic Variability, Correlation and Path Analysis in Bread Wheat (Triticum aestivum L.) Genotypes for Yield and its Attributing Traits

This study investigated the genetic variability and agronomic traits influencing wheat yield across multiple genotypes. Conducted during the 2021-2022 rabi season at the Research Farm of BRD PG College, Deoria, the experiment included 31 treatments and a standard check variety, HD-2967, arranged in a randomized block design (RBD) with three replications. Analysis of variance (ANOVA) revealed significant genetic variation among the genotypes for traits such as Days to 50% Flowering (DF), Days to Maturity (DM), Plant Height (PH), and Grain Yield per Plant (GYP). Genotypic correlation analysis showed significant positive associations between DF and DM, and negative correlations between DF, DM, and GYP, highlighting the complex trade-offs among traits. Traits like Test Weight (TW) and Biological Yield (BY) were positively correlated with GYP, indicating their potential as key selection criteria for breeding. Path coefficient analysis identified DF and Test Weight as having strong direct effects on GYP, while traits such as Plant Height and Number of Grains per Spike had negative impacts. These results provide valuable insights into the genetic and phenotypic relationships that can guide the development of superior wheat genotypes with improved yield potential.

Identifying New Susceptibility Genes of Non-Syndromic Orofacial Cleft Based on Syndromes Accompanied With Craniosynostosis.

Orofacial cleft (OC) can be classified into syndromic orofacial cleft (SOC) and non-syndromic orofacial cleft (NSOC), depending on whether there are other congenital deformities. Craniosynostosis, the premature closure of cranial sutures, is a common phenotype of SOC resulting in abnormal ossification of skull and brain development disorders. Its correlation with OC offers a promising approach to identify susceptibility genes for NSOC by examining causative genes of SOCs with craniosynostosis. This study included 2556 patients with NSOC and 2255 normal controls from western Han Chinese with their genomic DNA samples. We selected 31 causative genes of 34 syndromes with both craniosynostosis and OC as candidate genes and performed quality control. Allelic and genotypic association analyses and haplotype analysis were performed to identify statistically significant single nucleotide polymorphisms (SNPs). In allelic association analysis performed with 1265 qualified SNPs in 20 genes, only rs2239936, located in MYH3 gene, was statistically associated with non-syndromic cleft lip only (NSCLO) (P = 1.70×10-07, OR = 1.33, 95%CI: 1.17-1.52) and non-syndromic cleft palate only (NSCPO) (P = 6.43×10-05, OR = 1.33, 95%CI: 1.16-1.52). The higher frequency of allele G in NSCPO suggesting that minor allele G at rs2239936 will result in an elevated risk of NSCPO. However, rs2239936 only exhibited a statistical association with NSCPO in genotypic association analysis (P = 8.06×10-06) and haplotype analysis (P = 1.43×10-05). This study identified that allele G at rs2239936 in MYH3 gene was significantly associated with NSCPO as a risk factor and MYH3 was a new susceptibility gene for NSCPO in western Han Chinese population.

Intrasporangium zincisolvens sp. nov., A Novel Actinobacterium Isolated from Rhizosphere Soil.

A novel phosphate-solubilizing and zinc-solubilizing actinobacterium strain YIM S08009T was isolated from rhizosphere soil collected from Pinus yunnanensis in Wuliangshan National Nature Reserve, Pu'er City, Yunnan Province, southwest PR China. Cells of strain YIM S08009T were Gram-stain-positive, non-motile, irregular rods to cocci, and formed yellow and white colonies on nutrient agar. Growth was observed at 10-40°C (optimum 25-35°C), pH 6.0-8.5 (optimum 7), and 0-4% (w/v) NaCl (optimum 1%). The cell wall peptidoglycan contained LL-diaminopimelic acid. The whole-cell sugars were mannose, ribose, glucose, and galactose. The predominant menaquinone was MK-8(H4). Major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown lipid, and 3 unknown phospholipids. The predominant fatty acids were iso-C14:0, iso-C15:0, and iso-C16:0. The DNA G + C content was 72.6%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM S08009T belonged to genus Intrasporangium, and was most closely related to Intrasporangium flavum MUSC 78T, with 99.0% 16S rRNA gene sequence similarity. Strain YIM S08009T shared 90.1% orthologous average nucleotide identity (OrthoANI) and 39.8% digital DNA-DNA hybridization (dDDH) with I. flavum MUSC 78T. The genome of strain YIM S08009T contained phosphate-solubilizing genes (SenX3, RegX3, pstSCAB, ugpBAEC, phoA) and zinc-solubilizing genes (znuABC, zupT), and the strain had also demonstrated in vitro phosphorus and zinc solubilization. Based on the genotypic and phenotypic analyses, strain YIM S08009T (= CGMCC 1.60168T = NBRC 116604T = KCTC 59021T) represents a novel Intrasporangium species, for which the name Intrasporangium zincisolvens sp. nov. is proposed.

Ongoing measles outbreak in Romania: Clinical investigation and molecular epidemiology performed on whole genome sequences.

Romania is currently facing a prolonged measles outbreak. The aim of the study was to analyse the circulating human measles virus (HMV) strains by combining whole genome sequencing (WGS) with phylogenetic analysis, with a focus on the haemagglutinin gene. We conducted an observational study in the first five months of 2024, in which 168 patients diagnosed with measles were randomly included. We have evaluated the clinical and epidemiological differences between children and adults. Screening for samples to be sequenced was performed with a commercial kit (PrimerDesign). WGS was done on Illumina MiSeq platform and phylogenetic analysis was performed with ML FastTree. No significant epidemiological and clinical differences between patients in the two age groups were identified. WGS was successfully performed for a number of 124 HMV strains. Genotype analysis indicated all the sequences as D8, except one that was B3. Phylogenetic analysis identified two well supported clusters, suggestive for at least two local transmission networks in Romania. One large transmission network (n = 108) consisted of sequences both from adults and children. Only one sequence from outside Romania (reported in Russia in 2023) clustered within this group. Another small transmission cluster was identified (14 sequences of which 11 from patients infected in the spring of 2024 and three in 2022). A few differences between the two co-circulating viral variants/clusters were observed. The median duration of hospitalisation was 2 days longer for patients in smaller cluster compared to those in the larger one (p = 0.019). Furthermore, these two clusters presented different mutation profiles in the hemagglutinin (HA) and neuraminidase (N) genes with implications for molecular surveillance. The current measles epidemic in Romania is driven mainly by two D8 genotype variants with different mutation profiles and slightly different severity of the disease, highlighting the usefulness of sustained molecular surveillance.

HIV-1 drug resistance and genetic transmission networks among patients with sexually transmitted HIV in Ningxia, China

BackgroundOver the past decade, sexual transmission has become a dominant source of new HIV-1 infection in China. However, very few studies have been conducted to characterize the two sexual transmissions, homosexual and heterosexual transmission. This study was conducted to better understand the relationship between genotypes, drug resistance, and molecular transmission networks in two groups of sexually transmitted HIV-1 in Ningxia, China.MethodsPlasma samples were collected from sexually transmitted HIV/AIDS patients in Ningxia between 2020 and 2021 for RNA extraction followed by HIV-1 genome sequencing, genotype and drug resistance analyses. The TN93 model in HyPhy2.2.4 with 1.25% as the threshold, was used to calculate the gene distance, and Cytoscape3.7.0 was used to generate a visual molecular transmission network.ResultsA total of 269 samples were successfully sequenced, and 10 HIV-1 subtypes were detected. The two most common subtypes were CRF07_BC and CRF01_AE. All 10 subtypes were detected in heterosexually transmitted patients, and 7 subtypes were found in homosexually transmitted patients who were exclusively men sex with men (MSM). The drug resistance rates of heterosexual individuals and MSMs were 45.34 and 33.33%, respectively. Sequences from 120 patients entered the molecular transmission network, forming 35 clusters. The clustering rate for MSM (52.78%) was higher than that of heterosexual individuals (39.13%). Some MSM and HSTs were involved in the same cluster and might act as bridges for transmission between the two populations.ConclusionOur data showed that heterosexually transmitted HIV-1 was more likely to be a drug-resistant virus, whereas MSM was more likely to contract viruses through network connection. It is strongly recommended that resistance testing be conducted before ART to improve effective treatment and reduce the spread of resistant viruses. Molecular networks can help to identify transmission clusters and provide more precise interventions.

Effective Mixed-Type Tissue Crusher and Simultaneous Isolation of RNA, DNA, and Protein from Solid Tissues Using a TRIzol-Based Method

One of the major challenges of studying biomarkers in tumor samples is the low quantity and quality of isolated RNA, DNA, and proteins. Additionally, the extraction methods ideally should obtain macromolecules from the same tumor biopsy, allowing better-integrated data interpretation. In this work, an in-house, low-cost, mixed-type tissue crusher combining blade and beating principles was made and the simultaneous isolation of macromolecules from human cells and tissues was achieved using TRIzol. RT-qPCR, genotyping, SDS-PAGE, and Western blot analysis were used to validate the approach. For tissue samples, RNA, DNA, and proteins resulted in an average yield of 677 ng/mg, 225 ng/mg, and 1.4 µg/mg, respectively. The same approach was validated using cell lines. The isolated macromolecule validation included the detection of mRNA levels of ATP-binding cassette (ABC) transporters through RT-qPCR, genotyping of TNFR1 (rs767455), and protein visualization through SDS-PAGE following Coomassie blue staining and Western blot. This work contributed to filling a gap in knowledge about TRIzol efficiency for the simultaneous extraction of RNA, DNA, and proteins from a single human tissue sample. A low-cost, high yield, and quality method was validated using target biomarkers of multidrug resistance mechanisms. This approach might be advantageous for future biomarker studies using different tissue specimens.

Diversity and Potential Cross-Species Transmission of Rotavirus A in Wild Animals in Yunnan, China.

Rotavirus A (RVA) is the primary enteric pathogen of humans and many other species. However, RVA interspecies transmission remains poorly understood. In this study, we conducted a comprehensive screening and genotyping analysis of RVA in 1706 wild animal samples collected from various regions within Yunnan Province, China. A total of 24 samples, originating from wild boars, rodents, bats, and birds tested positive for RVA. Next generation sequencing and phylogenetic analyses revealed a high degree of genetic diversity and reassortment, particularly for VP4 and VP7. Strains isolated from wild boars and rodents exhibited gene segments with high similarity to those found in humans and other mammalian RVA strains, indicating that RVA may undergo interspecies transmission and reassortment, resulting in novel strains with potential risks for human infection. This study provides critical data for understanding the transmission mechanisms and the RVA host range, and highlights the pivotal role of wildlife in viral evolution and dissemination. These findings have significant implications for public health policies and emphasize the need for enhanced surveillance to prevent interspecies RVA transmission.

Hybridization and diversity of the genus Vandenboschia in Korea insights from morphological, cytological, and genotype analyses

The genus Vandenboschia exhibits significant diversity, driven by complex hybridization events and varying ploidy levels in the natural habitats of Korea, leads to misidentifications that obscure its true distribution and classification. To address this issue, the present study employed morphological, cytological, and genotype analyses to clarify the taxonomical circumscription and distribution patterns of the Vandenboschia radicans complex in Korea. The V. radicans complex in the genus refers to V. radicans and its closely related species and exhibits significant morphological variation, making classification challenging. Previous molecular studies have revealed that it consists of several non-hybrid and hybrid species among them. Through the present study, comprehensive sampling from Jeju and Ulleung Islands identified five distinct taxa from the V. radicans complex: two non-hybrid species (Vandenboschia kalamocarpa and Vandenboschia nipponica), and three hybrids (Vandenboschia × stenosiphon, Vandenboschia × quelpaertensis, and Vandenboschia kalamocarpa × Vandenboschia nipponica × Vandenboschia striata). Notably, hybrids exhibited broader geographic distributions compared to non-hybrid species, which were confined to specific microhabitats. While overlapping morphological traits among the species complicate identification without genetic analysis, rhizome diameter and the width-to-length ratio of the involucre can serve as key morphological traits for distinguishing members of the Vandenboschia radicans complex in Korea. Additionally, cleaved amplified polymorphic sequence (CAPS) markers and cloning techniques were employed for species identification, particularly when morphological traits were inconclusive. These findings highlight the need to integrate genetic tools with traditional taxonomic methods to resolve complex species relationships within Vandenboschia in Korea and emphasize the importance of conservation efforts for geographically restricted and genetically distinct populations.

Genetic dissection of flag leaf morphology traits and fine mapping of a novel QTL (Qflw.sxau-6BL) in bread wheat (Triticum aestivum L.).

Total 60-QRC for FLM traits were detected by meta-genomics analysis, nine major and stable QTL identified by DH population and validated, and a novel QTL Qflw.sxau-6BL was fine mapped. The flag leaf is an "ideotypic" morphological trait providing photosynthetic assimilates in wheat. Although flag leaf morphology (FLM) traits had been extensively investigated through genetic mapping, there is a desire for FLM-related loci to be validated in multi-environments and fine mapping. In order to identify the stable genomic regions for FLM traits, we conducted a meta-genomic analysis based on reports from 2008 to 2024. Experimentally, a doubled haploid (DH) population was used to assess the genetic regions associated with FLM traits in nine environments. The meta-genomic analysis extracted 60 QTL-rich clusters (QRC), 45 of which were verified in marker-trait association (MTA) study. Nine major and stable QTL were found being associated with FLM traits across three-to-seven environments including BLUP, with phenotypic variance explained (PVE) ranging from 5.05 to 34.95%. The KASP markers of the nine QTL were validated (P < 0.005) in more than three environments using a panel of diverse wheat collections from Shanxi Province in China. Two co-located major and stable QTL viz. Qflw.sxau-6B.5 and Qfla.sxau-6B.4 were found novel and contributed to increaseFLW by 12.09-19.21% and FLA by 5.45-13.28%. They also demonstrated high recombination rates in LD analysis based on the resequencing of 145 wheat landmark cultivars. The fine mapping of Qflw.sxau-6BL narrowed it down to a 1.27Mb region as a result of the combined genotypic and phenotypic analysis for secondary mapping population. Comparing to NIL-ND3338, the NIL-LF5064 showed higher FLW by 20.45-27.37%, thousand-grain weight by 1.88-2.57% and grain length by 0.47-2.30% across all environments. The expression analysis of 11 tissues revealed seven highly expressed genes within the fine map region. This study provides a genetic basis for the FLM traits for further map-based cloning of FLW genes in wheat.

Multi-index based analysis of genotype × environment interaction and selection of superior maize (Zea mays L.) hybrids

Multi-index based analysis of genotype × environment interaction and selection of superior maize (Zea mays L.) hybrids

Whole-Genome Sequencing of Resistance, Virulence and Regulation Genes in Extremely Resistant Strains of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a clinically significant opportunistic pathogen, renowned for its ability to acquire and develop diverse mechanisms of antibiotic resistance. This study examines the resistance, virulence, and regulatory mechanisms in extensively drug-resistant clinical strains of P. aeruginosa. Antibiotic susceptibility was assessed using the Minimum Inhibitory Concentration (MIC) method, and whole-genome sequencing (WGS) was performed on the Illumina NovaSeq platform. The analysis demonstrated a higher prevalence of virulence genes compared to resistance and regulatory genes. Key virulence factors identified included secretion systems, motility, adhesion, and biofilm formation. Resistance mechanisms observed comprised efflux pumps and beta-lactamases, while regulatory systems involved two-component systems, transcriptional regulators, and sigma factors. Additionally, phenotypic profiles were found to correlate with resistance genes identified through genotypic analysis. This study underscores the significant resistance and virulence of the clinical P. aeruginosa strains analyzed, highlighting the urgent need for alternative strategies to address infections caused by extensively drug-resistant bacteria.

Susceptibility assessment and genetic analysis of cucumber genotypes to damping-off disease caused by Phytophthora melonis

Susceptibility assessment and genetic analysis of cucumber genotypes to damping-off disease caused by Phytophthora melonis

Clostridium sediminicola sp. nov., a crude oil aggregation-forming anaerobic bacterium isolated from marine sediment.

A crude oil aggregation-forming, strictly anaerobic, Gram-stain-positive, spore-forming, rod-shaped, motile and mesophilic bacterium, named strain SH18-2T, was isolated from marine sediment near Sado Island in the Sea of Japan. The temperature, salinity and pH ranges of this strain for the growth were 15-40 °C (optimum 35 °C), 0.5-6.0% NaCl (w/v; optimum 2.0%) and pH 6.0-8.0 (optimum 7.5), respectively. A phylogenetic analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Clostridium. It was most closely related to Clostridium grantii A-1T (97.02% homology). The draft genome size was 5616089 bp, with a G+C content of 29.7 mol%. The digital DNA-DNA hybridization values determined using the Genome-to-Genome Distance Calculator and the average nucleotide identity between this strain and C. grantii A-1T were 20.30 and 78.24%, respectively. Whole-organism hydrolysates of strain SH18-2T contained meso-diaminopimelic acid; the major fatty acid was C16:0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and three unidentified polar lipids. From the results of genotypic, phenotypic and chemotaxonomic analyses, SH18-2T (=NBRC 116030T=DSM 115762T) is the type strain and represents a novel species of the genus Clostridium, and the name Clostridium sediminicola sp. nov. is proposed.

Isolation, genotyping and antibiotic resistance analysis in Salmonella species isolated from turkey meat in Isfahan, Iran

Isolation, genotyping and antibiotic resistance analysis in Salmonella species isolated from turkey meat in Isfahan, Iran

Genetic signatures of ERCC1 and ERCC2 expression, along with SNPs variants, unveil favorable prognosis in SCLC patients undergoing platinum-based chemotherapy.

Platinum chemotherapy (CT) remains the backbone of systemic therapy for patients with small-cell lung cancer (SCLC). The nucleotide excision repair (NER) pathway plays a central role in the repair of the DNA damage exerted by platinum agents. Alteration in this repair mechanism may affect patients' survival. We conducted a retrospective analysis of data from 38 patients with extensive disease (ED)-SCLC who underwent platinum-CT at the Clinical Oncology Unit, Careggi University Hospital, Florence (Italy), from 2015 to 2020. mRNA expression analysis and single nucleotide polymorphism (SNP) characterization of three NER pathway genes-namely ERCC1, ERCC2, and ERCC5-were performed on patient tumor samples. Overall, elevated expression of ERCC genes was observed in SCLC patients compared to healthy controls. Patients with low ERCC1 and ERCC5 expression levels exhibited a better median progression-free survival (mPFS = 7.1 vs. 4.9 months, p = 0.39 for ERCC1 and mPFS = 6.9 vs. 4.8 months, p = 0.093 for ERCC5) and overall survival (mOS = 8.7 vs. 6.0 months, p = 0.4 for ERCC1 and mOS = 7.2 vs. 6.2 months, p = 0.13 for ERCC5). Genotyping analysis of five SNPs of ERCC genes showed a longer survival in patients harboring the wild-type genotype or the heterozygous variant of the ERCC1 rs11615 SNP (p = 0.24 for PFS and p = 0.14 for OS) and of the rs13181 and rs1799793 ERCC2 SNPs (p = 0.43 and p = 0.26 for PFS and p = 0.21 and p = 0.16 for OS, respectively) compared to patients with homozygous mutant genotypes. The comprehensive analysis of ERCC gene expression and SNP variants appears to identify patients who derive greater survival benefits from platinum-CT.

Retrospective detection of ITGB7 gene mutation in a Holstein calf with chronic diarrhea that was suspected of hereditary cholesterol deficiency.

A homozygous individual for ITGB7 gene mutation, an autosomal recessive congenital disorder in Holstein cattle, was retrospectively identified by genotyping of 195 stored blood from patients less than 12 months of age. Other 24 patients (12.3%) showed heterozygous. The homozygous individual was a 107-day-old female calf born on March 2017, who presented with chronic diarrhea and severe hypocholesterolemia suggesting hereditary cholesterol deficiency (CD), but genotyping analysis showed negative for CD. The patient showed watery diarrhea, dehydration, and extreme emaciation. Necropsy revealed no apparent cause of chronic diarrhea. Histopathological examination revealed mild mucosal inflammation from the jejunum to the colon. Seven years after the patient's death, the availability of ITGB7 gene mutation testing revealed the patient to be homozygous.

High Frequency of Detection of NDM‐Producing Enterobacterales Among Companion Animals Hospitalized in an Italian Veterinary Teaching Hospital

Carbapenems are considered one of the most important last‐resort classes of antibiotics, and the spread of carbapenem‐resistant Enterobacterales (CRE) is a serious concern worldwide. From a One Health point of view, reports on CRE in companion animals are increasing, requiring attention regarding their role in maintenance and direct transmission to humans. The aim of this study was to assess the frequency of detection at admission and the in‐hospital acquisition of CRE from perirectal swabs in dogs and cats hospitalized in an Italian Veterinary Teaching Hospital (VTH). Of the 150 patients sampled, 11.3% (n = 17) were CRE carriers at admission, 25.6% (n = 34) acquired CRE in their commensal microbiota during their hospital stay, and 2% (n = 3) developed an infection caused by CRE. Genotypical analysis showed that in 100% (78/78) of the CRE isolates (44 Escherichia coli, 33 Klebsiella pneumoniae, and 1 Klebsiella aerogenes) carbapenem resistance was conferred by the carbapenemase gene blaNDM, suggesting an endemic presence of such gene within the hospital. Co‐occurrent β‐lactamase‐encoding genes were found in most of the isolates. Risk factors associated with CRE acquisition were length of hospitalization (p = 0.0002) and treatment with piperacillin–tazobactam (PTZ; p = 0.0380), indicating potential cross‐selection of CRE. These results reinforce the suspicion that companion animals could silently contribute to the maintenance and dissemination of CRE in the local community, posing a threat to global health.