Trycycler: consensus long-read assemblies for bacterial genomes

Are reads required? High-precision variant calling from bacterial genome assemblies

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related Staphylococcus aureus isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.

Genome sequences of polar Carnobacterium maltaromaticum strains 2857 and 2862 with genes for glycerol and 1,2-propanediol pathways

We report genome sequences of two polar Carnobacterium maltaromaticum strains: 2857 (draft, 3.54 Mb, 34.4% GC) and 2862 (complete, 3.61 Mb, 34.6% GC, five plasmids). Sequencing used Illumina (both) and Nanopore (2862). Genome analysis revealed genes for glycerol conversion to 1,2-propanediol, suggesting potential for sustainable bioprocessing in cold environments.

Differences in complement activation of serum-resistant and serum-sensitive Klebsiella pneumoniae isolates

The gram-negative bacteria Klebsiella pneumoniae are genetically heterogeneous and a common cause of sepsis and bacteremia in humans. The complement system is the first line of defence against bacteria when they invade the body. We previously investigated K. pneumoniae isolates from sepsis patients. We found that complement factor (C) 3 is deposited on all isolates independent of serum sensitivity, but the membrane attack complex (MAC) was only formed on the serum-sensitive isolates. To investigate the mechanism for serum resistance, we incubated one serum-sensitive and one serum-resistant isolate in human serum and identified bound complement factors by mass spectrometry. The serum-sensitive isolate had all expected complement factors bound, including C4, while the serum-resistant isolate had only C3 bound. The serum resistance was caused by a fast cleavage of C3b to iC3b. Thereby, the C5 convertase, and thus MAC, cannot be formed. To confirm the role of C4 in serum sensitivity, C4 was inhibited by the nanobody hC4Nb8, resulting in the survival of the serum-sensitive isolate. This suggests that C4 is indispensable for MAC formation through the classical and lectin pathways. In contrast, when activated selectively, the alternative pathway primarily leads to the generation of iC3b, thereby enabling serum resistance by bypassing MAC assembly.

Complete genomes of 568 diverse Klebsiella pneumoniae species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020

We report 578 hybrid genome assemblies (568 complete) of Klebsiella pneumoniae species complex isolates from human, animal, and marine sources in Norway collected from 2001 to 2020, belonging to five phylogroups including K. pneumoniae (n = 492) and K. variicola (n = 69) and 364 unique sequence types.

Genomic insights into novel predatory myxobacteria isolated from human feces

Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35T and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35T. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy

Chrysochromulina parva (C. parva) is a eukaryotic freshwater haptophyte algae found in lakes and rivers worldwide. It is known to be infected by viruses, yet knowledge of the diversity and activity of these viruses is still very limited. Based on sequences of PCR-amplified DNA polymerase B (polB) gene fragments, Chrysochromulina parva virus BQ1 (CpV-BQ1) was the first known lytic agent of C. parva, and was considered a member of the virus family Phycodnaviridae, order Algavirales. However, the genome of a different C. parva-infecting virus (CpV-BQ2, or Tethysvirus ontarioense) from another virus family, the Mesomimiviridae, order Imitervirales, was the first sequenced. Here, we report the complete genome sequence of the putative phycodnavirus CpV-BQ1, accession PQ783904. The complete CpV-BQ1 genome sequence is 165,454 bp with a GC content of 32.32% and it encodes 193 open reading frames. Phylogenetic analyses of several virus hallmark genes including the polB, the late gene transcription factor (VLTF-3), and the putative A32-like virion packaging ATPase (Viral A32) all demonstrate that CpV-BQ1 is most closely related to other viruses in the phylum Megaviricetes within the order Algavirales, family Phycodnaviridae.

Isolation of Mycobacterium europaeum from a clinical sample in China: report of genome sequence and literature review

Mycobacterium europaeum, of Mycobacterium simiae complex, is a rare nontuberculous mycobacterium associated with human diseases. We report a case with an isolate from bronchoalveolar lavage fluid and summarize M. europaeum cases from literature. M. europaeum may cause respiratory infections and colonization in immunocompromised, elderly, and/or chronic pulmonary illness patients.

Evolution of an extensively antibiotic resistant sublineage of lineage 1 of GC1 Acinetobacter baumannii

The multiply antibiotic-resistant lineage 1 of Acinetobacter baumannii global clone 1 (GC1) emerged in the 1970s, and subsequently more extensively resistant sublineages have emerged. Here, we examined the evolution of the extensively resistant MRSN56 sublineage and showed it is characterised by insertions carrying resistance genes at specific chromosomal positions. An evolved form of the sublineage carries KL17 replacing KL1 at the capsule locus and includes an additional integrative element Aci-IE1 carrying further resistance genes including blaNDM. Further members of the modified sublineage (isolated 2014-2021) identified among publicly available genomes were from several countries and appear to have replaced the original form (2007-2010). Some KL17 type isolates had acquired even more resistance genes including blaPER. The blaNDM and blaPER genes contribute to reduced susceptibility to cefiderocol and/or sulbactam/durlobactam. The phylogeny indicated that separation of the sublineage into KL1 and KL17 groups coincided with the KL switch and Aci-IE1 was acquired later.

Characterization and De Novo Genome Assembly for New Rhizobium Ruizarguesonis Rhizobial Strain Vst36-3 Involved in Symbiosis with Pisum and Vicia Plants

Pea and vetch are the important legume crops used as food, forage, and green manure in agriculture. Several new rhizobial isolates were obtained from vetch Vicia sativa root nodules. For one of them, Vst36-3, the nodulation test showed various specificity in relation to plant hosts from the Fabeae tribe, such as pea and vetch. It is in contrast to typical strains of the Rhizobium leguminosarum species complex (Rlc), which formed effective nodules as in pea and vetch. Here, whole genome sequencing was performed followed by de novo genome assembly for Vst36-3 strain. As a result of de novo genome assembly, seven contigs were generated using Oxford Nanopore Technology long reads and subsequently Illumina short reads. Phylogenetic analysis allowed us to identify this strain as Rhizobium ruizarguesonis Vst36-3. Analysis of the Sym plasmid containing the nod and nif genes revealed that R. ruizarguesonis Vst36-3 has a complete suite of essential genes for the development of symbiosis. Nevertheless, this new strain forms ineffective nodules in pea. This makes Rhizobium ruizarguesonis Vst36-3 attractive for the search and investigation of new factors of host specificity in future.

Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail

Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promise in treating P. aeruginosa infections, the development of bacteriophage-insensitive mutants (BIMs) in the presence of bacteriophages has been described. The aim of this study was to examine the genetic changes associated with the BIM phenotype. Biofilms of three genetically distinct P. aeruginosa strains, including PAO1 (ATCC 15692), and two clinical respiratory isolates (one CF and one non-CF) were grown for 7 days and treated with either a cocktail of four bacteriophages or a vehicle control for 7 consecutive days. BIMs isolated from the biofilms were detected by streak assays, and resistance to the phage cocktail was confirmed using spot test assays. Comparison of whole genome sequencing between the recovered BIMs and their respective vehicle control-treated phage-sensitive isolates revealed structural variants in two strains, and several small variants in all three strains. These variations involved a TonB-dependent outer membrane receptor in one strain, and mutations in lipopolysaccharide synthesis genes in two strains. Prophage deletion and induction were also noted in two strains, as well as mutations in several genes associated with virulence factors. Mutations in genes involved in susceptibility to conventional antibiotics were also identified in BIMs, with both decreased and increased antibiotic sensitivity to various antibiotics being observed. These findings may have implications for future applications of lytic phage therapy.IMPORTANCELytic bacteriophages are viruses that infect and kill bacteria and can be used to treat difficult-to-treat bacterial infections, including biofilm-associated infections and multidrug-resistant bacteria. Pseudomonas aeruginosa is a bacterium that can cause life-threatening infections. Lytic bacteriophage therapy has been trialed in the treatment of P. aeruginosa infections; however, sometimes bacteria develop resistance to the bacteriophages. This study sheds light on the genetic mechanisms of such resistance, and how this might be harnessed to restore the sensitivity of multidrug-resistant P. aeruginosa to conventional antibiotics.

Genomic insights and phenotypic characterization of three multidrug resistant Cupriavidus strains from the cystic fibrosis lung

AIMS

We aimed to investigate phenotypic and genomic traits of three Cupriavidus spp. isolates recovered from people with cystic fibrosis (PWCF). These bacteria are recognized as emerging pathogens in PWCF.

METHODS AND RESULTS

Using short and long sequencing reads, we assembled three hybrid complete genomes for the genus Cupriavidus, adding to the 45 published currently, describing multipartite genomes and plasmids. The isolates likely represent three different species, and they carry a cumulative total of 30 antibiotic resistance genes with high homology to well-characterized resistance determinants from other bacteria. Multidrug resistance to antibiotics used in CF management was observed in all three isolates. However, two treatments were active across all isolates: cefotaxime and piperacillin/tazobactam. Biofilm formation was only seen at physiological temperatures (37°C) and lost at 20°C and all isolates had low lethality in Galleria mellonella larvae. Isolates demonstrated variable motility, with one non-motile isolate carrying a disrupted flhD transcriptional regulator, abolishing flagella expression.

CONCLUSIONS

Our Cupriavidus spp. isolates showed considerable genomic and phenotypic variability that may impact their virulence and treatment in PWCF, where multidrug resistance will negate treatments and biofilm formation and motility play key roles in infection establishment, as seen in CF pathogens like Pseudomonas aeruginosa. More detailed investigation of clinical Cupriavidus isolates is needed for full understanding of the risk they pose to PWCF.

Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov

Whole-genome sequencing of cultures at the American Type Culture Collection (ATCC®) is ongoing, with reference-quality genome sequences for our microbial strains added to the ATCC® Genome Portal on a quarterly basis. Following genome assembly, authentication and taxonomy verification are needed for taxonomic updates based on the circumscription of genomic metrics for a species. Moraxella sp. ATCC 23246T was originally identified as an atypical Moraxella catarrhalis; however, an analysis of the complete and closed genome of this strain indicates that it represents a novel species within the Moraxella genus. We propose the name of Moraxella veridica sp. nov. for this long-mischaracterized strain as whole-genome sequencing was used to uncover the truth of this strain's identity. The type strain is ATCC 23246T (=NCTC 4103T).

Janthinobacterium aestuarii sp. nov., a novel violacein-producing bacterium isolated from the Tidal Basin in Washington, D.C., USA

Strain TB1-E2-13T was isolated from water collected from the Tidal Basin in Washington, D.C., USA, due to the bright purple colour of its colonies, and was taxonomically evaluated with a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain TB1-E2-13T was most similar to species in the Janthinobacterium genus. For more precise taxonomic inference, a phylogenomic analysis was conducted and indicated that strain TB1-E2-13T was most closely related to Janthinobacterium lividum, 'Janthinobacterium kumbetense', Janthinobacterium rivuli and Janthinobacterium violaceinigrum. Analyses of genomic indices found that pairwise comparisons between strain TB1-E2-13T and other members of the Janthinobacterium genus returned values below the threshold of species novelty. Based on a polyphasic characterization and identifying differences in genomic and taxonomic data, strain TB1-E2-13T represents a novel species, for which the name Janthinobacterium aestuarii sp. nov. is proposed. The type strain is TB1-E2-13T (=ATCC TSD-339T=JCM 36076T).

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.

The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family

The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis. Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii.IMPORTANCEUsing long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.

Often in silico, rarely in vivo: characterizing endemic plant-associated microbes for system-appropriate biofertilizers

The potential of phosphate-solubilizing microbes (PSMs) to enhance plant phosphorus uptake and reduce fertilizer dependency remains underutilized. This is partially attributable to frequent biofertilizer-farming system misalignments that reduce efficacy, and an incomplete understanding of underlying mechanisms. This study explored the seed microbiomes of nine Australian lucerne cultivars to identify and characterize high-efficiency PSMs. From a library of 223 isolates, 94 (42%) exhibited phosphate solubilization activity on Pikovskaya agar, with 15 showing high efficiency (PSI > 1.5). Genomic analysis revealed that the "high-efficiency" phosphate-solubilizing microbes belonged to four genera (Curtobacterium, Pseudomonas, Paenibacillus, Pantoea), including novel strains and species. However, key canonical genes, such as pqq operon and gcd, did not reliably predict phenotype, highlighting the limitations of in silico predictions. Mutagenesis of the high-efficiency isolate Pantoea rara Lu_Sq_004 generated mutants with enhanced and null solubilization phenotypes, revealing the potential role of "auxiliary" genes in downstream function of solubilization pathways. Inoculation studies with lucerne seedlings demonstrated a significant increase in shoot length (p < 0.05) following treatment with the enhanced-solubilization mutant, indicating a promising plant growth-promotion effect. These findings highlight the potential of more personalized "system-appropriate" biofertilizers and underscore the importance of integrating genomic, phenotypic, and in planta analyses to validate function. Further research is required to investigate links between genomic markers and functional outcomes to optimize the development of sustainable agricultural inputs.

Nanopore Environmental Analysis

As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.

Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens

Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376T = CCM 8659T = DSM 111350T) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.

Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume

Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study

BACKGROUND

Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity.

METHODS

In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from five hospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream S pyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity.

FINDINGS

We identified 500 cases of invasive S pyogenes infection in patients in the Top End and 495 cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5·97 (95% CI 4·61-7·73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5·41, 4·28-6·89). The odds of in-hospital mortality (OR 0·43, 95% CI 0·26-0·70), 30-day mortality (0·38, 0·23-0·63), and ICU admission (0·42, 0·30-0·59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 S pyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hyperendemic Top End. Using a lower transmission rate, larger population size, and lower levels of migration similar to those of communities in urbanised southeast Australia, the transmission model qualitatively reproduced a pattern of dominant lineages that cycled in frequency. Despite distinct circulating lineages, the prevalence of accessory genes in the bacterial population was maintained across geographies and temporal periods.

INTERPRETATION

In a hyperendemic setting, the replacement of distinct S pyogenes lineages occurred in waves, which could be linked to the disproportionate burden of disease and sparse human population in this setting. The maintenance of bacterial gene frequency could be consistent with multilocus selection. These findings suggest that lineage-specific interventions-such as vaccines under development-should consider disease setting and, without broad cross-protection, might lead to lineage replacement.

FUNDING

National Health and Medical Research Council, and Leducq Foundation.

Isolation and characterization of Sporomusa carbonis sp. nov.: a carboxydotrophic hydrogenogen in the genus of Sporomusa isolated from a charcoal-burning pile

A Gram-negative bacterial strain, designated ACPtT, was isolated from the top of the covering soil of an active charcoal-burning pile. The cells of ACPtT were strictly anaerobic, rod-shaped and grew optimally at 40 °C and pH 7. The substrates ribose, glucose, sucrose, raffinose, melezitose, pyruvate, vanillate, syringate, methanol and CO were utilized for growth. Phylogenomic analysis of the 4.1 Mb genome showed that strain ACPtT represented a novel species of the genus Sporomusa. The most closely related species to ACPtT was Sporomusa malonica, with an average amino acid identity of 80.1%. The genome of ACPtT encoded cytochromes, ubiquinones, the Wood-Ljungdahl gene cluster and an Rnf complex, which were identified as common features of all Sporomusa type strains. However, strain ACPtT did not ferment H2+CO2 via acetogenesis as other Sporomusa species but employed the metabolism of a carboxydotrophic hydrogenogen, converting CO to H2+CO2. Based on the genomic, morphological and physiological features presented in this study, strain ACPtT is proposed as a novel species in the genus Sporomusa, with the name Sporomusa carbonis sp. nov. (DSM 116159T and CCOS 2105T).

Quorum sensing and DNA methylation play active roles in clinical Burkholderia phase variation

Phenotypic diversity in bacteria often results from adaptation to changing environmental conditions, exemplified by variable colony morphotypes. In Burkholderia pseudomallei, discrete genomic alterations and modulation of gene expression facilitate adaptation. Adapted variants of species within the Burkholderia cepacia complex (Bcc) often lose the pC3 virulence megaplasmid, impacting their colony morphology and their production of virulence factors. In this study, we characterize variants arising in Burkholderia ambifaria clinical isolates using proteomics and phenotypic tests and show that some of them have retained the pC3, indicating a distinct phase variation mechanism at play in this Bcc species. Interestingly, variants of B. ambifaria strains CEP0996 (pC3-null) and HSJ1 (pC3-positive) still share similarities in phenotypes controlled by the Cep quorum-sensing (QS) system. We further investigated the role of QS in B. ambifaria HSJ1 phase variation and confirmed that the Cep QS system is important for the emergence of variants. Given that DNA methylation is a key epigenetic factor regulating virulence factors in Burkholderia cenocepacia, we hypothesized that adenosine DNA methylation also governs phase variation in B. ambifaria HSJ1. By deleting the genes encoding putative adenosine DNA methyltransferases, we discovered that an orphan type II DNA methyltransferase inhibits the emergence of phase variants. This study is the first to demonstrate that quorum sensing and adenosine DNA methylation are two antagonistic systems independently controlling phase variation in B. ambifaria.IMPORTANCESome Burkholderia species are pathogenic to plants, animals, or humans. In immunocompromised individuals, and people suffering from cystic fibrosis, infection from the Burkholderia cepacia complex (Bcc) can lead to "cepacia syndrome." In northern Australia and southeast Asia, melioidosis caused by Burkholderia pseudomallei is prevalent among native population, particularly among people with diabetes, chronic lung or kidney disease or alcoholism. Burkholderia's phenotypic plasticity, including colony morphotype variation (CMV), enables rapid adaptation to diverse environments, enhancing its survival and pathogenicity. This study reveals phase variation as a new CMV mechanism within the Bcc group and is the first to report that quorum sensing and DNA methylation are involved in phase variation. Understanding the underlying mechanisms of CMV could lead to the development of targeted therapies against these highly antibiotic-tolerant bacteria.

Complete genome sequences of Yersinia pestis 6/69 strain isolated from a bubonic plague patient in Madagascar and its isogenic strain cured of pPCP1

We report the complete genome sequences of two valuable strains to investigate plague pathogenesis: (i) Yersinia pestis strain 6/69, which was isolated from a bubonic plague patient in Madagascar and contains pCD1, pMT1, and pPCP1 virulence plasmids, and (ii) the 6/69 strain cured of pPCP1.

Complete genome sequences of Castellaniella ginsengisoli associated with mortality events in avian species

Castellaniella ginsengisoli is a potential bacterial pathogen that affects chickens. We present 22 complete genome sequences of clinical isolates to facilitate the genomic analysis and the development of diagnostic tools.

Characterization of FosA13, a novel fosfomycin glutathione transferase identified in a Morganella morganii isolate from poultry

Background

M. morganii is a species of the genus Morganella in the family Enterobacteriaceae. This species primarily causes infections of postoperative wounds and the urinary tract. Some isolates of M. morganii exhibit resistance to multiple antibiotics due to multidrug resistance traits, complicating clinical treatment; thus, there is a growing need to elucidate the resistance mechanisms of this pathogen.

Methods

A total of 658 bacterial strains were isolated from anal fecal swabs from poultry and livestock and from the surrounding environment in Wenzhou, China, via plate streaking. The full genome sequences of the bacteria were obtained via next-generation sequencing platforms. The standard agar dilution method was employed to determine the minimum inhibitory concentrations (MICs) of various antimicrobial agents. The resistance gene (fosA13) of the isolate was identified using the Comprehensive Antibiotic Resistance Database (CARD) and confirmed via molecular cloning. The FosA13 protein encoded by the novel resistance gene fosA13 was expressed with the vector pCold I, and its enzyme kinetics parameters were characterized. The genetic background and evolutionary process of the sequence of this novel resistance gene were analyzed by means of bioinformatics methods.

Results

In this study, we identified a new chromosomally encoded fosfomycin resistance gene, designated fosA13, from the M. morganii isolate DW0548, which was isolated from poultry on a farm in Wenzhou, China. Compared with the control strain (pUCP19/DH5α), the recombinant strain carrying fosA13 (pUCP19-fosA13/DH5α) presented a fourfold increase in the MIC value for fosfomycin. The enzyme kinetics data of FosA13 revealed effective inactivation of fosfomycin, with a k cat /K m of (1.50 ± 0.02)×104 M-1·s-1. Among functionally characterized resistance proteins, FosA13 presented the highest amino acid (aa) homology (55.6%) with FosA. FosA13 also contained essential functional residues of FosA proteins. The isolate M. morganii DW0548 presented high MIC values (≥ 8 μg/mL) for 5 classes of antimicrobials, namely, aminoglycosides, β-lactams, quinolones, tetracycline, and chloramphenicol, but only two functionally characteristic antimicrobial resistance genes (ARGs) have been identified in the complete genome: a β-lactam resistance gene (bla DHA-16) and a phenol resistance gene (catII). These findings indicate that in addition to the novel resistance gene identified in this work, other uncharacterized resistance mechanisms might exist in M. morganii DW0548.

Conclusion

A novel chromosomal fosfomycin resistance gene, fosA13, was identified in an animal M. morganii isolate, and its enzymatic parameters were characterized. This protein shares the highest aa identity of 55.6% with the functionally characterized protein FosA and has all the essential functional residues of FosA proteins. Exploring more antimicrobial resistance mechanisms of this pathogen would help clinicians choose effective drugs to treat infectious diseases in animal husbandry and clinical practice and facilitate the development of methods to prevent the spread of resistance between bacteria of different species.

Complete genome sequencing and probiotic trait analysis of Lacticaseibacillus rhamnosus LR110, a human stool isolate from the NORDBIOTIC collection

We present the complete genome of Lacticaseibacillus rhamnosus strain LR110, a human stool isolate from the NORDBIOTIC strain collection. The genome consists of a 2,867,184-bp chromosome with 46.8% GC content. Genomic analysis revealed genes related to thiamine salvage, lactose metabolism, and putrescine biosynthesis, providing insight into the strain's potential probiotic properties.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.

Haemophilus influenzae Type b Meningitis in Infants, New York, New York, USA, 2022-2023

Two unvaccinated infants residing in the same borough of New York, New York, USA, had Haemophilus influenzae type b meningitis develop 1 year apart. Whole-genome sequencing and phylogenetic analysis revealed the isolates shared a previously undescribed multilocus sequence type and were more closely related to each other than to other sequenced strains.

Mycobacterium servetii sp. nov., a novel rapid-growing nontuberculous mycobacterial species recovered from a human patient in Zaragoza, Spain

In this study, we describe a novel rapid-growing Mycobacterium species isolated from a clinical specimen obtained from the lower respiratory tract of a patient with ciliary dysfunction, bronchiectasis and exacerbated respiratory symptoms. A comprehensive phenotypic characterization was conducted, including the establishment of a MALDI-TOF MS profile. Additionally, whole-genome sequencing was performed to assess overall genomic relatedness indices and conduct phylogenetic comparative analyses. These findings allowed us to characterize a previously unrecognized rapid-growing Mycobacterium species, for which we propose the name Mycobacterium servetii (=DSM 118141; =CECT 31091).

Enterobacter hormaechei replaces virulence with carbapenem resistance via porin loss

Pathogenic Enterobacter species are of increasing clinical concern due to the multidrug-resistant nature of these bacteria, including resistance to carbapenem antibiotics. Our understanding of Enterobacter virulence is limited, hindering the development of new prophylactics and therapeutics targeting infections caused by Enterobacter species. In this study, we assessed the virulence of contemporary clinical Enterobacter hormaechei isolates in a mouse model of intraperitoneal infection and used comparative genomics to identify genes promoting virulence. Through mutagenesis and complementation studies, we found two porin-encoding genes, ompC and ompD, to be required for E. hormaechei virulence. These porins imported clinically relevant carbapenems into the bacteria, and thus loss of OmpC and OmpD desensitized E. hormaechei to the antibiotics. Our genomic analyses suggest porin-related genes are frequently mutated in E. hormaechei, perhaps due to the selective pressure of antibiotic therapy during infection. Despite the importance of OmpC and OmpD during infection of immunocompetent hosts, we found the two porins to be dispensable for virulence in a neutropenic mouse model. Moreover, porin loss provided a fitness advantage during carbapenem treatment in an ex vivo human whole blood model of bacteremia. Our data provide experimental evidence of pathogenic Enterobacter species gaining antibiotic resistance via loss of porins and argue antibiotic therapy during infection of immunocompromised patients is a conducive environment for the selection of porin mutations enhancing the multidrug-resistant profile of these pathogens.

Genomic and Transcriptomic Profiling of Bacillus cereus in Milk: Insights into the Sweet Curdling Defect

Bacillus cereus sensu lato (B. cereus s.l.) are significant spoilage and pathogenic microorganisms found in various foodstuffs. They are responsible for defects like sweet curdling in milk, which impacts dairy product storage and distribution. Nevertheless, the genetic mechanisms underlying B. cereus-induced sweet curdling remain poorly characterized. In this study, we investigated the genetic and functional basis underlying this phenomenon through whole genome sequencing of the newly isolated B. cereus strain BC46 and transcriptome sequencing at two phases of its growth in milk. Hybrid assembly of Illumina and Nanopore reads resulted in a 5.6 Mb genome with 35.1% GC content, classifying BC46 as B. cereus sensu stricto (B. cereus s.s.) within the panC group IV. Several virulence factors, antimicrobial resistance genes, and cold shock proteins were identified in the genome. A distinct functional profile of BC46 was observed before and after the development of sweet curdling in milk. Genes associated with sporulation, toxin production, hydrolysis, and proteolysis were upregulated in sweet-curdled samples. Our findings highlight potential gene targets that may play an important role in the BC46-induced sweet curdling in milk, enhancing our understanding of its molecular basis and supporting the development of new genetic approaches for early spoilage detection.

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Lignin contains a variety of interunit linkages, leading to a range of potential decomposition products that can be used as carbon and energy sources by microbes. β-O-4 linkages are the most common in native lignin, and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from β-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains of Novosphingobium aromaticivorans with improved catabolism of a model aromatic dimer containing a β-O-4 linkage, guaiacylglycerol-β-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide polymorphism in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, β-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.IMPORTANCELignin degradation is a key step for both carbon cycling in nature and biomass conversion to fuels and chemicals. Bacteria can catabolize lignin-derived aromatic compounds, but the complexity of lignin means that full mineralization requires numerous catabolic pathways and often results in slow growth. Using experimental evolution, we identified an uncharacterized enzyme for the catabolism of a lignin-derived aromatic monomer, β-hydroxypropiovanillone. A single nucleotide polymorphism in the promoter of the associated gene significantly increased bacterial growth with either β-hydroxypropiovanillone or a related lignin-derived aromatic dimer. This work expands the repertoire of known aromatic catabolic genes and demonstrates that slow catabolism of lignin-derived aromatic compounds may be due to misregulation under laboratory conditions rather than inherent catabolic challenges.

Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates

OBJECTIVE

Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.

DATA DESCRIPTION

We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.

Complete genome sequence of fluoroacetate-degrading Caballeronia sp. S22 strain (DSM 8341) as a reference resource for investigations of microbial defluorination

A complete genome sequence of Caballeronia sp. strain S22 capable of growing with fluoroacetate as the sole source of carbon and energy was obtained by PacBio technology. It consists of seven circular replicons totaling 9,367 kb, with a gene cluster involved in fluoroacetate utilization on its smallest 172 kb plasmid.

Complete genome sequences of two actinomycetes containing abyssomicin-like gene clusters: Kutzneria buriramensis DSM 45791 and Streptomyces sp. NL15-2K

Here, we report the resequencing, assembly, and annotation of two actinomycete genomes containing abyssomicin gene clusters. Kutzneria buriramensis DSM 45791 with a circular chromosome of 11,681,598 bp and 4 circular plasmids (14,175-207,548 bp) and Streptomyces sp. NL15-2K with a 12,368,159 bp linear genome and circular plasmid (11,584 bp).

Complete genome sequence of Bifidobacterium animalis subsp. lactis BI040, a probiotic strain with multiple health benefits from the NORDBIOTIC collection

The complete genome of Bifidobacterium animalis subsp. lactis BI040-a human stool isolate, was sequenced using Illumina and Oxford Nanopore technologies. The BI040 genome is composed of a circular 1,944,141-bp chromosome which carries genes potentially involved in vitamin synthesis and gut health.

Complete genome sequence of Dorea formicigenerans JCM 31256

We describe a complete genome sequence of Dorea formicigenerans JCM 31256. The genome consists of a single circular chromosome with a length of 3,090,452 base pairs and a GC content of 40.8%, and was predicted to contain 3,061 total genes, encoding for 2,907 proteins.

Complete genome sequence of Roseburia faecis M72/1T

We describe a complete genome sequence of Roseburia faecis strain M72/1T (= JCM 17581T = DSM 16840T = NCIMB 14031T). The genome assembly consists of a single circular chromosome with a length of 3,385,415 base pairs and was predicted to contain 3,338 genes and encode for 3,180 proteins.

Genomic Biosurveillance of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 3 Reveals Adaptation to Selective Pressures in New Zealand Orchards

In the late 2000s, a pandemic of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) devastated kiwifruit orchards growing susceptible, yellow-fleshed cultivars. New Zealand's kiwifruit industry has since recovered, following the deployment of the tolerant cultivar 'Zesy002'. However, little is known about the extent to which the Psa population is evolving since its arrival. Over 500 Psa3 isolates from New Zealand kiwifruit orchards were sequenced between 2010 and 2022, from commercial monocultures and diverse germplasm collections. While effector loss was previously observed on Psa-resistant germplasm vines, effector loss appears to be rare in commercial orchards, where the dominant cultivars lack Psa resistance. However, a new Psa3 variant, which has lost the effector hopF1c, has arisen. The loss of hopF1c appears to have been mediated by the movement of integrative conjugative elements introducing copper resistance into this population. Following this variant's identification, in-planta pathogenicity and competitive fitness assays were performed to better understand the risk and likelihood of its spread. While hopF1c loss variants had similar in-planta growth to wild-type Psa3, a lab-generated ∆hopF1c strain could outcompete the wild type on select hosts. Further surveillance was conducted in commercial orchards where these variants were originally isolated, with 6.6% of surveyed isolates identified as hopF1c loss variants. These findings suggest that the spread of these variants is currently limited, and they are unlikely to cause more severe symptoms than the current population. Ongoing genome biosurveillance of New Zealand's Psa3 population is recommended to enable early detection and management of variants of interest.

Complete genome characterization of mcr-1-mediated colistin-resistant Escherichia coli from outpatients in Bulgaria

INTRODUCTION

This study reports the emergence of mcr-1-mediated colistin resistance in human Escherichia coli isolates from Bulgaria.

METHODS

Three colistin-resistant E. coli isolates were obtained from outpatient urine specimens. They were subjected to PCR for detection of mcr genes and conjugation experiments. Whole-genome sequencing was employed to analyze the genomic characteristics of the isolates.

RESULTS

PCR identified mcr-1 in all isolates. In E. coli of sequence type (ST) 2067, mcr-1.1 was found on a self-transmissible IncI2 plasmid, while mcr-1.32 was chromosomal in the remaining two ST131 E. coli isolates. E. coli ST2067 co-harbored quinolones resistance mutations (gyrAD87N, gyrAS83L, parCS80I), β-lactam (blaTEM-30) and aminoglycoside (aadA1, aac(3)-IId) resistance genes.

CONCLUSION

This report further confirms the role of IncI2 conjugative plasmids in the dissemination of mcr genes. Our findings involving chromosomal mcr-1 in high-risk ST131 E. coli strains from outpatients underscores the need for enhanced surveillance and systematic screening to combat colistin resistance.

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.

Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans

Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

Leptospira gorisiae sp. nov, L. cinconiae sp. nov, L. mgodei sp. nov, L. milleri sp. nov and L. iowaensis sp. nov: five new species isolated from water sources in the Midwestern United States

Isolates of Leptospira spp. were cultured from water sources at five different sites in central Iowa in the Midwestern United States and characterized by whole-genome sequencing. Isolates were helix-shaped and motile. Genome sequence analyses determined that the isolates could be clearly distinguished from other species described in the genus Leptospira and included one species that belonged to the pathogen subclade P1, one species that belonged to the pathogen subclade P2 and three species that belonged to the saprophyte subclade S1. The names Leptospira gorisiae sp. nov. (type strain WS92.C1T=NVSL-WS92.C1T=KIT0303T), Leptospira cinconiae sp. nov. (type strain WS58.C1T=NVSL-WS58.C1T=KIT0304T), Leptospira mgodei sp. nov. (type strain WS4.C2T=NVSL.WS4.C2T=KIT0305T), Leptospira iowaensis sp. nov. (type strain WS39.C2T=NVSL-WS39.C2T=KIT0306T) and Leptospira milleri sp. nov. (type strain WS60.C2T=NVSL-WS60.C2T=KIT0307T) are proposed.

A Step-by-Step Guide to Sequencing and Assembly of Complete Bacterial Genomes Using the Oxford Nanopore MinION

The Oxford Nanopore (ONT) MinION enables sequencing of longer DNA/RNA fragments compared to other sequencers, such as Illumina, etc. This nanopore method provides distinct advantages for generating complete genome assemblies from microorganisms. Specifically, the R9.4 flow cells used for MinION sequencing have much lower error rates compared with earlier versions of the ONT platform. Coupled with base calling using Dorado software, higher-quality long reads can now be generated for complete bacterial genome assembly. In this chapter, we describe a detailed MinION method to assemble a complete genome from a microorganism, polish the final assembly, and evaluate the genome quality using various software tools. Because of the low cost for MinION sequencing, this platform could be an asset for virtually any laboratory interested in generating complete genomes from microorganisms.

Scrofimicrobium appendicitidis sp. nov., isolated from a patient with ruptured appendicitis

A clinical isolate, R131, was isolated from the peritoneal swab of a patient who suffered from ruptured appendicitis with abscess and gangrene in Hong Kong in 2018. Cells are facultatively anaerobic, non-motile, Gram-positive coccobacilli. Colonies were small, grey, semi-translucent, low convex and alpha-haemolytic. The bacterium grew on blood agar but not on Brain Heart Infusion (BHI) and Mueller-Hinton agars. It was negative for catalase, oxidase, indole and aesculin hydrolysis. The initial identification attempts via matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S rRNA gene sequencing yielded inconclusive results. The 16S rRNA gene analysis showed that R131 shared >99% nucleotide identity with certain uncultured Actinomycetales bacteria. In this retrospective investigation, a complete genome of R131 was constructed, disclosing a DNA G+C content of 64%. Phylogenetic analysis showed that the bacterium was mostly related to Scrofimicrobium canadense WB03_NA08, which was first described in 2020. However, its 16S rRNA gene shared only 94.15% nucleotide identity with that of S. canadense WB03_NA08. Notably, the orthoANI between R131 and S. canadense WB03_NA08 was 67.81%. A pan-genome analysis encompassing R131 and 4 Scrofimicrobium genomes showed 986 core gene clusters shared with the Scrofimicrobium species, along with 601 cloud genes. The average nucleotide identity comparisons within the pan-genome analysis ranged from 59.78 to 62.51% between R131 and the other Scrofimicrobium species. Correspondingly, the dDDH values ranged from 19.20 to 22.30%, while the POCP values spanned from 57.48 to 60.94%. Therefore, a novel species, Scrofimicrobium appendicitidis sp. nov., is proposed. The type strain is R131T (=JCM 36615T=LMG 33627T).

Genome analysis reveals diverse novel psychrotolerant Mucilaginibacter species in Arctic tundra soils

As Arctic soil ecosystems warm due to climate change, enhanced microbial activity is projected to increase the rate of soil organic matter degradation. Delineating the diversity and activity of Arctic tundra microbial communities active in decomposition is thus of keen interest. Here, we describe novel cold-adapted bacteria in the genus Mucilaginibacter (Bacteroidota) isolated from Artic tundra soils in Finland. These isolates are aerobic chemoorganotrophs and appear well adapted to the low-temperature environment, where they are also exposed to desiccation and a wide regime of annual temperature variation. Initial 16S ribosomal RNA (rRNA)-based phylogenetic analysis suggested that five isolated strains represent new species of the genus Mucilaginibacter, confirmed by whole genome-based phylogenomic and average nucleotide identity. Five novel species are described: Mucilaginibacter geliditolerans sp. nov., Mucilaginibacter tundrae sp. nov., Mucilaginibacter empetricola sp. nov., Mucilaginibacter saanensis sp. nov., and Mucilaginibacter cryoferens sp. nov. Genome and phenotype analysis showed their potential in complex carbon degradation, nitrogen assimilation, polyphenol degradation, and adaptation to their tundra heath habitat. A pangenome analysis of the newly identified species alongside known members of the Mucilaginibacter genus sourced from various environments revealed the distinctive characteristics of the tundra strains. These strains possess unique genes related to energy production, nitrogen uptake, adaptation, and the synthesis of secondary metabolites that aid in their growth, potentially accounting for their prevalence in tundra soil. By uncovering novel species and strains within the Mucilaginibacter, we enhance our understanding of this genus and elucidate how environmental fluctuations shape the microbial functionality and interactions in Arctic tundra ecosystems.

An exploration of unusual antimicrobial resistance phenotypes in Salmonella Typhi from Blantyre, Malawi reveals the ongoing role of IncHI1 plasmids

Typhoid fever is a significant public health problem endemic in Southeast Asia and Sub-Saharan Africa. Antimicrobial treatment of typhoid is however threatened by the increasing prevalence of antimicrobial resistant (AMR) S. Typhi, especially in the globally successful lineage (4.3.1) which has rapidly spread in East and Southern Africa. AMR elements can be found either on plasmids or in one of the three chromosomal integration sites, and there is variability of this across the lineage. Several previous studies with Malawian isolates indicated a clonal, locally spreading lineage with chromosomally integrated resistance genes. In a recent study however we noted three isolates with predicted resistance genes unusual for the region, and we here present the resolved genomes of these isolates using long- and short-read sequencing. Our work shows that these isolates are potentially imported cases, most closely related to the recently described sub-lineage 4.3.1.EA1, although they encode IncHI1 plasmids with reduced resistance gene repertoire compared to the main IncHI1 plasmids spreading in East Africa. Similar reduced plasmids were reported in a recent large-scale study in five isolates from Tanzania, highlighting the urgency for better coverage of the African continent in genome studies to better understand the dynamics of these potentially co-circulating plasmids.

Sequencing Strategy to Ensure Accurate Plasmid Assembly

Despite the wide use of plasmids in research and clinical production, the need to verify plasmid sequences is a bottleneck that is too often underestimated in the manufacturing process. Although sequencing platforms continue to improve, the method and assembly pipeline chosen still influence the final plasmid assembly sequence. Furthermore, few dedicated tools exist for plasmid assembly, especially for de novo assembly. Here, we evaluated short-read, long-read, and hybrid (both short and long reads) de novo assembly pipelines across three replicates of a 24-plasmid library. Consistent with previous characterizations of each sequencing technology, short-read assemblies had issues resolving GC-rich regions, and long-read assemblies commonly had small insertions and deletions, especially in repetitive regions. The hybrid approach facilitated the most accurate, consistent assembly generation and identified mutations relative to the reference sequence. Although Sanger sequencing can be used to verify specific regions, some GC-rich and repetitive regions were difficult to resolve using any method, suggesting that easily sequenced genetic parts should be prioritized in the design of new genetic constructs.

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

Background

The study of sample taxonomic composition has evolved from direct observations and labor-intensive morphological studies to different DNA sequencing methodologies. Most of these studies leverage the metabarcoding approach, which involves the amplification of a small taxonomically-informative portion of the genome and its subsequent high-throughput sequencing. Recent advances in sequencing technology brought by Oxford Nanopore Technologies have revolutionized the field, enabling portability, affordable cost and long-read sequencing, therefore leading to a significant increase in taxonomic resolution. However, Nanopore sequencing data exhibit a particular profile, with a higher error rate compared with Illumina sequencing, and existing bioinformatics pipelines for the analysis of such data are scarce and often insufficient, requiring specialized tools to accurately process long-read sequences.

Results

We present PRONAME (PROcessing NAnopore MEtabarcoding data), an open-source, user-friendly pipeline optimized for processing raw Nanopore sequencing data. PRONAME includes precompiled databases for complete 16S sequences (Silva138 and Greengenes2) and a newly developed and curated database dedicated to bacterial 16S-ITS-23S operon sequences. The user can also provide a custom database if desired, therefore enabling the analysis of metabarcoding data for any domain of life. The pipeline significantly improves sequence accuracy, implementing innovative error-correction strategies and taking advantage of the new sequencing chemistry to produce high-quality duplex reads. Evaluations using a mock community have shown that PRONAME delivers consensus sequences demonstrating at least 99.5% accuracy with standard settings (and up to 99.7%), making it a robust tool for genomic analysis of complex multi-species communities.

Conclusion

PRONAME meets the challenges of long-read Nanopore data processing, offering greater accuracy and versatility than existing pipelines. By integrating Nanopore-specific quality filtering, clustering and error correction, PRONAME produces high-precision consensus sequences. This brings the accuracy of Nanopore sequencing close to that of Illumina sequencing, while taking advantage of the benefits of long-read technologies.