Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Дек. 12, 2022

Abstract Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids clonal expansion, yet the distribution dynamics of ESC-R in different ecological compartments poorly understood. Here we use whole genome sequence data Enterobacterales isolates animal origin from Europe North America identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant humans farm animals, only later emerging Europe. In contrast, specific extended-spectrum (ESBLs) common animals emerged America. This study identifies differences relative importance expansion across genes. Understanding mechanisms transmission will be critical design interventions to reduce resistance.

Язык: Английский

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Genomic Insights into Global bla _CTX-M-55 -Positive Escherichia coli Epidemiology and Transmission Characteristics

Microbiology Spectrum, Год журнала: 2023, Номер 11(4)

Опубликована: Июнь 26, 2023

In recent years, blaCTX-M-55-positive Escherichia coli has been widely reported in multiple locations with an increasing trend prevalence, yet few studies have comprehensively analyzed the transmission characteristics and epidemiological patterns of E. coli. Here, we constructed a global genomic data set as completely possible explored epidemiology potential impact on scale by high-resolution bioinformatics methods. The results show that spread worldwide, especially Asia, rich sequence typing (ST) diversity high proportion auxiliary genome occupancy indicating degree openness. phylogenetic tree suggests is frequently clonally transmitted between three human-animal environments often cotransmitted fosA, mcr, blaNDM, tet(X). stable presence InclI1 InclI2 different hosts from sources this part plasmid drives widespread We inductively clustered all blaCTX-M-55 flanking environmental gene structures obtained five types. Notably, "ISEcp1-blaCTX-M-55-orf477-(Tn2)" "IS26(IS15DI)-hp-hp-blaCTX-M-55-orf477-hp-blaTEM-IS26-hp-IS26-Tn2" are dominant "humans" "animals related foods," respectively. Overall, our findings highlight importance whole-genome sequencing-based surveillance exploring evolution context "One Health," they serve reminder to strengthen order address risk future large outbreaks. IMPORTANCE CTX-M-55 was first discovered Thailand 2004, today, enzyme most common CTX-M subtype animal origin China. Thus, getting growing public health problem. Although prevalence surveys remain insufficient Health" comprehensive perspective. database 2144 used methods resolve suggest rapid long-term continuous should be emphasized.

Язык: Английский

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Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features

Microbiology Spectrum, Год журнала: 2023, Номер 11(3)

Опубликована: Май 16, 2023

Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several silico methods to predict plasmid sequences assembled genomes. However, existing have evident shortcomings, such as unbalance sensitivity specificity, dependency on species-specific models, performance reduction shorter than 10 kb, which has limited their scope applicability. In this work, we proposed Plasmer, a novel predictor based machine-learning shared k-mers genomic features. Unlike k-mer or genomic-feature methods, Plasmer employs the random forest algorithm make predictions using percent with chromosome databases combined other features, alignment E value replicon distribution scores (RDS). can multiple species achieved an average area under curve (AUC) 0.996 accuracy 98.4%. Compared tests both sliding simulated de novo assemblies consistently shown that outperforming stable across long short contigs above 500 bp, demonstrating its applicability fragmented assemblies. also excellent balanced specificity (both >0.95 bp) highest F1-score, eliminated bias was common methods. provides taxonomy classification help identify origin plasmids. IMPORTANCE study, prediction tool named Plasmer. Technically, unlike features-based first combine advantages score This given (i) improvement compared best F1-score sequences, contigs, assemblies; (ii) bp accuracy, enabling short-read (iii) between commonly existed methods; (iv) no training models. We believe more reliable alternative genome

Язык: Английский

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Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

Scientific Reports, Год журнала: 2021, Номер 11(1)

Опубликована: Апрель 26, 2021

Abstract Campylobacter , a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract wide range animals.Although antimicrobial treatment is restricted to severe cases, increase resistance (AMR) concern. Considering significant contribution ruminants as reservoirs resistant Illumina whole-genome sequencing was used characterise mechanisms AMR jejuni and coli recovered from beef cattle, dairy sheep northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn ABRicate, additional sequence alignments performed search for frameshift mutations gene modifications. A high correlation observed between phenotypic given presence corresponding known genes. Detailed allowed us detect recently described mosaic tet (O/M/O) one C. describe possible new alleles bla OXA-61 -like genes, decipher context aminoglycoside well plasmid/chromosomal location different genes their implication spread. Updated databases detailed matched open reading frames are needed avoid errors when using WGS-based pipelines detection absence data.

Язык: Английский

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Multidrug resistance and virulence genes carried by mobile genomic elements in Salmonella enterica isolated from live food animals, processed, and retail meat in North Carolina, 2018–2019

International Journal of Food Microbiology, Год журнала: 2022, Номер 378, С. 109821 - 109821

Опубликована: Июнь 23, 2022

Язык: Английский

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Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 6, 2023

Abstract The analysis of microbial genomes from human archaeological samples offers a historic snapshot ancient pathogens and provides insights into the origins modern infectious diseases. Here, we analyze metagenomic datasets 38 identify bacterial genomic sequences related to modern-day Clostridium tetani , which produces tetanus neurotoxin (TeNT) causes disease tetanus. These assemblies had varying levels completeness, subset them displayed hallmarks DNA damage. Phylogenetic analyses revealed known C. clades as well potentially new lineages closely . encode 13 TeNT variants with unique substitution profiles, including subgroup found exclusively in South America. We experimentally tested variant selected an Chilean mummy sample that it induced muscle paralysis mice, potency comparable TeNT. Thus, our identifies neurotoxigenic samples, novel can cause mammals.

Язык: Английский

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Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review

Journal of Veterinary Diagnostic Investigation, Год журнала: 2024, Номер 36(3), С. 400 - 417

Опубликована: Март 8, 2024

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was synthesize knowledge on the direct application of long-read metagenomic sequencing respiratory samples detect bacterial pathogens and resistance genes (ARGs) compared PCR, loop-mediated isothermal amplification, recombinase polymerase amplification. scoping review protocol followed Joanna Briggs Institute PRISMA Scoping Review reporting guidelines. Included studies reported these methods from animals or humans ±ARGs included turnaround time (TAT) analytical sensitivity. We excluded not that were focused exclusively bioinformatics. identified 5,636 unique articles 5 databases. Two-reviewer screening 3,964, 788, 784 at 3 levels, leaving 100 (19 animal 81 human), which only 7 studied (only 1 animals). Thirty-two investigated ARGs one Reported TATs ranged minutes 2 d; steps did always include sample collection results, sensitivity varied by study. reveals a gap research for detection using sequencing. There is an opportunity harness rapid development this space multiple single run. Long-read tools show potential address urgent need into support stewardship production.

Язык: Английский

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Effects of antibiotic resistance genes on health risks of rivers in habitat of wild animals under human disturbance – based on analysis of antibiotic resistance genes and virulence factors in microbes of river sediments

Ecology and Evolution, Год журнала: 2024, Номер 14(5)

Опубликована: Май 1, 2024

Abstract Studying the ecological risk of antibiotic resistance genes (ARGs) to wild animals from human disturbance (HD) is an important aspect “One Health”. The highest level ARGs reflected in pathogenic antibiotic‐resistant bacteria (PARBs). Metagenomics was used analyze characteristics PARBs river sediments. Then, total contribution and virulence factors (VFs) were assessed determine health rivers. Results showed that HD increased diversity relative abundance ARG groups, as well kinds PARBs, their abundance, gene numbers VFs. risks habitat group (CK group), agriculture (WA grazing (WG domestic sewage (WS group) 0.067 × 10 −3 , −1.55 87.93 153.53 respectively. Grazing PARBs. However, did not increase rivers, but also introduced new mechanisms range drug resistance. More serious transfer rivers under grazing. If are transferred animals, then may face severe challenges acquiring developing antibiotics. Further analysis phosphorus (TP) dissolved organic nitrogen (DON) related ARGs. Therefore, controlling emissions TP DON could reduce

Язык: Английский

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Molecular and geochemical basis of microbially induced carbonate precipitation for treating acid mine drainage: The case of a novel Sporosarcina genomospecies from mine tailings

Journal of Hazardous Materials, Год журнала: 2024, Номер 476, С. 135005 - 135005

Опубликована: Июнь 28, 2024

Язык: Английский

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Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages

Microbial Genomics, Год журнала: 2025, Номер 11(3)

Опубликована: Март 5, 2025

Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug-resistant (MDR) methicillin-resistant (MRSP) lineages have disseminated globally in last decade present significant treatment challenges. However, little known regarding factors that contribute to success MDR lineages. In this study, we compared genome sequence 110 UK isolates S. with 2166 genomes populations from different continents. A novel core multi-locus typing scheme was generated allow large-scale, rapid detailed analysis phylogenies used show population structure broadly segregated into an a non-MDR population. MRSP are predicted encode certain resistance genes either chromosomally or on plasmids, associated their MLST type. comparison most frequently implicated disease, ST-45 ST-71, phylogenetically related ST-496 lineage has comparatively low disease rate, revealed ST-71 distinct combinations phage-defence systems concurrently high number intact prophages. contrast, wider array phage defence lack complete These findings indicate structural genomic differences prophage integration differential antiviral correlate emergence successful genotypes.

Язык: Английский

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