Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Июль 8, 2024

Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed correct these errors, but it is uncertain if they obtain accuracy needed for high-resolution source tracking foodborne illness outbreaks.

Язык: Английский

---

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Nucleic Acids Research, Год журнала: 2021, Номер 50(3), С. e17 - e17

Опубликована: Окт. 25, 2021

Abstract Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many genomes have been sequenced short read sequencers resulted mix contigs derive from plasmids or chromosomes. New tools accurately identify needed to elucidate new plasmid-borne genes high biological importance. We developed Deeplasmid, deep learning tool for distinguishing bacterial chromosomes based on the DNA sequence its encoded data. It requires input only assembled sequences generated any sequencing platform assembly algorithm runtime scales linearly with number sequences. Deeplasmid achieves an AUC–ROC over 89%, it was more accurate than five other plasmid classification methods. Finally, proof concept, we used predict fish pathogen Yersinia ruckeri ATCC 29473 has no annotated plasmids. predicted reliability long contig is part plasmid. Using indeed validated existence 102 kb plasmid, demonstrating Deeplasmid's ability detect novel

Язык: Английский

---

Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage

Gut Pathogens, Год журнала: 2023, Номер 15(1)

Опубликована: Фев. 24, 2023

The prophylactic use of antimicrobials and zinc oxide (ZnO) in pig production was prohibited by the European Union 2022 due to potential associations between antimicrobial heavy metal usage with resistance (AMR) concerns regarding environmental pollution. However, effects their on bacterial AMR profiles commercial farms are still not fully understood previous studies examining effect ZnO have reported contrasting findings. objective this study examine farms. Faecal samples were taken 10 Irish farms, which 5 regularly used (amoxicillin or sulphadiazine-trimethoprim) for prevention disease. other did any form prophylaxis. Escherichia coli numbers quantified from all using non-supplemented supplemented Tryptone Bile X-glucuronide agar.In total 351 isolates phenotypically analysed, genomes 44 AmpC/ESBL-producing E. 4 characterised whole-genome sequencing. Phenotypic analysis suggested higher multi-drug resistant (MDR) Furthermore, prophylaxis associated apramycin, trimethoprim, tetracycline, streptomycin, chloramphenicol, while ciprofloxacin more Thirty-four strains harboured blaCTX-M-1 gene multi drug (MDR). Moreover, network plasmids integrons showed that biocide genes frequently co-located mobile genetic elements, indicating possibility co-selection during as a contributor occurrence persistence farms.The results evidence treatment pigs post-weaning can favour selection development MDR coli. Co-location elements observed. This demonstrated usefulness phenotypic genotypic detection combining sequencing microbiological methods.

Язык: Английский

---

Insights into the ecology of the infant gut plasmidome

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

Опубликована: Авг. 13, 2024

Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow understand impact plasmids on microbiome. We create phylogenetic tree, devise method for assigning hosts, and examine potential transfer networks. Our research discovers wide variety previously unidentified sequences, indicating current databases do not fully represent plasmidome. Interestingly, infants display greater diversity compared mothers other healthy adults. find Bacteroidota, major bacterial phylum, serves as primary host plays dominant in events. Additionally, broaden genetic capabilities bacteria, with influence function becoming more apparent children's develop. This study sheds light infant microbiome, making significant contribution our understanding biology. Here, authors characterize plasmidome cohort mother-infant dyads showing exhibit adults, Bacteroidota representing transfer.

Язык: Английский

---

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Journal of Hazardous Materials, Год журнала: 2021, Номер 418, С. 126384 - 126384

Опубликована: Июнь 10, 2021

Язык: Английский

---