Genomic epidemiology and phenotypic characterisation of Salmonella enterica serovar Panama in Victoria, Australia DOI Creative Commons

Samriddhi Thakur,

Sarah L. Baines,

Cheryll M Sia

et al.

PLoS neglected tropical diseases, Journal Year: 2024, Volume and Issue: 18(11), P. e0012666 - e0012666

Published: Nov. 20, 2024

Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one several serovars that causes invasive NTS disease (iNTS) in humans. S . Panama an understudied pathogen, with its pathobiology poorly understood. It predominant iNTS Australia, high-income country high rates salmonellosis, where has been documented to have odds ratio (13.9–15.26) for causing iNTS. This study investigates the genomic epidemiology and antimicrobial resistance profiles all isolates recovered Victoria, between 2000 2021. We examined infection dynamics seven isolates, representing genetic diversity population. Two sub-lineages, encompassed within previously described Asian lineage, were identified. Multi-drug (resistance ≥3 drug classes) was detected 46 (51.7%) Australian isolates. The plasmid-mediated colistin gene, mcr1 1 , isolate, carried by IncI plasmid reported Escherichia coli collected from poultry South-East Asia. Examination intracellular replication demonstrated diverse phenotypes. In THP-1 derived macrophages, despite low host cell uptake, showed higher over time compared Typhimurium. However, genotype could not be identified explain this observed phenotype. provides insights into circulating Australia two-decades, finding 78% linked international travel suggesting importation Australia. shows MDR common serovar, first time. data on host-pathogen interactions which will aid our collective understanding more broadly.

Language: Английский

Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era DOI
Salvador Castañeda-Barba, Eva M. Top, Thibault Stalder

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(1), P. 18 - 32

Published: July 10, 2023

Language: Английский

Citations

121
Genomic surveillance for antimicrobial resistance — a One Health perspective DOI
Steven P. Djordjevic, Veronica M. Jarocki, Torsten Seemann

et al.

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(2), P. 142 - 157

Published: Sept. 25, 2023

Language: Английский

Citations

106
Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies DOI Creative Commons
George Bouras, Ghais Houtak, Ryan R. Wick

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(5)

Published: May 8, 2024

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- long-reads) assembly approaches. Complete allow a deeper understanding evolution genomic variation beyond single nucleotide variants. They also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids missed or misassembled by algorithms. Here, we present Hybracter allows fast, automatic scalable recovery near-perfect first approach. can be run either as assembler only assembler. We compared to existing automated tools diverse panel samples varying levels with manually curated ground truth reference genomes. demonstrate is more accurate faster than gold standard Unicycler. show long-reads most comparable methods accurately recovering plasmids.

Language: Английский

Citations

19
Degradation of plasmid-mediated resistance genes in poultry slaughterhouse wastewater employing a UV/H2O2 process: A metagenomic approach DOI
Beatriz Oliveira de Farias, Enrico Mendes Saggioro,

Kaylanne S. Montenegro

et al.

Chemosphere, Journal Year: 2025, Volume and Issue: 372, P. 144109 - 144109

Published: Jan. 17, 2025

Language: Английский

Citations

0
Characterization of antibiotic determinants and heavy metal resistance genes in Escherichia coli from pigs in Catalonia DOI Creative Commons

Biel Garcias,

William Monteith,

Anna Vidal

et al.

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(3)

Published: March 25, 2025

More antibiotics are administered to livestock animals than treat human infections. Industrialization, large animal densities and early weaning mean pigs exposed more any other animal. Consequently, antimicrobial resistance (AMR) is common among commensal pathogenic bacteria. Heavy metals (HMs) also often used as feed additives for growth promotion infection prevention alongside antimicrobials, increased exposure copper, zinc cadmium can further encourage AMR through co-selection. In this study, we sequenced an archived collection of 112 Escherichia coli isolates from in Catalonia using short- long-read sequencing methods detect HM tolerance genes. The most genes were mdfA (84.8%), aph(3″)-Ib (52.7%), bla TEM-1B (45.6%) aph(6)-Id (45.6%). Genes relevant public health, such the extended-spectrum β -lactamases (15.4%), CTX-M type or SHV , mobile colistin ( mcr ) (13.4%), mcr-1 found. present almost every genome but rarely located plasmids, and, cases, not on same plasmids. Of predicted increase HMs, only those with activity mercury co-located plasmids determinants. However, pig farming does support a scenario where co-selected. Finally, identified exclusive association between mcr-4 ColE10 plasmid, which may help target interventions curtail its spread .

Language: Английский

Citations

0
Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital DOI Creative Commons

Nicole L. Kavanagh,

Peter M. Kinnevey,

Gráinne I. Brennan

et al.

JAC-Antimicrobial Resistance, Journal Year: 2025, Volume and Issue: 7(3)

Published: April 17, 2025

Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse vanA-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient diversity could confound surveillance. This study investigated the intra-host genetic among colonized hospital patients. Rectal (n = 150) from 10 patients (15 isolates each) were by WGS, core-genome MLST and split k-mer (SKA)-SNP analysis. Plasmids vanA-transposons 39 representative of CTs identified resolved hybrid assembly short-read (Illumina) long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible E. (VSEfm) four VREfm-positive also investigated. All clade A1 most ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent (7/10) harboured either two 4), three 2) or 1) CTs. Individual patient isolate pairs different differed significantly (median SKA-SNPs 2933), but differences minimal between same CT 0). In total, 193 plasmids in Near-identical (≥99.5% average nucleotide identity) divergent multiple Most (28/39, 72%) vanA closely related transferable, linear plasmids. Divergent within individual indistinguishable with distinct organizational iterations. Four VSEfm similar to VREfm. within-host is highly prevalent patients, which complicates Linear play an important role emergence

Language: Английский

Citations

0
What are the missing pieces needed to stop antibiotic resistance? DOI Creative Commons
José Luis Martínez, Fernando Baquero

Microbial Biotechnology, Journal Year: 2023, Volume and Issue: 16(10), P. 1900 - 1923

Published: July 7, 2023

Abstract As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with introduction new antibiotics into market in golden age antimicrobial discovery, few are pipeline. Under these circumstances, a deep understanding on mechanisms emergence, evolution and transmission resistance, as well consequences bacterial physiology acquiring needed to implement novel strategies, beyond development or restriction use current ones, more efficiently treat infections. There still aspects field that not fully understood. In article, we make non‐exhaustive critical review some them consider special relevance, aim presenting snapshot studies need be done tackle resistance.

Language: Английский

Citations

8
Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies DOI Creative Commons
George Bouras, Ghais Houtak, Ryan R. Wick

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 13, 2023

Abstract Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- long-reads) assembly approaches. Complete allow a deeper understanding evolution genomic variation beyond single nucleotide variants (SNVs). They also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids missed or misassembled by algorithms. Here, we present Hybracter allows fast, automatic, scalable recovery near-perfect first approach. can be run either as assembler only assembler. We compared to existing automated tools diverse panel samples varying levels with manually curated ground truth reference genomes. demonstrate is more accurate faster than gold standard Unicycler. show long-reads most comparable methods accurately recovering plasmids. Data Summary developed Python Snakemake command-line software tool Linux MacOS systems. freely available under an MIT License on GitHub ( https://github.com/gbouras13/hybracter ) documentation at Read Docs https://hybracter.readthedocs.io/en/latest/ ). install via PyPI https://pypi.org/project/hybracter/ Bioconda https://anaconda.org/bioconda/hybracter A Docker/Singularity container https://quay.io/repository/gbouras13/hybracter . All code used benchmark Hybracter, including genomes, publicly https://github.com/gbouras13/hybracter_benchmarking released DOI https://zenodo.org/doi/10.5281/zenodo.10910108 Zenodo. The subsampled FASTQ files benchmarking Zenodo https://doi.org/10.5281/zenodo.10906937 super simplex ATCC reads sequenced part this study found BioProject PRJNA1042815. Hall et al. fast duplex read (prior subsampling) SRA PRJNA1087001. raw Lermaniaux PRJNA1020811. Staphylococcus aureus JKD6159 PRJNA50759. Mycobacterium tuberculosis H37R2 PRJNA836783. list BioSample accession numbers each benchmarked sample Supplementary Table 1. output Pypolca outputs https://zenodo.org/doi/10.5281/zenodo.10072192 Impact Statement genome routine vital genomics, especially identification mobile genetic elements As becomes cheaper, easier access accurate, crucial. With new widely-used both only. Additionally, it solves problems assemblers struggling plasmid from performing par methods. natively exploit parallelisation high-performance computing (HPC) clusters cloud-based environments, enabling users assemble hundreds thousands one line code. source GitHub, PyPi.

Language: Английский

Citations

7
Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020 DOI Creative Commons
Nicholas Duggett, Manal AbuOun, Emma Stubberfield

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 14

Published: Jan. 30, 2024

Introduction Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures humans and animals treat infections. In a One Health context, AMR from livestock food can transfer through chain humans, vice versa, which be characterized detail genomics. We investigated critical aspects dynamics poultry UK. Methods this study, we performed whole genome sequencing genomic characterization 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated caeca meat EU harmonized zoonotic commensal 2016 2018 UK national 2020. Results The most common ESC was blaCTX-M-1; however, 2020 had greater diversity ESCs with blaCTX-M-55 dominant chickens blaCTX-M-15 more prevalent turkeys. Co-resistance sulphonamides, tetracycline, trimethoprim widespread, there were several positive correlations between sequence types (STs) genes. identified certain genotypes STs that frequent each year but not as successful subsequent years, e.g., ST350 blaCTX-M-1, sul2, tetA-v4.Phylogenetic comparison isolates our panel global ones same available public databases showed generally clustered together, suggesting within-country than between-country transmission. Discussion conclude future surveillance indicator organisms will invaluable it enable detailed comparisons within neighboring countries, potentially identifying types, plasmids, or emerging threats.

Language: Английский

Citations

1
An eco-evolutionary perspective on antimicrobial resistance in the context of One Health. DOI Creative Commons
Misshelle Bustamante, Siyu Mei,

Inès M. Daras

et al.

iScience, Journal Year: 2024, Volume and Issue: 28(1), P. 111534 - 111534

Published: Dec. 5, 2024

Language: Английский

Citations

1