1
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Li J, Sun Z, Sun F, Lai Y, Yi X, Wang Z, Yuan J, Hu Y, Pan A, Pan XF, Zheng Y, Chen D. Gut antibiotic resistome during pregnancy associates with the risk of gestational diabetes mellitus: New evidence from a prospective nested case-control study. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135434. [PMID: 39146585 DOI: 10.1016/j.jhazmat.2024.135434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 07/24/2024] [Accepted: 08/04/2024] [Indexed: 08/17/2024]
Abstract
Antibiotic resistome has emerged as a global threat to public health. However, gestational antibiotic resistome and potential link with adverse pregnancy outcomes remains poorly understood. Our study reports for the first time an association between gut antibiotic resistome during early pregnancy and the risk of gestational diabetes mellitus (GDM) based on a prospective nested case-control cohort including 120 cases and 120 matched controls. A total of 214 antibiotic resistance gene (ARG) subtypes belonging to 17 ARG types were identified in > 10 % fecal samples collected during each trimester. The data revealed dynamic profiles of gut antibiotic resistome through pregnancy, and significant positive associations between selected features (i.e., ARG abundances and a GDM-ARG score which is a new feature characterizing the association between ARGs and GDM) of gut antibiotic resistome during early pregnancy and GDM risk as well as selected endogenous metabolites. The findings demonstrate ubiquitous presence of ARGs in pregnant women and suggest it could constitute an important risk factor for the development of GDM.
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Affiliation(s)
- Jing Li
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China; School of Public Health, Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Zhonghan Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 200433, Shanghai, China
| | - Fengjiang Sun
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yuwei Lai
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou 510631, Guangdong, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou 510631, Guangdong, China
| | - Jiaying Yuan
- Department of Science and Education, Shuangliu Maternal and Child Health Hospital, Chengdu 610200, Sichuan, China
| | - Yayi Hu
- Department of Gynecology and Obstetrics, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - An Pan
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiong-Fei Pan
- Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu 610041, Sichuan, China; Section of Epidemiology and Population Health & Department of Gynecology and Obstetrics, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products In Vitro and In Vivo Correlation, West China Second University Hospital, Sichuan University, Shuangliu Maternal and Child Health Hospital, Chengdu 610041, Sichuan, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 200433, Shanghai, China.
| | - Da Chen
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China.
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2
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Kim SG, Kim BE, Lee JH, Kim DW. Novel Qnr Families as Conserved and Intrinsic Quinolone Resistance Determinants in Aeromonas spp. J Microbiol Biotechnol 2024; 34:1276-1286. [PMID: 38693047 PMCID: PMC11239419 DOI: 10.4014/jmb.2403.03043] [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: 03/24/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/03/2024]
Abstract
The environment has been identified as an origin, reservoir, and transmission route of antibiotic resistance genes (ARGs). Among diverse environments, freshwater environments have been recognized as pivotal in the transmission of ARGs between opportunistic pathogens and autochthonous bacteria such as Aeromonas spp. In this study, five environmental strains of Aeromonas spp. exhibiting multidrug resistance (MDR) were selected for whole-genome sequencing to ascertain their taxonomic assignment at the species-level and to delineate their ARG repertoires. Analyses of their genomes revealed the presence of one protein almost identical to AhQnr (A. hydrophila Qnr protein) and four novel proteins similar to AhQnr. To scrutinize the classification and taxonomic distribution of these proteins, all Aeromonas genomes deposited in the NCBI RefSeq genome database (1,222 genomes) were investigated. This revealed that these Aeromonas Qnr (AQnr) proteins are conserved intrinsic resistance determinants of the genus, exhibiting species-specific diversity. Additionally, structure prediction and analysis of contribution to quinolone resistance by AQnr proteins of the isolates, confirmed their functionality as quinolone resistance determinants. Given the origin of mobile qnr genes from aquatic bacteria and the crucial role of Aeromonas spp. in ARG dissemination in aquatic environments, a thorough understanding and strict surveillance of AQnr families prior to the clinical emergence are imperative. In this study, using comparative genome analyses and functional characterization of AQnr proteins in the genus Aeromonas, novel Aeromonas ARGs requiring surveillance has suggested.
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Affiliation(s)
- Sang-Gyu Kim
- Department of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Bo-Eun Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea
| | - Dae-Wi Kim
- Department of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Saibu S, Uhanie Perera I, Suzuki S, Rodó X, Fujiyoshi S, Maruyama F. Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective. ENVIRONMENT INTERNATIONAL 2024; 183:108377. [PMID: 38103344 DOI: 10.1016/j.envint.2023.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.
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Affiliation(s)
- Salametu Saibu
- Department of Microbiology, Lagos State University of Ojo, Lagos, Nigeria
| | - Ishara Uhanie Perera
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan
| | - Satoru Suzuki
- Graduate School of Science and Engineering, Center for Marine Environmental Studies, Ehime University, Japan
| | - Xavier Rodó
- ICREA and CLIMA Program, Barcelona Institute for Global Health (-ISGlobal), Barcelona, Spain
| | - So Fujiyoshi
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan
| | - Fumito Maruyama
- Section of Microbial Genomics and Ecology, Planetary Health and Innovation Science Center (PHIS), The IDEC Institute, Hiroshima University, Japan.
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4
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Chen C, Cai J, Shi J, Wang Z, Liu Y. Resensitizing multidrug-resistant Gram-negative bacteria to carbapenems and colistin using disulfiram. Commun Biol 2023; 6:810. [PMID: 37537267 PMCID: PMC10400630 DOI: 10.1038/s42003-023-05173-7] [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: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
The increasing incidence of bacterial infections caused by multidrug-resistant (MDR) Gram-negative bacteria has deepened the need for new effective treatments. Antibiotic adjuvant strategy is a more effective and economical approach to expand the lifespan of currently used antibiotics. Herein, we uncover that alcohol-abuse drug disulfiram (DSF) and derivatives thereof are potent antibiotic adjuvants, which dramatically potentiate the antibacterial activity of carbapenems and colistin against New Delhi metallo-β-lactamase (NDM)- and mobilized colistin resistance (MCR)-expressing Gram-negative pathogens, respectively. Mechanistic studies indicate that DSF improves meropenem efficacy by specifically inhibiting NDM activity. Moreover, the robust potentiation of DSF to colistin is due to its ability to exacerbate the membrane-damaging effects of colistin and disrupt bacterial metabolism. Notably, the passage and conjugation assays reveal that DSF minimizes the evolution and spread of meropenem and colistin resistance in clinical pathogens. Finally, their synergistic efficacy in animal models was evaluated and DSF-colistin/meropenem combination could effectively treat MDR bacterial infections in vivo. Taken together, our works demonstrate that DSF and its derivatives are versatile and potent colistin and carbapenems adjuvants, opening a new horizon for the treatment of difficult-to-treat infections.
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Affiliation(s)
- Chen Chen
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jinju Cai
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jingru Shi
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China.
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5
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Wang Q, Tan L, Sun S, Lu X, Luo Y. Land-derived wastewater facilitates antibiotic resistance contamination in marine sediment of semi-closed bay: A case study in Jiaozhou Bay, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117870. [PMID: 37084540 DOI: 10.1016/j.jenvman.2023.117870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
The emergence of antibiotic resistance is a severe threat to public health. There are few studies on the effects of sewage discharge on antibiotics and antibiotic resistance genes (ARGs) contamination in Jiaozhou Bay sediment. Herein, a total of 281 ARG subtypes, 10 mobile genetic elements (MGEs), 10 antibiotics and bacterial communities in marine sediments from Jiaozhou Bay were characterized. Similar bacterial community structures and ARG profiles were identified between the various sampling sites inside the bay, which were both dominated by multidrug and (fluoro)quinolone resistance genes and harbored lower relative abundances of ARGs than those in the sampling sites near the bay exit. Compared with antibiotics and MGEs, bacterial community composition was a more important driver of ARG diversity and geographic distribution. The abundance of pathogens carrying genetic information increased dramatically in southern Jiaozhou Bay is affected by sewage discharge, which indicating that wastewater discharge facilitated ARG contamination of marine sediments. This study highlights the risk of disseminating antibiotic resistance-influencing factors from treated wastewater discharge into marine environment there is an urgent need to optimize or improve wastewater treatment processes to enhance the removal of antibiotics and ARGs. This study has necessary implications for filling the gap in information on antibiotic resistance in Jiaozhou Bay and developing future pollution regulation and control measures.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China; College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan, 056038, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Shaojing Sun
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan, 056038, China
| | - Xueqiang Lu
- Tianjin International Joint Research Center for Environmental Biogeochemical Technology and Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China
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6
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Flint A, Cooper A, Rao M, Weedmark K, Carrillo C, Tamber S. Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood. Front Microbiol 2023; 14:1188872. [PMID: 37520363 PMCID: PMC10373929 DOI: 10.3389/fmicb.2023.1188872] [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: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.
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Affiliation(s)
- Annika Flint
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Ashley Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mary Rao
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Catherine Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
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7
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Alekseeva MG, Rudakova NN, Ratkin AV, Mavletova DA, Danilenko VN. Resistome in Streptomyces rimosus - A Reservoir of Aminoglycoside Antibiotics Resistance Genes. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:723-730. [PMID: 37748869 DOI: 10.1134/s0006297923060019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 09/27/2023]
Abstract
Investigation of aminoglycoside acetyltransferases in actinobacteria of the genus Streptomyces is an integral part of the study of soil bacteria as the main reservoir and possible source of drug resistance genes. Previously, we have identified and biochemically characterized three aminoglycoside phosphotransferases, which cause resistance to kanamycin, neomycin, paromomycin, streptomycin, and hygromycin B in the strain Streptomyces rimosus ATCC 10970 (producing oxytetracycline), which is resistant to most natural aminoglycoside antibiotics. In the presented work, it was shown that the resistance of this strain to other AGs is associated with the presence of the enzyme aminoglycoside acetyltransferase, belonging to the AAC(2') subfamily. Induction of the expression of the gene, designated by us as aac(2')-If, in Escherichia coli cells determines resistance to a wide range of natural aminoglycoside antibiotics (neomycin, gentamicin, tobramycin, sisomycin, and paromomycin) and increases minimum inhibitory concentrations of these antibiotics.
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Affiliation(s)
- Maria G Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Natalya N Rudakova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anatoly V Ratkin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dilara A Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Valeriy N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
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8
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Chatterjee S, More M. Cyanobacterial Harmful Algal Bloom Toxin Microcystin and Increased Vibrio Occurrence as Climate-Change-Induced Biological Co-Stressors: Exposure and Disease Outcomes via Their Interaction with Gut-Liver-Brain Axis. Toxins (Basel) 2023; 15:289. [PMID: 37104227 PMCID: PMC10144574 DOI: 10.3390/toxins15040289] [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: 12/08/2022] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
The effects of global warming are not limited to rising global temperatures and have set in motion a complex chain of events contributing to climate change. A consequence of global warming and the resultant climate change is the rise in cyanobacterial harmful algal blooms (cyano-HABs) across the world, which pose a threat to public health, aquatic biodiversity, and the livelihood of communities that depend on these water systems, such as farmers and fishers. An increase in cyano-HABs and their intensity is associated with an increase in the leakage of cyanotoxins. Microcystins (MCs) are hepatotoxins produced by some cyanobacterial species, and their organ toxicology has been extensively studied. Recent mouse studies suggest that MCs can induce gut resistome changes. Opportunistic pathogens such as Vibrios are abundantly found in the same habitat as phytoplankton, such as cyanobacteria. Further, MCs can complicate human disorders such as heat stress, cardiovascular diseases, type II diabetes, and non-alcoholic fatty liver disease. Firstly, this review describes how climate change mediates the rise in cyanobacterial harmful algal blooms in freshwater, causing increased levels of MCs. In the later sections, we aim to untangle the ways in which MCs can impact various public health concerns, either solely or in combination with other factors resulting from climate change. In conclusion, this review helps researchers understand the multiple challenges brought forth by a changing climate and the complex relationships between microcystin, Vibrios, and various environmental factors and their effect on human health and disease.
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Affiliation(s)
- Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental and Occupational Health, Program in Public Health, University of California–Irvine, Irvine, CA 92697, USA
- Toxicology Core, NIEHS Center for Oceans and Human Health on Climate Change Interactions, Department of Environmental and Occupational Health, Program in Public Health, University of California–Irvine, Irvine, CA 92697, USA
- Division of Infectious Disease, Department of Medicine, UCI School of Medicine, University of California–Irvine, Irvine, CA 92697, USA
| | - Madhura More
- Environmental Health and Disease Laboratory, Department of Environmental and Occupational Health, Program in Public Health, University of California–Irvine, Irvine, CA 92697, USA
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Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century. Microorganisms 2023; 11:1050. [PMID: 37110473 PMCID: PMC10144039 DOI: 10.3390/microorganisms11041050] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.
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Affiliation(s)
- Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel D. Fernández-de-Bobadilla
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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10
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Vatlin AA, Bekker OB, Shur KV, Ilyasov RA, Shatrov PA, Maslov DA, Danilenko VN. Kanamycin and Ofloxacin Activate the Intrinsic Resistance to Multiple Antibiotics in Mycobacterium smegmatis. BIOLOGY 2023; 12:biology12040506. [PMID: 37106707 PMCID: PMC10135989 DOI: 10.3390/biology12040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/16/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
Drug resistance (DR) in Mycobacterium tuberculosis is the main problem in fighting tuberculosis (TB). This pathogenic bacterium has several types of DR implementation: acquired and intrinsic DR. Recent studies have shown that exposure to various antibiotics activates multiple genes, including genes responsible for intrinsic DR. To date, there is evidence of the acquisition of resistance at concentrations well below the standard MICs. In this study, we aimed to investigate the mechanism of intrinsic drug cross-resistance induction by subinhibitory concentrations of antibiotics. We showed that pretreatment of M. smegmatis with low doses of antibiotics (kanamycin and ofloxacin) induced drug resistance. This effect may be caused by a change in the expression of transcriptional regulators of the mycobacterial resistome, in particular the main transcriptional regulator whiB7.
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O’Connor L, Heyderman R. The challenges of defining the human nasopharyngeal resistome. Trends Microbiol 2023:S0966-842X(23)00056-2. [DOI: 10.1016/j.tim.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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12
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Li T, Wang Z, Guo J, de la Fuente-Nunez C, Wang J, Han B, Tao H, Liu J, Wang X. Bacterial resistance to antibacterial agents: Mechanisms, control strategies, and implications for global health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160461. [PMID: 36435256 DOI: 10.1016/j.scitotenv.2022.160461] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
The spread of bacterial drug resistance has posed a severe threat to public health globally. Here, we cover bacterial resistance to current antibacterial drugs, including traditional herbal medicines, conventional antibiotics, and antimicrobial peptides. We summarize the influence of bacterial drug resistance on global health and its economic burden while highlighting the resistance mechanisms developed by bacteria. Based on the One Health concept, we propose 4A strategies to combat bacterial resistance, including prudent Application of antibacterial agents, Administration, Assays, and Alternatives to antibiotics. Finally, we identify several opportunities and unsolved questions warranting future exploration for combating bacterial resistance, such as predicting genetic bacterial resistance through the use of more effective techniques, surveying both genetic determinants of bacterial resistance and the transmission dynamics of antibiotic resistance genes (ARGs).
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Affiliation(s)
- Ting Li
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing 100071, PR China
| | - Zhenlong Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
| | - Jinquan Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Bing Han
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Hui Tao
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Jie Liu
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China
| | - Xiumin Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, PR China.
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13
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Murray AK, Zhang L, Snape J, Gaze WH. Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100184. [PMID: 36908773 PMCID: PMC9995290 DOI: 10.1016/j.crmicr.2023.100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) -like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.
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Affiliation(s)
- Aimee K. Murray
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
- Corresponding author.
| | - Lihong Zhang
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Jason Snape
- AstraZeneca Global Environment, Alderly Park, Macclesfield, United Kingdom
| | - William H. Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10 9FE, United Kingdom
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14
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. THE ISME JOURNAL 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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15
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Shi X, Xia Y, Wei W, Ni BJ. Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms. WATER RESEARCH 2022; 224:119060. [PMID: 36096030 DOI: 10.1016/j.watres.2022.119060] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/28/2022] [Accepted: 09/04/2022] [Indexed: 05/28/2023]
Abstract
The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.
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Affiliation(s)
- Xingdong Shi
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
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16
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Anti-Restriction Gene Homologs Are Highly Represented in Methicillin-Resistant and Multidrug-Resistant Staphylococcus aureus ST239 and ST398: Implications for Resistance Gene Acquisitions. Antibiotics (Basel) 2022; 11:antibiotics11091217. [PMID: 36139996 PMCID: PMC9495042 DOI: 10.3390/antibiotics11091217] [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: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug resistance is commonly acquired by transferring DNA from one bacterium to another. However, the mechanisms that enhance the acquisitions of foreign genes are poorly understood, as well as the dynamics of their transmission between hosts in different environments. Here, genomic approaches were applied to evaluate the enrichment of the S. aureus chromosome with resistance traits in groups of genomes with or without anti-restriction genes and to analyze some evolutionary aspects of these acquisitions. Furthermore, the role played by an anti-restriction gene in improving multiresistance in MRSA was investigated by molecular cloning. A strong association was observed between the presence of anti-restriction gene homologs and patterns of multidrug resistance. Human isolates, mainly ST239-SCCmecIII, carry ardA-H1, and from animal sources, mainly CC398, carry ardA-H2. Increased DNA transfer was observed for clones that express the ardA-H1 allele, corroborating its role in promoting gene transfer. In addition, ardA-H1 was expressed in the dsDNA format in the BMB9393 strain. The evolution of successful multidrug-resistant MRSA lineages of the ST239 and ST398 was initiated not only by the entry of the mec cassette but also by the acquisition of anti-restriction gene homologs. Understanding the mechanisms that affect DNA transfer may provide new tools to control the spread of drug resistance.
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17
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Aljeldah MM. Antimicrobial Resistance and Its Spread Is a Global Threat. Antibiotics (Basel) 2022; 11:antibiotics11081082. [PMID: 36009948 PMCID: PMC9405321 DOI: 10.3390/antibiotics11081082] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) is a challenge to human wellbeing the world over and is one of the more serious public health concerns. AMR has the potential to emerge as a serious healthcare threat if left unchecked, and could put into motion another pandemic. This establishes the need for the establishment of global health solutions around AMR, taking into account microdata from different parts of the world. The positive influences in this regard could be establishing conducive social norms, charting individual and group behavior practices that favor global human health, and lastly, increasing collective awareness around the need for such action. Apart from being an emerging threat in the clinical space, AMR also increases treatment complexity, posing a real challenge to the existing guidelines around the management of antibiotic resistance. The attribute of resistance development has been linked to many genetic elements, some of which have complex transmission pathways between microbes. Beyond this, new mechanisms underlying the development of AMR are being discovered, making this field an important aspect of medical microbiology. Apart from the genetic aspects of AMR, other practices, including misdiagnosis, exposure to broad-spectrum antibiotics, and lack of rapid diagnosis, add to the creation of resistance. However, upgrades and innovations in DNA sequencing technologies with bioinformatics have revolutionized the diagnostic industry, aiding the real-time detection of causes of AMR and its elements, which are important to delineating control and prevention approaches to fight the threat.
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Affiliation(s)
- Mohammed M Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafar al-Batin 31991, Saudi Arabia
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18
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Bose D, Chatterjee S, Older E, Seth R, Janulewicz P, Saha P, Mondal A, Carlson JM, Decho AW, Sullivan K, Klimas N, Lasley S, Li J, Chatterjee S. Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation. Commun Biol 2022; 5:552. [PMID: 35672382 PMCID: PMC9174162 DOI: 10.1038/s42003-022-03494-7] [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: 06/14/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022] Open
Abstract
Chronic multisymptom illness (CMI) affects a subsection of elderly and war Veterans and is associated with systemic inflammation. Here, using a mouse model of CMI and a group of Gulf War (GW) Veterans' with CMI we show the presence of an altered host resistome. Results show that antibiotic resistance genes (ARGs) are significantly altered in the CMI group in both mice and GW Veterans when compared to control. Fecal samples from GW Veterans with persistent CMI show a significant increase of resistance to a wide class of antibiotics and exhibited an array of mobile genetic elements (MGEs) distinct from normal healthy controls. The altered resistome and gene signature is correlated with mouse serum IL-6 levels. Altered resistome in mice also is correlated strongly with intestinal inflammation, decreased synaptic plasticity, reversible with fecal microbiota transplant (FMT). The results reported might help in understanding the risks to treating hospital acquired infections in this population.
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Affiliation(s)
- Dipro Bose
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Somdatta Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Ethan Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Ratanesh Seth
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Patricia Janulewicz
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Punnag Saha
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Ayan Mondal
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jeffrey M Carlson
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Alan W Decho
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Kimberly Sullivan
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Nancy Klimas
- Department of Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Stephen Lasley
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
- Columbia VA Medical Center, Columbia, SC, USA.
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19
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Activation of class 1 integron integrase is promoted in the intestinal environment. PLoS Genet 2022; 18:e1010177. [PMID: 35482826 PMCID: PMC9090394 DOI: 10.1371/journal.pgen.1010177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/10/2022] [Accepted: 03/30/2022] [Indexed: 11/21/2022] Open
Abstract
Class 1 integrons are widespread genetic elements playing a major role in the dissemination of antibiotic resistance. They allow bacteria to capture, express and exchange antibiotic resistance genes embedded within gene cassettes. Acquisition of gene cassettes is catalysed by the class 1 integron integrase, a site-specific recombinase playing a key role in the integron system. In in vitro planktonic culture, expression of intI1 is controlled by the SOS response, a regulatory network which mediates the repair of DNA damage caused by a wide range of bacterial stress, including antibiotics. However, in vitro experimental conditions are far from the real lifestyle of bacteria in natural environments such as the intestinal tract which is known to be a reservoir of integrons. In this study, we developed an in vivo model of intestinal colonization in gnotobiotic mice and used a recombination assay and quantitative real-time PCR, to investigate the induction of the SOS response and expression and activity of the class 1 integron integrase, IntI1. We found that the basal activity of IntI1 was higher in vivo than in vitro. In addition, we demonstrated that administration of a subinhibitory concentration of ciprofloxacin rapidly induced both the SOS response and intI1 expression that was correlated with an increase of the activity of IntI1. Our findings show that the gut is an environment in which the class 1 integron integrase is induced and active, and they highlight the potential role of integrons in the acquisition and/or expression of resistance genes in the gut, particularly during antibiotic therapy. Class 1 integrons are genetic systems allowing bacteria to acquire antibiotic resistance genes through the recombination activity of the IntI1 integrase. These genetic platforms are involved in the spread of antibiotic resistance among bacteria. So far, most of the studies for understanding the mechanistic of integrons have been performed in vitro, experimental conditions which are far from the lifestyle of bacteria in natural environments such as the gut. We developed a new in vivo model using gnotobiotic mice and we showed that in the gut, the basal activity of IntI1 is significantly higher than in in vitro conditions. In addition, we showed that a subinhibitory concentration of ciprofloxacin rapidly triggers the SOS response, leading to increased activity of IntI1 in the mouse gut. Our results demonstrate that the intestinal environment promotes the acquisition/expression of antibiotic resistance genes through the integron system and that this phenomenon can be enhanced by antibiotic therapy.
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20
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Mullowney MW, Maltseva NI, Endres M, Kim Y, Joachimiak A, Crofts TS. Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens. Microbiol Spectr 2022; 10:e0013922. [PMID: 35195438 PMCID: PMC8941942 DOI: 10.1128/spectrum.00139-22] [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: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 11/20/2022] Open
Abstract
Phylogenetically diverse bacteria can carry out chloramphenicol reduction, but only a single enzyme has been described that efficiently catalyzes this reaction, the NfsB nitroreductase from Haemophilus influenzae strain KW20. Here, we tested the hypothesis that some NfsB homologs function as housekeeping enzymes with the potential to become chloramphenicol resistance enzymes. We found that expression of H. influenzae and Neisseria spp. nfsB genes, but not Pasteurella multocida nfsB, allows Escherichia coli to resist chloramphenicol by nitroreduction. Mass spectrometric analysis confirmed that purified H. influenzae and N. meningitides NfsB enzymes reduce chloramphenicol to amino-chloramphenicol, while kinetics analyses supported the hypothesis that chloramphenicol reduction is a secondary activity. We combined these findings with atomic resolution structures of multiple chloramphenicol-reducing NfsB enzymes to identify potential key substrate-binding pocket residues. Our work expands the chloramphenicol reductase family and provides mechanistic insights into how a housekeeping enzyme might confer antibiotic resistance. IMPORTANCE The question of how new enzyme activities evolve is of great biological interest and, in the context of antibiotic resistance, of great medical importance. Here, we have tested the hypothesis that new antibiotic resistance mechanisms may evolve from promiscuous housekeeping enzymes that have antibiotic modification side activities. Previous work identified a Haemophilus influenzae nitroreductase housekeeping enzyme that has the ability to give Escherichia coli resistance to the antibiotic chloramphenicol by nitroreduction. Herein, we extend this work to enzymes from other Haemophilus and Neisseria strains to discover that expression of chloramphenicol reductases is sufficient to confer chloramphenicol resistance to Es. coli, confirming that chloramphenicol reductase activity is widespread across this nitroreductase family. By solving the high-resolution crystal structures of active chloramphenicol reductases, we identified residues important for this activity. Our work supports the hypothesis that housekeeping proteins possessing multiple activities can evolve into antibiotic resistance enzymes.
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Affiliation(s)
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structure Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Michael Endres
- Structure Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structure Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Structure Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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21
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The Bacterial Urban Resistome: Recent Advances. Antibiotics (Basel) 2022; 11:antibiotics11040512. [PMID: 35453263 PMCID: PMC9030810 DOI: 10.3390/antibiotics11040512] [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: 03/24/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens’ behaviors all support persistence and transfer of antimicrobial resistances (AMR). Various unique aspects of urban settings that promote spread and resilience of ARGs/ARB are discussed: (i) the role of hospitals and recreational parks as reservoirs; (ii) private and public transportation as carriers of ARGs/ARB; (iii) the role of built environments as a hub for horizontal gene transfer even though they support lower microbial biodiversity than outdoor environments; (iv) the need to employ ecological and evolutionary concepts, such as modeling the fate of a specific ARG/ARB, to gain enhanced health risk assessments. Our understanding and our ability to control the rise of AMR in an urban setting is linked to our knowledge of the network connecting urban reservoirs and the environment.
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22
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2022; 10:80. [PMID: 35847383 PMCID: PMC9243550 DOI: 10.12688/f1000research.39214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Affiliation(s)
| | - Marco Fabbri
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Guy Van den Eede
- European Commission Joint Research Centre, Ispra, Italy
- European Commission Joint Research Centre, Geel, Belgium
| | - Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Catherine Carrillo
- Ottawa Laboratory – Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | | | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teresa Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, Madrid, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul Hammer
- BIOMES. NGS GmbH c/o Technische Hochschule Wildau, Wildau, Germany
| | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, Lyon, France
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Thierry Naas
- French-NRC for CPEs, Service de Bactériologie-Hygiène, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | | | - John Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Lukas M. Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Present address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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23
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Cui H, Smith AL. Impact of engineered nanoparticles on the fate of antibiotic resistance genes in wastewater and receiving environments: A comprehensive review. ENVIRONMENTAL RESEARCH 2022; 204:112373. [PMID: 34774508 DOI: 10.1016/j.envres.2021.112373] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Nanoparticles (NPs) and antibiotic resistance elements are ubiquitous in wastewater and consequently, in receiving environments. Sub-lethal levels of engineered NPs potentially result in a selective pressure on antibiotic resistance gene (ARG) propagation in wastewater treatment plants. Conversely, emergent NPs are being designed to naturally attenuate ARGs based on special physical and electrochemical properties, which could alleviate dissemination of ARGs to the environment. The complex interactions between NPs and antibiotic resistance elements have heightened interest in elucidating the potential positive and negative implications. This review focuses on the properties of NPs and ARGs and how their interactions could increase or decrease antibiotic resistance at wastewater treatment plants and in receiving environments. Further, the potential for sub-lethal level NPs to facilitate horizontal gene transfer of ARGs and increase mutagenesis rates, which adds a layer of complexity to combatting antibiotic resistance associated with wastewater management, is discussed. Notably, the literature revealed that sub-lethal exposure of engineered NPs may facilitate conjugative transfer of ARGs by increasing cell membrane permeability. The enhanced permeability is a result of direct damage via NP attachment and indirect damage by generating reactive oxygen species (ROS) and causing genetic changes relevant to conjugation. Finally, current knowledge gaps and future research directions (e.g., deciphering the fate of NPs in the environment and examining the long-term cytotoxicity of NPs) are identified for this emerging field.
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Affiliation(s)
- Hanlin Cui
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA, 90089, United States
| | - Adam L Smith
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA, 90089, United States.
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24
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Jiang Q, Feng M, Ye C, Yu X. Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150568. [PMID: 34627113 DOI: 10.1016/j.scitotenv.2021.150568] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 05/17/2023]
Abstract
Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.
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Affiliation(s)
- Qi Jiang
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Mingbao Feng
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chengsong Ye
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Xin Yu
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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25
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Hernández-González IL, Mateo-Estrada V, Castillo-Ramirez S. The promiscuous and highly mobile resistome of Acinetobacter baumannii. Microb Genom 2022; 8. [PMID: 35075990 PMCID: PMC8914355 DOI: 10.1099/mgen.0.000762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.
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Affiliation(s)
- Ismael L Hernández-González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Santiago Castillo-Ramirez,
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26
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Brindangnanam P, Sawant AR, Prashanth K, Coumar MS. Bacterial effluxome as a barrier against antimicrobial agents: structural biology aspects and drug targeting. Tissue Barriers 2021; 10:2013695. [PMID: 34957912 DOI: 10.1080/21688370.2021.2013695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. The bacterial membrane is the first layer of defense for the bacteria against antimicrobial agents (AMA), specifically transporters in the membrane efflux these AMA out of the bacteria and plays a significant role in the AMR development. Understanding the structure and the functions of these efflux transporters is essential to overcome AMR. This review discusses efflux transporters (primary, secondary, and tripartite), their domain architectures, substrate specificities, and efflux pump inhibitors (EPI). Special emphasis on nosocomial ESKAPEE (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli) pathogens, their multidrug efflux targets and inhibitors are discussed. Deep knowledge about the functioning of efflux pumps and their structural aspects will open up opportunities for developing new EPI, which could be used along with AMA as combination therapy to overcome the emerging AMR crisis.
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Affiliation(s)
- Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [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: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
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Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model. mSystems 2021; 6:e0098821. [PMID: 34726494 PMCID: PMC8562478 DOI: 10.1128/msystems.00988-21] [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
Assembly of a resistome in parallel with the establishment of a microbial community is not well understood. Germfree models can reveal microbiota interactions and shed light on bacterial colonization and resistance development under antibiotic pressure. In this study, we exposed germfree soil (GS), GS with diluted nontreated soil (DS), and nontreated soil (NS) to various concentrations of tetracycline (TET) in a nongermfree environment for 10 weeks, followed by 2 weeks of exposure to water. High-throughput sequencing was used to profile bacterial communities and antibiotic resistance genes (ARGs) in the soils. The initial bacterial loads were found to shape the profiles of bacterial communities and the resistomes. GS and DS treated with TET and the same soils left untreated had similar profiles, whereas NS showed different profiles. Soils with the same initial bacterial loads had their profiles shifted by TET treatment. Multidrug resistance (MDR) genes were the most abundant ARG types in all soils, with multidrug efflux pump genes being the discriminatory ARGs in GS regardless of different TET treatments and in GS, DS, and NS after TET. Furthermore, MDR genes were significantly enriched by TET treatment. In contrast, tetracycline resistance genes were either absent or low in relative abundance. The family Burkholderiaceae was predominant in all soils (except in NS treated with water) and was positively selected for by TET treatment. Most importantly, Burkholderiaceae were the primary carrier of ARGs, including MDR genes. IMPORTANCE This is the first study to examine how resistomes develop and evolve using GS. GS can be used to study the colonization and establishment of bacterial communities under antibiotic selection. Surprisingly, MDR genes were the main ARGs detected in GS, and TET treatments did not positively select for specific tetracycline resistance genes. Additionally, Burkholderiaceae were the key bacterial hosts for MDR genes in the current GS model under the conditions investigated. These results show that the family Burkholderiaceae underpins the development of resistome and serves as a source of ARGs. The ease of establishment of Burkholderiaceae and MDR genes in soils has serious implications for human health, since these bacteria are versatile and ubiquitous in the environment.
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Wang Z, Chen Q, Zhang J, Yan H, Chen Y, Chen C, Chen X. High prevalence of unstable antibiotic heteroresistance in cyanobacteria causes resistance underestimation. WATER RESEARCH 2021; 202:117430. [PMID: 34298276 DOI: 10.1016/j.watres.2021.117430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Both cyanobacterial bloom and antibiotic resistance have aggravated worldwide and posed a global threat to public health in recent years. Cyanobacteria can exhibit discrepancy between their resistance genotype and susceptible phenotype due to antibiotic heteroresistance, which leads to difficulties in unambiguously classifying cyanobacterial strains as susceptible or resistant. Here we profiled the prevalence and mechanisms of antibiotic heteroresistance in cyanobacterial strains isolated from 50 sites across four eutrophicated lakes in China. Among 300 cyanobacterial isolates tested against 19 different antibiotics, over 90% of cyanobacterial isolates exhibited HR to multiple antibiotics and 19.5% of isolate/antibiotic interactions classified as susceptible by traditional minimum inhibitory concentration (MIC) estimates were designated heteroresistant. Over 97% of these monoclonal HR cases were unstable, with an increased resistance of subpopulations due to amplification of known resistance genes with high fitness cost. Wide-type cyanobacterial isolates of Synechococcus, Synechocystis, Anabaena and Microcystis aeruginosa exposed to sub-MIC level of four antibiotics evolved high-level resistance with little fitness cost, resulting in stable polyclonal HR. Both stable polyclonal HR and unstable monoclonal HR observed in different cyanobacterial strains can be promoted under environmental levels of antibiotic pressure. The highly prevalent and unstable monoclonal HR with the potential for susceptibility misclassification highlighted underestimation of cyanobacteria-derived antibiotic resistance. Cost-effective strategies should be developed to identify heteroresistance in cyanobacteria and to avoid false positive or negative results in traditional susceptibility testing.
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Affiliation(s)
- Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China.
| | - Jianyun Zhang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China.
| | - Hanlu Yan
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Yuchen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Cheng Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Xiaoxue Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
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Lebeaux RM, Coker MO, Dade EF, Palys TJ, Morrison HG, Ross BD, Baker ER, Karagas MR, Madan JC, Hoen AG. The infant gut resistome is associated with E. coli and early-life exposures. BMC Microbiol 2021; 21:201. [PMID: 34215179 PMCID: PMC8252198 DOI: 10.1186/s12866-021-02129-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs. RESULTS Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally. CONCLUSIONS Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.
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Affiliation(s)
- Rebecca M. Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Modupe O. Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Oral Biology Department, Rutgers School of Dental Medicine, Newark, NJ USA
| | - Erika F. Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Thomas J. Palys
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | | | - Benjamin D. Ross
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Orthopaedics Geisel School of Medicine at Dartmouth , NH Hanover, USA
| | - Emily R. Baker
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
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The innate resistome of “recalcitrant” Acinetobacter baumannii and the role of nanoparticles in combating these MDR pathogens. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning. Sci Rep 2021; 11:7736. [PMID: 33833319 PMCID: PMC8032699 DOI: 10.1038/s41598-021-87300-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/26/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus uberis is one of the leading pathogens causing mastitis worldwide. Identification of S. uberis strains that fail to respond to treatment with antibiotics is essential for better decision making and treatment selection. We demonstrate that the combination of supervised machine learning and matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) mass spectrometry can discriminate strains of S. uberis causing clinical mastitis that are likely to be responsive or unresponsive to treatment. Diagnostics prediction systems trained on 90 individuals from 26 different farms achieved up to 86.2% and 71.5% in terms of accuracy and Cohen’s kappa. The performance was further increased by adding metadata (parity, somatic cell count of previous lactation and count of positive mastitis cases) to encoded MALDI-TOF spectra, which increased accuracy and Cohen’s kappa to 92.2% and 84.1% respectively. A computational framework integrating protein–protein networks and structural protein information to the machine learning results unveiled the molecular determinants underlying the responsive and unresponsive phenotypes.
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Qiu T, Wu D, Zhang L, Zou D, Sun Y, Gao M, Wang X. A comparison of antibiotics, antibiotic resistance genes, and bacterial community in broiler and layer manure following composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:14707-14719. [PMID: 33219508 DOI: 10.1007/s11356-020-11469-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Animal manure is an important source of antibiotics and antibiotic resistance genes (ARGs) in the environment. However, the difference of antibiotic residues and ARG profiles in layer and broiler manure as well as their compost remains unexplored. In this study, we investigated the profiles of twelve antibiotics, seventeen ARGs, and class 1 integrase gene (intI1) in layer and broiler manure, and the corresponding compost at large-scale. Compared with layer manure, broiler manure exhibited approximately six times more residual tetracyclines, especially chlortetracycline. The relative abundances of qnrS and ermA genes in broiler manure were significantly higher than those in layer manure. The concentration of tetracyclines not only had a significantly positive correlation with tetracycline resistance genes (tetA and tetC) but was also positively correlated with quinolone resistance (qepA, qnrB, and qnrS) and macrolide resistance (ermA and ermT). Most ARGs in manure were reduced after composting. However, the relative abundance of sulfonamide resistance gene sul1 increased up to 2.41% after composting, which was significantly higher than that of broiler (0.41%) and layer (0.62%) manure. The associated bacterial community was characterized by high-throughput 16S rRNA gene sequencing. The relative abundances of thermophilic bacteria had significant positive correlations with the abundance of sul1 in compost. The composting has a significant impact on the ARG-associated gut microbes in poultry manure. Variation partitioning analysis indicated that the change of bacterial community compositions and antibiotics contributed partially to the shift in ARG profiles. The results indicate that at industry-scale production broiler manure had more antibiotics and ARGs than layer manure did, and composting decreased most ARG abundances in poultry manure except for sulfonamide resistance genes.
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Affiliation(s)
- Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Banjing, Haidian District, Beijing, 100097, People's Republic of China
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Dan Wu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Banjing, Haidian District, Beijing, 100097, People's Republic of China
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Dexun Zou
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Yanmei Sun
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Banjing, Haidian District, Beijing, 100097, People's Republic of China
| | - Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Banjing, Haidian District, Beijing, 100097, People's Republic of China
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Banjing, Haidian District, Beijing, 100097, People's Republic of China.
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Kim DW, Cha CJ. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 2021; 53:301-309. [PMID: 33642573 PMCID: PMC8080597 DOI: 10.1038/s12276-021-00569-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.
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Affiliation(s)
- Dae-Wi Kim
- grid.411545.00000 0004 0470 4320Division of Life Sciences, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Chang-Jun Cha
- grid.254224.70000 0001 0789 9563Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546 Republic of Korea
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Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization. Braz J Microbiol 2021; 52:675-686. [PMID: 33590447 DOI: 10.1007/s42770-021-00437-y] [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: 04/15/2020] [Accepted: 02/02/2021] [Indexed: 01/28/2023] Open
Abstract
Poultry litter is widely applied as agricultural fertilizer and can affect the soil microbiome through nutrient overload and antibiotic contamination. In this study, we assessed changes in soil bacterial diversity using high-throughput sequencing approaches. Four samples in triplicate were studied: soils with short- and long-term fertilization by poultry litter (S1 = 10 months and S2 = 30 years, respectively), a soil inside a poultry shed (S3), and a forest soil used as control (S0). Samples S0, S1, and S2 revealed a relatively high richness, with confirmed operational taxonomic units (OTUs) in the three replicates of each sample ranging from 1243 to 1279, while richness in S3 was about three times lower (466). The most abundant phyla were Proteobacteria, Bacteroidetes, and Actinobacteria. Acidobacteria, Planctomycetes, and Verrucomicrobia were also abundant but highly diminished in S3, while Firmicutes was less abundant in S0. Changes in bacterial communities were very evident at the genera level. The genera Gaiella, Rhodoplanes, Solirubacter, and Sphingomonas were predominant in S0 but strongly decreased in the other soils. Pedobacter and Devosia were the most abundant in S1 and were diminished in S2, while Herbiconiux, Brevundimonas, Proteiniphilum, and Petrimonas were abundant in S2. The most abundant genera in S3 were Deinococcus, Truepera, Rhodanobacter, and Castellaniella. A predictive analysis of the metabolic functions with Tax4Fun2 software suggested the potential presence of enzymes associated with antibiotic resistance as well as with denitrification pathways, indicating that the S3 soil is a potential source of nitrous oxide, a powerful greenhouse gas.
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021; 10:80. [DOI: 10.12688/f1000research.39214.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 01/12/2023] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Ondon BS, Li S, Zhou Q, Li F. Sources of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in the Soil: A Review of the Spreading Mechanism and Human Health Risks. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 256:121-153. [PMID: 33948742 DOI: 10.1007/398_2020_60] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Soil is an essential part of our ecosystem and plays a crucial role as a nutrient source, provides habitat for plants and other organisms. Overuse of antibiotics has accelerated the development and dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). ARB and ARGs are recognized as emerging environmental contaminants causing soil pollution and serious risks to public health. ARB and ARGs are discharged into soils through several pathways. Application of manure in agriculture is one of the primary sources of ARB and ARGs dissemination in the soil. Different sources of contamination by ARB and ARGs were reviewed and analyzed as well as dissemination mechanisms in the soil. The effects of ARB and ARGs on soil bacterial community were evaluated. Furthermore, the impact of different sources of manure on soil microbial diversity as well as the effect of antibiotics on the development of ARB and ARGs in soils was analyzed. Human health risk assessments associated with the spreading of ARB and ARGs in soils were investigated. Finally, recommendations and mitigation strategies were proposed.
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Affiliation(s)
- Brim Stevy Ondon
- Key Laboratory of Pollution Processes and Environmental Criteria at Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China
| | - Shengnan Li
- Key Laboratory of Pollution Processes and Environmental Criteria at Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria at Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China
| | - Fengxiang Li
- Key Laboratory of Pollution Processes and Environmental Criteria at Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, People's Republic of China.
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Maurya AP, Rajkumari J, Bhattacharjee A, Pandey P. Development, spread and persistence of antibiotic resistance genes (ARGs) in the soil microbiomes through co-selection. REVIEWS ON ENVIRONMENTAL HEALTH 2020; 35:371-378. [PMID: 32681784 DOI: 10.1515/reveh-2020-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/13/2020] [Indexed: 05/28/2023]
Abstract
Bacterial pathogens resistant to multiple antibiotics are emergent threat to the public health which may evolve in the environment due to the co-selection of antibiotic resistance, driven by poly aromatic hydrocarbons (PAHs) and/or heavy metal contaminations. The co-selection of antibiotic resistance (AMR) evolves through the co-resistance or cross-resistance, or co-regulatory mechanisms, present in bacteria. The persistent toxic contaminants impose widespread pressure in both clinical and environmental setting, and may potentially cause the maintenance and spread of antibiotic resistance genes (ARGs). In the past few years, due to exponential increase of AMR, numerous drugs are now no longer effective to treat infectious diseases, especially in cases of bacterial infections. In this mini-review, we have described the role of co-resistance and cross-resistance as main sources for co-selection of ARGs; while other co-regulatory mechanisms are also involved with cross-resistance that regulates multiple ARGs. However, co-factors also support selections, which results in development and evolution of ARGs in absence of antibiotic pressure. Efflux pumps present on the same mobile genetic elements, possibly due to the function of Class 1 integrons (Int1), may increase the presence of ARGs into the environment, which further is promptly changed as per environmental conditions. This review also signifies that mutation plays important role in the expansion of ARGs due to presence of diverse types of anthropogenic pollutants, which results in overexpression of efflux pump with higher bacterial fitness cost; and these situations result in acquisition of resistant genes. The future aspects of co-selection with involvement of systems biology, synthetic biology and gene network approaches have also been discussed.
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Affiliation(s)
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, India
| | | | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, India
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Wang Z, Chen Q, Zhang J, Guan T, Chen Y, Shi W. Critical roles of cyanobacteria as reservoir and source for antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2020; 144:106034. [PMID: 32777621 DOI: 10.1016/j.envint.2020.106034] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
The widespread occurrence of antibiotic resistance genes (ARGs) throughout aquatic environments has raised global concerns for public health, but understanding of the emergence and propagation of ARGs in diverse environmental media remains limited. This study investigated the occurrence and spatio-temporal patterns of six classes of ARGs in cyanobacteria isolated from Taihu Lake. Tetracycline and sulfonamide resistance genes were identified as dominant ARGs. The abundance of ARGs in cyanobacteria was significantly higher in the bloom period than in the non-bloom period. The contribution and persistence of ARGs were higher in extracellular DNA (eDNA) than in intracellular DNA (iDNA) from cyanobacteria. Cyanobacteria-associated eDNA carrying ARGs was more stable at lower temperature. The relative abundances of ARGs in Microcystis and Synechococcus, the dominant genera of cyanobacterial blooms in Taihu Lake, were significantly higher than those in other cyanobacterial strains. The conjugative transfer efficiency for bacterial assimilation of ARGs in cyanobacteria was facilitated by increasing temperature and cyanobacterial cell concentration. Our results demonstrated that cyanobacteria could act as a significant reservoir and source for the acquisition and dissemination of ARGs in aquatic environments, hence the definition of negative ecological effects of cyanobacterial blooms was expanded.
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Affiliation(s)
- Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China.
| | - Jianyun Zhang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Tiesheng Guan
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Yuchen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Wenqing Shi
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
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40
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Hernando-Amado S, Coque TM, Baquero F, Martínez JL. Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health. Front Microbiol 2020; 11:1914. [PMID: 32983000 PMCID: PMC7483582 DOI: 10.3389/fmicb.2020.01914] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.
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Affiliation(s)
- Sara Hernando-Amado
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M. Coque
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José L. Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Acquired Genetic Elements that Contribute to Antimicrobial Resistance in Frequent Gram-Negative Causative Agents of Healthcare-Associated Infections. Am J Med Sci 2020; 360:631-640. [PMID: 32747008 DOI: 10.1016/j.amjms.2020.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/26/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is a worldwide public health problem that reduces therapeutic options and increases the risk of death. The causative agents of healthcare-associated infections (HAIs) are drug-resistant microorganisms of the nosocomial environment, which have developed different mechanisms of AMR. The hospital-associated microbiota has been proposed to be a reservoir of genes associated with AMR and an environment where the transfer of genetic material among organisms may occur. The ESKAPE group (Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter aerogenes and Escherichia coli) is a frequent causative agents of HAIs. In this review, we address the issue of acquired genetic elements that contribute to AMR in the most frequent Gram-negative of ESKAPE, with a focus on last resort antimicrobial agents and the role of transference of genetic elements for the development of AMR.
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42
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Perri R, Kolvenbach BA, Corvini PFX. Subsistence and complexity of antimicrobial resistance on a community-wide level. Environ Microbiol 2020; 22:2463-2468. [PMID: 32286010 PMCID: PMC7383678 DOI: 10.1111/1462-2920.15018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/26/2022]
Abstract
There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well-understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. β-lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.
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Affiliation(s)
- Riccardo Perri
- Institute for Ecopreneurship, School of Life SciencesUniversity of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
| | - Boris A. Kolvenbach
- Institute for Ecopreneurship, School of Life SciencesUniversity of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
| | - Philippe F. X. Corvini
- Institute for Ecopreneurship, School of Life SciencesUniversity of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
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Wang L, Wang J, Wang J, Zhu L, Conkle JL, Yang R. Soil types influence the characteristic of antibiotic resistance genes in greenhouse soil with long-term manure application. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122334. [PMID: 32092657 DOI: 10.1016/j.jhazmat.2020.122334] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/10/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Composted livestock and poultry manure, which may contain antibiotic resistance genes (ARGs), is widely used as natural fertilizer in China. But the influence of soil types on ARGs is not well characterized, particularly at greenhouse sites with long-term manure application. We investigated the distribution of ARGs in the cinnamon, fluvo-aquic and saline-alkali soils in greenhouse of Yellow River Delta region, China. A total of 193 ARGs subtypes were detected, with multidrug and aminoglycoside resistance genes as the most universal ARGs subtypes. Soil types influenced the ARGs distribution, where higher levels of diversity and relative abundance of ARGs in the fluvo-aquic and saline-alkali soils compared with those in the cinnamon soils. Among abiotic factors, sand, pH and Zn contributed more to the pattern of ARGs in the cinnamon soils, whereas sand and Cd, clay and Pb contributed the most in the fluvo-aquic and saline-alkali soils respectively. Furthermore, positive correlations between the relative abundances of ARGs and mobile genetic elements (MGEs) in the fluvo-aquic soils, suggesting higher dissemination potential of ARGs in this type of soil. Overall, MGEs played a positive primary role in the ARGs distribution in greenhouse soil than heavy metal co-selection and soil physicochemical properties.
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Affiliation(s)
- Lanjun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jinhua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lusheng Zhu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jeremy L Conkle
- Department of Physical & Environmental Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States.
| | - Rui Yang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
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Jorge P, Magalhães AP, Grainha T, Alves D, Sousa AM, Lopes SP, Pereira MO. Antimicrobial resistance three ways: healthcare crisis, major concepts and the relevance of biofilms. FEMS Microbiol Ecol 2020; 95:5532357. [PMID: 31305896 DOI: 10.1093/femsec/fiz115] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
Worldwide, infections are resuming their role as highly effective killing diseases, as current treatments are failing to respond to the growing problem of antimicrobial resistance (AMR). The social and economic burden of AMR seems ever rising, with health- and research-related organizations rushing to collaborate on a worldwide scale to find effective solutions. Resistant bacteria are spreading even in first-world nations, being found not only in healthcare-related settings, but also in food and in the environment. In this minireview, the impact of AMR in healthcare systems and the major bacteria behind it are highlighted. Ecological aspects of AMR evolution and the complexity of its molecular mechanisms are explained. Major concepts, such as intrinsic, acquired and adaptive resistance, as well as tolerance and heteroresistance, are also clarified. More importantly, the problematic of biofilms and their role in AMR, namely their main resistance and tolerance mechanisms, are elucidated. Finally, some of the most promising anti-biofilm strategies being investigated are reviewed. Much is still to be done regarding the study of AMR and the discovery of new anti-biofilm strategies. Gladly, considerable research on this topic is generated every day and increasingly concerted actions are being engaged globally to try and tackle this problem.
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Affiliation(s)
- Paula Jorge
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Andreia Patrícia Magalhães
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tânia Grainha
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Alves
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana Margarida Sousa
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Susana Patrícia Lopes
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Olívia Pereira
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Abstract
The human gut is home to a myriad of organisms. While some are harmless commensals, others are transient, pathogenic flora. The gut microbiome is composed of diverse bacterial flora, and apart from playing a major role in protecting from various infectious and non-infectious diseases, it plays an important role in resistance to antimicrobials. The collection of genes or genetic material that confers antimicrobial resistance constitutes the gut resistome, and it may involve the pathogens or commensals of the intestinal tract. The diversity of this gut resistome is influenced by various environmental factors including the diet and antibiotic exposure. This review highlights the recent concepts pertaining to the human gut resistome, factors affecting it, how it impacts human health and diseases, methods to study the resistome and potential therapeutic approaches.
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Affiliation(s)
- Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nipun Verma
- Department of Hepatology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. ENVIRONMENT INTERNATIONAL 2020; 138:105667. [PMID: 32234679 DOI: 10.1016/j.envint.2020.105667] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.
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Affiliation(s)
- Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel
| | - Rohit Kumar Tiwari
- Department of Biosciences, Integral University, Lucknow 226026, UP, India
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel.
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47
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Palma E, Tilocca B, Roncada P. Antimicrobial Resistance in Veterinary Medicine: An Overview. Int J Mol Sci 2020; 21:E1914. [PMID: 32168903 PMCID: PMC7139321 DOI: 10.3390/ijms21061914] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
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Affiliation(s)
| | | | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (E.P.); (B.T.)
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Oikonomou G, Addis MF, Chassard C, Nader-Macias MEF, Grant I, Delbès C, Bogni CI, Le Loir Y, Even S. Milk Microbiota: What Are We Exactly Talking About? Front Microbiol 2020; 11:60. [PMID: 32117107 PMCID: PMC7034295 DOI: 10.3389/fmicb.2020.00060] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022] Open
Abstract
The development of powerful sequencing techniques has allowed, albeit with some biases, the identification and inventory of complex microbial communities that inhabit different body sites or body fluids, some of which were previously considered sterile. Notably, milk is now considered to host a complex microbial community with great diversity. Milk microbiota is now well documented in various hosts. Based on the growing literature on this microbial community, we address here the question of what milk microbiota is. We summarize and compare the microbial composition of milk in humans and in ruminants and address the existence of a putative core milk microbiota. We discuss the factors that contribute to shape the milk microbiota or affect its composition, including host and environmental factors as well as methodological factors, such as the sampling and sequencing techniques, which likely introduce distortion in milk microbiota analysis. The roles that milk microbiota are likely to play in the mother and offspring physiology and health are presented together with recent data on the hypothesis of an enteromammary pathway. At last, this fascinating field raises a series of questions, which are listed and commented here and which open new research avenues.
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Affiliation(s)
- Georgios Oikonomou
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | | | | | - I Grant
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Celine Delbès
- Université Clermont Auvergne, INRAE, UMRF, Aurillac, France
| | - Cristina Inés Bogni
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Yves Le Loir
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
| | - Sergine Even
- STLO, UMR 1253, INRAE, Agrocampus Ouest, Rennes, France
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Lopez CM, Callegari ML, Patrone V, Rebecchi A. Assessment of antibiotic resistance in staphylococci involved in fermented meat product processing. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2019.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dahanayake PS, Hossain S, Wickramanayake MVKS, Heo GJ. Prevalence of virulence and antimicrobial resistance genes in Aeromonas species isolated from marketed cockles (Tegillarca granosa) in Korea. Lett Appl Microbiol 2020; 71:94-101. [PMID: 31943254 DOI: 10.1111/lam.13261] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022]
Abstract
This study aimed to examine incidence, virulence and antimicrobial properties in Aeromonas spp. isolated from cockles (Tegillarca granosa) in Korea. Firstly, genomic DNA was extracted from 32 Aeromonas spp. isolates, and PCR screening for virulence, antimicrobial resistance genes was carried out. The disk diffusion assay was used to examine antimicrobial susceptibility. Aeromonas spp. isolates comprised, A. hydrophila (n = 8), A. veronii (n = 15), A. media (n = 2), A. salmonicida (n = 2), A. allosaccharophila (n = 1), A. bestiarum (n = 1), A. culicicola (n = 1), A. enteropelogenes (n = 1) and A. rivipollensis (n = 1). High prevalence of virulence-related genes reported as; act (69%), alt (47%), ast (41%), aerA (56%), lip (50%), ahyB (47%), ser (28%), fla (66%), gcat (44%), ascV (50%) and hlyA (72%). All isolates were multidrug resistant, while highest resistance level observed for ampicillin (100%), followed by imipenem (81%), rifampicin (78%), cephalothin (72%), piperacillin (47%) and Colistin sulfate (31%). The presence of blaSHV , blaCTX , tetE, aac(6')-Ib, strA-strB, qnrS, qnrB and IntI1 genes were reported in varying combinations. Nevertheless, blaTEM , blaIMP , tetA, tetB, qnrA, qnrB and aphAI-IAB genes and the class1 integron were not detected. The high occurrence of virulence and antimicrobial resistance genes in cockles reveals that it can be a potential health risk source for consumers.
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Affiliation(s)
- P S Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - S Hossain
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - M V K S Wickramanayake
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - G-J Heo
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
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