1
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Ott LC, Mellata M. Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants. Front Microbiol 2024; 15:1414401. [PMID: 38903782 PMCID: PMC11187007 DOI: 10.3389/fmicb.2024.1414401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.
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Affiliation(s)
- Logan C. Ott
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
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2
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Anjum F, Maherchandani S, Gahlot K, Purva M. Clonal diversity and zoonotic potential of MDR Escherichia coli isolated from poultry at different age intervals. Br Poult Sci 2023; 64:650-657. [PMID: 37450277 DOI: 10.1080/00071668.2023.2236038] [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: 06/22/2022] [Revised: 06/02/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
1. A pool of 480 E. coli isolates of poultry (broilers and ducks) representing different time intervals (0, 10, 20 and 30 days) was selected for ribotyping and used to determine polymorphism of 16-23S ribosomal RNA intergenic space. All the isolates were multidrug-resistant (MDR).2. Out of these, 10 isolates were tested for MultiLocus Sequence Typing (MLST) among which novel allelic combinations and therefore new sequence types were identified in seven isolates.3. This work showed the changes in E. coli strains structure at farm level and individual bird level in host species raised on organised farms with similar parental lineage and environmental housing. The statistical results showed that the structure of variation is very different by farm, supporting a strong effect of location, which confirms the temporal clustering.4. There were significant differences between E. coli strains in chickens and ducks, indicating host specificity of the E. coli strains.5. Some of the pathogenic E. coli strains found using MLST belonged to ST735, ST2796 and a pandemic clone ST752 of ST10 clonal complex. The results strongly suggested the clonal expansion and establishment of specific MDR clones that have zoonotic relevance.
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Affiliation(s)
- F Anjum
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - S Maherchandani
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - K Gahlot
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - M Purva
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
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3
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Spatially and Temporally Confined Response of Gastrointestinal Antibiotic Resistance Gene Levels to Sulfadiazine and Extracellular Antibiotic Resistance Gene Exposure in Mice. BIOLOGY 2023; 12:biology12020210. [PMID: 36829487 PMCID: PMC9953105 DOI: 10.3390/biology12020210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023]
Abstract
This work aims to investigate the impact of antibiotics and extracellular antibiotic resistance genes (eARGs) on the dynamics of gastrointestinal antimicrobial resistance (AMR). The antibiotic resistance gene (ARG) levels of different segments of the gastrointestinal tract of mouse models were analyzed and compared after exposure to clinical concentrations of sulfadiazine and environmental levels of eARGs carried by the conjugative plasmid pR55. Exposure to sulfadiazine and eARGs led to significant changes in ARG levels by as many as four log-folds. Further analysis showed that the response of ARG levels appeared from 12-16 days after exposure and diminished 20 days after exposure. The responses in ARG levels were also restricted to different gastrointestinal segments for sulfadiazine and eARGs. Combined exposure of sulfadiazine and eARGs was unable to further increase ARG levels. From these findings, we concluded that the short-term consumption of environmental levels of eARGs and uptake of clinical levels of antibiotics lead to a spatially and temporally confined response in gastrointestinal AMR. These findings further clarify the detrimental impacts of antibiotic and eARG uptake, and the complexity of AMR development and dissemination dynamics in the gastrointestinal tract.
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. THE ISME JOURNAL 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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Orlova EG, Maslennikova IL, Pospelova JS, Starčič Erjavec M, Loginova NP, Troinich YN, Kuznetsova MV. The effect of Escherichia coli ŽP strain with a conjugation-based colicin E7 delivery on growth performance, hematological, biochemical, and histological parameters, gut microbiota, and nonspecific immunity of broilers. Can J Microbiol 2022; 68:687-702. [PMID: 36121064 DOI: 10.1139/cjm-2022-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli ŽP strain (ŽP) was constructed based on the known probiotic E. coli strain Nissle 1917. It was genetically modified to carry the colicin E7 synthesis gene encoding DNase on a conjugative plasmid and the colicin E7 immunity gene in the chromosome. The aim of this study was to evaluate the effects of the daily ŽP per oral administration (5 × 108 or 5 × 1010 CFU per bird) on the growth performance, hematological, biochemical, histological parameters, gut microbiota, and nonspecific immunity of the 4-24 days old broilers. The ŽP administration increased the abundance of genera Bacillus, Butyrivibrio, and Clostridium and did not influence the weight gain of 4-16 days old broilers. The biochemical parameters were within normal ranges for poultry in experimental and control groups. The ŽP administration had no effect on the erythrocyte numbers, hemoglobin and immunoglobulin Y concentrations, but significantly increased the serum lysozyme concentration, leukocyte numbers, and reactive oxygen species production by phagocytes compared with the control group. It did not cause inflammatory changes in intestinal mucosa, Peyer's patches, and spleen. Thus, the ŽP had no detrimental effects on broiler health and could be an efficient probiotic for the broiler colibacillosis prophylaxis.
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Affiliation(s)
- E G Orlova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch, Russian Academy of Science, Perm, Russia
| | - I L Maslennikova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch, Russian Academy of Science, Perm, Russia
| | - J S Pospelova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch, Russian Academy of Science, Perm, Russia
| | | | | | | | - M V Kuznetsova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch, Russian Academy of Science, Perm, Russia.,Perm State Medical University, Perm, Russia
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7
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Lu J, Zhang H, Pan L, Guan W, Lou Y. Environmentally relevant concentrations of triclosan exposure promote the horizontal transfer of antibiotic resistance genes mediated by Edwardsiella piscicida. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:64622-64632. [PMID: 35474424 PMCID: PMC9041674 DOI: 10.1007/s11356-022-20082-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Aquaculture pathogen and antibiotic resistance genes (ARGs) co-occur in the aquatic environment. Accumulated evidence suggests that aquaculture pathogens can facilitate the horizontal transfer of plasmid-mediated ARGs. However, the role of Edwardsiella piscicida (E. piscicida) in ARG dissemination is still not fully understood. In addition, the potential impact of triclosan (TCS) on the spread of ARGs mediated by E. piscicida is still unknown, so a mating model system was established to investigate the transfer process of ARGs. The results showed that E. piscicida disseminated ARGs on RP4 by horizontal gene transfer (HGT). Furthermore, TCS exposure promoted this process. The conjugative transfer frequencies were enhanced approximately 1.2-1.4-fold by TCS at concentrations from 2 to 20 μg/L, when compared with the control. TCS promoted the HGT of ARGs by stimulating reactive oxygen species (ROS) production, increasing cell membrane permeability, and altering expressions of conjugative transfer-associated genes. Together, the results suggested that aquaculture pathogens spread ARGs and that the emerging contaminant TCS enhanced the transfer of ARGs between bacteria.
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Affiliation(s)
- Jinfang Lu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - He Zhang
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China
| | - Liangliang Pan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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8
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Sharma NK, Wu SB, Morgan NK, Crowley TM. Artificial gut and the applications in poultry: A review. ANIMAL NUTRITION 2022; 10:156-166. [PMID: 35757559 PMCID: PMC9184286 DOI: 10.1016/j.aninu.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/26/2022]
Abstract
Artificial gut models including both the gastric and intestinal phases have been used in poultry research for decades to predict the digestibility of nutrients, the efficacy of feed enzymes and additives, and caecal fermentation. However, the models used in the past are static and cannot be used to predict interactions between the feed, gut environment and microbiome. It is imperative that a standard artificial gut model for poultry is established, to enable these interactions to be examined without continual reliance on animals. To ensure the validity of an artificial model, it should be validated with in vivo studies. This review describes current practices in the use of artificial guts in research, their importance in poultry nutrition studies and highlights an opportunity to develop a dynamic gut model for poultry to reduce the number of in vivo experiments.
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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Dorr M, Silver A, Smurlick D, Arukha A, Kariyawasam S, Oladeinde A, Cook K, Denagamage T. Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli. J Glob Antimicrob Resist 2022; 30:88-95. [PMID: 35489678 DOI: 10.1016/j.jgar.2022.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/12/2022] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to sequence, assemble and annotate three plasmids (two IncN and one IncI1) carrying the blaCTX-M-1 gene and assess their transmissibility rates between homologous and heterologous serovars and/or species of bacteria. METHODS First, the plasmids were sequenced, assembled, and annotated. They were then transferred from three donor strains (E. coli/IncN, S. Heidelberg/IncN, and S. Heidelberg/IncI1) into nine recipient strains (S. Enteritidis, S. Heidelberg, S. Saint Paul, S. Cero, S. Infantis, S. Braenderup, E. coli 50, and E. coli 2010). The blaCTX-M-1 gene PCR, plasmid isolation, and antimicrobial susceptibility testing were used on the transconjugants to confirm the successful transfer of ESBL plasmids into the recipient strains. RESULTS Both IncN plasmids were 42,407 bp in size and showed >99.4% similarity to the S. Bredeney pET1.2-IncN (GenBank accession CP043224.1) whereas the IncI1 plasmid was 107,635 bp in size and demonstrated >99.9% similarity to the E. coli pCOV33 plasmid (GenBank accession MG649046.1). Successful plasmid transfer was observed between donor E. coli (IncN) and all recipient strains except for E. coli 50 and between donor S. Heidelberg (IncN) and all recipient strains. Successful plasmid transfer was also observed between S. Heidelberg (IncI1) and E. coli 50. CONCLUSIONS Transfer of the bla CTX-M-1 encoding IncN and IncI1 plasmids via conjugation is possible yet occurs at different frequencies depending on the donor strain of bacteria with S. Heidelberg (IncN) having the highest donor-dependent transfer frequency, followed by E. coli 9079 (IncN) and S. Heidelberg (IncI1).
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Affiliation(s)
- Mackenzie Dorr
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Aryeh Silver
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Dylan Smurlick
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Ananta Arukha
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Subhashinie Kariyawasam
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | | | - Kimberly Cook
- U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Thomas Denagamage
- Department of Large Animal Clinical Sciences, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA.
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11
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Storey N, Cawthraw S, Turner O, Rambaldi M, Lemma F, Horton R, Randall L, Duggett NA, AbuOun M, Martelli F, Anjum MF. Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage. Microb Genom 2022; 8:000782. [PMID: 35344479 PMCID: PMC9176276 DOI: 10.1099/mgen.0.000782] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials is low or absent. We monitored antimicrobial-resistant Escherichia coli over 1 year in a UK outdoor pig farm with low antimicrobial usage (AMU) compared to conventional pig farms in the United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed to identify AMR genes, phylogeny and mobile elements in 385 E. coli isolates purified mainly from pig and some seagull faeces. Generally, low levels of antimicrobial-resistant E. coli were present, probably due to low AMU. Those present were likely to be multi-drug resistant (MDR) and belonging to particular Sequence Types (STs) such as ST744, ST88 or ST44, with shared clones (<14 Single Nucleotide Polymorphisms (SNPs) apart) isolated from different time points indicating epidemiological linkage within pigs of different ages, and between pig and the wild bird faeces. Although importance of horizontal transmission of AMR is well established, there was limited evidence of plasmid-mediated dissemination between different STs. Non-conjugable MDR plasmids or large AMR gene-bearing transposons were stably integrated within the chromosome and remained associated with particular STs/clones over the time period sampled. Heavy metal resistance genes were also detected within some genetic elements. This study highlights that although low levels of antimicrobial-resistant E. coli correlates with low AMU, a basal level of MDR E. coli can still persist on farm potentially due to transmission and recycling of particular clones within different pig groups. Environmental factors such as wild birds and heavy metal contaminants may also play important roles in the recycling and dissemination, and hence enabling persistence of MDR E. coli. All such factors need to be considered as any rise in AMU on low usage farms, could in future, result in a significant increase in their AMR burden.
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Affiliation(s)
- Nathaniel Storey
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Great Ormond Street Hospital for Children, London WC1N 3JH, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Olivia Turner
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Margherita Rambaldi
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Bologna, Via Zamboni, 33, 40126 Bologna BO, Italy
| | - Fabrizio Lemma
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Robert Horton
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicholas A. Duggett
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- Teeside University, Campus Heart, Middlesbrough TS1 3BX, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Francesca Martelli
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Muna F. Anjum
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
- *Correspondence: Muna F. Anjum,
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12
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Saraiva MMS, Silva NMV, Ferreira VA, Moreira Filho ALB, Givisiez PEN, Freitas Neto OC, Berchieri Júnior A, Gebreyes WA, Oliveira CJB. Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli. Lett Appl Microbiol 2022; 74:831-838. [PMID: 35138674 DOI: 10.1111/lam.13671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2x5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), and AGPs monensin (MON), lincomycin (LCM), and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively.The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared to sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.
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Affiliation(s)
- M M S Saraiva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - N M V Silva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Instituto Federal do Sertão Pernambucano - Campus Petrolina
| | - V A Ferreira
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - A L B Moreira Filho
- Department of Animal Science, Center for Human, Social and Agricultural Sciences, Federal University of Paraiba (CCHSA/UFPB), Bananeiras, PB, Brazil
| | - P E N Givisiez
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - O C Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - A Berchieri Júnior
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - W A Gebreyes
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - C J B Oliveira
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
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13
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Asare PT, Greppi A, Pennacchia A, Brenig K, Geirnaert A, Schwab C, Stephan R, Lacroix C. In vitro Modeling of Chicken Cecal Microbiota Ecology and Metabolism Using the PolyFermS Platform. Front Microbiol 2022; 12:780092. [PMID: 34987487 PMCID: PMC8721126 DOI: 10.3389/fmicb.2021.780092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Continuous in vitro fermentation models provide a useful tool for a fast, reproducible, and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. In this study, we used the PolyFermS model to mimic the conditions of the chicken cecum and evaluated three nutritive media for in vitro modeling of the chicken cecal microbiota ecology and metabolism. We observed that our model inoculated with immobilized cecal microbiota and fed with a modified Viande Levure medium (mVL-3) reached a high bacterial cell density of up to approximately 10.5 log cells per mL and stable microbiota composition, akin to the host, during 82 days of continuous operation. Relevant bacterial functional groups containing primary fibrolytic (Bacteroides, Bifidobacteriaceae, Ruminococcaceae), glycolytic (Enterococcus), mucolytic (Bacteroides), proteolytic (Bacteroides), and secondary acetate-utilizing butyrate-producing and propionate-producing (Lachnospiraceae) taxa were preserved in vitro. Besides, conserved metabolic and functional Kyoto Encyclopedia of Genes and Genomes pathways were observed between in vitro microbiota and cecal inoculum microbiota as predicted by functional metagenomics analysis. Furthermore, we demonstrated that the continuous inoculation provided by the inoculum reactor generated reproducible metabolic profiles in second-stage reactors comparable to the chicken cecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. In conclusion, we showed that PolyFermS is a suitable model for mimicking chicken cecal microbiota fermentation allowing ethical and ex vivo screening of environmental factors, such as dietary additives, on chicken cecal fermentation. We report here for the first time a fermentation medium (mVL-3) that closely mimics the substrate conditions in the chicken cecum and supports the growth and metabolic activity of the cecal bacterial akin to the host. Our PolyFermS chicken cecum model is a useful tool to study microbiota functionality and structure ex vivo.
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Affiliation(s)
- Paul Tetteh Asare
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Anna Greppi
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Alessia Pennacchia
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Katharina Brenig
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Hygiene and Safety, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
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14
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Duxbury SJN, Alderliesten JB, Zwart MP, Stegeman A, Fischer EAJ, de Visser JAGM. Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli. Proc Biol Sci 2021; 288:20212027. [PMID: 34727719 PMCID: PMC8564601 DOI: 10.1098/rspb.2021.2027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/12/2021] [Indexed: 12/17/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.
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Affiliation(s)
| | - Jesse B. Alderliesten
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mark P. Zwart
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arjan Stegeman
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Egil A. J. Fischer
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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15
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Abstract
Horizontal gene transfer (HGT) is a driving force of microbial evolution. The gut of animals acts as a potent reservoir for the lateral transfer of virulence, fitness, and antimicrobial resistance genes through plasmids. Reduced-complexity models for the examination of host-microbe interactions involved in plasmid transfer are greatly desired. Thus, this study identifies the use of Drosophila melanogaster as a model organism for the conjugation of plasmids of various incompatibility groups in the gut. Enterobacteriaceae conjugation pairs were identified in vitro and used for oral inoculation of the Drosophila gut. Flies were enumerated for the donor, recipient, and transconjugant populations. Each donor-recipient pair was observed to persist in fly guts for the duration of the experiment. Gut concentrations of the donors and recipients were significantly different between male and female flies, with females generally demonstrating increased concentrations. Furthermore, host genetics significantly altered the concentrations of donors and recipients. However, transconjugant concentrations were not affected by host sex or genetics and were detected only in the IncPε and IncI1 plasmid groups. This study demonstrates Drosophila melanogaster as a model for gut-mediated plasmid transfer. IMPORTANCE Microbial evolution in the gut of animals due to horizontal gene transfer (HGT) is of significant interest for microbial evolution as well as within the context of human and animal health. Microbial populations evolve within the host, and factors from the bacteria and host interact to regulate this evolution. However, little is currently known about how host and bacterial factors regulate plasmid-mediated HGT in the gut. This study demonstrates the use of Drosophila and the roles of sexual dimorphism as well as plasmid incompatibility groups in HGT in the gut.
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16
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Tate H, Li C, Nyirabahizi E, Tyson GH, Zhao S, Rice-Trujillo C, Jones SB, Ayers S, M'ikanatha NM, Hanna S, Ruesch L, Cavanaugh ME, Laksanalamai P, Mingle L, Matzinger SR, McDermott PF. A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States. J Food Prot 2021; 84:1749-1759. [PMID: 34015113 DOI: 10.4315/jfp-21-005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria. HIGHLIGHTS
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Affiliation(s)
- Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Epiphanie Nyirabahizi
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Crystal Rice-Trujillo
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sonya Bodeis Jones
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sherry Ayers
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Nkuchia M M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, 7th and Forster Streets, Harrisburg, Pennsylvania 17120
| | - Samir Hanna
- Tennessee Department of Health, 710 James Robertson Parkway, Nashville, Tennessee 37243
| | - Laura Ruesch
- Animal Disease Research and Diagnostic Lab, South Dakota State University, Brookings, South Dakota 57007
| | | | - Pongpan Laksanalamai
- Laboratories Administration, Maryland Department of Health, 1770 Ashland Avenue, Baltimore, Maryland 21205
| | - Lisa Mingle
- Wadsworth Center Division of Infectious Diseases, New York State Department of Health, Albany, New York 12208
| | - Shannon R Matzinger
- Colorado Department of Public Health and Environment, 8100 Lowry Boulevard, Denver, Colorado 80230, USA
| | - Patrick F McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
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17
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Kazlauskaite R, Cheaib B, Heys C, Ijaz UZ, Connelly S, Sloan W, Russel J, Rubio L, Sweetman J, Kitts A, McGinnity P, Lyons P, Llewellyn M. SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities. MICROBIOME 2021; 9:179. [PMID: 34465363 PMCID: PMC8408954 DOI: 10.1186/s40168-021-01134-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/15/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. There is still a lack of knowledge surrounding the importance and functionality of the teleost gut microbiome in fish nutrition. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host's microbial communities. Several in vitro gut models targeted at monogastric vertebrates are now in operation. Here, we report the development of an Atlantic salmon gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum, and midgut) and associated microbial communities. RESULTS The gut model was established in a series of linked bioreactors seeded with biological material derived from farmed adult marine-phase salmon. We first aimed to achieve a stable microbiome composition representative of founding microbial communities derived from Atlantic salmon. Then, in biological triplicate, the response of the in vitro system to two distinct dietary formulations (fishmeal and fishmeal free) was compared to a parallel in vivo trial over 40 days. Metabarcoding based on 16S rDNA sequencing qPCR, ammoniacal nitrogen, and volatile fatty acid measurements were undertaken to survey the microbial community dynamics and function. SalmoSim microbiomes were indistinguishable (p = 0.230) from their founding inocula at 20 days and the most abundant genera (e.g., Psycrobacter, Staphylococcus, Pseudomonas) proliferated within SalmoSim (OTUs accounting for 98% of all reads shared with founding communities). Real salmon and SalmoSim responded similarly to the introduction of novel feed, with majority of the taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa (e.g., a small fraction of Psychrobacter) was differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acid profiles were not significantly different in SalmoSim pre- and post-feed switch. CONCLUSION By establishing stable and representative salmon gut communities, this study represents an important step in the development of an in vitro gut system as a tool for the improvement of fish nutrition and welfare. The steps of the system development described in this paper can be used as guidelines to develop various other systems representing other fish species. These systems, including SalmoSim, aim to be utilised as a prescreening tool for new feed ingredients and additives, as well as being used to study antimicrobial resistance and transfer and fundamental ecological processes that underpin microbiome dynamics and assembly. Video abstract.
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Affiliation(s)
- Raminta Kazlauskaite
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, Scotland.
| | - Bachar Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Chloe Heys
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Stephanie Connelly
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - William Sloan
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Julie Russel
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | | | - John Sweetman
- Alltech Aqua, Eindhoven, Netherlands
- Alltech, Lexington, KY, USA
| | - Alex Kitts
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, T23 N73K, Cork, Ireland
- Marine Institute, Foras na Mara, F28 PF65, Newport, Ireland
| | - Philip Lyons
- Alltech Aqua, Eindhoven, Netherlands
- Alltech, Lexington, KY, USA
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, Scotland
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18
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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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19
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Habib S, Swaby AM, Gaisawat MB, Kubow S, Agellon LB. A novel, scalable, and modular bioreactor design for dynamic simulation of the digestive tract. Biotechnol Bioeng 2021; 118:4338-4346. [PMID: 34297349 DOI: 10.1002/bit.27902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 11/06/2022]
Abstract
In vitro gut model systems permit the growth of gut microbes outside their natural habitat and are essential to the study of gut microbiota. Systems available today are limited by a lack of scalability and flexibility in the mode of operation. Here, we describe the development of a versatile bioreactor module that can be easily adjusted for culture size and capable of sensing and controlling of environmental parameters such as pH control of culture medium, rate of influx and efflux of the culture medium, and aerobic/anaerobic atmosphere. Bioreactor modules can be operated as single units or linked in series to construct a model of a digestive tract with multiple compartments to allow the growth of microbiota in vitro. We tested the growth of synthetic and natural bacterial communities in a multicompartment continuous dynamic culture model simulation of the mammalian gut. The distal compartments of a sterile system inoculated with the synthetic bacterial community at the proximal module attained a stable bacterial density by 24 h, and all the genera present in the inoculum were firmly established in the distal modules simulating the large intestine at 5 days of continuous culture. A natural bacterial community simultaneously inoculated into the distal modules attained a stable bacterial composition at the phylum level by Day 7 of continuous culture. The findings illustrate the utility of the system to culture mixed bacterial communities which can be used to study the collective biological activities of the cultured microbiota in the absence of host influence.
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Affiliation(s)
- Salam Habib
- School of Human Nutrition, McGill University, Montreal, Quebec, Canada
| | - Anikka M Swaby
- School of Human Nutrition, McGill University, Montreal, Quebec, Canada
| | - Mohd B Gaisawat
- School of Human Nutrition, McGill University, Montreal, Quebec, Canada
| | - Stan Kubow
- School of Human Nutrition, McGill University, Montreal, Quebec, Canada
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Montreal, Quebec, Canada
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20
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Teymurazov MG, Petrova NV, Karelina EA, Ganina KK, Tarasov SA, Epstein OI. Nonclinical study of the new immunotropic drug effectiveness in salmonella infection treatment. BULLETIN OF SIBERIAN MEDICINE 2021. [DOI: 10.20538/1682-0363-2021-2-95-101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M. G. Teymurazov
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB)
| | - N. V. Petrova
- Institute of General Pathology and Pathophysiology (IGPP);
MATERIA MEDICA HOLDING LLC, Research and Production Company
| | - E. A. Karelina
- MATERIA MEDICA HOLDING LLC, Research and Production Company
| | - K. K. Ganina
- MATERIA MEDICA HOLDING LLC, Research and Production Company
| | - S. A. Tarasov
- Institute of General Pathology and Pathophysiology (IGPP);
MATERIA MEDICA HOLDING LLC, Research and Production Company
| | - O. I. Epstein
- Institute of General Pathology and Pathophysiology (IGPP);
MATERIA MEDICA HOLDING LLC, Research and Production Company
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21
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Mehat JW, van Vliet AHM, La Ragione RM. The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes. Avian Pathol 2021; 50:402-416. [PMID: 34047644 DOI: 10.1080/03079457.2021.1915960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Avian Pathogenic E. coli (APEC) is the causative agent of avian colibacillosis, resulting in economic losses to the poultry industry through morbidity, mortality and carcass condemnation, and impacts the welfare of poultry. Colibacillosis remains a complex disease to manage, hampered by diagnostic and classification strategies for E. coli that are inadequate for defining APEC. However, increased accessibility of whole genome sequencing (WGS) technology has enabled phylogenetic approaches to be applied to the classification of E. coli and genomic characterization of the most common APEC serotypes associated with colibacillosis O1, O2 and O78. These approaches have demonstrated that the O78 serotype is representative of two distinct APEC lineages, ST-23 in phylogroup C and ST-117 in phylogroup G. The O1 and O2 serotypes belong to a third lineage comprised of three sub-populations in phylogroup B2; ST-95, ST-140 and ST-428/ST-429. The frequency with which these genotypes are associated with colibacillosis implicates them as the predominant APEC populations and distinct from those causing incidental or opportunistic infections. The fact that these are disparate clusters from multiple phylogroups suggests that these lineages may have become adapted to the poultry niche independently. WGS studies have highlighted the limitations of traditional APEC classification and can now provide a path towards a robust and more meaningful definition of the APEC pathotype. Future studies should focus on characterizing individual APEC populations in detail and using this information to develop improved diagnostics and interventions.
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Affiliation(s)
- Jai W Mehat
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Roberto M La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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22
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Lone A, Mottawea W, Mehdi Y, Hammami R. Bacteriocinogenic probiotics as an integrated alternative to antibiotics in chicken production - why and how? Crit Rev Food Sci Nutr 2021; 62:8744-8760. [PMID: 34060404 DOI: 10.1080/10408398.2021.1932722] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The misuse of antibiotics in the livestock industry has played an important role in the spread of resistant superbugs with severe health implications for humans. With the recent ban on the use of antibiotics in poultry and poultry feed in Canada and the USA, poultry farmers will have to rely on the use of alternatives to antibiotics (such as feed acidifiers, antibodies, bacteriophages, antimicrobial peptides, prebiotics, and probiotics) to maintain the same productivity and health of their livestock. Of particular interest are bacteriocinogenic probiotics, that is, bacterial strains capable of producing bacteriocins that confer health benefits on the host. These bacterial strains have multiple promising features, such as the ability to attach to the host mucosa, colonize, proliferate, and produce advantageous products such as bacteriocins and short-chain fatty acids. These not only affect pathogenic colonization but improve poultry phenotype as well. Bacteriocins are antimicrobial peptides with multiple promising features such as being non-harmful for human and animal consumption, non-disruptive to the host microbiota eubiosis, non-cytotoxic, and non-carcinogenic. Therefore, bacteriocinogenic probiotics are at the forefront to be excellent candidates for effective replacements to antibiotics. While evidence of their safety and effectiveness is accumulating in vitro and in vivo in inhibiting pathogens while promoting animal health, their safety and history of use in livestock remains unclear and requires additional investigations. In the present paper, we review the safety assessment regulations and commercialization policies on existing and novel bacteriocinogenic and bacteriocin products intended to be used in poultry feed as an alternative to antibiotics.
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Affiliation(s)
- Ayesha Lone
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Faculty of Pharmacy, Department of Microbiology and Immunology, Mansoura University, Mansoura, Egypt
| | - Youcef Mehdi
- Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada
| | - Riadh Hammami
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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23
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In Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture Device. Appl Environ Microbiol 2021; 87:AEM.02659-20. [PMID: 33361364 DOI: 10.1128/aem.02659-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-resistant (MDR) Escherichia coli to a community of pathogenic Salmonella enterica was investigated using a continuous-culture device, and the behaviors of dissemination dynamics under different levels of antibiotic stress were investigated. Three MDR E. coli invasion events were analyzed in this work: MDR E. coli-S. enterica cocolonization, MDR E. coli invasion after antibiotic treatment of S. enterica, and MDR E. coli invasion before antibiotic treatment of S. enterica It was found that both horizontal gene transfer (HGT) and vertical gene transfer (VGT) play significant roles in AMR dissemination, although different processes contribute differently under different circumstances, that environmental levels of antibiotics promote AMR dissemination by enhancing HGT rather than leading to selective advantage for resistant bacteria, and that early invasion of MDR E. coli completely and quickly sabotages the effectiveness of antibiotic treatment. These findings contribute to understanding the drivers of AMR dissemination under different antibiotic stresses, the detrimental impact of environmental tetracycline contamination, and the danger of nosocomial presence and dissemination of MDR nonpathogens.IMPORTANCE Antimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits. The dissemination dynamics and behaviors of this threat, however, have not been rigorously investigated. In this work, with a continuous-culture device, we studied antimicrobial resistance dissemination processes by simulating antimicrobial-resistant Escherichia coli invasion to a pathogenic Salmonella enterica community. Using this novel tool, we provide evidence on the drivers of antimicrobial resistance dissemination, on the detrimental impact of environmental antibiotic contamination, and on the danger of antimicrobial resistance in hospitals, even if what harbors the antimicrobial resistance is not a pathogen. This work furthers our understanding of antimicrobial resistance and its dissemination between bacteria and of antibiotic therapy, our most powerful tool against bacterial infection.
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24
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Wei B, Cha SY, Shang K, Zhang JF, Jang HK, Kang M. Genetic diversity of extended-spectrum cephalosporin resistance in Salmonella enterica and E. coli isolates in a single broiler chicken. Vet Microbiol 2021; 254:109010. [PMID: 33631701 DOI: 10.1016/j.vetmic.2021.109010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Extended-spectrum cephalosporin (ESC) resistance investigated in Salmonella and E. coli from the same chicken was to improve the understanding of the inter-species transmission of ESC resistance determinants in Salmonella and E. coli from a single chicken individual. Fifteen (13.6%) farms and 44 (8.0%) chicken individuals were positive for ESC-resistant E. coli and/or Salmonella, 8 farms (7.3%) and 12 (2.2%) individuals were simultaneously positive for ESC-resistant E. coli and Salmonella. The genetic diversity of ESC resistance determinants in E. coli and Salmonella was observed. Most E. coli isolates (67.6%) produced CTX-M-type of blaCTX-M-55, and 9 isolates (24.3%) produced CMY-type of blaCMY-2. Most Salmonella isolates (94.1%) produced blaCTX-M-15. Two broiler chicken farms were simultaneously positive for blaCMY-2- and blaCTX-M-15-harboring E. coli and Salmonella isolates. Whole-plasmid sequence for the transferable plasmid harboring blaCMY-2 showed genomic diversity of the plasmids from Salmonella and E. coli sourced from the same chicken. The genetic arrangement of blaCMY-2 in Salmonella was IS1294b-ΔISEcp1-blaCMY-2-blc-sugE and ISEcp1-blaCMY-2-blc-sugE in E. coli located on multi-host plasmids of IncI1-pST-2 and IncI1-pST-12. In conclusion, the study illustrates the genetic diversity of ESC resistance determinants in E. coli and Salmonella in a single chicken. Considering the possibility of transmission of antimicrobial resistance to humans through the food chain, a large reservoir of ESC resistance in chicken which could be co-infected with ESC-resistant E. coli and Salmonella poses a serious risk of potential transmission of ESC-resistant E. coli and Salmonella, and their transferable ESC resistant gene, to human simultaneously.
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Affiliation(s)
- Bai Wei
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea
| | - Se-Yeoun Cha
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea
| | - Ke Shang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea
| | - Jun-Feng Zhang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea
| | - Hyung-Kwan Jang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea; Bio Disease Control(BIOD) Co., Ltd., Iksan, South Korea.
| | - Min Kang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan, South Korea; Bio Disease Control(BIOD) Co., Ltd., Iksan, South Korea.
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25
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Mageiros L, Méric G, Bayliss SC, Pensar J, Pascoe B, Mourkas E, Calland JK, Yahara K, Murray S, Wilkinson TS, Williams LK, Hitchings MD, Porter J, Kemmett K, Feil EJ, Jolley KA, Williams NJ, Corander J, Sheppard SK. Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nat Commun 2021; 12:765. [PMID: 33536414 PMCID: PMC7858641 DOI: 10.1038/s41467-021-20988-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
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Affiliation(s)
- Leonardos Mageiros
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
- MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK
| | - Johan Pensar
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Jessica K Calland
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Koji Yahara
- Antimicrobial Resistance Research Centre, National Institute of Infectious Diseases, Tokyo, Japan
| | - Susan Murray
- Uppsala University, Department for medical biochemistry and microbiology, Uppsala University, Uppsala, Sweden
| | - Thomas S Wilkinson
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Lisa K Williams
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Matthew D Hitchings
- Swansea University Medical School, Institute of Life Science, Swansea, SA2 8PP, UK
| | - Jonathan Porter
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kirsty Kemmett
- Department of Epidemiology and Population Health, Institute of Infection & Global Health, University of Liverpool, Leahurst Campus, Wirral, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Keith A Jolley
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Nicola J Williams
- Department of Epidemiology and Population Health, Institute of Infection & Global Health, University of Liverpool, Leahurst Campus, Wirral, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK.
- MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK.
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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26
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Puvača N, de Llanos Frutos R. Antimicrobial Resistance in Escherichia coli Strains Isolated from Humans and Pet Animals. Antibiotics (Basel) 2021; 10:69. [PMID: 33450827 PMCID: PMC7828219 DOI: 10.3390/antibiotics10010069] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Throughout scientific literature, we can find evidence that antimicrobial resistance has become a big problem in the recent years on a global scale. Public healthcare systems all over the world are faced with a great challenge in this respect. Obviously, there are many bacteria that can cause infections in humans and animals alike, but somehow it seems that the greatest threat nowadays comes from the Enterobacteriaceae members, especially Escherichia coli. Namely, we are witnesses to the fact that the systems that these bacteria developed to fight off antibiotics are the strongest and most diverse in Enterobacteriaceae. Our great advantage is in understanding the systems that bacteria developed to fight off antibiotics, so these can help us understand the connection between these microorganisms and the occurrence of antibiotic-resistance both in humans and their pets. Furthermore, unfavorable conditions related to the ease of E. coli transmission via the fecal-oral route among humans, environmental sources, and animals only add to the problem. For all the above stated reasons, it is evident that the epidemiology of E. coli strains and resistance mechanisms they have developed over time are extremely significant topics and all scientific findings in this area will be of vital importance in the fight against infections caused by these bacteria.
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Affiliation(s)
- Nikola Puvača
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
- Department of Engineering Management in Biotechnology, Faculty of Economics and Engineering Management in Novi Sad, University Business Academy in Novi Sad, Cvećarska 2, 21000 Novi Sad, Serbia
| | - Rosa de Llanos Frutos
- Faculty of Biomedical and Health Sciences, Jaume I University, Avinguda de Vicent Sos Baynat, s/n, 12071 Castelló de la Plana, Spain;
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27
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Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms. Microorganisms 2021; 9:microorganisms9010141. [PMID: 33435450 PMCID: PMC7826917 DOI: 10.3390/microorganisms9010141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/27/2022] Open
Abstract
Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY
was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY
was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment.
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28
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Aljahdali NH, Sanad YM, Han J, Foley SL. Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota. BMC Microbiol 2020; 20:353. [PMID: 33203384 PMCID: PMC7673091 DOI: 10.1186/s12866-020-02008-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/12/2020] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.
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Affiliation(s)
- Nesreen H Aljahdali
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.,Biological Science Department, College of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Yasser M Sanad
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.,Department of Agriculture, University of Arkansas, Pine Bluff, AR, USA.,Department of Parasitology and Animal Diseases, Veterinary Research Division, National Research Centre, Giza, Egypt
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
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29
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Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources. Genes (Basel) 2020; 11:genes11111307. [PMID: 33158112 PMCID: PMC7716204 DOI: 10.3390/genes11111307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.
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30
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Redweik GAJ, Jochum J, Mellata M. Live Bacterial Prophylactics in Modern Poultry. Front Vet Sci 2020; 7:592312. [PMID: 33195630 PMCID: PMC7655978 DOI: 10.3389/fvets.2020.592312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022] Open
Abstract
Commercial poultry farms frequently use live bacterial prophylactics like vaccines and probiotics to prevent bacterial infections. Due to the emergence of antibiotic-resistant bacteria in poultry animals, a closer examination into the health benefits and limitations of commercial, live prophylactics as an alternative to antibiotics is urgently needed. In this review, we summarize the peer-reviewed literature of several commercial live bacterial vaccines and probiotics. Per our estimation, there is a paucity of peer-reviewed published research regarding these products, making repeatability, product-comparison, and understanding biological mechanisms difficult. Furthermore, we briefly-outline significant issues such as probiotic-label accuracy, lack of commercially available live bacterial vaccines for major poultry-related bacteria such as Campylobacter and Clostridium perfringens, as well research gaps (i.e., probiotic-mediated vaccine adjuvancy, gut-brain-microbiota axis). Increased emphasis on these areas would open several avenues for research, ranging from improving protection against bacterial pathogens to using these prophylactics to modulate animal behavior.
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Affiliation(s)
- Graham A. J. Redweik
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Jared Jochum
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
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31
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Nyirabahizi E, Tyson GH, Dessai U, Zhao S, Kabera C, Crarey E, Womack N, Crews MK, Strain E, Tate H. Evaluation of Escherichia coli as an indicator for antimicrobial resistance in Salmonella recovered from the same food or animal ceca samples. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Suresh G, Pakdel H, Rouissi T, Brar SK, Diarra M, Roy C. Evaluation of pyroligneous acid as a therapeutic agent against Salmonella in a simulated gastrointestinal tract of poultry. Braz J Microbiol 2020; 51:1309-1316. [PMID: 32468399 PMCID: PMC7455633 DOI: 10.1007/s42770-020-00294-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 10/24/2022] Open
Abstract
Pyroligneous acid (PA) was evaluated as a potential alternative to therapeutic antibiotics in poultry. Antimicrobial activity of PA was studied at acidic pH (2.0) and neutral pH (7.0) of the liquid against Salmonella enterica and Lactobacillus acidophilus. Acidic PA gave a MIC value of 0.8% (v/v) and 1.6% (v/v), and neutralized PA gave a MIC value of 1.6% (v/v) and 3.2% (v/v) against S. enterica and L. acidophilus respectively. Acidic PA was evaluated at different concentrations in a simulated poultry digestive tract and cecal fermentation to study its effect on the cecal microflora and fermentation profile. PA at a concentration of 1.6% (v/v) completely inhibited S. enterica and was also found to have a similar effect on lactobacilli count as compared with the control (p = 0.17). Additionally, PA at this concentration was found not to have a significant effect on acetic acid production after 24 h of cecal fermentation (p = 0.20). Graphical abstract.
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Affiliation(s)
- Gayatri Suresh
- Centre - Eau Terre Environnement, 490, Rue de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Hooshang Pakdel
- Pyrovac Inc, 176-2 rue Damase-Breton, Saint-Lambert-de-Lauzon, QC, G0S 2W0, Canada
| | - Tarek Rouissi
- Centre - Eau Terre Environnement, 490, Rue de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Satinder Kaur Brar
- Centre - Eau Terre Environnement, 490, Rue de la Couronne, Québec, QC, G1K 9A9, Canada.
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, M3J 1P3, Canada.
| | - Moussa Diarra
- Guelph Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Christian Roy
- Pyrovac Inc, 176-2 rue Damase-Breton, Saint-Lambert-de-Lauzon, QC, G0S 2W0, Canada
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33
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Sidiropoulou E, Skoufos I, Marugan-Hernandez V, Giannenas I, Bonos E, Aguiar-Martins K, Lazari D, Blake DP, Tzora A. In vitro Anticoccidial Study of Oregano and Garlic Essential Oils and Effects on Growth Performance, Fecal Oocyst Output, and Intestinal Microbiota in vivo. Front Vet Sci 2020; 7:420. [PMID: 32851011 PMCID: PMC7411182 DOI: 10.3389/fvets.2020.00420] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/11/2020] [Indexed: 01/01/2023] Open
Abstract
This study investigated the in vitro effects of Greek oregano and garlic essential oils on inhibition of Eimeria parasites and their in vivo effects on production performance, intestinal bacteria counts, and oocyst output. An inhibition assay was performed in vitro using Eimeria tenella Wisconsin strain sporozoites and Madin-Darby bovine kidney (MDBK) cells. Intracellular sporozoite invasion was quantified by detection of E. tenella DNA using qPCR from cell monolayers harvested at 2 and 24 h post-infection. Parasite invasion was inhibited by the oregano essential oil at the concentration of 100 μg/ml by 83 or 93% after 2 or 24 h, respectively. Garlic essential oil reached a maximum inhibition of 70% after 24 h with the 50 μg/ml concentration. Normal morphology was observed in MDBK cells exposed to concentrations of 100 μl/ml of garlic or oregano for over 24 h. In the in vivo trial, 180 male broiler chicks (45.3 ± 0.7 g) were allocated into two treatments (6 pens of 15 chicks per treatment). Control treatment was fed commercial diets without antibiotics or anticoccidials. The ORE-GAR treatment was fed the same control diets, further supplemented with a premix (1 g/kg feed) containing the oregano (50 g/kg premix) and garlic (5 g/kg premix) essential oils. At day 37, all birds were slaughtered under commercial conditions, and intestinal samples were collected. ORE-GAR treatment had improved final body weight (1833.9 vs. 1.685.9 g; p < 0.01), improved feed conversion ratio (1.489 vs. 1.569; p < 0.01), and reduced fecal oocyst excretion (day 28: 3.672 vs. 3.989 log oocysts/g, p < 0.01; day 37: 3.475 vs. 4.007 log oocysts/g, p < 0.001). In the caecal digesta, ORE-GAR treatment had lower total anaerobe counts (8.216 vs. 8.824 CFU/g; p < 0.01), whereas in the jejunum digesta the ORE-GAR treatment had higher counts of E. coli (5.030 vs. 3.530 CFU/g; p = 0.01) and Enterobacteriaceae (5.341 vs. 3.829 CFU/g; p < 0.01), and lower counts of Clostridium perfringens (2.555 vs. 2.882 CFU/g; p < 0.01). In conclusion, the combined supplementation of oregano and garlic essential oils had a potent anticoccidial effect in vitro and a growth-promoting effect in broilers reared in the absence of anticoccidial drugs.
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Affiliation(s)
- Erasmia Sidiropoulou
- Laboratory of Nutrition, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Skoufos
- Laboratory of Animal Production, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Arta, Greece
| | - Virginia Marugan-Hernandez
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| | - Ilias Giannenas
- Laboratory of Nutrition, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Bonos
- Laboratory of Animal Production, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Arta, Greece
| | - Kelsilandia Aguiar-Martins
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| | - Diamanto Lazari
- Laboratory of Pharmacognosy, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Damer P. Blake
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| | - Athina Tzora
- Laboratory of Animal Production, Nutrition and Biotechnology, Department of Agriculture, School of Agriculture, University of Ioannina, Arta, Greece
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Cuevas-Ferrando E, Guirado P, Miró E, Iglesias-Torrens Y, Navarro F, Alioto TS, Gómez-Garrido J, Madrid C, Balsalobre C. Tetracycline resistance transmission in Campylobacter is promoted at temperatures resembling the avian reservoir. Vet Microbiol 2020; 244:108652. [PMID: 32402330 DOI: 10.1016/j.vetmic.2020.108652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 11/26/2022]
Abstract
Campylobacter is the causal agent of campylobacteriosis in humans, a self-limiting gastroenteritis. Campylobacteriosis is a zoonosis, commonly transmitted from contaminated chicken meat by either direct consumption or cross contamination during food manipulation. Presence of plasmids encoding for resistance to antibiotics such as tetracycline is common among Campylobacter isolates. In this report, we studied the effect of the temperature in the conjugation frequency of several tet(O) carrying plasmids, providing tetracycline resistance to the recipient cells. The conjugation frequency from donor cells carrying three previously characterized plasmids (pCjA13, pCjA9 and pTet) and from two clinical isolates was determined. Two temperatures, 37 and 42 °C, mimicking the conditions encountered by C. jejuni in the human and broiler chicken gastrointestinal tracts, respectively, were assessed. Our results clearly indicate that the conjugation process is promoted at high temperature. Accordingly, the transcriptional expression of some putative conjugative apparatus genes is thermoregulated, being induced at 42 °C. The two plasmids present in the clinical isolates were sequenced and assembled. Both plasmids are highly related among them and to the pTet plasmid. The high identity of the genes putatively involved in the conjugation process among the plasmids is in agreement with the similar behavior regarding the temperature dependency of the conjugative process. This report suggest that conjugation of plasmids carrying antibiotic resistance genes occurs preferentially at temperatures that resemble the gastrointestinal tract of birds, the main reservoir of C. jejuni.
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Affiliation(s)
- E Cuevas-Ferrando
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona Spain
| | - P Guirado
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona Spain
| | - E Miró
- Hospital de la Santa Creu i Sant Pau and Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Y Iglesias-Torrens
- Hospital de la Santa Creu i Sant Pau and Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain; Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - F Navarro
- Hospital de la Santa Creu i Sant Pau and Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain; Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - T S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - J Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - C Madrid
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona Spain.
| | - C Balsalobre
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona Spain.
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Sood U, Gupta V, Kumar R, Lal S, Fawcett D, Rattan S, Poinern GEJ, Lal R. Chicken Gut Microbiome and Human Health: Past Scenarios, Current Perspectives, and Futuristic Applications. Indian J Microbiol 2020; 60:2-11. [PMID: 32089569 PMCID: PMC7000578 DOI: 10.1007/s12088-019-00785-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022] Open
Abstract
Sustainable poultry practices are needed to maintain an adequate supply of poultry products to the increasing human population without compromising human wellbeing. In order to achieve the understanding of the core microbiome that assumes an imperative role in digestion, absorption, and assimilation of feed as well as restrict the growth of pathogenic strains, a proper meta-data survey is required. The dysbiosis of the core microbiome or any external infection in chickens leads to huge losses in the poultry production worldwide. Along with this, the consumption of infected meat also impacts on human health as chicken meat is a regular staple in many diets as a vital source of protein. To tackle these losses, sub-therapeutic doses of antibiotics are being used as a feed additive along with other conventional approaches including selective breeding and modulation in feed composition. Altogether, these conventional approaches have improved the yield and quality of poultry products, however, the use of antibiotics encompasses the risk of developing multi-drug resistant pathogenic strains that can be harmful to human beings. Thus, there is an urgent need to understand the chicken microbiome in order to modulate chicken gut microbiome and provide alternatives to the conventional methods. Although there is now emerging literature available on some of these important microbiome aspects, in this article, we have analysed the relevant recent developments in understanding the chicken gut microbiome including the establishment of integrated gene catalogue for chicken microbiome. We have also focussed on novel strategies for the development of a chicken microbial library that can be used to develop novel microbial consortia as novel probiotics to improve the poultry meat production without compromising human health. Thus, it can be an alternative and advanced step compared to other conventional approaches to improve the gut milieu and pathogen-mediated loss in the poultry industry.
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Affiliation(s)
- Utkarsh Sood
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Roshan Kumar
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
- South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Sukanya Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Derek Fawcett
- Physics and Nanotechnology, Murdoch University, Perth, WA Australia
| | - Supriya Rattan
- Physics and Nanotechnology, Murdoch University, Perth, WA Australia
| | | | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
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Saraiva M, Moreira Filho A, Vasconcelos P, Nascimento P, Azevedo P, Freitas Neto O, Givisiez P, Gebreyes W, Oliveira C. Chemical treatment of poultry litter affects the conjugation of plasmid-mediated extended-spectrum beta-lactamase resistance genes in E. coli. J APPL POULTRY RES 2020. [DOI: 10.1016/j.japr.2019.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Clinically important microbial diversity and its antibiotic resistance pattern towards various drugs. J Infect Public Health 2019; 12:783-788. [DOI: 10.1016/j.jiph.2019.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 08/03/2019] [Accepted: 08/20/2019] [Indexed: 10/26/2022] Open
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Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca. Appl Environ Microbiol 2019; 85:AEM.01903-19. [PMID: 31471306 DOI: 10.1128/aem.01903-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022] Open
Abstract
The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between S Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one S Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-β-lactamase gene (bla CMY-2). In vitro, this plasmid was transferable between Escherichia coli and S Heidelberg strains but transfer was unsuccessful between S Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome.IMPORTANCE S. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC β-lactamase (bla CMY-2) gene to an important foodborne pathogen, S Heidelberg. The potential role for bacteriophage transduction is also discussed.
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An in vitro chicken gut model for the assessment of phytase producing bacteria. 3 Biotech 2019; 9:294. [PMID: 31297307 DOI: 10.1007/s13205-019-1825-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/02/2019] [Indexed: 01/08/2023] Open
Abstract
An in vitro simulated chicken gut model was proposed for studying the phytase activity of selected bacteria such as Streptococcus thermophilus, Sporosarcina pasteurii, Sporosarcina globispora, and Sporosarcina psychrophila using known probiotic bacterium, Lactobacillus helveticus as a control. The selected bacteria were viable in the intestinal lumen and produced extracellular phytase at optimal phytate concentration of 6.25 mM when compared to 3.125 mM and 12.5 mM. These bacteria demonstrated significantly higher (p < 0.05) phosphate liberation (up to 387 µM) due to better phytase activity in the production medium, when compared to the growth medium (339 µM). The phytase activity showed a steady increase in phosphate liberation up to 150 min after which it became constant. This trend is observed for the selected bacteria at pH 5, 6 and 7. However, the liberation of phosphates showed no significant difference (p > 0.05) at the tested pH. Among the analyzed bacteria, the members of the genus Sporosarcina showed better phytate degradation when compared to S. thermophilus. The proposed model can be extended to analyze any extracellular enzymes produced by gut microbes.
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Monte DF, Lincopan N, Berman H, Cerdeira L, Keelara S, Thakur S, Fedorka-Cray PJ, Landgraf M. Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016. Sci Rep 2019; 9:11058. [PMID: 31363103 PMCID: PMC6667439 DOI: 10.1038/s41598-019-45838-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
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Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. .,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Hanna Berman
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil.
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41
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Collineau L, Boerlin P, Carson CA, Chapman B, Fazil A, Hetman B, McEwen SA, Parmley EJ, Reid-Smith RJ, Taboada EN, Smith BA. Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Front Microbiol 2019; 10:1107. [PMID: 31231317 PMCID: PMC6558386 DOI: 10.3389/fmicb.2019.01107] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/01/2019] [Indexed: 12/20/2022] Open
Abstract
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures. This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR. We describe how WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling. Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. WGS results can be used to stratify hazards into strains with similar genetic profiles that are expected to behave similarly, e.g., in terms of growth, survival, virulence or response to antimicrobial treatment. The QMRA input distributions can be tailored to each strain accordingly, making it possible to capture the variability in the strains of interest while decreasing the uncertainty in the model. WGS also allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption. WGS therefore has the potential to substantially improve the utility of foodborne AMR QMRA models. However, some degree of uncertainty remains in relation to the thresholds of genetic similarity to be used, as well as the degree of correlation between genotypic and phenotypic profiles. The latter could be improved using a functional approach based on prediction of microbial behavior from a combination of 'omics' techniques (e.g., transcriptomics, proteomics and metabolomics). We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.
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Affiliation(s)
- Lucie Collineau
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Brennan Chapman
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Benjamin Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Scott A. McEwen
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - E. Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ben A. Smith
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
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Bythwood TN, Soni V, Lyons K, Hurley-Bacon A, Lee MD, Hofacre C, Sanchez S, Maurer JJ. Antimicrobial Resistant Salmonella enterica Typhimurium Colonizing Chickens: The Impact of Plasmids, Genotype, Bacterial Communities, and Antibiotic Administration on Resistance. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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43
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Xavier BB, Renzi G, Lammens C, Cherkaoui A, Goossens H, Schrenzel J, Harbarth S, Malhotra-Kumar S. Potential in vivo transfer of a blaCTX-M14-harbouring plasmid established by combining long- and short-read sequencing. J Microbiol Methods 2019; 159:1-4. [DOI: 10.1016/j.mimet.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/28/2019] [Accepted: 02/05/2019] [Indexed: 12/26/2022]
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Lee HJ, Cho SH, Shin D, Kang HS. Prevalence of Antibiotic Residues and Antibiotic Resistance in Isolates of Chicken Meat in Korea. Korean J Food Sci Anim Resour 2018; 38:1055-1063. [PMID: 30479511 PMCID: PMC6238038 DOI: 10.5851/kosfa.2018.e39] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 11/06/2022] Open
Abstract
The aim of study was to investigate the correlation between the level of 17 antibiotic residues and 6 antibiotic resistances of Escherichia coli isolates in chicken meats. A total of 58 chicken meats were collected from retail grocery stores in five provinces in Korea. The total detection rate of antibiotic residues was 45% (26 out of 58). Ten out of 17 antibiotics were detected in chicken meats. None of the antibiotics exceeded the maximum residue level (MRLs) in chicken established by the Ministry of Food and Drug Safety (MFDS). The most detected antibiotics were amoxicillin (15.5%), followed by enrofloxacin (12.1%) and sulfamethoxazole (10.3%). In a total of 58 chicken meats, 51 E. coli strains were isolated. E. coli isolates showed the highest resistance to ampicillin (75%), followed by tetracycline (69%), ciprofloxacin (65%), trimethoprim/ sulfamethoxazole (41%), ceftiofur (22%), and amoxicillin/clavulanic acid (12%). The results of study showed basic information on relationship between antibiotic residue and resistance for 6 compounds in 13 chicken samples. Further investigation on the antibiotic resistance patterns of various bacteria species is needed to improve food safety.
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Affiliation(s)
- Hyo-Ju Lee
- Department of Emergency Medical Services, Sun Moon University, Asan 31460, Korea
| | - Seung-Hak Cho
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Cheongju 28159, Korea
| | - Dasom Shin
- Pesticide and Veterinary Drugs Residue Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea
| | - Hui-Seung Kang
- Pesticide and Veterinary Drugs Residue Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea
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Anjum M, Madsen JS, Espinosa-Gongora C, Jana B, Wiese M, Nielsen DS, Sørensen SJ, Moodley A, Bortolaia V, Guardabassi L. A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities. J Microbiol Methods 2018; 152:18-26. [PMID: 30030013 DOI: 10.1016/j.mimet.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022]
Abstract
IncI1 plasmids play a central role in the transfer of antimicrobial resistance genes among Enterobacteriaceae in animals and humans. Knowledge on the dynamics of IncI1 plasmid transfer is limited, mainly due to lack of culture-independent methods that can quantify donor strain survival and plasmid transfer in complex microbial communities. The aim of this study was to develop a culture-independent method to study the dynamics of IncI1 plasmids transfer by fluorescence-activated cell sorting. We genetically modified three wild-type Escherichia coli of animal (n = 2) and human (n = 1) origin carrying blaCMY-2 or blaCTX-M-1 on two epidemic IncI1 plasmids (pST12 and pST7). Non-coding regions on the chromosome and on the IncI1 plasmid of each strain were tagged with mCherry (red) and GFPmut3 (green) fluorescent proteins, respectively, using lambda recombineering. A gene cassette expressing mCherry and lacIq was inserted into the chromosome, whereas the plasmid was marked with a GFPmut3 cassette with LacIq repressible promoter. Therefore, gfpmut3 was repressed in donor strains but expressed in recipient strains acquiring the plasmids. We demonstrated that genetic engineering of the strains did not affect the growth rate and plasmid transfer-ability in filter and broth matings. A proof-of-concept experiment using the CoMiniGut, an in vitro model of the colon, proved the validity of our method for studying the survival of wild-type E. coli and horizontal transfer of IncI1 plasmids under different pH and oxygen conditions. The dual-labeling method by fluorescent proteins is useful to determine persistence of exogenous E. coli and transfer dynamics of IncI1 plasmids in microbial communities.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Jonas Stenløkke Madsen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Dennis Sandris Nielsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs. Lyngby, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark.
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Microbial degradation of myo-inositol hexakisphosphate (IP6): specificity, kinetics, and simulation. 3 Biotech 2018; 8:268. [PMID: 29868306 DOI: 10.1007/s13205-018-1302-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 05/21/2018] [Indexed: 01/08/2023] Open
Abstract
Microbial degradation of myo-inositol hexakisphosphate (IP6) is crucial to deal with nutritional problems in monogastric animals as well as to prevent environmental phosphate pollution. The present study deals with the degradation of IP6 by microorganisms such as Sporosarcina spp. pasteurii, globiospora, psychrophila, Streptococcus thermophilus and Saccharomyces boulardii. These microbes were screened for phytase production under laboratory conditions. The specificity of the enzyme was tested for various phosphorylated substrates such as sodium phytate (IP6), sodium hexametaphosphate, phenyl phosphate, α-d-glucose-6 phosphate, inosine 5' monophosphate and pyridoxal 5' phosphate. These enzymes were highly specific to IP6. The influence of modulators such as phytochemicals and metal ions on the enzymatic activity was assessed. These modulators in different concentrations had varying effect on microbial phytases. Calcium (in optimal concentration of 0.5 M) played an important role in enzyme activation. The enzymes were then characterized based on their molecular weight 41~43 kDa. The phytase-producing microbes were assessed for IP6 degradation in a simulated intestinal setup. Among the selected microbes, Sporosarcina globiospora hydrolyzed IP6 effectively, as confirmed by colorimetric time-based analysis.
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Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
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Hadziabdic S, Fischer J, Malorny B, Borowiak M, Guerra B, Kaesbohrer A, Gonzalez-Zorn B, Szabo I. In Vivo Transfer and Microevolution of Avian Native IncA/C 2blaNDM-1-Carrying Plasmid pRH-1238 during a Broiler Chicken Infection Study. Antimicrob Agents Chemother 2018; 62:e02128-17. [PMID: 29437622 PMCID: PMC5913973 DOI: 10.1128/aac.02128-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
The emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) in wildlife and livestock animals pose an important safety concern for public health. With our in vivo broiler chicken infection study, we investigated the transfer and experimental microevolution of the blaNDM-1-carrying IncA/C2 plasmid (pRH-1238) introduced by avian native Salmonella enterica subsp. enterica serovar Corvallis without inducing antibiotic selection pressure. We evaluated the dependency of the time point of inoculation on donor (S Corvallis [12-SA01738]) and plasmid-free Salmonella recipient [d-tartrate-fermenting (d-Ta+) S Paratyphi B (13-SA01617), referred to here as S Paratyphi B (d-Ta+)] excretion by quantifying their excretion dynamics. Using plasmid profiling by S1 nuclease-restricted pulsed-field gel electrophoresis, we gained insight into the variability of the native plasmid content among S Corvallis reisolates as well as plasmid acquisition in S Paratyphi B (d-Ta+) and the enterobacterial gut microflora. Whole-genome sequencing enabled us to gain an in-depth insight into the microevolution of plasmid pRH-1238 in S Corvallis and enterobacterial recipient isolates. Our study revealed that the fecal excretion of avian native carbapenemase-producing S Corvallis is significantly higher than that of S Paratyphi (d-Ta+) and is not hampered by S Paratyphi (d-Ta+). Acquisition of pRH-1238 in other Enterobacteriaceae and several events of plasmid pRH-1238 transfer to different Escherichia coli sequence types and Klebsiella pneumoniae demonstrated an interspecies broad host range. Regardless of the microevolutionary structural deletions in pRH-1238, the single carbapenem resistance marker blaNDM-1 was maintained on pRH-1238 throughout the trial. Furthermore, we showed the importance of the gut E. coli population as a vector of pRH-1238. In a potential scenario of the introduction of NDM-1-producing S Corvallis into a broiler flock, the pRH-1238 plasmid could persist and spread to a broad host range even in the absence of antibiotic pressure.
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Affiliation(s)
- Sead Hadziabdic
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Jennie Fischer
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Beatriz Guerra
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Annemarie Kaesbohrer
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
| | - Bruno Gonzalez-Zorn
- Departamento de Sanidad Animal and Centro de Vigilancia Sanitaria Veterinaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Istvan Szabo
- German Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Berlin, Germany
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