Comparative Genomic Analysis Research Articles

Comparative chloroplast genomes analysis of nine Primulina (Gesneriaceae) rare species, from karst region of southwest China

Guizhou Province is one of the most important karst regions of southwest China, with 22 Primulina species. These species are highly habitat-specialized and dependent on the soils of the karst region, and many inter-species classifications are unclear. Therefore, studying the chloroplast genomes and estimating the divergence times of there species can not only provide a better understanding of interspecific relationships but also help to know the species speciation and divergence in the karst environment. So, we sequenced and assembled the chloroplast genomes of nine Primulina species (including six endemic species of Guizhou) and conducted chloroplast genome comparison analysis and phylogenetic study. The chloroplast genome structures of the nine Primulina species were quadripartite with total lengths of 152,869–153,364 base pairs (bp) and GC content of 37.55–37.64%. There are 132 functional genes annotated, respectively. A total of 375 simple sequence repeats and 375 interspersed nuclear elements were identified. The 30 highly preferred codons identified were used at similar frequencies in different species, respectively. A phylogenetic tree constructed on the basis of the 38 chloroplast genomes showed that Primulina species form a monophyletic group. Eleven mutational hotspot regions that could serve as potential molecular markers were identified, of which two regions near the 3′ and 5′ ends of the ycf1 gene were of appropriate size and can serve as molecular markers for phylogenetic studies of Primulina. The results of molecular clock analyses indicate that the three major branches of Primulina begin to diverge in the Miocene, and the number of species proliferated in the Pliocene and Pleistocene. Most of the species of Primulina in Guizhou Province were formed in the Pleistocene and rapidly diverged within a short period of time. This research study enriches the genetic resource information of Primulina and deepens the understanding of the phylogenetic relationships of the genus.

Genomic Insights into Fusarium verticillioides Diversity: The Genome of Two Clinical Isolates and Their Demethylase Inhibitor Fungicides Susceptibility

Fusarium verticillioides is an important plant pathogen in maize and other cereals that is seldom detected as the cause of human fusariosis. Here, we provide the analysis of the available diversity of F. verticillioides sequenced worldwide and report the first two genome assemblies and annotations (including mitochondrial DNA) of Fusarium verticillioides from clinical settings. Fusarium verticillioides 05-0160 (IUM05-0160) and Fusarium verticillioides 09-1037 (IUM09-1037) strains were obtained from the bone marrow and blood of two immunocompromised patients, respectively. The phylogenomic analysis confirmed the species identity of our two strains. Comparative genomic analyses among the reannotated F. verticillioides genomes (n = 46) did not lead to the identification of unique genes specific to the clinical samples. Two subgroups in the F. verticillioides clade were also identified and confirmed by a mitochondrial diversity study. Clinical strains (n = 4) were positioned in the multigene phylogenetic tree without any correlation between the host and the tree branches, grouping with plant-derived strains. To investigate the existence of a potential fitness advantage of our two clinical strains, we compared demethylase inhibitor fungicides susceptibility against the reference Fusarium verticillioides 7600, showing, on average, lower susceptibility to agricultural and medical-used antifungals. A significant reduction in susceptibility was observed for itraconazole and tetraconazole, which might be explained by structural changes in CYP51A and CYP51C sequences. By providing the first two annotated genomes of F. verticillioides from clinical settings comprehensive of their mitogenomes, this study can serve as a base for exploring the fitness and adaptation capacities of Fusarium verticillioides infecting different kingdoms.

Novel Variant of New Delhi Metallo-Beta-Lactamase (blaNDM-60) Discovered in a Clinical Strain of Escherichia coli from the United Arab Emirates: An Emerging Challenge in Antimicrobial Resistance

Background/Objectives: Carbapenem resistance poses a significant health threat. This study reports the first detection and characterization of a novel variant of New Delhi metallo-β-lactamase (blaNDM-60) in Escherichia coli from the United Arab Emirates (UAE), including its genetic context and relationship to global strains. Methods: NDM-60-producing E. coli was isolated from a rectal swab during routine screening. Characterization involved whole-genome sequencing, antimicrobial susceptibility testing, and comparative genomic analysis with 66 known NDM variants. Core genome analysis was performed against 42 global E. coli strains, including the single other reported NDM-60-positive isolate. Results: The strain demonstrated extensive drug resistance, including resistance to novel β-lactam/β-lactamase inhibitor combinations, notably taniborbactam. NDM-60 differs from the closely related NDM-5 by a single amino acid substitution (Asp202Asn) and two amino acid substitutions (Val88Leu and Met154Leu) compared to NDM-1. NDM-60 is located on a nonconjugative IncX3 plasmid. The strain belongs to sequence type 940 (ST940). Phylogenetic analysis revealed high diversity among the global ST940 strains, which carry a plethora of resistance genes and originated from humans, animals, and the environment from diverse geographic locations. Conclusions: NDM-60 emergence in the UAE represents a significant evolution in carbapenemase diversity. Its presence on a nonconjugative plasmid may limit spread; however, its extensive resistance profile is concerning. Further studies are needed to determine the prevalence, dissemination, and clinical impact of NDM-60. NDM evolution underscores the ongoing challenge in managing antimicrobial resistance and the critical importance of vigilant molecular surveillance. It also highlights the pressing demand to discover new antibiotics to fight resistant bacteria.

Genomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2

Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636. Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined.

Characterization of an Enterococcus sp. SMC-9 strain isolated from bile of a patient with cholangitis.

The genus Enterococcus is increasingly recognized for its involvement in various human infections, with several species known to be pathogenic. This study characterized Enterococcus sp. SMC-9, isolated from bile of a patient with cholangitis, and compared its characteristics with those of Enterococcus montenegrensis CoE-012-22T, recently isolated from dried beef sausage. A comprehensive analysis, encompassing phylogenetic, genomic, and phenotypic studies, confirmed that strain SMC-9 belongs to the same species as E. montenegrensis CoE-012-22T. However, comparative genomic analysis revealed key differences in virulence and antibiotic resistance gene profiles between the two strains. Notably, genes related to exopolysaccharide biosynthesis and the L-rhamnose biosynthesis pathway were found exclusively in strain SMC-9, suggesting their role in the strain's colonization of the biliary tract and its involvement in cholangitis. Additionally, the tetracycline resistance gene tet(M), which was absent in E. montenegrensis CoE-012-22T, was identified in strain SMC-9, explaining its high tetracycline minimum inhibitory concentration (>16 μg/mL). These findings highlight the unique pathogenic traits of strain SMC-9 compared to E. montenegrensis CoE-012-22T. Our study underscores the significant genetic and phenotypic variations that can exist among strains within the same species, highlighting the critical need for strain typing to assess their potential impact on patient outcomes and public health.

Expanding the Stenotrophomonas maltophilia complex: phylogenomic insights, proposal of Stenotrophomonas forensis sp. nov. and reclassification of two Pseudomonas species.

A novel Stenotrophomonas species was isolated as a contaminant in viral transport media at the District of Columbia Department of Forensic Sciences Public Health Laboratory. Phylogenomic and biochemical analyses of the isolate determined that it represented a novel species within Stenotrophomonas. Related strains in public genome databases suggested that this novel species is associated with clinically acquired infections, similar to closely related Stenotrophomonas maltophilia. The name Stenotrophomonas forensis sp. nov. is proposed. Comparative genomic and phylogenetic analyses of the S. maltophilia complex reveal that Stenotrophomonas africana is an independent species and is not a later heterotypic synonym of S. maltophilia. We also propose the transfer of two misclassified Pseudomonas species into Stenotrophomonas as Stenotrophomonas beteli comb. nov. and Stenotrophomonas hibiscicola comb. nov. The type strain for S. forensis sp. nov. is DFS-20110405T (=ATCC TSD-272T=NCTC 14893T).

097 Comparative genomic analysis of the skin mycobiome

097 Comparative genomic analysis of the skin mycobiome

Overview of β-Lactam-Resistance Genes in Pandemic Multidrug-Resistant Acinetobacter baumannii: A Troublesome Pathogen in the Indian Intensive Care Unit

Objectives: Acinetobacter baumannii is responsible for many infections in admitted patients, especially in the intensive care unit (ICU). Several risk factors may lead to an enhanced risk of A. baumannii colonization and infections. β-lactam antibiotics are frequently administered to treat Gram-positive and Gram-negative bacterial infections due to their minimum side effects, but the acquisition of β-lactamase genes has been the most challenging and troublesome situation and an imminent threat to the world as it increases mortality, medical expenses, and hospital stays. Hence, the present systematic review focused on the screening of β-lactam resistance genes that have been identified in the A. baumannii isolates’ genome and the nosocomial infections they cause in the Indian ICU. Material and Methods: This review has been done according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline 2020. After screening, 317 genomes were included in this systematic review. We downloaded data from the bv-brc.org website on an Excel spreadsheet for statistical analysis. We presented categorical data in percentages (%) and in the form of a graph and pie chart. Results: Among the 317 isolates, pneumonia was caused by 189 strains (59.62%), bacteremia was caused by 109 strains (34.38%), respiratory infection by 12 isolates (3.79%), sepsis by 5 isolates (1.58%), and wound infection by 2 isolates (0.63%), which indicated that A. baumannii strains are highly involved in pneumonia followed by bacteremia. We did comparative genome analysis and found 26 β-lactamase genes; among them, the ADC2 gene was found to be in higher frequency (312) and was identified in 98.42% of A. baumannii isolates, followed by the OXA23 gene (303), which was found in 95.58% of isolates. The NDM-1 gene was identified in 181 (57.09%) isolates. OXA66 was found in 156 (49.21%) isolates. Our findings show a higher frequency of the ADC2 gene, followed by the OXA23 gene, in all these nosocomial infections. We have found that NDM-1, ADC2, OXA23, and OXA-66 genes coexisted in higher frequency in the A. baumannii isolates (137; 43.21%), followed by OXA23, OXA-66, and ADC2 (52; 16.40%). Conclusion: A. baumannii is a notorious pandemic pathogen, designated as a “priority of concern” by the World Health Organization. Our study indicates a high prevalence of the ADC2 gene, which gives resistance against the cephalosporin group and co-existence of β-lactamase genes (ADC2, OXA23, OXA66, and NDM-1) in various A. baumannii isolates’ genomes. This is a worrisome situation. Global molecular surveillance and the “One Health Concept” are crucial, as are research studies on plant extracts’ in vitro and in vivo efficacy against A. baumannii. Combating multidrug-resistant A. baumannii requires a multifaceted approach that involves infection control measures, antimicrobial stewardship, surveillance, education, research, and collaboration. Implementing these strategies and staying vigilant in the face of this resilient pathogen is essential to minimize its impact on health-care systems and public health.

Investigation of chromosomal anomalies and copy number variations in children diagnosed with autism spectrum disorder by array CGH method.

This study aimed to identify the chromosomal anomalies and copy number variations (CNVs) in autism spectrum disorder (ASD) and to provide genotype/phenotype correlations. Fifty-four patients diagnosed with ASD between March 2021 and June 2022 were included in the study. Patients were evaluated by cytogenetic analysis and array comparative genomic hybridisation analysis (aCGH). The structural and numerical chromosomal anomaly was detected in 3.7%, and the CNVs were identified in 18.52% of patients. Of the CNVs detected, 27.3% were identified as pathogenic, 18.2% as likely pathogenic and 54.5% as VUS. The copy number gain rate of the detected CNVs was higher than the copy number losses rate, 70% and 30% respectively. As an important finding in the study, a new pathogenic CNV with a 6.3-mb copy number gain in the 3p22.3p22.2 region, whose gene region had not been previously defined in OMIM, was detected. Identifying a genetic aetiology may provide clinicians with more information about disease prognosis and risk of recurrence.

Comparative genomic analysis of Chinese Erwinia amylovora strains reveals genetic variations, plasmid diversity, and potential common ancestor

Comparative genomic analysis of Chinese <i>Erwinia amylovora</i> strains reveals genetic variations, plasmid diversity, and potential common ancestor

Comparative chloroplast genome analysis of two Desmodesmus species reveals genome diversity within Scenedesmaceae (Sphaeropleales, Chlorophyceae)

Desmodesmus (Sphaeropleales, Chlorophyceae) is a genus of freshwater green algae widely distributed in aquatic ecosystems and known for its potential in biotechnology and bioremediation. We present the complete chloroplast genome sequences of two Desmodesmus species, D. hystrix and D. perforatus . Comparative analysis revealed significant differences in their quadripartite structures, particularly in the lengths of the small single copy regions. We observed variations in G + C content across genomic regions, with inverted repeat regions showing a higher G + C content. Microsatellite analysis revealed that A/T mononucleotides were the most abundant type, while dispersed repeat analysis suggested a potential link to expansion of the single-copy region in D. perforatus. Gene annotation, codon usage analysis, and comparison of genome rearrangement highlighted both similarities and differences between the species. Nucleotide diversity analysis revealed higher variability in intergenic regions than in coding regions, with IR regions displaying relative conservation. Comparative analyses of genomes and IR border arrangements demonstrated that the Desmodesmus species exhibit substantial differences in genome structure and gene arrangement among Scenedesmaceae. Phylogenetic analysis, based on 51 single-copy genes from 34 species of Sphaeropleales provided additional information about phylogenetic relationships within Sphaeropleales. These findings contribute to our understanding of comparative plastid genomics in green algae.

Comparative genomics analyses reveal selection on neuronal and cuticular hydrocarbon genes is associated with aggression in ants (Hymenoptera: Formicidae)

Abstract Aggression is an essential component of survival and fitness, although the expression of aggression behaviors can also carry fitness costs. As a result, aggressive behaviors vary significantly across animals and are likely acted on by natural selection to produce this variation. Aggression, and associated traits like nestmate discrimination, both complex traits, have well studied genetic components, with links to genes involved in processes like neuronal function, metabolism, and hormone and cuticular hydrocarbon (CHC) production and reception. However, whether and how natural selection acts on these genes to produce variation across species is not fully understood. Using a comparative genomics approach, we analyzed natural selection in ants (Hymenoptera: Formicidae) with candidate genes previously linked to these traits. We find that aggression is associated with shifts in selection intensity, including positive selection on neurotransmitter receptors, and that ants with low levels of nestmate discrimination experience positive or relaxed selection on several CHC genes. Interestingly, we find that most candidate genes analyzed experience positive selection across ants, regardless of aggression level or discrimination ability. Our results shed new light on the means by which natural selection may act to produce variation in aggression across the ants.

Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple

A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.

Genomic Features of Taiwanofungus gaoligongensis and the Transcriptional Regulation of Secondary Metabolite Biosynthesis

Fungal secondary metabolites (SMs) have broad applications in biomedicine, biocontrol, and the food industry. In this study, whole-genome sequencing and annotation of Taiwanofungus gaoligongensis were conducted, followed by comparative genomic analysis with 11 other species of Polyporales to examine genomic variations and secondary metabolite biosynthesis pathways. Additionally, transcriptome data were used to analyze the differential expression of polyketide synthase (PKS), terpene synthase (TPS) genes, and transcription factors (TFs) under different culture conditions. The results show that T. gaoligongensis differs from other fungal species in genome size (34.58 Mb) and GC content (50.72%). The antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analysis reveals significant variation in the number of SM biosynthetic gene clusters (SMBGCs) across the 12 species (12–29), with T. gaoligongensis containing 25 SMBGCs: 4 PKS, 6 non-ribosomal peptide synthetase (NRPS), and 15 TPS clusters. The TgPKS1 gene is hypothesized to be involved in the biosynthesis of orsellinic acid or its derivatives, while TgPKS2 might catalyze the synthesis of 6-methylsalicylic acid (6MSA) and its derivatives. The TgTRI5 genes are suggested to synthesize tetracyclic sesquiterpene type B trichothecene compounds, while TgPentS may be involved in the synthesis of δ-cadinol, β-copaene, and α-murolene analogs or derivatives. Comparative genomic analysis shows that the genome size of T. gaoligongensis is similar to that of T. camphoratus, with comparable SMs. Both species share four types of PKS domains and five distinct types of TPS. Additionally, T. gaoligongensis exhibits a high degree of similarity to Laetiporus sulphureus, despite belonging to a different genus within the same family. Transcriptome analysis reveals significant variation in the expression levels of PKS and TPS genes across different cultivation conditions. The TgPKS1 and TgPKS4 genes, along with nine TgTFs, are significantly upregulated under three solid culture conditions. In contrast, under three different liquid culture conditions, the TgPKS3, TgTRI5-1, and TgTRI5-2 genes, along with twelve TgTFs, exhibit higher activity. Co-expression network analysis and TgTFs binding site prediction in the promoter regions of TgPKS and TgTPS genes suggest that TgMYB9 and TgFTD4 regulate TgPKS4 expression. TgHOX1, TgHSF2, TgHSF3, and TgZnF4 likely modulate TgPKS3 transcriptional activity. TgTRI5-1 and TgTRI5-5 expression is likely regulated by TgbZIP2 and TgZnF15, respectively. This study provides new insights into the regulatory mechanisms of SMs in T. gaoligongensis and offers potential strategies for enhancing the biosynthesis of target compounds through artificial intervention.

Genomic Characterization and Comparative Genomic Analysis of the Foodborne Burkholderia gladioli pv. cocovenenans.

The Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases, which could produce the deadly toxin of bongkrekic acid (BA). However, genomic characterization and toxin production pathways of B. cocovenenans strains remain elusive. This study aimed to explore the BA-producing ability associated with the evolution of the bon gene cluster and to analyze the intraspecies genomic diversity and phylogenetic relationships of B. gladioli based on the 17 genomes of B. cocovenenans strains isolated from Shenzhen City, China. Genome sequencing results suggested that the genome sizes of these B. cocovenenans strains were mostly approximately 8 Mb, with a GC content of approximately 68%. The evolutionary tree analysis of the whole-genome sequences showed that significant divergences and distinct cluster were exhibited among these B. cocovenenans strains. Comparative genomic analysis indicated that the genomes of strains 2020051, 2021031, and 2021067 contained the complete and entire bon gene cluster, supporting that these strains displayed obviously BA-producing ability. The genomes of strains 2021028 and 2020041 lacked the entire bon gene cluster. However, the genomes of strains 2021037, 2021024, 2021035, and 2021031 exhibited disruptions in their bon gene clusters. This finding indicated the loss of specific genes within the cluster, suggesting a reduced capability for BA production in these strains. The present results indicated that the bon gene cluster in the genome played a key role in the toxin BA biosynthesis of different B. cocovenenans strains. This study provided a comprehensive understanding of the relationship between genomic diversity and BA production of this lethal foodborne pathovar, which will potentially contribute to the risk identification and food poisoning outbreak prevention of B. cocovenenans.

Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management.

Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393bp and 1527 to 1541bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.

Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface

On the deep and dark seafloor, a cryptic and yet untapped microbial diversity flourishes around hydrothermal vent systems. This remote environment of difficult accessibility exhibits extreme conditions, including high pressure, steep temperature- and redox gradients, limited availability of oxygen and complete darkness. In this study, we analysed the genomes of three aerobic strains belonging to the phylum Planctomycetota that were isolated from two deep-sea iron- rich hydroxide deposits with low temperature diffusive vents. The vents are located in the Arctic and Pacific Ocean at a depth of 600 and 1,734 m below sea level, respectively. The isolated strains Pr1dT, K2D and TBK1r were analyzed with a focus on genome-encoded features that allow phenotypical adaptations to the low temperature iron-rich deep-sea environment. The comparison with genomes of closely related surface-inhabiting counterparts indicates that the deep-sea isolates do not differ significantly from members of the phylum Planctomycetota inhabiting other habitats, such as macroalgae biofilms and the ocean surface waters. Despite inhabiting extreme environments, our “deep and dark”-strains revealed a mostly non-extreme genome biology.

Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken

Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including blaCTX−M−55, blaTEM−141, blaTEM−1B, aph(3’)-IIa, aph(3’’)-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain.

First Detection of a Novel Posavirus 2 Strain Identified from Pigs in China

Porcine stool-associated RNA virus (Posavirus) is an unclassified virus with sequence similarity to viruses in the order of Picornaviridae. In China, lineage 1 Posavirus (Posavirus 1) has been circulating in the field since its initial emergence in 2014 however no other lineages have been reported. To investigate the genetic diversity of Posavirus in China, 1200 diarrheic samples were collected from pigs in China. Following high-throughput and Sanger sequencing, one complete genome sequence of a Posavirus (designated SC01) strain was obtained. The genome of SC01 strain was 10217 nucleotides in length and encoded a polyprotein of 3346 amino acids. Genome comparative analysis revealed that SC01 shared 85.6% nucleotide similarity to Posavirus 2 strains, but only 35.2–58.0% sequence identity with Posavirus 1 and 3–12 strains. Phylogenetic analysis showed that the SC01 was classified in Posavirus 2 and clustered into a separate branch with the American Posavirus 2 isolates, indicating that the SC01 is a Posavirus 2 strain. Notably, a novel 1-amino acid deletion was observed in polyprotein at amino acid position 147. This is the first report of the presence of Posavirus 2 in China, and the genomic data of SC01 provides insights into the genetic diversity and evolution of Posavirus in the region.

Hydin as the Candidate Master Sex Determination Gene in Channel Catfish (Ictalurus punctatus) and Its Epigenetic Regulation.

Sex determination is a fascinating area of research. To date, more than 20 master sex determination (SD) genes have been reported from vertebrate animals. With channel catfish (Ictalurus punctatus), much work has been conducted to determine its master SD gene, ranging from genetic linkage mapping, genome-wide association (GWA) analysis, genome sequencing, comparative genome analysis, epigenomic analysis, transcriptome analysis, and functional studies. Here in this mini review, we provide positional, expression, regulatory, and functional evidence supporting hydin (hydrocephalus-inducing protein or HYDIN axonemal central pair apparatus protein-like) as a master SD gene in channel catfish. Hydin is located within the sex determination region (SDR) within a mapped 8.9-Mb non-recombinational segment on chromosome 4 of channel catfish. It is highly expressed in genetic males, but not in genetic females. The alleles of X and Y are highly differentially methylated with the X chromosome being hypermethylated and the Y chromosome hypomethylated. The hypomethylated Y allele of hydin is expressed while the hypermethylated X allele is not expressed. Such allelic expression fits well with the XY sex determination system of channel catfish. Functional analysis using a methylation blocker, 5-aza-dC, demonstrated that demethylation, especially within the SDR, is accompanied with increased expression of hydin, which led to sex reversal of genetic females into phenotypic males. These evidences support the candidacy of hydin as a master SD gene in channel catfish. Future knockout and analysis of affected genes after hydin knockout should provide insights into how hydin functions as a master SD gene.