QUAST: quality assessment tool for genome assemblies

Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering

Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.

IMPORTANCE

This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.

The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments

This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management.

IMPORTANCE

Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.

Large-scale phenotypic and genomic analysis of Listeria monocytogenes reveals diversity in the sensitivity to quaternary ammonium compounds but not to peracetic acid

Listeria monocytogenes presents a significant concern for the food industry due to its ability to persist in the food processing environment. One of the factors contributing to its persistence is decreased sensitivity to disinfectants. Our objective was to assess the diversity of L. monocytogenes sensitivity to food industry disinfectants by testing the response of 1,671 L. monocytogenes isolates to quaternary ammonium compounds (QACs) and 414 isolates to peracetic acid (PAA) using broth microdilution and growth curve analysis assays, respectively, and to categorize the isolates into sensitive and tolerant. A high phenotype-genotype concordance (95%) regarding tolerance to QACs was obtained by screening the genomes for the presence of QAC tolerance-associated genes bcrABC, emrE, emrC, and qacH. Based on this high concordance, we assessed the QAC genes' dissemination among publicly available L. monocytogenes genomes (n = 39,196). Overall, QAC genes were found in 23% and 28% of the L. monocytogenes collection in this study and in the global data set, respectively. bcrABC and qacH were the most prevalent genes, with bcrABC being the most detected QAC gene in the USA, while qacH dominated in Europe. No significant differences (P > 0.05) in the PAA tolerance were detected among isolates belonging to different lineages, serogroups, clonal complexes, or isolation sources, highlighting limited variation in the L. monocytogenes sensitivity to this disinfectant. The present work represents the largest testing of L. monocytogenes sensitivity to important food industry disinfectants at the phenotypic and genomic level, revealing diversity in the tolerance to QACs while all isolates showed similar sensitivity to PAA.

IMPORTANCE

Contamination of Listeria monocytogenes within food processing environments is of great concern to the food industry due to challenges in eradicating the isolates once they become established and persistent in the environment. Genetic markers associated with increased tolerance to certain disinfectants have been identified, which alongside other biotic and abiotic factors can favor the persistence of L. monocytogenes in the food production environment. By employing a comprehensive large-scale phenotypic testing and genomic analysis, this study significantly enhances the understanding of the L. monocytogenes tolerance to quaternary ammonium compounds (QACs) and the genetic determinants associated with the increased tolerance. We provide a global overview of the QAC genes prevalence among public L. monocytogenes sequences and their distribution among clonal complexes, isolation sources, and geographical locations. Additionally, our comprehensive screening of the peracetic acid (PAA) sensitivity shows that this disinfectant can be used in the food industry as the lack of variation in sensitivity indicates reliable effect and no apparent possibility for the emergence of tolerance.

Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness

Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media.

IMPORTANCE

Innovative solutions are needed to address emerging challenges in agriculture while reducing its environmental footprint. Management of soil microbiomes could contribute to this effort, as plant growth-promoting microorganisms provide key ecosystem services that support crops. Yet, inoculating beneficial microbes into farm soils yields unreliable results. We require a greater knowledge of the ecology of these taxa to improve their functioning in sustainable agroecosystems. In this report, we demonstrate that exposure to laboratory media and lingering adaptation to another soil can negatively impact the in-soil survival of a phosphorus-solubilizing bacterial species. We go further to highlight the underlying mutations that give rise to these patterns. These insights can be leveraged to improve our understanding of how soil-dwelling beneficial microorganisms adapt to different evolutionary pressures.

Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers

Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.

Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance

Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.

Prevalence of Shiga Toxin-Producing Escherichia coli (STEC) and Risk Characterization Based on Virulence Genes in Retail Raw Ground Meat of Beef, Veal, and Lamb in Canada

Shiga toxin-producing Escherichia coli (STEC) are potentially pathogenic E. coli that may cause mild to severe gastrointestinal illnesses. STEC-contaminated foods of animal origin have been the most frequently implicated sources of foodborne outbreaks. A multiyear (2016 to 2021) targeted survey was conducted to investigate the prevalence of STEC in retail ground meats (beef, veal, and lamb). Samples were screened for the presence of Shiga toxin genes (stx) to identify presumptive samples, followed by culture and molecular confirmation of isolates to confirm the presence of stx genes and subsequent characterization by whole-genome-sequencing (WGS) for O serogroup and virulence genes (e.g., stx, eae, aggR). A total of 175 STEC strains were isolated from a total of 148 samples where the presence of viable STEC was confirmed out of 2,398 ground meat samples. This represented 1.2% (7/589 positive, 8 unique strains) of the beef samples, 4.7% (58/1,241 positive, 67 unique strains) of the veal samples, and 14.6% (83/568 positive, 100 unique strains) of the lamb samples. The intimin virulence gene, eae, was identified in the STEC strains of veal origin (9/67, 13.4%) only and were classified as belonging to risk level 1 (1/67), level 3 (2/67), and level 4 (6/67) according to the FAO/WHO risk categories. Risk level 2 STEC strains were of beef (2/8, 25.0%), veal (8/67, 11.9%), and lamb (1/100, 1.0%) origin. The majority of the STEC strains, 75.0% (6/8) of the beef, 67.2% (45/67) of the veal, and 94.0% (94/100) of the lamb STEC strains were classified as risk level 5 (lowest level) of the FAO/WHO risk categories. This study's findings indicate that the current food safety control measures implemented for ground meats in Canada are effective at maintaining an acceptable level of possible contamination with STEC strains associated with severe clinical outcomes. Continued application of effective control measures and safe food handling practices by consumers will minimize the potential risk of foodborne infections from raw ground meats.

Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata)

The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.

Genomic Characterization of Serratia fonticola (EBS19) as a Biocontrol Agent against Botrytis cinerea

Botrytis cinerea (Bc), a plant pathogenic fungus, is the causative agent of gray mold disease, which rapidly develops resistance to fungicides in cultivation areas. This study explores the biocontrol potential of various bacterial isolates collected from the rhizosphere of tomato plants (Solanum lycopersicum). Bacterial isolates were purified and neutralized through phenol vaporization for 2 days. Colonies that inhibited pathogen spore growth were confirmed via antibiosis effect using in vitro bioassays. Bacterial colonies demonstrated up to 84% inhibition of pathogen growth at 7-day post-inoculation (dpi) with a one-layer agar diffusion test and up to 70% inhibition with a double-layer agar diffusion test, compared to control plates. Both bacterial suspension and filtrate significantly suppressed pathogen mycelium growth at 11 and 14 dpi. The isolate used in further studies was identified as Serratia fonticola (EBS19) through whole-genome sequencing. Annotated genome data revealed the presence of genes encoding enzymes crucial for pathogen inhibition. Carbon preference analyses identified specific carbon sources unique to the bacterial strain. These findings are advantageous for developing effective biopreparations that ensure bacterial strain stability in practical applications. In addition, the primary focus was on the interaction between the pathogen's major stress regulator protein (BAG1) and the bacterial glycoside hydrolase. Protein-protein docking analyses elucidated strong interaction between BAG1 and bacterial glycoside hydrolase. In conclusion, this study provides a knowledge for further research using recombinant DNA and gene cloning techniques on the bacterium's mapped genome.

Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis

BACKGROUND

Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.

RESULTS

WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.

CONCLUSIONS

The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.

The first chromosome-scale genome assembly of a microcyclic rust, Puccinia silphii

BACKGROUND

Rust fungi are destructive pathogens in crop plants, having led to epidemics and damaging crops all over the world. The rust Puccinia silphii (Basidiomycota) infects Silphium integrifolium, which is a member of the most speciose plant family, Asteraceae.

RESULTS

This study analyzes the first chromosome-scale genome sequence of a rust that infects any dicot, or any species outside of the Poaceae (grasses). We found it to be the smallest genome among the available Pucciniales genome assemblies. Our final assembly was 41.7 Mb in size and consisted of 19 pseudomolecules. The genome had a BUSCO completeness score of 92.1%, with nearly all BUSCO gene losses shared with other Puccinia genomes, and gene losses concentrated in the sulfate assimilation categories. Other gene losses were unique to P. silphii, whose genome contained by far the fewest protein coding genes. A total of 10,399 protein coding genes were predicted, compared to 14,257 in the next smallest genome. Gene losses in P. silphii were concentrated in categories related to meiosis.

CONCLUSION

This newly assembled genome provides insights into the size limitations of Puccinia genus genomes, as well as important protein gene families that are evolving within the genus including sulphate assimilation genes and DNA replication and its role in the evolution of microcyclic rusts.

Comparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental Pseudomonas aeruginosa strains

Background

Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation. Pseudomonas aeruginosa can degrade hydrocarbons through emulsification ( rhl genes) and tolerance ( mla genes). However, genomic organization of these systems in environmental P. aeruginosa strains remains unclear. This study aimed to investigate the rhl and mla systems in six strains isolated from hydrocarbon-contaminated sites in Peru.

Methods

Six Pseudomonas aeruginosa strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality Pseudomonas genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL.

Results

The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as P. aeruginosa by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had rhlABRI genes in a conserved 3'-5' orientation. Most of them contained duplicated rhlB gene, except C1BHIC5 strain. However, rhlG varied in position and orientation, it was often near rhlC, with C1BHIC5 also displaying an exception in rhlG orientation.100% of strains presented mla system, associated with toluene tolerance, with two copies of mlaA, mlaFEDC, and mlaEFD genes arranged with high synteny but variable orientations. In comparison to Pseudomonas putida, where mla genes are positioned between murA and ppcD with an additional toluene tolerance gene ( ttg2D).

Conclusions

In conclusion, the presence of the rhlABC genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of P. aeruginosa to survive in polluted environments.

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres

Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.

Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces

Among the emerging issues in probiotic safety, the possible presence of pks, a gene cluster synthetizing a genotoxin known as colibactin, is one of the most alarming. Indeed, indigenous E. coli strain pks-positive are found in 60% of patients with colorectal cancer, and the most widely used E. coli-based probiotic, known as E. coli Nissle 1917 (DSM 6601), is pks-positive. Starting from 25 potential candidates selected by screening 25 infant stool samples, we have selected an E. coli strain (named 5C, deposited as LMG S-33222) belonging to the phylotype A and having the serovar O173:H1. Having been previously completely sequenced by our group, we have further characterized this strain, demonstrating that it is (i) devoid of the most known potential pathogenic-related genes, (ii) devoid of possible plasmids, (iii) antibiotic-sensitive according to the EFSA panel, (iv) resistant in gastric and enteric juice, (v) significantly producing acetate, (vi) poorly producing histamine, (vii) endowed with a significant in vitro antipathogenic profile, (viii) promoting a significant in vitro immunological response based on IL-10 and IL-12, and (ix) devoid of the pks genes. A comparative genomics versus E. coli Nissle 1917 is also provided. Considering that the other two most commonly used E. coli-based probiotics (E. coli DSM 17252 and E. coli A0 34/86) are respectively pks-positive and alpha-hemolysin-(hly) and cytotoxic necrotizing factor-1-(cnf1) positive, this novel strain (E. coli 5C) is likely the probiotic E. coli strain with the best safety profile available to date for human use.

Mediterranean monk seal (Monachus monachus) and leopard seal (Hydrurga leptonyx) de novo genomes to study the demographic history and genetic diversity of southern seals

BACKGROUND

The Monachinae, or southern seals, are one of two subfamilies within the Phocidae and are home to iconic pinnipeds such as the leopard seal, a fierce Antarctic top predator, and the Mediterranean monk seal, one of the world's most endangered mammals. These two species are difficult to study and sample, due to their hidden lives in extreme environments or, in case of the monk seal, their critically reduced population sizes; consequently, genetic data from these two species is scarce. However, cost developments and advances in genome sequencing have made it possible to generate continuous genome assemblies from DNA of even stranded individuals, allowing to assemble the first reference genomes of such rarely observed species.

RESULTS

In this study, we have sequenced the genomes of the leopard seal and the Mediterranean monk seal using PacBio's CCS technology to assemble the very first genomes for these species. Four additional Mediterranean monk seal individuals were sequenced using Illumina short-read technology. These data allowed analysis of their demography and genomic diversity based on whole-genome data, confirming low genetic variability and small numbers of individuals for the Mauritanian population of the Mediterranean monk seal. In contrast, the relatively abundant leopard seal shows a high degree of heterozygosity, comparable in the range of other common carnivores.

CONCLUSIONS

The first genome assemblies for these seals will lay the groundwork for population-level and other studies to better understand their evolutionary history and biology and to aid conservation efforts.

A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Integrated genomic and transcriptomic analysis reveals the mechanisms underlying leaf variegation in 'Gonggan' mandarin

BACKGROUND

The 'Gonggan' mandarin, an elite local cultivar from Zhaoqing City, Guangdong Province, combines the qualities of mandarin and sweet orange. A leaf-variegated mutant enhances its ornamental and economic value, providing an excellent model for studying chloroplast development and photosynthetic pigment metabolism in citrus.

RESULTS

We found that, in this variegated mutant, chloroplasts are severely deficient or absent in mesophyll cells. Physiological assessments revealed lower levels of chlorophyll, carotenoids, net photosynthetic rate (Pn), and stomatal conductance (Gs), alongside significantly higher non-photochemical quenching (NPQ) and the non-photochemical quenching coefficient (qN), reflecting increased photoprotective energy dissipation. To uncover the molecular basis of leaf variegation, high-quality genome assemblies and transcriptomes were generated for both the normal and variegated 'Gonggan' mandarin, enabling comparative multi-omics analysis. Key genes involved in chloroplast development, such as TOC159, PDV2, THA8, and SIG5, were downregulated in the variegated leaves. Similarly, structural genes linked to chlorophyll degradation, including CLH2, SGR, NOL, and NYC1, exhibited altered expression. Downregulation of transcription factors GLK, GNC, and GNC-LIKE (GNL), known regulators of chloroplast development and chlorophyll biosynthesis, was also observed.

CONCLUSIONS

These findings suggest that disrupted expression of critical genes impacts chloroplast development and pigment metabolism, causing the leaf variegation phenotype. Overall, this study lays a foundation for functional genomics research and potential germplasm improvement of 'Gonggan' mandarin, and provides new insights into the mechanisms driving color variation in citrus.

First Report of a Fatal Septicemia Case Caused by Vibrio metoecus: A Comprehensive Functional and Genomic Study

BACKGROUND

In recent years, we have witnessed an unprecedented increase in the incidence of vibriosis due to global warming. Vibrio metoecus is a recently described Vibrio cholerae-like species that has not been associated with septicemia death in humans. During follow-up of human vibriosis, we received a blood isolate from a patient with secondary septicemia who died a few hours after admission.

METHODS

Phenotypic and genotypic methods failed to identify the isolate, which could only be identified by average nucleotide identity after genome sequencing. The isolate was subjected to in vitro and ex vivo assays, complemented by comparative genomics focused on the identification of unique genetic traits. Strains and genomes from the same and related species (V. cholerae and Vibrio mimicus) were used for analyses.

RESULTS

The isolate was the only one able to resist and multiply in human serum. Its genome contained virulence genes shared with V. mimicus and/or V. cholerae, with those associated with sialic acid degradation within pathogenicity island 2 standing out. However, it also presented a unique gene cluster, flanked by a transposase gene, putatively related to surface polysaccharide pseudosialyzation.

CONCLUSIONS

We document the first case of death caused by septicemia due to V. metoecus and propose that the acquisition of surface pseudosialyzation genes explains the ability of certain isolates of this species to survive in blood. Our discovery underscores the urgent need to monitor and study newly emerging pathogenic species, as climate change may be facilitating their spread and increasing the risk of serious infections in humans.

Description of Pseudomonas imrae sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel (Scomber scombrus)

Three β-lactam resistant bacterial strains isolated from gut samples of wild Atlantic mackerel (Scomber scombrus) collected from the northern North Sea were characterized by polyphasic analyses. The strains were determined to belong to the genus Pseudomonas but could not be assigned to a known species. The nearly-complete 16S rRNA gene sequence showed the highest similarity (99.9%) to four different species, although partial rpoD sequence exhibited relatively low similarities to Pseudomonas proteolytica (93.4%) and other Pseudomonas spp. Genome sequencing and subsequent digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) analysis and core genome analysis confirmed that these strains represent a novel species within the genus Pseudomonas. The three strains demonstrated ANIb values >99.5% with each other, confirming that all three strains (CCUG 74779T = CECT 30571T, CCUG 74780 and CCUG 74781) belong to the same genomospecies. Phylogenomic analysis confirmed that the strains form a distinct genomic clade, representing a novel taxonomic species, for which the name Pseudomonas imrae sp. nov., is proposed, with strain CCUG 74779T (=CECT 30571T) designated as the type strain. We report the complete genome sequence of the type strain of P. imrae sp. nov. and show that it carries a gene encoding a novel variant of a chromosomally-encoded class C β-lactamase, which has been designated as PFL-7.

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China

In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology has hindered understanding of its population dynamics. Here, we analyzed 1506 non-repetitive BSI-causing A. baumannii isolates from 76 Chinese hospitals over a decade (2011-2021). We identified 149 sequence types (STs) and 101 K-locus types (KLs), revealing increased population diversity. International clone (IC) 2 accounted for 81.74% of isolates, with a notable shift in prevalent STs: ST208 increased while ST191 and ST195 declined, aligning with global trends. ST208 exhibited higher virulence, greater antibiotic resistance, enhanced desiccation tolerance, and more complex transmission patterns compared to ST191 and ST195. Its genomic plasticity drives its adaptation and spread. Using the high-resolution Oxford MLST scheme, this study uncovered greater diversity and genetic factors behind ST208's rise. A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one, highlighting the urgent need to address its growing threat. These findings have critical implications for infection control and public health policies.

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy k-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each cluster, and (6) generates a consensus assembly from the overlap graph of the assembled contigs. Here, we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually curated Telomere-to-Telomere human genome assembly. Across more than 250 synthetic data sets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates, and depth of sequencing.

First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying blaIMI-4 carbapenemase in Costa Rica

OBJECTIVE

All carbapenem-resistant Gram-negative bacterial isolates obtained in the Costa Rican National Network of Bacteriology Laboratories are routinely referred to the National Reference Center for Bacteriology for the national-laboratory for the surveillance and characterization of their carbapenem-related mechanism of resistance. As a result of this healthcare-associated infection surveillance, two bacterial isolates with unknown mechanisms for carbapenem resistance were investigated.

METHODS

The isolates were subjected to taxonomic identification, antimicrobial susceptibility testing, and whole-genome characterization, using Illumina and Oxford Nanopore technologies, and bioinformatic analyses.

RESULTS

The isolates were identified as Enterobacter roggenkampii and Enterobacter sichuanensis. Although the isolates presented different antimicrobial resistance profiles, both were resistant to carbapenems, positive for the modified carbapenem inactivation method (mCIM), and showed inhibition of carbapenem resistance with boronic acid. The full characterization of the isolates' genomes, revealed the presence of the rare chromosomal blaIMI-4 gene inserted within 25-kb integrative mobile elements, closely related to EcloIMEX-2.

CONCLUSIONS

The limited global distribution of the blaIMI-4 variant, along with its identification in two distinct bacterial species in Costa Rica within integrative mobile elements, underscores the critical need for regular antibiotic resistance surveillance using next-generation sequencing technologies. This study demonstrates that this practice allows the timely detection of novel or rare mechanisms of antibiotic resistance.

Detection of a novel SME-6 Carbapenemase in Serratia ureilytica in Germany

BACKGROUND

Carbapenem resistance in Serratia species is occasionally mediated by the serine carbapenemase Serratia marcescens enzymes (SMEs). During microbiological diagnostics, we identified a carbapenem-resistant Serratia ureilytica isolate in which resistance was not mediated by any known SME variants or other characterized carbapenemases.

OBJECTIVES

To identify and characterize the underlying resistance mechanism in a carbapenem-resistant Serratia ureilytica isolate that lacks known SME variants or other characterized carbapenemases.

METHODS

Antimicrobial susceptibility testing (AST) was performed using Vitek, gradient strips, broth microdilution, and disc diffusion methods. WGS was performed to identify the resistance mechanisms. Growth curve analysis and RT-qPCR were performed at 30°C and 37°C.

RESULTS

WGS identified a novel SME variant, SME-6, which differed from a known variant, SME-2, by two amino acids (G117R and G147E). AST showed carbapenem resistance at 30°C but susceptibility at 37°C. Growth curve analysis showed a shorter lag phase at 30°C compared with 37°C, and RT-qPCR showed a ∼3-fold higher blaSME expression at 30°C.

CONCLUSIONS

To the best of our knowledge, this study reports the first identification of SME-6 and the first detection of an SME-type carbapenemase in Germany. Resistance was found to be temperature-dependent, with faster growth and higher SME-6 expression at lower temperatures contributing to the phenotype. These findings suggest SME variants may be underdiagnosed using current diagnostic protocols, highlighting the need for adjustments to improve detection of temperature-sensitive resistance mechanisms.

The endophytic fungus Cosmosporella sp. VM-42 from Vinca minor is a source of bioactive compounds with potent activity against drug-resistant bacteria

Medicinal plants serve as valuable resources for the isolation of endophytic fungi. Vinca minor is a well-known producer of important vinca alkaloids and emerges as a promising source of endophytic fungi with antibacterial potential and biosynthetic capacity. In this study, we isolated an endophytic fungus from V. minor and identified it as Cosmosporella sp. VM-42. To date, relatively little is known about this fungal genus. The ethyl acetate extract of this isolate selectively inhibited Gram-positive bacteria, such as methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). Therefore, we isolated the most abundant compound from the crude extract and identified it as nectriapyrone with MIC and MBC values ranging from 125 to 62.5 µg/mL against MSSA and MRSA strains. We further sequenced and annotated the 39.07 Mb genome of the isolate, revealing that it encodes 9842 protein-coding genes, including 415 genes for carbohydrate-active enzymes and various biosynthetic gene clusters. Our untargeted metabolomic analysis shows that the fungus produces various secondary metabolites, including cyclodepsipeptides, dimeric naphtho-γ-pyrones, and macrolactones, which are known to have antifungal and antibacterial activities. In addition, we used small-molecule epigenetic modulators to activate the expression of silent biosynthetic gene clusters to broaden the chemical profile of Cosmosporella sp. VM-42. Taken together, we provide a first systematic analysis of Cosmosporella sp. VM-42, and our results show that it is a promising source of compounds with pharmacological potential against drug resistant bacteria.

Staphylococcus hominis as a source of antimicrobial peptides: identification of a new peptide with potential antimicrobial properties using in silico approach

The rapid progression of antimicrobial resistance, fueled by the excessive use of antibiotics, has become a major public health concern. Among the pathogens contributing to this crisis, Staphylococcus aureus stands out as a significant therapeutic challenge, especially with the rise of resistant strains like Methicillin-Resistant S. aureus (MRSA). In this context, antimicrobial peptides (AMPs) emerge as a promising alternative, thanks to their unique mechanisms of action. Exploring the genomes of species such as Staphylococcus hominis, known for producing AMPs effective against S. aureus, offers promising opportunities for discovering novel therapeutic agents. In this study, Average Nucleotide Identity (ANI) combined with phylogenetic analysis identified a potential emerging subspecies of Staphylococcus hominis. The core genome analysis led to the identification of a potential antimicrobial peptide. The peptide model simulated with the S. aureus membrane model in molecular dynamics revealed that it interacts primarily with the lipids head groups, leading to an overall rigidification of the bacterial membrane.

Draft genomes of three bacteria capable of growing on cocamidopropyl betaine or N,N,N-trimethylglycine (betaine): Cupriavidus sp. CuC1, Variovorax sp. VaC1, and Pseudomonas sp. PsB

We report three draft genome sequences of Pseudomonas sp. PsB, Cupriavidus sp. CuC1, and Variovorax sp. VaC1. Pseudomonas sp. PsB can grow on N,N,N-trimethylglycine (betaine), but not on cocamidopropyl betaine (CPB), as a sole carbon source. Cupriavidus sp. CuC1 and Variovorax sp. VaC1 can grow only on CPB.

Draft genomes of Klebsiella pneumoniae and Streptococcus anginosus strains found in the urine of the same female patient

Here, we report the draft genomes of Klebsiella pneumoniae 5008-1 and Streptococcus anginosus 5008-2 strains isolated from a catheterized urine sample obtained from an asymptomatic postmenopausal woman diagnosed with recurrent urinary tract infection and receiving vaginal estrogen cream.

Genome sequence of Eubacterium callanderi AM6, isolated from a Parkinson's disease patient

Here, we report the genome sequence of Eubacterium callanderi AM6, isolated from a fecal sample obtained from a Parkinson's disease patient. The bacterial genome was sequenced using Illumina technology on a NextSeq 500 platform. The assembled genome of Eubacterium callanderi comprises 4,318,463 base pairs with a G + C content of 47.5%.

Draft genome sequences of a strain of Clostridium neuense and four Candidatus Clostridium species

We report the draft genomes of five Clostridium isolates from soil and agricultural by-products, four of which are proposed as Candidatus species. Members of the genus Clostridium are of significant industrial interest, and the availability of their genome sequences facilitates the understanding and exploration of their functional potential.

Complete genome and transcriptome of Mycobacterium bovis 3488, a clinical isolate with a novel deletion at the RD1 locus

In members of the Mycobacterium tuberculosis complex, the RD1 locus encodes a type VII secretion system involved in virulence. Herein, we describe the genome and transcriptomic analysis of Mycobacterium bovis 3488, a clinical isolate from a cat, with a 14.2 kb deletion that encompasses the RD1 locus.

Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379

We report the complete genome sequences of five bacteria associated with the marine cyanobacterium Capilliphycus salinus ALCB114379 of the phylum Pseudomonadota. This genetic diversity offers insights into the cyanosphere, shedding light on potential relationships between these microorganisms and their cyanobacterial hosts.

Draft genome sequences of five glacial fungi from Styx Glacier, Antarctica

We generated four high-quality draft genomes of fungi isolated from Styx Glacier, Antarctica. The genome announcement of these fungal strains offers insights into their evolution and adaptation to extreme glacial environments, as well as their potential biotechnological applications.

Draft genome sequence of Vreelandella stevensii strain BS235 isolated from hypersaline lakes from Brazilian pantanal

Mitigating climate crisis has driven biotechnology research toward capturing and utilizing CO2. Production of biosurfactants by microorganisms' metabolism offers a promising solution. We present the draft genome of Vreelandella stevensii strain BS235 from a hypersaline alkaline lake (Pantanal biome, Brazil). We identified genes related to CO2 metabolism and biosurfactant production.

Draft genome sequence of benzo[a]pyrene degrading Bacillus altitudinis strain AR19 isolated from Digboi oil refinery (India)

Bacillus altitudinis AR19, isolated from the Digboi oil refinery (India), has a genome size of 3,630,000 bp with a G+C content of 42.45%. The genome encodes 3,755 protein-coding genes, including those for ring-cleaving dioxygenases and biofilm formation. These genes likely play crucial roles in the bacterium's survival in hydrocarbon-enriched environments.

Draft genomes of six methicillin-resistant Staphylococcus aureus in a Philippine tertiary hospital with insights on putative antimicrobial and phage resistance mechanisms

The genomes of six methicillin-resistant Staphylococcus aureus (MRSA) revealed CC5(ST5)-SCCmec-IVc-spa-t105-PVL+ (n = 3), CC5(ST6)-SCCmec-IVc-spa-t10002 (n = 1), CC5(ST5)-SCCmec-IVa-spa-t002 (n = 1), and CC8(ST8)-SCCmec-IVa-spa-t008-PVL+ (n = 1) genotypes. All possessed multiple antibiotic resistance genes (putative mecA and blaZ, and dfrG for cotrimoxazole-resistant strains), intact staphylococcal prophages, and putative antiphage systems. The results could aid in MRSA infection management and control.

Draft genomes of five putative biosurfactant-producing Serratia sp. isolates from Laguna de Bay, Philippines

Here, we report on the draft genomes of five putative biosurfactant-producing isolates of Serratia sp. from the East, West, and South bays of Laguna de Bay, Philippines. The contigs ranged from 20 to 21, and the genome lengths ranged from 5,175,553 to 5,214,031 bp.

Draft genome sequence of the Serratia liquefaciens strain UNJFSC002, isolated from the soil of a potato field of the Bicentenaria variety

In this study, we present the draft genome assembly of the Serratia liquefaciens strain UNJFSC002, isolated from the experimental potato field of the Bicentenaria variety at the Universidad Nacional José Faustino Sánchez Carrión, Lima, Peru.

Draft genome sequence of a novel species of Radiobacillus (strain PE A8.2) isolated from a red Antarctic seaweed

We report the draft genome sequence of Radiobacillus sp. nov. PE A8.2, an endospore-forming bacterium isolated from the surface of the red seaweed Pyropia endiviifolia collected in King George Island, Antarctica. The genome assembly comprised 5,183,530 bp, with a 37.5% G+C content and 5,077 coding sequences.

Complete genome sequence of Escherichia marmotae F12YCO47 isolated from a healthy human fecal sample

Escherichia marmotae has been found in animals and the environment. Here, we isolated it from a healthy human fecal sample. The 4.91 Mb circular genome (GC content = 50.34%) is associated with three plasmids: pF12YCO47-2 (89.9 kb, 50.2% GC), pF12YCO47-3 (47.9 kb, 44.3% GC), and pF12YCO47-1 (95.4 kb, 47.2% GC).

Draft genome sequence of the naphthalene-degrading bacterium Rhodococcus pyridinivorans RA1 isolated from an industrial soil sample in Mosul, Iraq

Rhodococcus pyridinivorans RA1 was isolated for the ability to grow on naphthalene from an industrial site near Mosul, Iraq. The draft genome is 5,419,924 bp with a GC content of 67.5%.

Complete genome sequence of Trueperella bernardiae strain UMB8254, isolated from the bladder of a female with metabolic syndrome and nephrolithiasis

Trueperella bernardiae is infrequently isolated, usually in polymicrobial communities, from human hosts with a wide variety of symptoms and diseases. Here, we report a complete genome sequence of Trueperella bernardiae (UMB8254), isolated from the bladder of a human female with metabolic syndrome and nephrolithiasis.

Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds

Lactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the genera Pediococcus and Lactiplantibacillus.

Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex

The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi.

Genome assembly of multidrug-resistant Enterococcus gallinarum IFEGHNEK1 isolated from bighead carp, Hypophthalmichthys nobilis

Enterococcus gallinarum IFEGHNEK1 is a multidrug-resistant bacterium belonging to the Enterococcaceae family isolated from bighead carp in 2023. We report the complete genome sequence of E. gallinarum (CP169314) containing a 3.15 Mb genome.

Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCCmecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes

Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health menace. The global spread of MRSA is characterized by successive waves of epidemic clones dominating specific geographical regions. The acquisition of genes encoding resistance to heavy metals (HMRGs) is thought to be a key feature in the geographic divergence of MRSA. However, the cause-effect relationship between the presence of HMRGs and the divergence of MRSA clones remains to be clarified. In this study, we assessed the role that HMRGs may have played in the evolutionary divergence of the MRSA ST5-SCCmecI lineage in Latin America. We conducted a genomic characterization of 113 MRSA clinical isolates from six Latin American healthcare centers, including 53 isolates collected from two cities in Chile (Santiago and Concepción). We found a plasmid (pSCL4752) harboring arsenic, cadmium, and mercury resistance genes in 65% (n = 71) of the ST5-SCCmecI isolates. We also observed a geographic divergence associated with the presence of pSCL4752 in Chilean isolates, with a higher frequency in isolates from Concepción (88%) compared to Santiago (29%). Interestingly, a molecular clock analysis revealed that this divergence occurred in the aftermath of an 8.8 Mw earthquake and tsunami that struck the Concepción area in 2010. Moreover, our results demonstrate that the carriage of pSCL4752 can be beneficial or detrimental for ST5-SCCmecI isolates, depending on the environmental availability of these heavy metals. Our results suggest that the divergence of the ST5-SCCmecI MRSA lineage in Latin America could have been fostered by environmental disasters and influenced by the presence/absence of HMRGs harbored in a plasmid.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) is a major cause of life-threatening infections worldwide and a growing public health concern. The rise of antibiotic-resistant bacteria, such as MRSA, is often linked to genetic adaptations that enhance their survival. Our research sheds light on how environmental changes, such as those triggered by a natural disaster, can influence the evolution and geographic spread of a highly resistant MRSA lineage in Latin America. We identified a plasmid carrying genes for resistance to arsenic, cadmium, and mercury, which was associated with the geographic divergence of the ST5-SCCmecI MRSA lineage, with striking differences in its prevalence between regions affected by a major earthquake and tsunami. By linking environmental events to pathogen evolution, our study highlights the role of ecological pressures in the spread of MRSA. These findings emphasize the need to integrate environmental monitoring into public health strategies to better understand the global challenge of antimicrobial resistance.

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.

Rubrolithibacter danxiaensis gen. nov., sp. nov. isolated from red sandy conglomerate in the Danxia Mountain

A Gram-stain-negative, rod-shaped and non-motile bacterium, designated as strain SYSU DXS3258T, was isolated from red sandy conglomerate sample collected from the Danxia Mountain in Guangdong Province, PR China. The bacterium was found to grow optimally at 28 °C, pH 7.0, and with 0-1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain SYSU DXS3258T within the family Sphingobacteriaceae. Strain SYSU DXS3258T showed the highest 16S rRNA gene sequence similarity to Pararcticibacter tournemirensis TF5-37.2-LB10T (95.5%), Paradesertivirga mongoliensis 1-32 T (95.3%) and Desertivirga xinjiangensis 12157 T (95.2%). Digital DNA-DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain SYSU DXS3258T and the closest related members within the Sphingobacteriaceae were ≤ 13%, 70.3% and 69.9%, respectively. The genomic DNA G + C content was 38.8%. The major fatty acid was iso-C15:0, C18:0 and C15:0 2-OH. The predominant polar lipids were phosphatidylethanolamine, three glycolipids, one phospholipid and one unidentified polar lipid. The major respiratory quinone was Q-7. Based on phenotypic, phylogenetic, chemotaxonomic and genomic results, we propose that strain SYSU DXS3258T represents a novel species of a novel genus within the family Sphingobacteriaceae, for which the name Rubrolithibacter danxiaensis gen. nov., sp. nov. was proposed. The type strain is SYSU DXS3258T (= MCCC 1K09420T = KCTC 102322 T).

Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot

The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00300-025-03380-y.

An outbreak in week-old broiler chicks caused by a highly virulent and multidrug-resistant strain of Salmonella Gallinarum

RESEARCH HIGHLIGHTS

Salmonella Gallinarum infection in chicks resulted in a mortality rate of 42%.Chicks had unusual lesions such as haemorrhagic enteritis and interstitial pneumonia.Whole genome analysis of the SG isolate revealed exclusive antimicrobial resistance genes.Higher number of exclusive virulence genes were related to severe fowl typhoid in chicks.