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Amine Mohamed BOUKERB, PhD LMSM - EA431255 Rue Saint-Germain27000 Evreux, Franceamine.boukerb@univ-rouen.fr+33 (0) 650 878 112

MICROBIAL ECOLOGY AND META-OMICS

PROFESSIONAL SKILLS

Scientific & technical Molecular biology

Bioinformatics

Bacteriology

Plant biology

Animal testing

Biostatistics

Metrology

Project management

Communication

Supervision

Languages

High-throughput PCR, q/ddPCR, cloning, microbiome studies with DNA extraction, libraries preparation & sequencing (Illumina & MinION technologies)

Comparative genomics (SeqSphere, MaGe...), metagenomics (Qiime, Mothur, Frogs, MetaVelvet, MetaQuast...), virulome/resistome screenings (CGE toolbox...)

Isolation (microaerophilic bacteria), enumeration (MPN-PCR, Idexx) and identification (Vitek2, Omnilog, API), confocal microscopy, laboratory level P2

Cultivation of macrophytes and in vitro colonization (adhesion-biofilm) assays

Development and practice of animal experimentation protocols

Rtudio, Statistica, xlstat

Experimental site: maintenance, quality assurance control, calibration of measuring instruments, safety, sampling, metadata management

Multidisciplinary projects: co-writing project reports, fund raising, organizing meeting and field trips, order management and inventory Oral presentations in team meetings and national/international conferences. Research synthesis, writing of scientific publications

BTS, License, Master and PhD students: general rules in P2-level laboratory, bacteriology, molecular biology and bioinformatics

Arabic (mother tongue), French and English (fluent; professional languages)

RESEARCH EXPERIENCE

Dec 2016 – May 2018

Sep 2016 - Nov 2016

Apr 2012 - Dec 2015

Since June 2018

PostDoc – Health and Environment Microbiology Laboratory – IFREMER Brest - Bacterial communities in river/seawaters, shellfish, sea birds and seals feces- MST (Microbial Source Tracking) tools for fecal pollution management- Campylobacter spp. culture and genomics

Invited early career researcher – Environmental & Public Health Microbiology Laboratory – Monash University, Melbourne (Australia) - Campylobacter spp. culture and genomics

PhD in Microbial Ecology – UMR 5557 Microbial Ecology Laboratory – Lyon - Ecology and genomics of Pseudomonas aeruginosa in aquatic environments- Antiadhesive properties of glycoclusters against P. aeruginosa lung infection

Research Associate – Microbiology, Signals and Microenvironment Lab - Rouen University and Evreux IUT-Skin microbiome and air pollution : effects of nitrogen dioxide (NO2)-Food microbiome: dynamics of microbial contaminants and phage signatures-Whole genome sequencing and analysis of bacterial pathogens

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TRAININGS

2013 (3 weeks) Inter-university diploma: Animal experimentation level 1 - Health and safety rules, writing experimental protocols and handling of animals

2013 (2 days) Excel: data and pivot tables bases 2013 (3 days) Analysis of genomic sequences and phylogeny: PARABI Lyon 2013(1 week) Statistics : R, PCA, time series, spatial and space-time data 2013 (4 days) Annotation and analysis of bacterial genomes: Génoscope (MAGE platform)

PUBLICATIONS (on June 2018)APPENDIX

Peer-reviewed papers

Published papers

1. Boukerb AM, Décor A, Ribun S, Tabaroni S, Rousset A, Commin L, Buff S, Doléans-Jordheim A, VidalA, Varrot A, Imberty A and Cournoyer B. 2016. Genomic rearrangements and functional diversification oflecA and lecB lectin-coding regions impacting the efficacy of glycomimetics directed againstPseudomonas aeruginosa. Frontiers in Microbiology, 7: 811 (cited 5 times, IF 4.1)

2. Boukerb AM, Marti R and Cournoyer B. 2015. Genome sequences of three strains of thePseudomonas aeruginosa PA7 clade. ASM Genome Announcement, 3: e01366-15 (cited 7 times)

3. Boukerb AM, Rousset A, Galanos N, Méar JB, Gillon E, Cecioni S, Abderrahmen C, Faure K, RedelbergerD, Kipnis E, Dessein R, Matthews SE, de Bentzmann S, Guéry B, Cournoyer B, Imberty A, Havet S, DarbladeB and Vidal S. 2014. Anti-adhesive properties of glycoclusters against Pseudomonas aeruginosa lunginfection. Journal of Medicinal Chemistry, 57(24): 10275-89 (cited 46 times, IF 6.2)

4. Petit SM, Lavenir R, Colinon-Dupuich C, Boukerb AM, Cholley P, Bertrand X, Freney J, Doléans-Jordheim A, Nazaret S, Laurent F and Cournoyer B. 2013. Lagooning of wastewaters favors disseminationof clinically relevant Pseudomonas aeruginosa. Research in Microbiology, 164:856-66 (cited 9 times, IF2.5)

Under internal review or in preparation papers

1. Boukerb AM, Petit SM, Marjolet L, Gleizal A, Moulin B, Fantino G, Schmitt L, Navratil O, McCarthyDT, Prigent-Combaret C, Breil P and Cournoyer B. Hydrologically-driven population changes ofclinically relevant Pseudomonas aeruginosa adhering on river macrophytes and inert surfaces.Under internal review (for Environmental Pollution Journal, IF 5.1)

2. Boukerb AM, Jayaprakash B, Quenot E, Pitkänen P and Gourmelon M. Diversity of ribosomal 16SDNA- and RNA-based bacterial communities in shellfish and waters in a shellfish-harvesting area and itscatchment in France. Under internal review (for Journal of Applied Microbiology, IF 2.1)

3. Henry R, Edmunds M, Boukerb AM, Bulach B, Korman T, Prosser T, Grant T, Crosbie N andMcCarthy DT. The river runs through: Understanding the human health risks of Campylobacterjejuni and Campylobacter coli in recreational waters. Under internal review (for Water Research, IF 6.9)

4. Meng Z, Henry R, Boukerb AM, Deletic A and McCarthy DT. Understanding the sources and risks ofCampylobacter to stormwater constructed wetlands. Under internal review (for Water Research, IF6.9)

5. Boukerb AM, Navratil O, Breil P, Caurel C, Perret F, Lejot J, Petit SM, Marjolet L and Cournoyer B.Dynamic dispersion of Pseudomonas aeruginosa in response to cycles of low-flows and erosivefloods of a small peri-urban stream. In preparation

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6. Boukerb AM, Quenot E and Gourmelon M. Development of a novel qPCR assay-set for identifyingfecal pollution originating from a selection of sea-birds in France. In preparation

7. Boukerb AM, Gourmelon M, Cozien J, Walczak C, Cauchie HM, Miller WG, Losch S, Ragimbeau C,Mossong J, Mégraud F, Lehours P and Penny C. Campylobacter armorica sp. nov., a novel pathogenicmember of the Campylobacter lari group isolated from surface water and human diseased faeces. Inpreparation

Scientific newsletters (in French)

1. Boukerb AM et Cournoyer B. 2013. Pseudomonas aeruginosa, une espèce pathogène à forte fréquencede recombinaisons génétiques, abritant des lignées spécialisées et largement disséminées. Bulletin deveille scientifique ANSES. 20: 20-24

2. Boukerb AM et Cournoyer B. 2012. Exposition aux bactéries pathogènes : cas de la pluie et du sablede plage. Bulletin de veille scientifique ANSES. 18: 14-18

CONGRESSES AND CONFERENCES

Oral Presentations

1. Navratil O, Boukerb AM, Caurel C, Breil P, Perret F, Lejot J, Petit SM et Cournoyer B. Réponses descommunautés bactériennes fécales benthiques à la variabilité hydrologique d'un petit cours d'eau péri-urbain : La Chaudanne, ouest lyonnais. 42èmes Journées Scientifiques du GFHN. 28-29 novembre2017 ; Lyon, France

2. Boukerb AM, Jayaprakash B, Quenot E, Pitkänen T et Gourmelon M. Diversité des communautésbactériennes présentes dans les coquillages et les eaux d'une zone conchylicole et de son bassin versanten Bretagne. 8e Colloque de l’Association Francophone d’Ecologie Microbienne. 17-20 octobre2017 ; Camaret-sur-Mer, France

3. Henry R, Edmunds M, Boukerb AM, Bulach D, Korman T, Prosser T, Grant T, Crosbie N andMcCarthy.DT. The river runs through: Understanding the human health risks of C. jejuni and C. coli inrecreational waters. 19th International Workshop on Campylobacter, Helicobacter and RelatedOrganisms. September 10-14, 2017 ; Nantes, France

4. Penny C, Cozien J, Walczak C, Hubert C, Boukerb AM, Rincé A, Ragimbeau C, Mossong J, Mégraud F,Cauchie HM and Gourmelon M. Diversity of Campylobacter lari in a One-Health context: Focus onshellfish, wild birds, surface water and human health risk. 19th International Workshop onCampylobacter, Helicobacter and Related Organisms. September 10-14, 2017 ; Nantes, France

5. Gourmelon M, Cozien J, Walczak C, Hubert C, Boukerb AM, Rincé A, Ragimbeau C, Mossong J,Cauchie HM and Penny C. Diversity of Campylobacter lari, the most frequent Campylobacter species inshellfish and marine waters, in a shellfish-harvesting area and its catchment in France. UNC Water &Microbiology Conference. May 15-19, 2017 ; Chapel Hill, North Carolina, USA

6. Boukerb AM, Jayaprakash B, Quenot E, Pitkänen T and Gourmelon M. Bacterial communityprofiling of shellfish and waters in a shellfish-harvesting area and its catchment in France. UNC Water& Microbiology Conference. May 15-19, 2017 ; Chapel Hill, North Carolina, USA

7. Boukerb AM et Marti R. Animaux en ville: quel impact sanitaire pour l’écosystème urbain?Ateliers Expérimentaux IMUalpha - penser les circulations animales en milieu urbain. 13 février2015 ; Lyon, France

8. Boukerb AM et Cournoyer B. Pseudomonas aeruginosa dans les milieux aquatiques: sources,diversité et colonisation des macrophytes. GDR Pseudomonas. 23-25 novembre 2014 ; Carry-le-Rouet,France

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9. Navratil O, Boukerb AM, Lejot J, Breil P and Cournoyer B. Aquatic habitat analysis of a humanopportunistic pathogen in a small peri-urban river. Ecohydraulics Conference. June 23-27, 2014 ;Trondheim, Norway

10. Boukerb AM, Ribun S, Rousset A, Prigent-Combaret C, Imberty A, Vidal S et Cournoyer B. Etude desphénomènes d’agrégation de Pseudomonas aeruginosa en interaction avec des glycoconjuguéscalix[4]arène : rôle des lectines. 17e Journée Scientifique du Groupe Lyonnais des Glyco-Sciences. 5décembre 2013 ; Lyon, France

11. Breil P, Petit SM, Boukerb AM, Namour P, McCarthy DT and Cournoyer B. An approach topathogens flux simulation in a combined sewer system. Novatech’ 2013 International Conference.June 23-27 2013 ; Lyon, France

12. Boukerb AM et Cournoyer B. Pseudomonas aeruginosa dans les milieux aquatiques: sources,diversité et colonisation des macrophytes. GDR Pseudomonas. 11-12 octobre 2012 ; Autrans, France

Posters

1. Gourmelon M, Cozien J, Walczak C, Boukerb AM, Rincé A, Ragimbeau C, Mossong J, Megraud F,Cauchie HM et Penny C. Diversité des Campylobacter lari en zone littorale : étude au niveau d'une zoneconchylicole en Bretagne. 8e Colloque de l’Association Francophone d’Ecologie Microbienne. 17-20octobre 2017 ; Camaret-sur-Mer, France

2. Gourmelon M, Thépault A, Cozien J, Boukerb AM, Chemaly M and Rivoal K. Campylobacter jejuni atthe level of a coastal catchment in France. 19th International Workshop on Campylobacter, Helicobacter and Related Organisms. September 10-14, 2017 ; Nantes, France

3. Boukerb AM, Petit SM, McCarthy DT, Breil P et Cournoyer B. Amplitude du transfert par undéversoir d’orage de P. aeruginosa et devenir en milieu aquatique. 9e congrès de la société Françaisede Microbiologie. Février 2013 ; Lille, France