Search Results (464)

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with nosocomial infections and environmental dissemination. Among its high-risk clones, ST244 is notable for its global distribution and distinctive genomic traits. This study reports whole-genome sequencing of ten ST244 isolates from hospitalized patients and wastewater in a healthcare complex in Southeastern Brazil. Genomic comparisons revealed a highly conserved clonal group, with nine isolates forming a tight monophyletic cluster based on rMLST, SNP phylogeny, and average nucleotide identity (>99.5%). One isolate showed close phylogenetic proximity to strains from Asia and North America, suggesting international dissemination. Serotype analysis revealed both O5 and O12 variants, indicating intra-lineage antigenic diversity. Resistance profiling identified multidrug-resistant phenotypes carrying carbapenemase genes (bla_OXA-494, bla_OXA-396) and diverse insertion sequences (ISPa1, ISPa6, ISPa22, ISPa32, and ISPa37), facilitating horizontal gene transfer. Virulence gene analysis showed conserved elements related to adhesion, iron uptake, secretion systems, and quorum sensing, while the cytotoxin gene exoU was absent. These results highlight clonal persistence, possible intra-hospital transmission, and links to globally circulating ST244 sublineages. Our findings underscore the importance of genomic surveillance to track high-risk P. aeruginosa clones at the clinical–environmental interface. Full article

The historic Rockborn strain of the canine distemper virus was widely used as a vaccine, but its use was discontinued due to safety concerns. Yet, Rockborn-like canine distemper virus strains are still used in some vaccine formulations. Genetic analysis of this strain was previously limited to the H gene, leaving its full evolutionary and pathogenic potential unclear. This study aimed to determine the complete genome sequence of the Rockborn strain to reconstruct its origin, understand its evolution, and provide a reference for improving diagnostics and future research on virulence markers. An amplicon-based sequencing protocol using MinION nanopore technology was employed to determine the complete genome of the Rockborn-46th laboratory strain. The genome was assembled, annotated, and analyzed in comparison with 223 genomes. The complete genome of the Rockborn strain was 15,690 nucleotides in length. Phylogenetic analysis revealed that Rockborn forms a unique lineage with field isolates from a masked civet in China and a dog in the United States. Crucially, a significant recombination event was identified, showing that the Rockborn strain acted as a parental strain, contributing its F and H genes to create mosaic viruses. The full-genome characterization of the Rockborn strain confirms that Rockborn-like viruses persist and actively contribute to the evolution of canine distemper virus through recombination. This finding highlights the inadequacy of single-gene analysis for diagnostics and surveillance, and underscores the necessity of whole-genome sequencing to accurately track the virus epidemiology and evolution. Full article

The extended application of pesticides has intensified the resistance problem in Liriomyza trifolii within Hainan Province. This study aimed to elucidate the underlying mechanisms contributing to the elevated resistance observed in this pest by employing Whole-Genome Re-sequencing (WGR) technology. Through the analysis and comparison of WGR data focusing on voltage-gated sodium channel (VGSC) from diverse regions and LT-S of L. trifolii in Hainan Province, we identified a total of six nonsynonymous single nucleotide polymorphisms (nsSNPs) and thirty-one synonymous single nucleotide polymorphisms (sSNPs) in five wild populations MY, TS, DA, TY, and JY. Among the six nsSNPs, three (PyR1: M918T, L1014F, and PyR2: T933I) have been confirmed as linked to pyrethroid resistance, while one (D IVS6: V1845I) was associated with resistance to indoxacarb. Moreover, the frequency of these four mutations generally increases with decreasing latitude. Additionally, under sustained pesticide selection pressure, L. trifolii exhibits an evolutionary pattern characterized by a dN/dS ratio (nsSNP/sSNP = 6/31 ≈ 0.19) of less than 1. Among the 31 sSNPs that held an absolute quantitative advantage, the highest occurrence frequency reached 94.44% (G2033: JY), and this sSNP occurred in all populations. In contrast, among a limited number of 6 nsSNPs, the highest occurrence frequency attained 100% (L1014F: all populations). This study substantiates that the elevated resistance observed in L. trifolii within Hainan Province can be ascribed to the presence of four nsSNPs-M922T, T933I, L1018F, and V1845I in their VGSC. Furthermore, the emergence of cross-resistance between pyrethroids and indoxacarb has been identified. This research offers a novel theoretical foundation for future investigations into the resistance mechanisms of L. trifolii. Full article

Human adenovirus type 3 (HAdV-3) in the species Mastadenovirus blackbeardi is a frequent cause of hundreds of respiratory infections in Japan, with outbreaks varying in clinical severity. Such a high frequency of cases could be due to regular migration of novel variants or persistent circulation of endemic strains. Either scenario would require different measures to ameliorate the burden on public health. We designed a new cost-effective whole-genome sequencing protocol based on tiled amplicons and nanopore sequencing to clarify the circumstances behind the frequent outbreaks. This protocol was used with clinical samples collected between 2011 and 2020 from Japanese patients with acute respiratory illness (n = 110), resulting in near whole-genome sequences (~99% length) for 105 samples with high read coverage (~262.6 ± 192 reads). Phylogenetic analysis indicated sustained circulation of endemic strains in Japan during the analyzed decade and their relation to other strains worldwide with publicly available genome sequences. However, a comparison with other Japanese HAdV-3 strains circulating since 2023 suggested the public health measures introduced during the COVID-19 pandemic (2020–2022) indirectly affected the prevalence of circulating HAdV-3 variants. Additionally, our approach enabled the detection and partial sequencing (~71% completion) of co-infecting strains from the species Mastadenovirus caesari (n = 4) in the examined samples. The detection of adenoviruses belonging to different species in the same sample highlights how our protocol enhances the distinction of circulating viruses. In conclusion, these results and the introduced protocol will enable timely characterization and clinical interventions to mitigate this virus. Full article

Antimicrobial resistance is a serious problem in veterinary medicine worldwide. Given that farm animals are considered to be among the sources of infectious disease pathogens in humans, studying the genetic diversity of pathogenic microorganisms isolated from them and identifying strains that are potentially pathogenic to humans is a primary research task nowadays. The current paper provides a comprehensive characterization of 4 Escherichia coli strains that caused colibacillosis in farm animals. Along with a description of morphological and biochemical characteristics, data on antibiotic sensitivity are presented, and a multiple antibiotic resistance index is calculated. In order to identify the genetic basis of antimicrobial resistance (AMR), whole-genome sequencing was performed, followed by phylogenetic analysis and identification of antibiotic resistance genes. It is shown that the studied strains possess genetic determinants of virtually all major molecular mechanisms of antibiotic resistance, a significant number of which are phenotypically expressed. The pronounced potential for acquiring new variants of resistance, in combination with the strains’ virulence potential, determines the etiological significance of the E. coli isolates in relation to both farm animals and human beings. A comparison of the results obtained with other researchers’ data indicates a coincidence in the trends of the multiple antibiotic-resistant strains spread in different countries and points to the need for the development and implementation of a unified global strategy to combat AMR. Full article

Sclerotium rolfsii Sacc. is a soil-borne fungus that causes southern blight on many crops in the tropical and subtropical regions. In 2018, southern blight was reported as the most prevalent bean root rot in Uganda. Earlier studies ascertained the morphological and pathogenic diversity of S. rolfsii, but a limited understanding of its genetic diversity exists. Knowledge of S. rolfsii genetic diversity is a critical resource for pathogen surveillance and developing common bean varieties with durable resistance. A total of 188 S. rolfsii strains from infected common bean plants were collected from seven agro-ecological zones of Uganda in 2013, 2020 and 2021, and characterized morphologically and pathogenically. The genetic diversity of the strains was assessed using single-nucleotide polymorphisms (SNPs) obtained from whole-genome sequencing. The growth rate of the strains ranged between 1.1 and 3.6 cm per day, while the number of sclerotia produced ranged from 0 to 543 per strain. The strains had fluffy, fibrous, and compact colony texture. The strains were pathogenic on common bean and caused disease severity indices ranging from 10.1% to 93.3%. Average polymorphic information content across all chromosomes was 0.27. Population structure analysis identified five genetically distinct clusters. The results of analysis of molecular variance revealed that 54% of the variation was between clusters while 46% of variation was within clusters. Pairwise comparison of Wright’s fixation indices between genetic clusters ranged from 0.31 to 0.78. The findings of this study revealed moderate genetic diversity among S. rolfsii strains, which should be taken into consideration when selecting strains for germplasm screening. Full article

Wastewater-based surveillance is gaining interest worldwide as a complementary tool informing human surveillance of pathogens, among which are antibiotic-resistant bacteria. The current study investigated whether CPE detected within the Dutch human CPE surveillance could be identified among isolates that were independently retrieved from Dutch wastewater. Whole genomes of 203 wastewater- and 1278 human-retrieved isolates were compared using whole-genome multilocus sequence typing (wgMLST), resistome, and plasmid analyses. Overall, 25 clusters (16 E. coli, 9 K. pneumoniae) with genetically highly related variants from both niches were detected. The maximum allelic difference between human- and wastewater-derived isolates in clusters was on average 0.51% (23/4503 alleles, E. coli) and 0.22% (11/4978 alleles K. pneumoniae). For seven clusters, in-depth plasmid analysis was performed, showing highly homologous (87–100%) carbapenemase-containing plasmids from human- and wastewater-retrieved isolates. Six clusters contained wastewater and human isolates that were spatiotemporally related. The sequence identity at chromosomal and plasmid level confirms the presence of human-associated CPE variants in wastewater. Ongoing comparisons between isolates from the national human CPE surveillance and wastewater surveillance will shed more light on the added value of wastewater-based surveillance for monitoring of CPE and other (emerging) antibiotic resistances. Full article

Bloodstream infections (BSIs) pose a significant global health challenge, particularly due to the increasing prevalence of antimicrobial resistance (AMR). Timely and accurate identification of pathogens and resistance determinants is critical for guiding appropriate therapy and improving patient outcomes. Traditional culture-based diagnostics are limited by prolonged turnaround times and reduced sensitivity, especially in culture-negative or polymicrobial infections. This review systematically examined current and emerging sequencing technologies for AMR detection in BSIs, including whole-genome sequencing (WGS), targeted next-generation sequencing (tNGS), metagenomic next-generation sequencing (mNGS), and long-read sequencing platforms (Oxford Nanopore, PacBio). We compared their clinical performance using key metrics such as diagnostic sensitivity, turnaround time, and cost, highlighting contexts in which each technology is most effective. For example, tNGS can achieve the rapid detection of known resistance genes within 8–24 h, while WGS provides comprehensive genome-wide resistance profiling over 24–48 h. mNGS offers broader detection, including rare or unexpected pathogens, although at higher cost and longer processing times. Our analysis identifies specific strengths and limitations of each approach, supporting the use of context-specific strategies, such as combining rapid targeted sequencing for common pathogens with broader metagenomic approaches for complex cases, to improve diagnostic yield and guide antimicrobial therapy. Quantitative comparisons indicate that sequencing technologies can complement conventional methods, particularly in cases where culture-based approaches fail. In conclusion, sequencing-based diagnostics offer measurable improvements in sensitivity and speed over traditional methods for AMR detection in BSIs. Future work should focus on optimizing workflows, integrating sequencing data into clinical decision-making, and validating approaches in prospective studies. Full article

Outbreaks of hemorrhagic septicemia (HS) caused by Pasteurella multocida serogroup B are endemic in Kazakhstan. These outbreaks have repeatedly led to mass mortality events among wild saigas and economic losses to farms. The aim of this study was to conduct the first whole-genome sequencing (WGS) and analysis of P. multocida genomes associated with HS cases in saigas and livestock in Kazakhstan. In this study, WGS was performed on 22 P. multocida isolates obtained from saigas and livestock. A comparative genomic analysis of P. multocida isolates from Kazakhstan and publicly available genomes was performed. All isolates belonged to the B:2:ST122 genotype and formed distinct phylogenetic clusters based on outbreaks in saiga populations and livestock. Clustering also corresponded to identified mutations in virulence genes. Isolates recovered from the 2015 mass mortality of saigas in the Betpak-Dala population were found to have a deletion of the flp1 gene. This observation emphasizes the study of the role of Flp pili in HS pathogenesis. Comparison of the P. multocida B:L2:ST122 genomes revealed low virulence gene diversity and an open pangenome. Prophage annotation did not identify virulence or pathogenicity genes. The obtained results will be useful for future studies of HS pathogenesis. Full article

Avian pathogenic Escherichia coli (APEC) infections cause substantial economic losses in the poultry industry, primarily due to high mortality rates, reduced productivity, and increased treatment costs. With the emergence of antibiotic-resistant APEC strains, including multidrug-resistant (MDR) variants, alternative therapeutic strategies have gained increasing attention. This study reports the isolation and characterization of an Escherichia phage, vB_EcoG_APECPW12 (phage vAPECPW12), which specifically targets MDR APEC. Both antibacterial and antibiofilm activities of the phage were evaluated. Phage vAPECPW12 produced small plaques with halos and exhibited strong lytic activity against MDR APEC. Whole-genome sequencing revealed a genome size of 77,812 base pairs with 123 open reading frames. No tRNA, antibiotic-resistant, or lysogenic genes were identified. Phylogenetic analysis and genome comparison suggest that phage vAPECPW12 is a novel member of the genus Kuravirus within the Gordonclarkvirinae family. It also demonstrated good stability across a range of temperatures and pH levels and remained viable after exposure to UV radiation. Phage vAPECPW12 showed a high adsorption rate, a short latent period of 10 min, and a burst size of 258 plaque-forming units per cell. A depolymerase domain was identified in the genome, prompting investigation of its antibiofilm efficacy. Results showed that vAPECPW12 significantly inhibited biofilm formation and removed preformed biofilms, indicating its potential as an alternative antimicrobial agent for controlling MDR APEC and their biofilms in poultry farming. Full article

Marinesco–Sjögren syndrome (MSS) is a rare autosomal recessive disorder characterized by cerebellar ataxia, congenital cataracts, developmental delay, hypotonia, and progressive myopathy. Most reported cases are linked to pathogenic variants in SIL1, a gene encoding a co-chaperone essential for protein folding in the endoplasmic reticulum. Here, we present a comprehensive case study of a Turkish pediatric patient diagnosed with MSS, supported by genetic, bioinformatic, and structural modeling analyses. Whole-exome sequencing revealed a homozygous splice-site variant (SIL1 c.453+1G>T), confirmed by Sanger sequencing and segregation analysis. In silico annotation using Genomize, InterVar, Franklin, VarSome, ClinVar, OMIM, and PubMed classified the variant as pathogenic according to ACMG guidelines. Structural modeling by Phyre2 and I-TASSER demonstrated that the variant abolishes the intron 5 donor site, leading to truncation of the wild-type 461-amino-acid protein into a shortened ~189-amino-acid polypeptide. This truncation results in the loss of critical Armadillo (ARM) repeats required for HSPA5 interaction, explaining the observed instability and impaired chaperone function. Clinically, the patient presented with congenital cataracts, ataxia, developmental delay, and progressive muscle weakness, consistent with previously reported MSS cases. Comparison with the literature confirmed that splice-site variants frequently correlate with severe phenotypes, including early-onset ataxia and cataracts. This report highlights the importance of integrating genomic, structural, and clinical data to better understand genotype–phenotype correlations in MSS. Our findings expand the mutational spectrum of SIL1, reinforce the role of splicing defects in disease pathogenesis, and emphasize the necessity of comprehensive molecular diagnostics for rare neurogenetic syndromes. Full article

Three episodes of sylvatic plague occurred in Yunnan from April to November 2022, and nine Yersinia pestis strains were isolated. Whole-genome sequencing was performed on these isolates, and phylogenetic analysis based on SNP comparisons included 234 publicly available genomes from NCBI. All nine 2022 strains clustered within the 1.IN5 lineage, together with historical isolates from the Lijiang wild rodent plague focus. The Heqing strain HQ1 was most closely related to previous Heqing isolates, while seven Lijiang 2022 strains formed a monophyletic cluster with historical Lijiang strains; the remaining strain LJ4 was the closest relative to this cluster. Whole-genome comparison of HQ1 with historical Heqing strains revealed six SNPs and two indels. Of these, one nonsynonymous SNP and both indels—one being a deletion in the flagellin gene flgF—were located in coding regions. Comparison of the Lijiang strain 2022YL002 with historical local isolates identified ten SNPs and three indels. Five nonsynonymous SNPs were found in coding regions, including one at position 1566343 causing an amino acid change in the iron uptake regulator Fur, a virulence-associated mutation. All three indels were in coding regions. These findings confirm that the 2022 outbreaks originated from local plague reservoirs, while genetic differences indicate ongoing bacterial evolution. The results underscore the persistent activity of sylvatic plague in the Lijiang area and highlight the need for continued surveillance to prevent human spillover. Full article

Caleosins (CLOs) or peroxygenases (PXGs), a class of structural proteins of lipid droplets (LDs), comprise a small family of multifunctional proteins widely involved in oil accumulation, organ development, and stress responses. Despite the proposal of two clades termed H and L in Arabidopsis thaliana, their evolution in the order Brassicales has not been well established. In this study, the first genome-wide analysis of the caleosin family was conducted in papaya (Carica papaya), a Caricaceae plant without any recent whole-genome duplication (WGD). A high number of five members representing both H and L clades were identified from the papaya genome. Further identification and comparison of 68 caleosin genes from 14 representative plant species revealed seven orthogroups, i.e., H1–4 and L1–3, where H1 and L1 have already appeared in the basal angiosperm Amborella trichopoda, supporting their early divergence before angiosperm radiation. Five CpCLO genes belong to H1 (1) and L1 (4), and extensive expansion of the L1 group was shown to be contributed to by species-specific tandem and transposed duplications, which may contribute to environmental adaptation. Orthologous and syntenic analyses uncovered that lineage-specific expansion of the caleosin family in Brassicales relative to A. trichopoda was largely contributed to by tandem duplication and recent WGDs, as well as the ancient γ whole-genome triplication (WGT) shared by all core eudicots. Independent gain or loss of certain introns and apparent expression divergence of caleosin genes were also observed. Tissue-specific expression analysis showed that CpCLO2 and −5 are constitutively expressed, whereas others appear to be tissue-specific, implying function divergence. Interestingly, the H-forms CpCLO1 and RcCLO1 were shown to exhibit similar expression profiles to most oleosin genes that are preferentially expressed oil-rich tissues such as seeds/endosperms, shoots, and calluses, implying their putative involvement in oil accumulation, as observed in Arabidopsis. The results obtained from this study provide a global view of CpCLO genes and insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in papaya and other non-model species. Full article

Infections caused by nontuberculous mycobacteria are becoming significant due to the increasing number of vulnerable individuals worldwide. Understanding the evolutionary relationships within the genus Mycobacterium is critical for improving species identification and, consequently, enhancing diagnosis, treatment, and epidemiological tracking. Pairwise comparisons of average nucleotide identity, genome–genome distance calculations, Mash values, multilocus sequence analyses, and average amino acid identities (AAIs) revealed that the AAI metric is the best to distinguish Mycobacterium from other genera of Mycobacteriales. Furthermore, genes encoding 16S and 23S rRNAs could also be used for the genus delineation: the previously established threshold of 94.5–95.0% of the rrs was confirmed, and the value for the rrl gene was estimated at 88.5–89.0%. The genus-delineating thresholds do not confirm the proposed splitting of the Mycobacterium into five genera, and the overall performance of conserved signatures used for splitting was not satisfactory. We estimated that Mycobacterium contains at least 402 distinct species, 246 of which were identified in clinical human specimens. The obtained tree and the corresponding list of species with proposed corrections to the names made from whole-genome sequences provide a reliable framework for the identification and taxonomic positioning of novel species within the genus. Full article

Background: Antimicrobial resistance (AMR) in Legionella pneumophila is emerging as a concern, particularly with resistance to macrolides and fluoroquinolones. Although clinically significant resistance in Legionella pneumophila remains uncommon, systematic genomic surveillance using whole-genome sequencing (WGS) is needed to anticipate treatment failure as metagenomic diagnostics move toward routine use. Objectives: We assessed the UK Health Security Agency AMR pipeline for predicting resistance in L. pneumophila by analysing 522 L. pneumophila isolates from England and Wales (2020–2023) together with nine database sequences that carry confirmed 23S rRNA mutations conferring high-level azithromycin resistance. The objective of the present study was to examine the presence of antimicrobial resistance genes (ARGs) in L. pneumophila isolates and to determine whether they exhibited phenotypic resistance through minimum inhibitory concentration (MIC) testing. Methods: Serogroups (sgs) were determined using an in-house qPCR assay, and L. pneumophila non-sg1 isolates were serogrouped using the Dresden monoclonal antibody (mAb) typing method. Sequence types were determined using the standard sequence-based typing method by Sanger sequencing. WGS reads were screened against standard AMR databases to identify resistance genes and resistance-mediating mutations. Agar dilution measured MICs for azithromycin, erythromycin, ampicillin, levofloxacin, tetracycline and spectinomycin in isolates possessing the bla_OXA-29, lpeAB or aph(9)-Ia gene. Results: AMR screening detected lpeAB, two allelic β-lactamase variants (bla_OXA-29 and bla_LoxA) and aph(9)-Ia in 165 of the 522 L. pneumophila isolates, while all high-azithromycin MIC reference sequences contained the expected 23S mutation. Only lpeAB was associated with a significant twofold elevation in macrolide MICs. Neither β-lactamase variant increased ampicillin MICs, and aph(9)-Ia carriage did not correlate with higher spectinomycin MICs. Conclusions: Advanced genomic analytics can now deliver timely therapeutic guidance, yet database-flagged genes may not translate into phenotypic resistance. Continuous pairing of curated mutation catalogues with confirmatory testing remains essential for distinguishing clinically actionable determinants such as 23S mutations and lpeAB from silent markers like bla_OXA-29 and aph (9)-Ia. Full article