QUAST: quality assessment tool for genome assemblies

Engineering regiospecific methylation of the pladienolides

Well-recognized for the ability to modulate spliceosome activity, the pladienolide family of polyketide natural products has been the recent subject of intense synthetic and bioactivity studies. However, our understanding of their biosynthesis remains incomplete. Here, we report the biosynthetic gene cluster of FD-895 from Streptomyces hygroscopicus A-9561 and explore the installation of a key methylation important for metabolite stability. We demonstrate the in vitro and in vivo application of an O-methyltransferase for regioselective methylation of pladienolide B at the C21 position, a post-synthase modification critical for compound stability. These findings provide a crucial next step in developing systems to engineer this important family of splicing modulatory anti-tumor agents.

A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi Māori (Māori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any except Orcinus orca, more single-copy complete BUSCOs than any except Phocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future, the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.

Exploring fecal microbial activity in zoo felids of varying body mass on a similar diet

Under human care, felids are typically fed similar diets, unlike wild counterparts whose diets vary by body mass and ecology. This study evaluated fecal microbiota and fermentation products in 18 zoo felids from Pairi Daiza Zoo, Belgium, grouped by body mass: under 100 kg ("small") and over 100 kg ("large"), with 9 animals in each group. Fresh feces were collected from the rectum under anesthesia. Microbial composition was assessed via 16S rRNA gene sequencing, while the fecal volatile fatty acids were quantified using gas chromatography. At the phylum level, regardless of body mass, the gut microbiota of zoo felids was predominantly composed of Firmicutes (61.7%), Actinobacteria (16.4%) and Bacteroidetes (12.5%). At the genus level, the most abundant genus was Clostridium sensu stricto 1 (15.9%), followed by Collinsella (15.7%). Although no significant differences in microbial composition or alpha diversity were found, beta diversity showed body mass influenced overall microbial structure. Smaller felids had significantly higher acetate levels than larger felids (p < 0.01). Additionally, acetate proportions were positively correlated with Clostridium sensu stricto 13 (r = 0.6, p < 0.01) and Peptoniphilus (r = 0.5, p < 0.05). These results show particular associations between body mass and the response of the intestinal microbiome to diet, suggesting that a uniform diet may not suit all felids under human care.

Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma

Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.

An annotated near-complete sequence assembly of the Magnaporthe oryzae 70-15 reference genome

Magnaporthe oryzae is a devastating fungal pathogen that causes substantial yield losses in rice and other cereal crops worldwide. A high-quality genome assembly is critical for addressing challenges posed by this pathogen. However, the current widely used MG8 assembly of the M. oryzae strain 70-15 reference genome contains numerous gaps and unresolved repetitive regions. Here, we report a complete 44.82 Mb high-quality nuclear genome and a 35.95 kb circular mitochondrial genome for strain 70-15, generated using deep-coverage PacBio high-fidelity sequencing (HiFi) and high-resolution chromatin conformation capture (Hi-C) data. Notably, we successfully resolved one or both telomere sequences for all seven chromosomes and achieved telomere-to-telomere (T2T) assemblies for chromosomes 2, 3, 4, 6, and 7. Based on this T2T assembly, we predicted 12,100 protein-coding genes and 493 effectors. This high-quality T2T assembly represents a significant advancement in M. oryzae genomics and provides an enhanced reference for studies in genome biology, comparative genomics, and population genetics of this economically important plant pathogen.

VanB transposon analysis detects horizontal gene transfer in vancomycin resistant Enterococcus faecium: description of two outbreaks

BACKGROUND

Outbreaks with vancomycin resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation.

AIM

Developing a method for sequence analysis of vancomycin resistance genes in parallel to wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.

METHODS

We developed a bioinformatics pipeline to compare the sequences of transposons containing vanB resistance genes. We used this pipeline in addition to wgMLST to investigate two separate ongoing VRE outbreaks. We also sequenced five separate colonies from 15 different samples and 10 vancomycin sensitive isolates.

FINDINGS

Of 46 strains collected during two outbreaks, we identified 26 and 9 strains to be part of the two outbreaks based on wgMLST clustering. In 6 strains we identified an identical vanB transposon but a different wgMLST cluster, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. We found no variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. We identified 1 vancomycin sensitive E. faecium in blood culture with a similar wgST as one of the outbreak strains.

CONCLUSIONS

Real-time analysis of transposons containing vancomycin resistance genes provides additional information for analysis of vanB-VRE outbreaks. It detects possible horizontal gene transfer which would not be detected using conventional methods. Transposon analysis is a valuable addition to whole genome sequence analysis during vanB-VRE outbreaks.

Antimicrobial Potential of Marine Sponge-Associated Bacillus velezensis and Stutzerimonas stutzeri from the Indian Coast: A Genome Mining and Metabolite Profiling Approach

Antimicrobial resistance (AMR) is one of the leading health crises worldwide that demands new antimicrobials to enter the clinical pipeline. Marine sponges are a rich source of promising bioactive compounds. Due to their sessile nature and filter-feeding lifestyle, sponges are prone to attack by competitors, predators, and pathogens. To combat these threats, they produce a diverse array of bioactive compounds. Notably, the microbial communities residing within the sponges make many of these beneficial compounds. Twenty-one bacterial isolates from various marine sponges from the Indian coast were selected for this study. The bacterial isolates were fermented to obtain crude extracts, which were then screened against critical bacterial pathogens. Based on the MIC (minimum inhibitory concentration) results, two isolates, Bacillus velezensis NIO_002 and Stutzerimonas stutzeri NIO_003 showing good activity, were characterized by morphological, biochemical, and molecular methods. Genome mining predicted multiple antibiotic biosynthetic gene clusters, most of which showed a high degree of similarity to known gene clusters, and some with low or no similarity which may be indicative of novel gene clusters. LC-MS (liquid chromatography-mass spectrometry) data revealed the putative presence of certain antibacterial compounds previously reported in the literature. To our knowledge, this is the first study to report the antimicrobial activity of marine sponge-associated Bacillus velezensis and Stutzerimonas stutzeri strains characterized by whole genome sequencing, thereby indicating the novelty of our strains. This study emphasizes the potential of our bacterial isolates for further development as a source of promising antibiotics to address the escalating challenge of drug-resistant pathogens.

Salmonella in Swiss and Imported Retail Chicken Meat - A Cross-Sectional Study

Non-typhoidal Salmonella enterica (NTS) are significant foodborne pathogens responsible for many cases of enterocolitis worldwide, with the increasing threat of antimicrobial resistance (AMR) posing a growing public health concern. Salmonella Infantis has emerged as a predominant multidrug-resistant (MDR) serotype, particularly in poultry. This study investigated the Salmonella prevalence in 200 chicken meat samples from Swiss retail stores. Six (3%) samples tested positive; all were imported, and the isolates were all identified as S. Infantis. Whole genome sequencing confirmed the presence of the pESI (plasmid of emerging S. Infantis) megaplasmid, which is associated with enhanced persistence, biofilm formation, and multidrug resistance. Statistical analysis revealed a significant correlation between Salmonella prevalence and imported, unlabeled products. These findings highlight the effectiveness of Swiss control measures in the poultry production but underscore the importance of maintaining consumer awareness to mitigate Salmonella transmission and MDR risks.

Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp

Background

Vibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy.

Methods

Phage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis.

Results

Phage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent.

Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China

Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice

Large genomic rearrangements, such as chromosomal inversions, can play a key role in evolution, but the mechanisms by which these rearrangements arise remain poorly understood. To study the origins of inversions, we generated chromosome-level de novo genome assemblies for four subspecies of the deer mouse (Peromyscus maniculatus) with known inversion polymorphisms. We identified ∼8,000 inversions, including 47 megabase-scale inversions, that together affect ∼30% of the genome. Analysis of inversion breakpoints suggests that while most small (<1 Mb) inversions arose via ectopic recombination between retrotransposons, large (>1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of retrotransposons in pericentromeric regions driving SDs. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, suggesting that centromeric repeats may also facilitate inversions. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.

Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies

INTRODUCTION

Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.

AIM AND METHODS

Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.

RESULTS

Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.

CONCLUSION

Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20 + sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.

Pathogenomics Insights into Phytophthora capsici and Phytophthora tropicalis -Sibling Species Causing Black Pepper Foot Rot: Genomic Architecture, Metabolic Pathways, and Effector Diversity

Foot rot disease in black pepper, caused by Phytophthora species, is a major threat to cultivation. Along with the well-known Phytophthora capsici, a newly identified species, Phytophthora tropicalis, has also been implicated. Comparative genome analysis of P. capsici 05-06 from Kerala (80.51 Mb, 626 scaffolds) and P. tropicalis 98-93 from Karnataka (73.54 Mb, 302 scaffolds) revealed similar GC content (∼50.5%) and gene counts (19,639 and 17,716, respectively). Genomic ANI analysis clustered them with P. capsici LT1534-B, suggesting a species complex. Both species contain transposable elements (19.35% and 21.31%), indicating adaptive evolution. Pathway mapping highlights roles in carbohydrate metabolism, carbohydrate-active enzymes (CAZymes: 575 and 566), energy production, effector biosynthesis, and molecular signaling. The presence of unique protein families and shared orthologous genes underscores their pathogenic potential. These findings enhance understanding of their evolution and pathogenicity, aiding in the development of targeted management strategies for black pepper foot rot.

Genome Sequencing of a Fusarium Endophytic Isolate from Hazelnut: Phylogenetic and Metabolomic Implications

This study reports on the whole genome sequencing of the hazelnut endophytic Fusarium isolate Hzn5 from Poland. It was identified as a member of the Fusarium citricola species complex based on a phylogenetic analysis which also pointed out that other hazelnut isolates, previously identified as F. lateritium and F. tricinctum, actually belong to this species complex. Genome annotation allowed the mapping of 4491 different protein sequences to the genome assembly. A further in silico search for their potential biosynthetic activity showed that predicted genes are involved in 1110 metabolic pathways. Moreover, the analysis of the genome sequence carried out in comparison to another isolate, previously identified as an agent of hazelnut gray necrosis in Italy, revealed a homology to several regions containing biosynthetic gene clusters for bioactive secondary metabolites. The resulting indications for the biosynthetic aptitude concerning some emerging mycotoxins, such as the enniatins and culmorin, should be taken into consideration with reference to the possible contamination of hazelnuts and derived products.

Colistin-resistant Klebsiella pneumoniae species complex: The scenario in Mexico

OBJECTIVES

Characterize the colistin-resistance mechanisms, determine the molecular epidemiology, and genomic traits of the colistin-resistant Klebsiella pneumoniae species complex (ColR-KpSC) clinical isolates in Mexico.

METHODS

In this study, 1,539 KpSC isolates were collected in Mexico from 2016 to 2021. We conducted a comprehensive analysis that included microbiological, genetic, molecular, and genomic approaches.

RESULTS

A total of 50 isolates (3.25%) were colistin-resistant; of which 49 (98%) corresponded to K. pneumoniae and 1 (2%) to Klebsiella quasipneumoniae. Whole genome sequencing of these resistant isolates revealed intra- and inter-hospital dissemination, and the mgrB inactivation was the main resistance mechanism. Some KpSC isolates carried plasmid-borne mcr-1 gene found in Escherichia coli from piglets in Mexico. The colistin-resistant isolates presented a high prevalence of ESBL- and NDM-1 genes, and one hypervirulent strain also produced ESBL CTX-M-15.

CONCLUSION

This study provides a comprehensive snapshot of the epidemiology of ColR-KpSC in Mexico, highlighting a high prevalence of NDM-1 carbapenemase among ColR-KpSC isolates; this is in line with previous reports identifying NDM-1 as the most prevalent carbapenemase in K. pneumoniae species complex. This problem is particularly concerning in Mexico because of the lack of therapeutic options.

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the genomes and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across seven species, the total size of which is 33.1% longer than that of a single cichlid genome. Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid genome is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations, both of which merit study to understand their interplay in cichlid evolution.

Unraveling the genetic traits and functional diversity of the pan-genome in Pantoea dispersa

BACKGROUND

Medical devices are crucial in modern healthcare, but commonly used clinical tools such as cotton swabs can be easily contaminated by microorganisms (such as Pantoea), becoming vectors for pathogens and leading to patient infections or more severe outcomes. Despite the dual nature of the Pantoea that has garnered significant attention, research investigating Pantoea dispersa (P. dispersa) remains limited. This study conducted a pan-genome analysis of three isolates and 57 P. dispersa strains from NCBI to investigate their evolutionary relationships, population structure, and functional characteristics.

RESULTS

Whole-genome analysis revealed high genomic diversity among 60 strains of P. dispersa, identifying 6,791 orthologous gene clusters (OGs), with core genes accounting for 45.1% and accessory genes accounting for 54.9%. Additionally, 2,185 gene clusters were not annotated in the reference genome. Further analysis demonstrated that 782 gene clusters were annotated as 406 VFs that were unevenly distributed among different strains and primarily associated with nutritional or metabolic factors, motility, and immune modulation. This study also identified four VFs genes related to the type III secretion system (T3SS) and observed some VFs present only in specific genetic clusters. In the analysis of antibiotic resistance genes (ARGs), 12 ARGs were identified, with nine being highly conserved across all isolates, and resistance mechanisms primarily involved antibiotic efflux and antibiotic target alteration. Secondary metabolite analysis identified 289 gene clusters, with 23 matching known gene clusters, while the rest were new discoveries, including arylpolyene, NRPS, and terpene types. These results reveal the complex virulence factors (VFs) and secondary metabolite genes in P. dispersa, providing significant insights into its genetic diversity and biological significance.

CONCLUSION

This study provides the first pan-genome framework for P. dispersa, along with a map of its VFs, ARGs, and secondary metabolite gene clusters. This study provides a deep insight into the genetic diversity and potential biological significance of P. dispersa, offering valuable references for leveraging its unique strain characteristics and metabolic capabilities in industrial production and clinical therapy.

Misidentification of Raoultella spp. (R. terrigena, R. planticola) and Klebsiella spp. (K. variicola, K. grimontii) as Klebsiella pneumoniae: Retrospective study of a necropsy-associated bacterial collection from horses

Misidentifications as Klebsiella pneumoniae were observed during a French retrospective study of a necropsy-associated K. pneumoniae bacterial collection from horses. Accordingly, the present study aimed to further characterise the 12 Raoultella spp. and Klebsiella spp. strains involved in these misidentifications. The strains were identified and characterised using the Api 20E system, K. pneumoniae PCR detection, matrix-assisted laser desorption/ionisation time-of-flight mass spectroscopy and whole-genome sequencing. Antimicrobial susceptibilities were tested by the disc diffusion method with a panel of 40 antibiotics. Thus, misidentifications as K. pneumoniae mainly concerned Raoultella spp. (R. terrigena, R. planticola) rather than Klebsiella spp. (K. variicola, K. grimontii), with a dominance of R. terrigena. Among the 12 strains, only K. grimontii was multi-drug resistant and none were considered hypervirulent. MALDI-TOF was sufficient to avoid misidentification but commercial spectra databases should be expanded with K. grimontii and R. terrigena reference spectra to improve identification accuracy. This is probably (i) the first report of K. grimontii and R. planticola isolations from horses and (ii) the second report of R. terrigena and K. variicola isolations from horses.

Genomic characterization of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021

Listeria monocytogenes is a saprophytic gram-positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania, and up to 20 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterization of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021 : 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, 5 (7.1%) from wounds, 1 (1.4%) from pleural fluid and 1 (1.4%) from a brain abscess. Two phylogenetic lineages were identified-I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)-along with three serogroups-IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2) and singletons for ST37, ST451 and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6-48 core SNPs from reference and 0, 4 or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights the complementary value of whole-genome sequencing in routine PCR-based surveillance in Lithuania. This is the first study to characterize and compare genomes for L. monocytogenes associated with neuroinfections in Lithuania using whole-genome sequencing. The retrospective detection of the ST155 clone underscores the need for a review and strengthening of epidemiological surveillance strategies in clinical and non-clinical settings in Lithuania.

Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States

Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.

Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota

In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.

Characterization of a multidrug-resistant hypovirulent ST1859-KL35 klebsiella quasipneumoniae subsp. similipneumoniae strain co-harboring tmexCD2-toprJ2 and blaKPC-2

OBJECTIVES

The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24).

METHODS

Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships.

RESULTS

KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1), an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination.

CONCLUSIONS

KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.

Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules

Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.

An expanded metabolic pathway for androgen production by commensal bacteria

Commensal bacteria have been implicated in the modulation of steroid hormones, including circulating androgen levels in the host. However, the microbial genetic pathways involved in androgen production have not been fully characterized. Here we identify a microbial gene encoding an enzyme that catalyses the conversion of androstenedione to epitestosterone in the gut microbiome member Clostridium scindens and named this gene desF. We demonstrate that epitestosterone impacts androgen receptor-dependent prostate cancer cell proliferation in vitro. We also demonstrate that stool desF levels are elevated in patients with prostate cancer who are unresponsive to abiraterone/prednisone therapy. Bacterial isolates from urine or prostatectomy tissue produced androgens, and 17β-hydroxysteroid dehydrogenase activity encoded by the desG gene was detected in strains of the urinary tract bacterium Propionimicrobium lymphophilum. Furthermore, we demonstrate that urinary androgen-producing bacterial strains can promote prostate cancer cell growth through metabolism of cortisol and prednisone. Abiraterone, which targets host desmolase (CYP17A1), a rate-limiting enzyme in adrenal steroidogenesis, does not inhibit bacterial desmolase (DesAB), whereas the conversion of prednisone to androgens by DesAB, DesF and DesG drives androgen-receptor-dependent prostate cancer cell line proliferation in vitro. Our results are a significant advance in steroid microbiology and highlight a potentially important role for gut and urinary tract bacteria in host endocrine function and drug metabolism.

Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis

Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside, which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a telomere-to-telomere (T2T) C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb of repetitive sequences and 25 200 protein-coding genes. Comparative genomic analyses revealed C. asiatica as an early-diverging genus within the Apiaceae family with a single whole-genome duplication (WGD, Apiaceae-ω) event following the ancient γ-triplication, contrasting with Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω). We further constructed 3D chromatin structures, A/B compartments, and topologically associated domains (TADs) in C. asiatica leaves, elucidating the influence of chromatin organization on expression WGD-derived genes. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene coexpression network analysis (WGCNA) further highlighted the pathways modulated in response to methyl jasmonate (MeJA), offering insights into the regulatory networks governing saponin biosynthesis. This work not only provides a valuable genomic resource for C. asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites.

Deciphering the genetic context of the emerging OXA-484-producing carbapenem-resistant Escherichia coli from ST167 high-risk clone in the United Arab Emirates

PURPOSE

The evolution of new carbapenemase variants is alarming. We aimed to investigate the genetic context and molecular epidemiology of the emerging OXA-484 carbapenemase in the United Arab Emirates, to decipher its resistance mechanisms and evolutionary relationships.

METHODS

Antimicrobial susceptibility testing was performed for an E. coli isolate recovered from an intrauterine contraceptive device of a patient returning to the UAE after a trip to Pakistan. Whole genome sequencing was used to characterize the genetic environment of blaOXA-484, resistance and virulence determinants. Southern blotting was used to localize OXA-484 gene. Phylogenetic analysis established the sequence type (ST) and used to investigate relationships with global strains, and differences from other OXA-48-like types.

RESULTS

The strain demonstrated selective resistance against ertapenem while maintaining susceptibility to imipenem and meropenem. OXA-484 exhibited R214G substitution affecting the enzyme's activity and distinguishing it from closely related variants like OXA-181 (214R) and OXA-232 (214 S). blaOXA-484 was located on two non-conjugative plasmids (∼ 65 and 100 kb) within a genetic environment containing multiple insertion sequences. It belonged to the high-risk clone ST167, recognized for its enhanced capacity to acquire and maintain resistance determinants. The gene was mostly prevalent in the Western part of the world with limited distribution in the Middle East.

CONCLUSION

This study presents the first comprehensive characterization of OXA-484-producing E. coli ST167 in the UAE. The presence of blaOXA-484 in high-risk clone warrants concern on its dissemination potential and underscores the importance of genomic surveillance and targeted infection control to prevent the spread of emerging resistance determinants.

Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation

Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.

Genomic characterization of Pseudomonas aeruginosa from canine otitis highlights the need for a One Health approach to this opportunistic pathogen

In humans, Pseudomonas aeruginosa is well known as a prominent opportunistic pathogen associated with antimicrobial resistance (AMR), which presents a major challenge to successful treatment. This is also the case in animals, particularly in companion dogs where P. aeruginosa is a common cause of otitis. Despite its clinical significance, little data are available on the genomics and epidemiology of P. aeruginosa in dogs. To address this, we have genome-sequenced 34 canine otitis P. aeruginosa isolates from a veterinary referral hospital and analysed these along with a further 62 publicly available genomes from canine isolates. Phylogenetic analysis revealed that all three P. aeruginosa phylogroups, A-C, are represented amongst a diverse bacterial population isolated from dogs. We identify examples of persistent or recurrent infection by the same strain of up to 309 days between sampling, demonstrating the difficulty of successfully eradicating infection. Isolates encoded a variety of AMR genes with genomic and phenotypic AMR correlating poorly for β-lactams but showing complete concordance between fluoroquinolone resistance and quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV. Pangenome-wide analysis between 80 canine otitis isolates (34 newly sequenced here and a further 46 publicly available) and a reference collection of 491 human isolates found no genes which were over-represented or specific to either host species, indicating similar strains infect both humans and dogs. This agrees with the sharing of multilocus sequence types between dogs and humans, including the isolation here of ST235 from three dogs, a lineage prominent among the multidrug resistant (MDR) and extensively drug-resistant (XDR) international high-risk clones of P. aeruginosa causing human infections. The presence of such 'high-risk' clones in companion dogs is concerning given their potential impact on animal health and the potential for zoonotic spread. These data provide new insight into this difficult-to-treat veterinary pathogen and promote the need for a One Health approach to tackling it.

Genomic diversity and tracing of Paenibacillus larvae in Australia: implications for American foulbrood outbreak surveillance in low-diversity populations

Paenibacillus larvae is the causative agent of American foulbrood (AFB) in honeybees (Apis mellifera) and a devastating pathogen for honey and pollination industries worldwide. Despite this threat, a genomic survey of P. larvae has not been attempted within Australia. To examine the diversity of Australian populations, we sequenced 368 P. larvae genomes sourced primarily from south-eastern Australia. Multilocus sequencing typing analysis identified only 4 sequence types across all 368 samples, with 2 sequence types (ST18 and ST5) representing 96% of all isolates. In comparison to European-sourced P. larvae, sequences revealed much less genetic diversity in Australian isolates. However, Australian genotypes were very similar to those found in New Zealand populations. All Australian isolates were identified as enterobacterial repetitive intergenic consensus (ERIC) type I. To determine the feasibility of a genomic tracing system in a low-diversity genetic background, we investigated core-genome SNP (cgSNP) genotyping of isolates from a single beekeeper and from isolates across multiple apiaries and sample sites. We identified highly related cgSNP clusters, one with known epidemiological links, but another highly related cluster spanned several decades. Results strongly suggest that cgSNP analysis does have the discriminatory power to assist in the trace-forward and trace-back of AFB outbreaks, but importantly, the inclusion of background sequences and careful consideration of multiple analysis methods are required to avoid erroneous conclusions.

Macrolactin a is an inhibitor of protein biosynthesis in bacteria

Macrolactin A (McA) is a secondary metabolite produced by Bacillus species. It has been known for its antimicrobial properties since the late 1980s, although the exact mechanism of its antibacterial activity remains unknown. In this study, we have found that McA is an inhibitor of protein synthesis in bacteria. Our conclusion is based on the results obtained by in vivo and in vitro bioreporter systems. We demonstrated that the inhibitory activity of McA is independent of bacterial species. However, the concentration of McA required to inhibit protein synthesis in the E. coli cell-free translational model was found to be 50 times lower than the concentration required in the S. aureus cell-free translational model. To investigate the mechanism of McA's inhibitory activity, we conducted a toe-printing assay, sequenced and annotated the genomes of McA-resistant Bacillus pumilus McAR and its parental strain. The results showed that McA inhibits the initial step of the elongation phase of protein synthesis. We identified single and multiple nucleotide polymorphisms in the gene encoding the translation elongation factor Tu (EF-Tu). Molecular modeling showed that the McA molecule can form non-covalent bonds with amino acids at the interface of domains 1 and 2 of EF-Tu. A cross-resistance assay was conducted using kirromycin on B. pumilus McAR. The results confirmed the assumption that McA has a mode of action similar to that of other elfamycin-like antibiotics (targeting EF-Tu). Overall, our study addresses a significant gap in our understanding of the mechanism of action of McA, a representative member of the macrolide antibiotics.

Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam

BACKGROUND

Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam.

METHODS

Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential.

RESULTS

Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 µg/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple β-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.

CONCLUSIONS

This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.

Imbroritus primus gen. nov., sp. nov., a facultatively autotrophic bacterium from environmental water samples

A Gram-stain-negative coccobacillus, LMG 32992T, was isolated from water that had collected in a tyre in Pingtung, Donggang Township, Taiwan. Upon preliminary 16S rRNA gene sequence analysis, it was most closely related to members of the genus Ralstonia (16S rRNA gene sequence similarities of 96.7-97.5%). The present study aimed to elucidate its taxonomic position and to propose a formal classification. To this end, the complete genome sequence was determined, and taxonomic, phylogenomic, metabolic and physiological analyses were performed. Comparative genomic analyses demonstrated that strain LMG 32992T and another unclassified strain, Burkholderiaceae bacterium PBA, which was isolated earlier from textile wastewater in Malaysia, represented a single novel species within a novel genus of the family Burkholderiaceae. The G+C content of the LMG 32992T genomic DNA was 63.77 mol%. Genomic analyses and growth tests demonstrated that LMG 32992T had an asaccharolytic metabolism but that it was well-equipped to synthetize, if necessary autotrophically, and transform all required carbohydrates and that it used the Krebs and related cycles to generate reductive power for a heterotrophic energy metabolism. We propose the name Imbroritus primus gen. nov., sp. nov. with strain LMG 32992T (=CIP 112179T=BCRC 81361T=A30B1T) as the type strain, for this novel taxon.

Genomic characterization of Streptococcus suis serotype 31 isolated from one human and 17 clinically asymptomatic pigs in Thailand

Streptococcus suis is a zoonotic pathogen capable of causing severe diseases in humans and pigs. Frequently, S. suis serotype 31 strains have been isolated from pigs. The first human case of S. suis was reported in Thailand in 2015. In total, 18 strains from one human and 17 clinically asymptomatic pigs in Thailand were analyzed to characterize S. suis serotype 31. In total, 11 different STs were identified, with the major ST being ST2767 (38.89 %; 7/18). The minimum core-genome (MCG) classification revealed that almost all of the serotype 31 strains belonged to MCG7 (94.44 %; 17/18). Genomic analysis revealed that the serotype 31 isolates were major clusters with the porcine-healthy strains from China, Viet Nam, and Thailand. The human serotype 31 ST221 isolate was closely related to S. suis serotype 5 and 24 strains (CC221/234) isolated from Thailand. All serotype 31 strains were multidrug resistant with resistance to azithromycin (100 %; 18/18) and tetracycline (100 %; 18/18). Notably, 10 (55.56 %) of the serotype 31 strains were resistant to penicillin, while 8 strains (44.44 %) showed intermediate resistance to this agent. High substitutions were observed in three penicillin-binding proteins (1 A, 2B, and 2X) of these serotype 31 strains. The most prevalent antimicrobial resistance genes were erm(B) (100 %; 18/18) and tet(O) (66.67 %; 12/18). Overall, 7 strains carried integrative conjugative elements (ICEs) that harbored antimicrobial resistance genes, such as erm(B), tet(O), and tet(W). This study contribute to understanding the genomic diversity and provide valuable information for public health awareness of multidrug-resistant S. suis serotype 31.

Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis

Bacteriophage (phage) therapy, which uses lytic viruses as antimicrobials, is a potential strategy to address the antimicrobial resistance crisis. Cystic fibrosis, a disease complicated by recurrent Pseudomonas aeruginosa pulmonary infections, is an example of the clinical impact of antimicrobial resistance. Here, using a personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off, nine adults with cystic fibrosis (eight women and one man) of median age 32 (range 22-46) years were treated with phages on a compassionate basis because their clinical course was complicated by multidrug-resistant or pan-drug-resistant Pseudomonas that was refractory to prior courses of standard antibiotics. The individuals received a nebulized cocktail or single-phage therapy without adverse events. Five to 18 days after phage therapy, sputum Pseudomonas decreased by a median of 104 CFU ml-1, or a mean difference of 102 CFU ml-1 (P = 0.006, two-way analysis of variance with Dunnett's multiple-comparisons test), without altering sputum microbiome, and an analysis of sputum Pseudomonas showed evidence of trade-offs that decreased antibiotic resistance or bacterial virulence. In addition, an improvement of 6% (median) and 8% (mean) predicted FEV1 was observed 21-35 days after phage therapy (P = 0.004, Wilcoxon signed-rank t-test), which may reflect the combined effects of decreased bacterial sputum density and phage-driven trade-offs. These results show that a personalized, nebulized phage therapy trade-off strategy may affect clinical and microbiologic endpoints, which must be evaluated in larger clinical trials.

Analysis of two Nocardia brasiliensis class A β-lactamases (BRA-1 and BRS-1) and related resistance to β-lactam antibiotics

OBJECTIVE

Molecular determinants of β-lactam resistance are poorly explored for most Nocardia species, such as Nocardia brasiliensis. In this study, we characterised resistance mediated by two β-lactamases in the reference strain N. brasiliensis HUJEG-1 and extended our analysis to nine N. brasiliensis clinical strains.

METHODS

The susceptibility of N. brasiliensis HUJEG-1 was determined by measuring the MIC via microdilution for five β-lactam antibiotics that were or were not associated with β-lactamase inhibitors (clavulanate and avibactam, 4 µg/mL). Two putative class A β-lactamase-encoding genes (blaBRA-1 and blaBRS-1) were identified in the HUJEG-1 genome. The kinetic parameters of purified BRA-1 and BRS-1 were determined by spectrophotometry. Measurement of β-lactam resistance was then extended to nine clinical strains. These phenotypic data were compared with the genomic diversity of whole genomes (next-generation sequencing).

RESULTS

N. brasiliensis HUJEG-1 was resistant to amoxicillin, cefuroxime, and cefotaxime, but susceptible to their combination with clavulanate or avibactam. This strain was resistant to imipenem (with or without inhibitors) and susceptible to meropenem. BRA-1 showed high catalytic efficiencies against penams (penicillin, ampicillin) and cephems (cephaloridine, cephalothin, and cefamandole), but not against penems (imipenem, meropenem), suggesting that imipenem resistance was mediated by another mechanism. The hydrolytic activity of BRS-1 was 100-1000-fold lower than that of BRA-1 for all β-lactams tested, suggesting that BRS-1 has a minor contribution to β-lactam resistance. Analysis of the nine clinical strains showed variations in susceptibility to cefotaxime, as well as diversity in genetic backgrounds and BRA-1 sequences.

CONCLUSIONS

N. brasiliensis HUJEG-1 resistance to penams and cephems is mainly due to the class A β-lactamase BRA-1.

Emergence of an XDR Klebsiella pneumoniae ST5491 strain co-harboring NDM-5, MCR-1.1, tmexCD1-toprJ1, and a novel plasmid carrying CTX-M-15

Objective

The rapid emergence of antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a significant global health threat. The study aimed to analyze and describe the genomic architecture and resistance mechanisms of an extensively drug-resistant (XDR) K. pneumoniae isolate, KP09, by focusing on plasmids that harbor multiple resistance genes, including tmexCD1-toprJ1, blaCTX-M-15 , blaNDM-5 , and mcr-1.1.

Methods

The KP09 strain, isolated from a clinical sample, was subjected to antimicrobial susceptibility testing and conjugation experiments. Whole-genome sequencing with both long- and short-read methods facilitated hybrid assembly for complete genome reconstruction. Bioinformatics analyses identified resistance genes, plasmid structures, and sequence types (STs), whereas comparative genomic analysis elucidated the context and dissemination mechanisms of resistance determinants.

Results

KP09 exhibited broad-spectrum resistance to carbapenems, colistin, eravacycline, and tigecycline, and only remained susceptible to cefiderocol. The conjugation experiments successfully produced four transconjugants, each carrying specific plasmids: JKP09-1 harbored the tmexCD1-toprJ1 gene, JKP09-2 harbored tmexCD1-toprJ1 and mcr-1.1 genes, JKP09-3 harbored the mcr-1.1 gene, and JKP09-4 harbored blaNDM-5 and mcr-1.1 genes. Genomic analysis revealed a novel IncFIA/IncFII/IncQ1 hybrid plasmid carrying bla CTX-M-15, along with a large conjugative plasmid encoding the tmexCD1-toprJ1 efflux pump. The bla NDM-5 and mcr-1.1 genes were located in separate IncX-type plasmids, suggesting independent dissemination pathways. Furthermore, KP09 was identified as a new sequence type, ST5491, closely related to the endemic ST15 clone. The comparative analysis highlighted the role of mobile genetic elements, such as IS26 and ISEcp1, in facilitating the spread of resistance genes.

Conclusion

This study provides critical information on the genetic mechanisms that drive AMR in K. pneumoniae, including the identification of a novel bla CTX-M-15 encoding IncFIA/IncFII/IncQ1 hybrid plasmid and the emergence of the ST5491 strain. Understanding the genetic basis of resistance is essential to inform public health interventions and mitigate the impact of AMR.

Phylogenetic analysis of pathogenic algae reveals lineage-dependent patterns of phagocytosis

Prototheca is an unusual genus of algae that lack chlorophyll and are obligate heterotrophs. To date, six paraphyletic pathogenic species have been identified in the context of vertebrates, principally in cattle-associated and human-associated infections. Together with the genus Auxenochlorella and Helicosporidium, rDNA sequence analysis currently favors grouping Prototheca under a clade known as the Auxenochlorella, Helicosporidium and Prototheca (AHP) lineage. Most studies so far have focused only on Prototheca bovis and Prototheca ciferrii as cattle-associated species and on Prototheca wickerhamii as a human-associated species. However, such studies remain limited in scope as they focus on only three species of Prototheca, which is not representative of the total number of species within the AHP lineage. In this study, we employ a phylogenetics approach based on five new organelle-encoded genes to delineate higher-level relationships within the AHP lineage. We use the resultant data to then guide a live-cell imaging-based investigation of aspects of the mammalian innate immune response to 11 Prototheca species and four Auxenochlorella species. Our data reveal varying patterns of phagocytosis dynamics that are both host cell type- and algal species-dependent. Together, these findings reveal the interaction between pathogen phylogeny and host immune response, revealing ways to identify new therapeutic targets in the future.

IMPORTANCE

Protothecosis is a rare algal infection caused by members of the genus Prototheca, which is comprised of unusual non-photosynthetic algae. Six pathogenic species have been identified so far that can cause infection in vertebrates, primarily cattle and humans. The phylogeny of this genus remains obscure and has been revised multiple times recently. However, this phylogeny has largely been based on only three species of Prototheca. To resolve this phylogenetic conundrum, here, we employ a phylogenetics approach based on five new organelle-encoded genes. We then use these data to perform live-cell imaging of a selected range of Prototheca species co-cultured with mammalian immune cells. Visualizing these phagocytic interactions in this context helps delineate both host cell-type- and species-dependent differences in phagocytic uptake, thereby providing novel insight into lineage-based differences.

Draft whole-genome sequence of multidrug-resistant Enterococcus faecium strain MKL_BAU_Fe01 isolated from chicken meat

We report the draft genome sequence of Enterococcus faecium MKL_BAU_Fe01 from chicken meat in Bangladesh. The 2,953,746 bp genome, with 37.99% GC content across 264 contigs, contains 3,117 genes, including 3,007 Coding Sequences (CDSs), 17 rRNAs, and 89 tRNAs, along with several antibiotic resistance and pathogenic genes.

Characterization and whole genome sequencing of Saccharomyces cerevisiae strains lacking several amino acid transporters: Tools for studying amino acid transport

Saccharomyces cerevisiae mutants have been used since the early 1980s as a tool for characterizing genes from other organisms by functional complementation. This approach has been extremely successful in cloning and studying transporters; for instance, plant amino acid, sugar, urea, ammonium, peptide, sodium, and potassium transporters were characterized using yeast mutants lacking these functions. Over the years, new strains lacking even more endogenous transporters have been developed, enabling the characterization of transport properties of heterologous proteins in a more precise way. Furthermore, these strains provide the added possibility of characterizing a transporter belonging to a family of proteins in isolation, and thus can be used to study the relative contribution of redundant transporters to the whole function. We focused on amino acid transport, starting with the yeast strain 22 ∆ 8AA, which was developed to clone plant amino acid transporters in the early 2000s. We recently deleted two additional amino acid permeases, Gnp1 and Agp1, creating 22 ∆ 10α. In the present work, five additional permeases (Bap3, Tat1, Tat2, Agp3, Bap2) were deleted from 22 ∆ 10α genome, in a combination of up to three at a time. Unexpectedly, the amino acid transport properties of the new strains were not very different from the parent, suggesting that these amino acid permeases play a minor role in amino acid uptake, at least in our conditions. Furthermore, the inability to utilize certain amino acids as sole nitrogen source did not correlate with reduced uptake activity, questioning the well-accepted relationship between lack of growth and loss of transport properties. Finally, in order to verify the mutations and the integrity of 22 ∆ 10α genome, we performed whole-genome sequencing of 22 ∆ 10α using long-read PacBio sequencing technology. We successfully assembled 22 ∆ 10α's genome de novo, identified all expected mutations and precisely characterized the nature of the deletions of the ten amino acid transporters. The sequencing data and genome will serve as a valuable resource to researchers interested in using these strains as a tool for amino acid transport study.

Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments

The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.

Paramutation-Like Behavior of Genic piRNA-Producing Loci in Drosophila virilis

Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of a paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversions remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the subtelomeric RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Importantly, the maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. The present findings suggest that the paramutation-like behavior of piRNA clusters may be influenced not only by piRNAs but also by structural features and the chromatin environment in the proximity to telomeres, providing new insights into the epigenetic regulation of the Drosophila genome.

Complete genome sequence of a Neisseria meningitidis isolate from an ankle joint with septic arthritis

Neisseria meningitidis has been identified as the causative agent of a wide variety of infections. We report the complete genome sequence of an N. meningitidis isolate from a joint fluid sample collected from a patient with primary meningococcal septic arthritis. This strain belongs to the sequence type 17488 of the ST-11 clonal complex, and its assembled genome consists of 2,242,622 base pairs with 51.75% GC content.

Chromosome-level genomes of Arctic and Antarctic mosses: Aulacomnium turgidum and Polytrichastrum alpinum

Bryophytes play a crucial role in the ecosystems of polar regions. These simple plants are among the predominant vegetation types in both Arctic and Antarctic landscapes, where they contribute significantly to biodiversity and ecological stability. Here, we report the chromosome-level genomes of two polar moss species, the Arctic Aulacomnium turgidum and Antarctic Polytrichastrum alpinum. Utilizing a combination of Illumina short reads, Nanopore long reads, and Hi-C data, we assembled genomes of 277.84 Mb for A. turgidum and 498.33 Mb for P. alpinum, respectively. These assemblies were anchored to 11 chromosomes for A. turgidum and 8 chromosomes for P. alpinum. Both species exhibited a sex chromosome with distinct genomic characteristics. Gene annotations revealed 25,999 protein-coding genes in A. turgidum and 28,070 in P. alpinum. The high completeness of the gene space was validated via BUSCO, achieving impressive scores of 98.2% and 98.0%. These high-quality genomes provide critical resources for studying the adaptive evolution and stress tolerance mechanisms of mosses in extreme polar environments.

Whole-genome analysis of Streptococcus mutans GDP01 isolate of dental caries tooth

Dental caries is a multifactorial infectious disease primarily driven by Streptococcus mutans. Here, we present the whole-genome sequence of Streptococcus mutans GDP01, which was isolated from the dental caries-infected children from Madurai, Tamil Nadu, India.

De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family

BACKGROUND

Aeluropus littoralis is considered a valuable natural forage plant for ruminant livestock and is highly tolerant to extreme abiotic stresses, especially salinity, drought, and heat. It is a monocotyledonous halophyte, has salt glands, performs C4-type photosynthesis and has a close genetic relationship with cereal crops. Moreover, previous studies have shown its huge potential as a reservoir of genes and promoters to understand and improve abiotic stress tolerance in crops.

RESULTS

The sequencing and hybrid assembly of the A. littoralis genome (2n = 2X = 20) using short and long reads from the BGISeq-500 and PacBio high-fidelity (HiFi) sequencing platforms, respectively. Using the k-mer analysis method, the haploid genome size of A. littoralis was estimated to be 360 Mb (with a heterozygosity rate of 1.88%). The hybrid assembled genome included 4,078 contigs with a GC content of 44% and covered 348 Mb. The longest contig and the N50 values were 5.1 Mb and 133.77 kb, respectively. The Benchmarking Universal Single Copy Ortholog (BUSCO) value was 91.1%, indicating good integrity of the assembled genome. The discovered repetitive elements accounted for 90.6 Mb, representing 26.03% of the total genome, and included a significant component of transposable elements (11.48%, ~40 Mb). Using a homology-based approach, 35,147 genes were predicted from the genome assembly. We next focused our analysis on the zinc-finger A20/AN1 gene family, a member of which (AlSAP) was previously shown to confer increased tolerance to osmotic and salt stresses when it was over-expressed in tobacco, wheat, and rice. Here, we identified the complete set of members of this family in the Aeluropus littoralis genome, thereby laying the foundation for their future functional analysis in cereal crops. In addition, the expression patterns of four novel genes from this family were analyzed by qPCR.

CONCLUSION

This resource and our findings will contribute to improve the current understanding of salinity tolerance in halophytes while providing useful genes and allelic variation to improve salinity and drought tolerance in cereals through genetic engineering and gene editing, respectively.

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change.IMPORTANCEAnthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Identification of pandemic ST147, ESBL-type β-lactamases, carbapenemases, and virulence factors in Klebsiella pneumoniae isolated from southern Peru

Multidrug-resistant Klebsiella pneumoniae (MDR K. pneumoniae) is a significant pathogen associated with nosocomial infections, often leading to high morbidity and mortality. This resistance is largely due to the efficient horizontal transfer of mobile genetic elements such as plasmids, which carry resistance genes and virulence factors. These elements contribute to the production of extended-spectrum β-lactamases (ESBL) and carbapenemases, which further complicates treatment. Despite the high prevalence of MDR K. pneumoniae in Peruvian hospitals, the genomic characterization of these strains remains limited. This study investigated the phenotypic and molecular identification of extended-spectrum β-lactamases (ESBLs), carbapenemases, and virulence factors in 91 MDR K. pneumoniae strains collected from three hospitals between 2022 and 2023. Phenotypic detection of ESBLs was performed using the Jarlier method, while carbapenemases were identified via double-disk synergy testing with boronic acid, EDTA, and Carba NP test. The positive isolates were further analyzed for resistance genes (blaCTX-M, blaTEM, blaSHV, blaKPC, blaNDM, blaIMP, and blaVIM). Four isolates were subjected to whole-genome sequencing (WGS) for further characterization. All multidrug-resistant K. pneumoniae strains (100%) were ESBL-positive, with 14.3% producing carbapenemases, primarily KPC-type and metallo-β-lactamases (MBLs). The virulence factor analyses revealed that only 7.7% exhibited hypermucoviscosity. Protease activity was detected in 19.8% of the strains, and lipase activity in 1.1%. Regarding biofilm formation, 85.7% of the strains showed moderate adherence. Molecular analysis identified ESBL (blaCTX-M, 78%; blaTEM, 71.4%; blaSHV, 82.4%) and carbapenemase genes (blaKPC 7.7%, blaNDM 4.4%). Genomic analysis revealed various antimicrobial resistance mechanisms, including porin-coding gene mutations, aminoglycoside resistance linked to fluoroquinolone resistance, and multidrug efflux pump regulators. Sequence typing has identified high-risk clones (ST147, ST629, and ST37) associated with hospital outbreaks globally. These findings underscore the considerable concern of MDR and hypervirulent K. pneumoniae in Peruvian hospitals. These findings emphasize the pressing need for sustained genomic surveillance, enhanced infection control measures, and strategies to address the expanding problem of MDR K. pneumoniae.

Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code

Trypanosomatids are among the most extensively studied protists due to their parasitic interactions with insects, vertebrates, and plants. Recently, Blastocrithidia nonstop was found to depart from the canonical genetic code, with all three stop codons reassigned to encode amino acids (UAR for glutamate and UGA for tryptophan), and UAA having dual meaning also as a termination signal (glutamate and stop). To explore features linked to this phenomenon, we analyzed the genomes of four Blastocrithidia and four Obscuromonas species, the latter representing a sister group employing the canonical genetic code. We found that all Blastocrithidia species encode cognate tRNAs for UAR codons, possess a distinct 4 bp anticodon stem tRNATrpCCA decoding UGA, and utilize UAA as the only stop codon. The distribution of in-frame reassigned codons is consistently non-random, suggesting a translational burden avoided in highly expressed genes. Frame-specific enrichment of UAA codons immediately following the genuine UAA stop codon, not observed in Obscuromonas, points to a specific mode of termination. All Blastocrithidia species possess specific mutations in eukaryotic release factor 1 and a unique acidic region following the prion-like N-terminus of eukaryotic release factor 3 that may be associated with stop codon readthrough. We infer that the common ancestor of the genus Blastocrithidia already exhibited a GC-poor genome with the non-canonical genetic code. Our comparative analysis highlights features associated with this extensive stop codon reassignment. This cascade of mutually dependent adaptations, driven by increasing AU-richness in transcripts and frequent emergence of in-frame stops, underscores the dynamic interplay between genome composition and genetic code plasticity to maintain vital functionality.

IMPORTANCE

The genetic code, assigning amino acids to codons, is almost universal, yet an increasing number of its alterations keep emerging, mostly in organelles and unicellular eukaryotes. One such case is the trypanosomatid genus Blastocrithidia, where all three stop codons were reassigned to amino acids, with UAA also serving as a sole termination signal. We conducted a comparative analysis of four Blastocrithidia species, all with the same non-canonical genetic code, and their close relatives of the genus Obscuromonas, which retain the canonical code. This across-genome comparison allowed the identification of key traits associated with genetic code reassignment in Blastocrithidia. This work provides insight into the evolutionary steps, facilitating an extensive departure from the canonical genetic code that occurred independently in several eukaryotic lineages.

Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens

Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the different resolution power of allele-based schemas led to marked discrepancies. Still, we identified non-negligible differences in outbreak detection and demonstrated how a threshold flexibilization favors the detection of similar outbreak signals by different laboratories. These results, together with the observation that different traditional typing groups (e.g., serotypes) exhibit a remarkably different genetic diversity, represent valuable information for future outbreak case-definitions and WGS-based nomenclature design. This study reinforces the need, while demonstrating the feasibility, of conducting continuous pipeline comparability assessments, and opens good perspectives for a smoother international and intersectoral cooperation towards an efficient One Health FWD surveillance.

An Outbreak of Multidrug-Resistant Shigella flexneri Serotype 2a Among People Experiencing Homelessness in Vancouver

Background: We describe a community-based outbreak of multidrug-resistant Shigella flexneri serotype 2a among people experiencing homelessness (PEH) in Vancouver's Downtown Eastside during the COVID-19 pandemic. Methods: In this observational cohort study, we followed the Outbreak Reports and Intervention Studies of Nosocomial Infection (ORION) reporting guidelines. We identified cases by laboratory surveillance and collected demographic and clinical data from the medical charts or patient interviews. We implemented enhanced surveillance and disseminated testing and management guidelines. Shigella flexneri isolates were serotyped, and whole-genome sequencing was performed. Results: We identified 101 confirmed cases of Shigella flexneri 2a (80% male; median age 43) between 31 January and 16 December 2021. All the affected individuals experienced homelessness, and substance use disorder was the most common comorbidity (88%). Five patients required ICU hospitalization, and one death occurred within 30 days. Core-genome multilocus sequence typing analysis confirmed a clonal outbreak. All S. flexneri isolates were phenotypically and genotypically multidrug-resistant. Conclusions: COVID-19 exacerbated longstanding public health concerns around the dearth of hygiene and sanitation resources available to PEH. Preventing similar outbreaks will require addressing these risks and finding solutions to the crisis of homelessness in Canada.