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  1. Article: Editorial: "One Health" approach for revealing reservoirs and transmission of antimicrobial resistance, volume II.

    Daoud, Ziad / Rolain, Jean-Marc

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1170407

    Language English
    Publishing date 2023-03-06
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1170407
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Editorial: "One Health" Approach for Revealing Reservoirs and Transmission of Antimicrobial Resistance.

    Daoud, Ziad / Rolain, Jean-Marc

    Frontiers in microbiology

    2022  Volume 12, Page(s) 830211

    Language English
    Publishing date 2022-01-17
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.830211
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Mechanisms of acquisition of the vanA operon among vancomycin-resistant Staphylococcus aureus genomes: The tip of the iceberg?

    Vo, Tram / Pontarotti, Pierre / Rolain, Jean-Marc / Merhej, Vicky

    International journal of antimicrobial agents

    2024  Volume 63, Issue 6, Page(s) 107154

    Abstract: Background: Vancomycin is frequently used as a last line of defence against infections due to multidrug-resistant Staphylococcus aureus (S. aureus). A recent finding described the acquisition of vancomycin-resistant S. aureus strains by the integration ... ...

    Abstract Background: Vancomycin is frequently used as a last line of defence against infections due to multidrug-resistant Staphylococcus aureus (S. aureus). A recent finding described the acquisition of vancomycin-resistant S. aureus strains by the integration of an enterococcal plasmid containing the vanA operon into the S. aureus chromosome via homologous recombination involving a specific integration site called locus L2.
    Methods: To characterise all mechanisms of acquisition of vanA, this study analysed the 15 706 S. aureus genomes to look for vanA and described its genetic environment.
    Results: A complete vanA operon was found in 25 S. aureus strains isolated from 12 patients, including nine co-isolated with vancomycin-resistant Enterococcus strains. VanA was found within transposon Tn1546-like elements on 17 plasmids and eight chromosomes. VanA might be acquired through conjugation of enterococcal and staphylococcal plasmids, transposition of Tn1546 carrying vanA and plasmid integration into the chromosome. Further, L2 was detected in 2087 genomes (13.3%) of S. aureus strains across different continents. Six potential chromosomal hotspots for integration of the entire vanA-containing enterococcal plasmid were identified by homologous recombination via L2.
    Conclusions: These findings suggest that the recently described scenario in a New York patient could be reproduced anywhere. Surveillance of this possibility is mandatory, especially in patients with vancomycin-resistant S. aureus and vancomycin-resistant Enterococcus infection or colonisation.
    Language English
    Publishing date 2024-04-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2024.107154
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation.

    Maatouk, Mohamad / Rolain, Jean-Marc / Bittar, Fadi

    Microorganisms

    2023  Volume 11, Issue 5

    Abstract: Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent ... ...

    Abstract Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
    Language English
    Publishing date 2023-05-07
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11051231
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants.

    Khabthani, Sami / Rolain, Jean-Marc / Merhej, Vicky

    International journal of molecular sciences

    2022  Volume 23, Issue 4

    Abstract: Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including ... ...

    Abstract Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance.
    Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases.
    Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance.
    Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Humans ; Microbiota/drug effects ; Microbiota/genetics
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2022-02-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23042137
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: In Vitro Screening of a 1280 FDA-Approved Drugs Library against Multidrug-Resistant and Extensively Drug-Resistant Bacteria.

    Peyclit, Lucie / Baron, Sophie Alexandra / Hadjadj, Linda / Rolain, Jean-Marc

    Antibiotics (Basel, Switzerland)

    2022  Volume 11, Issue 3

    Abstract: Alternative strategies against multidrug-resistant (MDR) bacterial infections are suggested to clinicians, such as drug repurposing, which uses rapidly available and marketed drugs. We gathered a collection of MDR bacteria from our hospital and performed ...

    Abstract Alternative strategies against multidrug-resistant (MDR) bacterial infections are suggested to clinicians, such as drug repurposing, which uses rapidly available and marketed drugs. We gathered a collection of MDR bacteria from our hospital and performed a phenotypic high-throughput screening with a 1280 FDA-approved drug library. We used two Gram positive (Enterococcus faecium P5014 and Staphylococcus aureus P1943) and six Gram negative (Acinetobacter baumannii P1887, Klebsiella pneumoniae P9495, Pseudomonas aeruginosa P6540, Burkholderia multivorans P6539, Pandoraea nosoerga P8103, and Escherichia coli DSM105182 as the reference and control strain). The selected MDR strain panel carried resistance genes or displayed phenotypic resistance to last-line therapies such as carbapenems, vancomycin, or colistin. A total of 107 compounds from nine therapeutic classes inhibited >90% of the growth of the selected Gram negative and Gram positive bacteria at a drug concentration set at 10 µmol/L, and 7.5% were anticancer drugs. The common hit was the antiseptic chlorhexidine. The activity of niclosamide, carmofur, and auranofin was found against the selected methicillin-resistant S. aureus. Zidovudine was effective against colistin-resistant E. coli and carbapenem-resistant K. pneumoniae. Trifluridine, an antiviral, was effective against E. faecium. Deferoxamine mesylate inhibited the growth of XDR P. nosoerga. Drug repurposing by an in vitro screening of a drug library is a promising approach to identify effective drugs for specific bacteria.
    Language English
    Publishing date 2022-02-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics11030291
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Screening of Colistin-Resistant Bacteria in Domestic Pets from France.

    Hamame, Afaf / Davoust, Bernard / Rolain, Jean-Marc / Diene, Seydina M

    Animals : an open access journal from MDPI

    2022  Volume 12, Issue 5

    Abstract: Background: Pets are the closest animals to humans with a considerable risk of zoonotic transmission. This study aimed to screen colistin-resistant bacteria from stools of dogs and cats from Marseille, France. Screening of : Methods: Fecal samples (!# ...

    Abstract Background: Pets are the closest animals to humans with a considerable risk of zoonotic transmission. This study aimed to screen colistin-resistant bacteria from stools of dogs and cats from Marseille, France. Screening of
    Methods: Fecal samples (
    Results: A total of 218 bacteria were identified. For cats, intrinsically colistin-resistant bacteria were significantly higher than
    Conclusions: The current study opens a new perspective: the spread of colistin resistance is independent of colistin use. What are the most factors related to the emergence of colistin resistance? The surveillance of pets must be considered a priority to avoid the spread of
    Language English
    Publishing date 2022-03-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani12050633
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France.

    Hamame, Afaf / Davoust, Bernard / Rolain, Jean-Marc / Diene, Seydina M

    Journal of global antimicrobial resistance

    2022  Volume 28, Page(s) 174–179

    Abstract: Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted ... ...

    Abstract Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mcr genes in France. Samples collected from a pig farm in Avignon (Vaucluse department) were subjected to molecular screening targeting mcr variants.
    Methods: Samples were cultured on selective Lucie-Bardet-Jean-Marc-Rolain medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing. Whole-genome sequencing and bioinformatic genome analysis were performed.
    Results: Selective culture of stools revealed the presence of an E. coli strain named Q4552 harbouring mcr-1.1 and mcr-3.5 genes, which is also resistant to 14 antibiotics. Genome sequencing and assembly yielded a complete and circular chromosome and eight different plasmids. Sequence analysis demonstrated an integration of a mobile genetic element carrying mcr-1.1 in the chromosome, whereas mcr-3.5 was in the plasmid and its resistome was composed of 22 resistance genes. The Q4552 strain was identified as an ST-843 clone that belonged to the clonal complex Cplx-568 and is the only ST type of this cplx-568 that has been isolated from animals, humans, and the environment.
    Conclusion: We report the first co-occurrence of mcr-1 and mcr-3 genes in France from a pathogenic E. coli isolated from a pig. Because this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor the bacterium are urgently required to avoid its spread and zoonotic transmission to humans.
    MeSH term(s) Animals ; Anti-Bacterial Agents/pharmacology ; Colistin/pharmacology ; Drug Resistance, Bacterial ; Escherichia coli ; Escherichia coli Infections/microbiology ; Escherichia coli Infections/veterinary ; Escherichia coli Proteins/genetics ; Genomics ; Swine
    Chemical Substances Anti-Bacterial Agents ; Escherichia coli Proteins ; MCR-1 protein, E coli ; Colistin (Z67X93HJG1)
    Language English
    Publishing date 2022-01-24
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2710046-7
    ISSN 2213-7173 ; 2213-7173
    ISSN (online) 2213-7173
    ISSN 2213-7173
    DOI 10.1016/j.jgar.2022.01.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens.

    Khabthani, Sami / Rolain, Jean-Marc / Merhej, Vicky

    Microorganisms

    2021  Volume 9, Issue 11

    Abstract: Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high- ... ...

    Abstract Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.
    Language English
    Publishing date 2021-11-05
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9112297
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges.

    Hamel, Mouna / Rolain, Jean-Marc / Baron, Sophie Alexandra

    Microorganisms

    2021  Volume 9, Issue 2

    Abstract: Since 2015, the discovery of colistin resistance genes has been limited to the characterization of new mobile colistin resistance ( ...

    Abstract Since 2015, the discovery of colistin resistance genes has been limited to the characterization of new mobile colistin resistance (
    Language English
    Publishing date 2021-02-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9020442
    Database MEDical Literature Analysis and Retrieval System OnLINE

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