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Vincent J, Tenore A, Mattei MR, Frunzo L. Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms. Bull Math Biol 2024; 86:63. [PMID: 38664322 DOI: 10.1007/s11538-024-01289-x] [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: 12/11/2023] [Accepted: 03/27/2024] [Indexed: 05/23/2024]
Abstract
In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.
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Affiliation(s)
- Julien Vincent
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
- Microbial Ecology Laboratory, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Alberto Tenore
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
| | - Maria Rosaria Mattei
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy.
| | - Luigi Frunzo
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
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2
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Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
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Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
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3
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Sanz-García F, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. The Pseudomonas aeruginosa Resistome: Permanent and Transient Antibiotic Resistance, an Overview. Methods Mol Biol 2024; 2721:85-102. [PMID: 37819517 DOI: 10.1007/978-1-0716-3473-8_7] [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] [Indexed: 10/13/2023]
Abstract
One of the most concerning characteristics of Pseudomonas aeruginosa is its low susceptibility to several antibiotics of common use in clinics, as well as its facility to acquire increased resistance levels. Consequently, the study of the antibiotic resistance mechanisms of this bacterium is of relevance for human health. For such a study, different types of resistance should be distinguished. The intrinsic resistome is composed of a set of genes, present in the core genome of P. aeruginosa, which contributes to its characteristic, species-specific, phenotype of susceptibility to antibiotics. Acquired resistance refers to those genetic events, such as the acquisition of mutations or antibiotic resistance genes that reduce antibiotic susceptibility. Finally, antibiotic resistance can be transiently acquired in the presence of specific compounds or under some growing conditions. The current article provides information on methods currently used to analyze intrinsic, mutation-driven, and transient antibiotic resistance in P. aeruginosa.
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Affiliation(s)
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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4
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Sang Y, Mo S, Zeng S, Wu X, Kashif M, Song J, Yu D, Bai L, Jiang C. Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167199. [PMID: 37734616 DOI: 10.1016/j.scitotenv.2023.167199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/23/2023]
Abstract
Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of "One Health."
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Affiliation(s)
- Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China; National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China; National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Sen Zeng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Xiaoling Wu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China; National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Jingjing Song
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China
| | - Dahui Yu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China
| | - Lirong Bai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China; National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China; Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China.
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5
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Brunetti F, Ghiglione B, Gudeta DD, Gutkind G, Guardabassi L, Klinke S, Power P. Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC β-Lactamases. Antimicrob Agents Chemother 2023; 67:e0006123. [PMID: 37272821 PMCID: PMC10353377 DOI: 10.1128/aac.00061-23] [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: 01/12/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
KPC-2 is one of the most relevant serine-carbapenemases among the carbapenem-resistant Enterobacterales. We previously isolated from the environmental species Chromobacterium haemolyticum a class A CRH-1 β-lactamase displaying 69% amino acid sequence identity with KPC-2. The objective of this study was to analyze the kinetic behavior and crystallographic structure of this β-lactamase. Our results showed that CRH-1 can hydrolyze penicillins, cephalosporins (except ceftazidime), and carbapenems with similar efficacy compared to KPC-2. Inhibition kinetics showed that CRH-1 is not well inhibited by clavulanic acid, in contrast to efficient inhibition by avibactam (AVI). The high-resolution crystal of the apoenzyme showed that CRH-1 has a similar folding compared to other class A β-lactamases. The CRH-1/AVI complex showed that AVI adopts a chair conformation, stabilized by hydrogen bonds to Ser70, Ser237, Asn132, and Thr235. Our findings highlight the biochemical and structural similarities of CRH-1 and KPC-2 and the potential clinical impact of this carbapenemase in the event of recruitment by pathogenic bacterial species.
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Affiliation(s)
- Florencia Brunetti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Barbara Ghiglione
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Dereje D. Gudeta
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sebastián Klinke
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Pablo Power
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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6
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Sierra TAO, Acosta AC, de Melo RPB, de Oliveira PRF, de Moraes Peixoto R, Cavalcanti EFTSF, Junior JWP, Mota RA. Occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae in raw milk from cows with subclinical mastitis in northeast Brazil. Braz J Microbiol 2023; 54:1303-1307. [PMID: 36964326 PMCID: PMC10235308 DOI: 10.1007/s42770-023-00955-x] [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: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram negative bacteria are becoming increasingly important in veterinary and human medicine because they can hydrolyze the third generation β-lactams, penicillins, and monobactams. The aim of this study was to identify ESBL-producing Enterobacteriaceae in raw cow milk samples from northeast Brazil. Twenty-six bacterial isolates belonging to the Enterobacteriaceae family were obtained from milk samples from 257 cows with subclinical mastitis. Using microbiological tests, 53.85% (14/26) were identified as Escherichia coli, 15.38% (4/26) as Proteus mirabilis, 26.92% (7/26) as Klebsiella spp., and 3.85% (1/26) as Citrobacter spp. Of all the isolates, 61.54% (16/26) were positive in the ESBL screening test, of which 12.5% (2/16) were positive in the double-disc synergy test using three types of cephalosporins and amoxicillin/clavulanic acid. The two isolates were identified as Klebsiella spp. Among all the isolates, 53.85% (14/26) were positive for one or both ESBL-encoding genes, blaSHV and blaTEM; among these, 71.43% (10/14) were identified as E. coli. This study demonstrates that ESBL-producing bacteria can be found in raw cow milk from northeast Brazil. Cows with subclinical mastitis should be recognized as reservoirs of these strains, which can propagate to humans.
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Affiliation(s)
| | - Atzel Candido Acosta
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
| | | | | | - Rodolfo de Moraes Peixoto
- Federal Institute of Education, Science and Technology of the Sertão Pernambucano (IF SERTÃO-PE)-R. Maria Luzia de Araújo Gomes Cabral, 791-João de Deus, CEP, Petrolina, PE, 56316-686, Brazil
| | | | - José Wilton Pinheiro Junior
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
| | - Rinaldo Aparecido Mota
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
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7
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Malin JJ, von Wintersdorff CJH, Penders J, Savelkoul PHM, Wolffs PFG. Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals. Int J Antimicrob Agents 2023; 61:106716. [PMID: 36640847 DOI: 10.1016/j.ijantimicag.2023.106716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/22/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
The human gut microbiome is an important reservoir of antimicrobial resistance genes (ARGs), collectively termed the 'resistome'. To date, few studies have examined the dynamics of the human gut resistome in healthy individuals. Previously, the authors observed high rates of ARG acquisition and significant abundance shifts during international travel. In order to provide insight into commonly occurring dynamics, this study investigated longitudinal fluctuations in prevalent ARGs (cfxA, tetM and ermB) in the resistomes of non-travelling healthy volunteers. In addition, this study assessed the prevalence of acquirable ARGs (blaCTX-M, qnrB, qnrS, vanA and vanB) over time. Faecal samples from 23 participants were collected at baseline and after 2 and 4 weeks. DNA was isolated, and ARG quantification was performed by quantitative polymerase chain reaction adjusting for the total amount of bacterial 16S rDNA. vanA and qnrS were not detected in any of the samples, while the prevalence rates of vanB of non-enterococcal origin and qnrB were 73.9% and 5.7%, respectively. The ß-lactamase encoding blaCTX-M was detected in 17.4% of healthy participants. The results were compared with previous data from 122 travellers. ARG acquisitions observed in travellers were rare in non-travelling individuals during 4 weeks of follow-up, supporting the hypothesis of ARG acquisition during international travel. However, median -1.04- to 1.04-fold abundance changes were observed for 100% of cfxA, tetM and ermB, which did not differ from those found in travellers. Thus, common abundance shifts in prevalent ARGs of the gut resistome were found to occur independent of travel behaviour.
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Affiliation(s)
- Jakob J Malin
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands.
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
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8
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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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Su W, Wang X, Yang J, Yu Q, Li X, Zhang S, Li H. Multi-omics methods reveal that putrescine and cadaverine cause different degrees of enrichment of high-risk resistomes and opportunistic pathogens in the water and sediment of the Yellow River. ENVIRONMENTAL RESEARCH 2023; 219:115069. [PMID: 36549489 DOI: 10.1016/j.envres.2022.115069] [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: 10/22/2022] [Revised: 11/28/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Contamination of antibiotic resistomes due to animal carcass decay has become a serious environmental concern. However, the relationship between main metabolite compounds of corpse decomposition (i.e., putrescine and cadaverine) and antibiotic resistomes remains unclear. To tackle this issue, the response of antibiotic resistance genes (ARGs) and microbiome in aquatic environment to excess putrescine, cadaverine and a mixture of both based on laboratory simulation experiment was investigated by high-throughput quantitative PCR and amplicon sequencing methods. Our results showed putrescine and cadaverine led to the increasing of TC (total carbon) and TN (total nitrogen) both in water and sediment. Under the exposure of putrescine and cadaverine, the total abundance of mobile genetic elements (MGEs) and most ARGs in water was higher than in sediment. In particular, putrescine and cadaverine caused significantly different decreases in alpha diversity of microbial community in water and sediment compared with the control group. Microbial community structures both in water and sediment were also significantly affected by cadaverine and putrescine. Furthermore, putrescine and cadaverine led to different degrees of increases of high-risk ARGs (like mecA) and opportunistic pathogens (like Delftia) in sediment, promoting the prevalence of antibiotic resistant bacteria. In conclusion, our findings revealed the influences of main metabolites of carcass decay on microbiome and resistomes, providing references for risk assessment and pollution management.
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Affiliation(s)
- Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaocheng Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoshan Li
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou 404120, China
| | - Shiheng Zhang
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou 404120, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu, 730000, China.
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10
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Miranda CD, Concha C, Godoy FA, Lee MR. Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance. Antibiotics (Basel) 2022; 11:1487. [PMID: 36358142 PMCID: PMC9687057 DOI: 10.3390/antibiotics11111487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 08/27/2023] Open
Abstract
The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.
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Affiliation(s)
- Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Félix A. Godoy
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile
| | - Matthew R. Lee
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile
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11
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A One Health approach to antimicrobial resistance. ASIAN BIOMED 2022; 16:151-152. [PMID: 37551170 PMCID: PMC10321163 DOI: 10.2478/abm-2022-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Machado D, Barbosa JC, Almeida D, Andrade JC, Freitas AC, Gomes AM. Insights into the Antimicrobial Resistance Profile of a Next Generation Probiotic Akkermansia muciniphila DSM 22959. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159152. [PMID: 35954507 PMCID: PMC9367757 DOI: 10.3390/ijerph19159152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/05/2023]
Abstract
Akkermansia muciniphila is a Gram-negative intestinal anaerobic bacterium recently proposed as a novel probiotic candidate to be incorporated in food and pharmaceutical forms. Despite its multiple health benefits, the data addressing its antimicrobial susceptibility profile remain scarce. However, the absence of acquired resistance in probiotic strains is a compulsory criterion for its approval in the qualified presumption of safety list. This study aimed at characterizing the A. muciniphila DSM 22959 strain’s antimicrobial susceptibility profile using phenotypic and in silico approaches. To establish the phenotypic antimicrobial susceptibility profile of this strain, minimum inhibitory concentrations of eight antimicrobials were determined using broth microdilution and E-test methods. Additionally, the A. muciniphila DSM 22959 genome was screened using available databases and bioinformatics tools to identify putative antimicrobial resistance genes (ARG), virulence factors (VF), genomic islands (GI), and mobile genetic elements (MGE). The same categorization was obtained for both phenotypic methods. Resistance phenotype was observed for gentamicin, kanamycin, streptomycin, and ciprofloxacin, which was supported by the genomic context. No evidence was found of horizontal acquisition or potential transferability of the identified ARG and VF. Thus, this study provides new insights regarding the phenotypic and genotypic antimicrobial susceptibility profiles of the probiotic candidate A. muciniphila DSM 22959.
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Affiliation(s)
- Daniela Machado
- CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (D.M.); (J.C.B.); (D.A.); (A.C.F.); (A.M.G.)
| | - Joana Cristina Barbosa
- CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (D.M.); (J.C.B.); (D.A.); (A.C.F.); (A.M.G.)
| | - Diana Almeida
- CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (D.M.); (J.C.B.); (D.A.); (A.C.F.); (A.M.G.)
| | - José Carlos Andrade
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence:
| | - Ana Cristina Freitas
- CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (D.M.); (J.C.B.); (D.A.); (A.C.F.); (A.M.G.)
| | - Ana Maria Gomes
- CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (D.M.); (J.C.B.); (D.A.); (A.C.F.); (A.M.G.)
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13
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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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14
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Chiș AA, Rus LL, Morgovan C, Arseniu AM, Frum A, Vonica-Țincu AL, Gligor FG, Mureșan ML, Dobrea CM. Microbial Resistance to Antibiotics and Effective Antibiotherapy. Biomedicines 2022; 10:biomedicines10051121. [PMID: 35625857 PMCID: PMC9138529 DOI: 10.3390/biomedicines10051121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.
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15
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Iskandar K, Murugaiyan J, Hammoudi Halat D, Hage SE, Chibabhai V, Adukkadukkam S, Roques C, Molinier L, Salameh P, Van Dongen M. Antibiotic Discovery and Resistance: The Chase and the Race. Antibiotics (Basel) 2022; 11:antibiotics11020182. [PMID: 35203785 PMCID: PMC8868473 DOI: 10.3390/antibiotics11020182] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
The history of antimicrobial resistance (AMR) evolution and the diversity of the environmental resistome indicate that AMR is an ancient natural phenomenon. Acquired resistance is a public health concern influenced by the anthropogenic use of antibiotics, leading to the selection of resistant genes. Data show that AMR is spreading globally at different rates, outpacing all efforts to mitigate this crisis. The search for new antibiotic classes is one of the key strategies in the fight against AMR. Since the 1980s, newly marketed antibiotics were either modifications or improvements of known molecules. The World Health Organization (WHO) describes the current pipeline as bleak, and warns about the scarcity of new leads. A quantitative and qualitative analysis of the pre-clinical and clinical pipeline indicates that few antibiotics may reach the market in a few years, predominantly not those that fit the innovative requirements to tackle the challenging spread of AMR. Diversity and innovation are the mainstays to cope with the rapid evolution of AMR. The discovery and development of antibiotics must address resistance to old and novel antibiotics. Here, we review the history and challenges of antibiotics discovery and describe different innovative new leads mechanisms expected to replenish the pipeline, while maintaining a promising possibility to shift the chase and the race between the spread of AMR, preserving antibiotic effectiveness, and meeting innovative leads requirements.
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Affiliation(s)
- Katia Iskandar
- Department of Mathématiques Informatique et Télécommunications, Université Toulouse III, Paul Sabatier, INSERM, UMR 1295, 31000 Toulouse, France
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573, Lebanon;
- Faculty of Pharmacy, Lebanese University, Beirut 6573, Lebanon
- Correspondence: (K.I.); (D.H.H.)
| | - Jayaseelan Murugaiyan
- Department of Biological Sciences, SRM University–AP, Amaravati 522502, India; (J.M.); (S.A.)
| | - Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Bekaa Campus, Beirut 1103, Lebanon
- Correspondence: (K.I.); (D.H.H.)
| | - Said El Hage
- Faculty of Medicine, Lebanese University, Beirut 6573, Lebanon;
| | - Vindana Chibabhai
- Division of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg 2193, South Africa;
- Microbiology Laboratory, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa
| | - Saranya Adukkadukkam
- Department of Biological Sciences, SRM University–AP, Amaravati 522502, India; (J.M.); (S.A.)
| | - Christine Roques
- Laboratoire de Génie Chimique, Department of Bioprocédés et Systèmes Microbiens, Université Paul Sabtier, Toulouse III, UMR 5503, 31330 Toulouse, France;
| | - Laurent Molinier
- Department of Medical Information, Centre Hospitalier Universitaire, INSERM, UMR 1295, Université Paul Sabatier Toulouse III, 31000 Toulouse, France;
| | - Pascale Salameh
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573, Lebanon;
- Faculty of Medicine, Lebanese University, Beirut 6573, Lebanon;
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia 2408, Cyprus
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16
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Abstract
Antimicrobial resistance is one of the most serious threats to medical science. Food supply is recognized as a potential source of resistant bacteria, leading to the development of surveillance programs targeting primarily poultry, pork, and beef. These programs are limited in scope, not only in the commodities tested, but also in the organisms targeted (Escherichia coli, Salmonella, and Campylobacter); consequently, neither the breadth of food products available nor the organisms that may harbour clinically relevant and (or) mobile resistance genes are identified. Furthermore, there is an inadequate understanding of how international trade in food products contributes to the global dissemination of resistance. This is despite the recognized role of international travel in disseminating antimicrobial-resistant organisms, notably New Delhi metallo-beta-lactamase. An increasing number of studies describing antimicrobial-resistant organisms in a variety of imported foods are summarized in this review.
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Affiliation(s)
- Dongyun Jung
- Department of Food Science and Agricultural Chemistry, McGill University, Montreal, Quebec, Canada
| | - Beverly J Morrison
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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18
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Wu KC, Hua KF, Yu YH, Cheng YH, Cheng TT, Huang YK, Chang HW, Chen WJ. Antibacterial and Antibiofilm Activities of Novel Antimicrobial Peptides against Multidrug-Resistant Enterotoxigenic Escherichia Coli. Int J Mol Sci 2021; 22:ijms22083926. [PMID: 33920239 PMCID: PMC8070514 DOI: 10.3390/ijms22083926] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Post-weaning diarrhea due to enterotoxigenic Escherichia coli (ETEC) is a common disease of piglets and causes great economic loss for the swine industry. Over the past few decades, decreasing effectiveness of conventional antibiotics has caused serious problems because of the growing emergence of multidrug-resistant (MDR) pathogens. Various studies have indicated that antimicrobial peptides (AMPs) have potential to serve as an alternative to antibiotics owing to rapid killing action and highly selective toxicity. Our previous studies have shown that AMP GW-Q4 and its derivatives possess effective antibacterial activities against the Gram-negative bacteria. Hence, in the current study, we evaluated the antibacterial efficacy of GW-Q4 and its derivatives against MDR ETEC and their minimal inhibition concentration (MIC) values were determined to be around 2~32 μg/mL. Among them, AMP Q4-15a-1 with the second lowest MIC (4 μg/mL) and the highest minimal hemolysis concentration (MHC, 256 μg/mL), thus showing the greatest selectivity (MHC/MIC = 64) was selected for further investigations. Moreover, Q4-15a-1 showed dose-dependent bactericidal activity against MDR ETEC in time–kill curve assays. According to the cellular localization and membrane integrity analyses using confocal microscopy, Q4-15a-1 can rapidly interact with the bacterial surface, disrupt the membrane and enter cytosol in less than 30 min. Minimum biofilm eradication concentration (MBEC) of Q4-15a-1 is 4× MIC (16 μg/mL), indicating that Q4-15a-1 is effective against MDR ETEC biofilm. Besides, we established an MDR ETEC infection model with intestinal porcine epithelial cell-1 (IPEC-1). In this infection model, 32 μg/mL Q4-15a-1 can completely inhibit ETEC adhesion onto IPEC-1. Overall, these results suggested that Q4-15a-1 may be a promising antibacterial candidate for treatment of weaned piglets infected by MDR ETEC.
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Affiliation(s)
- Kang-Chi Wu
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
| | - Kuo-Feng Hua
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
| | - Yu-Hsiang Yu
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
| | - Yeong-Hsiang Cheng
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
| | - Ting-Ting Cheng
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
| | - Yao-Kuan Huang
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hui-Wen Chang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan;
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Jung Chen
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (K.-C.W.); (K.-F.H.); (Y.-H.Y.); (Y.-H.C.); (T.-T.C.); (Y.-K.H.)
- Correspondence:
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19
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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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20
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Thomas SG, Abajorga M, Glover MA, Wengert PC, Parthasarathy A, Savka MA, Wadsworth CB, Shipman PA, Hudson AO. Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669-Potential Zoonotic Pathogens Isolated from Spotted Turtles. Microorganisms 2020; 8:microorganisms8111805. [PMID: 33212916 PMCID: PMC7698337 DOI: 10.3390/microorganisms8111805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest challenges of the 21st century, and biofilm formation enables bacteria to resist antibiotic at much higher concentrations than planktonic cells. Earlier, we showed that the Gram-negative Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669 (closely related to C. freundii NBRC 12681) from infected spotted turtles (Clemmys guttata), formed biofilms and upregulated toxin expression on plastic surfaces, and were predicted to possess multiple antibiotic resistance genes. Here, we show that they each resist several antibiotics in the planktonic phase, but were susceptible to neomycin, and high concentrations of tetracycline and cotrimoxazole. The susceptibility of their biofilms to neomycin and cotrimoxazole was tested using the Calgary device. For A. hydrophila, the minimum inhibitory concentration (MIC) = 500-1000, and the minimum biofilm eradication concentration (MBEC) > 1000 μg/mL, using cotrimoxazole, and MIC = 32.3-62.5, and MBEC > 1000 μg/mL, using neomycin. For C. freundii MIC = 7.8-15.6, and, MBEC > 1000 μg/mL, using cotrimoxazole, and MIC = 7.8, and MBEC > 1000 μg/mL, using neomycin. Both A. hydrophila and C. portucalensis activated an acyl homoserine lactone (AHL) dependent biosensor, suggesting that quorum sensing could mediate biofilm formation. Their multidrug resistance in the planktonic form, and weak biofilm eradication even with neomycin and cotrimoxazole, indicate that A. hydrophila and C. portucalensis are potential zoonotic pathogens, with risks for patients living with implants.
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21
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Expression of a Shiga-Like Toxin during Plastic Colonization by Two Multidrug-Resistant Bacteria, Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669, Isolated from Endangered Turtles ( Clemmys guttata). Microorganisms 2020; 8:microorganisms8081172. [PMID: 32752245 PMCID: PMC7465454 DOI: 10.3390/microorganisms8081172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669 were isolated from endangered spotted turtles (Clemmys guttata). Whole-genome sequencing, annotation and phylogenetic analyses of the genomes revealed that the closest relative of RIT668 is A. hydrophila ATCC 7966 and Citrobacter portucalensis A60 for RIT669. Resistome analysis showed that A. hydrophila and C. freundii harbor six and 19 different antibiotic resistance genes, respectively. Both bacteria colonize polyethylene and polypropylene, which are common plastics, found in the environment and are used to fabricate medical devices. The expression of six biofilm-related genes—biofilm peroxide resistance protein (bsmA), biofilm formation regulatory protein subunit R (bssR), biofilm formation regulatory protein subunit S (bssS), biofilm formation regulator (hmsP), toxin-antitoxin biofilm protein (tabA) and transcriptional activator of curli operon (csgD)—and two virulence factors—Vi antigen-related gene (viaB) and Shiga-like toxin (slt-II)—was investigated by RT-PCR. A. hydrophila displayed a > 2-fold increase in slt-II expression in cells adhering to both polymers, C. freundii adhering on polyethylene displayed a > 2-fold, and on polypropylene a > 6-fold upregulation of slt-II. Thus, the two new isolates are potential pathogens owing to their drug resistance, surface colonization and upregulation of a slt-II-type diarrheal toxin on polymer surfaces.
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22
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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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23
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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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Baquero F, Coque TM, Martínez JL, Aracil-Gisbert S, Lanza VF. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance. Front Microbiol 2019; 10:2892. [PMID: 31921068 PMCID: PMC6927996 DOI: 10.3389/fmicb.2019.02892] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - José-Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sonia Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp. Microorganisms 2019; 7:microorganisms7090363. [PMID: 31540466 PMCID: PMC6780555 DOI: 10.3390/microorganisms7090363] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/24/2022] Open
Abstract
The evolution of multidrug resistant bacteria to the most diverse antimicrobials known so far pose a serious problem to global public health. Currently, microorganisms that develop resistant phenotypes to multiple drugs are associated with high morbidity and mortality. This resistance is encoded by a group of genes termed ‘bacterial resistome’, divided in intrinsic and extrinsic resistome. The first one refers to the resistance displayed on an organism without previous exposure to an antibiotic not involving horizontal genetic transfer, and it can be acquired via mutations. The latter, on the contrary, is acquired exclusively via horizontal genetic transfer involving mobile genetic elements that constitute the ‘bacterial mobilome’. This transfer is mediated by three different mechanisms: transduction, transformation, and conjugation. Recently, a problem of public health due to implications in the emergence of multi-drug resistance in Aeromonas spp. strains in water environments has been described. This is derived from the genetic material transfer via conjugation events. This is important, since bacteria that have acquired antibiotic resistance in natural environments can cause infections derived from their ingestion or direct contact with open wounds or mucosal tissue, which in turn, by their resistant nature, makes their eradication complex. Implications of the emergence of resistance in Aeromonas spp. by horizontal gene transfer on public health are discussed.
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Liu X, Zhang G, Liu Y, Lu S, Qin P, Guo X, Bi B, Wang L, Xi B, Wu F, Wang W, Zhang T. Occurrence and fate of antibiotics and antibiotic resistance genes in typical urban water of Beijing, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:163-173. [PMID: 30543942 DOI: 10.1016/j.envpol.2018.12.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/01/2018] [Accepted: 12/02/2018] [Indexed: 05/21/2023]
Abstract
The pollution of antibiotics and antibiotic resistance genes (ARGs) has been highlighted on a global scale because of their serious threats to the environment and human health. Typical urban water in cities with high population density are ideal mediums for the acquisition and spread of antibiotics and ARGs. The pollution level of a broad range of antibiotics and ARGs in hospital wastewater, groundwater and the Wenyu River, and their fates through three sewage treatment plants (STPs) were investigated in this study. The concentrations of the 11 detected antibiotics ranged from not detected (ND)-16800 ng L-1 in diverse water samples from Beijing, and fluoroquinolones were detected at the highest concentration, especially in the hospital samples. The maximum concentrations of antibiotics in STPs and hospital were 1-3 orders of magnitude higher than those in the surface water from Wenyu River and groundwater. Good removal efficiencies by treatment processes were observed for tetracyclines and quinolones, and low removal efficiencies were observed for sulfonamides and macrolides. These results also revealed that the sulfonamide resistance genes (sul1, sul2) and macrolide resistance genes (ermB) were detected at the highest relative abundances (7.11 × 10-2-1.18 × 10-1) in the water bodies of Beijing. It was worth noting that sul1 abundance was the highest in groundwater samples. The relative abundance of most ARGs in STPs exhibited a declining trend in the order of influent > secondary effluents > effluent. However, the relative abundance of sul 1, sul 2 and tetC in the effluent was higher than those in the influent. The incomplete removal of antibiotics and ARGs in STPs poses a serious threat to the receiving rivers, and affects ecosystem security. Overall, our findings provide favorable support for a further investigation of the spread and risk of antibiotics and ARGs from diverse sources (e.g., STPs and hospitals) to the aquatic environment.
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Affiliation(s)
- Xiaohui Liu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guodong Zhang
- School of Geography and Environment, Shandong Normal University, Jinan, Shandong, 250358, China
| | - Ying Liu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shaoyong Lu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Pan Qin
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiaochun Guo
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Bin Bi
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lei Wang
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria an Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Weiliang Wang
- School of Geography and Environment, Shandong Normal University, Jinan, Shandong, 250358, China
| | - Tingting Zhang
- School of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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Abstract
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
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Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM. In-depth resistome analysis by targeted metagenomics. MICROBIOME 2018; 6:11. [PMID: 29335005 PMCID: PMC5769438 DOI: 10.1186/s40168-017-0387-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/17/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. METHODS We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. CONCLUSIONS ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role.
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Affiliation(s)
- Val F Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
- National Center of Biotechnology, CSIC, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - José Luís Martínez
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain
- National Center of Biotechnology, CSIC, Madrid, Spain
| | | | - Bruno González-Zorn
- Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Bacteriology Laboratory, Hospital Bichat, AP-HP, Paris, France
| | - Antonio Sánchez-Valenzuela
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Stanislav Dusko Ehrlich
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
- Center of Host Microbiome Interactions, King's College, London, UK
| | - Sean Kennedy
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
- Present Address: Bioinformatics and Biostatistics HUB, C3BI and Biomics Pole, CITECH Pasteur Institute, Centre François Jacob, Paris, France
| | - Etienne Ruppé
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Bacteriology Laboratory, Hospital Bichat, AP-HP, Paris, France
- MGP MetaGénoPolis, INRA, University of Paris-Saclay, Jouy-en-Josas, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center, Utrecht, Netherlands
- Present Address: Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rob J Willems
- Department of Medical Microbiology, University Medical Center, Utrecht, Netherlands
| | - Fernando de la Cruz
- Department of Molecular Biology, University of Cantabria, Santander, Spain
- Institute of Biomedicine and Biotechnology of Cantabria, IBBTEC (UC-CSIC), Santander, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.
- Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC), Madrid, Spain.
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
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Brown-Jaque M, Calero-Cáceres W, Espinal P, Rodríguez-Navarro J, Miró E, González-López JJ, Cornejo T, Hurtado JC, Navarro F, Muniesa M. Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates. Int J Antimicrob Agents 2017; 51:434-442. [PMID: 29180282 DOI: 10.1016/j.ijantimicag.2017.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/07/2017] [Accepted: 11/18/2017] [Indexed: 12/31/2022]
Abstract
Phage particles have emerged as elements with the potential to mobilise antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. This study aimed to determine the occurrence of ARGs in phage particles present in faecal matter and induced from strains isolated from faeces. Nine ARGs (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 faecal samples obtained from healthy individuals who had not received antibiotic treatment or travelled abroad in the 3 months prior to sample collection. On the suspicion that the detected particles originated from bacterial flora, 82 Escherichia coli and Klebsiella pneumoniae isolates possessing at least one identified ARG (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, armA, qnrA, qnrS and sul1) were isolated and their capacity to produce phage particles carrying these ARGs following induction was evaluated. Of 150 samples, 72.7% were positive for at least one ARG, with blaTEM and blaCTX-M-9 group being the most prevalent and abundant. Of the 82 isolates, 51 (62%) showed an increase in the number of copies of the respective ARG in the phage fraction following induction, with blaTEM, blaCTX-M-1 group, blaCTX-M-9 group and sul1 being the most abundant. Phages induced from the isolates were further purified and visualised using microscopy and their DNA showed ARG levels of up to 1010 gene copies/mL. This study highlights the abundance of phage particles harbouring ARGs and indicates that bacterial strains in the intestinal habitat could be source of these particles.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Judith Rodríguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Juan José González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Thais Cornejo
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan Carlos Hurtado
- ISGlobal, Barcelona Centre for International Health Research, Department of Microbiology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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30
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Rodríguez MM, Herman R, Ghiglione B, Kerff F, D’Amico González G, Bouillenne F, Galleni M, Handelsman J, Charlier P, Gutkind G, Sauvage E, Power P. Crystal structure and kinetic analysis of the class B3 di-zinc metallo-β-lactamase LRA-12 from an Alaskan soil metagenome. PLoS One 2017; 12:e0182043. [PMID: 28750094 PMCID: PMC5531557 DOI: 10.1371/journal.pone.0182043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 12/02/2022] Open
Abstract
We analyzed the kinetic properties of the metagenomic class B3 β-lactamase LRA-12, and determined its crystallographic structure in order to compare it with prevalent metallo-β-lactamases (MBLs) associated with clinical pathogens. We showed that LRA-12 confers extended-spectrum resistance on E. coli when expressed from recombinant clones, and the MIC values for carbapenems were similar to those observed in enterobacteria expressing plasmid-borne MBLs such as VIM, IMP or NDM. This was in agreement with the strong carbapenemase activity displayed by LRA-12, similar to GOB β-lactamases. Among the chelating agents evaluated, dipicolinic acid inhibited the enzyme more strongly than EDTA, which required pre-incubation with the enzyme to achieve measurable inhibition. Structurally, LRA-12 contains the conserved main structural features of di-zinc class B β-lactamases, and presents unique structural signatures that differentiate this enzyme from others within the family: (i) two loops (α3-β7 and β11-α5) that could influence antibiotic entrance and remodeling of the active site cavity; (ii) a voluminous catalytic cavity probably responsible for the high hydrolytic efficiency of the enzyme; (iii) the absence of disulfide bridges; (iv) a unique Gln116 at metal-binding site 1; (v) a methionine residue at position 221that replaces Cys/Ser found in other B3 β-lactamases in a predominantly hydrophobic environment, likely playing a role in protein stability. The structure of LRA-12 indicates that MBLs exist in wild microbial populations in extreme environments, or environments with low anthropic impact, and under the appropriate antibiotic selective pressure could be captured and disseminated to pathogens.
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Affiliation(s)
- María Margarita Rodríguez
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Raphaël Herman
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Barbara Ghiglione
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Frédéric Kerff
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Gabriela D’Amico González
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fabrice Bouillenne
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Moreno Galleni
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Jo Handelsman
- Department of Molecular, Cellular and Development Biology, Yale University, New Haven, CT, United States of America
| | - Paulette Charlier
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Gabriel Gutkind
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eric Sauvage
- InBioS, Centre d’Ingénierie des Protéines, Université de Liège, Liège, Belgium
| | - Pablo Power
- Cátedra de Microbiología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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31
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Yılmaz Ç, Özcengiz G. Antibiotics: Pharmacokinetics, toxicity, resistance and multidrug efflux pumps. Biochem Pharmacol 2017; 133:43-62. [DOI: 10.1016/j.bcp.2016.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/14/2016] [Indexed: 02/03/2023]
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32
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Klahn P, Brönstrup M. Bifunctional antimicrobial conjugates and hybrid antimicrobials. Nat Prod Rep 2017; 34:832-885. [PMID: 28530279 DOI: 10.1039/c7np00006e] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.
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Affiliation(s)
- P Klahn
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany. and Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - M Brönstrup
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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33
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McArthur AG, Tsang KK. Antimicrobial resistance surveillance in the genomic age. Ann N Y Acad Sci 2016; 1388:78-91. [PMID: 27875856 DOI: 10.1111/nyas.13289] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022]
Abstract
The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings. To do so, efforts must be focused toward exploiting the advancements of genome sequencing and information technology. Currently, AMR bioinformatics software and databases reflect different scopes and functions, each with its own strengths and weaknesses. A review of the available tools reveals common approaches and reference data but also reveals gaps in our curated data, models, algorithms, and data-sharing tools that must be addressed to conquer the limitations and areas of unmet need within the AMR research field before DNA sequencing can be fully exploited for AMR surveillance and improved clinical outcomes.
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Affiliation(s)
- Andrew G McArthur
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Kara K Tsang
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
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34
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Martínez JL, Coque TM, Lanza VF, de la Cruz F, Baquero F. Genomic and metagenomic technologies to explore the antibiotic resistance mobilome. Ann N Y Acad Sci 2016; 1388:26-41. [PMID: 27861983 DOI: 10.1111/nyas.13282] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome. High-throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.
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Affiliation(s)
- José L Martínez
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
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35
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Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FSL, Wright GD, McArthur AG. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2016; 45:D566-D573. [PMID: 27789705 PMCID: PMC5210516 DOI: 10.1093/nar/gkw1004] [Citation(s) in RCA: 1529] [Impact Index Per Article: 191.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/30/2016] [Accepted: 10/17/2016] [Indexed: 11/30/2022] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis.
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Affiliation(s)
- Baofeng Jia
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Amogelang R Raphenya
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Brian Alcock
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Peiyao Guo
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Kara K Tsang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Briony A Lago
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Biren M Dave
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sheldon Pereira
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Arjun N Sharma
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sachin Doshi
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Mélanie Courtot
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Raymond Lo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Laura E Williams
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS U.S. National Poultry Research Center, U.S. Department of Agriculture, Athens, GA 30605, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS U.S. National Poultry Research Center, U.S. Department of Agriculture, Athens, GA 30605, USA
| | - Tariq Elsayegh
- School of Medicine, Royal College of Surgeons in Ireland, Dublin 2, Republic of Ireland
| | - Daim Sardar
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Erin L Westman
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Andrew C Pawlowski
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Timothy A Johnson
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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36
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Gillings MR. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 2016; 1389:20-36. [DOI: 10.1111/nyas.13213] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Michael R. Gillings
- Genes to Geoscience Research Centre, Department of Biological Sciences Macquarie University Sydney New South Wales Australia
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Using MALDI-TOF Mass Spectrometry to Identify Drug Resistant Staphylococcal Isolates from Nonhospital Environments in Brunei Darussalam. Interdiscip Perspect Infect Dis 2016; 2016:8685602. [PMID: 27127505 PMCID: PMC4834169 DOI: 10.1155/2016/8685602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/07/2016] [Indexed: 11/30/2022] Open
Abstract
Drug resistant bacteria have been a growing threat to the community and hospitals due to the misuse of antibiotics by humans, industrialization, and lack of novel antimicrobials currently available. Little is known about the prevalence of drug resistant bacteria in nonhealthcare environments in Brunei Darussalam and about how antibiotic resistant genes are transferred within these environments. Human contact points from different types of environments in Brunei Darussalam, varying from urban to jungle settings, were swabbed and cultured onto selective media to isolate staphylococci bacteria before performing antimicrobial susceptibility testing on the isolates. The identity of the isolates was determined using MALDI-TOF mass spectrometry (MS). Staphylococci isolates resistant to oxacillin were further tested for their minimum inhibitory concentration (MIC). PCR analysis of the mecA gene, a gene that confers resistance to oxacillin, is done to determine the level of resistance to oxacillin. Ten different staphylococcal species were identified by MALDI-TOF-MS analysis. Out of the 36 staphylococci isolates, 24 were resistant to multiple antibiotics including two isolates which were oxacillin resistant. Some staphylococci isolates had similar antibiotic resistance profiles to other staphylococci isolates of different species in the same location. This work provides the first-ever evidence of drug resistant staphylococci in the nonhospital environment in Brunei Darussalam.
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38
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Medvedeva ES, Davydova MN, Mouzykantov AA, Baranova NB, Grigoreva TY, Siniagina MN, Boulygina EA, Chernova OA, Chernov VM. Genomic and proteomic profiles of Acholeplasma laidlawii strains differing in sensitivity to ciprofloxacin. DOKL BIOCHEM BIOPHYS 2016; 466:23-7. [DOI: 10.1134/s1607672916010075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/23/2022]
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39
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Ruppé E, Baud D, Schicklin S, Guigon G, Schrenzel J. Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. Future Microbiol 2016; 11:427-39. [PMID: 26934540 DOI: 10.2217/fmb.15.144] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The increasing burden of multidrug-resistant bacteria affects the management of several infections. In order to prescribe adequate antibiotics, clinicians facing severe infections such as hospital-acquired pneumonia (HAP) need to promptly identify the pathogens and know their antibiotic susceptibility profiles (AST), which with conventional microbiology currently requires 24 and 48 h, respectively. Clinical metagenomics, based on whole genome sequencing of clinical samples, could improve the diagnosis of HAP, however, many obstacles remain to be overcome, namely the turn-around time, the quantification of pathogens, the choice of antibiotic resistance determinants (ARDs), the inference of the AST from metagenomic data and the linkage between ARDs and their host. Here, we propose to tackle those issues in a bottom-up, clinically driven approach.
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Affiliation(s)
- Etienne Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | - Damien Baud
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | - Stéphane Schicklin
- Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France
| | - Ghislaine Guigon
- Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland.,Bacteriology Lab, Service of Laboratory Medicine, Department of Genetics & Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
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40
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Klahn P, Brönstrup M. New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development. Curr Top Microbiol Immunol 2016; 398:365-417. [PMID: 27704270 DOI: 10.1007/82_2016_501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of bacterial resistance against current antibiotic drugs necessitates a continuous renewal of the arsenal of efficacious drugs. This imperative has not been met by the output of antibiotic research and development of the past decades for various reasons, including the declining efforts of large pharma companies in this area. Moreover, the majority of novel antibiotics are chemical derivatives of existing structures that represent mostly step innovations, implying that the available chemical space may be exhausted. This review negates this impression by showcasing recent achievements in lead finding and optimization of antibiotics that have novel or unexplored chemical structures. Not surprisingly, many of the novel structural templates like teixobactins, lysocin, griselimycin, or the albicidin/cystobactamid pair were discovered from natural sources. Additional compounds were obtained from the screening of synthetic libraries and chemical synthesis, including the gyrase-inhibiting NTBI's and spiropyrimidinetrione, the tarocin and targocil inhibitors of wall teichoic acid synthesis, or the boronates and diazabicyclo[3.2.1]octane as novel β-lactamase inhibitors. A motif that is common to most clinically validated antibiotics is that they address hotspots in complex biosynthetic machineries, whose functioning is essential for the bacterial cell. Therefore, an introduction to the biological targets-cell wall synthesis, topoisomerases, the DNA sliding clamp, and membrane-bound electron transport-is given for each of the leads presented here.
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Affiliation(s)
- Philipp Klahn
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
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41
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Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics 2015. [PMID: 26576951 DOI: 10.1186/s12864-015-2153-5/figures/9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems. RESULTS Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes. CONCLUSIONS This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.
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Affiliation(s)
- Chandan Pal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden.
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42
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Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics 2015; 16:964. [PMID: 26576951 PMCID: PMC4650350 DOI: 10.1186/s12864-015-2153-5] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems. RESULTS Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes. CONCLUSIONS This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.
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Affiliation(s)
- Chandan Pal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden.
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Gillings MR, Paulsen IT, Tetu SG. Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics. Genes (Basel) 2015; 6:841-57. [PMID: 26371047 PMCID: PMC4584332 DOI: 10.3390/genes6030841] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Abstract
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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44
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Moura de Sousa J, Sousa A, Bourgard C, Gordo I. Potential for adaptation overrides cost of resistance. Future Microbiol 2015; 10:1415-31. [PMID: 26343510 DOI: 10.2217/fmb.15.61] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To investigate the cost of antibiotic resistance versus the potential for resistant clones to adapt in maintaining polymorphism for resistance. MATERIALS & METHODS Experimental evolution of Escherichia coli carrying different resistance alleles was performed under an environment devoid of antibiotics and evolutionary parameters estimated from their frequencies along time. RESULTS & CONCLUSION Costly resistance mutations were found to coexist with lower cost resistances for hundreds of generations, contrary to the hypothesis that the cost of a resistance dictates its extinction. Estimated evolutionary parameters for the different resistance backgrounds suggest a higher adaptive potential of clones with costly antibiotic resistance mutations, overriding their initial cost of resistance and allowing their maintenance in the absence of drugs.
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Affiliation(s)
| | - Ana Sousa
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, Portugal
| | - Catarina Bourgard
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, Portugal
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45
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Abstract
The health care system is challenged by another serious issue: antimicrobial resistance. Clostridium difficile is the most common infection in health care institutions and is becoming resistant to standard treatment. Carbapenem-resistant enterobacteriaceae can be found in almost every state in the United States. Confounding the antimicrobial resistance issue is the fact that few new antimicrobials are being developed by pharmaceutical companies. The situation is so critical that the White House issued a strategic plan in September 2014 to deal with antimicrobial resistance. One challenge in that plan is to better understand how microbes have become resistant. Microbes have developed defense mechanisms such as bacteriophages and bacteriocins to survive for thousands of years. If science can start to use these mechanisms to help combat resistant organisms in combination with antimicrobials and strong epidemiological interventions, the battle against antimicrobial resistance may succeed.
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Affiliation(s)
- Nancy Munro
- Nancy Munro is Senior Acute Care Nurse Practitioner, Critical Care Medicine Department, National Institutes of Health, 10 Center Dr, Bldg 10-CRC Room 3-3677, Bethesda, MD 20892
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46
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von Wintersdorff CJH, Penders J, Stobberingh EE, Oude Lashof AML, Hoebe CJPA, Savelkoul PHM, Wolffs PFG. High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerg Infect Dis 2014. [PMID: 24655888 PMCID: PMC3966371 DOI: 10.3201/eid2004.131718] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated the effect of international travel on the gut resistome of 122 healthy travelers from the Netherlands by using a targeted metagenomic approach. Our results confirm high acquisition rates of the extended-spectrum β-lactamase encoding gene blaCTX-M, documenting a rise in prevalence from 9.0% before travel to 33.6% after travel (p<0.001). The prevalence of quinolone resistance encoding genes qnrB and qnrS increased from 6.6% and 8.2% before travel to 36.9% and 55.7% after travel, respectively (both p<0.001). Travel to Southeast Asia and the Indian subcontinent was associated with the highest acquisition rates of qnrS and both blaCTX-M and qnrS, respectively. Investigation of the associations between the acquisitions of the blaCTX-M and qnr genes showed that acquisition of a blaCTX-M gene was not associated with that of a qnrB (p = 0.305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance.
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von Wintersdorff CJH, Penders J, Stobberingh EE, Oude Lashof AML, Hoebe CJPA, Savelkoul PHM, Wolffs PFG. High rates of antimicrobial drug resistance gene acquisition after international travel, The Netherlands. Emerg Infect Dis 2014; 20:649-57. [PMID: 24655888 DOI: 10.3201/eid.2004.131718] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We investigated the effect of international travel on the gut resistome of 122 healthy travelers from the Netherlands by using a targeted metagenomic approach. Our results confirm high acquisition rates of the extended-spectrum β-lactamase encoding gene blaCTX-M, documenting a rise in prevalence from 9.0% before travel to 33.6% after travel (p<0.001). The prevalence of quinolone resistance encoding genes qnrB and qnrS increased from 6.6% and 8.2% before travel to 36.9% and 55.7% after travel, respectively (both p<0.001). Travel to Southeast Asia and the Indian subcontinent was associated with the highest acquisition rates of qnrS and both blaCTX-M and qnrS, respectively. Investigation of the associations between the acquisitions of the blaCTX-M and qnr genes showed that acquisition of a blaCTX-M gene was not associated with that of a qnrB (p = 0.305) or qnrS (p = 0.080) gene. These findings support the increasing evidence that travelers contribute to the spread of antimicrobial drug resistance.
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Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME JOURNAL 2014; 9:1269-79. [PMID: 25500508 PMCID: PMC4438328 DOI: 10.1038/ismej.2014.226] [Citation(s) in RCA: 790] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital, Truro, UK
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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Vaz-Moreira I, Nunes OC, Manaia CM. Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiol Rev 2014; 38:761-78. [PMID: 24484530 DOI: 10.1111/1574-6976.12062] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 12/14/2022] Open
Abstract
Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.
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Affiliation(s)
- Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Dr. António Bernardino Almeida, Porto, Portugal
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50
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Smith AME, Brennan JD. Simultaneous inhibition assay for human and microbial kinases via MALDI-MS/MS. Chembiochem 2014; 15:587-94. [PMID: 24478228 DOI: 10.1002/cbic.201300739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Indexed: 11/05/2022]
Abstract
Selective inhibition of one kinase over another is a critical issue in drug development. For antimicrobial development, it is particularly important to selectively inhibit bacterial kinases, which can phosphorylate antimicrobial compounds such as aminoglycosides, without affecting human kinases. Previous work from our group showed the development of a MALDI-MS/MS assay for the detection of small molecule modulators of the bacterial aminoglycoside kinase APH3'IIIa. Herein, we demonstrate the development of an enhanced kinase MALDI-MS/MS assay involving simultaneous assaying of two kinase reactions, one for APH3'IIIa, and the other for human protein kinase A (PKA), which leads to an output that provides direct information on selectivity and mechanism of action. Specificity of the respective enzyme substrates were verified, and the assay was validated through generation of Z'-factors of 0.55 for APH3'IIIa with kanamycin and 0.60 for PKA with kemptide. The assay was used to simultaneously screen a kinase-directed library of mixtures of ten compounds each against both enzymes, leading to the identification of selective inhibitors for each enzyme as well as one non-selective inhibitor following mixture deconvolution.
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Affiliation(s)
- Anne Marie E Smith
- Biointerfaces Institute and Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S 4L8 (Canada), Homepage: brennanlab.ca; biointerfaces.mcmaster.ca
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