Research team

Laboratory of Medical Microbiology (LMM)

Expertise

My research focuses on: (1) Investigating the impact of antibiotic use on human pathogens and commensal flora utilizing genetic, genomic and microbiomic approaches: Utilizing the oro-pharyngeal streptococcal flora in healthy and infected individuals as a model, we have demonstrated that antibiotic use is the single most important driver of antibiotic-resistance in vivo, that antibiotics belonging to the same class can differ widely in resistance gene selection, and that differences in predominance of certain resistance genes in geographically distinct areas might be linked to the preferential use of specific antibiotic subclasses. Now, we are studying changes in the resistome and in composition of the intestinal flora of patients in intensive care units undergoing selective oral or digestive decontamination utilizing metagenomic and functional genomic approaches. (2) Mechanisms of antibiotic resistance in pathogenic bacteria: The main focus is on investigating 'old' antibiotics that have been reintroduced into clinical practice and whose resistance mechanisms are not yet known such as colistin, nitrofurantoin and fosfomycin. Both clinical, patient derived strains as well as in vitro passaged strains undergo strain typing, whole genome sequencing, resistance stability studies and fitness cost assessments to understand emergence of the resistance mechanisms as well as their fate in the community. (3) Biofilms: As an increasing number of critical infections and their persistence are being linked to biofilm formation, investigations on bacterial isolates, while indispensable for species identification and metabolic and genetic studies, cannot give insights on disease pathogenesis. We have primarily chosen to study device-related infections, such as ventilator-associated pneumonia and catheter infections, where biofilm formation is most relevant, aiming to characterize mechanisms underlying biofilm formation and the microbial interactions in a biofilm both in vitro and in vivo. Several in vitro biofilm models, both static and dynamic shear-flow, have been set up in our laboratory for these studies. In vivo biofilms obtained from explanted catheters are being analysed using culture-dependent and -independent approaches as well as by confocal laser scanning microscopy.

Establishing innovative approaches for optimal infection prevention of resistant bacteria in NICUs by integrating research, implementation science and surveillance in a sustainable global platform (NeoIPC). 01/04/2021 - 31/03/2026

Abstract

Around 10% of newborns in Europe will be admitted to a neonatal intensive care unit (NICU). Critically ill babies are a highly vulnerable population for the acquisition of resistant bacteria. Sepsis is among the most common events in NICU and is known to be associated with high mortality and poor long-term outcomes. Despite rising awareness of high rates of resistant bacterial colonisation reported in NICU, there is very little robust specific data on globally applicable infection prevention and control (IPC) measures. NeoIPC focuses on new approaches to the prevention and management of resistant bacterial colonization and infection on NICU. The project builds on and further extends the collaboration between 13 partners with a proven track record in relevant areas, including neonatal infection, IPC, implementation science, microbiology and surveillance. NeoIPC aims to develop and implement an innovative approach towards the evaluation of IPC interventions combining a robust cost-efficient randomised trial combined with the evaluation of a suitable implementation science strategy and novel targeted clinical and genotypic surveillance. A further goal is to generate widely relevant pan-European network strategies to improve IPC in routine neonatal care. This will be achieved through six interrelated work packages to deliver a cluster randomised trialimplementation hybrid investigating the impact of skin antisepsis on infant hospital-acquired clinical sepsis and resistant bacterial colonisation, coupled with a comprehensive implementation strategy incorporating optimal targeted surveillance in a clinical network with tailored dissemination and exploitation to facilitate sustainable embedding of outputs. NeoIPC will generate globally transferrable outputs to reduce hospital transmission of resistant pathogens, foster and facilitate collaborative research and IPC implementation efforts with a broad and long-lasting impact for critically ill newborns and infants.

Researcher(s)

Research team(s)

Biology and ecology of bacterial and fungal biofilms in humans. 01/01/2021 - 31/12/2025

Abstract

The general objective of this research community is to better understand the origin and structure of bacterial and fungal biofilms in humans so that effective action can be taken against them in the long term.

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Research team(s)

Connecting European Cohorts to Increase Common and Effective Response to SARS-CoV-2 Pandemic (ORCHESTRA). 01/12/2020 - 30/11/2023

Abstract

The ORCHESTRA project provides an innovative approach to learn from the SARS-CoV-2 health crisis and derive recommendations for increasing preparedness for future outbreaks. The main outcome of the project is the creation of a new pan-European cohort built on existing and new large-scale population cohorts in European and non-European countries. Data analysis through a federated learning technique supported by advanced modelling capabilities will allow the integration of epidemiological, clinical, microbiological and genotypic aspects of population-based cohorts with environment and socio-economic features. The ORCHESTRA cohort will include SARS-CoV-2 infected and non-infected individuals of all ages and conditions and thereby enabling a retrospective evaluation of risk factors for the disease acquisition and progression of the disease and prospective follow-up aimed at exploring longterm consequences and analysis of vaccination response when vaccines will be available. To better address these research questions, the ORCHESTRA-cohort will include adequately sampled representatives of general populations, COVID-19 patients and special 'at risk' populations of fragile individuals and health-care workers. The project will assess also health costs of COVID-19 with special emphasis on delayed health services in the fragile populations. The participation of non-European and Low-Medium Income Countries and a Global COVID-19 Guidance group of major stakeholders and investigators from successful clinical trials addressing therapeutic approaches to COVID-19, ensures inclusion of all expertise needed and translation of recommendations to different social and economic settings. The project will significantly impact on the responsiveness to SARS-CoV-2 and can be used as a model for responsiveness for new public health threats.

Researcher(s)

Research team(s)

Connecting European Cohorts to Increase Common and Effective Response to SARS-CoV-2 Pandemic (ORCHESTRA). 01/12/2020 - 30/11/2023

Abstract

The ORCHESTRA project provides an innovative approach to learn from the SARS-CoV-2 health crisis and derive recommendations for increasing preparedness for future outbreaks. The main outcome of the project is the creation of a new pan-European cohort built on existing and new large-scale population cohorts in European and non-European countries. Data analysis through a federated learning technique supported by advanced modelling capabilities will allow the integration of epidemiological, clinical, microbiological and genotypic aspects of population-based cohorts with environment and socio-economic features. The ORCHESTRA cohort will include SARS-CoV-2 infected and non-infected individuals of all ages and conditions and thereby enabling a retrospective evaluation of risk factors for the disease acquisition and progression of the disease and prospective follow-up aimed at exploring longterm consequences and analysis of vaccination response when vaccines will be available. To better address these research questions, the ORCHESTRA-cohort will include adequately sampled representatives of general populations, COVID-19 patients and special 'at risk' populations of fragile individuals and health-care workers. The project will assess also health costs of COVID-19 with special emphasis on delayed health services in the fragile populations. The participation of non-European and Low-Medium Income Countries and a Global COVID-19 Guidance group of major stakeholders and investigators from successful clinical trials addressing therapeutic approaches to COVID-19, ensures inclusion of all expertise needed and translation of recommendations to different social and economic settings. The project will significantly impact on the responsiveness to SARS-CoV-2 and can be used as a model for responsiveness for new public health threats. Specifically, in this work package, different cytokines and chemokines from blood of COVID-19 patients will be studied and markers predicting disease severity, mortality, and/or long term sequalae will be identified in collaboration with other partners of ORCHESTRA.

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Mucin isoform-microbiome crosstalk shaping the course of COVID-19: a help in patient stratification? 01/11/2020 - 31/10/2021

Abstract

Infection with SARS-CoV-2 mostly leads to a mild self-limiting respiratory tract illness, however, some patients develop severe progressive pneumonia, multiorgan failure, and death. This project aims to determine factors that dictate the course of COVID19 beyond cytokines. We have prior data that specific aberrantly expressed mucins, triggered by SARS-CoV-2, regulate ACE2 expression and affect lung barrier integrity. Such mucin alterations are clinically relevant as excessive mucin production is seen in severe COVID-19 illness obstructing the respiratory tract and complicating recovery. Here, we will first identify differentially expressed mucin isoforms in COVID-19 patients exhibiting the entire spectrum of disease severity. Thereafter, therapeutics currently used for COVID-19 will be screened for their ability to reduce mucin abundance. As mucin expression is also a critical factor in microbiome homeostasis and dysbiosis might modulate COVID-19 severity, this project secondly aims to map the microbiome associated with different degrees of disease severity. Unravelling mucin isoform-microbiome interactions that shape the course of SARS-CoV-2 infection will lead to the future identification of those patients who are in danger of progressing to severe disease. This project will also improve the choice for an appropriate treatment as well as the time frame of treatment options once infection occurs.

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Research team(s)

Enhanced Networking on Antimicrobial Resistance Surveillance with Next Generation Sequencing (AmReSu). 01/10/2020 - 30/09/2023

Abstract

Antimicrobial resistance (AMR) is on the rise, resulting in 700 000 deaths worldwide every year. In Croatia and Hungary, AMR is responsible for the rapid increase in morbidity and mortality rates. The EU-funded AmReSu project will strengthen the innovation capacity in AMR surveillance in both countries, focussing on whole genome sequencing in correlation with next-generation sequencing techniques. It will also establish an "AMR surveillance vision." The project relies on the cooperation of Semmelweis University in Budapest and Klinika za infektivne bolesti "Dr. Fran Mihaljevic" in Zagreb with two internationally leading research institutions, the Laboratory of Medical Microbiology at the University of Antwerp and the Health Research Institute of the Balearic Islands. AmReSu will facilitate knowledge transfer, exchanges of best practices via training activities and the promotion of research excellence.

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Single-molecule long-read sequencing to enable high-resolution analysis and comparative genomics of the clinical Clostridioides difficile ECDC/Leeds-Leiden reference collection 14/11/2019 - 13/11/2021

Abstract

Clostridioides difficile constitutes the main source of healthcare-associated infectious diarrhea across the globe, causing a disease known as C. difficile infection (CDI) associated with prolonged hospital stay and increased mortality. Whole-genome sequencing (WGS) approaches applied to the study of C. difficile have revealed a highly variable 4.1-4.3 Mb genome that is not only rich in mobile genetic elements but is also highly complex to assemble due to the presence of numerous repeat regions. Thus, conventional short-read sequencing technologies have had limited success in resolving C. difficile genomes and have led to incomplete, and incorrectly assembled genomes. In this study, we intend to employ single-molecule real-time (SMRT) long-read sequencing to obtain complete, gapless C. difficile genomes and enable a high-resolution genome-wide analysis and comparison of clinical reference strains isolated from patients across Europe contained in the ECDC/Leeds-Leiden reference collection. This sequenced collection will be made publicly available in the European Nucleotide Archive (ENA)/NCBI to stimulate further research on different aspects, both fundamental and clinical, of CDI with the aim of developing better preventive, therapeutic/diagnostic, and typing strategies.

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Research team(s)

Investigating the complexity of resistance and heteroresistance mechanisms to colistin in Klebsiella pneumoniae and Escherichia coli. 01/10/2019 - 30/09/2023

Abstract

Colistin (CL) is a last line antibiotic used to treat hospital-associated infections due to multi- and extremely-drug resistant Gram-negative bacterial pathogens, and also in veterinary medicine to treat post-weaning diarrhoea in food animals. Increasing use has led to the emergence of both chromosomal and transferable plasmid-mediated (mcr) colistin resistance in pathogens. While the chromosomal mechanisms involve mutations in several genes, which also modify the bacterial metabolic pathways, the mcr-mediated mechanism confers low-level colistin resistance, and its role, relevance and fate in mediating colistin resistance in human pathogens remain to be explored. Another phenomenon that remains to be understood is of heteroresistance wherein bacterial subpopulations exhibit different susceptibilities to colistin and can lead to treatment failures during infection. Recent advances in next-generation sequencing have made it possible to study the genome and gene expression at the single cell level. In this project, we intend to study the complexities of resistance and heteroresistance evolution in a population utilizing whole genome sequencing and beyond state of the art NGS techniques of single-cell sequencing and gene expression analysis on pathogenic bacteria, Klebsiella pneumoniae and E. coli, evoluted in vitro under colistin pressure as well as in a mouse model of infection and finally in respiratory samples from patients treated with colistin.

Researcher(s)

Research team(s)

Vaccine & Infectious Diseases Excellence in Antwerp: Infectious disease prevention, control and management in a One Health policy context (VAX-IDEA). 03/07/2019 - 31/12/2023

Abstract

Infectious diseases (ID) and antimicrobial resistance (AMR) pose a continuous and serious threat to humans and animals (One Health). Five research units from the UAntwerpen, with strong international records and collaboration, will continue to jointly capitalize on their ID expertise. EVECO studies distribution, evolution and ecology of pathogens (plague, arenaviruses, …) and wildlife hosts, offering insights for emerging ID management. LMM has established large consortia (COMBACTE, PREPARE) leading to pan-European infrastructures for ID and antimicrobial consumption research. Next to developing rapid diagnostics, LMM investigates AMR mechanisms and pathogen dynamics in vitro, in humans/livestock, and in animal models to study host-immune response (biomarker discovery) and bacterial pathogenicity. LEH performs cutting-edge research on cell-based immunotherapies, in collaboration with the UZA Center for Cell Therapy & Regenerative Medicine. LEH investigates host-immune responses in vaccine trials using multi-parametric flow cytometry and systems biology to discover novel immune correlates of protection in next-generation vaccines. CEV studies the epidemiology of vaccine-preventable diseases and performs state-of-the-art vaccine trials with large national/international networks, including maternal immunization trials and quarantine studies with genetically-modified polioviruses. Given the global need for EID vaccines (Lassa, Ebola, …) , CEV engages in several innovative (non)-human challenge-phase 1-2 studies. CHERMID undertakes methodological and applied research on the intersection between health economics, biomedicine and mathematics. CHERMID is internationally renowned for developing models of dynamic ID processes within and between hosts and integrating these with cutting edge economic models. By integrating these complementary expertises, this COE will address current and future challenges in ID management.

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Research team(s)

Impact of duration of antibiotic therapy and of oral step-down to amoxicilin or co-amoxiclav on effectiveness, safety and selection of antimicrobial resistance in severe and very severe childhood community-acquired pneumonia (PediCAP Trial). 01/04/2019 - 31/03/2024

Abstract

Goals of PediCAP are Fill the knowledge gaps on antibiotic therapy of community-acquired pneumonia in pediatric age, in terms of optimal duration, oral step-down schedule evaluating effectiveness, safety and selection of antimicrobial resistance. Evaluate economic impact of antibiotic therapy in terms of cost-effectiveness. Implement the infrastructure that links study sites in order to share knowledge, develop study specific and general research skill straining programme and promote capacity development initiatives.

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Research team(s)

The value of diagnostics to combat antimicrobial resistance by optimising antibiotic use (VALUE-Dx). 01/04/2019 - 31/03/2023

Abstract

Antimicrobial resistance (AMR) is of great public health concern, causing numerous losses of lives worldwide and threatening to reverse many of the considerable strides modern medicine has made over the last century. There is a need to stratify antibiotic and alternative treatments in terms of the actual benefit for the patient, improving patient outcome and limit the impact on AMR. High quality, effective and appropriate diagnostic tests to steer appropriate use of antibiotics are available. However, implementation of these tests into daily healthcare practice is hampered due to lack of insight in the medical, technological and health economical value and limited knowledge about psychosocial, ethical, regulatory and organisational barriers to their implementation into clinical practice. VALUE-Dx will define and understand these value indicators and barriers to adoption of diagnostics of Community-Acquired Acute Respiratory Tract Infections (CA-ARTI) in order to develop and improve health economic models to generate insight in the whole value of diagnostics and develop policy and regulatory recommendations. In addition, efficient clinical algorithms and user requirement specifications of tests will be developed fuelling the medical and technological value of CA-ARTI diagnostics. The value of diagnostics will be tested and demonstrated in a unique pan-European clinical and laboratory research infrastructure allowing for innovative adaptive trial designs to evaluate novel CA-ARTI diagnostics. Close and continuous interaction with the VALUE-Dx multi-stakeholder platform provides for optimal alignment of VALUE-Dx activities with stakeholder opinions, expert knowledge and interests. A variety of dissemination and advocacy measures will promote wide-spread adoption of clinical and cost-effective innovative diagnostics to achieve more personalized, evidence-based antibiotic prescription in order to transform clinical practice, improve patient outcomes and combat AMR.

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Research team(s)

Preventing Resistance in Gonorrhoea (PReGo) Study. 01/10/2018 - 30/09/2022

Abstract

New interventions are required to prevent the emergence of antimicrobial resistance in contemporary sexually transmitted infection (STI) epidemics in men who have sex with men (MSM). Here, we perform a double-blinded single centre, crossover, randomized controlled trial of antibacterial vs. placebo mouthwash to study reduction in incidence of gonorrhoea/chlamydia/syphilis in MSM taking preexposure prophylaxis.

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Research team(s)

Harnessing a therapeutic microbiome as an alleviating strategy for dysbiosis and recurrence in colorectal cancer patients undergoing radiotherapy. 01/10/2018 - 30/09/2022

Abstract

Colorectal cancer (CRC) is the second most common malignancy in the world. With an estimated recurrence rate of 20-30%, CRC represents an important health and socioeconomical burden. Recent data based on metagenomics and experimental models suggest a strong contribution of the gut microbiome in modulating CRC development. This project aims to understand the role of microbiome in CRC development and recurrence, specifically in studying if CRC recurrence is significantly affected by the radiation induced dysbiosis and if faecal microbiota transplantation can resolve radiation-induced dysbiosis and attenuate CRC development.

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Research team(s)

Combatting Bacterial Resistance in Europe - Molecules Against Gram Negative Infections (COMBACTE-MAGNET). 01/01/2015 - 31/12/2021

Abstract

This project represents a formal research agreement between UA and on the other hand EU. UA provides EU research results mentioned in the title of the project under the conditions as stipulated in this contract.

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Research team(s)

Research in the field of medical microbiology. 01/10/2011 - 30/09/2021

Abstract

The research of Surbhi Malhotra has focused on the molecular epidemiology and genetics of resistance to antimicrobials in oral streptococci. Applying molecular biological techniques on oro-pharyngeal streptococcal flora in healthy individuals as a model, she demonstrated that antibiotic use is the single most important driver of antibiotic-resistance in vivo, that antibiotics belonging to the same class can differ widely in resistance gene selection, and that differences in predominance of certain resistance genes in geographically distinct areas might be linked to the preferential use of specific antibiotic subclasses. Her current research interests include studying the impact of antibiotic use on the naso-oro-pharyngeal and intestinal microflora, mechanisms of biofilm formation, bacterial pathogenetic mechanisms, and developing rapid diagnostic assays for pathogens causing community-acquired and nosocomial infections.

Researcher(s)

Research team(s)

Molecular insights in SARS-CoV-2 pathogenesis and epidemiology. 01/06/2020 - 31/05/2021

Abstract

Infection with SARS-CoV-2 mostly leads to a mild self-limiting respiratory tract illness, however, some patients progress to develop severe progressive pneumonia, multiorgan failure, and death. The project aims to determine factors that dictate the severity of COVID-19. Firstly, guided by our prior data of interaction of certain mucins with the ACE2 receptor and the clinical evidence of excessive mucin production in severe COVID-19 illness, we intend to characterize different mucins for their role in both the initiation and progression of COVID-19. Secondly, based on a severe degree of edematous interstitial lung tissue pathology observed in COVID-19 autopsies and its hypothesized link to abnormally low PaO2 observed clinically, the project intends to characterize aquaporin (AQP) water channels that are responsible for fluid transport across cells. This has important therapeutic relevance for COVID-19 as specific AQP inhibitors have been shown to attenuate inflammation and lung injury and to block mucin hypersecretion. Lastly, mucin expression is also a critical factor in microbiome homeostasis and based on, so far, scarce data that co-infection with other respiratory pathogens and other microbial interactions might modulate COVID-19 severity, the project aims to characterize the microbiome associated with different degrees of disease severity. Identifying factors that shape the course of SARS-CoV-2 infection will lead to identification of plausible targets to treat COVID-19.

Researcher(s)

Research team(s)

Studies in the field of medical and molecular microbiology and in basic science in connection to the CAP-IT samples. 01/02/2020 - 30/11/2020

Abstract

CAP-IT is a multicenter randomized double-blind 2x2 factorial noninferiority trial investigating the efficacy, safety and impact on antimicrobial resistance of amoxicillin administered as a shorter or longer course at a lower or higher dose for uncomplicated childhood pneumonia. The analysis at the University of Antwerp (UA) will comprise two parts: (i) research on S. pneumoniae colonization with respect to circulating (vaccine) serotypes in the UK and pneumococcal penicillin resistance; and (ii) evaluation of the microbial communities present in the respiratory tract of patients to identify and quantify the microbial shift as well as changes in the presence of antimicrobial resistance genes related to the effect of the different durations and doses of amoxicillin administered in CAP-IT. These data will be generated using metagenomics and metatranscriptomic sequencing using both PacBio and Illumina technologies.

Researcher(s)

Research team(s)

Assessment of the nasopharyngeal carriage of Streptococcus pneumoniae and other common pathogens in infants (6-30 months) with acute otitis media and in healthy infants (6-30 months) attending day-care centres in Belgium 01/10/2018 - 14/09/2020

Abstract

General use of vaccines against Streptococcus pneumoniae (S. pneumoniae) in infants has led to a decrease in the presence of the serotypes against which the vaccine was developed. It is a pathogen of which more than 90 different serotypes exist, of whom 10 to 13 are covered by the current vaccines. In order to gain a clear understanding of the S. pneumoniae serotypes carried by infants, and the impact of the vaccine used in the vaccination program, the current study was set up. As early as the first months of our lives S. pneumoniae is present in the nasal cavity and in the pharynx, mostly only temporary and innocuous, yet in some cases, in infants it may lead to infections such as otitis, pneumonia or meningitis. Since the presence of S. pneumoniae is more abundant in some circumstances, the current study focuses on infants between the age of 6 and 30 months either healthy and residing in day-care centres or suffering from an acute middle ear infection. Over a 4 year period, a swab will be taken from the nasal cavity of these infants (700 in first year, 900 in subsequent years, 6800 in total) to investigate presence, density and type of S. pneumoniae carriage, if any, as well as its resistance against antibiotics. The presence of some other pathogens that can cause airway or ear infections will be investigated too. The findings of this study will be extremely valuable to guide decisions on vaccine development, vaccine program, and recommendations on antibiotic treatment.

Researcher(s)

Research team(s)

Single molecule long-read sequencing technology: beyond state-of-the-art in biological and medical research. 01/05/2018 - 30/04/2021

Abstract

This project aims to advance the currently available sequencing technologies at the University of Antwerp (UA) by acquiring a third generation sequencing (3GS) platform. The flagship of the third generation, single-molecule longread sequencers, PacBio Sequel, harnesses the natural process of DNA replication and enables real-time observation of DNA synthesis. 3GS promises to open new avenues for sequencing-based research beyond the current state-of-the-art for this consortium, which consists of more than 14 UA research groups in various disciplines of medicine, biology and bioinformatics. Furthermore, several third parties have also committed to utilize this technology for their ongoing and future research studies. 3GS will be utilized by this consortium to (i) sequence prokaryotic and eukaryotic genomes, and difficult-to-sequence genome regions, (ii) identify new genes and mutations in various rare Mendelian disorders, (iii) identify epigenetic modifications to better understand biological processes like gene expression and host-pathogen interactions, (iv) precisely profile the human, murine, and environmental microbiome in disease and under various environmental stressors, and (v) develop novel preventive therapies for infection-prone disorders for better drug targeting. The analysis of the large amount of genomic and transcriptomic data generated by the various research groups will be coordinated by the UZA/UA bioinformatics group Biomina.

Researcher(s)

Research team(s)

Insight in methicillin-resistant Staphylococcus aureus (MRSA) biofilms: identification of key determinants in biofilm formation of highly pathogenic and globally successful MRSA clones 01/10/2017 - 30/09/2019

Abstract

Since two decades, methicillin-resistant Staphylococcus aureus (MRSA) has become a major cause of medical device-associated and postsurgical wound infections in hospitals and of pneumonia in the community. In these infections, MRSA favors the biofilm phenotype, living in a community encased in an extracellular matrix that affords protection against the host immune system and antibiotics, making these infections recalcitrant to treatment. Our laboratory has shown that two highly pathogenic and globally successful MRSA clones, USA300 and EMRSA-15, are prolific biofilm formers. Interestingly, our transcriptomics data has revealed spectacularly different mechanisms of biofilm formation between these two clones. For instance, in USA300-S391 biofilms, Hfq, a global regulator of small non-coding RNAs which in turn control rapid bacterial virulence gene expression as well as mecR, which regulates the expression of ß-lactam resistance conferring mecA gene, were both found to be highly upexpressed. EMRSA-15 biofilms, however, were not found to be MecR- or Hfq-dependent, but instead showed upexpression of multiple prophages. This fundamental project aims to dissect the role of mecR, Hfq, and prophages in mediating biofilm formation in USA300 and EMRSA-15. Identifying genes regulated by these key determinants could be better alternatives for biofilm disruption or additive therapies to antibiotics that are currently ineffective against MRSA.

Researcher(s)

Research team(s)

STARCS: Selection and transfer of antimicrobial resistance in complex systems. 01/01/2017 - 31/12/2019

Abstract

Selection and transmission are key determinants for the dissemination of antimicrobial resistance (AMR) across the planet. These determinants of AMR are frequently studied in laboratory settings while in reality they occur in complex systems, e.g. in microbial communities that colonize human and animal guts or in environmental ecosystems. The central aim of STARCS (Selection and Transmission of Antimicrobial Resistance in Complex Systems) is to characterize and quantify the processes of selection and transmission of AMR genes and drug-resistant bacteria in complex (eco)systems from a 'One Health' perspective and to integrate these elements into predictive mathematical models, which will be used to inform policy development. To reach this goal, the consortium will (i) develop and implement innovative metagenomic methodologies to map the expression of AMR genes and their linkage to bacterial hosts and mobile genetic elements in human, animal and environmental samples, (ii) use relevant animal models (using mice and ducks) and observational studies (in hospitals and in dogs and their owners) to analyse and quantify the processes of selection and transmission of drug-resistant Enterobacteriaceae (specifically Extended Spectrum Beta-Lactamase producing Escherichia coli) and (iii) implement state-of-the-art epidemiological modelling to quantify the spread of ESBL-producing E. coli between humans and animals. STARCS will develop technological breakthroughs to assess selection and transmission dynamics on the level of the resistance gene, the mobile genetic element, the bacterium, the human-animalenvironment interface and in clinical settings. This project will deliver important knowledge into selection and transmission of AMR, will provide the scientific community with novel tools to study selection and transfer of AMR in complex systems and will result in much-needed guidance towards policy decisions by international and national institutions. Ultimately the results from STARCS will form an evidence-based foundation for the development of new regulations, aimed at curbing the spread of AMR.

Researcher(s)

Research team(s)

Assessment of the nasopharyngeal carriage of Streptococcus pneumoniae and other common pathogens in infants (6-30 months) with acute otitis media and in healthy infants (6-30 months) attending day-care centres in Belgium. 01/10/2016 - 30/09/2018

Abstract

General use of vaccines against Streptococcus pneumoniae (S. pneumoniae) in infants has led to a decrease in the presence of the serotypes against which the vaccine was developed. It is a pathogen of which more than 90 different serotypes exist, of whom 10 to 13 are covered by the current vaccines. In order to gain a clear understanding of the S. pneumoniae serotypes carried by infants, and the impact of the vaccine used in the vaccination program, the current study was set up. As early as the first months of our lives S. pneumoniae is present in the nasal cavity and in the pharynx, mostly only temporary and innocuous, yet in some cases, in infants it may lead to infections such as otitis, pneumonia or meningitis. Since the presence of S. pneumoniae is more abundant in some circumstances, the current study focuses on infants between the age of 6 and 30 months either healthy and residing in day-care centres or suffering from an acute middle ear infection. Over a 4 year period, a swab will be taken from the nasal cavity of these infants (700 in first year, 900 in subsequent years, 6800 in total) to investigate presence, density and type of S. pneumoniae carriage, if any, as well as its resistance against antibiotics. The presence of some other pathogens that can cause airway or ear infections will be investigated too. The findings of this study will be extremely valuable to guide decisions on vaccine development, vaccine program, and recommendations on antibiotic treatment.

Researcher(s)

Research team(s)

    Biology and ecology of bacterial and fungal biofilms in humans. 01/01/2016 - 31/12/2020

    Abstract

    The general objective of this research group is to gain a better understanding of the formation process and structural characteristics of bacterial and fungal biofilms in humans to ensure future effective therapeutic interventions.

    Researcher(s)

    Research team(s)

    Key determinants of biofilm formation in two highly pathogenic and globally successful methicillin-resistant Staphylococcus aureus (MRSA) clones. 01/01/2016 - 31/12/2019

    Abstract

    Since two decades, methicillin-resistant Staphylococcus aureus (MRSA) are major causes of medical device-associated and postsurgical wound infections in hospitals and of pneumonia in the community. Recent research shows that in these infections, MRSA favour the biofilm phenotype, living in a community encased in an extracellular matrix that affords protection against the host immune system and antibiotics, making these infections recalcitrant to treatment. Recent data from our laboratory shows that the two most highly pathogenic and globally successful MRSA clones, USA300 and EMRSA-15, are also prolific biofilm formers. Interestingly, transcriptomics has revealed spectacularly different mechanisms of biofilm formation between the two clones. This fundamental project thus aims to dissect the role of novel regulators in mediating biofilm formation in USA300 and EMRSA-15. Identifying genes regulated by these key determinants would initialize identification of targets for biofilm disruption that might be better alternatives to antibiotics that are currently ineffective against MRSA.

    Researcher(s)

    Research team(s)

    Defining the burden of antibiotic resistance in Vietnam across different ecosystems. 01/01/2016 - 31/12/2017

    Abstract

    Global (mis)use of antibiotics has led to an alarming emergence and spread of antibiotic resistant bacteria (ARB). Countries like Vietnam with unrestricted, over-the-counter antibiotic use are especially prone to the emergence of pan-resistant 'superbugs' and alarmingly, very few treatment options for life-threatening infections. A burgeoning population and inadequate sanitation facilities have likely exacerbated the ARB reservoir in the Vietnamese environment. This study, carried out in Hanoi city and its surroundings, aims to obtain a longitudinal and holistic view of ARB in the community and hospital environments to identify the ARB selection hotspots in Vietnam. To achieve this, we will determine and finely dissect the ARB burden in various ecosystems (water, food, soil) and in the human gut, and link to the burden of ARB in nosocomial and community-related infections. Also, fitness costs of resistance and the impact of residual antibiotics in the maintenance of ARB in reservoirs and in patients will be elucidated. We will utilize state-of-the-art techniques to characterize ARB and beyond state-of-the-art functional metagenomics to elucidate the resistant metamobilome existing in Vietnamese ecosystems. This transnational study between IEHSD, Vietnam and UA, Belgium will not only facilitate extensive exchange of knowledge and expertise between partners but the results generated here will help to target intervention strategies to tackle this public health crisis.

    Researcher(s)

    Research team(s)

      Insight in methicillin-resistant Staphylococcus aureus (MRSA) biofilms: identification of key determinants in biofilm formation of two highly pathogenic and globally successful MRSA clones, USA300 and EMRSA-15. 01/10/2015 - 30/09/2017

      Abstract

      Since two decades, methicillin-resistant Staphylococcus aureus (MRSA) has become a major cause of medical device-associated and postsurgical wound infections in hospitals and of pneumonia in the community. In these infections, MRSA favors the biofilm phenotype, living in a community encased in an extracellular matrix that affords protection against the host immune system and antibiotics, making these infections recalcitrant to treatment. Our laboratory has shown that two highly pathogenic and globally successful MRSA clones, USA300 and EMRSA-15, are prolific biofilm formers. Interestingly, our transcriptomics data has revealed spectacularly different mechanisms of biofilm formation between these two clones. For instance, in USA300-S391 biofilms, Hfq, a global regulator of small non-coding RNAs which in turn control rapid bacterial virulence gene expression as well as mecR, which regulates the expression of ß-lactam resistance conferring mecA gene, were both found to be highly upexpressed. EMRSA-15 biofilms, however, were not found to be MecR- or Hfq-dependent, but instead showed upexpression of multiple prophages. This fundamental project aims to dissect the role of mecR, Hfq, and prophages in mediating biofilm formation in USA300 and EMRSA-15. Identifying genes regulated by these key determinants could be better alternatives for biofilm disruption or additive therapies to antibiotics that are currently ineffective against MRSA.

      Researcher(s)

      Research team(s)

        Methicillin-resistant Staphylococcus au reus (MRSA}: Development of in vitro and in vivo laboratory models as predictive bridge between in vitro drug discovery and clinical evaluation. 01/01/2015 - 31/12/2019

        Abstract

        This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

        Researcher(s)

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        COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe (COMPARE) 01/12/2014 - 30/11/2019

        Abstract

        COMPARE aims to harness the rapid advances in molecular technology to improve identification and mitigation of emerging infectious diseases and foodborne outbreaks. To this purpose COMPARE will establish a "One serves all" analytical framework and data exchange platform that will allow real time analysis and interpretation of sequencebased pathogen data in combination with associated data (e.g. clinical, epidemiological data) in an integrated inter-sectorial, interdisciplinary, international, "one health" approach.

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        Environmental and food reservoirs of antibiotic resistant organisms and its link with human disease. 01/11/2013 - 31/10/2015

        Abstract

        This project addresses the alarming rise of multiple resistant organisms in an holistic approach by analysing simultaneously different reservoirs of antibiotic resistant bacteria (ARB). These findings will be correlated to the presence of ARB in humans (healthy & patients).

        Researcher(s)

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          Mechanistic insights on colistin resistance in pathogenic Escherichia coli and Klebsiella species. 01/10/2012 - 30/09/2016

          Abstract

          Incidence of infections caused by multi- and pan-drug resistant Enterobacteriaceae, such as Escherichia coli and Klebsiella, is increasing worldwide. Consequently, colistin, an old and out-of-use antibiotic, had to be re-introduced into clinical practice as a last resort therapeutic option as it is the only antibiotic to which such bacteria still remain susceptible. However, increasing use has inevitably led to emergence of colistin resistance (CR) among Gram-negative bacteria. The main goal of this project is to examine key elements of colistin resistant Enterobacteriaceae (CRE) that have hitherto not been fully investigated. We have established a unique collection of CR E. coli and Klebsiella spp., originating from hospitalized patients and sick animals as well as generated in vivo in a Galleria mellonella moth model, that will form the basis of this project. With these isolates and their colistin sensitive counterparts, we plan to undertake the following: 1, Strain typing; 2, Selection of CR in-vitro; 3, Genome sequencing and comparative genome analysis; 4, Targeted gene sequencing and protein expression; 5, Stability studies; 6, Fitness studies and 7, Assessment of mortality and pathogenicity. While strain typing has been done on few Klebsiella, we will type other CRE to examine if CR is associated with certain strain types. Continuous culture experiments in a morbidostat set-up will allow in vitro selection of CRE under continuous drug pressure that will be studied temporally at various stages of resistance development. Whole genome sequencing of in-vivo and in-vitro CRE isogenic strains will identify the sites of mutations potentially responsible for CR. Gene targets identified by genome analysis will be re-sequenced to confirm the changes conferring CR and those will be further characterized by real-time PCR and proteomics. The stability of CR and fitness of such strains will be assessed either by passaging in colistin-free medium, or under constant colistin pressure on the morbidostat model. The effects of CR on mortality will be investigated in the high-throughput reproducible in vivo Galleria mellonella model. Finally, the impact of CR on virulence and pathogenicity will be studied in a higher animal model i.e., a ventilator-associated pneumonia rat model that is already established in our laboratory.

          Researcher(s)

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            Development of in vitro and in vivo laboratory models to analyse the dynamics of mono- and polymicrobial biofilm formation and treatment. 01/10/2012 - 30/09/2014

            Abstract

            Biofilm-related infections prove exceedingly difficult to treat because the organisms in a biofilm are protected from the circulating antimicrobials. Up till now, there have been relatively few studies investigating biofilm development in clinical isolates. Current in vitro methods for studying microbial adhesion and growth on biomaterial surfaces lack the influence of the host immune system, endorsing the specific need for animal models that allow temporal and spatial measurements based on non-invasive bio-imaging techniques using reporter strains. To improve our ability to prevent and/or treat biofilms, we need a better understanding of their formation and persistence. The specific goals of this research proposal are to i) understand the physiology of mono- and polymicrobial biofilms, with focus on staphylococci and Candida spp., isolated from indwelling devices from ICU patients and ii) implement in vitro and in vivo laboratory biofilm models that adequately reflect the real-life situation.

            Researcher(s)

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            Routine diagnostic tool for urinary tract infections caused by ESBL and carbapenamase producing bacteria (ROUTINE). 01/09/2012 - 29/02/2016

            Abstract

            In ROUTINE, 3 SMEs and 2 Universities will develop a prototype benchtop instrument that will rapidly (< 30 min) detect bacteria and characterize key antibiotics resistance profiles of ESBL (extended spectrum betalactamase) and carbapenemase producing GNB directly from the patient urine at the point of care in outpatients and hospitals at a low cost (~20 €/test) and with near 100% sensitivity and specificity.

            Researcher(s)

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              Characterizing host-pathogen interactions and biofilm formation in patients developing pneumonia on assisted ventilation. 01/01/2012 - 31/12/2015

              Abstract

              Our study proposes to firstly identify early predictors of pneumonia and secondly, utilize both human samples and rodent models to investigate distinct host-pathogen signatures during colonization and development of VAP by two marker organisms, Pseudomonas aeruginosa and Escherichia coli that not only show diverse pathogenetic profiles but are also most important for VAP etiology.

              Researcher(s)

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                Methicillin-resistant Staphylococcus aureus: Exploring the 'biofilmome' for markers of infection. 01/01/2012 - 31/12/2014

                Abstract

                In this project, we aim to: (1) Investigate gene expression profiles of planktonic cultures and of MRSA biofilms developed in vitro and, (2) Validate the identified 'biofilm markers' on patient samples (blood, wound swabs and sputum).

                Researcher(s)

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                  Resistance in gram-negative organisms: studying intervention strategies (R-GNOSIS). 01/10/2011 - 31/03/2017

                  Abstract

                  R-GNOSIS (2011-2015) combines 5 international clinical intervention studies, all supported by highly innovative microbiology and mathematical modelling, to determine - in the most relevant patient populations - the efficacy and effectiveness of cutting-edge interventions to reduce acquisition, carriage, infection and spread of Multi-Drug Resistant Gram-negative Bacteria (MDR-GNB). All clinical work-packages (WPs) will progress science beyond the state-of-the-art in generating new and translational clinically relevant knowledge, through hypothesis-driven studies with a focus on patient-centred outcomes that matter to the people of Europe and beyond. The studies and analyses proposed in R-GNOSIS will generate a step-change in identifying evidence-based preventive measures and clinical guidance for primary care and hospital-based physicians, as well as health-care authorities, to combat the spread and impact of the unprecedented rise of infections caused by MDR-GNB in Europe. The University of Antwerp (UA) is leading the work package on 'Functional microbiology and within-host transmission dynamics of genes, plasmids and clones of MDR-GNB'. Here, we will apply a "bedside-to-bench" translational approach to study the impact of antibiotics and gut decolonization on MDR-GNB pathogens and commensals in the community or hospital utilizing state-of-the-art microbiological tools. Our sophisticated in vitro analyses to investigate resistance gene transfer and the ecology and evolution of resistance will also facilitate ground-breaking modelling studies. Results from the diagnostic interventions planned here will revolutionize current screening practices for MDR-GNBs in hospitals and introduce the use of point-of-care testes (POCTs) in primary care.

                  Researcher(s)

                  Research team(s)

                    The role of bacterial biofilms as a major cause of therapeutic failure in intensive care units (ICU): an in vitro and in vivo study of 'biofilm' virulence factors. 01/01/2011 - 31/12/2014

                    Abstract

                    Bacterial isolates from intensive care unit patients will be collected from urinary and intravascular catheters and endotracheal tubes. The biofilm phenotype in relation to antibiotic treatment failure will be investigated using molecular biological, bio-imaging techniques and in vitro and in vivo biofilm models. Particular emphasis will be given to Escherichia coli for urinary tract infections (UTI), Pseudomonas aeruginosa for ventilation associated pneumonia (VAP) and Staphylococcus aureus for systemic infections related to venous catheters. The acquired library of fully typed strains will enable in depth study of putative virulence factors that contribute to biofilm formation and treatment failure.

                    Researcher(s)

                    Research team(s)

                    Characterizing the naso-oro-pharyngeal microbiome and resistome in the European population. 01/01/2011 - 31/12/2013

                    Abstract

                    The present study aims to combine culture-independent high-resolution sequencing techniques with functional screens to fully characterize the human naso-oro-pharyngeal microbiome and study variations in the antibiotic resistance reservoir in geographically diverse European populations.

                    Researcher(s)

                    Research team(s)

                      Antibiotic resistant pathogenic bacteria present in the environment and human commensal flora: is there a link with disease? 01/10/2010 - 09/05/2013

                      Abstract

                      The main aim of this study is to provide a comprehensive picture of the level of clinical relevant antibiotic resistant bacteria (ARB) in the environment and commensal flora in Gauteng/South Africa. Besides, the genetic relatedness of these ARB will be studied to understand the mechanisms of antibiotic resistance dissemination in the community.

                      Researcher(s)

                      Research team(s)

                        In vitro and in vivo study of mono- and polymicrobial biofilms as a major cause of therapeutic failure in intensive care units (ICU). 01/10/2010 - 30/09/2012

                        Abstract

                        Biofilm-related infections prove exceedingly difficult to treat because the organisms in a biofilm are protected from the circulating antimicrobials. Up till now, there have been relatively few studies investigating biofilm development in clinical isolates. Current in vitro methods for studying microbial adhesion and growth on biomaterial surfaces lack the influence of the host immune system, endorsing the specific need for animal models that allow temporal and spatial measurements based on non-invasive bio-imaging techniques using reporter strains. To improve our ability to prevent and/or treat biofilms, we need a better understanding of their formation and persistence. The specific goals of this research proposal are to i) understand the physiology of mono- and polymicrobial biofilms, with focus on staphylococci and Candida spp., isolated from indwelling devices from ICU patients and ii) implement in vitro and in vivo laboratory biofilm models that adequately reflect the real-life situation.

                        Researcher(s)

                        Research team(s)

                        Impact of specific antibiotic therapies on the prevalence of human host resistant bacteria (SATURN). 01/01/2010 - 31/12/2014

                        Abstract

                        SATURN (Impact of Specific Antibiotic Therapies on the prevalence of hUman host ResistaNt bacteria; 2010-2014) is a collaborative research project that is funded as part of the 7th framework programme by the EU. SATURN aims to improve methodological standards and conduct research that will help to better understand the impact of antibiotic use on acquisition, selection and transmission of antimicrobial resistance (AMR) in different environments, by combining analyses of molecular, individual patient-level as well as ecologic data. The anticipated results may guide clinical and policy decisions to ultimately reduce the burden of AMR in Europe. Several clinical trials conducted both in hospitals and in the community will serve as a platform for basic microbiological and pharmacological research carried out by several academic institutions throughout Europe. The University of Antwerp (UA) is coordinating the work package on bacterial genetics and functional studies. The main objective of this WP is to study the abilities of various antibiotics to select for resistance in the respiratory and intestinal flora of patients and their contacts or in nonantibiotic-treated controls and compare the persistence of the selected resistant bacteria over time following antibiotic administration. The functional and genetic studies planned here will utilize both in vitro and in vivo models to dissect the human microbiome. Further studies on the population biology, clonal fitness, and virulence potential of antibiotic-resistant and antibiotic-sensitive bacteria will uncover the mechanisms underlying the successful dissemination of major AMR clones in Europe.

                        Researcher(s)

                        Research team(s)

                          Identification of novel surface-expressed factors mediating virulence and biofilm formation in methicillin-resistant Staphylococcus aureus. 01/01/2010 - 31/12/2013

                          Abstract

                          A first objective of the project is the identification of genes encoding novel virulence factors, which are expressed at the bacterial surface of MRSA. A second objective is to study the differences in biofilm-forming capabilities between hospital-acquired (HA) and community-acquired (CA)-MRSA in the presence and absence of antibiotic pressure. A third objective of this project is to find an explanation why certain MRSA clones are highly epidemic.

                          Researcher(s)

                          Research team(s)

                            A highly integrated optical sensor for point of care label free identification of pathogenic bacteria strains and their antibiotic resistance. (InTopSens) 01/09/2008 - 31/08/2011

                            Abstract

                            InTopSens aims to design fast photonic label-free smart biosensors with detection limits below 1 pg/mm2, and integrate multiple biosensors on a disposable label-free photonic biochip capable of identifying and determining antibiotic resistance of bacteria causing sepsis. Severe sepsis or septic shock is characterized by multi-organ dysfunction, failure and finally death. In the EU, sepsis is estimated to cause a loss of up to 146,000 lives every year and up to EUR 7.6 billion in patient health care costs. The most important intervention is rapid diagnosis followed by appropriate antibiotic treatment. However, the currently available 'rapid' assays are laboratory based with a total assay time of up to 12 hours, e.g. PCR. Hence, more often than not, antibiotic treatment has to be instituted empirically before test results arrive and this non-targeted, and quite often inappropriate, antibiotic use has led to multidrug resistance amongst bacteria including those causing sepsis. We intend to develop the InTopSens device into a modular assay for sepsis to detect the causative pathogen and also profile its antibiotic resistance at the patient's bed-side in Emergency/Intensive Care Units in hospitals. Upon introduction of a large drop of blood (~ 50 µl) onto the chip, presence of bacteria and identification to the genus/species level will be obtained within 5-10 mins, while the antibiotic resistance profile of the bacterial pathogen will be available within 30 mins. Some 120 sensing areas/datapoints are needed to identify this profile and as such due to the very high integration up to 5 assays can be integrated onto a 1cm2 chip of the same bacteria for higher sensitivity and selectivity or for other bacteria. A final prototype consisting of a packaged biochip will be validated both preclinically and clinically to assess the potential of this sepsis assay in preventing/reducing inappropriate antibiotic therapy and mortality in sepsis patients.

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                              Project website

                              Evidence for a Novel Efflux Pump Mediating Telithromycin Resistance in Macrolide-Resistant Streptococcus pyogenes. 01/01/2008 - 31/12/2009

                              Abstract

                              Telithromycin (Tel), an advanced macrolide was developed to combat macrolide-resistant pathogens, although some S. pyogenes harbouring the erm(B) methylase can exhibit Tel resistance (Tel-R). However, we have evidenced, for the first time, Tel efflux mediated by a reserpine-sensitive pump in high-level Tel-R S. pyogenes that also harbour erm(B). Gene expression studies are planned to unequivocally establish the contribution of this pump to Tel-R.

                              Researcher(s)

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                                Mechanisms of antibiotic resistance and tolerance and the associated fitness costs in streptococci causing respiratory tract infections. 01/10/2007 - 30/09/2010

                                Abstract

                                The aim of this project is 1. Analyse baseline resistance and changes effected by amoxicillin use on the oropharyngeal bacteria of LRTI patients and study the mechanisms of phenotypic tolerance in this patient population. 2. Elucidate telithromycin resistance mechanisms in SPY. 3. Determine the fitness costs and any compensatory mutations in macrolide- (including telithromycin) resistant SPY and amoxicillin-resistant SPN.

                                Researcher(s)

                                Research team(s)