Taxonomic Distribution, Phylogenetic Relationship, and Domain Conservation of CRISPR-Associated Cas Proteins.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a naturally occurring genetic defense system in bacteria and archaea. It is comprised of a series of DNA sequence repeats with spacers derived from previous exposures to plasmid or phage. Further understanding and applications of CRISPR system have revolutionized our capacity for gene or genome editing of prokaryotes and eukaryotes. The CRISPR systems are classified into 3 distinct types: type I, type II, and type III, each of which possesses an associated signature protein, Cas3, Cas9, and Cas10, respectively. As the CRISPR loci originated from earlier independent exposures of foreign genetic elements, it is likely that their associated signature proteins may have evolved rapidly. Also, their functional domain structures might have experienced different selective pressures, and therefore, they have differentially diverged in their amino acid sequences. We employed genomic, phylogenetic, and structure-function constraint analyses to reveal the evolutionary distribution, phylogenetic relationship, and structure-function constraints of Cas3, Cas9, and Cas10 proteins. Results reveal that all 3 Cas-associated proteins are highly represented in the phyla Bacteroidetes, Firmicutes, and Proteobacteria, including both pathogenic and non-pathogenic species. Genomic analysis of homologous proteins demonstrates that the proteins share 30% to 50% amino acid identity; therefore, they are low to moderately conserved and evolved rapidly. Phylogenetic analysis shows that 3 proteins originated monophyletically; however, the evolution rates were different among different branches of the clades. Furthermore, structure-function constraint analysis reveals that both Cas3 and Cas9 proteins experiences low to moderate levels of negative selection, and several protein domains of Cas3 and Cas9 proteins are highly conserved. To the contrary, most protein domains of Cas10 proteins experience neutral or positive selection, which supports rapid genetic divergence and less structure-function constraints.

Identification and characterization of multiple novel viruses in fecal samples of ruddy shelducks using viral metagenomics methods.

The viral metagenomics approach is an effective technique for investigating and analysing both existing and emerging viruses in humans and diverse animal samples. The ruddy shelduck, a nationally protected secondary key species of wild animals, has become the predominant species among overwintering waterbirds in Qinghai Lake. Viruses carried by ruddy shelducks can potentially infect humans or other animals; however, limited research on the faecal virome of ruddy shelducks is currently available. In the present study, faecal samples of ruddy shelducks collected from Saga County, Shigatse City, Tibet, China, were subjected to viral metagenomic analysis. The predominant viral families identified in ruddy shelduck samples were Picornaviridae, Parvoviridae, Microviridae, Vilyaviridae, Astroviridae, and Caliciviridae. Among these, two picornavirus genomes have been identified as new strains of the genus Megrivirus in the family Parvoviridae. In addition, viruses that infect parasites and bacteria have been identified and characterised. The present study enhances our comprehension of the composition of the viral community in ruddy shelducks faeces and highlights the dynamic nature of viral evolution and the significance of continuous monitoring to assess potential risks to wildlife and public health.

Diversity of Marek's Disease Virus Strains in Infections in Backyard and Ornamental Birds.

Marek's disease is caused by Mardivirus gallidalpha2, commonly known as Marek's disease virus (MDV). This pathogen infects various bird species resulting in a range of clinical manifestations. The meq gene, which is crucial for oncogenesis, has been extensively studied, but molecular investigations of MDV in noncommercial South American birds are limited. This study detected MDV in backyard and ornamental birds from Brazil and Peru and characterized the meq gene. MDV was confirmed in all seven outbreaks examined. Three isoforms of meq (S-meq, meq, and L-meq) and two to seven proline repeat regions (PRRs) were detected among the sequenced strains. At the amino acid level, genetic profiles with low and high virulence potential were identified. Phylogenetic analysis grouped the sequences into three distinct clusters. Selection pressure analysis revealed 18 and 15 codons under positive and negative selection, respectively. The results demonstrate significant MDV diversity in the studied birds, with both high and low virulence potentials. This study highlights the importance of monitoring and characterizing circulating MDV in backyard and ornamental birds, as they can act as reservoirs for future epidemiological outbreaks.

The complete chloroplast genome sequence of Arytera littoralis (Sapindoideae, Sapindaceae).

Arytera littoralis Blume 1847 is an evergreen small tree belonging to the Sapindaceae family. It is distributed in South China to SE Asia and the Solomon Islands. However, the chloroplast genome of A. littoralis has yet to be reported. In this study, the complete chloroplast genome of Arytera littoralis was determined. The total genome size was 161,091 bp in length, consisting of two inverted repeats (IRs) (28,432 bp) separated by the large single-copy (LSC) (85,737 bp) and small single-copy (SSC) (18,490 bp) regions. The genome contained 133 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content of the complete chloroplast genome was 37.8%. A maximum-likelihood (ML) phylogenetic tree of A. littoralis and 13 related species from the family Sapindaceae indicated that A. littoralis was close to a clade composed of Sapindus, Nephelium, Litchi, and Dimocarpus. This study will offer essential genetic resources of A. littoralis and provide insights into the phylogeny and evolution of Sapindaceae.

Characterization of the complete chloroplast genome sequence of Artemisia sylvatica Maximowicz 1859 (Asteraceae).

Artemisia sylvatica Maximowicz 1859 is one of the medicinal herbs in Artemisia. This study presents the complete chloroplast genome of A. sylvatica, sequenced using the Illumina NovaSeq platform. The genome is 151,161 bp in length, featuring a GC content of 38%. It consists of a large single-copy (LSC) region of 82,892 bp, a small single-copy (SSC) region of 18,353 bp, and two inverted repeat (IR) regions of 24,958 bp each. In total, the genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis positions A. sylvatica within the subgenus Artemisia, highlighting its evolutionary relationships within this diverse genus. The first chloroplast genome of A. sylvatica was reported in this work contributes to the enrichment of genomic data for the genus Artemisia.

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications.

Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT- and GC-skews were - 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein-coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in "trnE-trnG" and "trnG-trnE". Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

Three novel Ascomycota (Saccharomycetes, Saccharomycetales) yeast species derived from the traditional Mexican alcoholic beverage Pulque.

The abundant variety of yeasts and their diverse applications have essential roles in traditional Mexican alcoholic beverage fermentation processes. During our investigation of yeast diversity associated with Pulque, 41 yeast strains were characterized. Among them, 31 strains were eight known species belonging to seven genera. According to morphological and phylogenetic analyses (ITS and LSU rDNA), ten unidentified yeast strains were identified to be three novel species and proposed: Starmerellaelongatum sp. nov., Kazachstaniaparagamospora sp. nov. and Pichiateotihuacanensis sp. nov. Our study has resulted in the isolation of yeast species not previously detected in Pulque, expanding our knowledge of the diversity of its associated yeast communities.

Genetic diversity and structure of Persicaria amphibia (Polygonaceae) in South Korea using genotyping by sequencing.

BACKGROUND: Persicaria amphibia, a member of the Polygonaceae family, exists both aquatic and terrestrial forms. It is native to North America, Asia, Europe, and some parts of Africa. OBJECTIVE: This study aimed to determine the genetic diversity within and among populations of P. amphibia and the distribution characteristics of each population to investigate insights into the genetic structure and conservation of P. amphibia. METHODS: In this study, the genetic diversity and structure of 84 P. amphibia individuals from 7 populations in South Korea were analyzed using genotyping-by-sequencing (GBS). We used 2,469 single nucleotide polymorphisms (SNPs) to analyze genetic diversity, principal components, structure, and phylogeny. RESULTS: Our results showed a mean observed heterozygosity and mean expected heterozygosity of 0.34409 and 0.34082, respectively. Genetic diversity analysis indicated that the variation among populations (60.08%) was greater than that within populations (39.92%). Fixation index values, principal components analysis, structure, and phylogeny analyses showed that the population in Gyodongdo, Ganghwa Island was highly different. CONCLUSION: These results provide important insights for better understand the population history and genetic structure of P. amphibia.

Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species.

Codon usage bias refers to the preferential use of synonymous codons, a widespread phenomenon found in bacteria, plants, and animals. Codon bias varies among species, families, and groups within kingdoms and between genes within an organism. Codon usage bias (CUB) analysis sheds light on the evolutionary dynamics of various species and optimizes targeted gene expression in heterologous host plants. As a significant order of gymnosperms, species within Gnetales possess extremely high ecological and pharmaceutical values. However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored. A systematic analysis was conducted to elucidate the codon usage patterns in 13 diverse Gnetales species based on the chloroplast genomes. Our results revealed that chloroplast coding sequences (cp CDSs) in 13 Gnetales species display a marked preference for AT bases and A/T-ending codons. A total of 20 predominantly high-frequency codons and between 2 and 7 optimal codons were identified across these species. The findings from the ENC-plot, PR2-plot, and neutrality analyses suggested that both mutation pressure and natural selection exert influence on the codon bias in these 13 Gnetales species, with natural selection emerging as the predominant influence. Correspondence analysis (COA) demonstrated variation in the codon usage patterns among the Gnetales species and indicated mutation pressure is another factor that could impact CUB. Additionally, our research identified a positive correlation between the measure of idiosyncratic codon usage level of conservatism (MILC) and synonymous codon usage order (SCUO) values, indicative of CUB's potential influence on gene expression. The comparative analysis concerning codon usage frequencies among the 13 Gnetales species and 4 model organisms revealed that Saccharomyces cerevisiae and Nicotiana tabacum were the optimal exogenous expression hosts. Furthermore, the cluster and phylogenetic analyses illustrated distinct patterns of differentiation, implying that codons, even with weak or neutral preferences, could affect the evolutionary trajectories of these species. Our results reveal the characteristics of codon usage patterns and contribute to an enhanced comprehension of evolutionary mechanisms in Gnetales species.

Changes in the Phylogenetic Structure of Alpine Grassland Plant Communities on the Qinghai-Tibetan Plateau with Long-Term Nitrogen Deposition.

Nitrogen (N) deposition rates have notably increased around the world, especially in high-altitude regions like the Qinghai-Tibetan Plateau (QTP). We conducted a six-year comprehensive experiment to simulate nitrogen deposition in an alpine grassland area near Qinghai Lake. Four levels of nitrogen depositions, i.e., 0 (CK), 8 kg N ha-1year-1 (N1), 40 kg N ha-1year-1 (N2), and 72 kg N ha-1year-1 (N3), with three replicates for each N treatment, were tested annually in early May and early July, with the meticulous collection of plant and soil samples during the peak growth period from 15 July to 15 August. We used the null model to evaluate the impact of environmental filtration and interspecific competition on the dynamics of the plant community was assessed based on the level of discrete species affinities within the plant community by constructing a phylogenetic tree. The results showed that the environmental filter was the predominant driver for the change of community's genealogical fabric. The N2 and N3 treatments increased the influence of soil factors on the change of plant community structure. Climatic factors played a crucial role on the change of plant community in the CK grassland area, while soil factors were dominant in the N1- and N3-treated grasslands.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny.

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

Positive Selection of Mitochondrial cytochrome b Gene in the Marine Bivalve Keenocardium buelowi (Bivalvia, Cardiidae).

The mitochondrial genome provides valuable data for phylogenetic analysis and evolutionary research. In this study, we sequenced, assembled, and annotated the mitochondrial genome of Keenocardium buelowi using the Illumina platform. The genome spanned 16,967 bp and included 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs. All PCGs utilized standard ATN start codons and TAN stop codons. The phylogenetic tree based on maximum likelihood and Bayesian inference analyses revealed Clinocardiinae as the sister group to Trachycardiinae, with the estimated divergence time being 44.5 million years ago (MYA) between K. buelowi and Vasticardium flavum. Notably, the cytochrome b gene (cob) exhibited a positive selection signal. Our findings provide valuable insights into the evolutionary history and molecular phylogeny of K. buelowi.

Molecular detection and genetic characteristics of porcine reproductive and respiratory syndrome virus in central China.

Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically devastating viral diseases in the global pork industry. To further clarify the epidemic characteristics of the virus, 365 clinical samples were collected from diseased pigs suffering from abortion and respiratory disease from 2018 to 2023 on 63 pig farms in Henan and Shanxi provinces, and screened for the presence of PRRSV using reverse transcription-polymerase chain reaction (RT-PCR). A total of 62 clinical samples (62/365, 16.99 %) were positive for PRRSV, and subsequently, full-length ORF5 gene sequences of 29 PRRSV strains and the complete genome sequence of one PRRSV HeN-HC isolate were obtained and analyzed. Phylogenetic analysis based on the ORF5 gene showed that 22 of the 29 PRRSV2 strains belonged to sublineage 1.8 (NADC30-like), 5 belonged to sublineage 8.5 (HP-PRRSV), and 2 belonged to sublineage 5.1 (VR-2332-like), indicating that both HP-PRRSV and NADC30-like strains were mainly circulating in Henan and Shanxi provinces. Compared to VR-2332 strain, different types of amino acid mutations were found in the GP5 protein of these 29 strains, and the amino acid deletions were displayed in the Nsp2 protein of the HeN-HC isolate, leading to the variation of protein structures. It is noteworthy that recombination events were identified in the HeN-Ping and HeN-B strains. In addition, a total of 60, 094 pig serum samples from Henan province were collected, and the positive rate of specific antibodies against PRRSV was 86.37 % from 2019 to 2022, and 86.66 %, 84.85 %, 87.54 % and 86.30 % in 2019, 2020, 2021 and 2022, respectively. Overall, this study provides valuable insights into the molecular epidemiology and evolution of PRRSV circulating in central China.

Molecular Characteristics and Expression Patterns of Carotenoid Cleavage Oxygenase Family Genes in Rice (Oryza sativa L.).

Carotenoid cleavage oxygenases (CCOs) cleave carotenoid molecules to produce bioactive products that influence the synthesis of hormones such as abscisic acid (ABA) and strigolactones (SL), which regulate plant growth, development, and stress adaptation. Here, to explore the molecular characteristics of all members of the OsCCO family in rice, fourteen OsCCO family genes were identified in the genome-wide study. The results revealed that the OsCCO family included one OsNCED and four OsCCD subfamilies. The OsCCO family was phylogenetically close to members of the maize ZmCCO family and the Sorghum SbCCO family. A collinearity relationship was observed between OsNCED3 and OsNCED5 in rice, as well as OsCCD7 and OsNCED5 between rice and Arabidopsis, Sorghum, and maize. OsCCD4a and OsCCD7 were the key members in the protein interaction network of the OsCCO family, which was involved in the catabolic processes of carotenoids and terpenoid compounds. miRNAs targeting OsCCO family members were mostly involved in the abiotic stress response, and RNA-seq data further confirmed the molecular properties of OsCCO family genes in response to abiotic stress and hormone induction. qRT-PCR analysis showed the differential expression patterns of OsCCO members across various rice organs. Notably, OsCCD1 showed relatively high expression levels in all organs except for ripening seeds and endosperm. OsNCED2a, OsNCED3, OsCCD1, OsCCD4a, OsCCD7, OsCCD8a, and OsCCD8e were potentially involved in plant growth and differentiation. Meanwhile, OsNCED2a, OsNCED2b, OsNCED5, OsCCD8b, and OsCCD8d were associated with reproductive organ development, flowering, and seed formation. OsNCED3, OsCCD4b, OsCCD4c, OsCCD8b, and OsCCD8c were related to assimilate transport and seed maturation. These findings provide a theoretical basis for further functional analysis of the OsCCO family.

Epidemiological investigation of equine rotavirus B outbreaks in horses in central Kentucky.

Using metagenomic sequencing we identified equine rotavirus group B (ERVB) of ruminant origin in foal diarrhea outbreaks in the 2021 foaling season. To further investigate ERVB occurrence and determine its environmental stability, we collected mare and foal fecal samples from different farms in Central Kentucky during the 2022 foaling season. The RT-qPCR-based analyses showed that ERVB genome was detected in 16.67 % (42/252) of surveyed mare samples and 26.56 % (34/128) of foal samples. Furthermore, 94.12 % (16/17) of collected soil samples and 100 % (13/13) of water samples obtained from the ERVB-positive farm premises also tested weakly positive. In addition, ERVB genome fragments were detected in 58.33 % (7/12) of indoor samples collected from the equipment/barn/hospital wards during the outbreak period. Finally, the seroprevalence study showed 87 % (113/130) of surveyed horse serum samples were positive for ERVB antibodies. Despite unsuccessful attempts in ERVB cultivation, phylogenetic analyses showed that fecal ERVB strains representing 2022 and 2023 foal diarrhea outbreaks, like 2021 strains, were more closely related to ruminant rotavirus B than other viruses. Further sequence analyses revealed that none of the three viral capsid proteins, the primary targets of virus-neutralizing antibodies, exhibited notable mutations among ERVB strains circulated over the past three years. Our data demonstrated that ERVB was widespread in horses on affected farms with extreme stability in the farm environment. These findings continue to support the need for future surveillance of ERVB in horses and the surrounding environment, and the development of effective countermeasures to protect horses against this new viral disease.

Six type-I PKS classes and highly conserved melanin and elsinochrome gene clusters found in diverse Elsinoë species.

Elsinoë species are phytopathogenic fungi that cause serious scab diseases on economically important plants. The disease symptoms arise from the effects of a group of phytotoxins known as elsinochromes, produced via a type-I polyketide synthase (PKS) biosynthetic pathway. The elsinochrome gene cluster was first annotated in Elsinoë fawcettii where the main type-I PKS gene was characterized as EfPKS1. A later study showed that this gene and the associated cluster had not been correctly annotated, and that EfPKS1 was actually the anchor gene of the melanin biosynthetic pathway. A new type-I PKS gene EfETB1 associated with elsinochrome production was also identified. The aim of this study was to identify all type-I PKS genes in the genomes of seven Elsinoë species with the goal of independently verifying the PKS containing clusters for both melanin and elsinochrome production. A total of six type-I PKS classes were identified, although there was variation between the species in the number and type of classes present. Genes similar to the E. fawcettii EfPKS1 and EfETB1 type-I PKS genes were associated with melanin and elsinochrome production respectively in all species. The complete melanin and elsinochrome PKS containing clusters were subsequently annotated in all the species with high levels of synteny across Elsinoë species. This study provides a genus-level overview of type-I PKS distribution in Elsinoë species, including an additional line of support for the annotation of the melanin and elsinochrome PKS containing clusters in these important plant pathogens.

Whole-genome-based taxonomy as the most accurate approach to identify Flavobacterium species.

The genus Flavobacterium comprises a diversity of species, including fish pathogens. Multiple techniques have been used to identify isolates of this genus, such as phenotyping, PCR genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using Average Nucleotide Identity (ANI) and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and F. psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.

Identification and Characterization of Bipolaris secalis and B. setariae Associated with Brown Stripe Disease on Saccharum officinarum in Yunnan, China.

Sugarcane (Saccharum officinarum L.) is the most important sugar crop that belongs to the Poaceae family and is mainly cultivated in tropical and subtropical regions worldwide. Brown stripe disease is a common and serious foliar fungal disease of sugarcane and has become a serious threat to sugarcane production in China. Yunnan Province is the second-largest sugar base in China. From 2022 to 2023, brown stripe-like symptoms from different sugarcane variety were observed in Yunnan. Thirty-nine Bipolaris-like isolates were obtained from symptomatic leaves of different sugarcane varieties and characterized by means of morphological identification combined with multilocus phylogeny comprising internal transcribed spacer rDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the translation elongation factor-1α (TEF-1α) gene sequence date. The analysis provided strong support for the delineation and identification of two Bipolaris species associated with sugarcane brown stripe, including Bipolaris secalis and B. setariae. Pathogenicity text in potted sugarcane plants confirmed that these two Bipolaris species can cause brown stripe of sugarcane, thus fulfilling Koch's postulates. This study confirmed that B. secalis and B. setariae were the pathogens of brown stripe in Yunnan Province. To the best of our knowledge, this is the first to report B. secalis as causal agents of brown stripe of sugarcane. Collectively, this finding provides a basis for sugarcane brown stripe disease accurate diagnosis and would be helpful to the development of effective management strategies.

The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.

Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are published in the literature, none of which are from Australia. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains sequenced using Oxford Nanopore Technologies and Illumina. Using in silico genotyping, we found that all strains were multi-drug resistant, including resistances to fluoroquinolones and cephalosporins. In vitro antibiotic susceptibility testing mostly correlated with individual genotypes. The exception was MS8320, which had additional in vitro resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a bla TEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular locus switch. Phenotypic confirmation of differing capsules in Australian ST1193 strains, coupled with genetic analysis revealing insertions downstream of the capsular locus, underscored the genetic distinctions between K5 and K1 capsule encoding strains. This study provides five new reference ST1193 genomes from Australia. These include the earliest complete K5-capsule ST1193 genomes on record (collected 2007), alongside our reference genome (MS10858), a clinical isolate obtained early during the ST1193 expansion and representative of the predominant K1-associated clade. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.