Revealing microbial community composition and disinfection efficacy evaluation in wholesale pork markets through 16S rDNA sequencing

References

• Andritsos, N., Mataragas, M., Mavrou, E., Stamatiou, A., & Drosinos, E. (2012). The microbiological condition of minced pork prepared at retail stores in Athens, Greece. Meat Science, 91(4), 486–11. https://doi.org/10.1016/j.meatsci.2012.02.036
   PubMed Web of Science ®Google Scholar
• Aráoz, R., Anhalt, E., René, L., Badet-Denisot, M.-A., Courvalin, P., & Badet, B. (2000). Mechanism-based inactivation of VanX, a d-alanyl-d-alanine dipeptidase necessary for vancomycin resistance. Biochemistry, 39(51), 15971–15979. https://doi.org/10.1021/bi001408b
   PubMed Web of Science ®Google Scholar
• Bassey, A., Chen, Y., Zhu, Z., Odeyemi, O., Gao, T., Olusola, O., Ye, K., Li, C., & Zhou, G. H. (2021). Evaluation of spoilage indexes and bacterial community dynamics of modified atmosphere packaged super-chilled pork loins. Food Control, 130, 108383. https://doi.org/10.1016/j.foodcont.2021.108383
   Web of Science ®Google Scholar
• Bessems, E. (1998). The effect of practical conditions on the efficacy of disinfectants. International Biodeterioration & Biodegradation, 41(3), 177–183. https://doi.org/10.1016/S0964-8305(98)00022-5
   Web of Science ®Google Scholar
• Brooks, B. W., Devenish, J., Lutze-Wallace, C. L., Milnes, D., Robertson, R. H., & Berlie-Surujballi, G. (2004). Evaluation of a monoclonal antibody-based enzyme-linked immunosorbent assay for detection of Campylobacter fetus in bovine preputial washing and vaginal mucus samples. Veterinary Microbiology, 103(1), 77–84. https://doi.org/10.1016/j.vetmic.2004.07.008
   PubMed Web of Science ®Google Scholar
• Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583. https://doi.org/10.1038/nmeth.3869
   PubMed Web of Science ®Google Scholar
• Camara, P. G. (2018). Methods and challenges in the analysis of single-cell RNA-sequencing data. Current Opinion in Systems Biology, 7, 47–53. https://doi.org/10.1016/j.coisb.2017.12.007
   Google Scholar
• Cauchie, E., Delhalle, L., Taminiau, B., Tahiri, A., Korsak, N., Burteau, S., Fall, P. A., Farnir, F., Baré, G., & Daube, G. (2020). Assessment of spoilage bacterial communities in food wrap and modified atmospheres-packed minced pork meat samples by 16S rDNA metagenetic analysis [Original Research]. Frontiers in Microbiology, 10, 10. https://doi.org/10.3389/fmicb.2019.03074
   Web of Science ®Google Scholar
• Charmpi, C., Van der Veken, D., Van Reckem, E., De Vuyst, L., & Leroy, F. (2020). Raw meat quality and salt levels affect the bacterial species diversity and community dynamics during the fermentation of pork mince. Food Microbiology, 89, 103434. https://doi.org/10.1016/j.fm.2020.103434
   PubMed Web of Science ®Google Scholar
• Cheung, P.-Y., Lo, K., Cheung, T., Yeung, W., Leung, P., & Kam, K. (2008). Streptococcus suis in retail markets: How prevalent is it in raw pork? International Journal of Food Microbiology, 127(3), 316–320. https://doi.org/10.1016/j.ijfoodmicro.2008.08.006
   PubMed Web of Science ®Google Scholar
• Cobo Díaz, J., Alvarez-Molina, A., Oniciuc, E., Walsh, C., Mencía-Ares, O., Puente-Gómez, P., Likotrafiti, E., Fernández-Gómez, P., Prieto, B., Crispie, F., Ruiz, L., Gonzalez-Raurich, M., López, M., Prieto, M., Cotter, P., & Alvarez-Ordóñez, A. (2021). Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity. Microbiome, 9(1), 204. https://doi.org/10.1186/s40168-021-01131-9
   PubMed Web of Science ®Google Scholar
• Correia Peres Costa, J., Bover-Cid, S., Bolívar, A., Cosano, G., & Pérez-Rodríguez, F. (2019). Modelling the interaction of the sakacin-producing Lactobacillus sakei CTC494 and listeria monocytogenes in filleted gilthead sea bream (Sparus aurata) under modified atmosphere packaging at isothermal and non-isothermal conditions. International Journal of Food Microbiology, 297, 72–84. https://doi.org/10.1016/j.ijfoodmicro.2019.03.002
   PubMed Web of Science ®Google Scholar
• De Filippis, F., Storia, A., Villani, F., & Ercolini, D. (2018). Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions. Applied and Environmental Microbiology, 85. https://doi.org/10.1128/AEM.02212-18
   Web of Science ®Google Scholar
• Del Blanco, A., Caro, I., Quinto, E. J., & Mateo, J. (2017). Quality changes in refrigerated stored minced pork wrapped with plastic cling film and the effect of glucose supplementation. Meat Science, 126, 55–62. https://doi.org/10.1016/j.meatsci.2016.12.007
   PubMed Web of Science ®Google Scholar
• Demaître, N., Van Damme, I., De Zutter, L., Geeraerd, A. H., Rasschaert, G., & De Reu, K. (2020). Occurrence, distribution and diversity of listeria monocytogenes contamination on beef and pig carcasses after slaughter. Meat Science, 169, 108177. https://doi.org/10.1016/j.meatsci.2020.108177
   PubMed Web of Science ®Google Scholar
• Emamjomeh, M., Mohd Hashim, A., Abdul-Mutalib, N., Khairil Mokhtar, N., Mustapha, N. A., Maeda, T., & Amin Nordin, S. (2023). Profiling bacterial communities and foodborne pathogens on food-associated surface following contact with raw beef, chicken and pork using 16S amplicon metagenomics. Food Control, 149, 109698. https://doi.org/10.1016/j.foodcont.2023.109698
   Web of Science ®Google Scholar
• Ercolini, D. (2013). High-throughput sequencing and metagenomics: Moving forward in the culture-independent analysis of food microbial ecology. Applied and Environmental Microbiology, 79(10), 3148–3155. https://doi.org/10.1128/AEM.00256-13
   PubMed Web of Science ®Google Scholar
• Ercolini, D., Casaburi, A., Nasi, A., Ferrocino, I., DiMonaco, R., Ferranti, P., Mauriello, G., & Villani, F. (2010). Different molecular types of Pseudomonas fragi have the same overall behaviour as meat spoilers. International Journal of Food Microbiology, 142(1–2), 120–131. https://doi.org/10.1016/j.ijfoodmicro.2010.06.012
   PubMed Web of Science ®Google Scholar
• Illikoud, N., Rossero, A., Chauvet, R., Courcoux, P., Pilet, M.-F., Charrier, T., Jaffrès, E., & Zagorec, M. (2019). Genotypic and phenotypic characterization of the food spoilage bacterium brochothrix thermosphacta. Food Microbiology, 81, 22–31. https://doi.org/10.1016/j.fm.2018.01.015
   PubMed Web of Science ®Google Scholar
• Janse, R. J., Hoekstra, T., Jager, K. J., Zoccali, C., Tripepi, G., Dekker, F. W., & van Diepen, M. (2021). Conducting correlation analysis: Important limitations and pitfalls. Clinical Kidney Journal, 14(11), 2332–2337. https://doi.org/10.1093/ckj/sfab085
   PubMed Web of Science ®Google Scholar
• Johansson, M., Azzouz, M., Häggendal, B., Säljö, K., Malmi, H., Zavialov, A., & Teneberg, S. (2020). Glycosphingolipids recognized by Acinetobacter baumannii. Microorganisms [Internet], 8(4), 612. https://doi.org/10.3390/microorganisms8040612
   PubMed Web of Science ®Google Scholar
• Kadariya, J., Smith, T. C., & Thapaliya, D. (2014). Staphylococcus aureus and Staphylococcal Food-Borne disease: An ongoing challenge in public health. Biomed Research International, 2014, 827965. https://doi.org/10.1155/2014/827965
   PubMed Web of Science ®Google Scholar
• Kameník, J., Dušková, M., Šedo, O., Saláková, A., Pavlík, Z., Zdráhal, Z., & Karpíšková, R. (2015). Lactic acid bacteria in hot smoked dry sausage (non-fermented salami): Thermal resistance of Weissella viridescens strains isolated from hot smoked dry sausages. LWT - Food Science and Technology, 61(2), 492–495. https://doi.org/10.1016/j.lwt.2014.12.012
   Web of Science ®Google Scholar
• Kang, G., Seong, P.-N., Moon, S., Cho, S., Ham, H.-J., Park, K., Kang, S. M., & Park, B.-Y. (2014). Distribution channel and microbial characteristics of pig by-products in Korea. Korean Journal for Food Science of Animal Resources, 34(6), 792–798. https://doi.org/10.5851/kosfa.2014.34.6.792
   PubMedGoogle Scholar
• Khatoon, Z., McTiernan, C. D., Suuronen, E. J., Mah, T.-F., & Alarcon, E. I. (2018). Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention. Heliyon, 4(12), e01067. https://doi.org/10.1016/j.heliyon.2018.e01067
   PubMed Web of Science ®Google Scholar
• Knight, R., Vrbanac, A., Taylor, B., Aksenov, A., Callewaert, C., Debelius, J., González, A., Kosciolek, T., McCall, L.-I., McDonald, D., Melnik, A., Morton, J., Navas, J., Quinn, R., Sanders, J., Swafford, A., Thompson, L., Tripathi, A. … Caporaso, J. G. (2018). Best practices for analysing microbiomes. Nature Reviews Microbiology, 16(7), 410–422. https://doi.org/10.1038/s41579-018-0029-9
   PubMed Web of Science ®Google Scholar
• Lagier, J.-C., Khelaifia, S., Tidjani Alou, M., Ndongo, S., Niokhor, D., Hugon, P., Caputo, A., Cadoret, F., Traore, S., Seck, E., Dubourg, G., Durand, G., Gaël, M., Guilhot, E., Togo, A., Bellali, S., Bachar, D., Cassir, N. … Levasseur, A. (2016). Culture of previously uncultured members of the human gut microbiota by culturomics. Nature Microbiology, 1(12). https://doi.org/10.1038/nmicrobiol.2016.203
   PubMed Web of Science ®Google Scholar
• Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G., & Huttenhower, C. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31(9), 814–821. https://doi.org/10.1038/nbt.2676
   PubMed Web of Science ®Google Scholar
• Li, N., Zhang, Y., Wu, Q., Gu, Q., Chen, M., Zhang, Y., Sun, X., & Zhang, J. (2019). High-throughput sequencing analysis of bacterial community composition and quality characteristics in refrigerated pork during storage. Food Microbiology, 83, 86–94. https://doi.org/10.1016/j.fm.2019.04.013
   PubMed Web of Science ®Google Scholar
• Li, Y., Tan, X., Zhao, X., Xu, Z.-F., Dai, W., Duan, W., Huang, S., Zhang, E., Liu, J., Zhang, S., Yin, R., Shi, X., Lu, Z., & Pan, Y. (2020). Composition and function of oral microbiota between gingival squamous cell carcinoma and periodontitis. Oral Oncology, 107, 104710. https://doi.org/10.1016/j.oraloncology.2020.104710
   PubMed Web of Science ®Google Scholar
• Lim, S.-M., Lee, N.-K., & Paik, H.-D. (2019). Antibacterial and anticavity activity of probiotic lactobacillus plantarum 200661 isolated from fermented foods against streptococcus mutans. LWT, 118, 108840. https://doi.org/10.1016/j.lwt.2019.108840
   Web of Science ®Google Scholar
• Mahros, M., Abd-Elghany, S., & Sallam, K. (2021). Multidrug-, methicillin-, and vancomycin-resistant Staphylococcus aureus isolated from ready-to-eat meat sandwiches: An ongoing food and public health concern. International Journal of Food Microbiology, 346, 109165. https://doi.org/10.1016/j.ijfoodmicro.2021.109165
   PubMed Web of Science ®Google Scholar
• Møretrø, T., & Langsrud, S. (2017). Residential bacteria on surfaces in the food industry and their implications for food safety and quality: Residential bacteria in food industry …. Comprehensive Reviews in Food Science and Food Safety, 16(5), 1022–1041. https://doi.org/10.1111/1541-4337.12283
   PubMed Web of Science ®Google Scholar
• Naïtali, M., Dubois-Brissonnet, F., Cuvelier, G., & Bellon-Fontaine, M.-N. (2009). Effects of pH and oil-in-water emulsions on growth and physicochemical cell surface properties of listeria monocytogenes: Impact on tolerance to the bactericidal activity of disinfectants. International Journal of Food Microbiology, 130(2), 101–107. https://doi.org/10.1016/j.ijfoodmicro.2009.01.008
   PubMed Web of Science ®Google Scholar
• Nearing, J. T., Connors, J., Whitehouse, S., Van Limbergen, J., Macdonald, T., Kulkarni, K., & Langille, M. G. I. (2019). Infectious complications are associated with alterations in the gut microbiome in pediatric patients with acute lymphoblastic leukemia [Original Research]. Frontiers in Cellular and Infection Microbiology, 9, 9. https://doi.org/10.3389/fcimb.2019.00028
   PubMed Web of Science ®Google Scholar
• O’Brien, T. (2002). Emergence, spread, and environmental effect of antimicrobial resistance: How use of an antimicrobial anywhere can increase resistance to any antimicrobial anywhere else. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 34(Suppl 3), S78–84. https://doi.org/10.1086/340244
   PubMedGoogle Scholar
• Peruzy, M. F., Houf, K., Joossens, M., Yu, Z., Therese, Y., Proroga, R., & Murru, N. (2020). Evaluation of microbial contamination of different pork carcass areas through culture-dependent and independent methods in small-scale slaughterhouses. International Journal of Food Microbiology, 336. https://doi.org/10.1016/j.ijfoodmicro.2020.108902
   PubMed Web of Science ®Google Scholar
• Sato, Y., Ishihara, M., Nakamura, S., Fukuda, K., Kuwabara, M., Takayama, T., Hiruma, S., Murakami, K., Fujita, M., & Yokoe, H. (2019). Comparison of various disinfectants on bactericidal activity under organic matter contaminated environments. Biocontrol Science, 24(2), 103–108. https://doi.org/10.4265/bio.24.103
   PubMed Web of Science ®Google Scholar
• Stellato, G., La Storia, A., De Filippis, F., Borriello, G., Villani, F., Ercolini, D., & Elkins, C. A. (2016). Overlap of spoilage-associated microbiota between meat and the meat processing environment in small-scale and large-scale retail distributions. Applied and Environmental Microbiology, 82(13), 4045–4054. https://doi.org/10.1128/AEM.00793-16
   PubMed Web of Science ®Google Scholar
• Tassou, C., Argyri, A., Doulgeraki, A., Nychas, G.-J., Chorianopoulos, N., Grounta, A., Dourou, D., & Spyrelli, E. (2021). Microbiota of chicken breast and thigh fillets stored under different refrigeration temperatures by next generation sequencing. Foods, 10(4), 10. https://doi.org/10.3390/foods10040765
   Web of Science ®Google Scholar
• Tong, C., Hu, H., Chen, G., Li, Z., Aifeng, L., & Zhang, J. (2021). Chlorine disinfectants promote microbial resistance in pseudomonas sp. Environmental Research, 199, 111296. https://doi.org/10.1016/j.envres.2021.111296
   PubMed Web of Science ®Google Scholar
• Tong, C., Hu, H., Chen, G., Li, Z., Li, A., & Zhang, J. (2021). Disinfectant resistance in bacteria: Mechanisms, spread, and resolution strategies. Environmental Research, 195, 110897. https://doi.org/10.1016/j.envres.2021.110897
   PubMed Web of Science ®Google Scholar
• Tong, S., Ma, L., Ronholm, J., Hsiao, W., & Lu, X. (2021). Whole genome sequencing of campylobacter in agri-food surveillance. Current Opinion in Food Science, 39, 130–139. https://doi.org/10.1016/j.cofs.2020.12.020
   Web of Science ®Google Scholar
• Velez, F. J., Bosilevac, J. M., & Singh, P. (2021). Validation of high-resolution melting assays for the detection of virulent strains of Escherichia coli O26 and O111 in beef and pork enrichment broths. Food Control, 128, 108123. https://doi.org/10.1016/j.foodcont.2021.108123
   Web of Science ®Google Scholar
• Vojkovska, H., Karpiskova, R., Kajsiková, M., & Drahovska, H. (2015). Characterization of cronobacter spp. isolated from food of plant origin and environmental samples collected from farms and from supermarkets in the Czech Republic. International Journal of Food Microbiology, 217, 130–136. https://doi.org/10.1016/j.ijfoodmicro.2015.10.017
   PubMed Web of Science ®Google Scholar
• Wang, Z., Fang, Y., Zhi, S., Simpson David, J., Gill, A., McMullen Lynn, M., Neumann Norman, F., Gänzle Michael, G., & Björkroth, J. (2020). The locus of heat resistance confers resistance to chlorine and other oxidizing chemicals in Escherichia coli. Applied and Environmental Microbiology, 86(4), e02123–02119. https://doi.org/10.1128/AEM.02123-19
   PubMed Web of Science ®Google Scholar
• Wickramasinghe, N. N., Ravensdale, J., Coorey, R., Dykes, G. A., & Chandry, P. S. (2021). Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793. Biofilm, 3, 100045. https://doi.org/10.1016/j.bioflm.2021.100045
   PubMedGoogle Scholar
• Wilson, C. N., Pulford, C. V., Akoko, J., Perez Sepulveda, B., Predeus, A. V., Bevington, J., Duncan, P., Hall, N., Wigley, P., Feasey, N., Pinchbeck, G., Hinton, J. C. D., Gordon, M. A., Fevre, E. M., & Bourret, T. J. (2020). Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets. PloS Neglected Tropical Diseases, 14(11), e0008796. https://doi.org/10.1371/journal.pntd.0008796
   PubMed Web of Science ®Google Scholar
• Wu, J., Li, R., Zhang, M., Shan, K., Jia, X., Zhao, D., Nian, Y., & Li, C. (2021). Microbiota changes on the surface of pig carcasses during refrigerated transportation and marketing. Food Materials Research[Cdata[food materials research]], 1(1), 1–9. https://doi.org/10.48130/FMR-2021-0004
   Google Scholar
• Xiao, X., Wang, W., Zhang, J., Liao, M., Rainwater, C., Yang, H., & Li, Y. (2021). A quantitative risk assessment model of salmonella contamination for the yellow-feathered broiler chicken supply chain in China. Food Control, 121, 107612. https://doi.org/10.1016/j.foodcont.2020.107612
   Web of Science ®Google Scholar
• Xu, L., Zhang, C. M., & Xu, P. (2017). Mechanisms of ultraviolet disinfection and chlorination of Escherichia coli: Culturability, membrane permeability, metabolism, and genetic damage. Journal of Environmental Sciences, 65. https://doi.org/10.1016/j.jes.2017.07.006
   Google Scholar
• Xu, S., Lu, W., Liu, Y., Ming, Z., Liu, Y., Meng, R., & Wang, H. (2016). Structure and diversity of bacterial communities in two large sanitary landfills in China as revealed by high-throughput sequencing (MiSeq). Waste Management, 63, 41–48. https://doi.org/10.1016/j.wasman.2016.07.047
   PubMed Web of Science ®Google Scholar
• Xu, Y., Yang, G., Xu, J., Guan, X., Li, R., & Wang, S. (2022). Influence of the combination of cinnamon essential oil nanoemulsions and epsilon-polylysine on microbial community and quality of pork during refrigerated period and radio frequency cooking. International Journal of Food Microbiology, 381, 109911. https://doi.org/10.1016/j.ijfoodmicro.2022.109911
   PubMed Web of Science ®Google Scholar
• Yang, C., Che, Y., Qi, Y., Liang, P., & Song, C. (2016). High-throughput sequencing of viable microbial communities in raw pork subjected to a fast cooling process. Journal of Food Science, 82. https://doi.org/10.1111/1750-3841.13566
   Web of Science ®Google Scholar
• Yi, Z., Yan, J., Ding, Z., & Xie, J. (2022). The HD-GYP domain protein of shewanella putrefaciens YZ08 regulates biofilm formation and spoilage activities. Food Research International, 157, 111466. https://doi.org/10.1016/j.foodres.2022.111466
   PubMed Web of Science ®Google Scholar
• Zhang, L., Fu, Y., Xiong, Z., Ma, Y., Wei, Y., Qu, X., Zhang, H., Zhang, J., & Liao, M. (2018). Highly prevalent multidrug-resistant salmonella from chicken and pork meat at retail markets in Guangdong, China. Frontiers in Microbiology, 9, 9. https://doi.org/10.3389/fmicb.2018.02104
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Hou, W., Yue, Q., Zhang, Y., Yi, Y., Min, T., & Wang, H. (2021). Effects of environmental humidity on microbial community and quality of chilled fresh pork. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.3964470
   Google Scholar
• Zhao, F., Wei, Z., Zhou, G., Kristiansen, K., & Wang, C. (2022). Effects of different storage temperatures on bacterial communities and functional potential in pork meat. Foods, 11(15), 2307. https://doi.org/10.3390/foods11152307
   PubMed Web of Science ®Google Scholar
• Zhao, F., Zhou, G., Ye, K., Wang, S., Xu, X., & Li, C. (2015). Microbial changes in vacuum-packed chilled pork during storage. Meat Science, 100, 145–149. https://doi.org/10.1016/j.meatsci.2014.10.004
   PubMed Web of Science ®Google Scholar
• Zhong, A., Chen, W., Duan, Y., Li, K., Tang, X., Tian, X., Wu, Z., Li, Z., Wang, Y., & Wang, C. (2021). The potential correlation between microbial communities and flavors in traditional fermented sour meat. LWT, 149, 111873. https://doi.org/10.1016/j.lwt.2021.111873
   Web of Science ®Google Scholar
• Zhou, J., Jin, Y., & Liang, Q. (2022). Effects of regulatory policy mixes on traceability adoption in wholesale markets: Food safety inspection and information disclosure. Food Policy, 107, 102218. https://doi.org/10.1016/j.foodpol.2022.102218
   Web of Science ®Google Scholar
• Zhu, Z., Shan, L., Zhang, X., Hu, F., Zhong, D., Yuan, Y., & Zhang, J. (2021). Effects of bacterial community composition and structure in drinking water distribution systems on biofilm formation and chlorine resistance. Chemosphere, 264, 128410. https://doi.org/10.1016/j.chemosphere.2020.128410
   PubMed Web of Science ®Google Scholar