E. Khamisse, O. Firmesse, S. Christieans, D. Chassaing, and B. Carpentier, Analysis of the microbial community of a meat processing plant before and after cleaning and disinfection. Affiche, SfAM Summer Meeting, pp.4-07, 2011.

E. Khamisse, O. Firmesse, S. Christieans, D. Chassaing, and B. Carpentier, Etude du microbiote susceptible de persister dans un atelier de la filière viande bovine avant et après nettoyage-désinfection. Communication orale, Commission R&D du SNIV- SNCP, 25 Novembre, 2011.

G. Agustí, F. Codony, M. Fittipaldi, B. Adrados, and J. Morató, Viability Determination of Helicobacter pylori Using Propidium Monoazide Quantitative PCR, Helicobacter, vol.17, issue.5, pp.473-476, 2010.
DOI : 10.1111/j.1523-5378.2010.00794.x

M. Alliot, Ecologie microbienne des sites industriels fromagers : identification, caractérisation des flores isolées et étude des facteurs régissant leur implantation, Ph. D, 1999.

R. I. Amann, W. Ludwig, and K. H. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiology and Molecular Biology Reviews, vol.59, p.143, 1995.

. Anonyme, Viandes et produits à base de viande-Dénombrements des micro-organismes, méthode par comptage des colonies obtenues à 25°C. Association Française de Normalisation NF V, pp.4-506, 1992.

. Anonyme, Salles propres et environnement maîtrisés apparentés Maîtrise de la biocontamination, 1999.

. Anonyme, Microbiologie des aliments -Méthodes horizontales pour les techniques de prélèvement sur des surfaces, au moyen de boîtes de contact et d'écouvillons. International Standard NF ISO 18593 Association Française de Normalisation, 2004.

C. D. Arajo, Mise au point d'une méthode de controle de l'efficacité du nettoyage et de la desinfection en élevage porcin, 2002.

A. Asséré, N. Oulahal, and B. Carpentier, Comparative evaluation of methods for counting surviving biofilm cells adhering to a polyvinyl chloride surface exposed to chlorine or drying, Journal of Applied Microbiology, vol.25, issue.6, pp.1692-1702, 2008.
DOI : 10.1007/BF02738539

S. Avrahami, R. Conrad, and G. Braker, Effect of soil ammonium concentration on N 2 O release and on the community structure of ammonia oxidizers and denitrifiers. Applied and environmental microbiology 68, p.5685, 2002.

D. Bagge-ravn, Y. Ng, M. Hjelm, J. N. Christiansen, C. Johansen et al., The microbial ecology of processing equipment in different fish industries???analysis of the microflora during processing and following cleaning and disinfection, International Journal of Food Microbiology, vol.87, issue.3, pp.239-250, 2003.
DOI : 10.1016/S0168-1605(03)00067-9

B. Baleux, A. Caro, J. Lesne, P. Got, S. Binard et al., Survie et maintien de la virulence de Salmonella Typhimurium VNC expos??e simultan??ment ?? trois facteurs stressants exp??rimentaux, Oceanologica Acta, vol.21, issue.6, pp.939-950, 1998.
DOI : 10.1016/S0399-1784(99)80017-6

N. Bano and J. T. Hollibaugh, Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean Applied and environmental microbiology 68, p.505, 2002.

F. Baruzzi, A. Matarante, L. Caputo, and M. Morea, Molecular and physiological characterization of natural microbial communities isolated from a traditional Southern Italian processed sausage, Meat Science, vol.72, issue.2, pp.261-269, 2006.
DOI : 10.1016/j.meatsci.2005.07.013

T. Benezech and M. Lalande, Le nettoyage en place (NEP) JY Leveau et M. Bouix: Nettoyage, désinfection et hygiène dans les bio-industries, pp.341-363, 1999.

A. Bernal, U. Ear, and N. Kyrpides, Genomes OnLine Database (GOLD): a monitor of genome projects world-wide, Nucleic Acids Research, vol.29, issue.1, pp.126-127, 2001.
DOI : 10.1093/nar/29.1.126

C. Bièche, M. De-lamballerie, D. Chevret, M. Federighi, and O. Tresse, Dynamic proteome changes in Campylobacter jejuni 81-176 after high pressure shock and subsequent recovery, Journal of Proteomics, vol.75, issue.4, pp.1144-1156, 2012.
DOI : 10.1016/j.jprot.2011.10.028

M. Bielaszewska, A. Mellmann, W. Zhang, R. Köck, A. Fruth et al., Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study, The Lancet Infectious Diseases, vol.11, issue.9, pp.671-676, 2011.
DOI : 10.1016/S1473-3099(11)70165-7

J. Bjorland, T. Steinum, B. Kvitle, S. Waage, M. Sunde et al., Widespread Distribution of Disinfectant Resistance Genes among Staphylococci of Bovine and Caprine Origin in Norway, Journal of Clinical Microbiology, vol.43, issue.9, p.4363, 2005.
DOI : 10.1128/JCM.43.9.4363-4368.2005

G. Bleve, L. Rizzotti, F. Dellaglio, and S. Torriani, Development of reverse transcription (RT)-PCR and real-time RT-PCR assays for rapid detection and quantification of viable yeasts and molds contaminating yogurts and pasteurized food products Applied and environmental microbiology 69, p.4116, 2003.

N. Boon, W. De-windt, W. Verstraete, and E. M. Top, Evaluation of nested PCR???DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants, FEMS Microbiology Ecology, vol.39, issue.2, pp.101-112, 2002.
DOI : 10.1016/S0168-6496(01)00198-2

E. Bossis, P. Lemanceau, X. Latour, and L. Gardan, : current status and need for revision, Agronomie, vol.20, issue.1, pp.51-63, 2000.
DOI : 10.1051/agro:2000112

L. Boulos, M. Prevost, B. Barbeau, J. Coallier, and R. Desjardins, LIVE/DEAD?? BacLight???: application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water, Journal of Microbiological Methods, vol.37, issue.1, pp.77-86, 1999.
DOI : 10.1016/S0167-7012(99)00048-2

F. Bourion and O. Cerf, Disinfection efficacy against pure-culture and mixed-population biofilms of Listeria innocua and Pseudomonas aeruginosa on stainless steel, Teflon and rubber, Sciences des Aliments, vol.16, pp.151-166, 1996.

J. Bowman, M. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer et al., The Genus Psychrobacter, pp.920-930, 2006.
DOI : 10.1007/0-387-30746-X_35

A. Bridier, R. Briandet, V. Thomas, and F. Dubois-brissonnet, Comparative biocidal activity of peracetic acid, benzalkonium chloride and ortho-phthalaldehyde on 77 bacterial strains, Journal of Hospital Infection, vol.78, issue.3, pp.208-213, 2011.
DOI : 10.1016/j.jhin.2011.03.014

URL : https://hal.archives-ouvertes.fr/hal-01004331

G. Brightwell, J. Boerema, J. Mills, E. Mowat, and D. Pulford, Identifying the bacterial community on the surface of Intralox??? belting in a meat boning room by culture-dependent and culture-independent 16S rDNA sequence analysis, International Journal of Food Microbiology, vol.109, issue.1-2, pp.47-53, 2006.
DOI : 10.1016/j.ijfoodmicro.2006.01.008

V. Brown and E. Lowbury, Use of an improved cetrimide agar medium and other culture methods for Pseudomonas aeruginosa, Journal of Clinical Pathology, vol.18, issue.6, p.752, 1965.
DOI : 10.1136/jcp.18.6.752

B. Lelieveld, H. L. Mostert, M. A. Holah, and J. T. , Aerosols as a contamination risk Handbook of Hygiene in The Food Industry, pp.93-102, 2005.

J. Byrd, J. Xu, H. Colwell, R. , and R. , Viable but nonculturable bacteria in drinking water, Applied and environmental microbiology, vol.57, pp.875-878, 1991.

C. , K. , S. , E. , W. et al., 16S rDNA analysis of bacterial diversity in three fractions of cow rumen, Journal of microbiology and biotechnology, vol.16, pp.92-101, 2006.

B. Carpentier, Biofilms in red meat processing, Biofilms in the food and beverage industries, pp.375-395, 2009.
DOI : 10.1533/9781845697167.4.375

B. Carpentier and O. Cerf, Persistence of Listeria monocytogenes in equipment and premises, pp.17-20, 2011.

E. O. Casamayor, H. Schafer, L. Baneras, C. Pedros-alio, and G. Muyzer, Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis, Applied and Environmental Microbiology, vol.66, issue.2, p.499, 2000.
DOI : 10.1128/AEM.66.2.499-508.2000

O. Cerf, B. Carpentier, and P. Sanders, Tests for determining in-use concentrations of antibiotics and disinfectants are based on entirely different concepts: ???Resistance??? has different meanings, International Journal of Food Microbiology, vol.136, issue.3, pp.247-254, 2010.
DOI : 10.1016/j.ijfoodmicro.2009.10.002

URL : https://hal.archives-ouvertes.fr/hal-00533747

M. C. Champomier-vergès, A. Stintzi, and J. M. Meyer, Acquisition of iron by the nonsiderophore-producing Pseudomonas fragi, Microbiology, vol.142, 1191.

K. Chen and L. Pachter, Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities, PLoS Computational Biology, vol.30, issue.2, p.24, 2005.
DOI : 0920-8569(2005)030[0151:AOTVPP]2.0.CO;2

N. T. Chen and C. W. Chang, Rapid quantification of viable legionellae in water and biofilm using ethidium monoazide coupled with real-time quantitative PCR, Journal of Applied Microbiology, vol.72, pp.623-634, 2010.
DOI : 10.1111/j.1365-2672.2010.04678.x

W. Chen, G. Martinez, and A. Mulchandani, Molecular Beacons: A Real-Time Polymerase Chain Reaction Assay for Detecting Salmonella, Analytical Biochemistry, vol.280, issue.1, pp.166-172, 2000.
DOI : 10.1006/abio.2000.4518

S. Christieans, P. Fravalo, and J. Frencia, Etude comparative de méthodes de prélèvement sur carcasses de bovins pour le dénombrement bactérien, 2006.

J. Chun, J. H. Lee, Y. Jung, M. Kim, S. Kim et al., EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences, International Journal of Systematic and Evolutionary Microbiology, vol.57, issue.10, pp.2259-2261, 2007.
DOI : 10.1099/ijs.0.64915-0

R. M. Clegg, Fluorescence resonance energy transfer, Current Opinion in Biotechnology, vol.6, issue.1, pp.103-110, 1995.
DOI : 10.1016/0958-1669(95)80016-6

L. Cocolin, M. Manzano, C. Cantoni, and G. Comi, Denaturing Gradient Gel Electrophoresis Analysis of the 16S rRNA Gene V1 Region To Monitor Dynamic Changes in the Bacterial Population during Fermentation of Italian Sausages, Applied and Environmental Microbiology, vol.67, issue.11, p.5113, 2001.
DOI : 10.1128/AEM.67.11.5113-5121.2001

R. R. Colwell, P. Brayton, D. Herrington, B. Tall, A. Huq et al., Viable but non-culturable Vibrio cholerae O1 revert to a cultivable state in the human intestine, World Journal of Microbiology and Biotechnology, vol.8, issue.1, pp.28-31, 1996.
DOI : 10.1007/BF00327795

C. Morot-bizot, S. Leroy, S. Talon, and R. , Staphylococcal community of a small unit manufacturing traditional dry fermented sausages, International Journal of Food Microbiology, vol.108, issue.2, pp.210-217, 2006.
DOI : 10.1016/j.ijfoodmicro.2005.12.006

E. Coton, N. Mulder, M. Coton, S. Pochet, H. Trip et al., Origin of the Putrescine-Producing Ability of the Coagulase-Negative Bacterium Staphylococcus epidermidis 2015B, Applied and Environmental Microbiology, vol.76, issue.16, pp.5570-5576, 2010.
DOI : 10.1128/AEM.00441-10

C. Cotte, S. Orenga, R. Andréa, and D. Robichon, Staphylococcus aureus specific detection media and identifying and/or counting method using same EP Patent 1, p.390524, 2006.

J. Criquelion, F. Durand, F. Olivier, G. Rauwel, and F. Sabat, Caractéristiques générales des fonctions chimiques désinfectantes, Nettoyage, désinfection et hygiène dans les bio-industries (Collection STAA), 1999.

B. C. Crump, C. S. Hopkinson, M. L. Sogin, and J. E. Hobbie, Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time, Applied and Environmental Microbiology, vol.70, issue.3, 1494.
DOI : 10.1128/AEM.70.3.1494-1505.2004

R. Dainty and B. Mackey, The relationship between the phenotypic properties of bacteria from chill-stored meat and spoilage processes, Journal of Applied Bacteriology, vol.62, pp.103-114, 1992.
DOI : 10.1111/j.1365-2672.1992.tb03630.x

I. Day, S. D. O-'dell, I. D. Cash, S. E. Humphries, and G. P. Weavind, Electrophoresis for genotyping: temporal thermal gradient gel electrophoresis for profiling of oligonucleotide dissociation, p.2404, 1995.

P. Deberghes, T. Kleiss, J. L. Cordier, J. P. Vincent, J. Hornez et al., Amelioration de l'efficacité du prélèvement de surface par utilisation d'éponges. Microbiologie-Aliments-Nutrition, pp.409-412, 1995.

C. Delbes and M. C. Montel, Design and application of a Staphylococcus-specific single strand conformation polymorphism-PCR analysis to monitor Staphylococcus populations diversity and dynamics during production of raw milk cheese, Letters in Applied Microbiology, vol.49, issue.2, pp.169-174, 2005.
DOI : 10.1016/0168-1605(96)00952-X

P. Dennis, E. A. Edwards, S. N. Liss, and R. Fulthorpe, Monitoring gene expression in mixed microbial communities by using DNA microarrays Applied and environmental microbiology 69, p.769, 2003.

L. Dijkshoorn, K. J. Towner, and M. Struelens, New approaches for the generation and analysis of microbial typing data Elsevier Science, 2001.

J. Doré and L. Rigottier-gois, Molecular analysis of the colonic microflora, Gastroenterol Clin Biol, vol.25, pp.74-78, 2001.

M. Drancourt, C. Bollet, A. Carlioz, R. Martelin, J. P. Gayral et al., 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates, Journal of clinical microbiology, vol.38, p.3623, 2000.

M. Drancourt and D. Raoult, rpoB Gene Sequence-Based Identification of Staphylococcus Species, Journal of Clinical Microbiology, vol.40, issue.4, 1333.
DOI : 10.1128/JCM.40.4.1333-1338.2002

F. Duthoit, J. J. Godon, and M. C. Montel, Bacterial Community Dynamics during Production of Registered Designation of Origin Salers Cheese as Evaluated by 16S rRNA Gene Single-Strand Conformation Polymorphism Analysis, Applied and Environmental Microbiology, vol.69, issue.7, p.3840, 2003.
DOI : 10.1128/AEM.69.7.3840-3848.2003

C. Eckert, J. Van-broeck, P. Spigaglia, B. Burghoffer, M. Delmee et al., Comparison of a commercially available rep-PCR system (Diversilab (R)) with PCR-ribotyping for typing of Clostridium difficile strains, Journal of clinical microbiology, pp.324-00311, 2011.

L. Ellerbroek, Airborne microflora in poultry slaughtering establishments, Food Microbiology, vol.14, issue.6, pp.527-531, 1997.
DOI : 10.1006/fmic.1997.0119

D. Ercolini, F. Russo, E. Torrieri, P. Masi, and F. Villani, Changes in the Spoilage-Related Microbiota of Beef during Refrigerated Storage under Different Packaging Conditions, Applied and Environmental Microbiology, vol.72, issue.7, pp.4663-4671, 2006.
DOI : 10.1128/AEM.00468-06

J. P. Euzéby, List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet, International Journal of Systematic and Evolutionary Microbiology, vol.47, issue.2, pp.590-592, 1997.
DOI : 10.1099/00207713-47-2-590

E. Fan, D. Levin, B. Glickman, and D. Logan, Limitations in the use of SSCP analysis, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.288, issue.1, pp.85-92, 1993.
DOI : 10.1016/0027-5107(93)90210-7

S. Fischer and L. Lerman, DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory., Proceedings of the National Academy of Sciences, vol.80, issue.6, p.1579, 1983.
DOI : 10.1073/pnas.80.6.1579

P. Forsman, A. Tilsaia-timisjärvi, and T. Alatossava, Identification of staphylococcal and streptococcal causes of bovine mastitis using 16S-23S rRNA spacer regions, Microbiology, vol.143, issue.11, p.3491, 1997.
DOI : 10.1099/00221287-143-11-3491

N. Y. Fortin, A. Mulchandani, and W. Chen, Use of Real-Time Polymerase Chain Reaction and Molecular Beacons for the Detection of Escherichia coli O157:H7, Analytical Biochemistry, vol.289, issue.2, pp.281-288, 2001.
DOI : 10.1006/abio.2000.4935

P. Frey, P. Frey-klett, J. Garbaye, O. Berge, and T. Heulin, Metabolic and genotypic fingerprinting of fluorescent pseudomonads associated with the Douglas fir-Laccaria bicolor mycorrhizosphere, Applied and environmental microbiology, vol.63, p.1852, 1997.

G. P. Gafan and D. A. Spratt, Denaturing gradient gel electrophoresis gel expansion (DGGEGE) ?????? An attempt to resolve the limitations of co-migration in the DGGE of complex polymicrobial communities, FEMS Microbiology Letters, vol.253, issue.2, pp.303-307, 2005.
DOI : 10.1016/j.femsle.2005.09.048

M. Garcia-lopez, M. Prieto, and A. Otero, The physiological attributes of Gram-negative bacteria associated with spoilage of meat and meat products. The microbiology of meat and poultry, pp.1-34, 1998.

J. García-martínez, I. Bescós, J. J. Rodríguez-sala, and F. Rodríguez-valera, RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions, Nucleic Acids Research, vol.29, issue.1, p.178, 2001.
DOI : 10.1093/nar/29.1.178

G. A. Gardner, T. , and A. , Psychotrophic micro-organisms in spoilage and pathogenicity, pp.139-173, 1982.

P. Giammarinaro, S. Leroy, J. P. Chacornac, J. Delmas, and R. Talon, Development of a New Oligonucleotide Array To Identify Staphylococcal Strains at Species Level, Journal of Clinical Microbiology, vol.43, issue.8, p.3673, 2005.
DOI : 10.1128/JCM.43.8.3673-3680.2005

S. Giglio, P. T. Monis, and C. P. Saint, Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR, Nucleic acids research 31, p.136, 2003.
DOI : 10.1093/nar/gng135

R. J. Gilbert, SUMMARY, Journal of Hygiene, vol.1964, issue.02, pp.221-232, 1970.
DOI : 10.1017/S0022172400041656

URL : https://hal.archives-ouvertes.fr/hal-00088487

I. Giovannacci, C. Ragimbeau, S. Queguiner, G. Salvat, J. L. Vendeuvre et al., Listeria monocytogenes in pork slaughtering and cutting plants, International Journal of Food Microbiology, vol.53, issue.2-3, pp.127-140, 1999.
DOI : 10.1016/S0168-1605(99)00141-5

A. N. Glazer and R. A. Mathies, Energy-transfer fluorescent reagents for DNA analyses, Current Opinion in Biotechnology, vol.8, issue.1, pp.94-102, 1997.
DOI : 10.1016/S0958-1669(97)80163-2

R. Gonzales, Etude comparative des différentes techniques manuelles de controle de l'état microbiologique des surfaces, XII-Institut National des Sciences et Techniques Nucléaires, 1995.

N. D. Gray, I. P. Miskin, O. Kornilova, T. P. Curtis, and I. M. Head, Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants, Environmental Microbiology, vol.5, issue.3, pp.158-168, 2002.
DOI : 10.1016/S0043-1354(97)00235-2

R. Grosskopf, P. H. Janssen, and W. Liesack, Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval, Applied and environmental microbiology, vol.64, p.960, 1998.

J. Handelsman, Metagenomics: Application of Genomics to Uncultured Microorganisms, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.669-685, 2004.
DOI : 10.1128/MMBR.68.4.669-685.2004

C. Haroux, Le nettoyage par voie enzymatique : vers une hygiene propre et douce, Nettoyage, désinfection et hygiène dans les bio-industries (Collection STAA), 1999.

J. Harvey, K. Keenan, and A. Gilmour, Assessing biofilm formation by Listeria monocytogenes strains, Food Microbiology, vol.24, issue.4, pp.380-392, 2007.
DOI : 10.1016/j.fm.2006.06.006

M. Healy, J. Huong, T. Bittner, M. Lising, S. Frye et al., Microbial DNA Typing by Automated Repetitive-Sequence-Based PCR, Journal of Clinical Microbiology, vol.43, issue.1, 0199.
DOI : 10.1128/JCM.43.1.199-207.2005

C. A. Heid, J. Stevens, K. J. Livak, and P. M. Williams, Real time quantitative PCR., Genome Research, vol.6, issue.10, p.986, 1996.
DOI : 10.1101/gr.6.10.986

H. G. Heilig, E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D. Akkermans et al., Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA Applied and environmental microbiology 68, 2002.

E. Heir, G. Sundheim, and A. L. Holck, Identification and characterization of quaternary ammonium compound resistant staphylococci from the food industry, International Journal of Food Microbiology, vol.48, issue.3, pp.211-219, 1999.
DOI : 10.1016/S0168-1605(99)00044-6

A. Hilton, J. Banks, and C. Penn, Random amplification of polymorphic DNA (RAPD) of Salmonella: strain differentiation and characterization of amplified sequences, Journal of Applied Microbiology, vol.99, issue.30, pp.575-584, 1996.
DOI : 10.1093/nar/18.22.6531

Y. Hirai, Survival of bacteria under dry conditions; from a viewpoint of nosocomial infection, Journal of Hospital Infection, vol.19, issue.3, pp.191-200, 1991.
DOI : 10.1016/0195-6701(91)90223-U

J. T. Holah and R. H. Thorpe, Cleanability in relation to bacterial retention on unused and abraded domestic sink materials, Journal of Applied Bacteriology, vol.1, issue.4, pp.599-608, 1990.
DOI : 10.1111/j.1365-2672.1990.tb01554.x

W. H. Holzapfel, The Gram-positive bacteria associated with meat and meat products. The microbiology of meat and poultry, pp.35-84, 1998.

T. Hoppe-seyler, B. Jaeger, W. Bockelmann, W. Noordman, A. Geis et al., Molecular Identification and Differentiation of Staphylococcus Species and Strains of Cheese Origin, Systematic and Applied Microbiology, vol.27, issue.2, pp.211-218, 2004.
DOI : 10.1078/072320204322881835

L. Imamovic, E. Balleste, J. Jofre, and M. Muniesa, Quantification of Shiga Toxin-Converting Bacteriophages in Wastewater and in Fecal Samples by Real-Time Quantitative PCR, Applied and Environmental Microbiology, vol.76, issue.17, p.5693, 2010.
DOI : 10.1128/AEM.00107-10

C. Jacquet and A. Reynaud, Differences in the sensitivity to eight disinfectants of Listeria monocytogenes strains as related to their origin (short note), International Journal of Food Microbiology, vol.22, issue.1, pp.79-83, 1994.
DOI : 10.1016/0168-1605(94)90010-8

P. Jaudon, Hygiène et propreté des surfaces en milieu agro-alimentaire: produits humides Éd, 2000.

A. Jawad, A. Snelling, J. Heritage, and P. Hawkey, spp., FEMS Microbiology Letters, vol.165, issue.2, pp.357-362, 1998.
DOI : 10.1111/j.1574-6968.1998.tb13170.x

D. K. Jeng, L. I. Lin, and L. V. Hervey, Importance of ultrasonication conditions in recovery of microbial contamination from material surfaces, Journal of Applied Bacteriology, vol.4, issue.5, pp.479-484, 1990.
DOI : 10.1111/j.1365-2672.1990.tb02899.x

Y. Jiang, F. Gao, X. Xu, Y. Su, K. Ye et al., Changes in the bacterial communities of vacuum-packaged pork during chilled storage analyzed by PCR???DGGE, Meat Science, vol.86, issue.4, pp.889-895, 2010.
DOI : 10.1016/j.meatsci.2010.05.021

Y. Jiang, F. Gao, X. Xu, K. Ye, and G. Zhou, Changes in the Composition of the Bacterial Flora on Tray-Packaged Pork during Chilled Storage Analyzed by PCR-DGGE and Real-Time PCR, Journal of Food Science, vol.146, issue.1, pp.27-33, 2011.
DOI : 10.1111/j.1750-3841.2010.01879.x

M. V. Jones, T. M. Herd, and H. J. Christie, Resistance of Pseudomonas aeruginosa to amphoteric and quaternary ammonium biocides, Microbios, vol.58, pp.49-61, 1989.

A. Karsai, S. Muller, S. Platz, and M. T. Hauser, Evaluation of a homemade SYBR® Green I reaction mixture for real-time PCR quantification of gene expression, Biotechniques, vol.32, pp.790-796, 2002.

J. Kaur, S. Radu, F. M. Ghazali, and C. Y. Kqueen, Real-time PCR-based detection and quantification of genetically modified maize in processed feeds commercialised in Malaysia, Food Control, vol.21, issue.11, pp.1536-1544, 2010.
DOI : 10.1016/j.foodcont.2010.03.018

A. Khamis, D. Raoult, L. Scola, and B. , rpoB Gene Sequencing for Identification of Corynebacterium Species, Journal of Clinical Microbiology, vol.42, issue.9, p.3925, 2004.
DOI : 10.1128/JCM.42.9.3925-3931.2004

K. Kogure, U. Simidu, and N. Taga, A tentative direct microscopic method for counting living marine bacteria, Canadian Journal of Microbiology, vol.25, issue.3, pp.415-420, 1978.
DOI : 10.1139/m79-063

J. Kozdrój and J. D. Van-elsas, Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches, Journal of Microbiological Methods, vol.43, issue.3, pp.197-212, 2001.
DOI : 10.1016/S0167-7012(00)00197-4

E. P. Krysinski, L. J. Brown, and T. J. Marchisello, Effect of Cleaners and Sanitizers on Listeria monocytogenes Attached to Product Contact Surfaces, Journal of Food Protection, vol.55, issue.4, pp.246-251, 1992.
DOI : 10.4315/0362-028X-55.4.246

Y. Kukita, T. Tahira, S. S. Sommer, and K. Hayashi, SSCP analysis of long DNA fragments in low pH gel, Human Mutation, vol.24, issue.5, pp.400-407, 1997.
DOI : 10.1002/(SICI)1098-1004(1997)10:5<400::AID-HUMU11>3.0.CO;2-3

L. Kulakova, A. Galkin, T. Nakayama, T. Nishino, and N. Esaki, Cold-active esterase from Psychrobacter sp. Ant300: gene cloning, characterization, and the effects of Gly???Pro substitution near the active site on its catalytic activity and stability, BBA) -Proteins &amp, pp.59-65, 2004.
DOI : 10.1016/j.bbapap.2003.09.008

I. V. Kutyavin, I. A. Afonina, A. Mills, V. V. Gorn, E. A. Lukhtanov et al., 3'-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures, Nucleic acids research 28, p.655, 2000.
DOI : 10.1093/nar/28.2.655

J. Labadie, Les écosystemes microbiens dans les produits carnés. Viandes et produits, 2004.

V. Lafarge, J. C. Ogier, V. Girard, V. Maladen, J. Y. Leveau et al., Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration, Applied and Environmental Microbiology, vol.70, issue.9, p.5644, 2004.
DOI : 10.1128/AEM.70.9.5644-5650.2004

S. Langsrud and G. Sundheim, Factors contributing to the survival of poultry associated Pseudomonas spp. exposed to a quaternary ammonium compound, Journal of Applied Microbiology, vol.82, issue.6, pp.705-712, 1997.
DOI : 10.1046/j.1365-2672.1997.00186.x

L. M. Lawrence and A. Gilmour, Characterization of Listeria monocytogenes isolated from poultry products and from the poultry-processing environment by random amplification of polymorphic DNA and multilocus enzyme electrophoresis, Appl Environ Microbiol, vol.61, pp.2139-2144, 1995.

J. L. Lee and R. E. Levin, A comparative study of the ability of EMA and PMA to distinguish viable from heat killed mixed bacterial flora from fish fillets, Journal of Microbiological Methods, vol.76, issue.1, pp.93-96, 2009.
DOI : 10.1016/j.mimet.2008.08.008

H. Lelieveld, I. Mostert, B. White, and J. Holah, Hygiene in food processing: principles and practice Woodhead, 2003.
DOI : 10.1533/9781855737051

Y. Lequette, G. Boels, M. Clarisse, and C. Faille, Using enzymes to remove biofilms of bacterial isolates sampled in the food-industry, Biofouling, vol.5, issue.1, pp.421-431, 2010.
DOI : 10.1099/mic.0.28165-0

V. Leriche and B. Carpentier, Viable but Nonculturable Salmonella typhimurium in Single- and Binary-Species Biofilms in Response to Chlorine Treatment, Journal of Food Protection, vol.58, issue.11, pp.1186-1191, 1995.
DOI : 10.4315/0362-028X-58.11.1186

S. Leroy, P. Giammarinaro, J. P. Chacornac, I. Lebert, and R. Talon, Biodiversity of indigenous staphylococci of naturally fermented dry sausages and manufacturing environments of small-scale processing units, Food Microbiology, vol.27, issue.2, pp.294-301, 2010.
DOI : 10.1016/j.fm.2009.11.005

S. Leroy, I. Lebert, J. P. Chacornac, P. Chavant, T. Bernardi et al., Genetic diversity and biofilm formation of Staphylococcus equorum isolated from naturally fermented sausages and their manufacturing environment, International Journal of Food Microbiology, vol.134, issue.1-2, pp.46-51, 2009.
DOI : 10.1016/j.ijfoodmicro.2008.12.012

K. Lewis, Persister cells, dormancy and infectious disease, Nature Reviews Microbiology, vol.71, issue.1, pp.48-56, 2007.
DOI : 10.1128/AAC.00684-06

M. Li, G. Zhou, X. Xu, C. Li, and W. Zhu, Changes of bacterial diversity and main flora in chilled pork during storage using PCR-DGGE, Food Microbiology, vol.23, issue.7, pp.607-611, 2006.
DOI : 10.1016/j.fm.2006.01.004

K. Liolios, N. Tavernarakis, P. Hugenholtz, and N. C. Kyrpides, The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide, Nucleic Acids Research, vol.34, issue.90001, pp.332-334, 2006.
DOI : 10.1093/nar/gkj145

S. R. Lyons, A. L. Griffen, and E. J. Leys, Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria, Journal of Clinical Microbiology, vol.38, p.2362, 2000.

N. Marouani-gadri, G. Augier, and B. Carpentier, Characterization of bacterial strains isolated from a beef-processing plant following cleaning and disinfection ??? Influence of isolated strains on biofilm formation by Saka?? and EDL 933 E. coli O157:H7, International Journal of Food Microbiology, vol.133, issue.1-2, pp.62-67, 2009.
DOI : 10.1016/j.ijfoodmicro.2009.04.028

N. Marouani-gadri, O. Firmesse, D. Chassaing, D. Sandris-nielsen, N. Arneborg et al., Potential of Escherichia coli O157:H7 to persist and form viable but non-culturable cells on a food-contact surface subjected to cycles of soiling and chemical treatment, International Journal of Food Microbiology, vol.144, issue.1, pp.96-103, 2010.
DOI : 10.1016/j.ijfoodmicro.2010.09.002

B. Martin, O. Humbert, M. Camara, E. Guenzi, J. Walker et al., A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae, p.3479, 1992.

A. Martinon, U. Cronin, J. Quealy, A. Stapleton, and M. Wilkinson, Swab sample preparation and viable real-time PCR methodologies for the recovery of Escherichia coli, Staphylococcus aureus or Listeria monocytogenes from artificially contaminated food processing surfaces, Food Control, vol.24, issue.1-2, 2011.
DOI : 10.1016/j.foodcont.2011.09.007

E. B. Masurovsky and W. K. Jordan, Studies on the Removal of Staphylococcus Aureus from Milk-Contact Surfaces by Ultrasonic Cleaning Methods, Journal of Dairy Science, vol.43, issue.11, pp.1545-1559, 1960.
DOI : 10.3168/jds.S0022-0302(60)90375-1

G. Mauriello, A. Casaburi, G. Blaiotta, and F. Villani, Isolation and technological properties of coagulase negative staphylococci from fermented sausages of Southern Italy, Meat Science, vol.67, issue.1, pp.149-158, 2004.
DOI : 10.1016/j.meatsci.2003.10.003

J. Mceniry, P. O-'kiely, N. J. Clipson, P. D. Forristal, and E. M. Doyle, Bacterial community dynamics during the ensilage of wilted grass, Journal of Applied Microbiology, vol.101, issue.Suppl., pp.359-371, 2008.
DOI : 10.1111/j.1365-2672.2008.03802.x

S. Mcguinness, E. Mccabe, E. O-'regan, A. Dolan, G. Duffy et al., Development and validation of a rapid real-time PCR based method for the specific detection of Salmonella on fresh meat, Meat Science, vol.83, issue.3, pp.555-562, 2009.
DOI : 10.1016/j.meatsci.2009.07.004

L. Mereghetti, R. Quentin, N. Marquet-van-der-mee, and A. Audurier, Low Sensitivity of Listeria monocytogenes to Quaternary Ammonium Compounds, Applied and Environmental Microbiology, vol.66, issue.11, pp.5083-5086, 2000.
DOI : 10.1128/AEM.66.11.5083-5086.2000

E. Mettler and B. Carpentier, Localisation, d??nombrement et identification de la contamination microbienne apr??s nettoyage de joints en EPDM d'un circuit de pasteurisation de l'industrie laiti??re, Le Lait, vol.77, issue.4, pp.489-503, 1997.
DOI : 10.1051/lait:1997435

E. Mettler and B. Carpentier, Variations over Time of Microbial Load and Physicochemical Properties of Floor Materials after Cleaning in Food Industry Premises, Journal of Food Protection, vol.61, issue.1, pp.57-65, 1998.
DOI : 10.4315/0362-028X-61.1.57

H. Meugnier, M. Bes, C. Vernozy-rozand, C. Mazuy, Y. Brun et al., Identification and ribotyping of Staphylococcus xylosus and Staphylococcus equorum strains isolated from goat milk and cheese, International Journal of Food Microbiology, vol.31, issue.1-3, pp.325-331, 1996.
DOI : 10.1016/0168-1605(96)00975-0

G. Midelet and B. Carpentier, Transfer of Microorganisms, Including Listeria monocytogenes, from Various Materials to Beef, Applied and Environmental Microbiology, vol.68, issue.8, pp.4015-4024, 2002.
DOI : 10.1128/AEM.68.8.4015-4024.2002

G. Midelet, A. Kobilinsky, and B. Carpentier, Construction and Analysis of Fractional Multifactorial Designs To Study Attachment Strength and Transfer of Listeria monocytogenes from Pure or Mixed Biofilms after Contact with a Solid Model Food, Applied and Environmental Microbiology, vol.72, issue.4, p.2313, 2006.
DOI : 10.1128/AEM.72.4.2313-2321.2006

M. M. Moeseneder, J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl, Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis, Applied and environmental microbiology, vol.65, p.3518, 1999.

R. M. Mokgatla, P. A. Gouws, and V. S. Brozel, Mechanisms contributing to hypochlorous acid resistance of a Salmonella isolate from a poultry-processing plant, Journal of Applied Microbiology, vol.81, issue.3, pp.566-573, 2002.
DOI : 10.1016/0966-842X(96)10054-8

G. Molin and A. Ternström, Numerical Taxonomy of Psychrotrophic Pseudomonads, Microbiology, vol.128, issue.6, 1249.
DOI : 10.1099/00221287-128-6-1249

G. Molin, A. Ternström, and J. Ursing, Notes: Pseudomonas lundensis, a New Bacterial Species Isolated from Meat, International Journal of Systematic Bacteriology, vol.36, issue.2, p.339, 1986.
DOI : 10.1099/00207713-36-2-339

C. Mollet, M. Drancourt, and D. Raoult, sequence analysis as a novel basis for bacterial identification, Molecular Microbiology, vol.26, issue.5, pp.1005-1011, 1997.
DOI : 10.1046/j.1365-2958.1997.6382009.x

E. R. Moore, M. Mau, A. Arnscheidt, E. C. Böttger, R. A. Hutson et al., The Determination and Comparison of the 16S rRNA Gene Sequences of Species of the Genus Pseudomonas (sensu stricto and Estimation of the Natural Intrageneric Relationships, Systematic and Applied Microbiology, vol.19, issue.4, pp.478-492, 1996.
DOI : 10.1016/S0723-2020(96)80021-X

G. Moore and C. Griffith, Factors Influencing Recovery of Micro-organisms from Surfaces by Use of Traditional Hygiene Swabbing, Dairy, Food and Environmental Sanitation, vol.22, pp.410-421, 2002.

G. Moore, C. Griffith, and L. Fielding, A Comparison of Traditional and Recently Developed Methods for Monitoring Surface Hygiene within the Food Industry : A Laboratory Study, Dairy, Food and Environmental Sanitation, vol.21, pp.478-488, 2001.

L. Moreau, Le plan de nettoyage et de désinfection en industrie alimentaire. Application à un atelier de jambons cuits, Th. : Med. vet. : Nantes : 1993-NAN 67, 1993.

M. A. Mosso, M. C. Rosa, C. Vivar, and M. R. Medina, Heterotrophic bacterial populations in the mineral waters of thermal springs in Spain, Journal of Applied Bacteriology, vol.32, issue.4, pp.370-381, 1994.
DOI : 10.1111/j.1365-2672.1994.tb03437.x

A. E. Murray, J. T. Hollibaugh, and C. Orrego, Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments, Applied and environmental microbiology, vol.62, pp.2676-2680, 1996.

G. Muyzer, DGGE/TGGE a method for identifying genes from natural ecosystems, Current Opinion in Microbiology, vol.2, issue.3, pp.317-322, 1999.
DOI : 10.1016/S1369-5274(99)80055-1

G. Muyzer, E. C. De-waal, and A. G. Uitterlinden, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Applied and environmental microbiology, vol.59, p.695, 1993.

G. Muyzer and K. Smalla, Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology, Antonie van Leeuwenhoek, vol.73, issue.1, pp.127-141, 1998.
DOI : 10.1023/A:1000669317571

T. Nieminen, E. Vihavainen, A. Paloranta, J. Lehto, L. Paulin et al., Characterization of psychrotrophic bacterial communities in modifiedatmosphere packed meat with terminal restriction fragment length polymorphism, International journal of food microbiology, 2010.

R. E. Nilsson, T. Ross, and J. P. Bowman, Variability in biofilm production by Listeria monocytogenes correlated to strain origin and growth conditions, International Journal of Food Microbiology, vol.150, issue.1, pp.14-24, 2011.
DOI : 10.1016/j.ijfoodmicro.2011.07.012

A. Nocker, M. Burr, and A. K. Camper, Genotypic Microbial Community Profiling: A Critical Technical Review, Microbial Ecology, vol.71, issue.2, pp.276-289, 2007.
DOI : 10.1007/s00248-006-9199-5

A. Nocker, C. Y. Cheung, and A. K. Camper, Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells, Journal of Microbiological Methods, vol.67, issue.2, pp.310-320, 2006.
DOI : 10.1016/j.mimet.2006.04.015

N. Nunan, T. J. Daniell, B. K. Singh, A. Papert, J. W. Mcnicol et al., Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques Applied and environmental microbiology 71, p.6784, 2005.

J. C. Ogier, V. Lafarge, V. Girard, A. Rault, V. Maladen et al., Molecular Fingerprinting of Dairy Microbial Ecosystems by Use of Temporal Temperature and Denaturing Gradient Gel Electrophoresis, Applied and Environmental Microbiology, vol.70, issue.9, p.5628, 2004.
DOI : 10.1128/AEM.70.9.5628-5643.2004

J. C. Ogier, O. Son, A. Gruss, P. Tailliez, and A. Delacroix-buchet, Identification of the Bacterial Microflora in Dairy Products by Temporal Temperature Gradient Gel Electrophoresis, Applied and Environmental Microbiology, vol.68, issue.8, p.3691, 2002.
DOI : 10.1128/AEM.68.8.3691-3701.2002

J. D. Oliver, The viable but nonculturable state in bacteria, Journal of Microbiology, vol.43, pp.93-100, 2005.

J. D. Oliver, D. Mcdougald, T. Barrett, A. Glover, L. Prosser et al., Effect of temperature and plasmid carriage on nonculturability in organisms targeted for release, FEMS Microbiology Ecology, vol.17, issue.4, pp.229-237, 1995.
DOI : 10.1111/j.1574-6941.1995.tb00147.x

A. Oppliger, N. Charrière, P. O. Droz, and T. Rinsoz, Exposure to bioaerosols in poultry houses at different stages of fattening; use of real-time PCR for airborne bacterial quantification, Annals of occupational hygiene, vol.52, p.405, 2008.

N. A. Oulahal-lagsir, M. , E. Boistier-', L. J. Blumand, and M. Bonneau, The development of an ultrasonic apparatus for the non-invasive and repeatable removal of fouling in food processing equipment, Letters in Applied Microbiology, vol.2, issue.1, pp.47-52, 2000.
DOI : 10.1016/0168-1605(94)90047-7

N. Oulahal, A. Martial-gros, M. Bonneau, L. J. Blum, and L. J. , Removal of meat biofilms from surfaces by ultrasounds combined with enzymes and/or a chelating agent. Innovative Food Science and Emerging Technologies, pp.192-196, 2006.

Y. Pan, F. Breidt-jr, and S. Kathariou, Resistance of Listeria monocytogenes biofilms to sanitizing agents in a simulated food processing environment Applied and environmental microbiology 72, p.7711, 2006.

S. Peneau, D. Chassaing, and B. Carpentier, First Evidence of Division and Accumulation of Viable but Nonculturable Pseudomonas fluorescens Cells on Surfaces Subjected to Conditions Encountered at Meat Processing Premises, Applied and Environmental Microbiology, vol.73, issue.9, pp.2839-2846, 2007.
DOI : 10.1128/AEM.02267-06

C. Pennacchia, D. Ercolini, and F. Villani, Spoilage-related microbiota associated with chilled beef stored in air or vacuum pack, Food Microbiology, vol.28, issue.1, pp.84-93, 2011.
DOI : 10.1016/j.fm.2010.08.010

J. Pinhassi, U. L. Zweifel, and A. Hagstrom, Dominant marine bacterioplankton species found among colony-forming bacteria Applied and environmental microbiology 63, p.3359, 1997.

E. Poitras and A. Houde, La PCR en temps réel: principes et applications, Rev. Biol. Biotechnol, vol.2, pp.2-11, 2002.

J. Puleo, R. Favero, M. , S. Petersen, N. et al., Use of ultrasonic energy in assessing microbial contamination on surfaces, Applied Microbiology, vol.15, pp.1345-1351, 1967.

C. L. Randazzo, S. Torriani, A. D. Akkermans, W. M. De-vos, and E. E. Vaughan, Diversity, Dynamics, and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis, Applied and Environmental Microbiology, vol.68, issue.4, p.1882, 2002.
DOI : 10.1128/AEM.68.4.1882-1892.2002

K. Rantsiou, L. Iacumin, C. Cantoni, G. Comi, and L. Cocolin, Ecology and characterization by molecular methods of Staphylococcus species isolated from fresh sausages, International Journal of Food Microbiology, vol.97, issue.3, pp.277-284, 2005.
DOI : 10.1016/j.ijfoodmicro.2004.02.018

G. Raponi, M. Ghezzi, G. Gherardi, G. Dicuonzo, D. Caputo et al., Antimicrobial susceptibility, biochemical and genetic profiles of Staphylococcus haemolyticus strains isolated from the bloodstream of patients hospitalized in critical care units, Journal of chemotherapy, vol.264, p.17, 2005.

D. A. Relman and S. Falkow, The meaning and impact of the human genome sequence for microbiology, Trends in Microbiology, vol.9, issue.5, pp.206-208, 2001.
DOI : 10.1016/S0966-842X(01)02041-8

M. Ritz, J. Tholozan, M. Federighi, and M. Pilet, Morphological and physiological characterization of Listeria monocytogenes subjected to high hydrostatic pressure Applied and environmental microbiology 67, 2001.

F. Rodr-guez-valera, Environmental genomics, the big picture? FEMS microbiology letters 231, pp.153-158, 2004.

D. B. Roszak and R. R. Colwell, Metabolic activity of bacterial cells enumerated by direct viable count, Applied and Environmental Microbiology, vol.53, pp.2889-2893, 1987.

K. Rudi, B. Moen, S. M. Dromtorp, and A. L. Holck, Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples Applied and environmental microbiology 71, 1018.

F. Russo, D. Ercolini, G. Mauriello, and F. Villani, Behaviour of Brochothrix thermosphacta in presence of other meat spoilage microbial groups, Food Microbiology, vol.23, issue.8, pp.797-802, 2006.
DOI : 10.1016/j.fm.2006.02.004

M. P. Ryan and C. C. Adley, Sphingomonas paucimobilis: a persistent Gram-negative nosocomial infectious organism, Journal of Hospital Infection, vol.75, issue.3, pp.153-157, 2010.
DOI : 10.1016/j.jhin.2010.03.007

S. Saha and B. Chopade, Studies on occurrence and distribution of Acinetobacter spp. and other gram-negative bacteria from meat, Journal of food science and technology, vol.38, pp.17-22, 2001.

P. D. Schloss and J. Handelsman, Metagenomics for studying unculturable microorganisms: cutting the Gordian knot, Genome Biology, vol.6, issue.8, p.229, 2005.
DOI : 10.1186/gb-2005-6-8-229

C. Schneeberger, P. Speiser, F. Kury, and R. Zeillinger, Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain., Genome Research, vol.4, issue.4, p.234, 1995.
DOI : 10.1101/gr.4.4.234

D. C. Schwartz and C. R. Cantor, Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis, Cell, vol.37, issue.1, pp.67-75, 1984.
DOI : 10.1016/0092-8674(84)90301-5

B. L. Scola, L. Bui, G. Baranton, A. Khamis, and D. Raoult, species, FEMS Microbiology Letters, vol.263, issue.2, pp.142-147, 2006.
DOI : 10.1111/j.1574-6968.2006.00377.x

URL : https://hal.archives-ouvertes.fr/hal-01466872

H. Sekiguchi, N. Tomioka, T. Nakahara, and H. Uchiyama, A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis, Biotechnology Letters, vol.23, issue.15, pp.1205-1208, 2001.
DOI : 10.1023/A:1010517117046

K. Shale, J. Lues, P. Venter, and E. Buys, The distribution of Staphylococcus sp. on bovine meat from abattoir deboning rooms, Food Microbiology, vol.22, issue.5, pp.433-438, 2005.
DOI : 10.1016/j.fm.2004.09.007

V. C. Sheffield, D. R. Cox, L. S. Lerman, and R. M. Myers, Attachment of a 40-base-pair G+ Crich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes, Proceedings of the National Academy of Sciences 86, p.232, 1989.

G. Sheridan, C. Masters, J. Shallcross, and B. Mackey, Detection of mRNA by reverse transcription-PCR as an indicator of viability in Escherichia coli cells, Applied and environmental microbiology, vol.64, 1313.

J. M. Short, Molecular Evolution: Recombinant approaches for accessing biodiversity, Nature Biotechnology, vol.260, issue.13, pp.1322-1323, 1997.
DOI : 10.1146/ANNUREV.IMMUNOL.12.1.433

C. K. Shutt, J. I. Pounder, S. R. Page, B. J. Schaecher, and G. L. Woods, Clinical Evaluation of the DiversiLab Microbial Typing System Using Repetitive-Sequence-Based PCR for Characterization of Staphylococcus aureus Strains, Journal of Clinical Microbiology, vol.43, issue.3, 1187.
DOI : 10.1128/JCM.43.3.1187-1192.2005

K. Smalla, M. Oros-sichler, A. Milling, H. Heuer, S. Baumgarte et al., Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results?, Journal of Microbiological Methods, vol.69, issue.3, pp.470-479, 2007.
DOI : 10.1016/j.mimet.2007.02.014

L. Smith and L. A. Burgoyne, Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper, BMC ecology, vol.4, issue.4, 2004.

A. G. Speksnijder, G. A. Kowalchuk, D. Jong, S. Kline, E. Stephen et al., Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences, Applied and Environmental Microbiology, vol.67, issue.1, p.469, 2001.
DOI : 10.1128/AEM.67.1.469-472.2001

S. Yan, S. Pendrak, M. L. Abela-ridder, B. Punderson, J. W. Fedorko et al., An overview of Salmonella typing: Public health perspectives, Clinical and Applied Immunology Reviews, vol.4, pp.189-204, 2004.

M. T. Suzuki, L. T. Taylor, and E. F. Delong, Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5'-Nuclease Assays, Applied and Environmental Microbiology, vol.66, issue.11, p.4605, 2000.
DOI : 10.1128/AEM.66.11.4605-4614.2000

P. ?vec, M. Vancanneyt, I. Sedlá?ek, K. Engelbeen, V. ?t?tina et al., Reclassification of Staphylococcus pulvereri Zakrzewska-Czerwinska et al. 1995 as a later synonym of Staphylococcus vitulinus Webster et al. 1994, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.54, issue.6, pp.2213-2215, 1994.
DOI : 10.1099/ijs.0.63080-0

H. Takahashi, B. Kimura, M. Yoshikawa, S. Gotou, I. Watanabe et al., Direct Detection and Identification of Lactic Acid Bacteria in a Food Processing Plant and in Meat Products Using Denaturing Gradient Gel Electrophoresis, Journal of Food Protection, vol.67, issue.11, pp.2515-2520, 2004.
DOI : 10.4315/0362-028X-67.11.2515

Y. Tanaka, H. Takahashi, N. Kitazawa, and B. Kimura, Rapid Estimation of Microbial Populations in Fish Samples by Using Terminal Restriction Fragment Length Polymorphism Analysis of 16S rDNA, Journal of Food Protection, vol.73, issue.1, pp.104-113, 2010.
DOI : 10.4315/0362-028X-73.1.104

N. Trachoo, J. Frank, and N. Stern, Survival of Campylobacter jejuni in Biofilms Isolated from Chicken Houses, Journal of Food Protection, vol.65, issue.7, pp.1110-1116, 2002.
DOI : 10.4315/0362-028X-65.7.1110

P. Tremonte, M. Succi, A. Reale, T. Di-renzo, E. Sorrentino et al., Interactions between strains of Staphylococcus xylosus and Kocuria varians isolated from fermented meats, Journal of Applied Microbiology, vol.44, issue.3, pp.743-751, 2007.
DOI : 10.1016/0300-9084(92)90128-2

C. Tse and J. Capeau, Quantification des acides nucléiques par PCR quantitative en temps réel, Ann Biol Clin, vol.61, pp.279-293, 2003.

Y. Van-de-peer, S. Chapelle, and R. De-wachter, A quantitative map of nucleotide substitution rates in bacterial rRNA, Nucleic acids research 24, p.3381, 1996.
DOI : 10.1093/nar/24.17.3381

S. Van-der-veen and T. Abee, Mixed species biofilms of Listeria monocytogenes and Lactobacillus plantarum show enhanced resistance to benzalkonium chloride and peracetic acid, International Journal of Food Microbiology, vol.144, issue.3, pp.421-431, 2011.
DOI : 10.1016/j.ijfoodmicro.2010.10.029

J. C. Venter, K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch et al., Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science, vol.304, issue.5667, p.66, 2004.
DOI : 10.1126/science.1093857

J. Versalovic, T. Koeuth, and J. R. Lupski, Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes, Nucleic Acids Research, vol.19, issue.24, p.6823, 1991.
DOI : 10.1093/nar/19.24.6823

A. Veulemans, E. Jacqmain, and D. Jacqmain, Etude d'une méthode simple pour la détermination du degré de pollution des surfaces et la comparaison du pouvoir désinfectant de divers produits d'entretien, pp.58-65, 1970.

J. Vincent, La chimie du nettoyage, Nettoyage, désinfection et hygiène dans les bio-industries (Collection STAA), 1999.

J. Walter, G. Tannock, A. Tilsala-timisjarvi, S. Rodtong, D. Loach et al., Detection and Identification of Gastrointestinal Lactobacillus Species by Using Denaturing Gradient Gel Electrophoresis and Species-Specific PCR Primers, Applied and Environmental Microbiology, vol.66, issue.1, p.297, 2000.
DOI : 10.1128/AEM.66.1.297-303.2000

K. Warriner, T. G. Aldsworth, S. Kaur, and C. E. Dodd, Cross-contamination of carcasses and equipment during pork processing, Journal of Applied Microbiology, vol.20, issue.1, pp.169-177, 2002.
DOI : 10.1046/j.1365-2672.2002.01678.x

K. Watanabe, J. Nelson, S. Harayama, and H. Kasai, ICB database: the gyrB database for identification and classification of bacteria, Nucleic Acids Research, vol.29, issue.1, p.344, 2001.
DOI : 10.1093/nar/29.1.344

S. Weidner, W. Arnold, and A. Puhler, Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes, Applied and environmental microbiology, vol.62, p.766, 1996.

W. G. Weisburg, S. M. Barns, D. A. Pelletier, and D. J. Lane, 16S ribosomal DNA amplification for phylogenetic study., Journal of Bacteriology, vol.173, issue.2, p.697, 1991.
DOI : 10.1128/jb.173.2.697-703.1991

N. Wilhelm, L. Coustumier, A. Fevrier, F. , L. Flèche et al., Bactéries d'identification difficile ou non cultivables en routine: Quelles solutions? Apport du séquençage du gène de l'ARN ribosomal 16, pp.49-54, 2005.

A. Willems, E. Falsen, B. Pot, E. Jantzen, B. Hoste et al., Acidovorax, a New Genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) Group 13, EF Group 16, and Several Clinical Isolates, with the Species Acidovorax facilis, Acidovorax delafieldii, and Acidovorax temperans International journal of systematic bacteriology, pp.384-398, 1990.

S. Yaron and K. Matthews, A reverse transcriptase-polymerase chain reaction assay for detection of viable Escherichia coli O157:H7: investigation of specific target genes, Journal of Applied Microbiology, vol.19, issue.4, pp.633-640, 2002.
DOI : 10.1128/AEM.66.10.4414-4420.2000

F. P. Yu and G. A. Mcfeters, Physiological responses of bacteria in biofilms to disinfection Applied and environmental microbiology 60, p.2462, 1994.

Z. Yu and M. Morrison, Comparisons of Different Hypervariable Regions of rrs Genes for Use in Fingerprinting of Microbial Communities by PCR-Denaturing Gradient Gel Electrophoresis, Applied and Environmental Microbiology, vol.70, issue.8, p.4800, 2004.
DOI : 10.1128/AEM.70.8.4800-4806.2004

R. Zhuang, L. Beuchat, and F. Angulo, Fate of Salmonella montevideo on and in raw tomatoes as affected by temperature and treatment with chlorine. Applied and environmental microbiology 61, p.2127, 1995.

E. G. Zoetendal, A. D. Akkermans, and W. M. De-vos, Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and hostspecific communities of active bacteria, Applied and environmental microbiology, vol.64, issue.3854, p.142, 1998.

S. Allegra, F. Berger, P. Berthelot, F. Grattard, B. Pozzetto et al., Use of flow 326 cytometry to monitor Legionella viability, Applied and environmental microbiology, vol.327, issue.7813, pp.74-328, 2008.

M. Alliot, Ecologie microbienne des sites industriels fromagers : identification, 329 caractérisation des flores isolées et étude des facteurs régissant leur implantation, p.331, 1999.

. Anonymous, NF V 04-506.Viandes et produits à base de vainde-Dénombrements des 332 micro-organismes, 1992.

A. Asséré, N. Oulahal, and B. Carpentier, Comparative evaluation of methods for counting surviving biofilm cells adhering to a polyvinyl chloride surface exposed to chlorine or drying, Journal of Applied Microbiology, vol.25, issue.6, pp.1692-1702, 2008.
DOI : 10.1007/BF02738539

H. J. Bach, J. Tomanova, M. Schloter, and J. Munch, Enumeration of total bacteria and 337 bacteria with genes for proteolytic activity in pure cultures and in environmental 338 samples by quantitative PCR mediated amplification, Journal of Microbiological Methods, vol.339, issue.49, pp.235-245, 2002.

D. Bagge-ravn, Y. Ng, M. Hjelm, J. N. Christiansen, C. Johansen et al., The 341 microbial ecology of processing equipment in different fish industries-analysis of the 342 microflora during processing and following cleaning and disinfection, International, vol.343, 2003.

N. T. Chen and C. W. Chang, Rapid quantification of viable legionellae in water and 353 biofilm using ethidium monoazide coupled with real-time quantitative PCR, Journal, p.354, 2010.

P. J. Eginton, H. Gibson, J. Holah, P. S. Handley, and P. Gilbert, Quantification of the ease of removal of bacteria from surfaces, Journal of Industrial Microbiology, vol.46, issue.4, pp.305-310, 1995.
DOI : 10.1007/BF01569984

P. J. Eginton, J. Holah, D. G. Allison, P. S. Handley, and P. Gilbert, Changes in the strength of attachment of micro-organisms to surfaces following treatment with disinfectants and cleansing agents, Letters in Applied Microbiology, vol.27, issue.2, pp.101-105, 1998.
DOI : 10.1046/j.1472-765X.1998.00390.x

A. H. Geeraerd, V. P. Valdramidis, and J. F. Van-impe, GInaFiT, a freeware tool to assess 361 non-log-linear microbial survivor curves, International Journal of Food Microbiology, vol.362, issue.102, pp.95-105, 2005.

H. Gibson, J. H. Taylor, K. E. Hall, and J. T. Holah, Effectiveness of cleaning techniques 364 used in the food industry in terms of the removal of bacterial biofilms, Journal, p.365, 1999.

F. Jorgensen, O. Nybroe, and S. Knochel, Effects of starvation and osmotic stress on 370 viability and heat resistance of Pseudomonas fluorescens AH9, Journal of Applied, vol.371, issue.77, pp.340-347, 1994.

K. Kogure, U. Simidu, and N. Taga, A tentative direct microscopic method for counting living marine bacteria, Canadian Journal of Microbiology, vol.25, issue.3, pp.415-420, 1978.
DOI : 10.1139/m79-063

V. Leriche and B. Carpentier, Viable but non culturable Salmonella typhimurium within 378 single and binary species biofilms in response to chlorine treatment, Journal of Food, vol.379, issue.58, pp.1186-1191, 1995.

D. Lindsay, I. Geornaras, and A. Vonholy, Biofilms associated with poultry processing 381 equipment, Microbios, vol.86, pp.105-116, 1996.

S. R. Lyons, A. L. Griffen, and E. J. Leys, Quantitative real-time PCR for Porphyromonas 383 gingivalis and total bacteria, Journal of Clinical Microbiology, vol.38, pp.2362-384, 2000.

E. Mettler and B. Carpentier, Variations over time of microbial load and physicochemical 385 properties of floor materials after cleaning in food industry premises, Journal of Food, vol.386, issue.61, pp.57-65, 1998.

G. Midelet and B. Carpentier, Transfer of microorganisms, including Listeria 388 monocytogenes, from various materials to beef Applied and environmental 389 microbiology 68, p.390, 2002.

G. Midelet, A. Kobilinsky, and B. Carpentier, Construction and analysis of fractional 391 multifactorial designs to study attachment strength and transfer of Listeria 392 monocytogenes from pure or mixed biofilms after contact with a solid model food, p.393, 2006.

A. Nocker, C. Y. Cheung, and A. K. Camper, Comparison of propidium monoazide with 395, 2006.

J. D. Oliver, The viable but nonculturable state in bacteria, Journal of Microbiology, vol.43, issue.398, pp.93-100, 2005.

J. D. Oliver, Recent findings on the viable but nonculturable state in pathogenic bacteria, FEMS Microbiology Reviews, vol.34, issue.4, pp.415-425, 2010.
DOI : 10.1111/j.1574-6976.2009.00200.x

N. Oulahal-lagsir, A. Martial-gros, M. Bonneau, and L. J. Blum, Ultrasonic methodology 402 coupled to ATP bioluminescence for the non-invasive detection of fouling in food 403 processing equipment -validation and application to a dairy factory, J Appl Microbiol, vol.404, pp.89-433, 2000.

J. T. Patterson, Microbiological assessment of surfaces, International Journal of Food Science & Technology, vol.30, issue.1, pp.63-72, 1971.
DOI : 10.1111/j.1365-2621.1971.tb01593.x

J. Richard, Observations on the value of a swab technique for determining the 408 bacteriological state of milking equipment surfaces, Journal of Applied Bacteriology, vol.409, pp.49-410, 1980.

E. M. Rossoni and C. C. Gaylarde, Comparison of sodium hypochlorite and peracetic 411 acid as sanitising agents for stainless steel food processing surfaces using 412, 2000.

D. B. Roszak and R. R. Colwell, Metabolic activity of bacterial cells enumerated by direct 414 viable count, Applied and Environmental Microbiology, vol.53, pp.2889-2893, 1987.

K. Rudi, B. Moen, S. M. Dromtorp, and A. L. Holck, Use of ethidium monoazide and PCR 416 in combination for quantification of viable and dead cells in complex samples, 2005.

M. T. Suzuki, L. T. Taylor, and E. F. Delong, Quantitative analysis of small-subunit rRNA 419 genes in mixed microbial populations via 5'-nuclease assays Applied and 420 environmental microbiology 66, p.421, 2000.

S. Van-der-veen and T. Abee, Mixed species biofilms of Listeria monocytogenes and 422, 2011.

F. Yu, . Philip, G. Mcfeters, and A. , Physiological responses of bacteria in biofillms to 429 disinfection, Applied and Environmental Microbiology, vol.60, pp.2462-2466, 1994.