Pathogenomic analysis and characterization of Pasteurella multocida strains recovered from human infections DOI Creative Commons
Thomas R. Smallman, Laura Perlaza-Jiménez,

Xiaochu Wang

и другие.

Microbiology Spectrum, Год журнала: 2024, Номер 12(4)

Опубликована: Март 1, 2024

ABSTRACT Pasteurella multocida is an upper respiratory tract commensal in several mammal and bird species but can also cause severe disease humans production animals such as poultry, cattle, pigs. In this study, we performed whole-genome sequencing of P. isolates recovered from a range human infections, the mouths cats, wounds on dogs. Together with publicly available genome sequences, phylogenetic comparative genomic analyses. While cats dogs were spread across tree, infections caused almost exclusively by subsp. septica strains. Most capsule type A LPS L1 L3; however, some strains lacked biosynthesis locus, contained novel outer-core distinct eight loci that currently be identified using multiplex PCR. addition, isolated mobile genetic elements. We compiled curated database known virulence factor antibiotic resistance genes (PastyVRDB) allowing for detailed characterization isolates. The majority encoded reduced iron receptors only one filamentous hemagglutinin gene. Finally, gene-trait analysis putative L-fucose uptake utilization pathway was over-represented may represent host predilection mechanism subspecies. Together, these analyses have pathogenic mechanisms likely important zoonotic infections. IMPORTANCE serious humans, including skin wound pneumonia, peritonitis, meningitis, bacteraemia. Cats are vectors pasteurellosis, transmitting via bite or contact animal saliva. underpin pathogenesis poorly understood. With increasing identification antibiotic-resistant strains, understanding vital developing treatments control strategies to combat infection. Here, show narrow while dogs, common harbor wide present -specific database, quick newly sequenced

Язык: Английский

Dnaapler: A tool to reorient circular microbial genomes DOI Creative Commons
George Bouras, Susanna R. Grigson, Bhavya Papudeshi

и другие.

The Journal of Open Source Software, Год журнала: 2024, Номер 9(93), С. 5968 - 5968

Опубликована: Янв. 11, 2024

Microorganisms found in natural environments are fundamental components of ecosystems and play vital roles various ecological processes.Studying their genomes can provide valuable insights into the diversity, functionality, evolution microbial life, as well impacts on human health.Once genetic material is extracted from environmental samples, it undergoes sequencing using technologies like whole genome (WGS).The raw sequence data then analysed, computational methods applied to assemble fragmented sequences reconstruct complete (Wick et al.,

Язык: Английский

Процитировано

35
Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication DOI Creative Commons
Enea Maffei,

Anne-Kathrin Woischnig,

Marco Burkolter

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 2, 2024

Abstract Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly a slow- or non-growing, dormant state. Here, we show diverse phages can infect deep-dormant bacteria and suspend replication until the host resuscitates (“hibernation”). newly isolated Pseudomonas aeruginosa phage, named Paride, directly replicate induce lysis While non-growing notoriously tolerant to antibiotic drugs, combination with Paride enables carbapenem meropenem eradicate vitro reduce resilient infection tissue cage implant mice. Our work might inspire new treatments for persistent infections and, more broadly, highlights two strategies (hibernation direct replication) will guide future studies on phage-host interactions.

Язык: Английский

Процитировано

32
Phage therapy DOI
Mikael Skurnik,

Sivan Alkalay‐Oren,

Maarten Boon

и другие.

Nature Reviews Methods Primers, Год журнала: 2025, Номер 5(1)

Опубликована: Фев. 13, 2025

Процитировано

3
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data DOI Creative Commons
Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew Millard

и другие.

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Апрель 21, 2023

Abstract Background The prediction of bacteriophage sequences in metagenomic datasets has become a topic considerable interest, leading to the development many novel bioinformatic tools. A comparative analysis ten state-of-the-art phage identification tools was performed inform their usage microbiome research. Methods Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, previously sequenced mock community containing four species, were used evaluate precision, recall, F1 scores We also dataset randomly shuffled quantify false-positive calls. In addition, set simulated viromes assess diversity bias each tool’s output. Results VIBRANT VirSorter2 achieved highest (0.93) artificial dataset, with several other performing well. Kraken2 had score (0.86) benchmark by large margin (0.3 higher than DeepVirFinder second place), mainly due its high precision (0.96). Generally, k-mer-based better reference similarity gene-based methods. Several tools, most notably PPR-Meta, called number false positives sequences. When analysing that tool predicted virome set, produced viral genome similar alpha- beta-diversity patterns original population, Seeker being notable exception. Conclusions This study provides key metrics performance detection offers framework for further comparison additional discovery discusses optimal strategies using these highlight choice phages datasets, as well parameters, can results provide pointers different use case scenarios. have made our benchmarking available download order facilitate future comparisons

Язык: Английский

Процитировано

34
Neutralizing antibodies after nebulized phage therapy in cystic fibrosis patients DOI Creative Commons
Mireia Bernabéu-Gimeno,

Marco Pardo-Freire,

Benjamin K. Chan

и другие.

Med, Год журнала: 2024, Номер 5(9), С. 1096 - 1111.e6

Опубликована: Июнь 24, 2024

Язык: Английский

Процитировано

14
Retron-Eco1 assembles NAD+-hydrolyzing filaments that provide immunity against bacteriophages DOI
Arturo Carabias, Sarah Camara-Wilpert, Mario Rodríguez Mestre

и другие.

Molecular Cell, Год журнала: 2024, Номер 84(11), С. 2185 - 2202.e12

Опубликована: Май 23, 2024

Язык: Английский

Процитировано

13
A long-context language model for deciphering and generating bacteriophage genomes DOI Creative Commons
Bin Shao, Jiawei Yan

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Окт. 30, 2024

Inspired by the success of large language models (LLMs), we develop a long-context generative model for genomes. Our multiscale transformer model, megaDNA, is pre-trained on unannotated bacteriophage genomes with nucleotide-level tokenization. We demonstrate foundational capabilities our including prediction essential genes, genetic variant effects, regulatory element activity and taxonomy sequences. Furthermore, it generates de novo sequences up to 96 K base pairs, which contain potential elements annotated proteins phage-related functions.

Язык: Английский

Процитировано

10
A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo DOI Creative Commons

Huanchang Chen,

Haifeng Liu, Yanchun Gong

и другие.

npj Biofilms and Microbiomes, Год журнала: 2024, Номер 10(1)

Опубликована: Ноя. 14, 2024

Bacteriophages (phages), viruses capable of infecting and lysing bacteria, are a promising alternative for treating infections from hypervirulent, antibiotic-resistant pathogens like Klebsiella pneumoniae, though narrow host range phage resistance remain challenges. In this study, the hypervirulent K. pneumoniae NTUH-K2044 was used to purify ΦK2044, while two ΦK2044-resistant strains were further phages: ΦKR1, ΦKR8 hospital sewage. A detailed characterization showed that ΦK2044 specifically killed KL1 capsule-type ΦKR1 targeted 13 different capsular serotypes. The cocktail (ΦK2044 + ΦKR8) effectively in biofilms, pre-treatment biofilm formation, delayed phage-resistance. improved 7-day survival Galleria mellonella mouse models therapeutic potential catheter model. summary, proof-of-principle has broad range, including highly drug-resistant serves as starting point optimizing therapy.

Язык: Английский

Процитировано

10
Exploration of the feasibility of clinical application of phage treatment for multidrug-resistant Serratia marcescens -induced pulmonary infection DOI Creative Commons
Xiangke Duan, Wenfeng Liu,

Yanyu Xiao

и другие.

Emerging Microbes & Infections, Год журнала: 2025, Номер 14(1)

Опубликована: Янв. 7, 2025

Serratia marcescens (S. marcescens) commonly induces refractory infection due to its multidrug-resistant nature. To date, there have been no reports on the application of phage treatment for S. infection. This study was conducted explore feasibility in treating by collaborating with a 59-year-old male patient pulmonary marcescens. Our experiments included three domains: i) selection appropriate phage, ii) verification efficacy and safety selected iii) confirmation phage-bacteria interactions. results showed that Spe5P4 is Treatment good efficacy, manifested as amelioration symptoms, hydrothorax examinations, chest computed tomography findings. Phage did not worsen hepatic renal function, immunity-related indices, or indices routine blood examination. It induce deteriorate drug resistance involved antibiotics. Importantly, adverse events were reported during follow-up periods. Thus, satisfactory safety. Finally, we found increase bacterial load, cytotoxicity, virulence, marcescens, indicating interactions between which are useful future against work provides evidence working basis further infections. We also provided methodological investigating clinical infections future.

Язык: Английский

Процитировано

2
“Sichuanvirus”, a novel bacteriophage viral genus, able to lyse carbapenem-resistant Klebsiella pneumoniae DOI Creative Commons
Juan Li, Qingqing Fang,

Huan Luo

и другие.

BMC Microbiology, Год журнала: 2025, Номер 25(1)

Опубликована: Янв. 13, 2025

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a severe threat for human health and urgently needs new therapeutic approaches. Lytic bacteriophages (phages) are promising clinically viable options against CRKP. We attempted to isolate lytic phages CRKP of sequence type 11 capsular 64 (ST11-KL64), the predominant in China. recovered phage from sewage collected at wastewater treatment station Sichuan province, obtained genome this found that it distinct all known with highest overall DNA similarity (12.5%, 16% coverage 78.4% identity) vB_EcoM_PHB05 (accession no. NC_052652) ICTV. This represents novel viral genus subfamily Stephanstirmvirinae, which we proposed "Sichuanvirus" as name. has narrow host range lyse specific KL64 Klebsiella. no genes referring antimicrobial resistance, virulence, lysogen stable wide pH temperatures. also three bacterial mutants resistant performed sequencing them. therefore discovered interruption polysaccharide biosynthesis-related gene wcaJ by insertion sequences mediated resistance phage. characterized "Sichuanvirus", suitable therapy. The discovery expands arsenal

Язык: Английский

Процитировано

2