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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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102
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Wang Y, Shen B, Zhang Z, Chen Y, Zhu L, Zhang Y, Huang H, Jiang L. Multifunctional fluorescent gold nanoclusters with enhanced aggregation-induced emissions (AIEs) and excellent antibacterial effect for bacterial imaging and wound healing. BIOMATERIALS ADVANCES 2022; 137:212841. [PMID: 35929270 DOI: 10.1016/j.bioadv.2022.212841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/11/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
To explore new alternatives to combat increasing risk of bacterial infection, in this work, a cationic antimicrobial peptide (HHC10) and glutathione (GSH) co-ligand protected ultra-small gold nanoclusters (Au NCs) was constructed by a simple one-pot method. The intrinsic luminescent property of GSH-protected Au NCs (AuxGSH) endowed enhanced aggregation-induced emissions (AIEs) of co-ligand-protected Au NCs (AuxGSH-HHC10), which exhibited a very strong orange luminescence. Based on the AIE effect, for one thing, AuxGSH could be applied to rapidly and selectively detect Gram-positive bacteria. For another, AuxGSH-HHC10 exhibited potential for multicolor imaging of both Gram-negative and Gram-positive bacteria. Besides, as-synthesized AuxGSH-HHC10 could act as potent nanoantibiotics against both Gram-negative and Gram-positive bacteria, which could not only avoid drug tolerance but also be effective toward drug-resistance bacteria. The antibacterial mechanism indicated that the synergetic effect of the generation of reactive oxygen species (ROS), binding with DNA, and broad-spectrum antibacterial activity of HHC10 led to the membrane damage, depolarization, and interference of biological function, thus enhancing the antibacterial effect. More importantly, such an Au NCs could realize excellent therapeutic outcomes for wound healing in vivo, and showed good biocompatibility and biosafety toward health tissues. The results will provide a great potential for the application of Au NCs for imaging-guided antibacterial platform.
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Affiliation(s)
- Yuxian Wang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Bowen Shen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengyi Zhang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yao Chen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yangheng Zhang
- Department of Periodontology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - He Huang
- College of Pharmaceutical Science, Nanjing Tech University, Nanjing 211816, China; School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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103
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Hsu YJ, Nain A, Lin YF, Tseng YT, Li YJ, Sangili A, Srivastava P, Yu HL, Huang YF, Huang CC, Chang HT. Self-redox reaction driven in situ formation of Cu 2O/Ti 3C 2T x nanosheets boost the photocatalytic eradication of multi-drug resistant bacteria from infected wound. J Nanobiotechnology 2022; 20:235. [PMID: 35590324 PMCID: PMC9117998 DOI: 10.1186/s12951-022-01428-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MXenes with interesting optical and electrical properties have been attractive in biomedical applications such as antibacterial and anticancer agents, but their low photogeneration efficiency of reactive oxygen species (ROS) and poor stability are major concerns against microbial resistance. METHODS Water-dispersible single layer Ti3C2Tx-based MXene through etching tightly stacked MAX phase precursor using a minimally intensive layer delamination method. After addition of Cu(II) ions, the adsorbed Cu(II) ions underwent self-redox reactions with the surface oxygenated moieties of MXene, leading to in situ formation of Cu2O species to yield Cu2O/Ti3C2Tx nanosheets (heterostructures). RESULTS Under NIR irradiation, the Cu2O enhanced generation of electron-hole pairs, which boosted the photocatalytic production of superoxide and subsequent transformation into hydrogen peroxide. Broad-spectrum antimicrobial performance of Cu2O/Ti3C2Tx nanosheets with sharp edges is attributed to the direct contact-induced membrane disruption, localized photothermal therapy, and in situ generated cytotoxic free radicals. The minimum inhibitory concentration of Cu2O/Ti3C2Tx nanosheets reduced at least tenfold upon NIR laser irradiation compared to pristine Cu2O/Ti3C2Tx nanosheets. The Cu2O/Ti3C2Tx nanosheets were topically administrated on the methicillin-resistant Staphylococcus aureus (MRSA) infected wounds on diabetic mice. CONCLUSION Upon NIR illumination, Cu2O/Ti3C2Tx nanosheets eradicated MRSA and their associated biofilm to promote wound healing. The Cu2O/Ti3C2Tx nanosheets with superior catalytic and photothermal properties have a great scope as an effective antimicrobial modality for the treatment of infected wounds.
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Affiliation(s)
- Ya-Ju Hsu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Amit Nain
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Feng Lin
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Ting Tseng
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Jia Li
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Arumugam Sangili
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Pavitra Srivastava
- School of Basic Sciences, Indian Institute of Technology, Kamand campus, Mandi, Himachal Pradesh, 175005, India
| | - Hui-Ling Yu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Fen Huang
- Institute of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202301, Taiwan. .,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
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104
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Liu H, Dong L, Zhao Y, Meng L, Wang J, Wang C, Zheng N. Antimicrobial Susceptibility, and Molecular Characterization of Staphylococcus aureus Isolated From Different Raw Milk Samples in China. Front Microbiol 2022; 13:840670. [PMID: 35633704 PMCID: PMC9136321 DOI: 10.3389/fmicb.2022.840670] [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: 12/21/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is one of the main pathogens in different raw milk and dairy products, which may lead to economic losses. Staphylococcus aureus is a significant and costly public health concern because it may enter the human food chain and contaminate milk causing foodborne illness. This study aimed to investigate the prevalence, antimicrobial susceptibility and virulence genes of S. aureus in raw milks. In total, 125 raw milk samples collected from goat (n = 50), buffalo (n = 25), camel (n = 25), and yak (n = 25) were collected from 5 provinces in China in 2016. Out of 125 samples, 36 (28.8%) S. aureus were isolated (16 from goat, 9 from buffalo, 6 from camel, and 5 from yak). Out of 36 S. aureus, 26 strains (26/36, 72.2%) showed antibiotics resistance, and 6 strains isolated from goats were identified as methicillin-resistant S. aureus (MRSA). The antimicrobial resistance against Penicillin G, tetracycline and gentamicin was 50% (18/36), 41.7% (15/36), and 36.1% (13/36), respectively. 19 S. aureus (52.8%) were considered as multidrug resistant. The highest prevalence of resistant S. aureus was observed in goat milk (13/36, 36.1%). Among the 36 strains, 16 isolates harbored three or more resistant genes. The resistance genes were detected in 25 S. aureus, including 13 strains in goat, 5 strains in buffalo, 4 strains in camel, and 3 strains in yak. Among the 26 resistant strains, 61.5% of isolates harbored three or more resistant genes. The resistance genes were detected in 25 S. aureus, including 13 strains in goat milk, 5 strains in buffalo milk, 4 strains in camel milk, and 3 strains in yak milk. The most predominant resistance genes were blaZ (18/26, 69.2%), aac6'-aph2″ (13/26, 50.0%), and tet(M) (10/26, 38.5%). The mecA, ant(6)-Ia and fexA gene were only detected in S. aureus from goat milk. The most predominant toxin gene were sec (8/26, 30.8%). The majority of S. aureus were multidrug resistant and carried multiple virulence genes, which may pose potential risk to public health. Our findings indicated that the prevalence and antimicrobial resistance of S. aureus was a serious concern in different raw milks in China, especially goat milks.
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Affiliation(s)
- Huimin Liu
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture—Milk and Dairy Product Inspection Center (Beijing), Beijing, China
| | - Lei Dong
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture—Milk and Dairy Product Inspection Center (Beijing), Beijing, China
| | - Yankun Zhao
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Lu Meng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture—Milk and Dairy Product Inspection Center (Beijing), Beijing, China
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture—Milk and Dairy Product Inspection Center (Beijing), Beijing, China
| | - Cheng Wang
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture—Milk and Dairy Product Inspection Center (Beijing), Beijing, China
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105
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Waskito LA, Rezkitha YAA, Vilaichone RK, Wibawa IDN, Mustika S, Sugihartono T, Miftahussurur M. Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge. Antibiotics (Basel) 2022; 11:antibiotics11050654. [PMID: 35625299 PMCID: PMC9137939 DOI: 10.3390/antibiotics11050654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 01/15/2023] Open
Abstract
The burden of bacterial resistance to antibiotics affects several key sectors in the world, including healthcare, the government, and the economic sector. Resistant bacterial infection is associated with prolonged hospital stays, direct costs, and costs due to loss of productivity, which will cause policy makers to adjust their policies. Current widely performed procedures for the identification of antibiotic-resistant bacteria rely on culture-based methodology. However, some resistance determinants, such as free-floating DNA of resistance genes, are outside the bacterial genome, which could be potentially transferred under antibiotic exposure. Metagenomic and metatranscriptomic approaches to profiling antibiotic resistance offer several advantages to overcome the limitations of the culture-based approach. These methodologies enhance the probability of detecting resistance determinant genes inside and outside the bacterial genome and novel resistance genes yet pose inherent challenges in availability, validity, expert usability, and cost. Despite these challenges, such molecular-based and bioinformatics technologies offer an exquisite advantage in improving clinicians’ diagnoses and the management of resistant infectious diseases in humans. This review provides a comprehensive overview of next-generation sequencing technologies, metagenomics, and metatranscriptomics in assessing antimicrobial resistance profiles.
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Affiliation(s)
- Langgeng Agung Waskito
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia;
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Department of Physiology and Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Yudith Annisa Ayu Rezkitha
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Department of Internal Medicine, Faculty of Medicine, Universitas Muhammadiyah Surabaya, Surabaya 60115, Indonesia
| | - Ratha-korn Vilaichone
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Khlong Nueng 12120, Pathumthani, Thailand;
- Digestive Diseases Research Center (DRC), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Department of Medicine, Chulabhorn International College of Medicine (CICM), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
| | - I Dewa Nyoman Wibawa
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Sanglah General Hospital, Faculty of Medicine, Universitas Udayana, Denpasar 80232, Indonesia;
| | - Syifa Mustika
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia;
| | - Titong Sugihartono
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya 60115, Indonesia;
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia;
- Correspondence: ; Tel.: +62-31-502-3865; Fax: +62-31-502-3865
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106
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Oluwole DO, Coleman L, Buchanan W, Chen T, La Ragione RM, Liu LX. Antibiotics-Free Compounds for Chronic Wound Healing. Pharmaceutics 2022; 14:pharmaceutics14051021. [PMID: 35631606 PMCID: PMC9143489 DOI: 10.3390/pharmaceutics14051021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/04/2022] [Accepted: 05/05/2022] [Indexed: 02/05/2023] Open
Abstract
The rapid rise in the health burden associated with chronic wounds is of great concern to policymakers, academia, and industry. This could be attributed to the devastating implications of this condition, and specifically, chronic wounds which have been linked to invasive microbial infections affecting patients' quality of life. Unfortunately, antibiotics are not always helpful due to their poor penetration of bacterial biofilms and the emergence of antimicrobial resistance. Hence, there is an urgent need to explore antibiotics-free compounds/formulations with proven or potential antimicrobial, anti-inflammatory, antioxidant, and wound healing efficacy. The mechanism of antibiotics-free compounds is thought to include the disruption of the bacteria cell structure, preventing cell division, membrane porins, motility, and the formation of a biofilm. Furthermore, some of these compounds foster tissue regeneration by modulating growth factor expression. In this review article, the focus is placed on a number of non-antibiotic compounds possessing some of the aforementioned pharmacological and physiological activities. Specific interest is given to Aloevera, curcumin, cinnamaldehyde, polyhexanide, retinoids, ascorbate, tocochromanols, and chitosan. These compounds (when alone or in formulation with other biologically active molecules) could be a dependable alternative in the management or prevention of chronic wounds.
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Affiliation(s)
- David O. Oluwole
- Chemical and Process Engineering Department, Faculty of Engineering and Physical Science, University of Surrey, Guildford GU2 7XH, UK; (L.C.); (T.C.)
- Correspondence: (D.O.O.); (L.X.L.)
| | - Lucy Coleman
- Chemical and Process Engineering Department, Faculty of Engineering and Physical Science, University of Surrey, Guildford GU2 7XH, UK; (L.C.); (T.C.)
| | | | - Tao Chen
- Chemical and Process Engineering Department, Faculty of Engineering and Physical Science, University of Surrey, Guildford GU2 7XH, UK; (L.C.); (T.C.)
| | - Roberto M. La Ragione
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK;
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Lian X. Liu
- Chemical and Process Engineering Department, Faculty of Engineering and Physical Science, University of Surrey, Guildford GU2 7XH, UK; (L.C.); (T.C.)
- Correspondence: (D.O.O.); (L.X.L.)
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107
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Koorakula R, Schiavinato M, Ghanbari M, Wegl G, Grabner N, Koestelbauer A, Klose V, Dohm JC, Domig KJ. Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives. Front Microbiol 2022; 13:833790. [PMID: 35495718 PMCID: PMC9048739 DOI: 10.3389/fmicb.2022.833790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.
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Affiliation(s)
- Raju Koorakula
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria.,Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI), Tulln, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | | | | | | | | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Konrad J Domig
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
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108
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Zhou Z, Li J, Tan L, Liu X, Zheng Y, Cui Z, Li C, Yeung KWK, Li Z, Liang Y, Zhu S, Wu S. Using tea nanoclusters as β-lactamase inhibitors to cure multidrug-resistant bacterial pneumonia: A promising therapeutic strategy by Chinese materioherbology. FUNDAMENTAL RESEARCH 2022; 2:496-504. [PMID: 38933406 PMCID: PMC11197604 DOI: 10.1016/j.fmre.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022] Open
Abstract
β-lactamase, a kind of hydrolase in multi-drug resistant pathogens, can hydrolyze β-lactam antibiotics and make these kinds of antibiotics invalid. Small-molecular inhibitors about the enzyme and their mechanism are widely investigated but they may result in unavoidable adverse reactions and drug-resistance. Herein, we propose a new therapeutic strategy of Chinese materioherbology, in which herbal medicine or traditional Chinese medicinal herbs can be employed as biological functional materials or refreshed/excited by means of materialogy. Natural tea nanoclusters (TNCs) were extracted from tea to inhibit β-lactamase. Different from the mechanism of small-molecular inhibitors inhibiting enzymes by binding to the corresponding active sites, the TNCs as a cap cover the protein pocket and create a spatial barrier between the active sites and antibiotics, which was named "capping-pocket" effect. TNCs were combined with amoxicillin sodium (Amo) to treat the methicillin-resistant Staphylococcus aureus (MRSA) pneumonia in mice. This combinatorial therapy remarkably outperforms antibiotic monotherapy in reducing MRSA infections and the associated inflammation in mice. The therapeutic strategy exhibited excellent biosafety, without any side effects, even in piglets. Hence, TNCs have great clinical value in potentiating β-lactam antibiotic activity for combatting multi-drug resistant pathogen infections and the "pocket capping" effect can guide the design of new enzyme inhibitors in near future.
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Affiliation(s)
- Ziao Zhou
- Biomedical Materials Engineering Research Center, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Jun Li
- School of Materials Science & Engineering, Peking University, Beijing 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
| | - Lei Tan
- Biomedical Materials Engineering Research Center, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Xiangmei Liu
- Biomedical Materials Engineering Research Center, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Yufeng Zheng
- School of Materials Science & Engineering, Peking University, Beijing 100871, China
| | - Zhenduo Cui
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
| | - Changyi Li
- Stomatological Hospital, Tianjin Medical University, No. 12, Qixiangtai Road, Heping District, Tianjin 300070, China
| | - Kelvin Wai Kwok Yeung
- Department of Orthopaedics & Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong 999077, China
| | - Zhaoyang Li
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
| | - Yanqin Liang
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
| | - Shengli Zhu
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
| | - Shuilin Wu
- School of Materials Science & Engineering, Peking University, Beijing 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Tianjin 300072, China
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109
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Huang Y, Zou L, Wang J, Jin Q, Ji J. Stimuli-responsive nanoplatforms for antibacterial applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1775. [PMID: 35142071 DOI: 10.1002/wnan.1775] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022]
Abstract
The continuously increasing bacterial resistance has become a big threat to public health worldwide, which makes it urgent to develop innovative antibacterial strategies. Nanotechnology-based drug delivery systems are considered as promising strategies in combating bacterial infections which are expected to improve the therapeutic efficacy and minimize the side effects. Unfortunately, the conventional nanodrug delivery systems always suffer from practical dilemmas, including incomplete and slow drug release, insufficient accumulation in infected sites, and weak biofilm penetration ability. Stimuli-responsive nanoplatforms are hence developed to overcome the disadvantages of conventional nanoparticles. In this review, we provide an extensive review of the recent progress of endogenous and exogenous stimuli-responsive nanoplatforms in the antibacterial area, including planktonic bacteria, intracellular bacteria, and bacterial biofilms. Taking advantage of the specific infected microenvironment (pH, enzyme, redox, and toxin), the mechanisms and strategies of the design of endogenous stimuli-responsive nanoplatforms are discussed, with an emphasis on how to improve the therapeutic efficacy and minimize side effects. How to realize controlled drug delivery using exogenous stimuli-responsive nanoplatforms especially light-responsive nanoparticles for improved antibacterial effects is another topic of this review. We especially highlight photothermal-triggered drug delivery systems by the combination of photothermal agents and thermo-responsive materials. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Lingyun Zou
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Jing Wang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Qiao Jin
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
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Zamir H, Ahmad B, Ali S, Khan SA, Sarwar R, Khan A, Ali J, Khan AA. Molecular characterization of Mycobacterium tuberculosis through MPT64 gene polymorphism using next-generation sequencing technology. Future Microbiol 2022; 17:763-772. [PMID: 35473398 DOI: 10.2217/fmb-2020-0231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To characterize and analyze polymorphism of the MPT64 gene and evaluate AgMPT64-based immunochromatographic assay (ICA) specificity associated with polymorphism. Materials & methods: A total of 1449 suspected samples were tested for tuberculosis (TB), and the MPT64/rv1980c gene was sequenced using next-generation sequencing for polymorphism analysis. Results: Of the TB-positive individuals, 200 (13.80%), 186 (12.84%) and 129 (8.90%) were positive using the liquid culture, GeneXpert and fluorescence microscopy assays, respectively. Liquid culture medium-based samples were confirmed using ICA, in which 193 (96.5%) were positive while seven (3.5%) were negative. Out of 14 sequenced samples, seven were positive and seven negative; 13 were identical to the reference and just one (ICA positive) showed a C477A point mutation (F159L). Conclusion: The results indicate that AgMPT64 can be considered as a potent vaccine candidate.
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Affiliation(s)
- Hina Zamir
- Centre of Biotechnology & Microbiology, University of Peshawar, KP, 25120, Pakistan
| | - Bashir Ahmad
- Centre of Biotechnology & Microbiology, University of Peshawar, KP, 25120, Pakistan
| | - Sajid Ali
- Provincial Tuberculosis Reference Laboratory, Peshawar, KP, 25120, Pakistan
| | - Saad A Khan
- Department of Medicine, Kabir Medical College, Peshawar, KP, 25120, Pakistan
| | - Raheela Sarwar
- Centre of Biotechnology & Microbiology, University of Peshawar, KP, 25120, Pakistan
| | - Alamzeb Khan
- Department of Pediatrics, Yale school of Medicine, Yale University, New Haven, CT 06511, USA
| | - Johar Ali
- Centre for Genomics Sciences, Rehman Medical Institute, Peshawar, KP, 25120, Pakistan
| | - Abid A Khan
- Centre of Biotechnology & Microbiology, University of Peshawar, KP, 25120, Pakistan.,Centre for Genomics Sciences, Rehman Medical Institute, Peshawar, KP, 25120, Pakistan.,Department of Chemical Sciences, University of Lakki Marwat, Lakki Marwat, KP, 28420, Pakistan
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111
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Wang Y, Chen G, Liu R, Fang X, Li F, Wu L, Wu Y. Synergistically enhanced photothermal transition of a polyoxometalate/peptide assembly improved the antibiofilm and antibacterial activities. SOFT MATTER 2022; 18:2951-2958. [PMID: 35348178 DOI: 10.1039/d2sm00092j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We successfully developed an antimicrobial assembly (Mo154/TK-14) using molybdenum-polyoxometalate and a positively charged peptide of TK-14. It was characterized and assayed using zeta-potential, dynamic light scattering (DLS), and TEM measurements. The Mo154/TK-14 assembly showed an enhanced 808 nm absorption and, therefore, improved the photothermal conversion efficiency of Mo154 (30.3%) to 38.6%. Consequently, in comparison to 5 μM Mo154 without irradiation, both the biofilm formation and bacterial viability of S. aureus were 24.6% and 20.2%, respectively, for the Mo154/TK-14 assembly; the biofilm formation and bacterial viability were further decreased to 7.7% and 4.4% under 808 nm irradiation, respectively. Therefore, the Mo154/TK-14 assembly reflects convincing antibacterial properties compared to Mo154. This is due to the synergistic effect between the peptide-binding enhanced 808 nm absorption and the improved PTT properties. The antimicrobial assembly offers a novel strategy for the rational design of light-responsive antibacterial materials.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, P. R. China
| | - Gang Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, P. R. China
| | - Rongrong Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, P. R. China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, No. 2 Liutiao Road, Changchun 130023, P. R. China
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Gude SS, Venu Gopal S, Marasandra Ramesh H, Vuppalapati S, Peddi NC, Gude SS. Unraveling the Nature of Antibiotics: Is It a Cure or a New Hurdle to the Patient Treatment? Cureus 2022; 14:e23955. [PMID: 35547462 PMCID: PMC9085652 DOI: 10.7759/cureus.23955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance is an increasing problem worldwide that has been exacerbated by antibiotic misuse worldwide. Growing antibiotic resistance can be attributed to as well as leads to severe infections, complications, prolonged hospital admissions, and higher mortality. One of the most important goals of administering antimicrobials is to avoid establishing antibiotic resistance during therapy. This can be done by drastically lowering worldwide antimicrobial usage, both in present and future. While current management methods to legislate antimicrobials and educate the healthcare community on the challenges are beneficial, they do not solve the problem of attaining an overall reduction in antimicrobial usage in humans. Application of rapid microbiological diagnostics for identification and antimicrobial susceptibility testing, use of inflammation markers to guide initiation and duration of therapies, reduction of standard antibiotic course durations, individualization of antibiotic treatments, and dosing considering pharmacokinetics are all possible strategies to optimize antibiotic use in everyday clinical practice and reduce the risk of inducing bacterial resistance. Furthermore, to remove any impediments to proper prescribing, strategies to improve antibiotic prescribing and antibiotic stewardship programs should enable clinical reasoning and enhance the prescribing environment. In addition, the well-established association between antimicrobial usage and resistance should motivate efforts to develop antimicrobial treatment regimens that facilitate the evolution of resistance. This review discusses the role of antibiotics, their current application in human medicine, and how the resistance has evolved to the existing antibiotics based on the existing literature.
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113
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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114
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Bartold PM, Ivanovski S. P4 Medicine as a model for precision periodontal care. Clin Oral Investig 2022; 26:5517-5533. [PMID: 35344104 PMCID: PMC9474478 DOI: 10.1007/s00784-022-04469-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/17/2022] [Indexed: 12/15/2022]
Abstract
Objectives P4 Medicine is based on a proactive approach for clinical patient care incorporating the four “pillars” of prediction, prevention, personalization, and participation for patient management. The purpose of this review is to demonstrate how the concepts of P4 medicine can be incorporated into the management of periodontal diseases (particularly periodontitis) termed P4 periodontics. Methods This is a narrative review that used current literature to explore how P4 periodontics can be aligned with the 2018 Classification of Periodontal Diseases, current periodontal treatment paradigms, and periodontal regenerative technologies. Results The proposed model of P4 periodontics is highly aligned with the 2018 Classification of Periodontal Diseases and represents a logical extension of this classification into treatment paradigms. Each stage of periodontitis can be related to a holistic approach to clinical management. The role of “big data” in future P4 periodontics is discussed and the concepts of a treat-to-target focus for treatment outcomes are proposed as part of personalized periodontics. Personalized regenerative and rejuvenative periodontal therapies will refocus our thinking from risk management to regenerative solutions to manage the effects of disease and aging. Conclusions P4 Periodontics allows us to focus not only on early prevention and intervention but also allow for personalized late-stage reversal of the disease trajectory and the use of personalized regenerative procedures to reconstruct damaged tissues and restore them to health. Clinical Significance P4 Periodontics is a novel means of viewing a holistic, integrative, and proactive approach to periodontal treatment.
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Affiliation(s)
- P Mark Bartold
- University of Queensland, 1 Milton Avenue, Beaumont, South Australia, 5066, Australia.
| | - Sašo Ivanovski
- University of Queensland, 1 Milton Avenue, Beaumont, South Australia, 5066, Australia
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. ENVIRONMENTAL MICROBIOME 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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116
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Review and Comparison of Antimicrobial Resistance Gene Databases. Antibiotics (Basel) 2022; 11:antibiotics11030339. [PMID: 35326803 PMCID: PMC8944830 DOI: 10.3390/antibiotics11030339] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however, can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation; however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.
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Ramírez C, Gutiérrez MS, Venegas L, Sapag C, Araya C, Caruffo M, López P, Reyes-Jara A, Toro M, González-Rocha G, Yáñez JM, Navarrete P. Microbiota composition and susceptibility to florfenicol and oxytetracycline of bacterial isolates from mussels (Mytilus spp.) reared on different years and distance from salmon farms. ENVIRONMENTAL RESEARCH 2022; 204:112068. [PMID: 34547250 DOI: 10.1016/j.envres.2021.112068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Chilean aquaculture mainly produces salmonids and molluscs. Salmonid production has been questioned by its excessive use of antimicrobials. This study aimed to investigate the bacterial microbiota composition of Mytilus spp. cultivated near salmonid farms and to determine the minimum inhibitory concentration (MIC) to florfenicol and oxytetracycline of its culturable bacteria. Seven Mytilus farming sites classified according to their proximity to salmon farms as close (CSF) or distant (DSF) were sampled in two years. We analyzed Mytilus microbiota composition through culture-independent methods, and isolated culturable bacteria, and identified those isolates with MIC values ≥ 64 μg mL-1 to florfenicol or oxytetracycline. Results revealed that the alpha diversity was affected by sampling year but not by Mytilus farming site location or its interaction. Nevertheless, in 2018, we observed a significant negative correlation between the alpha diversity of Mytilus microbiota in each farm sites and the tonnes of florfenicol reported for each phytosanitary management area. We detected significant differences in beta diversity and relative abundance of specific bacterial taxa in Mytilus microbiota depending on the proximity to salmon farms and years. A higher proportion of isolates with MIC values ≥ 64 μg mL-1 to both antibiotics was detected in 2019 compared to 2018, but not significant differences were detected according to Mytilus farming site location. However, in 2019, isolates from CSF sites showed higher MIC values for both antibiotics than those from DSF. Bacterial genera corresponding to isolates with MIC values ≥ 64 μg mL-1 represented a low proportion of Mytilus microbiota identified with the culture-independent approach, reflecting the need to implement new methodologies in the study of antimicrobial resistance. These results suggest that the proximity to salmonid farms and sampling year influence the Mytilus microbiota and MIC values of their bacterial isolates; however, other environmental variables should be considered in further studies.
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Affiliation(s)
- Carolina Ramírez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile
| | - Lucas Venegas
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | | | - Carolina Araya
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Mario Caruffo
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - José Manuel Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Núcleo Milenio INVASAL, Concepción, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile.
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Zhang X, Min Y, Zhang Q, Wu S, Fu W, Wu J, Li M, Wang Y, Zhang P. Functionalized Mn 3 O 4 Nanosheets with Photothermal, Photodynamic, and Oxidase-Like Activities Triggered by Low-Powered Near-Infrared Light for Synergetic Combating Multidrug-Resistant Bacterial Infections. Adv Healthc Mater 2022; 11:e2200121. [PMID: 35182457 DOI: 10.1002/adhm.202200121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/02/2022] [Indexed: 01/10/2023]
Abstract
Multidrug-resistant (MDR) pathogenic bacterial infections have become a major danger to public health. Synergetic therapy through multiple approaches is more powerful than the respective one alone, but has been rarely achieved in defeating MDR bacterial infections so far. Herein, indocyanine green-functionalized Mn3 O4 nanosheets are engineered as an efficient and safe antibacterial agent with photothermal, photodynamic, and oxidase-like activities, which display powerful ability in treating MDR bacterial infections. Therein, photothermal and photodynamic activities can be triggered by a single low-powered near-infrared laser (808 nm, 0.33 W cm-2 ), resulting in the generation of localized hyperthermia (photothermal conversion efficiency, 67.5%) and singlet oxygen. Meanwhile, oxidase-like activity of this material further leads to the generation of hydroxyl radical as well as superoxide radical. Sheet-like structure with rough surfaces make them tends to adhere on bacterial surface and thus damage membrane system as well as influence bacterial metabolism. As a result, Gram-positive and Gram-negative bacteria can both be eradicated. Animal experiments further indicate that the functionalized Mn3 O4 nanosheets can effectively treat methicillin-resistant Staphylococcus aureus-infected wounds through the triple synergetic therapy. Moreover, toxicity evaluation in vitro and in vivo has proved the superior biosafety of this material, which is promising to apply in clinical anti-infective therapy.
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Affiliation(s)
- Xinwen Zhang
- Chongqing Research Center for Pharmaceutical Engineering College of Pharmacy Chongqing Medical University Chongqing 400016 P. R. China
| | - Yuanhong Min
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education) Chongqing Key Laboratory of Green Synthesis and Applications College of Chemistry Chongqing Normal University Chongqing 401331 P. R. China
| | - Qi Zhang
- Chongqing Research Center for Pharmaceutical Engineering College of Pharmacy Chongqing Medical University Chongqing 400016 P. R. China
| | - Shiyue Wu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education) Chongqing Key Laboratory of Green Synthesis and Applications College of Chemistry Chongqing Normal University Chongqing 401331 P. R. China
| | - Wensheng Fu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education) Chongqing Key Laboratory of Green Synthesis and Applications College of Chemistry Chongqing Normal University Chongqing 401331 P. R. China
| | - Jiangling Wu
- Department of Clinical Laboratory University‐Town Hospital of Chongqing Medical University Chongqing 401331 P. R. China
| | - Ming Li
- Chongqing Research Center for Pharmaceutical Engineering College of Pharmacy Chongqing Medical University Chongqing 400016 P. R. China
| | - Yi Wang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education) Chongqing Key Laboratory of Green Synthesis and Applications College of Chemistry Chongqing Normal University Chongqing 401331 P. R. China
| | - Pu Zhang
- Chongqing Research Center for Pharmaceutical Engineering College of Pharmacy Chongqing Medical University Chongqing 400016 P. R. China
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Holm M, Zellweger RM, Poudyal N, Smith KHT, Joh HS, Marks F. Measuring the Link Between Vaccines and Antimicrobial Resistance in Low Resource Settings – Limitations and Opportunities in Direct and Indirect Assessments and Implications for Impact Studies. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.805833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The importance of vaccines in combatting antimicrobial resistance (AMR) is commonly accepted. Although scientific reasoning supports the putative connection between vaccines and reduction of AMR, reliably measuring the magnitude and effect of vaccines on antimicrobial resistance is inherently challenging, especially in low resource settings. We review the intrinsic challenges in estimating the effect of vaccines on AMR and discuss the limitations and opportunities in current methods from the host, pathogen, and environment perspectives. We highlight advantages and pitfalls in different epidemiological study designs with a specific focus on impact studies in low resource settings and suggest how these perspectives could be considered in future research.
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120
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Lu Y, Zou W, Wang L, Xi X, Ma C, Chen X, Chen T, Shaw C, Zhang X, Zhou M. Kassporin-KS1: A Novel Pentadecapeptide from the Skin Secretion of Kassina senegalensis: Studies on the Structure-Activity Relationships of Site-Specific “Glycine-Lysine” Motif Insertions. Antibiotics (Basel) 2022; 11:antibiotics11020243. [PMID: 35203845 PMCID: PMC8868508 DOI: 10.3390/antibiotics11020243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/07/2022] Open
Abstract
Due to the abuse of traditional antibiotics and the continuous mutation of microbial resistance genes, microbial infections have become serious problems for human health. Therefore, novel antibacterial agents are urgently required, and amphibian antimicrobial peptides (AMP) are among the most interesting potential antibacterial leads. In this research, a novel peptide, named kassporin-KS1 (generically QUB-1641), with moderate antibacterial activity against Gram-positive bacteria, was discovered in the skin secretion of the Senegal running frog, Kassina senegalensis. Using site-specific sequence enrichment with a motif “glycine-lysine” that frequently occurs in ranid frog temporin peptides, a series of QUB-1641 analogues were synthesized, and effects on selected bioactivities were studied. The greatest activity enhancement was obtained when the “glycine-lysine” motif was located at the eighth and ninth position as in QUB-1570.QUB-1570 had a broader antibacterial spectrum than QUB-1641, and was eight-fold more potent. Moreover, QUB-1570 inhibited S. aureus biofilm most effectively, and significantly enhanced the viability of insect larvae infected with S. aureus. When the “glycine-lysine” motif of QUB-1570 was substituted to reduce the helix ratio and positive charge, the antibacterial activities of these synthetic analogues decreased. These data revealed that the “glycine-lysine” motif at positions 8 and 9 had the greatest enhancing effect on the antibacterial properties of QUB-1570 through increasing positive charge and helix content. This research may provide strategies for the site’s selective amino acid modification of some natural peptides to achieve the desired enhancement of activity.
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Affiliation(s)
- Yueyang Lu
- School of Medicine & Holisitc Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Wanchen Zou
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Lei Wang
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Xinping Xi
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Chengbang Ma
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Xiaoling Chen
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Tianbao Chen
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Chris Shaw
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
| | - Xu Zhang
- School of Medicine & Holisitc Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
- Correspondence: (X.Z.); (M.Z.)
| | - Mei Zhou
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (W.Z.); (L.W.); (X.X.); (C.M.); (X.C.); (T.C.); (C.S.)
- Correspondence: (X.Z.); (M.Z.)
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Wang S, Yu Y, Li H, Huang Y, Wang J, Jin Q, Ji J. pH
‐sensitive polyion nanocomplexes for antimicrobial peptide delivery. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20210945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuting Wang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Yan Yu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Heyang Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Yan Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Jing Wang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Qiao Jin
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
| | - Jian Ji
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering Zhejiang University Hangzhou China
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Kesisoglou I, Tam VH, Tomaras AP, Nikolaou M. Discerning in vitro pharmacodynamics from OD measurements: A model-based approach. Comput Chem Eng 2022; 158:107617. [PMID: 35250117 PMCID: PMC8896896 DOI: 10.1016/j.compchemeng.2021.107617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Time-kill experiments can discern the pharmacodynamics of infectious bacteria exposed to antibiotics in vitro, and thus help guide the design of effective therapies for challenging clinical infections. This task is resource-limited, therefore typically bypassed in favor of empirical shortcuts. The resource limitation could be addressed by continuously assessing the size of a bacterial population under antibiotic exposure using optical density measurements. However, such measurements count both live and dead cells and are therefore unsuitable for declining populations of live cells. To fill this void, we develop here a model-based method that infers the count of live cells in a bacterial population exposed to antibiotics from continuous optical-density measurements of both live and dead cells combined. The method makes no assumptions about the underlying mechanisms that confer resistance and is widely applicable. Use of the method is demonstrated by an experimental study on Acinetobacter baumannii exposed to levofloxacin.
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Affiliation(s)
- Iordanis Kesisoglou
- Chemical & Biomolecular Engineering Department, University of Houston, 4226 MLK Blvd, Houston TX 77004, United States
| | - Vincent H Tam
- Chemical & Biomolecular Engineering Department, University of Houston, 4226 MLK Blvd, Houston TX 77004, United States
- Department of Pharmacy Practice and Translational Research, University of Houston, 4349 MLK Blvd, Houston TX 77204, United States
| | - Andrew P. Tomaras
- BacterioScan Inc. 2210 Welsch Industrial Ct, St. Louis, MO 63146 United States
| | - Michael Nikolaou
- Chemical & Biomolecular Engineering Department, University of Houston, 4226 MLK Blvd, Houston TX 77004, United States
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Baranova MN, Kudzhaev AM, Mokrushina YA, Babenko VV, Kornienko MA, Malakhova MV, Yudin VG, Rubtsova MP, Zalevsky A, Belozerova OA, Kovalchuk S, Zhuravlev YN, Ilina EN, Gabibov AG, Smirnov IV, Terekhov SS. Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint. Int J Mol Sci 2022; 23:ijms23031168. [PMID: 35163108 PMCID: PMC8835302 DOI: 10.3390/ijms23031168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.
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Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Vladislav V. Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Maria A. Kornienko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Maja V. Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Victor G. Yudin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, 690022 Vladivostok, Russia; (V.G.Y.); (Y.N.Z.)
| | - Maria P. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Yuriy N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, 690022 Vladivostok, Russia; (V.G.Y.); (Y.N.Z.)
| | - Elena N. Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
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Zhao Q, He H, Gao K, Li T, Dong B. Fate, mobility, and pathogenicity of drinking water treatment plant resistomes deciphered by metagenomic assembly and network analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150095. [PMID: 34509829 DOI: 10.1016/j.scitotenv.2021.150095] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/23/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance genes (ARGs) have been regarded as emerging environmental contaminants. The profile of resistome (collection of all ARGs) in drinking water and its fate during drinking water treatment remain unclear. This study applied metagenomic assembly combined with network analysis to decipher the profile, mobility, host, and pathogenicity of resistomes in two full-scale drinking water treatment plants (DWTPs), each applying conventional treatment and advanced treatment of ozonation followed by biological activated carbon filtration. In source waters and effluents of each treatment process collected from both DWTPs, 215 ARGs belonging to 20 types were detected with total concentration ranging from 6.30 ± 1.83 to 5.20 ± 0.26 × 104 copies/mL. Both the conventional and advanced DWTPs were revealed to effectively reduce the concentration of total ARGs, with the average removal efficiency of 3.61-log10 and 2.21-log10, respectively. Multiple statistical analyses (including network analysis) indicated drinking water resistome correlated tightly with mobile gene elements (MGEs) and bacterial community, with the latter acting as the premier driver of resistome alteration in DWTPs. Further analysis of ARG-carrying contigs (ACCs) assembled from drinking water metagenomes (i) tracked down potential bacterial hosts of ARGs (e.g., Proteobacteria phylum as the major pool of resistome), (ii) provided co-localization information of ARGs and MGEs (e.g., MacB-E7196 plasmid1), and (iii) identified ARG-carrying human pathogens (e.g., Enterococcus faecium and Ralstonia pickettii). This work firstly determined the concentration, mobility incidence, and pathogenicity incidence of DWTP resistomes, based on which the actual health risk regarding antibiotic resistance could be quantitatively assessed in further study, providing a useful direction for decision-making concerning the risk control of ARGs in DWTPs.
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Affiliation(s)
- Qingqing Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Huan He
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota - Twin Cities, 500 Pillsbury Dr. SE, Minneapolis, MN 55445, United States.
| | - Kuo Gao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Tian Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Bingzhi Dong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Liao Z, Xia Y, Zuo J, Wang T, Hu D, Li M, Shao N, Chen D, Song K, Yu X, Zhang X, Gao W. Metal-Organic Framework Modified MoS 2 Nanozyme for Synergetic Combating Drug-Resistant Bacterial Infections via Photothermal Effect and Photodynamic Modulated Peroxidase-Mimic Activity. Adv Healthc Mater 2022; 11:e2101698. [PMID: 34549554 DOI: 10.1002/adhm.202101698] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/11/2021] [Indexed: 12/13/2022]
Abstract
Bacterial infections have become major threats to public health all over the world. With the emergence of antibiotic resistance, it is urgent to develop novel antimicrobial materials to efficiently overcome drug resistance with high bactericidal activity. In this work, UiO-66-NH-CO-MoS2 nanocomposites (UNMS NCs) are constructed through the amidation reaction. The UNMS NCs are positively charged which is beneficial for capturing and restricting bacteria. Significantly, UNMS NCs possess a synergistic bactericidal efficiency based on near-infrared irradiation (808 nm) regulated combination of photothermal, photodynamic, and peroxidase-like enzymatic activities. Both the photodynamic property and nanozymatic activity of UNMS NCs can lead to the generation of reactive oxygen species. The UNMS NCs show high catalytic activity in a wide pH range and exhibit excellent antibacterial ability against ampicillin-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus with negligible cytotoxicity. Interestingly, due to the 808 nm irradiation-induced hyperthermia in the presence of UNMS NCs, the glutathione oxidation process can be accelerated, resulting in bacterial death more easily. Mice wound models are established to further manifest that UNMS NCs can promote wound healing with good biosafety in living systems.
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Affiliation(s)
- Zi‐Yang Liao
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Ya‐Mu Xia
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Jia‐Min Zuo
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Tao Wang
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Da‐Tong Hu
- College of Pharmacy Shan Dong University of Traditional Chinese Medicine Jinan 250355 China
| | - Ming‐Zhe Li
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Ning‐Ning Shao
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Dong Chen
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Kai‐Xin Song
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Xuan Yu
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Xin‐Yue Zhang
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
| | - Wei‐Wei Gao
- Key Laboratory of Multiphase Flow Reaction and Separation Engineering of Shandong Province College of Chemical Engineering Qingdao University of Science and Technology Qingdao 266042 China
- Chongqing Key Laboratory of Soft‐Matter Material Chemistry and Function Manufacturing Southwest University Chongqing 400715 China
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Fitzpatrick KJ, Rohlf HJ, Sutherland TD, Koo KM, Beckett S, Okelo WO, Keyburn AL, Morgan BS, Drigo B, Trau M, Donner E, Djordjevic SP, De Barro PJ. Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains. ACS Sens 2021; 6:4283-4296. [PMID: 34874700 DOI: 10.1021/acssensors.1c01973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
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Affiliation(s)
- Kira J. Fitzpatrick
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Hayden J. Rohlf
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Tara D. Sutherland
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kevin M. Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, Queensland 4029, Australia
| | - Sam Beckett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Walter O. Okelo
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony L. Keyburn
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, Victoria 3220, Australia
| | - Branwen S. Morgan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Steven P. Djordjevic
- Ithree Institute, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Paul J. De Barro
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health & Biosecurity, EcoSciences Precinct, Brisbane, Queensland 4001, Australia
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Wigand J, Tansirichaiya S, Winje E, Al-Haroni M. Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine. BMC Oral Health 2021; 21:632. [PMID: 34886820 PMCID: PMC8656073 DOI: 10.1186/s12903-021-02000-5] [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: 09/04/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022] Open
Abstract
Objective Many sections of the health care system are facing a major challenge making infectious disease problematic to treat; antimicrobial resistance (AMR). Identification and surveillance of the resistome have been highlighted as one of the strategies to overcome the problem. This study aimed to screen for AMR genes in an oral microbiota, a complex microbial system continuously exposed to antimicrobial agents commonly used in dental practice. Materials and methods As a significant part of the oral microbiome cannot be conventionally cultured, a functional metagenomic approach was chosen. The human oral metagenomic DNA was extracted from saliva samples collected from 50 healthy volunteers in Norway. The oral metagenomic library was then constructed by ligating partially digested oral metagenome into pSMART BAC vector and introducing into Escherichia coli. The library was screened against antimicrobials in dental practices. All resistant clones were selected and analyzed. Results Screening of the oral metagenomic library against different antimicrobials detected multiple clones with resistance against chlorhexidine, triclosan, erythromycin, tetracycline, and sodium hypochlorite. Bioinformatic analysis revealed both already known resistance genes, including msr, mef(A), tetAB(46), and fabK, and genes that were not previously described to confer resistance, including recA and accB conferring resistance to sodium hypochlorite and chlorhexidine, respectively. Conclusion Multiple clones conferring resistance to antimicrobials commonly used in dental practices were detected, containing known and novel resistant genes by functional-based metagenomics. There is a need for more studies to increase our knowledge in the field. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-021-02000-5.
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Affiliation(s)
- Johannes Wigand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Endre Winje
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway. .,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.
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Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics. Nat Commun 2021; 12:7085. [PMID: 34873166 PMCID: PMC8648761 DOI: 10.1038/s41467-021-27404-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics. Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.
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Eco-friendly bacteria-killing by nanorods through mechano-puncture with top selectivity. Bioact Mater 2021; 15:173-184. [PMID: 35386355 PMCID: PMC8941167 DOI: 10.1016/j.bioactmat.2021.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Nanorods can induce mechano-puncture of Staphylococcus aureus (S. aureus) that often impairs osseointegration of orthopedic implants, while the critical nanorod top sharpness able to puncture S. aureus and the predominant contributor between top sharpness and length to mechano-puncture activity remains elusive. Herein, we fabricated three kinds of Al2O3-wrapped nanorods patterned arrays with different lengths and top sharpness. The top-sharp nanorods have lengths of 469 and 884 nm and the shorter show a length identical to the top-flat nanorods. Driven by the equivalent adhesive force of S. aureus, the top-flat nanorods deform cell envelops, showing a bacteriostatic rate of 29% owing to proliferation-inhibited manner. The top-sharp nanorods puncture S. aureus, showing a bactericidal rate of 96% for the longer, and 98% for the shorter that simultaneously exhibits fair osseointegration in bacteria-infected rat tibias, identifying top sharpness as a predominate contributor to mechano-puncture activity. Based on finite-element simulation, such top-flat nanorod derives the maximum stress (Smax) of 5.65 MPa on cell wall, lower than its ultimate-tensile-strength (13 MPa); while such top-sharp and shorter nanorod derives Smax of 20.15 MPa to puncture cell envelop. Moreover, a critical top conical angle of 138° is identified for nanorods able to puncture S. aureus. Top sharpness depended mechano-puncture of nanorods against S. aureus is clarified. Top-flat nanorods deform bacterial cell envelop to inhibit their proliferation. Top-sharp nanorods (conical angle of 50°) puncture bacteria to intensely kill them. 138° is confirmed as critical top conical angle for nanorods to puncture S. aureus.
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Han S, Li X, Huang H, Wang T, Wang Z, Fu X, Zhou Z, Du P, Li X. Simultaneous Determination of Seven Antibiotics and Five of Their Metabolites in Municipal Wastewater and Evaluation of Their Stability under Laboratory Conditions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182010640. [PMID: 34682386 PMCID: PMC8535447 DOI: 10.3390/ijerph182010640] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
The selection and spread of antibiotic resistance poses risks to public health by reducing the therapeutic potential of antibiotics against human pathogens. Wastewater-based epidemiology (WBE) is potentially the most reliable approach to estimate antibiotics use. Previous WBE studies used parent antibiotics as biomarkers, which may lead to overestimation since parent antibiotics may be directly disposed of. Using metabolites as biomarkers can avoid this drawback. This study developed a simultaneous solid-phase extraction coupled with ultra-high-performance liquid chromatography tandem mass spectrometry method for analyzing 12 antibiotics and human metabolites in wastewater to help assess health risk. Optimum conditions were achieved using a PEP cartridge at pH 3.0. The extraction efficiencies were 73.3~95.4% in influent and 72.0~102.7% in effluent for most of the target analytes. Method detection limit ranged from 0.1 to 1.5 ng/L for influent wastewater and 0.03 to 0.7 ng/L for effluent wastewater. A stability experiment showed that sulfonamide parents and their metabolites were stable at 4 °C, −20 °C and −80 °C, while macrolides metabolites were more stable than their corresponding parents at 4 °C and −20 °C. Finally, the method was applied to measure these analytes in wastewater samples collected from three Beijing WWTPs and to derive apparent removal rates. All metabolites were detected in wastewater samples with concentrations ranging from 1.2 to 772.2 ng/L in influent, from <MDL to 235.6 ng/L in effluent. The apparent removal rates of five metabolites were above 72.6%. These results set a solid foundation for applying WBE to evaluate antibiotics use and its public health effects.
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Affiliation(s)
- Sheng Han
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; (S.H.); (H.H.); (T.W.); (X.F.)
| | - Xinyue Li
- Development Research Center, Ministry of Water Resources of China, Beijing 100036, China;
| | - Hongmei Huang
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; (S.H.); (H.H.); (T.W.); (X.F.)
| | - Ting Wang
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; (S.H.); (H.H.); (T.W.); (X.F.)
| | - Zhenglu Wang
- College of Oceanography, Hohai University, Nanjing 210098, China;
| | - Xiaofang Fu
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; (S.H.); (H.H.); (T.W.); (X.F.)
| | - Zilei Zhou
- Hubei Provincial Academy of Eco-Environmental Sciences, Wuhan 430070, China;
| | - Peng Du
- Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing 100875, China;
| | - Xiqing Li
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; (S.H.); (H.H.); (T.W.); (X.F.)
- Correspondence:
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Guernier-Cambert V, Chamings A, Collier F, Alexandersen S. Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia-A Descriptive Pilot Study. Front Microbiol 2021; 12:596984. [PMID: 34603219 PMCID: PMC8484959 DOI: 10.3389/fmicb.2021.596984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/18/2021] [Indexed: 11/27/2022] Open
Abstract
The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion AmpliseqTM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLSB (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion AmpliseqTM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.
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Affiliation(s)
- Vanina Guernier-Cambert
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Fiona Collier
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia.,Barwon Health, University Hospital Geelong, Geelong, VIC, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia.,Barwon Health, University Hospital Geelong, Geelong, VIC, Australia
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López-Catalina A, Atxaerandio R, García-Rodríguez A, Goiri I, Gutierrez-Rivas M, Jiménez-Montero JA, González-Recio O. Characterisation of the rumen resistome in Spanish dairy cattle. Anim Microbiome 2021; 3:63. [PMID: 34551823 PMCID: PMC8456196 DOI: 10.1186/s42523-021-00125-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/30/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to understand how they appear, their relationship with the host, how they behave as a whole in the ruminal ecosystem or how they spread to the environment or humans. We sequenced ruminal samples from 416 Holstein dairy cows in 14 Spanish farms using nanopore technology, to uncover the presence of resistance genes and their potential effect on human, animal and environmental health. RESULTS We found 998 antimicrobial resistance genes (ARGs) in the cow rumen and studied the 25 most prevalent genes in the 14 dairy cattle farms. The most abundant ARGs were related to the use of antibiotics to treat mastitis, metritis and lameness, the most common diseases in dairy cattle. The relative abundance (RA) of bacteriophages was positively correlated to the ARGs RA. The heritability of the RA of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW), similar to the heritability of the RA of microbes that carried those ARGs. Even though these genes are carried by the microorganisms, the host is partially controlling their RA by having a more suitable rumen pH, folds, or other physiological traits that promote the growth of those microorganisms. CONCLUSIONS We were able to determine the most prevalent ARGs (macB, msbA, parY, rpoB2, tetQ and TaeA) in the ruminal bacteria ecosystem. The rumen is a reservoir of ARGs, and strategies to reduce the ARG load from livestock must be pursued.
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Affiliation(s)
- Adrián López-Catalina
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña km 7.5, 28040, Madrid, Spain
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Raquel Atxaerandio
- Department of Animal Production, Neiker-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute, 01192, Arkaute, Spain
| | - Aser García-Rodríguez
- Department of Animal Production, Neiker-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute, 01192, Arkaute, Spain
| | - Idoia Goiri
- Department of Animal Production, Neiker-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute, 01192, Arkaute, Spain
| | - Mónica Gutierrez-Rivas
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Crta. de la Coruña km 7.5, 28040, Madrid, Spain.
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain.
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Zhang B, Yan H, Meng Z, Li P, Jiang X, Wu Z, Xiao JA, Su W. Photodynamic and Photothermal Ce6-Modified Gold Nanorod as a Potent Alternative Candidate for Improved Photoinactivation of Bacteria. ACS APPLIED BIO MATERIALS 2021; 4:6742-6757. [PMID: 35006976 DOI: 10.1021/acsabm.1c00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The global rise of antibiotic resistance of pathogenic bacteria has become an increasing medical and public concern, which is further urging the development of antimicrobial channels for treating infectious diseases. The combination of photodynamic therapy (PDT) with photothermal therapy (PTT) has been considered as a promising alternative way for the replacement of traditional antibiotic therapy. In this research, the newly fabricated Chlorin-e6 (Ce6) conjugated mesoporous silica-coated AuNRs, designated AuNR@SiO2-NH2-Ce6, exhibited synergistic photothermal effects and single oxygen localized generation property, and showed stronger photoinactivation for bacteria compared with Ce6. AuNR@SiO2-NH2-Ce6 can anchor to the cell membrane and accumulate in the interior of cells. Furthermore, the unique porous structure of AuNR@SiO2NH2 enabled Ce6 encapsulation in the mesopores and was subsequently released and activated by photothermic effect, allowing the generated single oxygen to penetrate into the cytoplasmic membrane or directly enter the interior of bacteria cells, thus overcoming the inherent defects of single oxygen. AuNR@SiO2-NH2-Ce6 not only damaged the integrity of the cell membrane of bacteria but also facilitated the cellular permeation and accumulation of external nanoagents in the bacteria upon light irradiation. In addition, AuNR@SiO2-NH2-Ce6 exhibited negligible cytotoxicity toward mammalian cells and hemolytic activity. Therefore, AuNR@SiO2-NH2-Ce6 may be highly promising candidates as topical antibacterial agents, and this study has wide implications on the design of next-generation antimicrobial agents.
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Affiliation(s)
- Baoqu Zhang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Hongjun Yan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Zhouting Meng
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Peiyuan Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Xiantao Jiang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Zihua Wu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Jun-An Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Wei Su
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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Cook A, Sharland M, Yau Y, Bielicki J. Improving empiric antibiotic prescribing in pediatric bloodstream infections: a potential application of weighted-incidence syndromic combination antibiograms (WISCA). Expert Rev Anti Infect Ther 2021; 20:445-456. [PMID: 34424116 DOI: 10.1080/14787210.2021.1967145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Background: Increasing antibiotic resistance to WHO-recommended first- and second-line treatments of pediatric sepsis requires adaptation of prescribing guidelines. We discuss the potential and limitations of a weighted-incidence syndromic combination antibiogram (WISCA) as a practical tool for incorporating local microbiology data when assessing empiric coverage of commonly used antibiotics.Research design and methods: A brief questionnaire of 18 clinically significant isolates from pediatric blood cultures (Jan-Dec 2018) was sent to a global network of pediatric hospitals in July 2019. Weighted coverage estimates of non-antipseudomonal third-generation cephalosporins (3GC) and meropenem were estimated using Monte-Carlo simulation for each site reporting >100 isolates.Results: 52 hospitals in 23 countries in 5 WHO regions responded to the questionnaire; 13 sites met the sample size requirement. The most common isolates were S. aureus, Klebsiella spp., E. coli and Enterococcus spp. Coverage of 3GC ranged from 39% [95%CrI: 34-43%] to 73% (two sites: [95%CrI: 65-80%]; [95%CrI: 68-86%]) and meropenem coverage ranged from 54% [95%CrI: 47-60%] to 88% [95%CrI:84-91%].Conclusions: A WISCA is a data-driven, clinically intuitive tool that can be used to compare empiric antibiotic regimens for pediatric sepsis using existing large datasets. The estimates can be further refined using more complex meta-analytical methods and patient characteristics.
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Affiliation(s)
- Aislinn Cook
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Mike Sharland
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Yasmine Yau
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | | | - Julia Bielicki
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
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Screening of Epidemiologically Significant Mechanisms of Antibiotics to β-Lactams in Enterobacteriaceae - Pathogens of Zoonoses. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among the acquired mechanisms of resistance to antibiotics of microorganisms, the production of beta-lactamases, enzymes that inactivate penicillins, cephalosporins, carbapenems, and monobactams, is widespread. Most often, such beta-lactamases, in particular ESBL (extended-spectrum beta-lactamases), are capable of destroying III and IV generations of cephalosporins. One of the important ESBL producers is Escherichia coli and, to a lesser extent, Salmonella enteritidis, which are clinically significant in animals and humans. The purpose of the study was to screen ESBL DDM using cephalosporin markers and screening of mobile extrachromosomal factors of bacterial heredity – plasmids (potentially dangerous factors of genetic transport) in isolates of E. coli and S. enteritidis, polyresistant to aminoderms, from environmental objects, patho- and biological material, raw materials and products of animal origin. Results of our studies have shown the level of their distribution among animals, poultry, since from 13 field isolates of E. coli isolated from the milk of cows with mastitis and pathological material from pigs, ESBL production was found in 3 strains (23.1%) and from 18 field isolates of S. enteritidis isolated from pathological material from poultry, ESBL production was found in 2 strains (11.1%). Based on the results of molecular genetics studies, the presence of resistance plasmids (R-plasmids) in 9 field E. coli isolates was confirmed, 4 of which produced acquired beta-lactamases, incl. ESBL and 8 field isolates of S. enteritidis, 7 of which confirmed the presence of acquired carbapenemases.
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Wang Y, Malkmes MJ, Jiang C, Wang P, Zhu L, Zhang H, Zhang Y, Huang H, Jiang L. Antibacterial mechanism and transcriptome analysis of ultra-small gold nanoclusters as an alternative of harmful antibiotics against Gram-negative bacteria. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:126236. [PMID: 34492988 DOI: 10.1016/j.jhazmat.2021.126236] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
In this work, a well-known Au25 NCs with high purity was prepared by simple one-pot reducing method. The as-synthesized Au25 NCs exhibited excellent antibacterial efficiency toward Gram-negative bacteria in a dose- and time-dependent manner, which could be used as nanoantibiotics to replace harmful antibiotics. The antibacterial assays showed that almost 100% bacteria were killed at lower concentration (100-150 μM) within a short time (30-60 min), providing a rapid and effective killing outcome for Gram-negative bacteria. After that, antibacterial mechanism was mainly investigated at cellular level via destruction of membrane integrity, disruption of antioxidant defense system, metabolic inactivation, DNA damage, as well as at molecular level via transcriptome analysis (RNA sequencing) for the first time. RNA sequencing results showed that differentially expressed genes (DEGs) related to biosynthesis of cell wall and membrane, glycolysis and TCA cycle, oxidative phosphorylation and DNA replication and repair were significantly affected. It was concluded that synergetic effect of membrane damage, oxidative stress, DNA damage and energy metabolism eventually led to the Gram-negative bacteria growth inhibition and death.
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Affiliation(s)
- Yuxian Wang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Matthew Jay Malkmes
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Cheng Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Peng Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Hongman Zhang
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yangheng Zhang
- Department of Periodontology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; College of Pharmaceutical Science, Nanjing Tech University, Nanjing 211816, China.
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Wang Y, Lyu N, Liu F, Liu WJ, Bi Y, Zhang Z, Ma S, Cao J, Song X, Wang A, Zhang G, Hu Y, Zhu B, Gao GF. More diversified antibiotic resistance genes in chickens and workers of the live poultry markets. ENVIRONMENT INTERNATIONAL 2021; 153:106534. [PMID: 33799229 DOI: 10.1016/j.envint.2021.106534] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Poultry farms and LPMs are a reservoir of antimicrobial resistant bacteria and resistance genes from feces. The LPM is an important interface between humans, farm animals, and environments in a typical urban environment, and it is considered a reservoir for ARGs and viruses. However, the antibiotic resistomes shared between chicken farms and LPMs, and that of LPM workers and people who have no contact with the LPMs remains unknown. METHODS We characterized the resistome and bacterial microbiome of farm chickens and LPMs and LPM workers and control subjects. The mobile ARGs identified in chickens and the distribution of the mcr-family genes in publicly bacterial genomes and chicken gut metagenomes was analyzed, respectively. In addition, the prevalence of mcr-1 in LPMs following the ban on colistin-positive additives in China was explored. RESULTS By profiling the microbiomes and resistomes in chicken farms, LPMs, LPM workers, and LPM environments, we found that the bacterial community composition and resistomes were significantly different between the farms and the LPMs, and the LPM samples possessed more diversified ARGs (59 types) than the farms. Some mobile ARGs, such as mcr-1 and tet(X3), identified in chicken farms, LPMs, LPM workers, and LPM environments were also harbored by human clinical pathogens. Moreover, we found that the resistomes were significantly different between the LPM workers and those who have no contact with the LPMs, and more diversified ARGs (188 types) were observed in the LPM workers. It is also worth noting that mcr-10 was identified in both human (5.2%, 96/1,859) and chicken (1.5%, 14/910) gut microbiomes. Although mcr-1 prevalence decreased significantly in the LPMs across the eight provinces in China, from 190/333 (57.1%) samples in September 2016-March 2017 to 208/544 (38.2%) samples in August 2018-May 2019, it is widespread and continuous in the LPMs. CONCLUSION Live poultry trade has a significant effect on the diversity of ARGs in LPM workers, chickens, and environments in China, driven by human selection with the live poultry trade. Our findings highlight the live poultry trade as ARG disseminators into LPMs, which serve as an interface of LPM environments even LPM workers, and that could urge Government to have better control of LPMs in China. Further studies on the factors that promote antibiotic resistance exchange between LPM environments, human commensals, and pathogens, are warranted.
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Affiliation(s)
- Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Zewu Zhang
- Dongguan Municipal Center for Disease Control and Prevention, Dongguan 523129, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing 100101, China; Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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139
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Saha SB, Gupta VK, Ramteke PW. uCARE Chem Suite and uCAREChemSuiteCLI: Tools for bacterial resistome prediction. Genes Dis 2021; 8:721-729. [PMID: 34291144 PMCID: PMC8278538 DOI: 10.1016/j.gendis.2020.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/08/2020] [Accepted: 06/21/2020] [Indexed: 11/23/2022] Open
Abstract
In the era of antibiotic resistance, in silico prediction of bacterial resistome profiles, likely to be associated with inactivation of new potential antibiotics is of utmost importance. Despite this, to the best of our knowledge, no tool exists for such prediction. Therefore, under the rationale that drugs with similar structures have similar resistome profiles, we developed two models, a deterministic model and a stochastic model, to predict the bacterial resistome likely to neutralize uncharacterized but potential chemical structures. The current version of the tool involves the prediction of a resistome for Escherichia coli and Pseudomonas aeruginosa. The deterministic model on omitting two diverse but relatively less characterized drug classes, polyketides and polypeptides showed an accuracy of 87%, a sensitivity of 85%, and a precision of 89%, whereas the stochastic model predicted antibiotic classes of the test set compounds with an accuracy of 72%, a sensitivity of 75%, and a precision of 83%. The models have been implemented in both a standalone package and an online server, uCAREChemSuiteCLI and uCARE Chem Suite, respectively. In addition to resistome prediction, the online version of the suite enables the user to visualize the chemical structure, classify compounds in 19 predefined drug classes, perform pairwise alignment, and cluster with database compounds using a graphical user interface. Availability uCARE Chem Suite can be browsed at: https://sauravsaha.shinyapps.io/ucarechemsuite2/, and uCAREChemSuiteCLI can be installed from: 1. CRAN (https://cran.r-project.org/package=uCAREChemSuiteCLI) and 2. GitHub (https://github.com/sauravbsaha/uCAREChemSuiteCLI).
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Affiliation(s)
- Saurav Bhaskar Saha
- Department of Computational Biology and Bioinformatics, JIBB, SHUATS, Prayagraj, Uttar Pradesh, 211007, India
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
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140
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A commentary on the development of engineered phage as therapeutics. Drug Discov Today 2021; 26:2095-2098. [PMID: 34237459 DOI: 10.1016/j.drudis.2021.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/21/2023]
Abstract
The use of engineered phages offers a unique opportunity to improve on wild-type (WT) phages to generate ever more successful therapeutics to combat bacterial infections. Here, we discuss how phage engineering could be used to overcome some of the technical challenges of phage therapy, and suggest some areas in which more research will be crucial to the development of further novel phage therapeutics.
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141
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Prosperi M, Marini S. KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. ... IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS. IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS 2021; 2021:10.1109/bhi50953.2021.9508479. [PMID: 34447942 PMCID: PMC8383893 DOI: 10.1109/bhi50953.2021.9508479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-throughput sequencing is widely used for strain detection and characterization of antibiotic resistance in microbial metagenomic samples. Current analytical tools use curated antibiotic resistance gene (ARG) databases to classify individual sequencing reads or assembled contigs. However, identifying ARGs from raw read data can be time consuming (especially if assembly or alignment is required) and challenging, due to genome rearrangements and mutations. Here, we present the k-mer-based antibiotic gene resistance analyzer (KARGA), a multi-platform Java toolkit for identifying ARGs from metagenomic short read data. KARGA does not perform alignment; it uses an efficient double-lookup strategy, statistical filtering on false positives, and provides individual read classification as well as covering of the database resistome. On simulated data, KARGA's antibiotic resistance class recall is 99.89% for error/mutation rates within 10%, and of 83.37% for error/mutation rates between 10% and 25%, while it is 99.92% on ARGs with rearrangements. On empirical data, KARGA provides higher hit score (≥1.5-fold) than AMRPlusPlus, DeepARG, and MetaMARC. KARGA has also faster runtimes than all other tools (2x faster than AMRPlusPlus, 7x than DeepARG, and over 100x than MetaMARC). KARGA is available under the MIT license at https://github.com/DataIntellSystLab/KARGA.
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Affiliation(s)
- Mattia Prosperi
- Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Simone Marini
- Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
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142
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Ventilation-Associated Particulate Matter Is a Potential Reservoir of Multidrug-Resistant Organisms in Health Facilities. Life (Basel) 2021; 11:life11070639. [PMID: 34209235 PMCID: PMC8307074 DOI: 10.3390/life11070639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 02/03/2023] Open
Abstract
Most healthcare-associated infections (HCAIs) develop due to the colonisation of patients and healthcare workers by multidrug-resistant organisms (MDRO). Here, we investigated whether the particulate matter from the ventilation systems (Vent-PM) of health facilities can harbour MDRO and other microbes, thereby acting as a potential reservoir of HCAIs. Dust samples collected in the ventilation grilles and adjacent air ducts underwent a detailed analysis of physicochemical properties and biodiversity. All Vent-PM samples included ultrafine PM capable of reaching the alveoli. Strikingly, >70% of Vent-PM samples were contaminated, mostly by viruses (>15%) or multidrug-resistant and biofilm-producing bacterial strains (60% and 48% of all bacteria-contaminated specimens, respectively). Total viable count at 1 m from the ventilation grilles was significantly increased after opening doors and windows, indicating an association between air flow and bacterial contamination. Both chemical and microbial compositions of Vent-PM considerably differed across surgical vs. non-surgical and intensive vs. elective care units and between health facilities located in coal and chemical districts. Reduced diversity among MDRO and increased prevalence ratio in multidrug-resistant to the total Enterococcus spp. in Vent-PM testified to the evolving antibiotic resistance. In conclusion, we suggest Vent-PM as a previously underestimated reservoir of HCAI-causing pathogens in the hospital environment.
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143
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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144
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Chen H, Li J, Yan S, Sun H, Tan C, Liu M, Liu K, Zhang H, Zou M, Xiao X. Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 2021; 9:e11699. [PMID: 34249516 PMCID: PMC8253115 DOI: 10.7717/peerj.11699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/08/2021] [Indexed: 02/01/2023] Open
Abstract
Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
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Affiliation(s)
- Huan Chen
- Postdoctoral Research Station of Clinical Medicine & Department of Hematology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Shanshan Yan
- Department of Intensive Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Hui Sun
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Chuyi Tan
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Meidong Liu
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ke Liu
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Huali Zhang
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Xianzhong Xiao
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
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145
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Léger A, Lambraki I, Graells T, Cousins M, Henriksson PJG, Harbarth S, Carson C, Majowicz S, Troell M, Parmley EJ, Jørgensen PS, Wernli D. AMR-Intervene: a social-ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective. J Antimicrob Chemother 2021; 76:1-21. [PMID: 33057678 DOI: 10.1093/jac/dkaa394] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The global threat of antimicrobial resistance (AMR) requires coordinated actions by and across different sectors. Increasing attention at the global and national levels has led to different strategies to tackle the challenge. The diversity of possible actions to address AMR is currently not well understood from a One Health perspective. AMR-Intervene, an interdisciplinary social-ecological framework, describes interventions to tackle AMR in terms of six components: (i) core information about the publication; (ii) social system; (iii) bio-ecological system; (iv) triggers and goals; (v) implementation and governance; and (vi) assessment. AMR-Intervene provides a broadly applicable framework, which can inform the design, implementation, assessment and reporting of interventions to tackle AMR and, in turn, enable faster uptake of successful interventions to build societal resilience to AMR.
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Affiliation(s)
- Anaïs Léger
- Global Studies Institute, University of Geneva, Sciences II, Quai Ernest-Ansermet 30, CH -1211 Genève 4, Switzerland
| | - Irene Lambraki
- School of Public Health and Health Systems, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Tiscar Graells
- Global Economic Dynamics and the Biosphere, The Royal Swedish Academy of Sciences, Box 50005, 104 05 Stockholm, Sweden.,Stockholm Resilience Centre, Stockholm University, Kräftriket 2B, 10691 Stockholm, Sweden
| | - Melanie Cousins
- School of Public Health and Health Systems, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Patrik J G Henriksson
- Stockholm Resilience Centre, Stockholm University, Kräftriket 2B, 10691 Stockholm, Sweden.,Beijer Institute of Ecological Economics, The Royal Swedish Academy of Sciences, PO Box 50005, SE-104 05 Stockholm, Sweden.,WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia
| | - Stephan Harbarth
- Infection Control Program and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Carolee Carson
- Canadian Integrated Program for Antimicrobial Resistance Surveillance; Public Health Agency of Canada, Guelph, Canada
| | - Shannon Majowicz
- School of Public Health and Health Systems, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Max Troell
- Stockholm Resilience Centre, Stockholm University, Kräftriket 2B, 10691 Stockholm, Sweden.,Beijer Institute of Ecological Economics, The Royal Swedish Academy of Sciences, PO Box 50005, SE-104 05 Stockholm, Sweden
| | - E Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Peter S Jørgensen
- Global Economic Dynamics and the Biosphere, The Royal Swedish Academy of Sciences, Box 50005, 104 05 Stockholm, Sweden.,Stockholm Resilience Centre, Stockholm University, Kräftriket 2B, 10691 Stockholm, Sweden
| | - Didier Wernli
- Global Studies Institute, University of Geneva, Sciences II, Quai Ernest-Ansermet 30, CH -1211 Genève 4, Switzerland
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146
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Affiliation(s)
- Jasmohan S Bajaj
- From Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond (J.S.B.); Mayo Clinic College of Medicine and Science, Rochester, MN (P.S.K.); and the University of Pennsylvania, Philadelphia (K.R.R.)
| | - Patrick S Kamath
- From Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond (J.S.B.); Mayo Clinic College of Medicine and Science, Rochester, MN (P.S.K.); and the University of Pennsylvania, Philadelphia (K.R.R.)
| | - K Rajender Reddy
- From Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond (J.S.B.); Mayo Clinic College of Medicine and Science, Rochester, MN (P.S.K.); and the University of Pennsylvania, Philadelphia (K.R.R.)
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147
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D'Souza AW, Boolchandani M, Patel S, Galazzo G, van Hattem JM, Arcilla MS, Melles DC, de Jong MD, Schultsz C, Dantas G, Penders J. Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. Genome Med 2021; 13:79. [PMID: 34092249 PMCID: PMC8182900 DOI: 10.1186/s13073-021-00893-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/22/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior studies have demonstrated travel-related acquisition of specific opportunistic pathogens and AMR genes, but the extent and magnitude of travel's effects on the gut resistome remain largely unknown. METHODS Using whole metagenomic shotgun sequencing, functional metagenomics, and Dirichlet multinomial mixture models, we investigated the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to diverse international locations. RESULTS Travel markedly increased the abundance and α-diversity of AMR genes in the travelers' gut resistome, and we determined that 56 unique AMR genes showed significant acquisition following international travel. These acquisition events were biased towards AMR genes with efflux, inactivation, and target replacement resistance mechanisms. Travel-induced shaping of the gut resistome had distinct correlations with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features. Finally, we identified and detailed specific acquisition events of high-risk, mobile genetic element-associated AMR genes including qnr fluoroquinolone resistance genes, blaCTX-M family extended-spectrum β-lactamases, and the plasmid-borne mcr-1 colistin resistance gene. CONCLUSIONS Our results show that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes. These broad acquisitions highlight the putative risks that international travel poses to public health by gut resistome perturbation and the global spread of locally endemic AMR genes.
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Affiliation(s)
- Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Manish Boolchandani
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gianluca Galazzo
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jarne M van Hattem
- Department of Medical Microbiology, Amsterdam University Medical Center, Location AMC, Amsterdam, The Netherlands
| | - Maris S Arcilla
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Damian C Melles
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Amsterdam University Medical Center, Location AMC, Amsterdam, The Netherlands
| | - Constance Schultsz
- Department of Medical Microbiology, Amsterdam University Medical Center, Location AMC, Amsterdam, The Netherlands
- Department of Global Health, Amsterdam Institute for Global Health and Development, AMC, Amsterdam, The Netherlands
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| | - John Penders
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands.
- School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, Maastricht, The Netherlands.
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148
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Kunhikannan S, Thomas CJ, Franks AE, Mahadevaiah S, Kumar S, Petrovski S. Environmental hotspots for antibiotic resistance genes. Microbiologyopen 2021; 10:e1197. [PMID: 34180594 PMCID: PMC8123917 DOI: 10.1002/mbo3.1197] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial resistance toward broad-spectrum antibiotics has become a major concern in recent years. The threat posed by the infectious bacteria and the pace with which resistance determinants are transmitted needs to be deciphered. Soil and water contain unique and diverse microbial communities as well as pools of naturally occurring antibiotics resistant genes. Overuse of antibiotics along with poor sanitary practices expose these indigenous microbial communities to antibiotic resistance genes from other bacteria and accelerate the process of acquisition and dissemination. Clinical settings, where most antibiotics are prescribed, are hypothesized to serve as a major hotspot. The predisposition of the surrounding environments to a pool of antibiotic-resistant bacteria facilitates rapid antibiotic resistance among the indigenous microbiota in the soil, water, and clinical environments via horizontal gene transfer. This provides favorable conditions for the development of more multidrug-resistant pathogens. Limitations in detecting gene transfer mechanisms have likely left us underestimating the role played by the surrounding environmental hotspots in the emergence of multidrug-resistant bacteria. This review aims to identify the major drivers responsible for the spread of antibiotic resistance and hotspots responsible for the acquisition of antibiotic resistance genes.
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Affiliation(s)
- Shalini Kunhikannan
- Department of Physiology, Anatomy and MicrobiologySchool of Life SciencesCollege of Science, Health and EngineeringLa Trobe UniversityBundooraVicAustralia
- Department of MicrobiologyJSS Medical College and HospitalMysuruIndia
| | - Colleen J. Thomas
- Department of Physiology, Anatomy and MicrobiologySchool of Life SciencesCollege of Science, Health and EngineeringLa Trobe UniversityBundooraVicAustralia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and MicrobiologySchool of Life SciencesCollege of Science, Health and EngineeringLa Trobe UniversityBundooraVicAustralia
| | | | - Sumana Kumar
- Department of MicrobiologyFaculty of Life SciencesJSS Academy of Higher Education and ResearchMysuruIndia
| | - Steve Petrovski
- Department of Physiology, Anatomy and MicrobiologySchool of Life SciencesCollege of Science, Health and EngineeringLa Trobe UniversityBundooraVicAustralia
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149
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Wang XR, Lian XL, Su TT, Long TF, Li MY, Feng XY, Sun RY, Cui ZH, Tang T, Xia J, Huang T, Liu YH, Liao XP, Fang LX, Sun J. Duck wastes as a potential reservoir of novel antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144828. [PMID: 33545481 DOI: 10.1016/j.scitotenv.2020.144828] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Overuse of antibiotics in animal husbandry has led to an increase of antibiotic resistance microorganisms as well as antibiotic-resistance genes (ARGs). Duck farming in China is practiced on a large and diverse scale and the overuse of antibiotics in this field is gaining attention recently. We evaluated the diversity of ARGs from five duck farms using a functional metagenomic approach and constructed five libraries. A total of seventy-six resistant determinants were identified, of which sixty-one were gene variants or novel genes. The novel genes contained five β-lactamase-encoding genes designated as blaDWA1, blaDWA2, blaDWA3, blaDWA4 and blaDWB1, respectively, and two genes conferring resistance to fosfomycin designated as fosA-like1 and fosA-like2. Three of the five β-lactamase-encoding genes were further identified as extended-spectrum β-lactamases (ESBL) that can hydrolyze both penicillins and cephalosporins. Besides, two of the five β-lactamase-encoding genes were associated with mobile genetic elements, indicating a high potential for transfer of the genes to other bacterial hosts. The two novel fosA-like genes were able to increase the MICs of the test Escherichia coli strain from 2 μg/mL to as high as 256 μg/mL(up to 128-fold increase). Our study provides a reference for ARGs prevalence in duck farm wastes and implies that they are an important resistome reservoir, especially for novel ARGs with high spread potential.
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Affiliation(s)
- Xi-Ran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xin-Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Tian-Tian Su
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Teng-Fei Long
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Meng-Yuan Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao-Yin Feng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ze-Hua Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Tian Tang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jing Xia
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ting Huang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.
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Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
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Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
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