Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

Article Infectious Diseases

Emergence of Cfr-Mediated Linezolid Resistance among Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) from Healthy Pigs in Portugal

Celia Leao et al.

Summary: This study characterized MRSA isolates from pig nasal swabs, revealing high rates of multi-drug resistance and genetic diversity.

ANTIBIOTICS-BASEL (2022)

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Article Food Science & Technology

Technical specifications for a baseline survey on the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in pigs

Marc Aerts et al.

Summary: The European Commission requested assistance in preparing a survey protocol on the prevalence of MRSA in pigs for a coordinated monitoring program. The objective is to estimate the MRSA prevalence in batches of fattening pigs at slaughter at both European and national levels.

EFSA JOURNAL (2022)

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Article Infectious Diseases

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Markus H. K. Johansson et al.

Summary: The study reveals that antimicrobial resistance in clinically relevant bacteria is a global public health threat. The MobileElementFinder tool enables rapid detection of MGEs and their genetic context, providing insights into bacterial spread and genetic variability potential.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2021)

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Article Biotechnology & Applied Microbiology

Linezolid-resistant MRSA-CC398 carrying the cfr gene, and MRSA-CC9 isolates from pigs with signs of infection in Spain

L. Ruiz-Ripa et al.

Summary: This study characterized 23 Staphylococcus aureus isolates from pigs with signs of infections in Spanish farms during 2018-2019. Two major livestock-associated genetic lineages were detected, with the presence of multidrug-resistant cfr gene among LA-MRSA-CC398 being a major concern. Continuous surveillance and awareness for LA-MRSA are necessary.

JOURNAL OF APPLIED MICROBIOLOGY (2021)

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Article Infectious Diseases

Livestock-Associated Methicillin-Resistant Staphylococcus aureus and Related Risk Factors in Holdings of Veal Calves in Northwest Italy

Simona Zoppi et al.

Summary: This study investigated the prevalence and characteristics of LA-MRSA in veal calf production in Italy, finding that about 30% of herds tested positive for MRSA with different clonal complexes and SCCmec types identified. Risk factors such as poor cleaning, importation from Austria, and animal age were identified, while the colonization of coagulase-negative staphylococci was predictive for MRSA occurrence. The ability of LA-MRSA clones to spread among different animal production systems in Italy was highlighted.

MICROBIAL DRUG RESISTANCE (2021)

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Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

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Article Microbiology

Carbapenemase IncF-borne blaNDM-5 gene in the E. coli ST167 high-risk clone from canine clinical infection, Italy

Patricia Alba et al.

Summary: The blaNDM-5-producing E. coli ST167 high-risk clone is emerging globally in human clinical cases, but has only been sporadically found in companion animals and has not been described in Italy. The sequence analysis revealed that the plasmid pMOL008 carrying blaNDM-5 is nearly identical to those found in human clinical cases in Italy and in colonized humans and a dog in Switzerland. The presence of carbapenem-resistance genes in the plasmid poses a public health threat and underscores the importance of the One Health approach for antimicrobial resistance surveillance.

VETERINARY MICROBIOLOGY (2021)

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Review Microbiology

Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria

Stefan Schwarz et al.

Summary: Mobile oxazolidinone resistance genes such as cfr, optrA, and poxtA are found on various platforms and may overlap with other resistance genes, contributing to the dissemination of resistance among microbial populations.

CLINICAL MICROBIOLOGY REVIEWS (2021)

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Letter Infectious Diseases

Detection of a chromosomal truncated cfr gene in a linezolid-susceptible LA-MRSA ST398 isolate of porcine origin, Italy

Simona Fioriti et al.

JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE (2021)

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Article Infectious Diseases

ResFinder 4.0 for predictions of phenotypes from genotypes

Valeria Bortolaia et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2020)

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Article Infectious Diseases

Novel IncFII plasmid harbouring blaNDM-4 in a carbapenem-resistant Escherichia coli of pig origin, Italy

Elena L. Diaconu et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2020)

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Article Infectious Diseases

Emergence of cfr-Mediated Linezolid Resistance in Staphylococcus aureus Isolated from Pig Carcasses

Hee Young Kang et al.

ANTIBIOTICS-BASEL (2020)

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Article Food Science & Technology

Molecular epidemiology of methicillin-resistant Staphylococcus aureus from dairy farms in North-eastern Italy

Paola Tomao et al.

INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY (2020)

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Article Microbiology

Characterization of the Multi-Drug Resistance Gene cfr in Methicillin-Resistant Staphylococcus aureus (MRSA) Strains Isolated From Animals and Humans in China

Shu-Min Li et al.

FRONTIERS IN MICROBIOLOGY (2018)

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Article Infectious Diseases

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

Ea Zankari et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2017)

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Article Biochemical Research Methods

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

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Article Biotechnology & Applied Microbiology

A Livestock-Associated, Multidrug-Resistant, Methicillin-Resistant Staphylococcus aureus Clonal Complex 97 Lineage Spreading in Dairy Cattle and Pigs in Italy

Fabiola Feltrin et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

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Letter Infectious Diseases

Linezolid-resistant cfr-positive MRSA, Italy

Alberto Antonelli et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2016)

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Article Microbiology

Antimicrobial Resistance, Biofilm Formation and mecA Characterization of Methicillin-Susceptible S. aureus and Non-S. aureus of Beef Meat Origin in Egypt

Kamelia M. Osman et al.

FRONTIERS IN MICROBIOLOGY (2016)

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Article Microbiology

Antimicrobial resistance and population structure of Staphylococcus aureus recovered from pigs farms

Laura E. J. Peeters et al.

VETERINARY MICROBIOLOGY (2015)

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Letter Infectious Diseases

MSSA ST398/t034 carrying a plasmid-mediated Cfr and Erm(B) in Brazil

Ana C. Gales et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2015)

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Article Multidisciplinary Sciences

Livestock-Associated Methicillin Resistant and Methicillin Susceptible Staphylococcus aureus Sequence Type (CC)1 in European Farmed Animals: High Genetic Relatedness of Isolates from Italian Cattle Herds and Humans

Patricia Alba et al.

PLOS ONE (2015)

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Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

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Article Microbiology

Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus

Mette Damkjaer Bartels et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2014)

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Article Microbiology

Dissemination of a pSCFS3-Like cfr-Carrying Plasmid in Staphylococcus aureus and Staphylococcus epidermidis Clinical Isolates Recovered from Hospitals in Ohio

Rodrigo E. Mendes et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)

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Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

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Review Infectious Diseases

The emerging problem of linezolid-resistant Staphylococcus

Bing Gu et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2013)

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Review Infectious Diseases

Presence and dissemination of the multiresistance gene cfr in Gram-positive and Gram-negative bacteria

Jianzhong Shen et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2013)

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Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

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Letter Biotechnology & Applied Microbiology

Integrative genomics viewer

James T. Robinson et al.

NATURE BIOTECHNOLOGY (2011)

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Article Multidisciplinary Sciences

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Aaron E. Darling et al.

PLOS ONE (2010)

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Article Microbiology

Heterogeneity among methicillin-resistant Staphylococcus aureus from Italian pig finishing holdings

A. Battisti et al.

VETERINARY MICROBIOLOGY (2010)

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Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

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Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

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Article Food Science & Technology

Analysis of the baseline survey on the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in holdings with breeding pigs, in the EU, 2008 Part A: MRSA prevalence estimates

[Anonymous]

EFSA JOURNAL (2009)

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Review Biotechnology & Applied Microbiology

The potential and challenges of nanopore sequencing

Daniel Branton et al.

NATURE BIOTECHNOLOGY (2008)

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Article Microbiology

IS21-558 insertion sequences are involved in the mobility of the multiresistance gene cfr

Corinna Kehrenberg et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2007)

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Article Microbiology

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

Johan Goris et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2007)

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Article Microbiology

Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: Rapid identification system for mec, ccr, and major differences in junkyard regions

Yoko Kondo et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2007)

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Article Microbiology

The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptograrnin A antibiotics

Katherine S. Long et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2006)

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Article Microbiology

Distribution of florfenicol resistance genes fexA and cfr among chloramphenicol-resistant Staphylococcus isolates

C Kehrenberg et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2006)

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Article Infectious Diseases

Nucleotide sequence and organization of the multiresistance plasmid pSCFS1 from Staphylococcus sciuri

C Kehrenberg et al.

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2004)

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Article Microbiology

Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus

MC Enright et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2000)

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Article Microbiology

Identification of a plasmid-borne chloramphenicol-florfenicol resistance gene in Staphylococcus sciuri

S Schwarz et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2000)

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Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

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