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Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E, Honkela A. Bacterial genomic epidemiology with mixed samples. Microb Genom 2021; 7:000691. [PMID: 34779765 PMCID: PMC8743562 DOI: 10.1099/mgen.0.000691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jarno Alanko
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UT The Arctic University of Norway, Tromsø, Norway
| | - Veli Mäkinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Eva Heinz
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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Presence of Antibiotic Residues and Antibiotic Resistant Bacteria in Cattle Manure Intended for Fertilization of Agricultural Fields: A One Health Perspective. Antibiotics (Basel) 2021; 10:antibiotics10040410. [PMID: 33918676 PMCID: PMC8069554 DOI: 10.3390/antibiotics10040410] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 01/19/2023] Open
Abstract
Antibiotic resistant bacteria and antibiotic residues can enter the environment when using animal manure as fertilizer. Twenty-five mixed beef cattle farmyard manure samples and 9 mixed fattening calf slurry samples from different farms across Belgium were investigated for the presence of 69 antibiotic residues, antibiotic resistant Escherichia coli and Salmonella spp. Doxycycline, oxytetracycline, ciprofloxacin, enrofloxacin, flumequine and lincomycin were detected in all fattening calf slurry samples with mean concentrations of 2776, 4078, 48, 31, 536 and 36 µg/kg manure, respectively. Sulfadiazine was detected at a mean concentration of 10,895 µg/kg. Further, antibiotic residues were found in only 4 of the 25 beef cattle farmyard manure samples. Oxytetracycline was detected twice below 500 µg/kg. Paromomycin, ciprofloxacin and enrofloxacin were detected in a concentration below 100 µg/kg. Of E. coli isolates, 88% and 23% from fattening calf slurry and beef cattle farmyard manure, respectively, were resistant to at least one of the antibiotics tested. Multi-drug resistance was observed at a maximum of 10 and 7 antibiotics, respectively. The occurrence of antibiotic resistant E. coli and antibiotic residues is shown to be higher in fattening calf slurry than in beef cattle farmyard manure used for agricultural field fertilization.
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Siqueira FM, De Carli S, Lopes CE, Machado L, Vieira TR, Pöppl ÁG, Cardoso MRI, Zaha A. Non-lactose-fermenting uropathogenic Escherichia coli from dogs: virulence profile characterization. Lett Appl Microbiol 2021; 72:596-603. [PMID: 33524173 DOI: 10.1111/lam.13454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 11/30/2022]
Abstract
Non-lactose-fermenting Escherichia coli (NLFEC) has a few descriptive studies restricted to human infections. In the present study, isolates of NLFEC obtained from urine samples of dogs with hyperadrenocorticism were characterized regarding their virulence ability, biofilm formation capacity and antimicrobial susceptibility profile. Escherichia coli lactose-fermenting strains from urinary infection in dogs with the same conditions were analysed to provide comparisons. The non-lactose-fermenting E. coli strains were classified as belonging to clade I E. coli, whereas the lactose-fermenting strains were classified in phylogroup B2. All strains presented virulence markers to adhesion, iron acquisition, toxins, colicin and cytotoxin production, and biofilm regulation. Components of the extracellular matrix in addition to the in vitro biofilm formation ability were observed in the strains. Multidrug resistance (MDR) profiles were observed by in vitro susceptibility tests to all NLFEC strains. In summary, non-lactose-fermenting uropathogenic E. coli from dogs behaves similar to lactose-fermenting E. coli, exhibiting MDR profile, and pathogenic potential of promote animal infections.
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Affiliation(s)
- F M Siqueira
- Laboratory of Veterinary Bacteriology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - S De Carli
- Laboratory of Veterinary Bacteriology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - C E Lopes
- Laboratory of Veterinary Bacteriology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - L Machado
- Veterinary Clinical Hospital, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - T R Vieira
- Laboratory of Veterinary Preventive Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Á G Pöppl
- Veterinary Clinical Hospital, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - M R I Cardoso
- Laboratory of Veterinary Preventive Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - A Zaha
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Brukner I, Oughton M. A Fundamental Change in Antibiotic Susceptibility Testing Would Better Prevent Therapeutic Failure: From Individual to Population-Based Analysis. Front Microbiol 2020; 11:1820. [PMID: 32973694 PMCID: PMC7461948 DOI: 10.3389/fmicb.2020.01820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/10/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ivan Brukner
- Department of Diagnostic Medicine, Jewish General Hospital, Montreal, QC, Canada.,Molecular and Regenerative Medicine, Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Matthew Oughton
- Department of Diagnostic Medicine, Jewish General Hospital, Montreal, QC, Canada.,Molecular and Regenerative Medicine, Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Faculty of Medicine, McGill University, Montreal, QC, Canada
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