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Whole Genome and Plasmid Sequencing for MDR Enterobacteriaceae Simultaneously Isolated from Multiple Human and Non-Human Settings: Deciphering Impact, Risks, and Dynamics for Resistance Transmission and Spread

English title Whole Genome and Plasmid Sequencing for MDR Enterobacteriaceae Simultaneously Isolated from Multiple Human and Non-Human Settings: Deciphering Impact, Risks, and Dynamics for Resistance Transmission and Spread
Applicant Endimiani Andrea
Number 177378
Funding scheme NRP 72 Antimicrobial Resistance
Research institution Institut für Infektionskrankheiten Universität Bern
Institution of higher education University of Berne - BE
Main discipline Infectious Diseases
Start/End 01.03.2018 - 30.04.2021
Approved amount 350'000.00
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All Disciplines (6)

Discipline
Infectious Diseases
Health Education
Methods of Epidemiology and Preventive Medicine
Molecular Biology
Medical Microbiology
Public Health and Health Services

Keywords (22)

ESBL; MDR; Meat; Carbapenemases; Whole genome sequencing, WGS; Whole plasmid sequencing, WPS; Environment; Food chain; MinION; Illumina; Risk factors; Colsitin; Pets; Enterobacteriaceae; Escherichia coli; Plasmids; Animals; Antibiotic resistance; Transmission; CTX-M; mcr-1; Nanopore

Lay Summary (Italian)

Lead
La prevalenza dei batteri resistenti agli antibiotici ha raggiunto livelli drammatici. In questo studio, analizzeremo una grossa collezione di batteri antibiotico-resistenti responsabili di infezione o colonizzazione intestinale (in umani e animali), o contaminazione (nella catena alimentare e ambiente). Questo approccio rivelerà le sorgenti dei geni di antibiotico resistenza e i loro meccanismi di trasmissione fra i vari ambienti umani e non umani. Questi dati saranno essenziali per studiare le epidemie e la diffusione dei “super batteri”. Inoltre, tali informazioni ci permetteranno di prevenire la propagazione di questi patogeni batterici in ospedali, comunità, catena alimentare, animali e ambiente.
Lay summary

La prevalenza dei batteri resistenti agli antibiotici ed inclusi nella famiglia delle Enterobacteriaceae ha raggiunto livelli drammatici, rendendo il trattamento delle infezioni molto difficoltoso. Inoltre, i viaggiatori e i pazienti ospedalizzati in altri paesi possono rimanere colonizzati a livello intestinale con questi “super batteri”. Gli ambienti non umani possono contribuire all’espansione e diffusione di questi organismi patogeni. Quindi, piccoli e limitati studi non sono in grado di identificare le sorgenti dei nuovi geni di resistenza e non riescono a definire le dinamiche di trasmissione dei “super batteri” fra i diversi ambienti umani e non umani. Oltre a ciò, solo pochissime nazioni stanno implementando le moderne tecniche di sequenziamento del genoma batterico e nessuna ha in programma di farlo in ceppi simultaneamente isolati da diverse sorgenti e associati con dati clinico-epidemiologici.

Per colmare tali gaps, analizzeremo una grossa collezione di batteri antibiotico-resistenti responsabili di infezione o colonizzazione intestinale (in umani e animali), o contaminazione (nella catena alimentare e ambiente).

Col nostro approccio multi-ambientale riveleremo le sorgenti dei nuovi geni di antibiotico resistenza e i loro meccanismi di trasmissione (clonale o plasmidico) fra i vari ambienti umani e non umani. Questi dati saranno essenziali per studiare le epidemie e la diffusione dei “super batteri”. Inoltre, tali informazioni ci permetteranno di prevenire la propagazione di questi patogeni batterici in ospedali, comunità, catena alimentare, animali e ambiente.  

Direct link to Lay Summary Last update: 17.01.2018

Lay Summary (English)

Lead
The prevalence of antibiotic-resistant bacteria has reached dramatic levels. We will investigate a large collection of resistant bacteria causing infection and intestinal colonization (humans, animals), or contamination (food chain, environment). This approach will reveal the sources of novel antibiotic resistance genes and their pathways of transmission among different settings. This will be essential for rapid outbreak investigations and for tracking national and global spread of clinically important “superbugs”. Different stakeholders will be able to take appropriate measures to prevent the spread of such “superbugs” in human/veterinary hospitals, community, food chain, companion/food animals, and in the environment.
Lay summary

The prevalence of antibiotic-resistant bacteria of the Enterobacteriaceae family has reached dramatic levels, making difficult the treatment of infections. Moreover, travelers and patients hospitalized abroad can get colonized at the gut level by such “multidrug-resistant Enterobacteriaceae (MDR-Ent)”. Non-human settings are also playing an important role in the expansion of these pathogens. Therefore, single and isolated analyses have limited ability to identify sources of antibiotic resistance genes and to discern the dynamics of “superbugs” transmission among different human and non-human settings. In addition, only few countries have national programs implementing whole genome (WGS) and whole plasmid sequencing (WPS) for MDR-Ent. Ample and simultaneous WGS/WPS analyses of strains from different settings coupled with clinical/epidemiological data are also lacking.

To fill up the above gaps, we will investigate a large collection of MDR-Ent causing infection and intestinal colonization (humans, animals), or contamination (food chain, environment) at the level of their genomes and analyze routes of transmission and associated risk factors based on curated clinical and epidemiological data for their human and animal hosts.

Our multi-setting One-Health approach will reveal the sources of novel antibiotic resistance genes, the genetic background of promiscuous bacterial clones and/or plasmids, and their pathways of transmission within and between different human and non-human settings in Switzerland. Our method will be also essential for rapid outbreak investigations and for tracking national and global spread of emerging and clinically important “superbugs”. This approach will provide rapid information to the different stakeholders to take appropriate measures to identify sources and risk factors and, therefore, to prevent the spread of epidemic MDR-Ent in human or veterinary hospitals, community, food chain, companion or food animals, and in the environment.

Direct link to Lay Summary Last update: 17.01.2018

Responsible applicant and co-applicants

Employees

Project partner

Publications

Publication
Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones
Campos-Madueno Edgar I., Moser Aline I., Jost Géraldine, Maffioli Carola, Bodmer Thomas, Perreten Vincent, Endimiani Andrea (2022), Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones, in Journal of Global Antimicrobial Resistance.
Duration of carriage of multidrug-resistant bacteria in dogs and cats in veterinary care and co-carriage with their owners
Dazio Valentina, Nigg Aurélien, Schmidt Janne S., Brilhante Michael, Campos-Madueno Edgar I., Mauri Nico, Kuster Stefan P., Brawand Stefanie Gobeli, Willi Barbara, Endimiani Andrea, Perreten Vincent, Schuller Simone (2021), Duration of carriage of multidrug-resistant bacteria in dogs and cats in veterinary care and co-carriage with their owners, in One Health, 13, 100322-100322.
A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC blaNDM-1- and armA-carrying Plasmid
Moser Aline, Keller Peter, Campos-Madueno Edgar I., Poirel Laurent, Nordmann Patrice, Endimiani Andrea (2021), A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC blaNDM-1- and armA-carrying Plasmid, in Pathogens and Immunity, 6(2), 119-134.
Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos
Moser Aline I., Kuenzli Esther, Campos-Madueno Edgar I., Büdel Thomas, Rattanavong Sayaphet, Vongsouvath Manivanh, Hatz Christoph, Endimiani Andrea (2021), Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos, in Frontiers in Microbiology, 12, 1-15.
Complete Genome Sequence of a Third- and Fourth-Generation Cephalosporin-Resistant Comamonas kerstersii Isolate.
Moser Aline I, Campos-Madueno Edgar I, Keller Peter M, Endimiani Andrea (2021), Complete Genome Sequence of a Third- and Fourth-Generation Cephalosporin-Resistant Comamonas kerstersii Isolate., in Microbiology resource announcements, 10(28), 0039121-0039121.
Exploring the global spread of Klebsiella grimontii isolates possessing blaVIM-1 and mcr-9
Campos-Madueno Edgar I., Moser Aline I., Risch Martin, Bodmer Thomas, Endimiani Andrea (2021), Exploring the global spread of Klebsiella grimontii isolates possessing blaVIM-1 and mcr-9, in Antimicrobial Agents and Chemotherapy.
First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis
Campos-Madueno Edgar I., Sigrist Thomas, Flückiger Ursula M., Risch Lorenz, Bodmer Thomas, Endimiani Andrea (2021), First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis, in Journal of Global Antimicrobial Resistance.
An XDR Proteus vulgaris isolate hosting a novel blaNDM-1- and armA-carrying plasmid.
Moser Aline I, Viaggi Valentina, Mauri Carola, Carattoli Alessandra, Luzzaro Francesco, Endimiani Andrea (2021), An XDR Proteus vulgaris isolate hosting a novel blaNDM-1- and armA-carrying plasmid., in The Journal of antimicrobial chemotherapy.
Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital
Brilhante Michael, Gobeli Brawand Stefanie, Endimiani Andrea, Rohrbach Helene, Kittl Sonja, Willi Barbara, Schuller Simone, Perreten Vincent (2021), Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital, in Journal of Antimicrobial Chemotherapy.
Characterization of a new bla VIM-1-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii.
Campos-Madueno Edgar I, Gmuer Christian, Risch Martin, Bodmer Thomas, Endimiani Andrea (2021), Characterization of a new bla VIM-1-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii., in Journal of global antimicrobial resistance.
Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland.
Dazio Valentina, Nigg Aurélien, Schmidt Janne S, Brilhante Michael, Mauri Nico, Kuster Stephan P, Brawand Stefanie Gobeli, Schüpbach-Regula Gertraud, Willi Barbara, Endimiani Andrea, Perreten Vincent, Schuller Simone (2021), Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland., in Journal of veterinary internal medicine.
Poor infection prevention and control standards are associated with environmental contamination with carbapenemase-producing Enterobacterales and other multidrug-resistant bacteria in Swiss companion animal clinics
Schmidt Janne S., Kuster Stefan P., Nigg Aurélien, Dazio Valentina, Brilhante Michael, Rohrbach Helene, Bernasconi Odette J., Büdel Thomas, Campos-Madueno Edgar I., Gobeli Brawand Stefanie, Schuller Simone, Endimiani Andrea, Perreten Vincent, Willi Barbara (2020), Poor infection prevention and control standards are associated with environmental contamination with carbapenemase-producing Enterobacterales and other multidrug-resistant bacteria in Swiss companion animal clinics, in Antimicrobial Resistance & Infection Control, 9(1), 93-93.
Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources.
Moser Aline I, Kuenzli Esther, Büdel Thomas, Campos-Madueno Edgar I, Bernasconi Odette J, DeCrom-Beer Susan, Jakopp Barbara, Mohammed Ali Haji, Hassan Nadir Khatib, Fehr Jan, Zinsstag Jakob, Hatz Christoph, Endimiani Andrea (2020), Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources., in The Journal of antimicrobial chemotherapy.
The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update.
Endimiani Andrea, Ramette Alban, Rhoads Daniel D, Jacobs Michael R (2020), The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update., in Infectious disease clinics of North America.
Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland: Spread of Common Plasmids and International Clones
Campos-Madueno Edgar I., Bernasconi Odette J., Moser Aline I., Keller Peter M., Luzzaro Francesco, Maffioli Carola, Bodmer Thomas, Kronenberg Andreas, Endimiani Andrea (2020), Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland: Spread of Common Plasmids and International Clones, in Antimicrobial Agents and Chemotherapy.
Environmental dissemination of carbapenemase-producing enterobacteriaceae in rivers in Switzerland
Bleichenbacher Stephanie, Stevens Marc J.A., Zurfluh Katrin, Perreten Vincent, Endimiani Andrea, Stephan Roger, Nüesch-Inderbinen Magdalena (2020), Environmental dissemination of carbapenemase-producing enterobacteriaceae in rivers in Switzerland, in Environmental Pollution, 115081-115081.
Investigating the Use of Bacteriophages as New Decolonization Strategy for Intestinal Carriage of CTX-M-15-producing ST131 Escherichia coli: An In Vitro Continuous Culture System Model
Bernasconi Odette J., Campos-Madueno Edgar I., Donà Valentina, Perreten Vincent, Carattoli Alessandra, Endimiani Andrea (2020), Investigating the Use of Bacteriophages as New Decolonization Strategy for Intestinal Carriage of CTX-M-15-producing ST131 Escherichia coli: An In Vitro Continuous Culture System Model, in Journal of Global Antimicrobial Resistance.
Whole-genome characterization of a Shewanella algae strain co-harboring blaCTX-M-15 and armA genes on a novel IncC plasmid
Endimiani Andrea, Bernasconi Odette J., Büdel Thomas, Campos-Madueno Edgar I., Kuenzli Esther, Hatz Christoph, Carattoli Alessandra (2020), Whole-genome characterization of a Shewanella algae strain co-harboring blaCTX-M-15 and armA genes on a novel IncC plasmid, in Antimicrobial Agents and Chemotherapy.
On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat
Büdel Thomas, Kuenzli Esther, Campos-Madueno Edgar I, Mohammed Ali Haji, Hassan Nadir Khatib, Zinsstag Jakob, Hatz Christoph, Endimiani Andrea (2020), On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat, in Journal of Antimicrobial Chemotherapy.
Employees of Swiss veterinary clinics colonized with epidemic clones of carbapenemase-producing Escherichia coli
Endimiani Andrea, Brilhante Michael, Bernasconi Odette J, Perreten Vincent, Schmidt Janne S, Dazio Valentina, Nigg Aurélien, Gobeli Brawand Stefanie, Kuster Stefan P, Schuller Simone, Willi Barbara (2019), Employees of Swiss veterinary clinics colonized with epidemic clones of carbapenemase-producing Escherichia coli, in Journal of Antimicrobial Chemotherapy.
Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018
Nigg Aurélien, Brilhante Michael, Dazio Valentina, Clément Mathieu, Collaud Alexandra, Gobeli Brawand Stefanie, Willi Barbara, Endimiani Andrea, Schuller Simone, Perreten Vincent (2019), Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018, in Eurosurveillance, 24(39), 1-12.
Intestinal Colonization with Multidrug-Resistant Enterobacteriaceae: Screening of Swiss Military Deployed to Kosovo
Kuenzli Esther, Büdel Thomas, Bernasconi Odette J., Schlagenhauf Patricia, Florek Peter, Gültekin Nejla, Hatz Christoph, Endimiani Andrea (2019), Intestinal Colonization with Multidrug-Resistant Enterobacteriaceae: Screening of Swiss Military Deployed to Kosovo, in Journal of Global Antimicrobial Resistance.
Symposium report: One Health meets sequencing.
Egli Adrian, Koch Daniel, Danuser Jürg, Hendriksen Rene S, Driesen Susanne, Schmid Diana Coman, Neher Richard, Mäusezahl Mirjam, Seth-Smith Helena Mb, Bloemberg Guido, Tschudin-Sutter Sarah, Endimiani Andrea, Perreten Vincent, Greub Gilbert, Schrenzel Jacques, Stephan Roger (2019), Symposium report: One Health meets sequencing., in Microbes and infection.
Polyclonal gut colonization with extended-spectrum cephalosporin- and/or colistin-resistant Enterobacteriaceae: a normal status for hotel employees on the island of Zanzibar, Tanzania
Büdel Thomas, Kuenzli Esther, Clément Mathieu, Bernasconi Odette J, Fehr Jan, Mohammed Ali Haji, Hassan Nadir Khatib, Zinsstag Jakob, Hatz Christoph, Endimiani Andrea (2019), Polyclonal gut colonization with extended-spectrum cephalosporin- and/or colistin-resistant Enterobacteriaceae: a normal status for hotel employees on the island of Zanzibar, Tanzania, in Journal of Antimicrobial Chemotherapy.
First Clinical Case of In Vivo Acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica subsp. enterica Isolate
Clément Mathieu, Keller Peter M., Bernasconi Odette J., Stirnimann Guido, Frey Pascal M., Bloemberg Guido V., Sendi Parham, Endimiani Andrea (2019), First Clinical Case of In Vivo Acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica subsp. enterica Isolate, in Antimicrobial Agents and Chemotherapy.
Characterization of the first ESBL-producing Shigella sonnei Clinical Isolate in Italy
Luzzaro Francesco, Clément Mathieu, Principe Luigi, Viaggi Valentina, Bernasconi Odette J., Endimiani Andrea (2019), Characterization of the first ESBL-producing Shigella sonnei Clinical Isolate in Italy, in Journal of Global Antimicrobial Resistance.
Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae.
Büdel Thomas, Clément Mathieu, Bernasconi Odette J, Principe Luigi, Perreten Vincent, Luzzaro Francesco, Endimiani Andrea (2018), Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae., in Microbial drug resistance (Larchmont, N.Y.), 25(4), 494-500.
Whole-Genome Sequence of the First Extended-Spectrum β-Lactamase-Producing Strain of Salmonella enterica subsp. enterica Serovar Napoli
Clément Mathieu, Ramette Alban, Bernasconi Odette J., Principe Luigi, Luzzaro Francesco, Endimiani Andrea (2018), Whole-Genome Sequence of the First Extended-Spectrum β-Lactamase-Producing Strain of Salmonella enterica subsp. enterica Serovar Napoli, in Microbiology Resource Announcements, 7(10), e00973.
Emergence of CTX-M-1-producing Salmonella enterica serovar Napoli: a novel “enzyme-pathogen association” in the Italian ESBL endemic context
Principe Luigi, Viaggi Valentina, Clément Mathieu, Meroni Elisa, Pini Beatrice, Endimiani Andrea, Luzzaro Francesco (2018), Emergence of CTX-M-1-producing Salmonella enterica serovar Napoli: a novel “enzyme-pathogen association” in the Italian ESBL endemic context, in Journal of Global Antimicrobial Resistance.
The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae
Clément Mathieu, Büdel Thomas, Bernasconi Odette J., Principe Luigi, Perreten Vincent, Luzzaro Francesco, Endimiani Andrea (2018), The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae, in Journal of Microbiological Methods.

Collaboration

Group / person Country
Types of collaboration
Dr. Peter Keller Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Nejla Gültekin -Centre of Competence for Military and Disaster Medicine, Federal Department of D Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Peter Florek - Armed Forces International Command SWISSINT Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Francesco Luzzaro - Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Prof. C. Hatz - Swiss TPH, Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Esther Kuenzli - TPH, Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Daniel D. Rhoads - University Hospitals Cleveland Medical Center United States of America (North America)
- Publication
Prof. Jan Fehr - Dept of Public Health, Epidem, Biostat Prevention Instit, Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Guido Bloemberg - Institute for Food Safety and Hygiene Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Mariagrazia Perilli Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. J. Zinsstag - Swiss TPH, Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Roger Stephan - Institute for Food Safety and Hygiene, Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Prof. Nordmann and Dr. Poirel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
31st European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna 9-12 July 2021 [online meeting due to Covid-19] Poster A novel blaNDM-1- and armA-carrying plasmid from an extensively drug-resistant Proteus vulgaris isolate 09.07.2021 Vienna (on-line due to Covid-19), Austria Endimiani Andrea; Carattoli Alessandra;
31st European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna 9-12 July 2021 [online meeting due to Covid-19] Poster Klebsiella grimontii isolates possessing blaVIM-1 and mcr-9 in Switzerland and their clonality in Europe. 09.07.2021 Vienna (on-line due to Covid-19), Austria Endimiani Andrea; Bodmer Thomas; Campos-Madueno Edgar;
31st European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna 9-12 July 2021 [online meeting due to Covid-19] Poster Multidrug-resistant Escherichia coli strains from people, poultry and chicken meat in Laos: comparison with those isolated from the gut of travellers visiting the country 09.07.2021 Vienna (on-line due to Covid-19), Austria Endimiani Andrea; Campos-Madueno Edgar;
Symposium Antibiotic Resistance StAR Individual talk MDROs: molecular diagnostic tools 22.11.2019 Bern, Switzerland Endimiani Andrea;
ECVIM-CA, 29th Annual Congress Talk given at a conference Prevalence, acquisition and persistence of rectal and naso-/oropharyngeal carriage of multidrug-resistant organisms in dogs and cats presented to veterinary practices and their owners 19.09.2019 Milan, Italy Clément Mathieu; Endimiani Andrea; Perreten Vincent;
77th Annual Meeting of Swiss Society of Microbiology (SSM) Talk given at a conference Whole genome sequencing of high-risk clones of OXA-48-producing Klebsiella pneumoniae from the veterinary setting in Switzerland 03.09.2019 Zurich, Switzerland Endimiani Andrea; Perreten Vincent;
Microbe Talk given at a conference Extended-Spectrum Cephalosporin- and Colistin-Resistant E. coli in Tanzania: High Prevalence of Gut Colonization in Healthy People and Chicken Meat Contamination 19.06.2019 San Francisco, United States of America Bernasconi Odette; Clément Mathieu; Endimiani Andrea;
Microbe Poster Extended-Spectrum Cephalosporin- and Colistin-Resistant E. coli in Tanzania: High Prevalence of Gut Colonization in Healthy People and Chicken Meat Contamination 19.06.2019 San Francisco, United States of America Bernasconi Odette; Endimiani Andrea; Clément Mathieu;
Microbe Poster First Case of In Vivo Acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica Clinical Isolate 19.06.2019 San Francisco, United States of America Clément Mathieu; Endimiani Andrea; Bernasconi Odette;
One Health meets Whole genome sequencing Individual talk Carbapenemase-producing Enterobacteriaceae in humans 21.05.2019 Luzern, Switzerland Endimiani Andrea;
3rd International Seminar on Animal and Plant Health (SISA 2019) and the 20th Congress of the Latin American Phytopathological Association Individual talk - Use of next generation sequencing (NGS) for antibiotic resistance surveillance 06.05.2019 Varadero, Cuba Perreten Vincent;
29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) Talk given at a conference High prevalence of gut colonization with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in healthy people in Zanzibar, Tanzania 13.04.2019 Amsterdam, Netherlands Endimiani Andrea; Bernasconi Odette; Clément Mathieu;
29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) Poster Low frequency of intestinal colonization with multidrug-resistant Enterobacteriaceae 13.04.2019 Amsterdam, Netherlands Endimiani Andrea; Clément Mathieu; Bernasconi Odette;
NRP72, Antimicrobial Resistance – Program Meeting Individual talk How to quickly identify sources and distribution pathways of resistance 27.03.2019 Lausanne, Switzerland Endimiani Andrea;
NRP72, Antimicrobial Resistance – Program Meeting Poster First Case of In Vivo Acquisition of DHA-1 plasmid-mediated AmpC in a Salmonella enterica Clinical Isolate 27.03.2019 Lausanne, Switzerland Bernasconi Odette; Clément Mathieu; Endimiani Andrea;
NRP72, Antimicrobial Resistance – Program Meeting Poster First ESBL-producing Shigella sonnei in Italy: a link with Switzerland 27.03.2019 Lausanne, Switzerland Clément Mathieu; Bernasconi Odette; Endimiani Andrea;
7° Congresso AMIT Internazionale. Argomenti di Malattie Infettive e Tropicali Poster First case of ESBL-producing Shigella sonnei infection in Italy 14.03.2019 Milan, Italy Endimiani Andrea; Clément Mathieu; Bernasconi Odette;
7° Congresso AMIT Internazionale. Argomenti di Malattie Infettive e Tropicali Individual talk Carbapenem-resistant Enterobacteriaceae in the community 14.03.2019 Milan, Italy Endimiani Andrea;
Annual meeting of the Swiss Societies for Infectious Diseases (SSI), Hospital Hygiene (SSHH), Tropical Medicine and Parasitology (SSTMP) and Tropical and Travel Medicine (SSTTM) Poster High prevalence of gut colonization with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in students in Bern. 13.09.2018 Interlaken, Switzerland Clément Mathieu; Endimiani Andrea; Ramette Alban;
Annual meeting of the Swiss Societies for Infectious Diseases (SSI), Hospital Hygiene (SSHH), Tropical Medicine and Parasitology (SSTMP) and Tropical and Travel Medicine (SSTTM) Poster Intestinal colonization with multidrug-resistant Enterobacteriaceae in Swiss military deployed to Kosovo. 13.09.2018 Interlaken, Switzerland Clément Mathieu; Endimiani Andrea;
76th Annual Meeting of Swiss Society of Microbiology (SSM) Poster An unusual colistin-resistant mcr-negative Escherichia coli strain 28.08.2018 Lausanne, Switzerland Endimiani Andrea; Clément Mathieu;
76th Annual Meeting of Swiss Society of Microbiology (SSM) Talk given at a conference Evaluation of EDTA- and DPA-based tests for detecting Mcr producers 28.08.2018 Lausanne, Switzerland Endimiani Andrea; Clément Mathieu; Perreten Vincent;
ASM Microbe 2018 Individual talk Carbapenemase Producers: Epidemiology in Travelers and Community-Associated Infections 07.06.2018 Atlanta, United States of America Endimiani Andrea;
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) Poster Microdilution tests to detect Enterobacteriaceae carrying mcr-1/-2 polymyxin resistance genes: Dipicolinic acid (DPA)-based versus EDTA-based assay 21.04.2018 Madrid, Spain Endimiani Andrea; Perreten Vincent;
28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) Poster Gut Decolonization with a Bacteriophage Cocktail against a CTX-M-15-producing ST131 Escherichia coli: an in vitro Continuous Culture System Model 21.04.2018 Madrid, Spain Endimiani Andrea; Perreten Vincent; Ramette Alban;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
1. NRP 72 Antimicrobial Resistance Synthesis Kick Off Meeting. Bern, Swiss National Science Foundation Workshop 27.01.2020 Bern, Switzerland Endimiani Andrea;


Self-organised

Title Date Place
Zwanzig Jahre Forschung über Antibiotika-Resistenzen „Twenty years of technology advancement for the identification of antibiotic resistance”. Veranstaltung der Alumni Vetsuisse-Fakultät Bern 16.05.2019 Bern, Switzerland
Antibiotikaresistenzen: Grundlagen der Resistenzentstehung, Verbreitung und –Messung. Fortbildungveranstaltung der Gesellschaft Zentral Scheizerischer Tierärzte (GZST) 13.09.2018 Rothenburg, Switzerland
Kickoff meeting with Risch laboratory for NRP72 project 31.05.2018 Bern-Liebefeld , Switzerland

Communication with the public

Communication Title Media Place Year
New media (web, blogs, podcasts, news feeds etc.) A patient from Macedonia imported 7 different multidrug-resistant bacteria in Switzerland. LinkedIn International 2022
New media (web, blogs, podcasts, news feeds etc.) Human and non-human settings may share high-risk clones of carbapenemase-producing Klebsiella pneumo LinkedIn International 2022
Media relations: radio, television The spread of antibiotic-resistant bacteria TSI - Swiss Italian Radio Italian-speaking Switzerland 2022
Media relations: print media, online media Emergence of carbapenemase-producing E. coli in hospitalized companion animals in Switzerland Newsletter to the National Reference Laboratories for Antimicrobial Resistance, No. 13 – December 20 International 2019
Media relations: print media, online media Expertise in beta-Lactams: Worldwide  Expertscape International 2019
Media relations: print media, online media Ein Souvenir, das keiner will Der Bund German-speaking Switzerland 2018

Associated projects

Number Title Start Funding scheme
192514 Multidrug-Resistant Enterobacterales Colonizing Swiss Embassy Employees and Relatives Worldwide: Molecular Features, Metagenomics, and Transmission to the Householders at Return 01.03.2021 Project funding

Abstract

The prevalence of MDR Enterobacteriaceae (MDR-Ent) has reached dramatic levels, negatively affecting the outcome of infections. Moreover, travelers and patients hospitalized abroad can get colonized at the gut level by MDR-Ent. Non-human settings are also playing an important role in the expansion of these pathogens. Therefore, single and isolated analyses have limited ability to identify sources of antibiotic resistance genes (ARGs) and to discern the dynamics of transmission. In addition, only few countries have national programs implementing whole genome (WGS) and whole plasmid sequencing (WPS) for MDR-Ent. Ample and simultaneous WGS/WPS analyses of strains from different settings coupled with clinical/epidemiological data are also lacking. To fill up the above gaps, we will investigate a large collection of MDR-Ent (n=1600) causing infection and intestinal colonization (humans, animals), or contamination (food chain, environment) at the level of their genomes and analyze routes of transmission and associated risk factors based on curated clinical and epidemiological data for their human and animal hosts. Aims: 1) Rapid characterization of emerging and epidemic MDR clones and plasmids via real-time sequencing (using MinION Oxford Nanopore) and real-time bioinformatic analyses; 2) High quality genome sequences (MinION scaffolds corrected by using Illumina MiSeq) and analysis of genomic features;3) Integration of genomic data with contextual data (demographic, clinical and epidemiological) to inform on routes and mechanisms of MDR-Ent and/or plasmid transmission among different settings.Impact of the study: Our multi-setting One-Health approach will reveal the sources of novel ARGs, the genetic background of promiscuous bacterial clones and/or plasmids, and their pathways of transmission within and between different human and non-human settings in Switzerland. The identification and characterization of new ARGs will also be essential for rapid outbreak investigations and for tracking national and global spread of emerging and clinically important MDR-Ent. This approach will provide rapid information to the different stakeholders to take appropriate measures to identify sources and risk factors and, therefore, to prevent the spread of epidemic MDR-Ent in human or veterinary hospitals, community, food chain, companion or food animals, and in the environment.
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