Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage DOI Creative Commons
Daniel Ekhlas, Juan M. Ortiz Sanjuán, Edgar García Manzanilla

et al.

Gut Pathogens, Journal Year: 2023, Volume and Issue: 15(1)

Published: Feb. 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.

Language: Английский

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus DOI
Landon J. Getz,

Sam R Fairburn,

Yundan Liu

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Language: Английский

Citations

1
Double carbapenemases in Klebsiella pneumoniae blood isolates: dissemination in a single medical center via multiple plasmids and a variety of highly efficient clones DOI Creative Commons

Anastasia Rigatou,

Ayorinde O. Afolayan, Elizabeth‐Barbara Tatsi

et al.

Antimicrobial Agents and Chemotherapy, Journal Year: 2025, Volume and Issue: 69(3)

Published: Feb. 3, 2025

Acquisition of multiple carbapenemase genes by Klebsiella pneumoniae (Kp) is an emerging public health threat. Here, we aim to elucidate the population structure Kp blood isolates carrying two different and identify mechanism facilitating their dissemination. The study was conducted in a tertiary healthcare center between 2014 2022. Twenty-four patients with bacteremia caused were identified. All 24 analyzed short-read genome sequences supplemented long reads selected number isolates. carried blaKPC (23 blaKPC-2, 1 blaKPC-3) blaVIM-1 genes, along variety antimicrobial resistance determinants. clustered six clonal lineages (ST39, ST147, ST323, ST258, ST3035, ST340). Long-read demonstrated that each gene located separate group plasmids: blaKPC-2 on fusion IncFIB(pQil) IncFII(K) plasmids, blaKPC-3 IncX3, IncC, or IncFIB(pNDM-Mar) IncHI1B(pNDM-MAR) plasmids. Comparison plasmid content eight single from previous present study, matched lineages, revealed second acquired addition another plasmid. Identical plasmids found within same lineage across lineages. These findings suggest dissemination our hospital setting driven highly efficient clones.

Language: Английский

Citations

1
Interactions and evolutionary relationships among bacterial mobile genetic elements DOI
Andrew S. Lang, Alison Buchan, Vincent Burrus

et al.

Nature Reviews Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Language: Английский

Citations

1
Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes DOI Creative Commons
Qin Qi, Vaheesan Rajabal, Timothy M. Ghaly

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Jan. 19, 2023

Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with and have plastic genomes extensive mosaicism. In this study, we present bioinformatic experimental evidence temperate virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites cassettes. Integrons normally found Bacteria, where they capture, express re-arrange cassettes via activity. We demonstrate experimentally a panel attC carried phage can be recognized by class 1 (IntI1) then integrated into paradigmatic attI1 site using an x attI assay. With increasing number projected to become available, more phage-associated integrons components will likely identified future. The discovery integron bacteriophages establishes new route for lateral transfer these cargo genes between host cells.

Language: Английский

Citations

21
Investigating the antibiotic resistance genes and their potential risks in the megacity water environment: A case study of Shenzhen Bay Basin, China DOI

Hebin Liang,

Jin Huang,

Tao Yi

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 465, P. 133536 - 133536

Published: Jan. 16, 2024

Language: Английский

Citations

8
In-depth analysis of Klebsiella aerogenes resistome, virulome and plasmidome worldwide DOI Creative Commons
Sérgio Morgado, Érica Fonseca, Fernanda Freitas

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 19, 2024

Abstract Klebsiella aerogenes is an emergent pathogen associated with outbreaks of carbapenem-resistant strains. To date, studies focusing on K. have been small-scale and/or geographically restricted. Here, we analyzed the epidemiology, resistome, virulome, and plasmidome this species based 561 genomes, spanning all continents. Furthermore, sequenced four new strains from Brazil (mostly Amazon region). Dozens STs occur worldwide, but pandemic clones ST93 ST4 prevailed in several countries. Almost genomes were clinical, however, most them did not carry ESBL or carbapenemases, instead, they carried chromosomal alterations ( omp 36, amp D, G, R) resistance to β-lactams. Integrons also identified, presenting gene cassettes yet reported bla IMP, VIM, GES). Considering virulence loci, yersiniabactin colibactin operons found ICEKp10 element, which disseminated STs, as well incomplete salmochelin cluster. In contrast, aerobactin hypervirulence trait was observed only one ST432 genome. Plasmids common, mainly ColRNAI replicon, some carrying genes mcr , TEM, NDM, KPC, VIM) (EAST1, sen B). Interestingly, 172 different presented putative plasmids containing colicin gene.

Language: Английский

Citations

8
Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk DOI Creative Commons
Pavel A. Andriyanov, Daria D. Kashina, Alena N. Menshikova

et al.

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

Published: Jan. 4, 2024

is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged opportunistic human pathogen. To date, the source of

Language: Английский

Citations

7
Flexible genomic island conservation across freshwater and marine Methylophilaceae DOI Creative Commons
Paul Layoun, Mario López‐Pérez, Jose M. Haro‐Moreno

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to and marine pelagial that resulted in genome reduction (genome-streamlining) the pelagic taxa. However, extent genetic similarities genomic structure microdiversity two genome-streamlined lineages (freshwater “Ca. Methylopumilus” OM43 lineage) has so far never been compared. Here, we analyzed complete genomes 91 strains isolated 14 lakes Central Europe 12 coastal strains. showed a remarkable niche differentiation with clear species-specific differences preference seasonal distribution. On other hand, observed synteny preservation their by having similar locations types flexible islands (fGIs). Three main fGIs were identified: replacement fGI acting as phage defense, an additive harboring metabolic resistance-related functions, tycheposon containing nitrogen-, thiamine-, heme-related functions. differed relative abundances metagenomic datasets suggesting different levels variability ranging strain-specific population-level adaptations. Moreover, variations one gene seemed be responsible for growth at low substrate concentrations potential biogeographic separation within species. Our study provides first insight into closely related taxa family revealed remarkably dynamics involving mobile elements recombination between members.

Language: Английский

Citations

7
Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems DOI Creative Commons
Egill Richard, Baptiste Darracq, Eloi Littner

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(2)

Published: Jan. 12, 2024

Integrons are adaptive bacterial devices that rearrange promoter-less gene cassettes into variable ordered arrays under stress conditions, thereby sampling combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat genome integrity. How this activity is regulated controlled, particularly through selective pressures, maintain such large cassette unknown. Here, we show key role promoter-containing toxin-antitoxin (TA) as systems kill the cell when overall rate too high. These results highlight importance TA regulating dynamics provide insight evolution success in genomes.

Language: Английский

Citations

7
Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids DOI Creative Commons
Roxana Zamudio,

Patrick Boerlin,

Michael R. Mulvey

et al.

EBioMedicine, Journal Year: 2024, Volume and Issue: 103, P. 105097 - 105097

Published: April 11, 2024

Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans animals to treat infections due multidrug-resistant (MDR) bacteria. Resistance ESCs (ESC-R) Enterobacterales is predominantly the production of extended-spectrum β-lactamases (ESBLs) plasmid-mediated AmpC (AmpCs). The dynamics ESBLs AmpCs changing across countries host species, result global transmission ESC-R genes. Plasmids known play a key role this dissemination, but relative importance different types plasmids not fully understood. In study, Escherichia coli with major genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 blaCMY-2 (AmpC), were selected from diverse species other sources Canada, France Germany, collected between 2003 2017. To examine detail vehicles genes, long- short-read sequences generated obtain complete contiguous chromosome plasmid (n = 192 E. coli). types, gene composition genetic relatedness these investigated, along association isolate year, source geographical origin, put context publicly available sequences. We identified five epidemic resistance subtypes distinct properties that associated dissemination multiple lineages species. IncI1 pST3 blaCTX-M-1 subtype was found more than main subtypes, whereas pST12 frequent Canadian German human chicken isolates. Clonal expansion also contributed ST131 ST117 harbouring plasmid. pST2 predominant isolates France, while IncF F31:A4:B1 blaCTX-M-15 F2:A-:B- cattle countries. Beyond their nature respect our collection almost all carried antimicrobial (AMR) conferring classes. Finally, we signatures regions surrounding specific identifying mechanisms movement, using databases, widespread bacterial continents. provide evidence contribute addition, some confer success suggests they may have fitness advantage over subtypes. Identification understanding AMR crucial develop target strategies interventions reduce spread AMR. This project supported by Joint Programming Initiative on Antimicrobial (JPIAMR), through Medical Research Council (MRC, MR/R000948/1), Institutes Health (CFC-150770), Genomics Development (Government Canada), Federal Ministry Education (BMBF) grant no. 01KI1709, French Agency for food environmental occupational health & safety (Anses), National Reference Center (CNR) resistance. Support provided Biotechnology Biological Sciences (BBSRC) BBSRC Institute Strategic Programme Microbes Food ChainBB/R012504/1 its constituent BBS/E/F/000PR10348 (Theme 1, Epidemiology Evolution Pathogens Chain).

Language: Английский

Citations

7