QUAST: quality assessment tool for genome assemblies

"Acceptable" concentrations of enrofloxacin in food lead to reduced enrofloxacin susceptibility in a mouse model of gastrointestinal Klebsiella pneumoniae

Concentrations of antimicrobials up to 1,000-fold lower than the minimum inhibitory concentration can select for antimicrobial resistance. This generates the hypothesis that the low concentrations of antimicrobials allowed in our food could select for resistance. We assessed if the dose of enrofloxacin allowed in food by the European Medicines Agency (6.2 µg/kg) could decrease susceptibility to enrofloxacin in a strain of Klebsiella pneumoniae colonizing the gastrointestinal tracts of Specific Opportunistic Pathogen-Free Naval Medical Research Institute (NMRI) mice. We found that one-tenth of this dose given daily was able to increase the K. pneumoniae enrofloxacin MIC 8-fold (from 0.047 µg/mL to 0.38 µg/mL). Our findings suggest the need for studies to assess if the same could occur in humans.IMPORTANCEAntimicrobial-resistant infections are responsible for over a million deaths a year. Reducing antimicrobial resistance requires addressing all the sources of unnecessary antimicrobial exposure. Because the antimicrobial concentration in our food frequently approaches or exceeds the maximum allowed limits, it is crucial to ensure that the legal concentrations of antimicrobials in food do not induce antimicrobial resistance. We found that enrofloxacin doses, 10 times lower than those classified as safe, could increase enrofloxacin MICs 8-fold in K. pneumoniae in the gastrointestinal tracts of mice. These findings suggest that we need to consider the induction of antimicrobial resistance when defining safe concentrations of antimicrobials in our food.

Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts

We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.

Draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis isolated from cattle swab in Dhaka, Bangladesh

Here, we present the draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis, isolated from cattle stool swab. The genome was sequenced using the Illumina MiSeq platform, yielding a 6.33 Mb assembly with 5,784 predicted coding sequences. The genome harbors multiple antibiotic-resistance genes and virulence factors, providing insights into P. aeruginosa colonization in livestock and potential implications for antimicrobial resistance dissemination through the food chain.

Bacterial nitrite production oxidizes Fe(II) bioremediating acidic abandoned coal mine drainage

Passive remediation systems (PRSs) treating either acidic or neutral abandoned coal mine drainage (AMD) are colonized by bacteria that can bioremediate iron (Fe) through chemical cycling. Due to the low pH in acidic AMD, iron oxidation from soluble Fe(II) to precipitated Fe(III) is mainly directed by microbial oxidation. Less well described are biotic reactions that lead to iron remediation through abiotic secondary reactions. We describe here iron oxidation in acidic AMD that is mediated by the bacterial reduction of nitrate to nitrite followed by the geochemical oxidation of Fe(II). Within an acidic PRS, 4,560 bacteria cultured from the microbial community were screened for their ability to oxidize iron and to perform nitrate-dependent iron oxidation (NDFO). Iron oxidation in the culturable community was observed in every pond of the system, ranging from 2.1% to 11.4%, and NDFO was observed in every pond, ranging from 1.4% to 6.0% of the culturable bacteria. Five NDFO isolates were purified and identified as Paraburkholderia spp. One of our isolates, Paraburkholderia sp. AV18 was shown to drive NDFO through the bacterial production of nitrite that in turn chemically oxidizes Fe(II) (nitrate reduction-iron oxidation; NRIO). AV18 expressed nitrate reductase, napA, concurrent to nitrite production. Burkholderiales are found by 16S rRNA gene sequencing in every pond of the PRS. The frequency of NDFO metabolism in the culturable microbial community and abundance of Burkholderiales in the PRS suggest nitrite producers contribute to the bioremediation of iron in acidic AMD and may be an unharnessed opportunity to increase iron bioremediation in acidic conditions.

IMPORTANCE

Our study sheds light on a poorly defined biogeochemical interaction, nitrate-dependent iron oxidation (NDFO), that has been described in several environments. We show that bacterial nitrate reduction produces nitrite, which can chemically oxidize ferrous iron, leading to insoluble ferric iron. We show that bacteria capable of the nitrate reduction-iron oxidation (NRIO) reactions are prevalent throughout multiple passive remediation systems that treat acidic coal mine drainage, indicating this may be a widespread mechanism for iron removal under acidic conditions. In acidic coal mine remediation, iron precipitation has been shown to be solely bacterially mediated, and NRIO provides a simple mechanism for aerobic oxidation of iron in these conditions.

Draft genome of Lactobacillus amylovorus KSAU with probiotic potential isolated from the gastrointestinal tract of industrial pigs

The Lactobacillus amylovorus KSAU strain was isolated from the chyme of the intestinal cecum of an industrial pig. Genes encoding the synthesis of bacteriocins were annotated and suggest their potential to improve the preparation and production of probiotics for pigs.

Genetic and phenotypic stability of Lacticaseibacillus paracasei DG (DSM 34154) over 10 years of industrial production

The commercialization of a probiotic microorganism requires genetic and phenotypic consistency across production lots. However, the large-scale industrial production of probiotic microbial biomasses over years poses a risk of genetic drift, potentially affecting the probiotic's ability to confer health benefits. This study assessed the stability of Lacticaseibacillus paracasei DG (DSM 34154), a commercial probiotic. Seven isolates from different commercial lots over 10 years, one 8-year-old laboratory subculture, one isolate from human feces, and the DG strain deposited at DSMZ were analyzed. Shotgun and PacBio sequencing were combined to obtain the complete genome of the 10 isolates. Comparative analysis showed that the seven commercial isolates had identical genomes, differing from the DSMZ isolate by one synonymous transition and one non-synonymous transversion. The laboratory subculture strain had two additional mutations. Phenotypic analyses, including antibiotic resistance, carbohydrate fermentation profile, survival to simulated gastrointestinal transit, immunomodulatory capacity, and radical scavenging ability, found no significant differences among isolates. Overall, this study demonstrates the substantial equivalence of L. paracasei DG over 10 years of industrial production, indicating that the current industrial practices help prevent genome alterations that could compromise probiotic performance. Similar studies should be part of continuous monitoring and quality control measures for the probiotic products on the market.IMPORTANCEThe genetic and functional stability of probiotic strains during years of industrial production is essential but has not been clearly demonstrated for many strains. This study shows that careful industrial practices can maintain the genetic integrity and functionality of probiotics. Using advanced genome sequencing and detailed laboratory tests, we confirmed that the probiotic Lacticaseibacillus paracasei DG (DSM 34154) has remained stable over a decade of production, consistently delivering its health-promoting properties. These findings support the quality and reliability of probiotic products, fostering consumer trust and highlighting the importance of continuous monitoring in probiotic manufacturing to sustain quality assurance.

Whole-Genome Sequencing and Comparative Genomic Analysis of Three Clinical Bloodstream Infection Isolates of Trichosporon austroamericanum

Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive fungal infections and comparative analyses with 13 related Trichosporon species. The three isolates yielded high-quality assemblies of 9-10 scaffolds (~21 Mb), facilitating reliable comparisons. While most species had comparable genome sizes, Trichosporon ovoides, Trichosporon coremiiforme, and Cutaneotrichosporon mucoides displayed large, fragmented genomes, suggestive of polyploidy. ANI analysis and phylogenetic trees based on ANI and single-copy orthologs supported the classification of T. austroamericanum as a distinct clade with moderate intraspecific divergence. Using the Galleria mellonella, a model for fungal pathogenicity, all T. austroamericanum strains reduced larval survival, and NIIDF 0077300 exhibited virulence comparable to T. asahii and greater than T. inkin. To explore the gene-level differences associated with pathogenicity, we performed ortholog analysis based on single-copy genes. This revealed a unique Zn(II)2Cys6-type transcription factor gene (OG0010545) present only in NIIDF 0077300 and T. asahii. These findings highlight the genomic diversity and infection-associated traits of T. austroamericanum, providing a framework for future functional studies.

Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential

Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39T, CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879T, confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.

Draft genome sequences of two Stenotrophomonas sp. isolates obtained from the venom of the tarantula Stichoplastoris elusinus (Araneae: Theraphosidae)

Genome sequences of two Stenotrophomonas sp. strains are reported. Isolates were obtained from the venom of the tarantula Stichoplastoris elusinus (Araneae: Theraphosidae) and are closely related to the recently described Stenotrophomonas muris. The announcement highlights the presence of multiple antibiotic resistance genes and their relevance to veterinary and human health.

CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies

Despite tremendous advances in long-read sequencing, some structurally complex and repeat-rich genomic regions remain challenging to assemble. Furthermore, we lack tools to assess local assembly quality, making it hard to identify problems and assess progress. Here we develop a new approach "CloseRead" for visualizing local assembly quality and diagnosing errors using multiple metrics. We apply CloseRead to evaluate how well immunoglobulin loci, paradigmatic cases of structurally complex regions, are assembled in 74 state-of-the-art vertebrate genomes. We then show that targeted, local re-assembly can correct the specific errors identified by CloseRead, highlighting the value of an iterative approach to genome assembly.

Molecular characteristics of chromosome-mediated colistin resistance in foodborne Salmonella isolates in China

OBJECTIVE

To determine the molecular characteristics and mechanisms of colistin-resistant (COLr) Salmonella isolates from 1224 chicken samples in Shanghai, China, between January 2021 and January 2022.

METHODS

Antimicrobial susceptibility testing, site-directed mutagenesis, RT-qPCR, and lipid A analysis was conducted to investigate the mechanisms of colistin resistance in Salmonella.

RESULTS

A total of 268 Salmonella isolates were obtained from chicken samples and 41 isolates were resistant to colistin. The uncommon extensively antimicrobial-resistant Salmonella Muenster was the predominant serotype, accounting for 87.8% (36/41) of the COLr isolates. Most (95.1%, 39/41) of the COLr isolates exhibited amino acid substitutions in the PmrAB. Ten different substitutions in PmrAB were identified, with Val161Gly (n = 14) and Gly206Glu (n = 10) in PmrB being the most prevalent. Four substitutions (Thr147Ser, Phe203Ser, Gly206Glu, and Asp250Tyr) in PmrB have not been reported before and were considered novel mutations. Additionally, it was demonstrated that these substitutions upregulated pmrE and pmrK expression, resulting in the production of L-Ara4N, which modified the lipid A and resulted in an 8-64-fold increase in the colistin MIC (2-8 mg/L). Finally, the deletion of pmrE or pmrK in mutants showed MIC values comparable to parental strains (0.25 mg/L), which suggested that colistin resistance may be conferred through the pmrE and pmrK pathways.

CONCLUSIONS

These findings illustrate the complex molecular mechanisms of colistin resistance in Salmonella, and the amino acid substitutions in PmrAB are the predominant molecular mechanisms. It is essential to implement monitoring and control measures for colistin resistance.

The effects of a prospective sink environmental hygiene intervention on Pseudomonas aeruginosa and Stenotrophomonas maltophilia burden in hospital sinks

BACKGROUND

Opportunistic premise plumbing pathogens (OPPPs) can establish reservoirs in hospital plumbing and cause healthcare associated infections (HAIs). There is currently no widely accepted protocol for sink drain cleaning to reduce OPPP burden.

METHODS

We implemented a sink cleaning intervention in 12 intensive care unit (ICU) rooms. At low frequency (1×/week) and high frequency (5×/week) intervals, we wiped sink surfaces with 10% bleach wipes and pumped a foamed preacid disinfectant into sink drains. We also maintained untreated rooms (0×/week). We used E-swabs to sample sink drains and surrounding surfaces during one baseline, two intervention, and two post-intervention periods over 23 months. Samples were selectively cultured for bacterial growth and antimicrobial resistant organism (ARO) isolation. We conducted whole-genome sequencing (WGS) on Pseudomonas spp. and Stenotrophomonas spp. isolates to track impacts on reservoirs over time. We also collected and analysed clinical isolates from patients occupying the study rooms and information about HAIs that occurred.

FINDINGS

The intervention reduced the proportion of sink drains yielding Gram-negative bacteria by up to 85% (95% CI: 56-114%) in high frequency rooms versus the baseline period, but this was not significant in low frequency rooms. It also reduced the proportion of sink drains yielding Pseudomonas spp. and Stenotrophomonas spp. by up to 100% (95% CI: 79-121%) and 95% (95% CI: 65-125%) versus the baseline period in high frequency rooms and up to 71% (95% CI: 50-92%, p < 0.001) and 66% (95% CI: 27-105%, p < 0.05) in low frequency rooms, respectively. WGS showed strains of Pseudomonas aeruginosa and Stenotrophomonas maltophilia that colonised sink drains for over 3 years across two studies. Following the intervention periods, P. aeruginosa reservoirs were replaced with new strains, while S. maltophilia reservoirs returned with the same strains.

INTERPRETATION

This environmental hygiene intervention may be effective in reducing the burden of OPPPs in hospital sinks.

FUNDING

Agency for Healthcare Research and Quality (R01HS027621), National Institute of Allergy and Infectious Diseases (U01AI123394, 1K23AI137321), Barnes-Jewish Hospital Foundation (5102), Washington University Institute of Clinical and Translational Sciences (4462) from the National Center for Advancing Translational Sciences (UL1TR002345).

Draft genome sequence of Acinetobacter junii strain ABJ_A23_1 isolated from soil in Gwagwalada, Nigeria

We report the draft genome sequence of Acinetobacter junii strain ABJ_A23_1 isolated from soil in Gwagwalada, Nigeria. The genome has a total size of 3,200,723 bp, 38.48% GC content, and 3,075 genes, including 2,975 protein-coding sequences, 73 RNA genes, and an integrative conjugative element.

Genomic description of Microbacterium mcarthurae sp. nov., a bacterium collected from the International Space Station that exhibits unique antimicrobial-resistant and virulent phenotype

A novel bacterial strain, designated as 1F8SW-P5T, was isolated from the wall of the crew quarters on the International Space Station. Cells were Gram-staining-positive, strictly aerobic, non-spore-forming, chemoheterotrophic, and mesophilic rods exhibiting catalase-positive and oxidase-negative reactivity. Strain 1F8SW-P5T shared the highest 16S rRNA gene similarity with Microbacterium proteolyticum CECT 8356T (99.34%) and the highest gyrB gene similarity with Microbacterium algihabitans KSW2-21T (91.34%). Its strongest matches via average nucleotide identity and DNA-DNA hybridization were to Microbacterium hydrothermale CGMCC_1.12512T (84.36% and 25.80%, respectively). 1F8SW-P5T formed a distinct lineage during phylogenetic and phylogenomic analysis. The biochemical, phenotypic, chemotaxonomic, and phylogenomic features substantiated the affiliation to 1F8SW-P5T as a new species of Microbacterium, for which we propose the name Microbacterium mcarthurae, with the type strain 1F8SW-P5T (=DSM 115934T =NRRL B-65667T). Based on metagenomic data collected during the Microbial Tracking mission series, M. mcarthurae was identified from all surfaces (n = 8) over an 8-year period, with an increase in relative abundance over time. This is of potential concern, as we observed resistance to all tested fluoroquinolone antibiotics (n = 6), two β-lactam antibiotics, and one macrolide antibiotic, which was not predicted based on isolate or plasmid genotype alone. Furthermore, we found an increase in virulence, compared to Escherichia coli, when tested within a Caenorhabditis elegans model. This pathogenic profile highlights the importance of continued characterization of spacecraft-associated microbes, the characterization of previously unidentified antimicrobial resistance and virulence genes, and the implementation of targeted mitigation strategies during spaceflight.

IMPORTANCE

Crew members are at an increased risk for exposure to and infection by pathogenic microbes during spaceflight. Therefore, it is imperative to characterize the species that are able to colonize and persist on spacecraft, how those organisms change in abundance and distribution over time, and their genotypic potential for and phenotypic expression of pathogenic traits (i.e., whether they encode for or exhibit traits associated with antibiotic resistance and/or virulence). Here, we describe a novel species of Microbacterium collected from the crew quarters on the International Space Station (ISS), 1F8SW-P5T, for which we propose the name Microbacterium mcarthurae. M. mcarthurae was found to be distributed throughout the ISS with an increase in relative abundance over time. Additionally, this bacterium exhibits a unique antibiotic resistance phenotype that was not predicted from whole-genome sequencing, as well as increased virulence, suggesting the need for the identification of previously undescribed antimicrobial resistance genes and monitoring/mitigation during spaceflight.

Comparative genomic analysis of Streptococcus suis sequence type 105 and development of a PCR diagnostic tool

Streptococcus suis serotype 14 is the second most prevalent serotype after serotype 2, and is highly prevalent in Southeast Asia. Among the serotype 14 strains, sequence type (ST) 105 is found in humans and pigs. We analysed the genome sequences of S. suis ST105 to identify unique sequences to develop a multiplex PCR (mPCR) -gel electrophoresis and mPCR-lateral flows trip (LFS) for epidemiological purposes. The ST105 genome was closely related to the ST1 genomes. All ST105 of Thai and Vietnamese strains were highly homologous. Of the 1818 genes found in all compared genomes, 36 unique sequences were detected only in the ST105 strain. Of these, two unique sequences encoding hypothetical proteins were selected as PCR targets. Only S. suis ST105 strains were positive for both mPCRs. mPCR-LFS had fewer complications, lower costs, and less time for testing, than those of mPCR-gel electrophoresis. This comparative genomic study demonstrates the usefulness of identifying unique sequences of ST105 S. suis. These unique sequences could be used to develop diagnostic or screening tools, such as PCR, for the detection of specific strains or clones for epidemiological purposes.

Saccharomycopsis yichangensis sp. nov., a Novel Predacious Yeast Species Isolated From Soil

Two yeast strains belonging to the ascomycetous yeast genus Saccharomycopsis were isolated from soil collected from a forest in Wufeng Tujia Autonomous County, Yichang, Hubei province, China. Phylogenetic analyzes of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene showed that they closely related to S. fermentans and S. babjevae but differed from S. fermentans by 17 (3.09%, 15 substitutions and two gaps) and 30 (4.85%, 22 substitutions and eight gaps) mismatches, and from S. babjevae by 13 (2.39%, eight substitutions and five gaps) and 21 (3.46%, 14 substitutions and seven gaps) mismatches in the D1/D2 domain and ITS region, respectively. A phylogenomic analysis based on 1260 single-copy orthologs confirmed the close relationship of the new Chinese strains with S. fermentans and S. babjevae. The whole genome average nucleotide identity (ANI) values of the new strains with the two species are 85.7% and 86.9%, respectively. The results suggest that the two strains represent a novel species, for which the name Saccharomycopsis yichangensis sp. nov. (holotype strain CGMCC 2.7390) is proposed. The Fungal Names number is FN 572295. The novel yeast is homothallic and produces asci containing four spheroidal ascospores with an equatorial or subequatorial ledge. This species can prey on cells of Jamesozyma jinghongensis, Meyerozyma carpophila and Saccharomyces cerevisiae through invasive infection pegs.

Draft genome sequences of Mycobacterium caprae strains linked to human tuberculosis in Canada

Mycobacterium caprae is a causative agent of tuberculosis that affects both humans and animals. Here, we present the draft genome sequences of two M. caprae strains. These genome sequences may improve understanding of M. caprae epidemiology and support diagnostic development.

Heterogeneity in recombination rates and accessory gene co-occurrence distinguish Pseudomonas aeruginosa phylogroups

Pseudomonas aeruginosa (class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It is also an opportunistic pathogen that causes a variety of chronic and acute infections in humans. Its ability to thrive in diverse environments and exhibit a wide range of phenotypes lies in part on its large gene pool, but the processes that govern inter-strain genomic variation remain unclear. Here, we aim to characterize the recombination features and accessory genome structure of P. aeruginosa using 840 globally distributed genome sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding to known phylogroups), two of which are most prominent. Notable epidemic clones are found in the two phylogroups: ST17, ST111, ST146, ST274, and ST395 in phylogroup 1, and ST235 and ST253 in phylogroup 2. The two phylogroups differ in the frequency and characteristics of homologous recombination in their core genomes, including the specific genes that most frequently recombine and the impact of recombination on sequence diversity. Each phylogroup's accessory genome is characterized by a unique gene pool, co-occurrence networks of shared genes, and anti-phage defense systems. Different pools of antimicrobial resistance and virulence genes exist in the two phylogroups and display dissimilar patterns of co-occurrence. Altogether, our results indicate that each phylogroup displays distinct histories and patterns of acquiring exogenous DNA, which may contribute in part to their predominance in the global population. Our study has important implications for understanding the genome dynamics, within-species heterogeneity, and clinically relevant traits of P. aeruginosa.

IMPORTANCE

The consummate opportunist Pseudomonas aeruginosa inhabits many nosocomial and non-clinical environments, posing a major health burden worldwide. Our study reveals phylogroup-specific differences in recombination features and co-occurrence networks of accessory genes within the species. This genomic variation partly explains its remarkable ability to exhibit diverse ecological and phenotypic traits, and thus contribute to circumventing clinical and public health intervention strategies to contain it. Our results may help inform efforts to control and prevent P. aeruginosa diseases, including managing transmission, therapeutic efforts, and pathogen circulation in non-clinical environmental reservoirs.

Comparative genomic analysis of Flavobacterium species causing columnaris disease of freshwater fish in Thailand: insights into virulence and resistance mechanisms

BACKGROUND

Columnaris disease, a prevalent disease among farmed and wild freshwater fish, is caused by the Flavobacterium columnare group, which includes four distinct species: F. columnare, F. oreochromis, F. covae, and F. davisii. Among these, F. oreochromis, F. covae, and F. davisii are particularly prevalent in farmed freshwater fish in Thailand. In this study, a comparative genomic analysis of 22 isolates was conducted to elucidate virulence factors, antibiotic resistance genes (ARGs), genomic islands (GIs), phages, insertion elements (ISs), and clustered regularly interspaced short palindromic repeats (CRISPRs).

RESULTS

A total of 212 putative virulence genes were predicted across three species with F. oreochromis exhibiting the highest number of unique virulence genes, followed by F. davisii, and F. covae. Moreover, 195 genes were predicted as ARGs, with F. oreochromis and F. covae showing an abundance of unique genes associated with resistance to quinolone, fluoroquinolone, and tetracycline antibiotics. Antimicrobial susceptibility testing, assessed with epidemiological cut-off values (ECVs), revealed decreased susceptibility to quinolones, fluoroquinolones and tetracycline in several isolates of F. oreochromis and F. covae. F. oreochromis and F. covae exhibited notable decreased susceptibility to quinolones, with mutations observed in the quinolone resistance-determining regions (QRDRs) of gyrA, including Ser83Phe, Ser83Val, Ser83Ala, and Asp87Tyr, the latter representing a novel mutation among isolates from Thailand. As a result, these findings suggest that gyrA is major target for quinolone in F. oreochromis, F. covae, and F. davisii, while gyrB, parC, parE might be less important to the decreased phenotypic susceptibility to this class of antimicrobials. Moreover, a tetracycline resistance gene (tetA_2) was found in only one F. covae isolate, which exhibited decreased phenotypic susceptibility to this drug, marking the first report of decreased susceptibility in this species.

CONCLUSIONS

This study provides insights into the genetic and pathogenic diversity of Flavobacterium species, aiding in the development of strategies to manage columnaris disease in farmed freshwater fish in Thailand.

Complete Mitochondrial Genome Characterization and Phylogenomics of the Stingless Bee, Heterotrigona itama (Apidae: Meliponini)

With increasing demand for stingless bee honey, meliponiculture has gained widespread attention. Heterotrigona itama is one of the most economically important species. However, excessive exploitation for commercial purposes has led to population declines, and the species is now considered vulnerable in Thailand. Despite its ecological and economic significance, genomic and taxonomic information on H. itama remains limited. In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of H. itama to explore its genome structure and phylogenetic position. The circular mitogenome is 15,318 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The genome exhibits a strong A+T bias (75.41%), which affects codon usage and amino acid composition. Isoleucine, methionine, and phenylalanine were the most commonly encoded amino acids. Gene arrangement was highly conserved and closely resembled that of Tetragonula species. Phylogenetic analyses confirmed that H. itama clusters with other stingless bees and is more closely related to bumblebees than to honeybees. Several gene rearrangements suggest a high degree of mitogenomic plasticity. This study provides essential genomic resources for future studies in systematics, phylogenetics, population genetics, and conservation of stingless bees in the Meliponini tribe.

Understanding the epidemiology and pathogenesis of Mycobacterium tuberculosis with non-redundant pangenome of epidemic strains in China

Tuberculosis is a major public health threat resulting in more than one million lives lost every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China including 344 Lineage 2 strains, 69 Lineage 4 strains, six Lineage 3 strains, and one Lineage 1 strain. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 are core genes. However, due to 99,694 interruptions in 2,447 coding genes, we can only confidently confirm 1,651 of these genes are translated in all samples. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structural variations, mostly small indels. Assuming a proportion of these interruptions are artifacts, the number of active core genes would still be much lower than 3,438. We further described differential evolutionary patterns of genes under the influences of selective pressure, population structure and purifying selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations are concentrated in 1,310 genes. Genes involved in cell wall biogenesis are under the strongest selective pressure, while the biological process of disruption of host organelles indicates the direction of the most intensive positive selection. This study provides a comprehensive view on the genetic diversity and evolutionary patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.

The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake

BACKGROUND

Venoms and their associated glands and delivery structures have evolved numerous times among animals. Within these venom systems, the molecular, cellular, and morphological components interact and co-evolve to generate distinct, venom phenotypes that are increasingly recognized as models for studying adaptive evolution. However, toxins are often unevenly distributed across venom-producing tissues in patterns that are not necessarily adaptive but instead likely result from constraints associated with protein secretion.

RESULTS

We generate a high-quality draft genome of the Cape coral snake (Aspidelaps lubricus) and combine analyses of venom gland single-cell RNA-seq data with spatial venom gland in situ toxin distributions. Our results reveal that while different toxin families are produced by distinct populations of cells, toxin expression is fine-tuned by regulatory modules that result in further specialization of toxin production within each cell population. We also find that the evolution of regulatory elements closely mirrors the evolution of their associated toxin genes, resulting in spatial association of closely related and functionally similar toxins in the venom gland. While this compartmentalization is non-adaptive, the modularity of the underlying regulatory network likely facilitated the repeated evolution of defensive venom in spitting cobras.

CONCLUSIONS

Our results provide new insight into the variability of toxin regulation across snakes, reveal the molecular mechanisms underlying the heterogeneous toxin production in snake venom glands, and provide an example of how constraints can result in non-adaptive character states that appear to be adaptive, which may nevertheless facilitate evolutionary innovation and novelty.

Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis

BACKGROUND

Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor protein bound to an adapter sequence, which is added either using ligation-based methods (ligation sequencing kit), or transposase-based methods (rapid sequencing kit). However, these methods have enzymatic steps that may be susceptible to motif bias, including the underrepresentation of adenine-thymine (AT) sequences due to ligation and biases from transposases. This study aimed to compare the recognition motif and relative interaction frequencies of these library preparation methods and assess their effects on relative sequencing coverage, microbiome, and methylation profiles. The impacts of DNA extraction kits and basecalling models on microbiome analysis were also investigated.

RESULTS

By using sequencing data generated by the ligation and rapid library kits, we identified the recognition motif (5'-TATGA-3') consistent with MuA transposase in the rapid kit and low frequencies of AT in the sequence terminus of the ligation kit. The rapid kit showed reduced yield in regions with 40-70% guanine-cytosine (GC) contents, while the ligation kit showed relatively even coverage distribution in areas with various GC contents. Due to longer reads, ligation kits showed increased taxonomic classification efficiency compared to the rapid protocols. Rumen microbial profile at different taxonomic levels and mock community profile showed significant variation due to the library preparation method used. The ligation kit outperformed the rapid kit in subsequent bacterial DNA methylation statistics, although there were no significant differences.

CONCLUSIONS

Our findings indicated that careful and consistent library preparation method selection is essential for quantitative methods such as bovine-related microbiome analysis due to the systematic bias induced by the enzymatic reactions in Oxford Nanopore library preparation.

Drug Susceptibility, Siderophore Production, and Genome Analysis of Staphylococcus aureus Clinical Isolates from a University Hospital in Chiang Mai, Thailand

Background/Objective:Staphylococcus aureus produces staphyloferrin A (Sfna) siderophores to sequester host iron during infection and rapid cell proliferation We examined drug susceptibility, siderophore production, and genome sequencing of clinical isolates of S. aureus. Methods: A total of 100 specimens, including pus, sputum, hemoculture, urine, tissue, fluid, and skin scrap specimens, were grown in iron-deprived Luria broth agar. The isolates were investigated for spectral signature using MALDI-TOF/MS, while antibiotic susceptibility and siderophore content were assessed using the chrome azurol S method. Whole genome and partial 16S rRNA DNA sequences were employed, and VITEK/MS revealed specific spectra. Results: Clindamycin, erythromycin, gentamicin, linezolid, moxifloxacin, oxacillin, trimethoprim/sulfamethoxazole, and vancomycin (100%) were the most common antibiotics to which the S. aureus isolates were susceptible. Sfna was not detectable in fluid and skin scrap isolates, which were encoded by sfnaB, sfnaD, and sfnaB/sfnaD genes. However, they were detectable in pus (73.8%), sputum (85.3%), hemoculture (50.0%), and urine (85.7%) isolates. The aureus subspecies, JKD6159, SA268, and MN8, were found to be 72.73% according to genome sequencing. Conclusion: most staphylococci in the isolates, including S. aureus JKD6159, SA268, and MN8, were sensitive to antibiotics and were detected by MALDI-TOF/MS, resulting in the production of Sfna encoded by sfna genes.

A hospital-wide outbreak of ESBL-producing Klebsiella oxytoca associated with contaminated sinks and associated plumbing: outbreak report, risk factor analysis and plasmid mapping

OBJECTIVES

To describe a sink-related outbreak of Klebsiella oxytoca and determine risk factors for acquiring the outbreak strain.

METHODS

Case-control analysis, environmental sampling from sinks, short-read whole genome sequencing and long-read whole genome sequencing of selected isolates.

RESULTS

Whole genome sequencing revealed genetic clustering of 47 patient cases over 26 months. The outbreak strain (Klebsiella oxytoca, sequence type 2, with or without blaCTX-M containing plasmid) was also identified in sinks or adjacent plumbing in four rooms in two wards. After adjustment for age, sex, and length of stay, four significant risk factors for infection or colonization of the outbreak strain were found: age (OR per additional year: 1.03 (95% CI: 1.00-1.07); length of stay (OR per additional day: 1.04 (95% CI: 1.02-1.08); urinary catheter (OR: 7.65 (95% CI: 2.10-27.8; OR per additional day: 1.06 (95% CI: 1.01-1.12); and diarrhoea (OR: 3.10 (1.03-9.35). Long-read plasmid sequencing revealed strong indications of plasmid transmission from the outbreak strain to other sequence types of Klebsiella oxytoca. Multifaceted interventions were employed, including exchange of sinks strainers, traps, and piping, behavioural interventions, and reinforced cleaning and disinfection. Outbreak control has so far not been achieved despite interventions.

CONCLUSIONS

Klebsiella oxytoca established in sink plumbing biofilm was associated with a prolonged outbreak difficult to control. Age, length of stay, urinary catheter and diarrhoea were risk factors for acquiring the outbreak strain. Both clonal and horizontal transmission occurred.

Genomic Features of E. ruysiae Associated with the Ecological Origin: Implications for the Environmental Hypothesis

Escherichia cryptic clades represent a relatively unexplored taxonomic cluster believed to exhibit characteristics associated with a free-living lifestyle, which is known as the environmental hypothesis. This hypothesis suggests that certain Escherichia strains harbour traits that favour their environmental persistence, thus expanding the ecological commensal niche of the genus. While surveying Escherichia diversity in an urban South American stream we isolated the first environmental cryptic clade IV strain in South America (339_SF). Here we report the genomic characterization of 339_SF strain in the context of existing genomic information for E. ruysiae (cryptic clades III and IV). A comparative analysis of genomes within the same species stemming from diverse ecological sources and geographical locations reveals close phylogenetic proximity between our isolate and strains of environmental origin. Based on genetic content, we observed two clusters associated with the environmental source within E. ruysiae. In addition, we identified genes relatively more represented in the environmental strains: genes associated with carbohydrate metabolism (ydjG), stress response and DNA damage repair (such as umuD, higA and yddM). On the other hand, the gene rrrQ, associated with defense against other microorganisms, was significatively enriched in genomes of commensal origin. Our findings suggest that genomic features within E. ruysiae favoring its persistence in open environments may have arisen more than once, with these events being associated with the use of alternative energy sources and the resistance to various stressors specific to these environments.

Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka

BACKGROUND

Antimicrobial resistance (AMR) is a major global challenge that disproportionately affects low- and middle-income countries (LMICs). Environmental contamination by resistant bacteria from animal production facilities is a major driver of the spread of AMR through the food chain, requiring a robust one-health control approach. Traditional culture-based AMR surveillance is time-consuming and less sensitive, and fails to fully capture the spectrum of AMR, evolutionary trends, and epidemiological patterns of AMR spread. Whole-genome sequencing (WGS) has revolutionized AMR surveillance capabilities. Rapid WGS captures the full AMR spectrum with minimum samples, aids source attribution, and provides insights into trends in AMR spread. The portable Oxford Nanopore® Technology (ONT) platform, coupled with open-source software such as Galaxy and Konstanz Information Miner (KNIME), enables the establishment of a potentially portable, transferable workflow for low-resource settings. This study aimed to assess the AMR burden on four dairy farms in Kandy, Sri Lanka, via a resource-limited LMIC using a low-cost high-throughput screening assay and rapid WGS via ONT with Galaxy and KNIME processing to obtain full antibiotic resistomes.

RESULTS

The four isolates exhibiting the highest minimum inhibitory concentrations for amoxicillin were identified as Enterobacter cloacae and E. hormaechei by WGS. Chromosomes (4.8 to 4.9 Mb) carry the strain-specific resistance genes blaCMH-1, blaACT-25, fosA_7, and ramA, which are associated with diverse antibiotic classes. Plasmids, including IncFIB (pECLA), IncFII (pECLA), and IncX3, carry multiple resistance genes, including AAC(3)-IIe, AAC(6')-Ib-cr, APH(3″)-Ib, APH(6)-Id, blaCTX-M-15, blaNDM, blaOXA-1, blaTEM-1, dfrA14, QnrB17, catII, determinant-of-bleomycin-resistance, and sul2. Novel arrangements of insertion sequences were observed in E. hormaechei plasmids. The phenotypic resistance of all the isolates matched the genotypic MDR profiles, including resistance to chloramphenicol, gentamicin, tetracycline, and cotrimoxazole.

CONCLUSIONS

ONT WGS with Galaxy and KNIME processing may be a feasible option for AMR surveillance in resource-limited LMICs. To the best of our knowledge, this is the first in-house whole-genome analysis workflow in the country tailored for AMR surveillance. The presence of potentially pathogenic high-MIC, MDR Enterobacter spp. with wide resistomes, including the blaNDM gene, emphasizes the urgent need to address AMR in animal production facilities within a one-health framework.

Occurrence and characteristics of extended-spectrum ß-lactamase-producing Escherichia coli in Swiss and imported retail chicken meat

OBJECTIVE

The occurrence of extended-spectrum ß-lactamase (ESBL) producing Enterobacterales in food is of concern because of the possibility of transmission of ESBL-producers and/or blaESBL genes to humans. This study aimed to investigate the presence of ESBL-producing Enterobacterales in Swiss and imported retail chicken meat.

METHODS

A total of 200 samples of different types of Swiss and imported chicken meat obtained at retail level in Switzerland were screened for ESBL-producing Enterobacterales using a selective culture medium. All non-intrinsically resistant isolates were characterised by antimicrobial susceptibility testing (AST), multilocus sequence typing (MLST), and whole genome sequencing (WGS).

RESULTS

Eighteen meat samples (9%) yielded a total of 19 ESBL-producing Escherichia coli (ESBL-EC). The proportion of samples containing ESBL-EC was higher in imported meat (14/55; 25%) than in Swiss meat (4/145; 3%). Co-resistance to ciprofloxacin was highly prevalent (18/19, 95%). E. coli sequence types (STs) included ST602, ST744, ST1844, and extraintestinal pathogenic (ExPEC) E. coli ST38. The blaESBL genes comprised blaCTX-M-1 (n=7), blaCTX-M-2 (n=1), blaCTX-M-8 (n=1), blaCTX-M-55 (n=1), blaSHV-12 (n=8), and blaTEM-52B (n=1). They were chromosomally (n=2) encoded or carried on plasmids belonging to IncB/O/K/Z (n=1), IncFII (n=1), IncI1-I(Alpha) (n=9), IncX1 (n=1), and IncX3 (n=5). Many of the plasmids were identical to those detected globally in ESBL-producers associated with broilers.

CONCLUSIONS

The contamination with ESBL-EC in retail chicken meat in Switzerland is moderate; nevertheless, domestic and imported chicken meat is a potential vehicle for MDR ESBL-EC and for genes conferring resistance to clinically important antimicrobials including 3rd-generation cephalosporins and fluoroquinolones.

Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features

Plesiomonas shigelloides, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on P. shigelloides PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (adeF, tet(A)), target modifiers (dfrA1, sul2), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (fliM, fliN, flhA) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of P. shigelloides PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.

Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis

High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.

IMPORTANCE

This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data

Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE

Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.

Molecular characterization of carbapenem resistance mechanisms and phenotypic correlations in clinical Klebsiella pneumoniae isolates from Ningbo, China

Objective

The purpose of this study is to understand the antimicrobial susceptibility and molecular distribution characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) in the region, and to evaluate their correlation. Additionally, the study aims to investigate the transmission status of these strains.

Methods

A total of 150 CRKP collected from January 2019 to December 2021 in the Ningbo region were included in this study. Antimicrobial susceptibility testing was performed using broth microdilution method following CLSI guidelines (CLSI, 2023). The tested agents included: (1) basic antimicrobials (tigecycline, polymyxin B, ceftazidime-avibactam); and (2) combination therapy candidates (ertapenem, imipenem, levofloxacin, piperacillin-tazobactam, ceftriaxone, cefepime, trimethoprim-sulfamethoxazole, fosfomycin, amikacin, aztreonam, chloramphenicol, amoxicillin-clavulanate, ceftazidime). Resistance genes were detected using polymerase chain reaction (PCR). Multi-locus sequence typing (MLST) was employed to analyze the molecular characteristics and evolutionary trends of the strains to determine their clonal relationships.

Results

The 150 strains of CRKP exhibit high resistance rates to various conventional drugs; The sensitivity rates to tigecycline, polymyxin B, and ceftazidime-avibactam were 98.7, 98.0, and 68%, respectively; Conversely, the sensitivity rates to fosfomycin, amikacin, and chloramphenicol were 72.0, 40.0, and 16.7%, respectively; The main proportions of carbapemen genes producing in CRKP are as follows: KPC-2 (61.3%), NDM-5 (14.7%), IMP-4 (8.0%), OXA-232 (6.0%), and OXA-181 (1.3%); The main proportions of β-lactamase resistance genes are as follows: CTX-M-1 (13.33%), CTX-M-3 (25.33%), CTX-M-9 (17.33%), CTX-M-14 (34.67%), SHV-1 (26.66%), SHV-11 (66.66%), SHV-12 (18.66%), and SHV-28 (10.00%); CRKP carrying class A, B, and D carbapenemases had a sensitivity rate greater than 96% for tigecycline and polymyxin B, while their sensitivities to ceftazidime-avibactam, aztreonam, and amikacin varied significantly (p < 0.01). Analysis of the MLST results for CRKP revealed that ST11 strains were predominant in the region. There was a significant difference in the resistance genes carried by ST11 strains compared to non-ST11 strains. While different healthcare institutions exhibited variations in ST types, the strains generally showed high homogeneity.

Conclusion

In the region, CRKP showed high sensitivity to tigecycline, polymyxin B, ceftazidime-avibactam, fosfomycin, amikacin, and chloramphenicol. The main carbapenemase genes identified were KPC-2 and NDM-5. The inhibitory effects of ceftazidime-avibactam, aztreonam, and amikacin varied for CRKP carrying different enzyme types. ST11 strains were predominant in the region. There was a significant difference in the resistance genes carried by ST11 strains compared to non-ST11 strains. Clonal dissemination was observed both within the same healthcare institution and between different institutions.

Whole-genome probe capture sequencing reveals genomic diversity and characteristics of Mycoplasma pneumoniae in Nanjing, China

Mycoplasma pneumoniae (M. pneumoniae), a slow-growing, fastidious Gram-negative bacterium and a leading cause of community-acquired pneumonia globally, remains understudied and underreported across numerous geographical areas in China despite its worldwide significance. This study employed probe capture sequencing for targeted enrichment and direct sequencing of M. pneumoniae from clinical samples, combined with comparative genomic analyses of contemporary and historical global genomes. Core genome and pan-genome revealed that the M. pneumoniae genomes were classified into two distinct clades, P1-I and P1-II, each associated with a specific sequence type (ST). Most of the genomes sequenced in this study were identified as P1-I (86.96%, 20/23), contrasting with the previously reported predominance of P1-II in the area. A limited number of single-nucleotide variations were identified in the virulence-associated genes between P1-I and P1-II, leading to amino acid substitutions. The A2063G point mutation in the 23S rRNA gene was detected in all sequenced genomes (23/23), demonstrating a 100% mutation rate. This study provides the first reported application of probe capture methodology for M. pneumoniae, highlighting the critical importance of sustained surveillance efforts to monitor the evolution and epidemiology of this pathogen.

Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix

Bacillus cereus sensu lato is frequently involved in foodborne toxico-infections and is found in various foodstuff. It is unclear whether certain strains have a higher affinity for specific food matrices, which can be of interest for risk assessment. This study reports the characterization by whole-genome sequencing of 169 B. cereus isolates, isolated from 12 food types and soil over two decades. Any potential links between the food matrix of isolation, the isolate's genetic lineage and/or their (putative) virulence gene reservoir were investigated. More than 20 % of the strains contained the genes for the main potential enterotoxins (nheABC, hblCDA and cytK_2). Cereulide biosynthesis genes and genes encoding hemolysins and phospholipases, were detected in multiple isolates. Strain typing revealed a high diversity, as illustrated by 84 distinct sequence types, including 26 not previously described. This diversity was also reflected in the detection of all seven panC types and 71 unique virulence gene profiles. Core-genome MLST was used for phylogenomic investigation of the entire collection and SNP-based clustering was performed on the four most abundant sequence types, which did not reveal a clear affinity for specific B. cereus lineages or (putative) virulence genes for certain food matrices. Additionally, minimal genetic overlap was observed between soil and foodborne isolates. Clusters of closely-related isolates with common epidemiological metadata were detected. However, some isolates from different food matrices or collected several years apart were found to be genetically identical. This study provides elements that can be used for risk assessment of B. cereus in food.

Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period

The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.

Genome diversity and signatures of natural selection in mainland Southeast Asia

Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age

BACKGROUND

Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS

Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS

We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.

Novel Anti-MRSA Peptide from Mangrove-Derived Virgibacillus chiguensis FN33 Supported by Genomics and Molecular Dynamics

Antimicrobial resistance (AMR) is a global health threat, with methicillin-resistant Staphylococcus aureus (MRSA) being one of the major resistant pathogens. This study reports the isolation of a novel mangrove-derived bacterium, Virgibacillus chiguensis FN33, as identified through genome analysis and the discovery of a new anionic antimicrobial peptide (AMP) exhibiting anti-MRSA activity. The AMP was composed of 23 amino acids, which were elucidated as NH3-Glu-Gly-Gly-Cys-Gly-Val-Asp-Thr-Trp-Gly-Cys-Leu-Thr-Pro-Cys-His-Cys-Asp-Leu-Phe-Cys-Thr-Thr-COOH. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for MRSA were 8 µg/mL and 16 µg/mL, respectively. FN33 AMP induced cell membrane permeabilization, suggesting a membrane-disrupting mechanism. The AMP remained stable at 30-40 °C but lost activity at higher temperatures and following exposure to proteases, surfactants, and extreme pH. All-atom molecular dynamics simulations showed that the AMP adopts a β-sheet structure upon membrane interaction. These findings suggest that Virgibacillus chiguensis FN33 is a promising source of novel antibacterial agents against MRSA, supporting alternative strategies for drug-resistant infections.

The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander

The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.

Multiplex polymerase chain reaction (PCR) with Nanopore sequencing for sequence-based detection of four tilapia pathogens

Background

Tilapia aquaculture faces significant threats posed by four prominent pathogens: tilapia lake virus (TiLV), infectious spleen and kidney necrosis virus (ISKNV), Francisella orientalis, and Streptococcus agalactiae. Currently, employed molecular diagnostic methods for these pathogens rely on multiple singleplex polymerase chain reactions (PCR), which are time-consuming and expensive.

Methods

In this study, we present an approach utilizing a multiplex PCR (mPCR) assay, coupled with rapid Nanopore sequencing, enabling the one-tube simultaneous detection and one-reaction Nanopore sequencing-based validation of four pathogens.

Results

Our one-tube multiplex assay exhibits a detection limit of 1,000 copies per reaction for TiLV, ISKNV, and S. agalactiae, while for F. orientalis, the detection limit is 10,000 copies per reaction. This sensitivity is sufficient for diagnosing infections and co-infections in clinical samples from sick fish, enabling rapid confirmation of the presence of pathogens. Integrating multiplex PCR and Nanopore sequencing provides an alternative approach platform for fast and precise diagnostics of major tilapia pathogens in clinically sick animals, adding to the available toolbox for disease diagnostics.

Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes

Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.

Persistence of mcr-1-carrying E. coli in rabbit meat production: Challenges beyond long-term colistin withdrawal

Colistin, a last-resort antibiotic in human medicine, has been banned in European food animal production to mitigate antimicrobial resistance. This study investigates the long-term effects of the colistin ban on the occurrence and genomic features (WGS) of colistin-resistant, mcr-carrying Escherichia coli across intensive rabbit farms (8 farms, ~600 animals/farm, fecal and farm environmental samples) in the north and center of Portugal. Colistin-resistant E. coli was detected in 25 % of groups from three farms in pre-slaughter fecal samples, with mcr-1-positive strains found throughout the lifecycle (does, offspring, and feed) in all fecal samples from one farm. A polyclonal multidrug-resistant (MDR) E. coli population carrying mcr-1 persisted over three years, mostly in pre-slaughter rabbits but also in newly arrived younger does (GP). Comparative genomic analysis (cgMLST) revealed four clusters, with closely related strains between rabbit feces and feed (ST1196, ST40) and between feces and GP (ST1196), suggesting external reservoirs, biosecurity concerns, and cross-contamination. WGS also revealed high load and diversity in virulence (EPEC and ExPEC), antibiotic resistance and genes related to metal decreased susceptibility. All mcr-1 genes were located on similar IncHI2 multireplicon plasmids, carrying sil + pco (copper) co-located with antibiotic resistance genes, and circulating in global sources. These results highlight that, despite colistin withdrawal, MDR mcr-carrying E. coli clones persist over three years in a single farm, underscoring complex co-selection pressure and biosecurity gaps. The findings underscore food safety risks via the food chain and environmental contamination. Enhanced biosecurity, feed monitoring, and One Health surveillance are essential to mitigate AMR dissemination and safeguard public health.

Emergence and characterization of a ST852 Klebsiella quasipneumoniae clinical isolate coharboring bla NDM-1 and bla KPC-2 in China

Objectives

To characterize a rare ST852 Klebsiella quasipneumoniae strain co-producing NDM-1 and KPC-2 isolated from a clinical patient.

Methods

Minimum inhibitory concentrations (MICs) were measured using a VITEK 2 compact system and broth microdilution. Conjugation experiments were conducted using film matings. Whole genome sequencing (WGS) was performed using Illumina and Nanopore platforms. Antimicrobial resistance determinants were identified using the ABRicate program in the ResFinder database. Insertion sequences (ISs) were identified using ISFinder. Bacterial virulence factors were identified using a virulence factor database (VFDB). Genome function annotation and classification were further analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups (COG) databases. Capsular polysaccharides (KL) and lipooligosaccharides (OCL) were tested using Kleborate with the Kaptive. Multilocus sequence typing (MLST) and replicon types were identified using the Center for Genomic Epidemiology website. Prophage region analysis was performed using PHASTEST software. Conjugation-related elements were predicted using oriTfinder. The plasmid structure was visualized using Circos and similar plasmids in the public database were tracked using BacWGSTdb. A global phylogeny for the ST852 K. quasipneumoniae isolates was further performed.

Results

K. quasipneumoniae KPSY isolate was identified as ST852, with KL18 and O3/O3a. It has an extensive drug-resistant (XDR) profile. WGS analysis revealed that it contained one circular chromosome and three plasmids. The results of the COG and KEGG functional classifications showed that most of the functions were associated with metabolism. pKPSY-2 is a 239,226-bp IncU plasmid carrying the carbapenem resistance gene bla NDM-1. pKPSY-3 is a smaller plasmid belonging to the IncN-type conjugative plasmid with bla KPC-2. Importantly, oriT sequence, the T4SS region, T4CP, and relaxase were identified. Tracking of the bla KPC-2 plasmids showed they were identified in different species in different countries, including E. coli, Leclercia sp., Pantoea sp., and E. hormaechei. Global analysis data showed 13 ST852 strains were mainly isolated from China (84.62%, 11/13), and the remaining isolates were collected from Switzerland.

Conclusions

This is the first study to identify an ST852 NDM-1-KPC-2 coproducing K. quasipneumoniae clinical isolate. Surveillance is warranted, and early detection of this high-risk clone in the clinic is recommended to avoid its extensive spread.

Exploratory Genomic Marker Analysis of Virulence Patterns in Listeria monocytogenes Human and Food Isolates

Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined the genotypic factors influencing the pathogenicity of L. monocytogenes, focusing on virulence gene profiles and key integrity genes like inlA to explain these divergences. The dataset included 958 strains isolated from human, food, and environmental samples. Whole-genome sequencing identified virulence genes, and principal component analysis (PCA) examined 92 virulence genes and inlA integrity to uncover potentially pathogenic patterns. The results highlight differences in virulence characteristics between strains of different origins. The integrity of inlA and genes such as inlD, inlG, and inlL were pivotal to pathogenicity. Strains with premature stop codons (PMSCs) in inlA, associated with reduced virulence, accounted for a low percentage of human cases but over 30% of food isolates. Sequence types (STs) like ST121, ST580, and ST199 showed unique profiles, while ST9, dominant in food, occasionally caused human cases, posing risks to vulnerable individuals. This research highlights the complexity of the pathogenicity of L. monocytogenes and emphasizes the importance of genomic surveillance for effective risk assessment.

Genomic analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causing infections in children-a Spanish multicenter study

Objectives

Staphylococcus aureus is one of the most common human pathogens causing skin and soft tissue infections (SSTIs) among children. This study investigated the molecular traits of community-associated methicillin-resistant S. aureus (CA-MRSA) isolates causing infections in children in Spain.

Methods

Antibiotic susceptibility testing and whole-genome sequencing were performed in 98 CA-MRSA isolates (4.2 median age, 52% males). The phylogenetic relationship, antibiotic resistance, virulence, and plasmid replicon genes content were investigated.

Results

Resistance rates were found as follows: Erythromycin, 42.9%, which could be explained due to the presence of erm(C), mph(C), and msr(A) genes; tobramycin, 27.5%, which could be explained due to the presence of aac(6')-Ie/aph(2″)-Ia and aadD1 genes; tetracycline, 25.5%, which could be explained mainly due to the presence of tet(K) genes; levofloxacin and moxifloxacin, 19.4%, which could be explained primarily due to the mutations in gyrA and parC genes; and gentamicin, 15.3%, which could be explained due to the presence of aac(6')-Ie/aph(2″)-Ia gene. The most prevalent lineage was ST8-IVc and t008. Most isolates were genetically diverse, except for three groups of isolates from the same hospital and one group of isolates from different hospitals. These had less than or equal to 5 allele differences by core-genome multilocus sequence typing (cgMLST) analysis or 0-6 core single-nucleotide polymorphisms (SNPs) by core-genome SNP-based analysis. Phage-encoded Panton-Valentine leukocidin (PVL) genes were found in 75.5% of the isolates. Other common virulence genes were related to adhesion (capA and capP), lipid degradation (geh), hemolysis (hlb, hld, hlgABC, and hly/hla), and tissue destruction (sspAB).

Conclusion

This study observed a high genetic diversity among CA-MRSA isolates causing community-acquired infections in children in Spain, with ST8-IVc as the most prevalent lineage. Nevertheless, genetic relatedness of some isolates from the same as well as different hospitals suggests the dissemination of CA-MRSA among children by contact.

In Silico Characterization of Resistance and Virulence Genes in Aeromonas jandaei Strains Isolated from Oreochromis niloticus in Brazil

Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.

Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback

Ash dieback caused by the fungus Hymenoscyphus fraxineus has devastated the European ash tree population since it arrived in Europe in 1992. Great effort has been put into breeding programs to increase the genetic diversity of ash trees and find heritable genetic markers associated with resistance, or tolerance mechanisms, to ash dieback. To facilitate identification of molecular markers, we used Oxford Nanopore Technologies combined with Illumina sequencing to obtain an accurate and contiguous ash genome. We used this genome to reanalyze transcriptome data from a Danish ash panel of 182 tree accessions. Using associative transcriptomics, we identified 175 gene expression markers, including 11 genes annotated as dormancy MADS-box transcription factors which are associated with ash bud dormancy, flowering, and senescence. We hypothesize that tolerant trees both break dormancy earlier in the year by increasing the expression of flowering-related SOC1 MADS-box and reducing the expression of SVP-like MADS-box, whilst also accelerating senescence by increasing the expression of JOINTLESS MADS-box genes. DNA methylation differences in the promoters of MADS-box genes between 1 tolerant and 1 susceptible tree indicate potential epigenetic regulation of these traits.

A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F. × ananassa)

BACKGROUND

Cultivated octoploid strawberry (Fragaria × ananassa) is one of the most economically important fruits worldwide due to its flavor, texture, and health benefits. However, bacterial angular leaf spot (ALS) causes economic losses in fruit production and plant nurseries. All commercial strawberry varieties are susceptible to ALS. A major resistance locus, RXf1, has been reported, but the genomic structure and candidate genes underlying this resistance remain known.

RESULTS

Fine-mapping was performed using three segregating populations containing 663 individuals that were genotyped with subgenome specific seven high-resolution melting (HRM) markers to narrow the RXf1 region to a 486-kb interval on chromosome 6C. We assembled a haplotype-phased chromosome-scale genome of ALS-resistant breeding selection FL17.68-110 using highly accurate long-read sequencing and trio-binning with parental short reads. The 1.62 Gbp genome containing two haplotypes, 56 chromosomes and 193,072 annotated genes. Transcriptome analysis in response to the ALS pathogen identified a candidate gene, Resistance gene analogue 3 (RGA3), associated with the RXf1 resistance. The gene structure and sequence variations within FaRGA3 were identified between resistant and susceptible genotypes.

CONCLUSIONS

Our results narrowed the RXf1 region, identified structural variations within this locus and pointed to FaRGA3 as a promising candidate gene. This information will be useful for breeders toward developing ALS-resistant strawberry varieties, and the high-quality genome will be a valuable resource for further genomics research in octoploid strawberry.

Complete genome sequence of Planococcus koreensis isolated from soil in Fort Collins, Colorado

The complete genome of Planococcus koreensis was obtained using Nanopore MinION sequencing after isolation from soil in Colorado. The assembled genome contains one circular contig with 3,519,105 bp, 3,606 genes, 419 pseudogenes, and 47.62% guanine-cytosine content. This discovery provides a fully assembled P. koreensis genome available at the National Center for Biotechnology Information.

The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus

For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.