QUAST: quality assessment tool for genome assemblies

Genomic insights into the rapid rise of Pseudomonas aeruginosa ST463: A high-risk lineage's adaptive strategy in China

High-risk lineages of Pseudomonas aeruginosa pose a serious threat to public health, causing severe infections with high mortality rates and limited treatment options. The emergence and rapid spread of the high-risk lineage ST463 in China have further exacerbated this issue. However, the basis of its success in China remains unidentified. In this study, we analyzed a comprehensive dataset of ST463 strains from 2000 to 2023 using whole genome sequencing to unravel the epidemiological characteristics, evolutionary trajectory, and antibiotic resistance profiles. Our findings suggest that ST463 likely originated from a single introduction from North America in 2007, followed by widespread domestic dissemination. Since its introduction, the lineage has undergone significant genomic changes, including the acquisition of three unique regions that enhanced its metabolism and adaptability. Frequent recombination events, along with the burden of bacteriophages, antibiotic resistance genes, and the spread of c1-type (blaKPC-2) plasmid-carrying strains, have played crucial roles in its expansion in China. Mutation analysis reveals adaptive responses to antibiotics and selective pressures on key virulence factors, indicating that ST463 is evolving toward a more pathogenic lifestyle.

Integrative and conjugative elements associated with antimicrobial resistance in multidrug resistant Pasteurella multocida isolates from bovine respiratory disease (BRD)-affected animals in Spanish feedlots

The emergence of multidrug-resistance (MDR) in Pasteurella multocida, a major contributor to bovine respiratory disease (BRD) is being increasingly reported, often linked to the carriage of antimicrobial resistance genes (ARGs) on integrative and conjugative elements (ICEs). The resistance phenotype for 19 antimicrobials was determined using broth microdilution in 75 Pasteurella multocida isolates from healthy and BRD-affected cattle from five feedlots. The genomes of 32 isolates were sequenced to identify ARG) and mobile genetic elements (MGEs) and assess their genetic diversity. MDR isolates (with phenotypic resistance to aminoglycosides, macrolides, fluoroquinolones and/or tetracyclines) were primarily found among BRD-affected compared to healthy animals. Non-susceptible isolates, belonging to ST79 and ST13, harbored point mutations and four to nine ARGs, including rarely reported mechanisms in Europe (mph(E), msr(E) and aadA31 ARGs and newly described mutations in the gyrA/parC genes). All ARGs were linked to the presence of MGEs including two ICEs, Tn7407 and the novel Tn7809, a prophage and a putative composite transposon. Clonally related isolates were found in different batches from the same feedlot, suggesting maintenance of MDR strains. Our findings demonstrate the diverse genetic basis of AMR in P. multocida from BRD-affected cattle in Spain, emphasizing the role of MGEs in the ARG dissemination.

Maternal probiotic exposure enhances CD8 T cell protective neonatal immunity and modulates offspring metabolome to control influenza virus infection

Maternal gut microbiota composition contributes to the status of the neonatal immune system and could influence the early life higher susceptibility to viral respiratory infections. Using a novel protocol of murine maternal probiotic supplementation, we report that perinatal exposure to Lacticaseibacillus rhamnosus (L.rh) or Bifidobacterium animalis subsp. lactis (B.lac) increases the influenza A/PR8 virus (IAV) clearance in neonates. Following either supplementation, type 1 conventional dendritic cells (cDC1) were amplified in the lymph nodes leading to an enhanced IAV antigen-experienced IFN-γ producing effector CD8 T cells in neonates and IAV-specific resident memory CD8 T cells in adulthood. This was compatible with a higher protection of the offspring upon a secondary infection. Interestingly, only mice born to L.rh supplemented mothers further displayed an increased activation of IFN-γ producing virtual memory CD8 T cells and a production of IL-10 by CD4 and CD8 T cells that could explain a better control of the lung damages upon infection. In the offspring and the mothers, no disturbance of the gut microbiota was observed but, as analyzed through an untargeted metabolomic approach, both exposures modified neonatal plasma metabolites. Among them, we further demonstrated that genistein and 3-(3-hydroxyphenyl)propionic acid recapitulate viral clearance or cDC1 activation in neonates exposed to IAV. We conclude that maternal L.rh or B.lac supplementation confers the neonates specific metabolomic modulations with a better CD8 T cell-mediated immune protection against IAV infection.

Novel insights into carbohydrate utilisation, antimicrobial resistance, and sporulation potential in Roseburia intestinalis isolates across diverse geographical locations

Roseburia intestinalis is one of the most abundant and important butyrate-producing human gut anaerobic bacteria that plays an important role in maintaining health and is a potential next-generation probiotic. We investigated the pangenome of 16 distinct strains, isolated over several decades, identifying local and time-specific adaptations. More than 50% of the genes in each individual strain were assigned to the core genome, and 77% of the cloud genes were unique to individual strains, revealing the high level of genome conservation. Co-carriage of the same enzymes involved in carbohydrate binding and degradation in all strains highlighted major pathways in carbohydrate utilization and reveal the importance of xylan, starch and mannose as key growth substrates. A single strain had adapted to use rhamnose as a sole growth substrate, the first time this has been reported. The ubiquitous presence of motility and sporulation gene clusters demonstrates the importance of these phenotypes for gut survival and acquisition of this bacterium. More than half the strains contained functional, potentially transferable, tetracycline resistance genes. This study advances our understanding of the importance of R. intestinalis within the gut ecosystem by elucidating conserved metabolic characteristics among different strains, isolated from different locations. This information will help to devise dietary strategies to increase the abundance of this species providing health benefits.

Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome

Breast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrading bacteria. This study investigated the metabolism of HMOs by bifidobacteria and lactobacilli isolated from human milk and mother-infant paired fecal samples, along with their antibiotic resistance profiles. Understanding these species- and sample-type-specific interactions will provide valuable insights into how bioactive components in human milk may shape the infant resistome during early life. A total of 39 Bifidobacterium and 14 Lactobacillaceae strains were isolated from paired mother-infant fecal and breast milk samples. Whole genome sequencing (WGS) allowed functional predictions on the HMO metabolism abilities and the resistance genotype of each strain. In vitro HMO utilization was assessed using growth kinetics assays combined with HMO glycoprofiling in culture supernatant. The minimum inhibitory concentration (MIC) was also determined for each strain. HMO metabolism by the bifidobacteria was species-specific. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium longum subsp. infantis (B. infantis) exhibited the highest capacity for HMO degradation, consistent with genomic predictions. In contrast, lactobacilli were unable to degrade HMOs in vitro but were predicted to metabolize the by-products of HMO degradation. Phenotypic analysis revealed that B. bifidum strains had the lowest levels of antibiotic resistance, while Bifidobacterium animalis subsp. lactis (B. lactis) strains were resistant to most tested antibiotics. Overall, B. bifidum demonstrated the strongest HMO-degrading ability while remaining the most antibiotic-susceptible species. Early-life colonizing bifidobacterial species possess the essential machinery required to degrade HMOs and are highly susceptible to antibiotics. A better understanding of these dynamics could inform clinical strategies to protect and restore the infant gut microbiome, particularly in neonates exposed to antibiotics.

Genetic diversity of Salmonella enterica during acute human infections

The ubiquitous bacterial pathogen Salmonella enterica is the causative agent of both enteric fever and gastroenteritis. Despite its significant global health burden, we lack an understanding of its genetic diversity during acute infection, with ramifications for treatment and prevention. Here, we investigated within-host infection diversity of acute salmonellosis using whole-genome sequencing of blood or stool isolates obtained from 23 different patients. We found that intestinal infections exhibited greater genetic variation than blood infections, including in their plasmid content. While same-patient isolates were separated by 10 single nucleotide polymorphisms or less, they often differed in the carriage of genes or alleles, including those associated with antibiotic resistance or virulence. Given the longstanding emphasis on single colony isolation in clinical and laboratory microbiology, these findings have implications for how we both study evolution and transmission and how we treat salmonellosis in an age of increasing antibiotic resistance.

First draft genome sequence of Vibrio rotiferianus isolated from diseased larvae of the spiny rock-scallop Spondylus limbatus during hatchery outbreaks

Scallop aquaculture is of economic importance along the east coast of the tropical Pacific. However, scallop diseases have been observed and there is limited knowledge about bacterial pathogens, especially in hatcheries. The objective of this study was to identify and characterize one of the predominant bacteria in outbreaks of vibriosis that occurred in a scallop hatchery in south-central Ecuador. The strain SA-10GR was isolated from moribund veliger larvae of the scallop Spondylus limbatus. SA-10GR was identified as Vibrio rotiferianus by phenotypic characterization and whole genome sequence analysis. SA-10GR is a strain with lytic activity, susceptible to many antibiotics except amoxicillin (25 μg), capable of producing siderophores and extracellular products with alkaline phosphatase, esterase, lipase esterase, leucine arylamidase, acid phosphatase, among others. The genome of V. rotiferianus consists of 5,579,217 bp; 5160 genes; 5086 protein-coding sequences (CDSs); 74 RNA genes (57 tRNA, 13 rRNA, and 4 ncRNA), and 40 pseudogenes. A total of six resistance genes vanT, adeF, E. coli parE, txR, CRP, and PBP3 were identified, and 110 virulence factors were detected. Functional characterization of SA-10GR shows extracellular products that cause damage to the fish model cell line (Epithelioma Papulosum Cyprini) and pathogenicity against larvae of the scallop Spondylus crassisquama and the oyster Magallana gigas (≥86 % mortality at a concentration of 104 CFU mL-1 at 24 h post-challenge). Both species of larvae infected with the SA-10GR strain showed clinical signs of vibriosis. This study represents the first documentation of a Vibrio rotiferianus strain as a potential pathogen of two important cultured bivalve species along the Pacific coast, expanding the susceptible host range and geographic distribution for this Vibrio species.

Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions

Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3-]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.

Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance

The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.

Genome-Wide association study to identify genetic markers associated with Campylobacter jejuni motility

The ability of Campylobacter jejuni to survive and persist under harsh conditions is linked to the presence of flagella. This structure promotes the motility of the bacteria towards their optimum environment. The aim of this study was to examine the genetic basis for motility within 136 C. jejuni isolates through two different Genome-Wide Association Studies, gene presence/absence and Single Nucleotide Polymorphisms (SNPs). The motility phenotype was widely distributed across the phylogeny with large intra-lineage swarming performance variabilities. Accessory genes significantly associated with motility were found in four key genomic regions. One of these regions affected the Cj0727-Cj0733 operon, that encodes a putative ABC transporter system for phosphate uptake, while other influenced the capsule biosynthesis locus. Multiple SNPs mostly linked to increased motility were also discovered in clusters of genes, with special relevance to transport and membrane proteins. Therefore, the capsule and membrane composition might influence nutrient transfer, further impacting the protonmotive force that drives flagellar motor rotation in C. jejuni. The study provides novel genetic markers with a potential role in the motility phenotype of the pathogen.

Microbial community development in an oil sands pit lake

Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.

Metagenomic analysis revealed community-level metabolic differences between full-scale EBPR and S2EBPR systems

Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) has emerged as a promising technology addressing certain challenges of conventional Enhanced Biological Phosphorus Removal (EBPR), notably stability in phosphorus removal, yet the underlying mechanisms are not fully understood. Metagenomic analysis presents a powerful approach to elucidate community-level metabolic differences between EBPR and S2EBPR configurations. In this study, we compared three EBPR and three S2EBPR activated sludge communities using metagenomic analysis at taxonomy, key functional pathways/genes, and polyphosphate-metabolism marker genes. Our analysis revealed larger genus-level diversity variance in S2EBPR communities, indicating distinct microbial community compositions influenced by different operational configurations. A higher diversity index in the S2EBPR than the EBPR was observed, and a higher Ca. Accumulibacter abundance was detected in EBPRs, whereas the fermentative candidate PAOs genera, including Ca. Phosphoribacter and Ca. Promineifilum, were more abundant in S2EBPR systems. EBPR and S2EBPR groups displayed similar gene and pathway abundance patterns related to core metabolisms essential for carbon and nitrogen metabolism. PolyP-metabolism marker gene phylogeny analysis suggested that exopolyphosphatase gene (ppx) showed better distinctions between EBPR and S2EBPR communities than polyphosphate kinase gene (ppk). This also highlighted the needs in fine-cale microdiversity analysis and finding novel Ca. Accumulibacter clades and species as resolved using the ppk gene. These findings provide valuable insights into AS community dynamics and metabolic functionalities, paving the way for further research into optimizing phosphorus removal processes in wastewater treatment systems.

Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water

The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.

Evolutionary insights into NDM variants: Identification and functional analysis of novel NDM-58 in Pseudomonas aeruginosa

The emergence of New Delhi Metallo-β-lactamase (NDM) variants in P. aeruginosa has significantly contributed to carbapenem resistance, posing a global threat to antimicrobial therapy. The catalytic activity of NDM, dependent on Zn (II), is enhanced by specific mutations. In this study, we report the identification and characterization of a novel NDM-58 variant (GenBank: OR081828.1) in P. aeruginosa BA24848, which exhibited resistance to multiple β-lactams, including cephalosporins, carbapenems, and BL/BLI combinations. WGS revealed that NDM-58 harbors a unique P185S substitution. This strain is associated with other ARGs (blaPAO, PME-1, fosA, blaOXA-396, blaOXA-494, blaOXA-50, sul1, dfrA1, qacE, aph(3')-VI, qnrVC1, and cat7), indicating a XDR phenotype. Comparative genomic analysis revealed the presence of MGEs (ISpre2, ISPa6, ISPa2, ISPsy29, IS26, Tn4661, ISPa37, and ISUnCu4) associated with NDM-58, which may facilitate the horizontal transfer of resistance determinants. Structural modeling and molecular dynamics simulations demonstrated that NDM-58 exhibits altered stability and compactness compared to NDM-1, likely influencing its enzymatic activity and resistance profile. Residual conservation analysis revealed that Pro185 is highly conserved, and its substitution to serine may impact protein stability and function. The molecular dynamics analysis indicated that NDM-58 has lower residual fluctuations and increased flexibility, which may enhance its adaptability under varying physiological conditions. Our findings provide novel insights into the evolutionary dynamics of NDM enzymes and the role of genetic environments in their dissemination. Understanding these mechanisms is crucial for developing effective surveillance and mitigation strategies against emerging carbapenem-resistant P. aeruginosa.

Cryo-EM Reveals Structural Diversity in Prolate-headed Mycobacteriophage Mycofy1

Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that Mycofy1 possesses a prolate head and a long non-contractile tail. We determined structures of its head, head-to-tail interface, terminator, and tail tube to resolutions of ∼3.5 Å. Unexpectedly, we identified two distinct types of prolate head structures, exhibiting a 36° relative rotation in the top cap region. Additionally, the head-to-tail interface demonstrated flexibility. Our structures provide high-resolution cryo-EM data of a mycobacteriophage with a prolate head, as well as detailed structural information of the head-to-tail interface and head-proximal tail region in this phage group. These findings advance our understanding of assembly mechanisms in tailed bacteriophages.

Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage

Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.

Marine plastic exposure triggers rapid recruitment of plastic-degrading bacteria and accelerates polymer-specific transformations

Plastic pollution in marine ecosystems is a growing concern, yet the degradation behavior of different plastic types and their interactions with microbial communities remain poorly understood. This study investigated the degradation kinetics and microbial colonization of four widely used plastic materials, surgical masks (most made of PP), PET bottles, PS foam, and PP cups, over 40 days of seawater exposure in the Central Atlantic of Morocco. Mass loss measurement revealed distinct degradation patterns, with PS foam showing the highest mass loss (13 %), followed by PET bottles (5 %), likely due to environmental stressors that promote mechanical fragmentation. Surgical masks and PP cups exhibited minimal degradation, retaining nearly all their original mass, as well as limited extent of biodegradation. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) analyses showed the formation of oxidative functional groups on PP cups and significant structural changes in PS foam and PET, particularly in their crystalline structures, correlating with their higher mass reduction rates. SEM/EDX biofilm imaging confirmed extensive microbial colonization, particularly on PS and PET surfaces. Using 16S rRNA metabarcoding, we identified a striking enrichment of Exiguobacterium, followed by Pseudomonas, Acinetobacter and Bacillus genera, containing reported plastic degrading strains, which were strongly correlated with the accelerated breakdown of plastics. However, its role in accelerating plastic breakdown in this study remains unclear and may warrant further investigation. Co-occurrence network analysis revealed a progressive shift in microbial community structure, evolving from highly interconnected networks at day 0 to more specialized, modular clusters by day 40, dominated by Proteobacteria and Firmicutes. Atomic Absorption Spectrometry (AAS) demonstrated significant heavy metal accumulation on plastic surfaces, potentially influencing microbial colonization and activity. While the observed fragmentation of PS foam and PET highlights the susceptibility of certain plastics to environmental stressors, this study also positions microbial colonization as a potential contributor to plastic surface changes, providing novel insights into the interplay between microbial communities and plastic degradation in marine environments.

Whole-genome sequence of Salmonella Typhimurium E-5591 and its methionine sulfoxide reductase (msr) gene deletion mutant strains

Salmonella Typhimurium is one of the leading causes of foodborne illness in humans. Poultry products are the main source of infection for humans. Here we report the whole-genome sequences of Salmonella Typhimurium strain E-5591 (a field poultry isolate) and its mutant strains lacking the various methionine sulfoxide reductase genes.

Complete and draft genome sequences of clinical Mycobacterium tuberculosis isolates from the Philippines

This study reports the complete and draft genomes of 71 Mycobacterium tuberculosis isolates from the Philippines. Hybrid assembly using Illumina and Nanopore sequencing produced six complete genomes, while others had 2-422 contigs. These data enhance understanding of M. tuberculosis diversity and drug resistance, supporting targeted treatment strategies.

Draft genome sequence of Rossellomorea marisflavi DL-A, a malathion-degrading bacterium

This study presents the draft genome of Rossellomorea marisflavi DL-A, a malathion-degrading bacterium isolated from the North Oconee River in Athens, GA, USA. The DL-A genome is 4.27 Mb in size and comprises 4,271 coding sequences with proteins.

Local Genomic Epidemiology of Acinetobacter baumannii Circulating in Hospital and Non-hospital Environments in Kano, Northwest Nigeria

Acinetobacter baumannii is a pathogenic bacterium of public health significance, capable of rapidly spreading within and between environments. The local epidemiology and transmission pattern of A. baumannii strains circulating in hospitals and non-hospital environments is rarely studied, and hence this is investigated in Kano, Nigeria. A cross-sectional study design was used to collect 172 samples from clinical, hospital, and non-hospital samples. Acinetobacter baumannii isolates were identified and confirmed using microbiological and molecular techniques. Variants of blaOXA-51 were determined through amplicon sequencing, while whole genome sequencing was performed on 22 isolates to determine their allelic variants/sequence types (ST), resistance/virulence genes, insertion sequences, plasmids, single-nucleotide polymorphism (SNPs) and investigate phylogenetic relationships between the isolates. Twenty-seven A. baumannii were isolated from door handle and toilet floors of student hostels (14), soil and sullage samples (3 each), bed, chair, and drawer of hospital environments (9), and 1 from the urine of a patient. All these isolates belong to only 2 variants of blaOXA51-like genes, 16 (48.8%) are blaOXA-66 and 11 (33.3%) are blaOXA-180. About 70% of the isolates were susceptible to many antibiotics, and 8 resistance genes encoding aminoglycoside, tetracycline, and sulphonamide resistance were acquired by only strains harbouring blaOXA-66, and between 37 and 39 virulence genes were harboured by all the variants. Intrinsic blaADC-25 encoding resistance to β-lactams was found in all A. baumannii strains. The 2 variants had Pasteur scheme MLST allelic profiles ST2 and 267, which are not commonly reported in Nigeria. Few isolates from hospital and non-hospital sources form a cluster with SNPs number distances within the two clusters in the range of 85-100, suggesting a close relationship. The 2 variants circulate in both environments, suggesting transmission in both directions. Detection of ST267 (blaOXA-180 variant) in a clinical sample indicates an environment-to-human transmission.

Localization of AbaR4-type genomic islands and multidrug resistance plasmids in multiple Acinetobacter baumannii clones and Acinetobacter pittii from infections of dogs and cats

The genomes of 39 clinical carbapenemase-producing A. baumannii (CP-Ab) and 2 A. pittii (CP-Ap) isolates from dogs and cats in Thailand (2016-2019) were analyzed for phylogenetic relationship and antimicrobial resistance gene (ARG) localization. Resistome and core genome multilocus sequence typing (cgMLST) analysis identified distinct ARG patterns within CP-Ab sequence type (ST) 2 (n = 4) and ST1575 (n = 1) of clonal complex (CC) 2, ST25 (n = 6), ST1576 (n = 1), and ST1581 (n = 2) of CC25, ST16 (n = 13), ST23 (n = 2), ST149 (n = 9), ST1093 (n = 1), along with CP-Ap (n = 2). Complete genome analysis of one CP-Ap strain and 15 representative CP-Ab strains from each clone identified strains with one to three copies of blaOXA-23 associated with Tn2006 and/or AbaR-type genomic islands (GIs). AbaR4 was chromosomally located in all other STs except CP-Ab of CC2, which carried AbaR4b. AbaR4 was found on conjugative OXA-23 plasmids in CP-Ab ST1093 and CP-Ap strains. Conjugative OXA-23 plasmids and multidrug resistance (MDR) mega-plasmids in CP-Ab ST149 and CC25 shared ancestry with the cryptic plasmid pCUVET16-467.1 in CP-Ab ST23. MDR mega-plasmids contained a bacteriophage exclusion (BREX) locus and Tn6172-derived elements. A Tn6172ISCR2::(ΔISCR2-ΔTn10-MARR) structure containing GR38 repM, a class 1 integron, and multiple ARGs were found in GR38 MDR mega-plasmids of ST149 and formed an AbGRI1 structure in CC25 plasmids. These findings highlight the role of AbaR4 in carbapenem resistance and the evolution of Acinetobacter plasmids, facilitating the blaOXA-23 dissemination and the development of extensive drug resistance in multiple clones of clinical CP-Ab and CP-Ap strains originating from companion animals.

Phenotypic plasticity in cell elongation among closely related bacterial species

Cell elongation in bacteria has been studied over many decades, in part because its underlying mechanisms are targets of numerous antibiotics. While multiple elongation modes have been described, little is known about how these strategies vary across species and in response to evolutionary and environmental influences. Here, we use fluorescent D-amino acids to track the spatiotemporal dynamics of bacterial cell elongation, revealing unsuspected diversity of elongation modes among closely related species of the family Caulobacteraceae. We identify species-specific combinations of dispersed, midcell and polar elongation that can be either unidirectional or bidirectional. Using genetic, cell biology, and phylogenetic approaches, we demonstrate that evolution of unidirectional-midcell elongation is accompanied by changes in the localization of the peptidoglycan synthase PBP2. Our findings reveal high phenotypic plasticity in elongation mechanisms, with implications for our understanding of bacterial growth and evolution.

Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen

Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.

An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP)

China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.

Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen

Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for 73 diverse Fusarium oxysporum genomes, a major fungal plant pathogen with a compartmentalized genome that includes conserved core as well as variable accessory chromosomes. To obtain insights into accessory chromosome dynamics, we first constructed a chromosome similarity network using all-vs-all similarity mapping. We identified eleven core chromosomes conserved across all strains and a substantial number of highly variable accessory chromosomes. Some of these accessory chromosomes are host-specific and likely play a role in determining host range. Using a k-mer based approach, we further identified the presence of these accessory chromosomes in all available (581) F. oxysporum assemblies and corroborated the occurrence of host-specific accessory chromosomes. To further analyze the evolution of chromosomes in F. oxysporum, we constructed a pangenome variation graph per group of homologous chromosomes. This reveals that accessory chromosomes are composed of different stretches of accessory regions, and possibly rearrangements between accessory regions gave rise to these mosaic accessory chromosomes. Furthermore, we show that accessory chromosomes are likely horizontally transferred in natural populations. Our findings demonstrate that a pangenome variation graph is a powerful approach to elucidate the evolutionary dynamics of accessory chromosomes in F. oxysporum, which is not only a useful resource for Fusarium but also provides a framework for similar analyses in other species containing accessory chromosomes.

Characterization of a new lytic bacteriophage (vB_KpnM_KP1) targeting Klebsiella pneumoniae strains associated with nosocomial infections

A new bacteriophage, vB_KpnM_KP1, was identified and characterized, exhibiting a strong lytic effect on Klebsiella pneumoniae. Host range analysis revealed its effectiveness against 77.4% of clinical strains, achieving complete lysis of those associated with urinary tract infections (UTIs). Phage stability tests demonstrated that vB_KpnM_KP1 remained stable at neutral pH and across all tested temperatures. However, inactivation was observed at high ethanol concentrations and extreme pH levels. Transmission electron microscopy (TEM) analysis identified vB_KpnM_KP1 as a Myo-type phage with an icosahedral head and a contractile tail. Moreover, genome annotation of vB_KpnM_KP1 revealed a linear DNA genome of 174,802 bp, containing 307 open reading frames. Functional predictions suggest the presence of genes involved in DNA replication, transcription, morphogenesis, and cell lysis. Phylogenetic analysis classified vB_KpnM_KP1 within the Slopekvirus genus of the Straboviridae family, showing high sequence identity with phages that infect Enterobacter, Escherichia and Klebsiella species. These findings highlight the potential of phage vB_KpnM_KP1 as an alternative treatment for multidrug-resistant K. pneumoniae infections, particularly in UTIs, while offering valuable insights into its stability and genetic composition.

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe

In high-income countries, dogs and cats are often considered members of the family. Because of this proximity, it has been suggested that pets and humans might exchange bacterial species from their gut microbiota, with multidrug resistant bacteria being of particular concern. The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe. Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. The acquired genes responsible for 3GC-R were identified. The sequence type (ST) of all genomes were assessed by multilocus sequence typing. Alpha and beta diversities were measured within and between the two populations. We included genomes of 1327 3GC-R E. coli isolated from humans and animals with 109 (8.2 %) being responsible for infections in dogs and cat, and 1218 (91.8 %) responsible for human infections. Alpha diversity analysis suggested greater diversity within ST and 3GC-R genes in the animal population. Beta diversity analysis by principal coordinate analysis separated animal and human strains. ST131 was more abundant in human strains (43.4 %) than in animal strains (14.7 %) (p < 0.001). Six STs, including ST372, were identified almost exclusively in 3GC-R E. coli from animal origin. The bla CTX-M-15 gene was more frequent in humans (49.24 %) than in companion animals (17.9 %) (p < 0.001). The resistance genes bla CMY-2 (30.8 %) and bla CTX-M-1 (15.4 %) were more frequent in E. coli isolated from pets (p < 0.001). We found that populations of 3GC-R E. coli responsible for human and pet infections in Europe do not overlap. Although it cannot rule out occasional transmission of bacteria between pets and humans within a household, it suggests that dogs and cats are not a major source of human infection with this antibiotic-resistant pathogen.

High Genetic Diversity of Histoplasma in the Amazon Basin, 2006-2017

Histoplasmosis is one of the most common pulmonary mycosis diseases in the world. Genome sequencing has revealed that Histoplasma, the cause of histoplasmosis, is composed of several phylogenetic species. The genetic diversity of the pathogen remains largely unknown, especially in the tropics. We sequenced the genomes of 91 Histoplasma isolates from the Amazon basin of South America and used phylogenomics and population genetic evidence to measure the genetic variation of the genus in South America. We report a previously unidentified clade of Histoplasma endemic to the Amazon basin. The lineage is widespread across the continent and contains 5 lineages that are sufficiently differentiated to be considered phylogenetic species. We found the geographic range of those lineages is largely but not completely overlapping. Finally, we found that the patient median age and sex ratio differs among species, suggesting differences in the epidemiology of histoplasmosis caused by each Histoplasma lineage.

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

BACKGROUND

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

METHODS

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

FINDINGS

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

INTERPRETATION

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

FUNDING

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

Genomic and phenotypic characterization of Chryseomicrobium imtechense from canine pyometra

Chryseomicrobium imtechense is a bacterium primarily isolated in environment samples. Here we demonstrated the virulent and antimicrobial resistant profile of the C. imtechense LBV029/19 strain, which was isolated in a pyometra infection in canines, being related as causal agent of that disease. The bacterium was recovered from purulent content of a uterus with pyometra and the identity was confirmed by both, biochemical tests followed MALDI-TOF MS and 16S-rDNA gene sequencing. Antimicrobial susceptibility test, biofilm formation assessment, genomic sequencing with Illumina MiSeq platform followed by the genome characterization and phylogenetic relationships were conducted with C. imtechense LBV029/19 strain. The phylogenetic analysis revealed a close evolutionary relationship between the C. imtechense LBV029/19 and the others publicly available 16S-rDNA genes of C. imtechense. The in vitro assays shown that C. imtechense LBV029/19 has a strong ability for biofilm formation. Additionally, the antimicrobial susceptibility tests revealed a smaller inhibition zone for novobiocin, cefuroxime, and erythromycin. To the best of our knowledge the C. imtechense LBV029/19 genome is the first genome sequenced and available of C. imtechense. Regarding the genotypic profile, resistance genes to tetracyclines, fluoroquinolones, beta-lactams, and multidrug resistance were present in this genome. Additionally, genes encoded to virulence factors, including biofilm formation, motility, and sporulation were identified. The phenotypic profile associated with the genotypic description indicates the potential of C. imtechense LBV029/19 as a primary agent of animal infectious diseases. The genomic description will contribute to the understanding of the biology of the bacterium and the pathogenesis process involved in the disease.

Draft genome sequence data on Bacillus safensis FB03 isolated from the rhizosphere soil of leguminous plant in Bangladesh

With the aim of investigating the biotechnological potential of Bacillus safensis' FB03, isolated from the rhizosphere soil of Bahrind region of Bangladesh, the current work focused on its complete genomic analysis and phenotypic description. The size of the genome of the isolate was 3.6 Mb with 41.59 % GC content. Genome annotation revealed the presence of many genes related to siderophore production, enzyme degradation, UV and stress tolerance. Six biosynthesis gene clusters for bacillibacin, bacilysin, bottromycin, Schizokinen, fengycin, and lychensin were identified through genome mining. Significantly, FB03 was found to contain only two acquired antimicrobial resistance genes and was anticipated to be non-pathogenic to humans. The openness of the Bacillus safensis pan-genome was demonstrated by the pan-genome analysis. According to this research, Bacillus safensis FB03 may be a good fit for a variety of biotechnological applications.

Evolutionary insights into adaptation of hemocyanins from deep-sea hydrothermal vent shrimps

Deep-sea hydrothermal vent shrimps inhabit environments with low oxygen levels and may even be exposed to hypoxic conditions. In response, their respiratory pigment, hemocyanin (Hc) may undergo molecular adaptations to enable them to survive in such extreme ecosystems. Therefore, we sampled four Alvinocarididae species from hydrothermal vents in the northern Central Indian Ridge and two types of Hc genes (α and γ) were observed. Employing the branch model, we detected positive selection for the deep-sea hydrothermal vent lineage, including 11 Decapoda species. Furthermore, using the branch-site model, we identified a putative mutant residue (Leu226, Ser377, and Ile390) close to the active site of Hc. Moreover, our results suggested potential molecular docking between two α-type Hc proteins. Thus, this study provides valuable and novel perspectives on the functional significance of the Hc gene in deep-sea hydrothermal vent shrimps, laying the foundation for future investigations in this intriguing area of research.

Multipronged impact of environmental temperature on Staphylococcus aureus infection by phage Kayvirus rodi: Implications for biofilm control

Environmental cues sometimes have a direct impact on phage particle stability, as well as bacterial physiology and metabolism, having a profound effect on phage infection outcome. Here, we explore the impact of temperature on the interplay between phage Kayvirus rodi (phiIPLA-RODI) and its host, Staphylococcus aureus. Our results show that phiIPLA-RODI is a more effective predator at room (25 °C) compared to body temperature (37 °C) against planktonic cultures of several strains with varying degrees of phage susceptibility. This result differs from most known examples of temperature-dependent phage infection, in which optimum infection is correlated with the host growth rate. Further characterization of this phenomenon was carried out with strains IPLA15 and IPLA16, whose respective MICs were 7 log units and a 1-log unit higher at 37 °C than at 25 °C. Our results demonstrated that the phage also had a greater impact at room temperature during biofilm development and for the treatment of preformed biofilms. There was no difference in phage adsorption between the two temperatures for strain IPLA16. Conversely, adsorption of phiIPLA-RODI to IPLA15 was reduced at 37 °C compared to 25 °C. Moreover, confocal microscopy analysis indicated that the biofilm matrix of both strains has a greater content of PIA/PNAG at 37 °C than at 25 °C. Regarding infection parameters, we observed longer duration of the lytic cycle at 25 °C for both strains, and infection of IPLA15 by phiIPLA-RODI resulted in a smaller burst size at 37 °C than at 25 °C. Finally, we also found that the rate of phage resistant mutant selection was higher at 37 °C for both strains. Altogether, this information highlights the impact that bacterial responses to environmental factors have on phage-host interactions. Moreover, phage phiIPLA-RODI appears to be a highly effective candidate for biofilm disinfection at room temperature, while its efficacy in biofilm-related infections will require combination with other antimicrobials.

Epidemiological and genomic characterisation of an outbreak of Streptococcus pyogenes emm5.23

OBJECTIVES

This retrospective cross-sectional study examined the epidemiology, clinical presentations, and genomics of Streptococcus pyogenes genotype emm5.23, linked to severe outcomes in Scotland.

METHODS

Between 2014 and 2022, 58 cases of invasive Group A Streptococcus (iGAS) disease associated with emm5.23 were reported in Scotland. Surveillance data from 45 cases were analysed for clinical characteristics and risk factors. Whole-genome sequencing (WGS) included all available emm5.23 strains from Scotland (n=58), a subset from England (n=29), and emm5 strains of non-5.23 subtypes from Scotland (n=10), England (n=2), and Canada (n=1).

RESULTS

Nearly all cases (96%, 43/45) were hospitalised, of whom 33% (15/45) required intensive care and 20% (9/45) died with iGAS. The most common presentations were bacteraemia (51%, 23/45) and pneumonia (24%, 11/45). WGS identified an emerging emm5.23 clade in Scotland, encompassing most isolates, which shared highly similar genomes and three non-synonymous polymorphisms.

CONCLUSIONS

Although genomic traits known to increase GAS virulence potential were not found, polymorphisms that may affect the emm5.23 phenotype were detected. This suggests this emm5.23 genotype was transiently successful rather than hypervirulent, with low population-level immunity contributing to its spread. This study emphasises the need for integration of real-time genomic data in public health surveillance to enhance source attribution and guide interventions.

Whole genome sequence analysis of multidrug-resistant Salmonella enterica Typhimurium ms203 provides insights into virulence and antibiotic resistance

Salmonella enterica subspecies enterica serovar Typhimurium, is a leading cause of gastroenteritis food-borne illness that leads to hospitalizations worldwide. These infections are further complicated because of the rapid development of antibiotic resistance and the spread of infections by the resistant strains. Thus, the overall aim of this study is to identify a multidrug-resistant strain of Salmonella Typhimurium, whole genome sequencing, and computational analysis of genome sequence. This study presents a comprehensive analysis of Salmonella Typhimurium ms203, isolated from a gastroenteritis patient in Odisha, India. The strain was characterized by microbiological and biochemical assays using a set of standard tests. An antibiotic-susceptibility test of the strain was carried out using VITEK system. Whole genome sequencing facilitated an in-depth examination of genomic architecture, distribution of pathogenic island regions, and antibiotic-resistant sequences. Utilizing diverse computational tools and bioinformatics analysis, including Prokka annotations, protein-protein interaction analysis, genomic island identification, plasmid and phage characterization, antibiotic resistance gene profiling, and average nucleotide identity (AAI) determination, this study elucidates key insights into the genetic makeup and pathogenic potential of S. Typhimurium ms203. These findings may provide valuable contributions to understanding the epidemiology, pathogenesis, and antibiotic resistance mechanisms of this Salmonella strain, with implications for public health interventions and surveillance strategies.

Unlocking the potential of Metschnikowia pulcherrima: a dive into the genomic and safety characterization of four plant-associated strains

Metschnikowia pulcherrima includes strains of applied agro-food interest, particularly due to the antimicrobial activity against plant pathogens, contribution to the aroma of fermented beverages, and preliminary evidence related to probiotic activity. This biotechnological relevance sheds new light of interest on the biology of this yeast. To better understand and expand its biotechnological potential and applicability, the genomes of M. pulcherrima NRRL Y-7111 T, NRRL Y-48695, CBS 10357, and NRRL Y-48712 were sequenced, and de-novo assembled. Between 10,671 and 14,548 genes were predicted and the cooperative genomic analyses were integrated with experimental assessments relating to traits relevant for biotechnological application and safety. In silico and in vitro safety assessment revealed intermediate sensitivity for itraconazole; furthermore, variants of the genes related to pulcherrimin production and transport were found in all the genomes. Moreover, an arsenal of carbohydrate-active enzymes (CAZymes) was unravelled, and their predicted localization was investigated. This study expands the body of knowledge on M. pulcherrima, including traits relevant for defining its safety as a bioresource, which is a pivotal aspect for its possible inclusion in the European Food Safety Authority (EFSA) Qualified Presumption of Safety (QPS) list and its application in REgulated food/feed PROducts (REPRO) both in the European Union & aligned European countries. KEY POINTS: • A pipeline for genomic characterisation and safety assessment of unconventional yeasts, using M. pulcherrima as a model species was developed. • M. pulcherrima strains can be considered safe and safety data can be used to develop a body of knowledge to include M. pulcherrima in EFSA QPS list. • Analysis of the predicted localization of CAZymes allowed the detection of compounds as potential biological control agents.

Flavobacterium algoriphilum sp. nov., Flavobacterium arabinosi sp. nov., Flavobacterium cryoconiti sp. nov., Flavobacterium galactosi sp. nov., Flavobacterium melibiosi sp. nov., and Flavobacterium algoris sp. nov., six novel cold-adapted bacteria isolated from glaciers

BACKGROUND

Six novel cold-adapted bacteria, LB3P122T, LT1R49T, ZT3R17T, ZT3R25T, XS2P12T, and GB2R13T, were isolated from glaciers on the Tibetan Plateau. This study aimed to characterize their taxonomic status and elucidate their molecular adaptations to cold environments using a polyphasic approach.

RESULTS

All strains were Gram-stain-negative, rod-shaped, and psychrophilic, growing at 0 °C with an optimum at 14-20 °C and at pH values of 6.0-8.0 (optimum pH 7.0). Analysis of the 16S rRNA gene sequences placed their taxonomic positions within the genus Flavobacterium, with similarities ranging from 97.2 to 98.4% to species with validly published names. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the six strains formed distinct clades with Flavobacterium gawalongense GSP16T. Phylogenomic analysis showed that these strains clustered with Flavobacterium gawalongense GSP16T and exhibited a close relationship with Flavobacterium urumqiense CGMCC 1.9230T and Flavobacterium xinjiangense CGMCC 1.2749T. Average nucleotide identity (ANI) values ranging from 82.5 to 93.6% and digital DNA-DNA hybridization (dDDH) values ranging from 26.1 to 51.5% between these strains and their closest relatives were well below the bacterial species delineation thresholds (95-96% ANI, 70% dDDH). The predominant fatty acids were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Genomic analysis identified genes associated with cryoprotection, oxidative stress response, cold-shock response, and osmoprotection in these strains, underscoring their adaptations to glacial environments.

CONCLUSIONS

Based on polyphasic taxonomic evidence, the strains represent six novel species within the genus Flavobacterium, with the proposed names Flavobacterium algoriphilum sp. nov. (LB3P122T = CGMCC 1.11443 T = NBRC 114820T), Flavobacterium arabinosi sp. nov. (LT1R49T = CGMCC 1.11617T = NBRC 114822T), Flavobacterium cryoconiti sp. nov. (ZT3R17T = CGMCC 1.11707T = NBRC 114824T), Flavobacterium galactosi sp. nov. (ZT3R25T = CGMCC 1.11711T = NBRC 114825T), Flavobacterium melibiosi sp. nov. (XS2P12T = CGMCC 1.23198T = NBRC 114826T), and Flavobacterium algoris sp. nov. (GB2R13T = CGMCC 1.24741T = NBRC 114830T). These findings enhance our understanding of Flavobacterium diversity and cold adaptation in cryospheric ecosystems.

Genome sequence of Cetobacterium somerae ATCC BAA-474 isolated from human feces

Cetobacterium somerae ATCC BAA-474 was first isolated from human feces and is emerging as an important species for animal and human health. Here, we report the complete genome sequence of this strain of C. somerae to improve the currently available genome sequence.

Complete genome sequence of Bacillus safensis strain BS22LVI isolated from the intestine of whiteleg shrimp, Litopenaeus vannamei

We report the complete genome sequence of Bacillus safensis strain BS22LVI, isolated from the mid-hindgut of whiteleg shrimp (Litopenaeus vannamei) in Korea. The 3,824,412 bp circular genome has a G + C content of 41.65% and encodes 3,828 predicted coding sequences, including genes associated with antimicrobial activity and quorum quenching.

Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration

Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.

Complete genome sequence of Cupriavidus sp. Agwp_2, isolated from soil in an iron mining area

Cupriavidus spp. is a Gram-negative bacterium belonging to the Burkholderia family. Here, we report the complete genome sequence of Cupriavidus sp. Agwp_2, whose genome consists of two chromosomes of 3,823,900 bp and 2,784,676 bp, respectively, and one plasmid of 847,469 bp with an average GC content of 66.17%.

Draft genome sequence of carbapenem-resistant Klebsiella pneumoniae ST6260 isolated from the catheter tip of a female patient in Nepal

Klebsiella pneumoniae is an opportunistic human pathogen, particularly associated with nosocomial infections and multidrug resistance. Here, we present a draft genome sequence of a carbapenem-resistant K. pneumoniae ST6260 isolated from the catheter tip of a female patient in a referral case received at Kathmandu Model Hospital, Kathmandu, Nepal.

Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps

BACKGROUND

Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited.

METHODS

The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species.

RESULTS

High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus.

CONCLUSION

This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.

Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance

A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_DT, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4AT, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8-1 and 97.4% similarity with the P. noertemannii strain BN9T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4AT, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_DT contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_DT tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0-4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C12:0, C16:0, C17:0 cyclo, and summed feature 2 (C12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_DT within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_DT = MCC 2506 T = KCTC 72453 T = JCM 34508 T) is proposed.

The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study

Background

IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases.

Methods

We comprehensively identified bla IMP genes in all publicly available bacterial genomes, then systematically analysed the distribution of variants across species, lineages, plasmids and mobile elements, examining patterns over time, across geographic regions and by source. Structural analysis of IMP variants was performed.

Findings

4,556 bla IMP -containing genomes were identified from 1996-2023, including 52 bla IMP variants across 93 bacterial species. Key variants ( bla IMP-1 , bla IMP-4 , bla IMP-7 , bla IMP-8 and bla IMP-13 ) achieved global endemicity, while bla IMP-26 and bla IMP-27 were regionally endemic in Southeast Asia and North America, respectively. bla IMP dissemination was driven by horizontal gene transfer, facilitating inter-species spread. Proliferation of multidrug-resistant Enterobacter hormaechei , Pseudomonas aeruginosa and Klebsiella pneumoniae lineages led to local outbreaks. Dereplication removed 3,175/4,556 (69.9%) genomes, indicating that most bla IMP -containing genomes were highly related. bla IMP variants were associated with mobile genetic element combinations including class 1 integrons and insertion sequences (99.7%), aiding mobilisation into ≥52 plasmid clusters, predominantly IncHI2A, IncN, IncL/M and IncC. Genomes of environmental and animal origin accounted for 10.0% and 1.1% of the dataset, respectively. Evidence of cross-source transmission was limited, with most spillover occurring between genomes of human and environmental origin. Structural analysis revealed a conserved carbapenemase structure (mean lDDT 0.977), with convergent missense mutations at seven catalytically relevant sites.

Interpretation

Global analysis enabled us to historically reconstruct the emergence and variant-specific epidemiologies of bla IMP carbapenemase genes. Intersecting mobile elements enabled bla IMP genes to spread across multiple plasmids and bacterial genera, facilitating global and multi-source spread within a One Health framework. Additionally, convergent evolutionary patterns indicate that IMP variants may continue evolving, potentially evading novel beta-lactam antimicrobial agents.

Funding

NHMRC EL1 (APP1176324) to N.M.; NHMRC PF (APP1117940) to A.Y.P.; NIH/NIAID R01AI175414 to A.G-S.

Research in context panel

Evidence before this study: Despite being a major cause of carbapenem resistance in Gram negative infections, little is known about the global epidemiology of IMP carbapenemases. IMP carbapenemases are metallo-beta-lactamases that were first identified in 1991 and have evolved into 96 different IMP variants. On May 21 2025, we searched all published reports available in PubMed using the terms "'IMP' and 'carbapenemase' genomics NOT (Review[Publication Type]) NOT (Case Reports[Publication Type]) NOT PCR" with no language restrictions and no publication date restrictions. We identified 223 articles, 62 and 121 of which reported single species or a single study centre/country, respectively. Only 6 articles employed genomics to examine multi-species and multi-geographical isolates, though this was in the context of carbapenem resistance more broadly rather than IMP carbapenemases specifically. The most relevant study included 38 globally distributed genomes across four species and tracked seven blaIMP variants across mobile genetic elements.Added value of this study: To our knowledge, this global characterisation provides the most comprehensive account of bla IMP carbapenemase gene epidemiology. To analyse the global distribution and diversity of bla IMP genes, we compiled all available public genome data resulting in a dataset of 4,646 genomes. This has allowed us to identify local, regional and international spread of bla IMP variants and determine the contributions of clonal expansion, plasmid proliferation and co-localised mobile genetic elements. We demonstrated that key bla IMP variants display global (IMP-1, IMP-4, IMP-7, IMP-8 and IMP-13) and regional (IMP-26 within Southeast Asia and IMP-27 within North America) endemicity and that these patterns have been previously unacknowledged, reframing the previous understanding that IMP carbapenemases were largely confined to the Asia-Pacific region. Our observation of convergent evolutionary patterns raise concern that IMP variants may continue to evolve, potentially evading new β-lactam antimicrobials. This analysis has revealed the under-recognised contribution IMP carbapenemases make to global carbapenem resistance. Implications of all the available evidence: These findings provide the first comprehensive atlas of bla IMP carbapenemase gene dissemination and underscore the silent global spread of IMP carbapenemases. We note the critical need for enhanced surveillance systems, particularly in low- and middle-income countries, that can detect complex plasmid-mediated and mobile genetic element-associated spread, as we noted with bla IMP carbapenemase genes. Moreover, our analyses show that systematic sampling across human, animal, and environmental reservoirs is crucial to address the One Health dimensions of emerging antimicrobial resistance threats. The study provides a framework for future interventions aimed at tracking and stopping the spread of IMP carbapenemases and calls for co-ordinated, real-time public health responses to this growing challenge.

Genomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome

Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.

Whole-genome sequencing analysis of Staphylococcus aureus isolated from female patients with mastitis in Henan, China

OBJECTIVES

To study the molecular characteristics, antibiotic resistance profiles and virulence features of Staphylococcus aureus (SA) isolates that cause mastitis.

METHODS

117 SA isolates were collected from women with mastitis. Strain identification and antimicrobial susceptibility testing were conducted using the Vitek 2 system. All SA isolates were sequenced on the Illumina HiSeq platform. For multilocus sequence typing, ResFinder, spaTyper, and SCCmecFinder were employed to analyse the strains.

RESULTS

Thirty-five methicillin-resistant Staphylococcus aureus (MRSA) strains and 82 methicillin-sensitive Staphylococcus aureus (MSSA) strains were isolated from women with acute breast abscesses. The rates of resistance to various antibiotics were significantly higher among MRSA isolates than among MSSA isolates. Twenty-two sequence types (STs), 35 staphylococcal protein A (spa) types, and 4 SCCmec types were identified. ST22, ST59, and ST398 were the major lineages, and t309 and t437 were the most common spa types. SCCmec-IVa was the predominant SCCmec type. Interestingly, toxin gene subtypes A (hlgA, hlgB, hlgC, lukF-PV, lukS-PV, seg, sei, sem, sen, seo, seu, n = 54), B (hlgA, hlgB, hlgC, seb, sek, seq, n = 13), C (hlgA, hlgB, hlgC, lukD, lukE, n = 10), and D (hlgA, hlgB, hlgC, n = 10) accounted for 74.4% (87/117) of all SA isolates, suggesting the high expression of virulence genes.

CONCLUSIONS

ST22, ST398, and ST59 are the main types that cause mastitis and have different virulence factor profiles. This study provides deeper insights into the molecular epidemiology of SA associated with acute mastitis.

Characterization of aquatic clade 2 and 3 Campylobacter coli isolates from Slovenia reveals admixture with other Campylobacter species

Campylobacter coli, a significant foodborne pathogen, has undergone extensive genetic exchange with its close relative, Campylobacter jejuni, leading to the emergence of three distinct clades. While clade 1 strains are commonly isolated from clinical and agricultural sources, clades 2 and 3 are primarily found in aquatic environments. This study aimed to enhance our understanding of C. coli clade 2 and 3 isolates through genomic and phenotypic characterization. A total of 48 surface water samples were collected from 19 different water bodies throughout Slovenia, and eleven Campylobacter isolates initially identified as C. coli from clades 2 and 3 were cultured. Whole genome sequencing was then performed on these isolates. Phylogenetic analysis was conducted using core genome multilocus sequence typing (cgMLST) and k-mer analysis. Phenotypic characterization included growth analysis, autoagglutination, biofilm formation, motility, antimicrobial susceptibility, water survival, and metabolic profiling. Genomic analysis revealed significant admixture with other Campylobacter species in the clade 2 and 3 isolates. One isolate was found to represent a new species related to C. coli. Besides C. jejuni and C. lari, this novel species appears to have contributed to introgression in the C. coli clades 2 and 3 isolates. Phenotypic characterization demonstrated diverse growth patterns, motility, autoagglutination abilities, and biofilm formation among the isolates. This study provides new insights into the genetic diversity and phenotypic characteristics of aquatic C. coli clade 2 and 3 isolates from Slovenia. The observed admixture with other Campylobacter species highlights the complex evolutionary history of these environmental strains and underscores the importance of continued surveillance and characterization of Campylobacter isolates from diverse ecological niches.

Genetic properties of mercury‑tolerant yeast, Pichia kudriavzevii 1P4

Mercury contamination in commercial products poses serious risks to human health and the environment. The in vitro detection methods using spectroscopy approaches are expensive and have limited practical use. Yeast-based biosensors provide a more affordable and user-friendly alternative. Therefore, the exploration of mercury tolerance yeast is essential to support the sensor properties. In this study, we investigated the mercury tolerance of 10 yeast isolates. Pichia kudriavzevii 1P4 exhibited tolerance up to 1.5 mM HgCl2 while showing slow growth phenotype as grown in 2 mM HgCl2. This is the first report to show the ability of this genus of the yeast Pichia to cope with HgCl2 stress. X-ray spectra showed Hg accumulation in yeast colonies grown in HgCl2, while none was detected in colonies grown without it. This data indicates the capability of 1P4 in the accumulation of Hg as one of the HgCl2-stress tolerance mechanisms. Whole-genome sequencing of isolate 1P4, using the MGI DNBSEQ-G400 platform, revealed a genome size of 10.8 Mbp across five chromosomes, with a GC content of 38.97%. The largest portions of the genome are involved in translation, amino acid transport, metabolism, and protein modification, based on COG analysis. Key genes potentially contributing to mercury tolerance involve efflux/inorganic ion transport system (e.g., FieF, Acr3/B, and CzcO/D-clusters) and glutathione-associated oxidative stress response (e.g., BtuE and LysX, which encoded glutathione peroxidase and glutathione synthase). Those genes were predominant in COG category of inorganic ion transport and metabolism (P) and defense mechanisms (V). The genome of 1P4 was assembled into 4753 gene clusters, where 2222 of which were shared with the other species of yeast, including Pichia membranifaciens, P. kluyveri, P. inconspicua, S. cerevisiae, and C. albicans. Meanwhile, 921 gene clusters were shared among genera of Pichia spp., only. These findings highlight the genetic profile and mercury-tolerance mechanisms of isolate 1P4, supporting its potential application as a mercury biosensor or bioremediation agent.