Microbiology Resource Announcements, Год журнала: 2024, Номер unknown
Опубликована: Дек. 20, 2024
ABSTRACT The Gram-negative bacterium Vibrio harveyi is a serious shrimp pathogen. Here, we present the genome sequence of TUMSAT-2019, which was isolated from kuruma ( Penaeus japonicus ) that originated farm in Okinawa Prefecture. assembly totaled 5.7 Mbp, consisting two chromosomes with no plasmid.
Язык: Английский
Microbial Genomics, Год журнала: 2024, Номер 10(6)
Опубликована: Июнь 4, 2024
It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing usually required for perfection. However, the effect of depth on performance not well understood. Here, we introduce Pypolca (with default and careful parameters) Polypolish v0.6.0 a new parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default Polypolish-careful commonly false-positive errors at low read depth; (2) most benefit occurs by 25× (3) almost never introduces any (4) Pypolca-careful single effective polisher. Overall, recommend following strategies: alone when very (<5×), (5–25×), sufficient (>25×).
Язык: Английский
Процитировано
20
Emerging infectious diseases, Год журнала: 2024, Номер 31(1)
Опубликована: Дек. 18, 2024
Cefiderocol (FDC), a siderophore-cephalosporin conjugate, is the newest option for treating infection with carbapenem-resistant gram-negative bacteria. We identified novel mechanism contributing to decreased FDC susceptibility in Klebsiella pneumoniae clinical isolates. The involves 2 coresident plasmids: pKpQIL, carrying variants of bla
Язык: Английский
Процитировано
4
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 8, 2025
The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for analysis methods bioinformatics expertise, which can be bottleneck many laboratories. At Sciensano, Belgian national institute, an intuitive user-friendly tool portal was implemented using Galaxy, open-source platform workflow creation. Galaxy @Sciensano instance is available to both internal external scientists offers wide range tools provided by community, complemented over 50 custom pipelines developed in-house. selection currently focused primarily on WGS generated Illumina microbial pathogen typing, characterization outbreak detection, but it also addresses specific use cases other types. Our includes several custom-developed 'push-button' pipelines, are stand-alone that perform complete bacterial isolates based generate interactive HTML output reports with key findings. These include quality control, de novo assembly, sequence antimicrobial resistance prediction relevant species-specific assays. They tailored pathogens active genomic surveillance programs, relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. Mycobacterium tuberculosis. utilize internationally recognized databases PubMLST, EnteroBase, NCBI National Database Antibiotic Resistant Organisms, automatically synchronized regular basis ensure up-to-date results. Many these part routine activities reference centers laboratories, some them under ISO accreditation. This resource publicly noncommercial at https://galaxy.sciensano.be/ help laboratories establish reliable, traceable reproducible analyses encountered settings.
Язык: Английский
Процитировано
0
Microbiology Resource Announcements, Год журнала: 2025, Номер unknown
Опубликована: Апрель 7, 2025
ABSTRACT The human gut microbiota is dominated by obligately anaerobic bacteria. A method based on species-targeted sorting using flow cytometry under conditions has been performed to analyze the microbiome. This report describes complete genome sequences of two Hominenteromicrobium mulieris strains CIP 112194 and 112527 that were isolated from feces a healthy adult France. volunteer young having vegetarian diet.
Язык: Английский
Процитировано
0
Microbiology Spectrum, Год журнала: 2025, Номер unknown
Опубликована: Апрель 10, 2025
ABSTRACT The emergence and spread of Salmonella Typhi ( S . Typhi) resistant to third-generation cephalosporins is a serious global health concern. In this study, we genomically characterized 142 cephalosporin-resistant strains isolated from India. Comparative genome analysis revealed the new clone ceftriaxone-resistant harboring three plasmids incompatibility groups IncFIB(K), IncX1, IncFIB(pHCM2). Among these, IncFIB(K) plasmid confers resistance through bla CTX-M-15 gene, along with other determinants such as aph(3") , aph(6') sul2 dfrA14 qnrS tet(A) Phylogenetic showed that isolates Gujarat n = 140/142) belong distinct subclade (genotype 4.3.1.2.2) within genotype 4.3.1.2 (H58 lineage II). Single nucleotide polymorphism-based phylogenetic core genes in suggested close relatedness backbone Enterobacteriales, indicating H58 II possesses capability acquire MDR these organisms. This could indicate potential onset wave implementation control measures—such vaccination improved water, sanitation, hygiene systems—is crucial areas where or extensively drug-resistant are prevalent curb impact strains. IMPORTANCE Typhoid fever remains concern, especially lacking sanitation clean water. rise complicates treatment, increasing illness, death, healthcare expenses. Travel facilitates worldwide. Multidrug-resistant (XDR) strains, including those first-line antibiotics fluoroquinolones, pose significant challenges. Azithromycin now preferred treatments. Recently, XDR typhoid emerged Pakistan, even cephalosporins. India also faces challenges, sporadic cases initially declining but re-emerging. New show due acquisition bacteria, particularly CTX-M -carrying IncFIB(K). Due ongoing nature outbreak, data study deserve further consideration order its
Язык: Английский
Процитировано
0
JAC-Antimicrobial Resistance, Год журнала: 2025, Номер 7(2)
Опубликована: Март 4, 2025
Abstract Objectives To analyse the intrahospital and global dissemination resistome dynamics of concerning NDM-1 MBL-producing ST773 P. aeruginosa high-risk clone. Methods A total 17 NDM-1-producing isolates recovered in 2022–24 from 10 patients at Hospital Clinic Barcelona (HCB), Spain, were studied through susceptibility testing WGS. Expression resistance genes was analysed quantitative (real-time) RT–PCR. Forty genomes worldwide also incorporated phylogenetic analysis. Results All HCB assigned to except one (ST357 additionally producing VEB-9 linked epidemiologically India). The index case a 41-year-old woman admitted oncology ward February 2022 after breast cancer surgery Ukraine. These closely related blaNDM-1 gene located same 117 kb integrative conjugative element. ST773-NDM-1 producers 40 shared acquired determinants [aadA11-like, rmtB4, qnrVC1 tet(G)], as well some antibiotic mutations (mexZ, mexT, gyrA parC). Other specific such an oprD deletion only with Ukrainian transferred Madrid or Netherlands. Lastly, evolved further during dissemination, including regulators AmpC (mpl) MexAB-OprM (nalD), acquisition aztreonam/avibactam resistance, thus remaining susceptible cefiderocol colistin. Conclusions This work evidences transborder spread evolution emerging
Язык: Английский
Процитировано
0
Access Microbiology, Год журнала: 2025, Номер 7(4)
Опубликована: Апрель 1, 2025
Klebsiella quasipneumoniae are Gram-negative bacteria of the family Enterobacteriaceae , distinguished from other members genus through a chromosomally encoded extended spectrum β-lactamase, bla OKP . Here, we report hybrid assembled genome novel sequence type K. subspecies similipneumoniae isolated faecal sample patient with sepsis.
Язык: Английский
Процитировано
0
Frontiers in Bacteriology, Год журнала: 2025, Номер 4
Опубликована: Апрель 25, 2025
Under climate change scenarios for temperate regions in Europe, prolonged droughts pose a major threat to barley production, but few studies have been conducted on stress mitigation strategies using plant-beneficial rhizobacteria. With this mind, we isolated and screened culture collection of drought-tolerant bacteria from the rhizosphere. From collection, assembled 16-member consortium based their relative abundances rhizosphere after drought vitro osmotic tolerance (Drought Tolerant Synthetic microbial Community/”DT-SynCom”). Members DT-SynCom range Proteobacteria Firmicutes Actinobacteria. We used Oxford Nanopore Illumina technologies assemble complete genomes. Whole genome annotation revealed presence number genes associated with plant growth promoting traits such as IAA biosynthesis, ACC deaminase activity siderophore production. In assays confirmed auxin activity, inorganic P solubilization, cellulase chitinase activities by selected bacterial strains. The members were not antagonistic each other, either neutral or beneficial shoot root when applied individually . To clarify effect designed tolerance, pot experiment was under conditions. reduced wilting leaves had positive drought. results research suggest that result improved stress.
Язык: Английский
Процитировано
0
Microbial Genomics, Год журнала: 2024, Номер 10(9)
Опубликована: Сен. 2, 2024
While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene bla KPC-2 . The pQEB1 lineage is concerning due to its conferral multidrug resistance, host range apparent transmissibility, potential for acquiring further genes. Representatives were found in three sequence types (STs) Citrobacter freundii , two STs Enterobacter cloacae species Klebsiella Hosts isolated 11 different patients who stayed various wards throughout hospital complex over a 13 month period January 2023 February 2024. At present, only representatives GenBank carried by hormaechei blood sample QE 2016 pneumoniae urine University Hospitals Coventry Warwickshire (UHCW) May 2023. UHCW had been treated QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison complete sequences. We structural variants defined molecular events responsible them. These have included IS 26 -mediated inversions acquisitions multiple insertion sequences transposons, carriers mercury or arsenic that particular inversion variant strongly associated with Liver speciality after appearing November 2023, but specialities January/February That has so far seen five bacterial hosts six patients, consistent recent ongoing inter-host inter-patient transmission this setting.
Язык: Английский
Процитировано
3
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июнь 8, 2024
Abstract While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPEs) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes including the carbapenemase gene bla KPC-2 . The pQEB1 lineage is concerning due to its conferral multi-drug resistance, host range apparent transmissibility, potential for acquiring further genes. Representatives were found in three sequence types (STs) Citrobacter freundii , two STs Enterobacter cloacae species Klebsiella Hosts isolated 11 different patients who stayed various wards throughout hospital complex over a 13-month period January 2023 February 2024. At present, only representatives GenBank carried by hormaechei blood sample QE 2016 pneumoniae urine University Hospitals Coventry Warwickshire (UHCW) May 2023. UHCW had been treated QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison complete sequences. We structural variants defined molecular events responsible them. These have included IS 26 -mediated inversions acquisitions multiple insertion sequences transposons, carriers mercury or arsenic that particular inversion variant strongly associated with Liver speciality after appearing November 2023, but specialities January/February That has so far seen five bacterial hosts six patients, consistent recent ongoing inter-host inter-patient transmission this setting.
Язык: Английский
Процитировано
2