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Botta C, Buzzanca D, Chiarini E, Chiesa F, Rubiola S, Ferrocino I, Fontanella E, Rantsiou K, Houf K, Alessandria V. Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp. Appl Environ Microbiol 2024; 90:e0029624. [PMID: 38647295 PMCID: PMC11107157 DOI: 10.1128/aem.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.
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Affiliation(s)
- Cristian Botta
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Elisabetta Chiarini
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Francesco Chiesa
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Selene Rubiola
- Department of Veterinary Sciences, University of Torino, Torino, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | | | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
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Faldynova M, Prikrylova H, Sebkova A, Volf J, Karasova D, Crhanova M, Babak V, Rychlik I. Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks. Poult Sci 2024; 103:103302. [PMID: 38052128 PMCID: PMC10746563 DOI: 10.1016/j.psj.2023.103302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore dependent on environmental sources only. However, since chickens evolved to be hatched in nests, in this study we evaluated the importance of contact between hens and chicks for the development of chicken skin and tracheal microbiota. Sequencing of PCR amplified V3/V4 variable regions of the 16S rRNA gene showed that contact with adult hens decreased the abundance of E. coli, Proteus mirabilis and Clostridium perfringens both in skin and the trachea, and Acinetobacter johnsonii and Cutibacterium acnes in skin microbiota only. These species were replaced by Lactobacillus gallinarum, Lactobacillus aviarius, Limosilactobacillus reuteri, and Streptococcus pasterianus in the skin and tracheal microbiota of contact chicks. Lactobacilli can be therefore investigated for their probiotic effect in respiratory tract in the future. Skin and respiratory microbiota of contact chickens was also enriched for Phascolarctobacterium, Succinatimonas, Flavonifractor, Blautia, and [Ruminococcus] torque though, since these are strict anaerobes from the intestinal tract, it is likely that only DNA from nonviable cells was detected for these taxa.
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Affiliation(s)
- Marcela Faldynova
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Hana Prikrylova
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Alena Sebkova
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Jiri Volf
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Daniela Karasova
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | | | - Vladimir Babak
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic.
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Vieira TR, de Oliveira EFC, Cibulski SP, Silva NMV, Borba MR, Oliveira CJB, Cardoso M. Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems. Poult Sci 2023; 102:103002. [PMID: 37713802 PMCID: PMC10511805 DOI: 10.1016/j.psj.2023.103002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023] Open
Abstract
The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.
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Affiliation(s)
- Tatiana R Vieira
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), 91540-000, Porto Alegre, RS, Brazil
| | - Esther F Cavinatto de Oliveira
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), 91540-000, Porto Alegre, RS, Brazil
| | - Samuel P Cibulski
- Department of Biotechnology, Center for Biotechnology (CBiotec), Federal University of Paraiba (UFPB), 58397-000, Areia, PB, Brazil
| | - Núbia M V Silva
- Federal Institute of Education, Science and Technology of Sertão Pernambucano, Campus Salgueiro (IF-Sertão Pernambucano), 56000-000, Salgueiro, PE, Brazil; Department of Animal Sciences, College of Agricultural Sciences (CCA), Federal University of Paraiba (UFPB), 58397-000, Areia, PB, Brazil
| | - Mauro R Borba
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), 91540-000, Porto Alegre, RS, Brazil
| | - Celso J B Oliveira
- Department of Animal Sciences, College of Agricultural Sciences (CCA), Federal University of Paraiba (UFPB), 58397-000, Areia, PB, Brazil
| | - Marisa Cardoso
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), 91540-000, Porto Alegre, RS, Brazil.
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Effects of bacterial-derived antimicrobial solutions on shelf-life, microbiota and sensory attributes of raw chicken legs under refrigerated storage condition. Int J Food Microbiol 2022; 383:109958. [DOI: 10.1016/j.ijfoodmicro.2022.109958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
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Lin WF, Guo HQ, Zhu LJ, Yang K, Li HZ, Cui L. Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129261. [PMID: 35739780 DOI: 10.1016/j.jhazmat.2022.129261] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
The massive food wastes pose a growing health concern for spreading of antibiotic resistance and pathogens due to food spoilage. However, little is known about these microbial hazards during collection, classification, and transportation before eventual treatment. Here, we profiled the temporal variations of antibiotic resistance genes (ARGs), pathogens, bacterial and fungal communities across four typical food wastes (vegetable, fish, meat, and rice) during storage at room temperature in summer (maximum 28-29 °C) of typical southeast city in China. A total of 171 ARGs and 32 mobile genetic elements were detected, and the absolute abundance of ARGs significantly increased by up to 126-fold with the storage time. Additionally, five bacterial pathogens containing virulence factor genes were detected, and Klebsiella pneumoniae was persistently detected throughout the storage time in all food types except rice. Moreover, fungal pathogens (e.g., Aspergillus, Penicillium, and Fusarium) were also frequently detected. Notably, animal food wastes were demonstrated to harbor higher abundance of ARGs and more types of pathogens, indicating a higher level of hazard. Mobile genetic elements and food types were demonstrated to mainly impact ARG profiles and pathogens, respectively. This work provides a comprehensive understanding of the microbial hazards associated with food waste recycling, and will contribute to optimize the food waste management to ensure biosecurity and benefit human health.
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Affiliation(s)
- Wen-Fang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong-Qin Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long-Ji Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing. Foods 2021; 10:foods10040765. [PMID: 33916748 PMCID: PMC8066510 DOI: 10.3390/foods10040765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Chicken is one of the most widely consumed meats worldwide. The exploration of the bacterial diversity of chicken meat may provide new insights into the chicken-associated microbiome that will lead to moderation of food spoilage or safety. This study was undertaken to explore the bacterial communities of chicken breast and thigh fillets stored at refrigeration (0 °C and 5 °C) and slightly abuse (10 °C) temperatures for 5 days through conventional cultural methods along with next-generation sequencing (NGS) analysis. Total viable counts (TVC), Brochothrix thermosphacta, Pseudomonas spp., and lactic acid bacteria (LAB) were enumerated, while the bacterial communities were mapped through 16S rRNA gene amplicon sequencing. Chicken breast and thigh fillets possessed a complex bacterial structure that incorporated a total of >200 Operational Taxonomic Units (OTUs) at the genus level. The core microbiota of fresh samples consisted of Acinetobacter, Brochothrix, Flavobacterium, Pseudomonas, Psychrobacter, and Vibrionaceae (family). These genera persisted until the end of storage in >80% of samples, except Psychrobacter and Flavobacterium, while Photobacterium was also identified. Hierarchical clustering showed a distinction of samples based on storage time and chicken part. Conventional plate counting with growth media commonly used in spoilage studies did not always correspond to the microbial community profiles derived from NGS analysis, especially in Pseudomonas, Acinetobacter, Photobacterium, and Vibrionaceae. Results of the present study highlight Photobacterium and Vibrionaceae, in general, as potent chicken meat spoilers and suggest the necessity to combine classical microbiological methods along with NGS technologies to characterize chicken meat spoilage microbiota.
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Huang Z, Shen Y, Huang X, Qiao M, He RK, Song L. Microbial diversity of representative traditional fermented sausages in different regions of China. J Appl Microbiol 2020; 130:133-141. [PMID: 32219941 DOI: 10.1111/jam.14648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/10/2020] [Accepted: 03/16/2020] [Indexed: 01/01/2023]
Abstract
AIMS The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety. METHODS AND RESULTS The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78·39, 13·13 and 7·14% in SC, 35·47, 30·36 and 28·04% in GD, 54·81, 28·91 and 14·00% in HN, 20·20, 58·16 and 17·31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions. CONCLUSIONS The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.
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Affiliation(s)
- Z Huang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
| | - Y Shen
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
| | - X Huang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
| | - M Qiao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
| | - R K He
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
| | - L Song
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China.,Zhengzhou City Key Laboratory for Soybean Refined Processing, Zhengzhou, China
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Wang Z, Shi Y, Zhou K, Zhou H, Li X, Li C, Wang Z, Xu B. Effects of different thermal temperatures on the shelf life and microbial diversity of Dezhou-braised chicken. Food Res Int 2020; 136:109471. [PMID: 32846556 DOI: 10.1016/j.foodres.2020.109471] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/25/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
This work investigated the effects of different thermal temperatures (84 °C for 35 min, 95 °C for 30 min, and 121 °C for 20 min) on the shelf life and microbial diversity of Dezhou-braised chicken. During refrigerated storage at 4 °C, the increase rate of total viable counts, pH and TVB-N value, was lower in 95 °C-treated and 121 °C-sterilized groups, when compared with 84 °C-treated group. Electronic nose revealed that the fresh odor of Dezhou-braised chicken treated by 84 °C and 95 °C could be maintained during storage. Additionally, 95 °C contributed to the maintenance of good texture of chicken. High throughput sequencing showed that Bacillus and Clostridium were only very active in 84 °C-treated samples, but not in 95 °C-treated and 121 °C-sterilized samples. Taken together, 95 °C can be developed as one potential thermal treatment temperature for Dezhou-braised chicken, due to its positive effects on maintaining fresh odor and texture together with extending shelf life while also protecting food safety.
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Affiliation(s)
- Zhaoming Wang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yuzhu Shi
- State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing 211806, China
| | - Kai Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hui Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing 211806, China
| | - Xinfu Li
- State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing 211806, China
| | - Cong Li
- State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing 211806, China
| | - Zhaobin Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; State Key Laboratory of Meat Processing and Quality Control, Yurun Group, Nanjing 211806, China; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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