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Thabet E, Dief AE, Arafa SAF, Yakout D, Ali MA. Antibiotic-induced gut microbe dysbiosis alters neurobehavior in mice through modulation of BDNF and gut integrity. Physiol Behav 2024; 283:114621. [PMID: 38925433 DOI: 10.1016/j.physbeh.2024.114621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/11/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
Gut microbiota is essential for intestinal integrity and brain functions. Herein we aimed to investigate the effects of alteration of gut microbiome using broad-spectrum antibiotics on CD 1 male mice (germ-modified group (GM). Moreover, we co-administrated probiotics with or without antibiotics for four weeks and evaluated if probiotics could reverse these behavioral and intestinal effects. GM, co-administered antibiotics and probiotics, and probiotics-only groups were compared to control mice of the same sex, age, and weight that did not receive either drug (n=12 in all groups). Cultivation of aerobic and anaerobic bacteria was evaluated by fecal culture of all groups. We tested exploratory behavior, anxiety, memory, depression-like behavior, and hippocampal and frontal lobe BDNF protein level alterations in response to antibiotics and its downstream effect on the PI3K/Akt1/Bcl2 pathway. Intestinal integrity was evaluated using gene expression analysis of ZO-1, claudin, and occludin genes. Additionally, the inflammatory TLR4 and p-p38 MAPK pathways in the intestines were investigated. Twice-daily administration of oral antibiotics for four weeks significantly reduced total bacterial count and upregulated TLR4 and p-p38.GM mice showed a significant reduction in BDNF(P =0.04), impaired spatial memory, and long-term memory as evidenced by decreased T maze correct alternation trails and shortened retention time in the passive avoidance test in GM(P =0.01). Passive avoidance showed significantly increased latency after probiotics intake. Depressive-like behavior was more pronounced in GM mice as assessed by the tail suspension test (P =0.01). GM showed significant upregulation(p<0.001) of the TLR4 and p-p38 MAPK pathway. Co-administration of probiotics with antibiotics showed an increase in BDNF levels, and upregulation of the cell survival PI3K/Akt1/Bcl2 pathway, significantly higher relative abundance in the firmucutes members, a significant decrease in the Firmicutes/Bacteroidetes ratio and downregulation of TLR4 and p-p38 MAPK. The tight junction proteins ZO-1, claudin and occludin were downregulated by antibiotic administration for four weeks and restored by probiotics. Collectively, the data suggest that long-term use of antibiotics appears to disrupt the intestinal epithelial barrier and alter neurobehavioral qualities specifically, long-term memory and exploratory drive, possibly through the reduction of BDNF, and probiotics partially reverse these effects. Our study emphasizes the effect of prolonged intake of antibiotics on production of dysbiosis as well as the impact of the antibiotic induced intestinal inflammation on neurobehavioral aspects in mice as the memory and anxiety-like behavior. We also reveal that co-administration of probiotics can reverse these changes.
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Affiliation(s)
- Eman Thabet
- Department of Medical Physiology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt.
| | - Abeer E Dief
- Department of Medical Physiology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Shams A-F Arafa
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Dalia Yakout
- Department of Clinical Pharmacology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Mennatallah A Ali
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
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2
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Liu X, Zhao H, Wong A. Accounting for the health risk of probiotics. Heliyon 2024; 10:e27908. [PMID: 38510031 PMCID: PMC10950733 DOI: 10.1016/j.heliyon.2024.e27908] [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: 07/10/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.
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Affiliation(s)
- Xiangyi Liu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Haiyi Zhao
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province, 325060, China
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Debnath N, Yadav P, Mehta PK, Gupta P, Kumar D, Kumar A, Gautam V, Yadav AK. Designer probiotics: Opening the new horizon in diagnosis and prevention of human diseases. Biotechnol Bioeng 2024; 121:100-117. [PMID: 37881101 DOI: 10.1002/bit.28574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/19/2023] [Accepted: 09/23/2023] [Indexed: 10/27/2023]
Abstract
Probiotic microorganisms have been used for therapeutic purposes for over a century, and recent advances in biotechnology and genetic engineering have opened up new possibilities for developing therapeutic approaches using indigenous probiotic microorganisms. Diseases are often related to metabolic and immunological factors, which play a critical role in their onset. With the help of advanced genetic tools, probiotics can be modified to produce or secrete important therapeutic peptides directly into mucosal sites, increasing their effectiveness. One potential approach to enhancing human health is through the use of designer probiotics, which possess immunogenic characteristics. These genetically engineered probiotics hold promise in providing novel therapeutic options. In addition to their immunogenic properties, designer probiotics can also be equipped with sensors and genetic circuits, enabling them to detect a range of diseases with remarkable precision. Such capabilities may significantly advance disease diagnosis and management. Furthermore, designer probiotics have the potential to be used in diagnostic applications, offering a less invasive and more cost-effective alternative to conventional diagnostic techniques. This review offers an overview of the different functional aspects of the designer probiotics and their effectiveness on different diseases and also, we have emphasized their limitations and future implications. A comprehensive understanding of these functional attributes may pave the way for new avenues of prevention and the development of effective therapies for a range of diseases.
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Affiliation(s)
- Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Pooja Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Praveen K Mehta
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok K Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
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Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024; 16:2297837. [PMID: 38217470 PMCID: PMC10793692 DOI: 10.1080/19490976.2023.2297837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024] Open
Abstract
Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.
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Affiliation(s)
- Dhrati V. Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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5
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Igo M, Xu L, Krishna A, Stewart S, Xu L, Li Z, Weaver JL, Stone H, Sacks L, Bensman T, Florian J, Rouse R, Han X. A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes. Gut Microbes 2023; 15:2271150. [PMID: 37908118 PMCID: PMC10621307 DOI: 10.1080/19490976.2023.2271150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.
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Affiliation(s)
- Matthew Igo
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Ashok Krishna
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sharron Stewart
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Lin Xu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Zhihua Li
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - James L. Weaver
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Heather Stone
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Leonard Sacks
- Office of Medical Policy, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Timothy Bensman
- Division of Infectious Disease Pharmacology, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jeffry Florian
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Rodney Rouse
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaomei Han
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U. S. Food and Drug Administration, Silver Spring, MD, USA
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6
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Weiss A, Wang T, You L. Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. Cell Syst 2023; 14:895-905.e5. [PMID: 37820728 PMCID: PMC10591896 DOI: 10.1016/j.cels.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/09/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.
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Affiliation(s)
- Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Quantitative Biodesign, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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7
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Tamés H, Sabater C, Margolles A, Ruiz L, Ruas-Madiedo P. Production of GABA in milk fermented by Bifidobacterium adolescentis strains selected on the bases of their technological and gastrointestinal performance. Food Res Int 2023; 171:113009. [PMID: 37330847 DOI: 10.1016/j.foodres.2023.113009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
There is an increasing interest in producing foods enriched in gamma-aminobutyric acid (GABA), due to their purported health promoting attributes. GABA is the main inhibitor neurotransmitter of the central nervous system, and several microbial species are capable to produce it through decarboxylation of glutamate. Among them, several lactic acid bacteria species have been previously investigated as an appealing alternative to produce GABA enriched foods via microbial fermentation. In this work we report for the first time an investigation into the possibility of utilizing high GABA-producing Bifidobacterium adolescentis strains as a mean to produce fermented probiotic milks naturally enriched in GABA. To this end, in silico and in vitro analyses were conducted in a collection of GABA-producing B. adolescentis strains, with the main goal to scrutinize their metabolic and safety traits, including antibiotic resistance patterns, as well as their technological robustness and performance to survive a simulated gastrointestinal passage. One of the strains, IPLA60004, exhibited better survival to lyophilization and cold storage (for up to 4 weeks at 4 °C), as well as survival to gastrointestinal passage, as compared to the other strains under investigation. Besides, the elaboration of milk drinks fermented with this strain, yielded products with the highest GABA concentration and viable bifidobacterial cell counts, achieving conversion rates of the precursor, monosodium glutamate (GMS), up to 70 %. To our knowledge, this is the first report on the elaboration of GABA enriched milks through fermentation with B. adolescentis.
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Affiliation(s)
- Héctor Tamés
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain; Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
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Shahali A, Soltani R, Akbari V. Probiotic Lactobacillus and the potential risk of spreading antibiotic resistance: a systematic review. Res Pharm Sci 2023; 18:468-477. [PMID: 37842520 PMCID: PMC10568962 DOI: 10.4103/1735-5362.383703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 10/17/2023] Open
Abstract
Background and purpose Lactobacillus, the most popular probiotic, has recently gained more attention because it is a potential reservoir of antibiotic resistance. This review summarized and discussed the phenotypic-genotypic characteristics of antibiotic resistance. Experimental approach Google Scholar, PubMed, Web of Science, and Scopus were searched up to February 2022. The inclusion criteria were all studies testing antibiotic resistance of probiotic Lactobacillus strains present in human food supplementation and all human/animal model studies in which transferring antibiotic-resistant genes from Lactobacillus strains to another bacterium were investigated. Findings/Results Phenotypic and genotypic characterization of Lactobacillus probiotics showed that the most antibiotic resistance was against protein synthesis inhibitors (fourteen studies, 87.5%) and cell wall synthesis inhibitors (ten studies, 62.5%). Nine of these studies reported the transfer of antibiotic resistance from Lactobacillus probiotic as donor species to pathogenic bacteria and mostly used in vitro methods for resistance gene transfer. Conclusion and implications The transferability of resistance genes such as tet and erm in Lactobacillus increases the risk of spreading antibiotic resistance. Further studies need to be conducted to evaluate the potential spread of antibiotic resistance traits via probiotics, especially in elderly people and newborns.
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Affiliation(s)
- Ali Shahali
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
- Department of Pharmaceutics, College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Rasool Soltani
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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9
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Fan X, Lu Y, Zhao Y, Miao H, Qi K, Wang R. An Insight into the Exploration of Antibiotic Resistance Genes in Calorie Restricted Diet Fed Mice. Nutrients 2023; 15:3198. [PMID: 37513616 PMCID: PMC10384538 DOI: 10.3390/nu15143198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/15/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance genes (ARGs) threaten the success of modern drugs against multidrug resistant infections. ARGs can be transferred to opportunistic pathogens by horizontal gene transfer (HGT). Many studies have investigated the characteristics of ARGs in various chemical stressors. Studies on the effects of dietary nutrition and dietary patterns on ARGs are rare. The study first demonstrated the effect of calorie restricted (CR) diet on the ARGs and mobile genetic elements (MGEs) in mouse feces and explored their relationship with gut microbiota and their functions. The results showed that the abundance of the total ARGs in mouse feces of the CR group increased, especially tetracycline ARGs (tetW-01). The abundance of the MLSB ARGs (ermB) decreased evidently in mouse feces of the CR group. In addition, the total abundance of MGEs decreased evidently in the CR group, especially tnpA-03. In the meantime, the abundance of Lactobacillus and Bifidobacterium in mouse feces of the CR group increased remarkably. The Spearman correlation analysis between gut microbiota and ARGs showed that several probiotics were significantly positively correlated with ARGs (tetW-01), which might be the main contribution to the increase in ARGs of the CR group.
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Affiliation(s)
- Xiuqin Fan
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yuanyuan Lu
- Department of Children's Health Care Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yunfeng Zhao
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Hongjian Miao
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Kemin Qi
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Rui Wang
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
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10
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Liu Y, Wu B, Cui X, Ren Q, Ren T, Zhou Y. Distribution and dynamics of antibiotic resistance genes in a three-dimensional multifunctional biofilm during greywater treatment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121533. [PMID: 36997145 DOI: 10.1016/j.envpol.2023.121533] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Antibiotic resistance genes (ARGs) have been identified as serious threats to public health. Despite the widespread in various systems, dynamics of ARGs in three-dimensional multifunctional biofilm (3D-MFB) treating greywater are largely undefined. This work tracked the distributions and dynamics of eight target genes (intI1, korB, sul1, sul2, tetM, ermB, blaCTX-M and qnrS) in a 3D-MFB during greywater treatment. Results showed that hydraulic retention times at 9.0 h achieved the highest linear alkylbenzene sulfonate (LAS) and total nitrogen removal rates at 99.4% and 79.6%, respectively. ARGs presented significant liquid-solid distribution feature, but non-significant with biofilm position. Intracellular ARGs (predominant by intI1, korB, sul1 and sul2) at bottom biofilm were 210- to 4.2 × 104- fold higher than that in cell-free liquid. Extracellular polymeric substances (EPS)-attached LAS showed linear relationship with most of ARGs (R2 > 0.90, P < 0.05). Sphingobacteriales, Chlamydiales, Microthrixaceae, SB-1, Cryomorphaceae, Chitinophagaceae, Leadbetterella and Niabella were tightly bound up with target ARGs. Key is that EPS-attached LAS considerably determines the occurrence of ARGs, and microbial taxa play an important role in the dissemination of ARGs in the 3D-MFB.
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Affiliation(s)
- Ying Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Beibei Wu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaocai Cui
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingqing Ren
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tian Ren
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yun Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Zhu L, Huang H, Avellán‐Llaguno RD, Qin Y, An X, Su J, Huang Q, Zhu Y. Diverse functional genes harboured in extracellular vesicles from environmental and human microbiota. J Extracell Vesicles 2022; 11:e12292. [PMID: 36463395 PMCID: PMC9719567 DOI: 10.1002/jev2.12292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/07/2022] Open
Abstract
Exchange of mobile functional genes within microbiota benefits the microbial community. However, the status of the mobile gene pool in environment is still largely unclear, impeding the understanding on the process of gene transfer in natural microbial communities. The release of extracellular vesicles (EVs) by diverse organisms has been proposed to be a vital way in the complex networks of interactions between microbes and their habitats. In this study, we hypothesized that microbial EVs encapsulating functional DNA are widely distributed in the environmental matrix. The prevalence, source and DNA cargoes of EVs in three types of typical microbial habitats were studied. High abundance of EVs comparable to the bacterial concentration was found in human faeces, wastewater and soil. Metagenomic analysis showed the diverse and differential taxonomy of EVs-associated DNA compared to source microbiome. An array of efficient EVs producing species was identified. A wide variety of mobile genes including glycoside hydrolase family 25 were enriched. Antibiotic resistance genes co-localizing with mobile genetic elements were abundant in the EVs. This study provides novel insights into the prevalent EVs as a reservoir for the mobile functional genes in the natural environment.
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Affiliation(s)
- Li‐Ting Zhu
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Hai‐Ning Huang
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Ricardo David Avellán‐Llaguno
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Yifei Qin
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Xin‐Li An
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Jian‐Qiang Su
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Qiansheng Huang
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- National Basic Science Data CenterBeijingChina
| | - Yong‐Guan Zhu
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
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12
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Voellmy IK, Lang C, Gasser M, Kronenberg A. Antibiotic resistance surveillance of Klebsiella pneumoniae complex is affected by refined MALDI-TOF identification, Swiss data, 2017 to 2022. Euro Surveill 2022; 27. [PMID: 36367012 PMCID: PMC9650708 DOI: 10.2807/1560-7917.es.2022.27.45.2200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Modern laboratory methods such as next generation sequencing and MALDI-TOF allow identification of novel bacterial species. This can affect surveillance of infections and antimicrobial resistance. From 2017, increasing numbers of medical microbiology laboratories in Switzerland differentiated Klebsiella variicola from Klebsiella pneumoniae complex using updated MALDI-TOF databases, whereas many laboratories still report them as K. pneumoniae or K. pneumoniae complex. Aim Our study explored whether separate reporting of K. variicola and the Klebsiella pneumoniae complex affected the ANRESIS surveillance database. Methods We analysed antibiotic susceptibility rates and specimen types of K. variicola and non-K. variicola-K. pneumoniae complex isolates reported by Swiss medical laboratories to the ANRESIS database (Swiss Centre for Antibiotic Resistance) from January 2017 to June 2022. Results Analysis of Swiss antimicrobial resistance data revealed increased susceptibility rates of K. variicola compared with species of the K. pneumoniae complex other than K. variicola in all six antibiotic classes tested. This can lead to underestimated resistance rates of K. pneumoniae complex in laboratories that do not specifically identify K. variicola. Furthermore, K. variicola strains were significantly more often reported from blood and primarily sterile specimens than isolates of the K. pneumoniae complex other than K. variicola, indicating increased invasiveness of K. variicola. Conclusion Our data suggest that refined differentiation of the K. pneumoniae complex can improve our understanding of its taxonomy, susceptibility, epidemiology and clinical significance, thus providing more precise information to clinicians and epidemiologists.
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Affiliation(s)
- Irene Katharina Voellmy
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Michael Gasser
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andreas Kronenberg
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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13
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Fei Y, Ma Y, Zhang H, Li H, Feng G, Fang J. Nanotechnology for research and treatment of the intestine. J Nanobiotechnology 2022; 20:430. [PMID: 36175955 PMCID: PMC9523975 DOI: 10.1186/s12951-022-01517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
The establishment of intestinal in vitro models is crucial for elucidating intestinal cell-microbe intrinsic connections and interaction mechanisms to advance normalized intestinal diagnosis and precision therapy. This review discusses the application of nanomaterials in mucosal therapy and mechanism research in combination with the study of nanoscaffold in vitro models of the gut. By reviewing the original properties of nanomaterials synthesized by different physicochemical principles and modifying the original properties, the contribution of nanomaterials to solving the problems of short survival period, low cell differentiation rate, and poor reduction ability in traditional intestinal models is explored. According to nanomaterials’ different diagnostic mediators and therapeutic targets, the current diagnostic principles in inflammatory bowel disease, intestinal cancer, and other diseases are summarized inductively. In addition, the mechanism of action of nanomedicines in repairing mucosa, inhibiting inflammation, and alleviating the disease process is also discussed. Through such systematic elaboration, it offers a basis for nanomaterials to help advance in vitro research on the intestine and provide precision treatments in the clinic.
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Affiliation(s)
- Yanquan Fei
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Yong Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Huaizu Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Hao Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Guangfu Feng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China.
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China.
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14
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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15
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Dou W, Abdalla HB, Chen X, Sun C, Chen X, Tian Q, Wang J, Zhou W, Chi W, Zhou X, Ye H, Bi C, Tian X, Yang Y, Wong A. ProbResist: a database for drug-resistant probiotic bacteria. Database (Oxford) 2022; 2022:6665407. [PMID: 35962763 PMCID: PMC9375527 DOI: 10.1093/database/baac064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/04/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022]
Abstract
Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing foods, many of which harbor antibiotic resistant determinants, has raised serious health concerns. Currently, the lack of accessibility to location-, drug- and species-specific information of drug-resistant probiotics has hampered efforts to combat the global spread of drug resistance. Here, we describe the development of ProbResist, which is a manually curated online database that catalogs reports of probiotic bacteria that have been experimentally proven to be resistant to antibiotics. ProbResist allows users to search for information of drug resistance in probiotics by querying with the names of the bacteria, antibiotic or location. Retrieved results are presented in a downloadable table format containing the names of the antibiotic, probiotic species, resistant determinants, region where the study was conducted and digital article identifiers (PubMed Identifier and Digital Object Identifier) hyperlinked to the original sources. The webserver also presents a simple analysis of information stored in the database. Given the increasing reports of drug-resistant probiotics, an exclusive database is necessary to catalog them in one platform. It will enable medical practitioners and experts involved in policy making to access this information quickly and conveniently, thus contributing toward the broader goal of combating drug resistance.
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Affiliation(s)
- Wanying Dou
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Hemn Barzan Abdalla
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xu Chen
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Changyi Sun
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuefei Chen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Qiwen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuan Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuechen Tian
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Yixin Yang
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
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16
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Bottery MJ. Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr Opin Microbiol 2022; 68:102152. [PMID: 35504055 PMCID: PMC9586876 DOI: 10.1016/j.mib.2022.102152] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
Plasmids are a major driver of horizontal gene transfer in prokaryotes, allowing the sharing of ecologically important accessory traits between distantly related bacterial taxa. Within microbial communities, interspecies transfer of conjugative plasmids can rapidly drive the generation genomic innovation and diversification. Recent studies are starting to shed light on how the microbial community context, that is, the bacterial diversity together with interspecies interactions that occur within a community, can alter the dynamics of conjugative plasmid transfer and persistence. Here, I summarise the latest research exploring how community ecology can both facilitate and impose barriers to the spread of conjugative plasmids within complex microbial communities. Ultimately, the fate of plasmids within communities is unlikely to be determined by any one individual host, rather it will depend on the interacting factors imposed by the community in which it is embedded.
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Affiliation(s)
- Michael J Bottery
- Division of Evolution Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
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17
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Zhou W, Zheng Y, Shang J, Wang H, Wang Y, Lu H, Wang X, Sui M. Intestinal microecology in mice bearing diethylnitrosamine-induced primary hepatocellular carcinoma. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:438-453. [PMID: 37202098 PMCID: PMC10265007 DOI: 10.3724/zdxbyxb-2022-0283] [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: 05/31/2022] [Accepted: 07/30/2022] [Indexed: 05/20/2023]
Abstract
OBJECTIVE To explore the characteristics of intestinal microecology in hepatocellular carcinoma (HCC) model mice. METHODS C57BL/6 male mice aged 2 weeks were divided into normal control group and HCC model group. Mice in HCC model group were exposed to a single intraperitoneal injection of diethylnitrosamine (DEN) 2 weeks after birth; the surviving mice were intraperitoneally injected with 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP), once every 2 weeks for 8 times starting from the 4 th week after birth. Mice in each group were randomly selected and sacrificed at 10 th, 18 th and 32 nd weeks after birth, respectively, the liver tissue samples were obtained for histopathological examination. At the 32 nd week, all mice in both groups were sacrificed and the feces samples were collected under sterile conditions right before the sacrifice. The feces samples were sequenced for the V3-V4 hypervariable regions of the 16S rRNA gene, and the species abundance, flora diversity and phenotype, as well as flora correlation and functional prediction were analyzed. RESULTS Alpha diversity analysis showed that all Good's coverage reached the maximum value of 1.00, and the differences in the Observed features, Chao1 index, Shannon index and Simpson index of the intestinal flora of mice between normal control group and HCC model group were all statistically significant (all P<0.05). Beta diversity analysis showed that PCoA based on weighted or unweighted Unifrac distances all yielded R>0, confirming that the intra-group differences of the samples were less than the inter-group differences; the trend of separation between the two groups was significant ( P<0.05). Bacteroidetes, Firmicutes, Actinobacteria and Patescibacteria were the dominant taxa at the phylum level in both normal control group and HCC model group. However, compared with normal control group, the abundance of Bacteroidetes in HCC model group was significantly decreased ( P<0.01), while the abundance of Patescibacteria was significantly increased ( P<0.05). Moreover, the dominant taxa at the genus level in normal control group mainly included Muribaculaceae_unclassified, Paramuribaculum, Muribaculum, Lachnospiraceae_NK4A 136 group, Olsenella. The dominant taxa at the genus level in HCC model group mainly included Akkermansia, Dubosiella, Muribaculaceae_unclassified, Lachnospiraceae_NK4A 136 group, Coriobacteriaceae_UCG-002. There were 30 genera with statistically significant differences in relative abundance at the genus level between the two groups (all P<0.05). LEfSe analysis of the intestinal flora of mice in the two groups revealed a total of 14 multi-level differential taxa (all P<0.05, LDA score>4.0), which were mainly enriched in Bacteroidetes. The enrichment of 10 differential taxa including Bacteroidetes, Bacteroidia, Bacteroidales, Muribaculaceae, etc. were found in normal control group, and the enrichment of 4 differential taxa including Dubosiella, Peptostreptococus, etc. were found in HCC model group. There were both positive and negative correlations between the dominant intestinal genera in normal control group (|rho|>0.5, P<0.05), while the correlations of the dominant intestinal genera in HCC model group, being less complex than that in normal control group, were all positive. The relative abundance of gram positive and mobile element containing in the intestinal flora of mice in HCC model group was significantly up-regulated compared with normal control group (both P<0.05), while that of gram negative ( P<0.05) and pathogenic potential ( P<0.05) was significantly down-regulated. The metabolic pathways of the intestinal flora in the two groups were significantly different. For instance, 18 metabolic pathways were enriched in normal control group (all P<0.005), including those related to energy metabolism, cell division, nucleotide metabolism, etc., while 12 metabolic pathways were enriched in HCC model group (all P<0.005), including those related to energy metabolism, amino acid metabolism, carbohydrate metabolism, etc. Conclusions: The amount of intestinal flora in DEN-induced primary HCC model mice decreased, and the composition, correlation, phenotype and function of the intestinal flora in mice were significantly altered. Bacteroidetes at the phylum level, as well as several microbial taxa at the genus level such as Muribaculaceae_unclassified, Muribaculum, Peptostreptococus and Dubosiella could be closely associated with DEN-induced primary HCC in mice.
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Affiliation(s)
- Wenbin Zhou
- 1. Qingdao Medical College, Qingdao University, Qingdao 266071, Shandong Province, China
| | - Yue Zheng
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Jia Shang
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Haiyang Wang
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Yisha Wang
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Huan Lu
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Xiaoxi Wang
- 5. Department of Pathology, the First Affiliated Hospital, Zhejiang University School Medicine, Hangzhou 310003, China
| | - Meihua Sui
- 2. School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
- 3. Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
- 4. Zhejiang University Cancer Center, Hangzhou 310058, China
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18
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Conteville LC, Vicente ACP. A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits. Sci Rep 2022; 12:12102. [PMID: 35840779 PMCID: PMC9287393 DOI: 10.1038/s41598-022-16392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups’ gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.
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Affiliation(s)
- Liliane Costa Conteville
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Ana Carolina Paulo Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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19
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Saha P, Bose D, Stebliankin V, Cickovski T, Seth RK, Porter DE, Brooks BW, Mathee K, Narasimhan G, Colwell R, Scott GI, Chatterjee S. Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models. Sci Rep 2022; 12:11516. [PMID: 35799048 PMCID: PMC9262933 DOI: 10.1038/s41598-022-15708-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
A strong association between exposure to the common harmful algal bloom toxin microcystin and the altered host gut microbiome has been shown. We tested the hypothesis that prior exposure to the cyanotoxin microcystin-LR may alter the host resistome. We show that the mice exposed to microcystin-LR had an altered microbiome signature that harbored antibiotic resistance genes. Host resistome genotypes such as mefA, msrD, mel, ant6, and tet40 increased in diversity and relative abundance following microcystin-LR exposure. Interestingly, the increased abundance of these genes was traced to resistance to common antibiotics such as tetracycline, macrolides, glycopeptide, and aminoglycosides, crucial for modern-day treatment of several diseases. Increased abundance of these genes was positively associated with increased expression of PD1, a T-cell homeostasis marker, and pleiotropic inflammatory cytokine IL-6 with a concomitant negative association with immunosurveillance markers IL-7 and TLR2. Microcystin-LR exposure also caused decreased TLR2, TLR4, and REG3G expressions, increased immunosenescence, and higher systemic levels of IL-6 in both wild-type and humanized mice. In conclusion, the results show a first-ever characterization of the host resistome following microcystin-LR exposure and its connection to host immune status and antimicrobial resistance that can be crucial to understand treatment options with antibiotics in microcystin-exposed subjects in clinical settings.
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Affiliation(s)
- Punnag Saha
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
- Columbia VA Medical Center, Columbia, SC, 29209, USA
| | - Dipro Bose
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
- Columbia VA Medical Center, Columbia, SC, 29209, USA
| | - Vitalii Stebliankin
- Knight Foundation School of Computing & Information Sciences, Florida International University, Miami, FL, 33199, USA
| | - Trevor Cickovski
- Knight Foundation School of Computing & Information Sciences, Florida International University, Miami, FL, 33199, USA
| | - Ratanesh K Seth
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
- Columbia VA Medical Center, Columbia, SC, 29209, USA
| | - Dwayne E Porter
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, Waco, TX, 76798, USA
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Giri Narasimhan
- Knight Foundation School of Computing & Information Sciences, Florida International University, Miami, FL, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Rita Colwell
- CosmosID Inc, Germantown, MD, 20874, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, 20742, USA
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, 20742, USA
| | - Geoff I Scott
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA.
- NIEHS Center for Oceans and Human Health and Climate Change Interactions, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA.
- Columbia VA Medical Center, Columbia, SC, 29209, USA.
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20
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Peng X, Ed-Dra A, Yue M. Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria. Crit Rev Food Sci Nutr 2022; 63:11244-11262. [PMID: 35694810 DOI: 10.1080/10408398.2022.2087174] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Probiotic bacteria exhibit beneficial effects on human and/or animal health, and have been widely used in foods and fermented products for decades. Most probiotics consist of lactic acid bacteria (LAB), which are used in the production of various food products but have also been shown to have the ability to prevent certain diseases. With the expansion of applications for probiotic LAB, there is an increasing concern with regard to safety, as cases with adverse effects, i.e., severe infections, transfer of antimicrobial resistance genes, etc., can occur. Currently, in vitro assays remain the primary way to assess the properties of LAB. However, such methodologies are not meeting the needs of strain risk assessment on a high-throughput scale, in the context of the evolving concept of food safety. Analyzing the complete genetic information, including potential virulence genes and other determinants with a negative impact on health, allows for assessing the safe use of the product, for which whole-genome sequencing (WGS) of individual LAB strains can be employed. Genomic data can also be used to understand subtle differences in the strain level important for beneficial effects, or protect patents. Here, we propose that WGS-based bioinformatics analyses are an ideal and cost-effective approach for the initial in silico microbial risk evaluation, while the technique may also increase our understanding of LAB strains for food safety and probiotic property evaluation.
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Affiliation(s)
- Xianqi Peng
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | | | - Min Yue
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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21
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Boahen A, Than LTL, Loke YL, Chew SY. The Antibiofilm Role of Biotics Family in Vaginal Fungal Infections. Front Microbiol 2022; 13:787119. [PMID: 35694318 PMCID: PMC9179178 DOI: 10.3389/fmicb.2022.787119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/25/2022] [Indexed: 11/15/2022] Open
Abstract
“Unity in strength” is a notion that can be exploited to characterize biofilms as they bestow microbes with protection to live freely, escalate their virulence, confer high resistance to therapeutic agents, and provide active grounds for the production of biofilms after dispersal. Naturally, fungal biofilms are inherently resistant to many conventional antifungals, possibly owing to virulence factors as their ammunitions that persistently express amid planktonic transition to matured biofilm state. These ammunitions include the ability to form polymicrobial biofilms, emergence of persister cells post-antifungal treatment and acquisition of resistance genes. One of the major disorders affecting vaginal health is vulvovaginal candidiasis (VVC) and its reoccurrence is termed recurrent VVC (RVVC). It is caused by the Candida species which include Candida albicans and Candida glabrata. The aforementioned Candida species, notably C. albicans is a biofilm producing pathogen and habitually forms part of the vaginal microbiota of healthy women. Latest research has implicated the role of fungal biofilms in VVC, particularly in the setting of treatment failure and RVVC. Consequently, a plethora of studies have advocated the utilization of probiotics in addressing these infections. Specifically, the excreted or released compounds of probiotics which are also known as postbiotics are being actively researched with vast potential to be used as therapeutic options for the treatment and prevention of VVC and RVVC. These potential sources of postbiotics are harnessed due to their proven antifungal and antibiofilm. Hence, this review discusses the role of Candida biofilm formation in VVC and RVVC. In addition, we discuss the application of pro-, pre-, post-, and synbiotics either individually or in combined regimen to counteract the abovementioned problems. A clear understanding of the role of biofilms in VVC and RVVC will provide proper footing for further research in devising novel remedies for prevention and treatment of vaginal fungal infections.
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22
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Antibiotic resistance and virulence factors in lactobacilli: something to carefully consider. Food Microbiol 2022; 103:103934. [DOI: 10.1016/j.fm.2021.103934] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 01/06/2023]
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23
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Hu B, Hou P, Teng L, Miao S, Zhao L, Ji S, Li T, Kehrenberg C, Kang D, Yue M. Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016. Front Med (Lausanne) 2022; 9:753085. [PMID: 35308507 PMCID: PMC8925297 DOI: 10.3389/fmed.2022.753085] [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: 08/04/2021] [Accepted: 02/04/2022] [Indexed: 12/27/2022] Open
Abstract
Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi (S. Typhi) and remains a significant public health burden in developing countries. In China, typhoid fever is endemic with a limited number of reported outbreaks. Recently, Chinese local Center for Disease Prevention and Control is starting to apply whole genome sequencing for tracking the source of outbreak isolates. In this study, we conducted a retrospective investigation into a community outbreak of typhoid fever in Lanling, China, in 2016. A total of 26 S. Typhi isolates were recovered from the drinking water (n = 1) and patients' blood (n = 24) and stool (n = 1). Phylogenetic analysis indicated the persistence of the outbreak isolates in drinking water for more than 3 months. The genomic comparison demonstrated a high similarity between the isolate from water and isolates from patients in their genomic content, virulence gene profiles, and antimicrobial resistance gene profile, indicating the S. Typhi isolate from drinking water was responsible for the examined outbreak. The result of pulsed-field gel electrophoresis (PFGE) revealed these isolates had identical PFGE pattern, indicating they are clonal variants. Additionally, phylogeographical analysis of global S. Typhi isolates suggested the outbreak isolates are evolutionarily linked to the isolates from the United Kingdom and Vietnam. Taken together, this study highlights the drinking water and international travel as critical control points of mitigating the outbreak, emphasizing the necessity of regular monitoring of this pathogen in China.
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Affiliation(s)
- Bin Hu
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Peibin Hou
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Lin Teng
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Song Miao
- Shandong Medical College, Jinan, China
| | - Lijiang Zhao
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Shengxiang Ji
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Tao Li
- Linyi Center for Disease Control and Prevention, Linyi, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dianmin Kang
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
- *Correspondence: Dianmin Kang
| | - Min Yue
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- The Hainan Institute of Zhejiang University, Sanya, China
- Min Yue
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24
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Howard-Jones AR, Rifaath Anver S, Tsang K, Branley J. Invasive extended-spectrum beta-lactamase (ESBL) related infection rates are not influenced by international travel restrictions. Pathology 2022; 54:792-795. [PMID: 35168811 DOI: 10.1016/j.pathol.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Annaleise R Howard-Jones
- NSW Health Pathology-Nepean, Nepean Hospital, Kingswood, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Samiha Rifaath Anver
- Department of Infectious Diseases and Microbiology, Nepean Hospital, Kingswood, NSW, Australia
| | - Kirsten Tsang
- Department of Pharmacy, Nepean Hospital, Kingswood, NSW, Australia
| | - James Branley
- NSW Health Pathology-Nepean, Nepean Hospital, Kingswood, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia; Department of Infectious Diseases and Microbiology, Nepean Hospital, Kingswood, NSW, Australia.
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25
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Wang Y, Dong J, Wang J, Chi W, Zhou W, Tian Q, Hong Y, Zhou X, Ye H, Tian X, Hu R, Wong A. Assessing the drug resistance profiles of oral probiotic lozenges. J Oral Microbiol 2022; 14:2019992. [PMID: 35024089 PMCID: PMC8745366 DOI: 10.1080/20002297.2021.2019992] [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] [Indexed: 12/17/2022] Open
Abstract
Background Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria. Aim To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro. Results Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments. Conclusion Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.
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Affiliation(s)
- Yi Wang
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Jingya Dong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Qiwen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Yue Hong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Xuan Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
| | - Rongdang Hu
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
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26
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Yan W, Hall AB, Jiang X. Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters. NPJ Biofilms Microbiomes 2022; 8:1. [PMID: 35013297 PMCID: PMC8748976 DOI: 10.1038/s41522-021-00260-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.
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Affiliation(s)
- Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - A Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure. Int J Hyg Environ Health 2021; 240:113882. [PMID: 34915282 PMCID: PMC8664710 DOI: 10.1016/j.ijheh.2021.113882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022]
Abstract
As the COVID-19 pandemic spread globally, the consumption of antibiotics increased. However, no studies exist evaluating the effect of antibiotics use on the antibiotic resistance of intestinal flora in COVID-19 patients during the pandemic. To explore this issue, we collected 15 metagenomic data of fecal samples from healthy controls (HCs) with no use history of antibiotics, 23 metagenomic data of fecal samples from COVID-19 patients who received empirical antibiotics [COVID-19 (abx+)], 18 metagenomic data of fecal samples from antibiotics-naïve COVID-19 patients [COVID-19 (abx-)], and six metagenomic data of fecal samples from patients with community-acquired pneumonia [PC (abx+)] from the Sequence Read Archive database. A total of 513 antibiotic-resistant gene (ARG) subtypes of 18 ARG types were found. Antibiotic treatment resulted in a significant increase in the abundance of ARGs in intestinal flora of COVID-19 patients and markedly altered the composition of ARG profiles. Grouped comparisons of pairs of Bray-Curtis dissimilarity values demonstrated that the dissimilarity of the HC versus the COVID-19 (abx+) group was significantly higher than the dissimilarity of the HC versus the COVID-19 (abx-) group. The mexF, mexD, OXA_209, major facilitator superfamily transporter, and EmrB_QacA family major facilitator transporter genes were the discriminative ARG subtypes for the COVID-19 (abx+) group. IS621, qacEdelta, transposase, and ISCR were significantly increased in COVID-19 (abx+) group; they greatly contributed toward explaining variation in the relative abundance of ARG types. Overall, our data provide important insights into the effect of antibiotics use on the antibiotic resistance of COVID-19 patients during the COVID-19 epidemic.
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28
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James C, Dixon R, Talbot L, James SJ, Williams N, Onarinde BA. Assessing the Impact of Heat Treatment of Food on Antimicrobial Resistance Genes and Their Potential Uptake by Other Bacteria-A Critical Review. Antibiotics (Basel) 2021; 10:1440. [PMID: 34943652 PMCID: PMC8698031 DOI: 10.3390/antibiotics10121440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
The dissemination of antibiotic resistance genes (ARGs) is a global health concern. This study identifies and critically reviews the published evidence on whether cooking (heating) food to eliminate bacterial contamination induces sufficient damage to the functionality of ARGs. Overall, the review found that there is evidence in the literature that Antimicrobial Resistant (AMR) bacteria are no more heat resistant than non-AMR bacteria. Consequently, recommended heat treatments sufficient to kill non-AMR bacteria in food (70 °C for at least 2 min, or equivalent) should be equally effective in killing AMR bacteria. The literature shows there are several mechanisms through which functional genes from AMR bacteria could theoretically persist in heat-treated food and be transferred to other bacteria. The literature search found sparce published evidence on whether ARGs may actually persist in food after effective heat treatments, and whether functional genes can be transferred to other bacteria. However, three publications have demonstrated that functional ARGs in plasmids may be capable of persisting in foods after effective heat treatments. Given the global impact of AMR, there is clearly a need for further practical research on this topic to provide sufficient evidence to fully assess whether there is a risk to human health from the persistence of functional ARGs in heat-treated and cooked foods.
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Affiliation(s)
- Christian James
- Food Refrigeration & Process Engineering Research Centre (FRPERC), Grimsby Institute, Nuns Corner, Grimsby DN34 5BQ, UK; (L.T.); (S.J.J.)
- National Centre for Food Manufacturing (NCFM), University of Lincoln, Park Road, Holbeach PE12 7PT, UK;
| | - Ronald Dixon
- Joseph Banks Laboratories, School of Life Sciences, University of Lincoln, Lincoln LN6 7DL, UK;
| | - Luke Talbot
- Food Refrigeration & Process Engineering Research Centre (FRPERC), Grimsby Institute, Nuns Corner, Grimsby DN34 5BQ, UK; (L.T.); (S.J.J.)
| | - Stephen J. James
- Food Refrigeration & Process Engineering Research Centre (FRPERC), Grimsby Institute, Nuns Corner, Grimsby DN34 5BQ, UK; (L.T.); (S.J.J.)
- National Centre for Food Manufacturing (NCFM), University of Lincoln, Park Road, Holbeach PE12 7PT, UK;
| | - Nicola Williams
- Institute of Infection, Veterinary and Ecological Sciences, Leahurst Campus, University of Liverpool, Neston CH64 7TE, UK;
| | - Bukola A. Onarinde
- National Centre for Food Manufacturing (NCFM), University of Lincoln, Park Road, Holbeach PE12 7PT, UK;
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Evaluation of Tetracycline Resistance and Determination of the Tentative Microbiological Cutoff Values in Lactic Acid Bacterial Species. Microorganisms 2021; 9:microorganisms9102128. [PMID: 34683449 PMCID: PMC8538481 DOI: 10.3390/microorganisms9102128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria (LAB) are widely used as probiotics in the food industry owing to their beneficial effects on human health. However, numerous antibiotic resistance genes have been found in LAB strains, especially tetracycline resistance genes. Notably, the potential transferability of these genes poses safety risks. To comprehensively evaluate tetracycline resistance in LAB, we determined the tetracycline susceptibility patterns of 478 LAB strains belonging to four genera and eight species. By comparing phenotypes with genotypes based on genome-wide annotations, five tetracycline resistance genes, tet(M), tet(W/N/W), tet(L), tet(S), and tet(45), were detected in LAB. Multiple LAB strains without tetracycline resistance genes were found to be resistant to tetracycline at the currently recommended cutoff values. Thus, based on the minimum inhibitory concentrations of tetracycline for these LAB strains, the species-specific microbiological cutoff values for Lactobacillus (para)gasseri, Lactobacillus johnsonii, and Lactobacillus crispatus to tetracycline were first developed using the Turnidge, Kronvall, and eyeball methods. The cutoff values for Lactiplantibacillus plantarum were re-established and could be used to better distinguish susceptible strains from strains with acquired resistance. Finally, we verified that these five genes play a role in tetracycline resistance and found that tet(M) and tet(W/N/W) are the most widely distributed tetracycline resistance genes in LAB.
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Abstract
Several studies have outlined that a balanced gut microbiota offers metabolic and protective functions supporting honeybee health and performance. The present work contributes to increasing knowledge on the impact on the honeybee gut microbiota of the three most common veterinary drugs (oxytetracycline, sulfonamides, and tylosin). The study was designed with a semi-field approach in micro-hives containing about 500 honeybees. Micro-hives were located in an incubator during the day and moved outdoors in the late afternoon, considering the restrictions on the use of antibiotics in the open field but allowing a certain freedom to honeybees; 6 replicates were considered for each treatment. The absolute abundance of the major gut microbial taxa in newly eclosed individuals was studied with qPCR and next-generation sequencing. Antimicrobial resistance genes for the target antibiotics were also monitored using a qPCR approach. The results showed that the total amount of gut bacteria was not altered by antibiotic treatment, but qualitative variations were observed. Tylosin treatment determined a significant decrease of α- and β-diversity indices and a strong depletion of the rectum population (lactobacilli and bifidobacteria) while favoring the ileum microorganisms (Gilliamella, Snodgrassella, and Frischella spp.). Major changes were also observed in honeybees treated with sulfonamides, with a decrease in Bartonella and Frischella core taxa and an increase of Bombilactobacillus spp. and Snodgrassella spp. The present study also shows an important effect of tetracycline that is focused on specific taxa with minor impact on alfa and beta diversity. Monitoring of antibiotic resistance genes confirmed that honeybees represent a great reservoir of tetracycline resistance genes. Tetracycline and sulfonamides resistance genes tended to increase in the gut microbiota population upon antibiotic administration. IMPORTANCE This study investigates the impact of the three most widely used antibiotics in the beekeeping sector (oxytetracycline, tylosin, and sulfonamides) on the honeybee gut microbiota and on the spread of antibiotic resistance genes. The research represents an advance to the present literature, considering that the tylosin and sulfonamides effects on the gut microbiota have never been studied. Another original aspect lies in the experimental approach used, as the study looks at the impact of veterinary drugs and feed supplements 24 days after the beginning of the administration, in order to explore perturbations in newly eclosed honeybees, instead of the same treated honeybee generation. Moreover, the study was not performed with cage tests but in micro-hives, thus achieving conditions closer to real hives. The study reaches the conclusion that the most common veterinary drugs determine changes in some core microbiota members and that incidence of resistance genes for tetracycline and sulfonamides increases following antibiotic treatment.
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Li X, Cheng Z, Dang C, Zhang M, Zheng Y. Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 7:100105. [PMID: 36160698 PMCID: PMC9488056 DOI: 10.1016/j.ese.2021.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 05/07/2023]
Abstract
Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.
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Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Corresponding author. School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055 China.
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Jani K, Sharma A. Targeted amplicon sequencing reveals the probiotic potentials of microbial communities associated with traditional fermented foods of northeast India. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mitchell S, Bull M, Muscatello G, Chapman B, Coleman NV. The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes. Crit Rev Microbiol 2021; 47:543-561. [PMID: 33899656 DOI: 10.1080/1040841x.2021.1907301] [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] [Indexed: 10/21/2022]
Abstract
Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.
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Affiliation(s)
- Scott Mitchell
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Gary Muscatello
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut. Appl Environ Microbiol 2021; 87:AEM.02735-20. [PMID: 33637574 DOI: 10.1128/aem.02735-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/20/2021] [Indexed: 01/12/2023] Open
Abstract
By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as the donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens P. shigelloides was unable to donate the plasmid, and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut, but only to Achromobacter, a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.IMPORTANCE To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.
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Borderes M, Gasc C, Prestat E, Galvão Ferrarini M, Vinga S, Boucinha L, Sagot MF. A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog. NAR Genom Bioinform 2021; 3:lqab009. [PMID: 33709074 PMCID: PMC7936653 DOI: 10.1093/nargab/lqab009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 01/19/2023] Open
Abstract
The human gut microbiota performs functions that are essential for the maintenance of the host physiology. However, characterizing the functioning of microbial communities in relation to the host remains challenging in reference-based metagenomic analyses. Indeed, as taxonomic and functional analyses are performed independently, the link between genes and species remains unclear. Although a first set of species-level bins was built by clustering co-abundant genes, no reference bin set is established on the most used gut microbiota catalog, the Integrated Gene Catalog (IGC). With the aim to identify the best suitable method to group the IGC genes, we benchmarked nine taxonomy-independent binners implementing abundance-based, hybrid and integrative approaches. To this purpose, we designed a simulated non-redundant gene catalog (SGC) and computed adapted assessment metrics. Overall, the best trade-off between the main metrics is reached by an integrative binner. For each approach, we then compared the results of the best-performing binner with our expected community structures and applied the method to the IGC. The three approaches are distinguished by specific advantages, and by inherent or scalability limitations. Hybrid and integrative binners show promising and potentially complementary results but require improvements to be used on the IGC to recover human gut microbial species.
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Affiliation(s)
- Marianne Borderes
- MaaT Pharma, 317 Avenue Jean Jaurès, 69007 Lyon, France
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
- Erable team, INRIA Grenoble Rhône-Alpes, 655 Avenue de l’Europe 38330 Montbonnot-Saint–Martin, France
| | - Cyrielle Gasc
- MaaT Pharma, 317 Avenue Jean Jaurès, 69007 Lyon, France
| | | | - Mariana Galvão Ferrarini
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
- INSA-Lyon, INRA, BF2i, UMR0203, F-69621 Villeurbanne, France
| | - Susana Vinga
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, 1000-029 Lisbon, Portugal
| | - Lilia Boucinha
- MaaT Pharma, 317 Avenue Jean Jaurès, 69007 Lyon, France
- EVOTEC ID (Lyon), 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Marie-France Sagot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
- Erable team, INRIA Grenoble Rhône-Alpes, 655 Avenue de l’Europe 38330 Montbonnot-Saint–Martin, France
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The shared resistome of human and pig microbiota is mobilized by distinct genetic elements. Appl Environ Microbiol 2021; 87:AEM.01910-20. [PMID: 33310720 PMCID: PMC8090867 DOI: 10.1128/aem.01910-20] [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] [Indexed: 01/16/2023] Open
Abstract
The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tract of human and farmed animals. Genetic exchange of resistance genes between the two ecosystems is now well documented for pathogenic bacteria, but the repertoire of shared resistance genes in the commensal bacterial community and by which genetic modules they are disseminated are still unclear. By analyzing metagenomics data of human and pig intestinal samples both collected in Shenzhen, China, a set of 27 highly prevalent antibiotic resistance genes was found to be shared between human and pig intestinal microbiota. The mobile genetic context for 11 of these core antibiotic resistance genes could be identified by mining their carrying scaffolds constructed from the two datasets, leading to the detection of seven integrative and conjugative/mobilizable elements and two IS-related transposons. The comparison of the relative abundances between these detected mobile genetic elements and their associated antibiotic resistance genes revealed that for many genes, the estimated contribution of the mobile elements to the gene abundance differs strikingly depending on the host. These findings indicate that although some antibiotic resistance genes are ubiquitous across microbiota of human and pig populations, they probably relied on different genetic elements for their dissemination within each population.IMPORTANCE There is growing concern that antibiotic resistance genes could spread from the husbandry environment to human pathogens through dissemination mediated by mobile genetic elements. In this study, we investigated the contribution of mobile genetic elements to the abundance of highly prevalent antibiotic resistance genes found in commensal bacteria of both human and pig intestinal microbiota originating from the same region. Our results reveal that for most of these antibiotic resistance genes, the abundance is not explained by the same mobile genetic element in each host, suggesting that the human and pig microbial communities promoted a different set of mobile genetic carriers for the same antibiotic resistance genes. These results deepen our understanding of the dissemination of antibiotic resistance genes among and between human and pig gut microbiota.
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Mazhar SH, Li X, Rashid A, Su J, Xu J, Brejnrod AD, Su JQ, Wu Y, Zhu YG, Zhou SG, Feng R, Rensing C. Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142702. [PMID: 33049532 DOI: 10.1016/j.scitotenv.2020.142702] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.
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Affiliation(s)
- Sohaib H Mazhar
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Denmark
| | - Azhar Rashid
- Nuclear Institute for Food and Agriculture (PAEC), Tarnab, Peshawar 25000, Pakistan
| | - JunMing Su
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqiang Xu
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Asker Daniel Brejnrod
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, United States
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China
| | - Yijian Wu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shun Gui Zhou
- Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
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Lessons and Considerations for the Creation of Universal Primers Targeting Non-Conserved, Horizontally Mobile Genes. Appl Environ Microbiol 2021; 87:AEM.02181-20. [PMID: 33277268 PMCID: PMC7851684 DOI: 10.1128/aem.02181-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica). Using sequence alignments and in silico PCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.IMPORTANCE Increasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during the in silico phase of primer design which will improve our gene annotations based on percent identities.
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A framework for identifying the recent origins of mobile antibiotic resistance genes. Commun Biol 2021; 4:8. [PMID: 33398069 PMCID: PMC7782503 DOI: 10.1038/s42003-020-01545-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome. Ebmeyer and colleagues developed a genomic framework for identification and scrutiny of the origins of antibiotic resistance genes. Using data scoured from the literature and publicly available genomes, their results indicate that only 81% of previously reported origins are valid, and that the majority of resistance genes of which the origin is known to date emerged in taxa that have been associated with infection in humans and domesticated animals.
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Probiotic Potential of Lactic Acid Starter Cultures Isolated from a Traditional Fermented Sorghum-Millet Beverage. Int J Microbiol 2020; 2020:7825943. [PMID: 32831844 PMCID: PMC7424372 DOI: 10.1155/2020/7825943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/10/2020] [Indexed: 01/29/2023] Open
Abstract
The purpose of this study was to establish the probiotic potential of lactic acid bacteria (LAB) starter cultures, Lb. plantarum MNC 21, L. lactis MNC 24, and W. confusa MNC 20, isolated from a traditionally fermented sorghum-millet beverage from Uganda. The cultures were examined for tolerance to acid and bile salts, bile salt hydrolase (BSH) activity, antibiotic susceptibility, biogenic amine production, mucin degradation, hydrophobicity, auto-aggregation, adherence to the ileum, coaggregation, and antimicrobial properties against selected pathogenic species. Lb. rhamnosus yoba 2012, a known probiotic, was the reference. The isolates were tolerant to acid (pH = 3) and bile (1%). W. confusa MNC 20 and Lb. plantarum MNC 21 exhibited medium BSH activity (11-15 mm diameter of hydrolysis zone) while L. lactis and Lb. rhamnosus yoba 2012 exhibited low BSH activity (<10 mm diameter of hydrolysis zone). All isolates lacked mucolytic activity. Lb. plantarum MNC 21 and W. confusa MNC 20 produced agmatine. The candidate and reference microorganisms were resistant to 10 of 21 and 5 of 21 antibiotics, respectively. The isolates exhibited hydrophobic, auto-aggregation and coaggregation properties. These three properties were exhibited more (p < 0.05) by the reference than the potential probiotics. The ability of the potential probiotics to attach onto the goat ileum (7.3-8.0 log cfu/cm2) was comparable to that of Lb. rhamnosus yoba 2012 (7.6 log cfu/cm2). The four LAB inhibited E. coli, S. aureus, and S. enterica to the same extent (p < 0.05). The findings indicated potential probiotic activity of the starter cultures. However, further in vivo examination of these isolates is required to confirm their probiotic capabilities.
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Huang WC, Liao YJ, Hashimoto M, Chen KF, Chu C, Hsu PC, Wang S, Teng CH. cjrABC-senB hinders survival of extraintestinal pathogenic E. coli in the bloodstream through triggering complement-mediated killing. J Biomed Sci 2020; 27:86. [PMID: 32762693 PMCID: PMC7412671 DOI: 10.1186/s12929-020-00677-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Extraintestinal pathogenic E. coli (ExPEC) is a common gram-negative organism causing various infections, including urinary tract infections (UTIs), bacteremia, and neonatal meningitis. The cjrABC-senB gene cluster of E. coli contributes to ExPEC virulence in the mouse model of UTIs. Consistently, the distribution of cjrABC-senB is epidemiologically associated with human UTIs caused by E. coli. cjrABC-senB, which has previously been proposed to encode an iron uptake system, may facilitate ExPEC survival in the iron availability-restricted urinary tract. Given that the bloodstream is also an iron limited environment to invading bacteria, the pathogenic role of cjrABC-senB in ExPEC bacteremia, however, remains to be investigated. METHODS The ability of ExPEC RS218 strains with and without cjrABC-senB to survive in the mouse bloodstream and human serum was evaluated. Subsequently, the role of this gene cluster in the ExPEC interaction with the complement system was evaluated. Finally, the distribution of cjrABC-senB in human clinical E. coli isolates was determined by PCR. The frequency of cjrABC-senB in bacteremia isolates that were not associated with UTIs (non-UTI bacteremia isolates) was compared with that in UTI-associated isolates and fecal isolates. RESULTS Expression of cjrABC-senB attenuated the survival of RS218 in the mouse bloodstream and human serum. The cjrABC-senB-harboring strains triggered enhanced classical- and alternative-complement pathway activation and became more vulnerable to complement-mediated killing in serum. cjrA was identified as the major gene responsible for the attenuated serum survival. Expressing cjrABC-senB and cjrA increased bacterial susceptibility to detergent and induced periplasmic protein leakage, suggesting that the expression of these genes compromises the integrity of the outer membrane of ExPEC. In addition, the frequency of cjrABC-senB in non-UTI bacteremia isolates was significantly lower than that in UTI-associated isolates, while the frequencies in non-UTI bacteremia isolates and fecal isolates showed no significant difference. Consistently, this epidemiological investigation suggests that cjrABC-senB does not contribute to E. coli bacteremia in humans. CONCLUSION The contribution of cjrABC-senB to the pathogenesis of ExPEC is niche dependent and contradictory because the genes facilitate ExPEC UTIs but hinder bacteremia. The contradictory niche-dependent characteristic may benefit the development of novel strategies against E. coli-caused infections.
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Affiliation(s)
- Wen-Chun Huang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Jyun Liao
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan City, Taiwan
| | - Kuan-Fu Chen
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan
| | - Chishih Chu
- Department of Microbiology, Immunology, and Biopharmaceuticals, National Chiayi University, Chiayi City, Taiwan
| | - Po-Chuen Hsu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan
| | - Shuying Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan City, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan City, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, 4th F, 367 Sheng Li Road, North District, Tainan City, Taiwan.
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan City, Taiwan.
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Liu Z, Luo G, Du R, Sun W, Li J, Lan H, Chen P, Yuan X, Cao D, Li Y, Liu C, Liang S, Jin X, Yang R, Bi Y, Han Y, Cao P, Zhao W, Ling S, Li Y. Effects of spaceflight on the composition and function of the human gut microbiota. Gut Microbes 2020; 11:807-819. [PMID: 31924114 PMCID: PMC7524348 DOI: 10.1080/19490976.2019.1710091] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Interaction between humans and the gut microbiota is important for human physiology. Here, the gut microbiota was analyzed via metagenomic sequencing, and the fluctuations in the gut microbiota under the conditions of spaceflight were characterized. The composition and function of the gut microbiota were substantially affected by spaceflight; however, individual specificity was uncompromised. We further confirmed the species fluctuations and functional genes from both missions. Resistance and virulence genes in the gut microbiota were affected by spaceflight, but the species attributions remained stable. Spaceflight markedly affected the composition and function of the human gut microbiota, implying that the human gut microbiota is sensitive to spaceflight.
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Affiliation(s)
- Zizhong Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Gui Luo
- Department of Rheumatology, Chinese PLA General Hospital, Beijing, China
| | - Ruikai Du
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Weijia Sun
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Jianwei Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Haiyun Lan
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Pu Chen
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Xinxin Yuan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Dengchao Cao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yuheng Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Caizhi Liu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Shuai Liang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xiaoyan Jin
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ping Cao
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Wei Zhao
- Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Shukuan Ling
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China,CONTACT Shukuan Ling Key Lab of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, China
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China,Yingxian Li
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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Kemp L, Adam L, Boehm CR, Breitling R, Casagrande R, Dando M, Djikeng A, Evans NG, Hammond R, Hills K, Holt LA, Kuiken T, Markotić A, Millett P, Napier JA, Nelson C, ÓhÉigeartaigh SS, Osbourn A, Palmer MJ, Patron NJ, Perello E, Piyawattanametha W, Restrepo-Schild V, Rios-Rojas C, Rhodes C, Roessing A, Scott D, Shapira P, Simuntala C, Smith RDJ, Sundaram LS, Takano E, Uttmark G, Wintle BC, Zahra NB, Sutherland WJ. Bioengineering horizon scan 2020. eLife 2020; 9:e54489. [PMID: 32479263 PMCID: PMC7259952 DOI: 10.7554/elife.54489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/14/2020] [Indexed: 01/01/2023] Open
Abstract
Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group of 38 participants. The final list of 20 issues includes topics spanning from the political (the regulation of genomic data, increased philanthropic funding and malicious uses of neurochemicals) to the environmental (crops for changing climates and agricultural gene drives). The early identification of such issues is relevant to researchers, policy-makers and the wider public.
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Affiliation(s)
- Luke Kemp
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | | | - Christian R Boehm
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Bioengineering, University of ManchesterManchesterUnited Kingdom
| | | | - Malcolm Dando
- Division of Peace Studies and International Development, University of BradfordBradfordUnited Kingdom
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, Royal (Dick) School of Veterinary StudiesEdinburghUnited Kingdom
| | - Nicholas G Evans
- Department of Philosophy, University of MassachusettsLowellUnited States
- Rogue BioethicsLowellUnited States
| | | | | | - Lauren A Holt
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Todd Kuiken
- Genetic Engineering and Society Center, North Carolina State UniversityRaleighUnited States
| | - Alemka Markotić
- University Hospital for Infectious DiseasesZagrebCroatia
- Medical School, University of RijekaRijekaCroatia
- Catholic University of CroatiaZagrebCroatia
| | - Piers Millett
- Future of Humanity Institute, University of OxfordOxfordUnited Kingdom
- iGem FoundationBostonUnited States
| | | | - Cassidy Nelson
- Future of Humanity Institute, University of OxfordOxfordUnited Kingdom
| | - Seán S ÓhÉigeartaigh
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | | | - Megan J Palmer
- Center for International Security and Cooperation (CSIAC), Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | | | | | - Wibool Piyawattanametha
- Biomedical Engineering Department, Faculty of Engineering, King Mongkut's Institute of Technology LadkrabangBangkokThailand
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
| | | | - Clarissa Rios-Rojas
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Ekpa’Palek: Empowering Latin-American Young ProfessionalsLimaPeru
| | - Catherine Rhodes
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Anna Roessing
- Department of Politics, Languages and International Studies, University of BathBathUnited Kingdom
| | - Deborah Scott
- Science, Technology & Innovation Studies, School of Social and Political Science, University of EdinburghEdinburghUnited Kingdom
| | - Philip Shapira
- Manchester Institute of Innovation Research, Alliance Manchester Business School, University of ManchesterManchesterUnited Kingdom
- SYNBIOCHEM, University of ManchesterManchesterUnited Kingdom
- School of Public Policy, Georgia Institute of TechnologyAtlantaUnited States
| | | | - Robert DJ Smith
- Science, Technology & Innovation Studies, School of Social and Political Science, University of EdinburghEdinburghUnited Kingdom
| | - Lalitha S Sundaram
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Faculty of Science and Bioengineering, University of ManchesterManchesterUnited Kingdom
| | - Gwyn Uttmark
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Bonnie C Wintle
- School of BioSciences, University of MelbourneMelbourneAustralia
| | - Nadia B Zahra
- Department of Biotechnology, Qarshi UniversityLahorePakistan
| | - William J Sutherland
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
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Citterio B, Andreoni F, Simoni S, Carloni E, Magnani M, Mangiaterra G, Cedraro N, Biavasco F, Vignaroli C. Plasmid Replicon Typing of Antibiotic-Resistant Escherichia coli From Clams and Marine Sediments. Front Microbiol 2020; 11:1101. [PMID: 32528456 PMCID: PMC7266932 DOI: 10.3389/fmicb.2020.01101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Unlike human isolates, environmental Escherichia coli isolates have not been thoroughly investigated for the diversity and transferability of antibiotic-resistant plasmids. In this study, antibiotic-resistant strains from marine sediment (n = 50) and clams (n = 53) were analyzed (i) for their plasmid content using a PCR-based plasmid replicon typing (PBRT) kit and (ii) for the transferability of plasmid-associated antibiotic resistance (AR) traits by mating experiments. Fifteen of the thirty replicons targeted by the PBRT kit were detected in the isolates; 8/15 were identified in both sediment and clam isolates, although at different frequencies. The most frequent replicons in sediment (74%) and in clam strains (66%) alike, were FIA, FIB, or FII, which are associated with the IncF group, followed by the I1α replicon, which was more frequent in clam (24.5%) than in sediment (10%) strains. More than 50% of the strains contained multiple replicons; although 15 were untypable, S1-PFGE analysis demonstrated that 14/15 carried no plasmids. All cryptic strains were successfully typed and were positive for IncF or IncI replicons. Antibiotic-resistant strains accounted for 63% of all isolates and were significantly (p < 0.05) more frequent in phylogroup A. Most (35%) multidrug-resistant (MDR) strains belonged to phylogroup A, too. Although 25/26 MDR strains were positive for IncF plasmids (the exception being a clam strain), the FII-FIB rep combination was predominant (63%) among the sediment isolates, whereas most clam isolates (40%) carried the FII replicon alone. In mating experiments, selected MDR strains carrying FIB, FII, and I1α replicons, used as the donors, transferred multiple ARs together with the IncF or IncI plasmids at high frequency. Since IncI plasmids are common in E. coli and Salmonella enterica isolates from poultry, our findings suggest an animal origin to the E. coli clam strains carrying IncI plasmids. They also suggest a role for IncI plasmids in the spread of ARs among environmental Enterobacteriaceae and, through the food chain, to human isolates. In conclusion, the PBRT kit proved to be a useful tool to identify plasmids carrying antibiotic-resistant genes and to shed light on the factors underpinning their diffusion.
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Affiliation(s)
- Barbara Citterio
- Department of Biomolecular Sciences, Biotechnology Section, University of Urbino "Carlo Bo", Urbino, Italy
| | - Francesca Andreoni
- Department of Biomolecular Sciences, Biotechnology Section, University of Urbino "Carlo Bo", Urbino, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Elisa Carloni
- Department of Biomolecular Sciences, Biotechnology Section, University of Urbino "Carlo Bo", Urbino, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, Biotechnology Section, University of Urbino "Carlo Bo", Urbino, Italy
| | - Gianmarco Mangiaterra
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Nicholas Cedraro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Sheng H, Huang J, Han Z, Liu M, Lü Z, Zhang Q, Zhang J, Yang J, Cui S, Yang B. Genes and Proteomes Associated With Increased Mutation Frequency and Multidrug Resistance of Naturally Occurring Mismatch Repair-Deficient Salmonella Hypermutators. Front Microbiol 2020; 11:770. [PMID: 32457709 PMCID: PMC7225559 DOI: 10.3389/fmicb.2020.00770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/31/2020] [Indexed: 11/23/2022] Open
Abstract
The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella. Our results indicated that the mutation frequency ranged from 3.39 × 10–4 to 5.46 × 10–2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes (mutS, mutT, mutL, and uvrD) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mutS, mutT, and mutL. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella.
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Affiliation(s)
- Huanjing Sheng
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jinling Huang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Zhaoyu Han
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Mi Liu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Zexun Lü
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Qian Zhang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jinlei Zhang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jun Yang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing, China
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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47
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Belas A, Menezes J, Gama LT, Pomba C. Sharing of Clinically Important Antimicrobial Resistance Genes by Companion Animals and Their Human Household Members. Microb Drug Resist 2020; 26:1174-1185. [PMID: 32354251 DOI: 10.1089/mdr.2019.0380] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The aims of this study were to implement a rapid easy methodology, to characterize the antimicrobial resistance gene (AMR) gut content associated with Enterobacteriales and staphylococci; and to evaluate statistical association between AMRs present in fecal samples from healthy companion animals and their human household members. Fecal samples were collected from 27 humans and 29 companion animals living in close contact in 20 households. Nineteen healthy humans without daily contact with companion animals were the control group. After DNA extraction, β-lactamase families and 10 genes of other antimicrobial classes were screened by PCR. Furthermore, third-generation cephalosporin-resistant, carbapenem-resistant, and colistin-resistant Enterobacteriales and methicillin-resistant staphylococci were screened by bacteriological methods. The blaTEM-1B gene with a P3 promotor was the most frequent β-lactam-resistant gene detected in humans and companion animals from households (33.3%, and 17.2%, respectively). The sul2 was the most frequently shared gene by humans and animals from the same household. In 50% of households at least one AMR was detected simultaneously in companion animal/owner pairs. Healthy humans and companion animals carried several AMRs of clinical importance. To the best our knowledge, this study reports the first detection of the blaSHV-27 gene in fecal samples from healthy humans in Portugal and in Europe.
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Affiliation(s)
- Adriana Belas
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Juliana Menezes
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Luís T Gama
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Constança Pomba
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
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Abstract
The interest in the therapeutic use of probiotic microorganisms has been increased during the last decade although the doubts have ascended about the probiotics mainly because their beneficial effects are not fully understood, and, in many cases, their usefulness has not been validated in clinical trials. Consequently, the notion got a considerable interest in those strains having proven probiotic potential to be engineered for improvement in their beneficial features. The process of genetic engineering can also be used for probiotic strains for the reversion of antimicrobial resistance and other modifications for their safer and effective human applications. The lactic acid bacilli are predominantly opposite as they already have gained attention owing to their health-promoting benefits and their safety for human consumption; therefore, their use, especially as a delivery agent of vaccines and drugs, is gaining attention. The tailoring of probiotic strains will not only improve the data regarding the probiotic potential of these strains but also clinch the doubts concerning these probiotics. This article focuses on the approaches of bioengineered probiotics and discusses the potential prospects for their therapeutic applications including immunomodulation, cognitive health, and anticancer therapeutics.
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49
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Wen X, Huang J, Cao J, Xu J, Mi J, Wang Y, Ma B, Zou Y, Liao X, Liang JB, Wu Y. Heterologous expression of the tetracycline resistance gene tetX to enhance degradability and safety in doxycycline degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110214. [PMID: 31968275 DOI: 10.1016/j.ecoenv.2020.110214] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Microbial remediation has the potential to inexpensively yet effectively decontaminate and restore contaminated environments, but the virulence of pathogens and risk of resistance gene transmission by microorganisms during antibiotic removal often limit its implementation. Here, a cloned tetX gene with clear evolutionary history was expressed to explore doxycycline (DOX) degradation and resistance variation during the degradation process. Phylogenetic analysis of tetX genes showed high similarity with those of pathogenic bacteria, such as Riemerella sp. and Acinetobacter sp. Successful tetX expression was performed in Escherichia coli and confirmed by SDS-PAGE and Western blot. Our results showed that 95.0 ± 1.0% of the DOX (50 mg/L) was degraded by the recombinant strain (ETD-1 with tetX) within 48 h, which was significantly higher than that for the control (38.9 ± 8.7%) and the empty plasmid bacteria (8.8 ± 5.1%) (P < 0.05). The tetX gene products in ETD-1 cell extracts also exhibited an efficient DOX degradation ability, with a degradation rate of 80.5 ± 1.2% at 168 h. Furthermore, there was no significant proliferation of the tetX resistance gene during DOX degradation (P > 0.05). The efficient and safe DOX-degrading capacity of the recombinant strain ETD-1 makes it valuable and promising for antibiotic removal in the environment.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Jielan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Junchao Cao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Jiangran Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing, 527400, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing, 527400, China
| | - Baohua Ma
- Nanhai Office of Foshan Customs House, Foshan, 528200, China
| | - Yongde Zou
- Nanhai Office of Foshan Customs House, Foshan, 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing, 527400, China
| | - Juan Boo Liang
- Laboratory of Animal Production, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, 43400, Malaysia
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Enterprise Lab of Healthy Animal Husbandry and Environment Control, Yunfu, Xinxing, 527400, China.
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50
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Wang Y, Jiang Y, Deng Y, Yi C, Wang Y, Ding M, Liu J, Jin X, Shen L, He Y, Wu X, Chen X, Sun C, Zheng M, Zhang R, Ye H, An H, Wong A. Probiotic Supplements: Hope or Hype? Front Microbiol 2020; 11:160. [PMID: 32184760 PMCID: PMC7058552 DOI: 10.3389/fmicb.2020.00160] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
Probiotic bacteria have been associated with various health benefits and included in overwhelming number of foods. Today, probiotic supplements are consumed with increasing regularity and record a rapidly growing economic value. With billions of heterogeneous populations of probiotics per serving, probiotic supplements contain the largest quantity of probiotics across all functional foods. They often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness. On the other hand, the human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains uncertain if probiotics from supplements can tolerate acids and bile salts that may undermine their effectiveness in conferring health benefits. Here, we put into perspective the perceived health benefits and the long-term safety of consuming probiotic supplements, specifically bringing intolerance to acids and bile salts, and the long-standing issue of antibiotic-resistant gene transfer into sharp focus. We report that probiotics from supplements examined in this study have poor tolerance to acids and bile salts while also displaying resistance to multiple antibiotics. They could also adapt and gain resistance to streptomycin in vitro. In an environment where consuming supplements is considered a norm, our results and that of others will put in perspective the persisting concerns surrounding probiotic supplements so that the current hype does not overpower the hope.
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Affiliation(s)
- Yuxuan Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yinyin Jiang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yuxin Deng
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Chen Yi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yangcan Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Mengnan Ding
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Jie Liu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xuanjing Jin
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Lishan Shen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Yue He
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xinyun Wu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Xuefei Chen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Changyi Sun
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Min Zheng
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Ruijia Zhang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Huiting An
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
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