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Yildirim M, Ozgeris B, Gormez A. The effect of novel β-lactam derivatives synthesized from substituted phenethylamines on resistance genes of MRSA isolates. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00769-5. [PMID: 39210001 DOI: 10.1038/s41429-024-00769-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
This study focuses on the activity of previously reported imine and β-lactam derivatives against methicillin-resistant Staphylococcus aureus (MRSA) isolates. The presence of mecA and blaZ genes in the isolates was determined, and the minimum inhibitory concentration (MIC) values were determined based on the antibacterial activity against these isolates. Active compounds were selected and their ability to act against resistant isolates in vitro was determined. Concurrently, biochemical (nitrocefin) and molecular (qRT-PCR) tests were used to investigate the ability of the compounds to induce resistance genes in MRSA isolates. The cytotoxicity of the compounds on human dermal fibroblasts (HDF) was investigated. The MIC values of compounds (10) and (12) against MSSA and MRSA isolates were 7.81 and 15.62 μg ml-1, respectively. The most active compounds were identified as (10) and (12), and it was observed that the isolates did not develop resistance to these compounds in vitro. These compounds were found to inhibit β-lactamase, reduce the expression of resistance genes, and exhibit reduced HDF cell toxicity in a dose-dependent manner. According to the findings of the study, it can be concluded that these compounds show promise as hits with an interesting mechanism of action for further chemical modifications to develop new MRSA inhibitors.
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Affiliation(s)
- Merve Yildirim
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, 25050, Turkey
| | - Bunyamin Ozgeris
- Department of Basic Sciences, Faculty of Science, Erzurum Technical University, Erzurum, 25050, Turkey
| | - Arzu Gormez
- Department of Biology, Faculty of Science, Dokuz Eylul University, Izmir, 35390, Turkey.
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2
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El Haddad L, Angelidakis G, Zhai Y, Yaghi L, Arias CA, Shelburne SA, Jeong KC, Chemaly RF. Persistence of Daptomycin-Resistant and Vancomycin-Resistant Enterococci in Hospitalized Patients with Underlying Malignancies: A 7-Year Follow-Up Study. Microorganisms 2024; 12:1676. [PMID: 39203518 PMCID: PMC11356748 DOI: 10.3390/microorganisms12081676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) commonly colonize the gut of individuals with hematologic malignancies or undergoing hematopoietic cell transplant (HCT) and may cause bacteremia. In 2012, we identified VRE isolates from patients and patients' rooms and showed transmission networks of highly genetically related daptomycin-resistant (DR)-VRE strains. This is a follow-up study performing whole-genome sequencing (WGS) and phylogenetic analyses on 82 clinical VRE strains isolated from stools and blood cultures of patients with leukemia and HCT between 2015 and 2019. Here, we observed transmission of highly genetically related strains between rooms on the same or on different floors, including a DR-VRE strain identified in 2012. Eleven of twenty-eight patients with DR-VRE were never exposed to daptomycin, suggesting horizontal transmission. Fifteen of the twenty-eight patients with DR-VRE died within 30 days of positive blood cultures. Amongst those, one DR-VRE strain belonging to ST1471 had the virulence gene bopD responsible for biofilm formation. Additionally, to our knowledge, this is the first report of a DR-VRE strain belonging to ST323 in the United States. In summary, our study demonstrated the emergence and persistence of VRE strains, especially DR-VRE, in our hospital. Adding WGS to routine infection control measures may timely identify potential horizontal VRE transmission including multi-drug-resistant isolates.
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Affiliation(s)
- Lynn El Haddad
- Department of Medicine, University of Florida, 2033 Mowry Rd, Gainesville, FL 32610, USA
| | - Georgios Angelidakis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuting Zhai
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Layale Yaghi
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX 77030, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kwangcheol Casey Jeong
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Roy F. Chemaly
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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3
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Patel A, Goswami S, Hazarika G, Sivaprakasam S, Bhattacharjee S, Manna D. Sulfonium-Cross-Linked Hyaluronic Acid-Based Self-Healing Hydrogel: Stimuli-Responsive Drug Carrier with Inherent Antibacterial Activity to Counteract Antibiotic-Resistant Bacteria. Adv Healthc Mater 2024; 13:e2302790. [PMID: 37909063 DOI: 10.1002/adhm.202302790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/22/2023] [Indexed: 11/02/2023]
Abstract
Augmentation of the activity of Food and Drug Administration-approved antibiotics by an adjuvant or antibiotic carrier is considered one of the promising strategies to fight against antibiotic-resistant bacteria. This study reports the development of sulfonium-cross-linked hyaluronic acid (HA)-based polymer (HA-SS-HA) as an inherent antimicrobial agent and antibiotic carrier. The HA-SS-HA polymer offers the potential for encapsulating various classes of antibiotics and accomplishing a stimuli-responsive release profile in the presence of hyaluronidase produced by bacterial cells within their extracellular environment. Systematic antibacterial studies reveal that the HA-SS-HA-encapsulated antibiotics (vancomycin, amoxicillin, and tetracycline) restore its activity against the antibiotic-resistant bacterial cells methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE), and Pseudomonas aeruginosa. The HA-SS-HA gel shows robust efficacy in eradicating the mature biofilm of Staphylococcus aureus (S. aureus). The membrane-disrupting activity reveals that HA-SS-HA can also counteract the antibiotic resistance mechanism of the bacterial cells. The in vivo studies reveal excellent wound-healing activity of HA-SS-HA in albino laboratory-bred (BALB/c) mice. The outcome of additional antibacterial studies reveals that antibiotics-encapsulated HA-SS-HA hydrogel can effectively combat Gram-negative, Gram-positive, and antibiotic-resistant bacterial strains. Therefore, revitalizing the activity of commercial antibiotics by HA-SS-HA can be considered a valuable and economically effective strategy to fight against antibiotic-resistant bacteria.
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Affiliation(s)
- Anjali Patel
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Sanghamitra Goswami
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Agartala, Tripura, 799022, India
| | - Gunanka Hazarika
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Senthilkumar Sivaprakasam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Surajit Bhattacharjee
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Agartala, Tripura, 799022, India
| | - Debasis Manna
- Centre for Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
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Faleye OS, Boya BR, Lee JH, Choi I, Lee J. Halogenated Antimicrobial Agents to Combat Drug-Resistant Pathogens. Pharmacol Rev 2023; 76:90-141. [PMID: 37845080 DOI: 10.1124/pharmrev.123.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Antimicrobial resistance presents us with a potential global crisis as it undermines the abilities of conventional antibiotics to combat pathogenic microbes. The history of antimicrobial agents is replete with examples of scaffolds containing halogens. In this review, we discuss the impacts of halogen atoms in various antibiotic types and antimicrobial scaffolds and their modes of action, structure-activity relationships, and the contributions of halogen atoms in antimicrobial activity and drug resistance. Other halogenated molecules, including carbohydrates, peptides, lipids, and polymeric complexes, are also reviewed, and the effects of halogenated scaffolds on pharmacokinetics, pharmacodynamics, and factors affecting antimicrobial and antivirulence activities are presented. Furthermore, the potential of halogenation to circumvent antimicrobial resistance and rejuvenate impotent antibiotics is addressed. This review provides an overview of the significance of halogenation, the abilities of halogens to interact in biomolecular settings and enhance pharmacological properties, and their potential therapeutic usages in preventing a postantibiotic era. SIGNIFICANCE STATEMENT: Antimicrobial resistance and the increasing impotence of antibiotics are critical threats to global health. The roles and importance of halogen atoms in antimicrobial drug scaffolds have been established, but comparatively little is known of their pharmacological impacts on drug resistance and antivirulence activities. This review is the first to extensively evaluate the roles of halogen atoms in various antibiotic classes and pharmacological scaffolds and to provide an overview of their ability to overcome antimicrobial resistance.
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Affiliation(s)
- Olajide Sunday Faleye
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Bharath Reddy Boya
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Inho Choi
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
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Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Bambakidis T, Singleton DM, Liu F, Edirisinghe JN, Faria JP, Leleiwi I, Daly RA, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Sullivan MB, Henry CS, Wood-Charlson EM, Ross MRV, Miller CS, Crump BC, Stegen JC, Wrighton KC. A functional microbiome catalog crowdsourced from North American rivers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550117. [PMID: 37502915 PMCID: PMC10370164 DOI: 10.1101/2023.07.22.550117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices.
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Venkateswaran P, Vasudevan S, David H, Shaktivel A, Shanmugam K, Neelakantan P, Solomon AP. Revisiting ESKAPE Pathogens: virulence, resistance, and combating strategies focusing on quorum sensing. Front Cell Infect Microbiol 2023; 13:1159798. [PMID: 37457962 PMCID: PMC10339816 DOI: 10.3389/fcimb.2023.1159798] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The human-bacterial association is long-known and well-established in terms of both augmentations of human health and attenuation. However, the growing incidents of nosocomial infections caused by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) call for a much deeper understanding of these organisms. Adopting a holistic approach that includes the science of infection and the recent advancements in preventing and treating infections is imperative in designing novel intervention strategies against ESKAPE pathogens. In this regard, this review captures the ingenious strategies commissioned by these master players, which are teamed up against the defenses of the human team, that are equally, if not more, versatile and potent through an analogy. We have taken a basketball match as our analogy, dividing the human and bacterial species into two teams playing with the ball of health. Through this analogy, we make the concept of infectious biology more accessible.
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Affiliation(s)
- Parvathy Venkateswaran
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sahana Vasudevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Helma David
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Adityan Shaktivel
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Karthik Shanmugam
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Prasanna Neelakantan
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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7
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AbdAlhafiz AI, Elleboudy NS, Aboshanab KM, Aboulwafa MM, Hassouna NA. Phenotypic and genotypic characterization of linezolid resistance and the effect of antibiotic combinations on methicillin-resistant Staphylococcus aureus clinical isolates. Ann Clin Microbiol Antimicrob 2023; 22:23. [PMID: 37013561 PMCID: PMC10069030 DOI: 10.1186/s12941-023-00574-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 03/12/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Methicillin-Resistant Staphylococcus aureus (MRSA) causes life-threatening infections, with narrow therapeutic options including: vancomycin and linezolid. Accordingly, this study aimed to characterize phenotypically and genotypically, the most relevant means of linezolid resistance among some MRSA clinical isolates. METHODS A total of 159 methicillin-resistant clinical isolates were collected, of which 146 were indentified microscopically and biochemically as MRSA. Both biofilm formation and efflux pump activity were assessed for linezolid-resistant MRSA (LR-MRSA) using the microtiter plate and carbonyl cyanide 3-chlorophenylhydrazone (CCCP) methods, respectively. Linezolid resistance was further characterized by polymerase chain reaction (PCR) amplification and sequencing of domain V of 23 S rRNA; rplC; rplD;and rplV genes. Meanwhile, some resistance genes were investigated: cfr; cfr(B); optrA; msrA;mecA; and vanA genes. To combat LR-MRSA, the effect of combining linezolid with each of 6 different antimicrobials was investigated using the checkerboard assay. RESULTS Out of the collected MRSA isolates (n = 146), 5.48% (n = 8) were LR-MRSA and 18.49% (n = 27) were vancomycin-resistant (VRSA). It is worth noting that all LR-MRSA isolates were also vancomycin-resistant. All LR-MRSA isolates were biofilm producers (r = 0.915, p = 0.001), while efflux pumps upregulation showed no significant contribution to development of resistance (t = 1.374, p = 0.212). Both mecA and vanA genes were detected in 92.45% (n = 147) and 6.92% (n = 11) of methicillin-resistant isolates, respectively. In LR-MRSA isolates, some 23 S rRNA domain V mutations were observed: A2338T and C2610G (in 5 isolates); T2504C and G2528C (in 2 isolates); and G2576T (in 1 isolate). Amino acids substitutions were detected: in L3 protein (rplC gene) of (3 isolates) and in L4 protein (rplD gene) of (4 isolates). In addition, cfr(B) gene was detected (in 3 isolates). In 5 isolates, synergism was recorded when linezolid was combined with chloramphenicol, erythromycin, or ciprofloxacin. Reversal of linezolid resistance was observed in some LR-MRSA isolates when linezolid was combined with gentamicin or vancomycin. CONCLUSIONS LR-MRSA biofilm producers' phenotypes evolved in the clinical settings in Egypt. Various antibiotic combinations with linezolid were evaluated in vitro and showed synergistic effects.
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Affiliation(s)
- Asmaa I AbdAlhafiz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nooran S Elleboudy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohammad M Aboulwafa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
- Faculty of Pharmacy, King Salman International University, South Sinai, Ras-Sudr, Egypt.
| | - Nadia A Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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8
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Sahoo S, Behera MR, Mishra B, Sahoo P, Kar S. Antibiotic-resistant bacteria in bovine milk in India. J Adv Vet Anim Res 2023; 10:21-29. [PMID: 37155547 PMCID: PMC10122944 DOI: 10.5455/javar.2023.j648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 05/10/2023] Open
Abstract
Antibiotic resistance (ABR) is a global issue that draws the attention of all healthcare experts in the veterinary and medical fields. Of various factors, indiscriminate and unregulated antibiotic usage in the animals reared for food production, especially in cows and buffaloes suffering from mastitis, contribute significantly to the rising incidence of resistant bacteria. A literature survey reveals the spread of resistant strains of mastitis-causing bacteria, like Staphylococcus aureus and Escherichia coli, to humans. In addition, antibiotic residues detected in milk samples against all major groups of antibiotics are likely to enter the human body through the food chain and aggravate the condition. The cumulative effects of ABR have emerged as a silent killer. The benefits of systematic surveillance on ABR in India are yet to be available. Here is an attempt to understand the ABR burden in India associated with bovine milk and its mitigation strategies.
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Affiliation(s)
- Sonali Sahoo
- School of Public Health, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Manas Ranjan Behera
- School of Public Health, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Biswajit Mishra
- Quality Assurance, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Priyadarshini Sahoo
- Veterinary Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Sonali Kar
- Department of Community Medicine, Kalinga Institute of Medical Sciences (KIMS), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
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9
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Zhao H, Zhang J, Chen X, Yang S, Huang H, Pan L, Huang L, Jiang G, Tang J, Xu Q, Dong K, Li N. Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158811. [PMID: 36115398 DOI: 10.1016/j.scitotenv.2022.158811] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.
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Affiliation(s)
- Huaxian Zhao
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xing Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shu Yang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Haifeng Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Lianghao Pan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536000, China
| | - Liangliang Huang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Gonglingxia Jiang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Jinli Tang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Qiangsheng Xu
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
| | - Ke Dong
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Nan Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China.
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Selvarajan R, Obize C, Sibanda T, Abia ALK, Long H. Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance. Antibiotics (Basel) 2022; 12:28. [PMID: 36671228 PMCID: PMC9855083 DOI: 10.3390/antibiotics12010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.
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Affiliation(s)
- Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Chinedu Obize
- Centre d’étude de la Forêt, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Timothy Sibanda
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Akebe Luther King Abia
- Department of Microbiology, Venda University, Thohoyando 1950, South Africa
- Environmental Research Foundation, Westville 3630, South Africa
| | - Haijun Long
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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Heterologous Expression Reveals Ancient Properties of Tei3—A VanS Ortholog from the Teicoplanin Producer Actinoplanes teichomyceticus. Int J Mol Sci 2022; 23:ijms232415713. [PMID: 36555354 PMCID: PMC9779433 DOI: 10.3390/ijms232415713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Glycopeptide antibiotics (GPAs) are among the most clinically successful antimicrobials. GPAs inhibit cell-wall biosynthesis in Gram-positive bacteria via binding to lipid II. Natural GPAs are produced by various actinobacteria. Being themselves Gram-positives, the GPA producers evolved sophisticated mechanisms of self-resistance to avoid suicide during antibiotic production. These self-resistance genes are considered the primary source of GPA resistance genes actually spreading among pathogenic enterococci and staphylococci. The GPA-resistance mechanism in Actinoplanes teichomyceticus—the producer of the last-resort-drug teicoplanin—has been intensively studied in recent years, posing relevant questions about the role of Tei3 sensor histidine kinase. In the current work, the molecular properties of Tei3 were investigated. The setup of a GPA-responsive assay system in the model Streptomyces coelicolor allowed us to demonstrate that Tei3 functions as a non-inducible kinase, conferring high levels of GPA resistance in A. teichomyceticus. The expression of different truncated versions of tei3 in S. coelicolor indicated that both the transmembrane helices of Tei3 are crucial for proper functioning. Finally, a hybrid gene was constructed, coding for a chimera protein combining the Tei3 sensor domain with the kinase domain of VanS, with the latter being the inducible Tei3 ortholog from S. coelicolor. Surprisingly, such a chimera did not respond to teicoplanin, but indeed to the related GPA A40926. Coupling these experimental results with a further in silico analysis, a novel scenario on GPA-resistance and biosynthetic genes co-evolution in A. teichomyceticus was hereby proposed.
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Determination of Enterococcus faecalis and Enterococcus faecium Antimicrobial Resistance and Virulence Factors and Their Association with Clinical and Demographic Factors in Kenya. J Pathog 2022; 2022:3129439. [PMID: 36405031 PMCID: PMC9668473 DOI: 10.1155/2022/3129439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background Enterococci are clinically significant because of their increasing antibiotic resistance and their ability to cause severe infections due to an arsenal of virulence genes. Few studies in the developing world have examined virulence factors that may significantly impact patient outcomes. This study describes the antimicrobial resistance profiles and prevalence of five key Enterococcal virulence genes gelE, asa, cylA, esp, and hyl in forty-four clinical Enterococcus faecalis and E. faecium isolates in Kenya and their association with patients' demographic and clinical characteristics. Results All E. faecium isolates were obtained from hospital-acquired skin and soft tissue infections. While E. faecalis was associated with community-acquired urinary tract infections. All isolates were resistant to erythromycin, whereas 11/44 (27.5%), 25/44 (56.8%), 28/44 (63.6%), 37/44 (84.1%), 40/44 (90.0%), and 43/44 (97.5%) were susceptible to tetracycline, levofloxacin, gentamicin, ampicillin, nitrofurantoin, and teicoplanin, respectively. All isolates were susceptible to tigecycline, vancomycin, and linezolid. There was little difference in the antibiotic resistance profiles between E. faecalis and E. faecium. The prevalence of the virulence genes among the 44 isolates were 27 (61.4%) for gelE, 26 (59.1%) for asa1, 16 (36.3%) for esp, 11 (25.0%) for cylA, and 1 (2.3%) for hyl. 72.9% of E. faecalis isolates had multiple virulence genes compared to 57% of E. faecium isolates with no virulence genes. The hyl gene was only detected in E. faecium, while cylA and asa1 were only detected in E. faecalis. A significant correlation was observed between the presence of asa1 and esp virulence genes and tetracycline resistance (P=0.0305 and 0.0363, respectively). A significant correlation was also observed between the presence of virulence genes gelE and asa1 and nitrofurantoin resistance (P=0.0175 and 0.0225, respectively) and ampicillin resistance (P=0.0005 and 0.0008, respectively). Conclusion The study highlights the high levels of erythromycin resistance in E. faecalis and E. faecium, the demographic factors influencing the species distribution among patients, and the accumulation of multiple virulence genes in E. faecalis. The significant association of gelE, asa1, and esp virulence genes with drug resistance could explain the pathogenic success of E. faecalis and provides a guide for future studies.
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Zhu L, Lian Y, Lin D, Huang D, Yao Y, Ju F, Wang M. Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129356. [PMID: 35728317 DOI: 10.1016/j.jhazmat.2022.129356] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.
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Affiliation(s)
- Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yulu Lian
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dan Huang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yanlai Yao
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Feng Ju
- Key laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310024, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China.
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14
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Xu M, Wang W, Wright GD. Glycopeptide antibiotic discovery in the genomic era. Methods Enzymol 2022; 665:325-346. [PMID: 35379441 DOI: 10.1016/bs.mie.2021.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Glycopeptide antibiotics are essential drugs used to treat infections caused by multi-drug resistant Gram-positive pathogens. There is a continuous need for new antibiotics, including GPAs, to address emerging resistance and offer desirable pharmacological profiles for improved efficacy. Microbial natural products are proven sources of antibiotics, and this source has dominated drug discovery over the past century. Bacteria from the phylum Actinobacteria are particularly renowned for producing a diverse range of bioactive natural products including glycopeptide antibiotics. The traditional approach to mining this resource is through the culture and extraction of natural products followed by assay for cell-killing activity. Unfortunately, this method no longer efficiently yields new antibiotic leads, delivering instead known compounds. Whole-genome sequencing programs on the other hand are revealing thousands of unexplored natural product biosynthetic gene clusters in the chromosomes of Actinobacteria. These gene clusters encode the necessary enzymes, transport and resistance mechanisms, along with regulatory elements for the biosynthesis of a variety of antibiotics. Identification of uncharacterized or cryptic biosynthetic gene clusters to unlock the chemical "dark matter" represents a new direction for the discovery of new drug candidates. This chapter discusses the identification of glycopeptide antibiotic biosynthetic gene clusters in microbial genomes, the improved production of these antibiotics using the GPAHex synthetic biology platform, and methods for their purification.
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Affiliation(s)
- Min Xu
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Wenliang Wang
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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15
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Yushchuk O, Zhukrovska K, Berini F, Fedorenko V, Marinelli F. Genetics Behind the Glycosylation Patterns in the Biosynthesis of Dalbaheptides. Front Chem 2022; 10:858708. [PMID: 35402387 PMCID: PMC8987122 DOI: 10.3389/fchem.2022.858708] [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] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Glycopeptide antibiotics are valuable natural metabolites endowed with different pharmacological properties, among them are dalbaheptides used to treat different infections caused by multidrug-resistant Gram-positive pathogens. Dalbaheptides are produced by soil-dwelling high G-C Gram-positive actinobacteria. Their biosynthetic pathways are encoded within large biosynthetic gene clusters. A non-ribosomally synthesized heptapeptide aglycone is the common scaffold for all dalbaheptides. Different enzymatic tailoring steps, including glycosylation, are further involved in decorating it. Glycosylation of dalbaheptides is a crucial step, conferring them specific biological activities. It is achieved by a plethora of glycosyltransferases, encoded within the corresponding biosynthetic gene clusters, able to install different sugar residues. These sugars might originate from the primary metabolism, or, alternatively, their biosynthesis might be encoded within the biosynthetic gene clusters. Already installed monosaccharides might be further enzymatically modified or work as substrates for additional glycosylation. In the current minireview, we cover recent updates concerning the genetics and enzymology behind the glycosylation of dalbaheptides, building a detailed and consecutive picture of this process and of its biological evolution. A thorough understanding of how glycosyltransferases function in dalbaheptide biosynthesis might open new ways to use them in chemo-enzymatic synthesis and/or in combinatorial biosynthesis for building novel glycosylated antibiotics.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Kseniia Zhukrovska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- *Correspondence: Flavia Marinelli,
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Berini F, Orlandi V, Gornati R, Bernardini G, Marinelli F. Nanoantibiotics to fight multidrug resistant infections by Gram-positive bacteria: hope or reality? Biotechnol Adv 2022; 57:107948. [PMID: 35337933 DOI: 10.1016/j.biotechadv.2022.107948] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/17/2022]
Abstract
The spread of antimicrobial resistance in Gram-positive pathogens represents a threat to human health. To counteract the current lack of novel antibiotics, alternative antibacterial treatments have been increasingly investigated. This review covers the last decade's developments in using nanoparticles as carriers for the two classes of frontline antibiotics active on multidrug-resistant Gram-positive pathogens, i.e., glycopeptide antibiotics and daptomycin. Most of the reviewed papers deal with vancomycin nanoformulations, being teicoplanin- and daptomycin-carrying nanosystems much less investigated. Special attention is addressed to nanoantibiotics used for contrasting biofilm-associated infections. The status of the art related to nanoantibiotic toxicity is critically reviewed.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via JH Dunant 3, 21100 Varese, Italy.
| | - Viviana Orlandi
- Department of Biotechnology and Life Sciences, University of Insubria, via JH Dunant 3, 21100 Varese, Italy.
| | - Rosalba Gornati
- Department of Biotechnology and Life Sciences, University of Insubria, via JH Dunant 3, 21100 Varese, Italy.
| | - Giovanni Bernardini
- Department of Biotechnology and Life Sciences, University of Insubria, via JH Dunant 3, 21100 Varese, Italy.
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via JH Dunant 3, 21100 Varese, Italy.
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Montaño ET, Nideffer JF, Brumage L, Erb M, Busch J, Fernandez L, Derman AI, Davis JP, Estrada E, Fu S, Le D, Vuppala A, Tran C, Luterstein E, Lakkaraju S, Panchagnula S, Ren C, Doan J, Tran S, Soriano J, Fujita Y, Gutala P, Fujii Q, Lee M, Bui A, Villarreal C, Shing SR, Kim S, Freeman D, Racha V, Ho A, Kumar P, Falah K, Dawson T, Enustun E, Prichard A, Gomez A, Khanna K, Trigg S, Pogliano K, Pogliano J. Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PLoS One 2022; 17:e0262354. [PMID: 35061755 PMCID: PMC8782336 DOI: 10.1371/journal.pone.0262354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare's most potent antibiotics are becoming obsolete. Approximately two-thirds of the world's antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 104 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
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Affiliation(s)
- Elizabeth T. Montaño
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jason F. Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marcella Erb
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Julia Busch
- Department of Immunology, Duke University, Durham, North Carolina, United Stated of America
| | - Lynley Fernandez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alan I. Derman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - John Paul Davis
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elena Estrada
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Fu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Le
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aishwarya Vuppala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Cassidy Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elaine Luterstein
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shivani Lakkaraju
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sriya Panchagnula
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Caroline Ren
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer Doan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jamielyn Soriano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Yuya Fujita
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Pranathi Gutala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Quinn Fujii
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Minda Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Anthony Bui
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Carleen Villarreal
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel R. Shing
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sean Kim
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Freeman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Vipula Racha
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alicia Ho
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Prianka Kumar
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kian Falah
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Thomas Dawson
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Amy Prichard
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Ana Gomez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shelly Trigg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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18
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Berini F, Orlandi VT, Gamberoni F, Martegani E, Armenia I, Gornati R, Bernardini G, Marinelli F. Antimicrobial Activity of Nanoconjugated Glycopeptide Antibiotics and Their Effect on Staphylococcus aureus Biofilm. Front Microbiol 2021; 12:657431. [PMID: 34925248 PMCID: PMC8674785 DOI: 10.3389/fmicb.2021.657431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
In the era of antimicrobial resistance, the use of nanoconjugated antibiotics is regarded as a promising approach for preventing and fighting infections caused by resistant bacteria, including those exacerbated by the formation of difficult-to-treat bacterial biofilms. Thanks to their biocompatibility and magnetic properties, iron oxide nanoparticles (IONPs) are particularly attractive as antibiotic carriers for the targeting therapy. IONPs can direct conjugated antibiotics to infection sites by the use of an external magnet, facilitating tissue penetration and disturbing biofilm formation. As a consequence of antibiotic localization, a decrease in its administration dosage might be possible, reducing the side effects to non-targeted organs and the risk of antibiotic resistance spread in the commensal microbiota. Here, we prepared nanoformulations of the 'last-resort' glycopeptides teicoplanin and vancomycin by conjugating them to IONPs via surface functionalization with (3-aminopropyl) triethoxysilane (APTES). These superparamagnetic NP-TEICO and NP-VANCO were chemically stable and NP-TEICO (better than NP-VANCO) conserved the typical spectrum of antimicrobial activity of glycopeptide antibiotics, being effective against a panel of staphylococci and enterococci, including clinical isolates and resistant strains. By a combination of different methodological approaches, we proved that NP-TEICO and, although to a lesser extent, NP-VANCO were effective in reducing biofilm formation by three methicillin-sensitive or resistant Staphylococcus aureus strains. Moreover, when attracted and concentrated by the action of an external magnet, NP-TEICO exerted a localized inhibitory effect on S. aureus biofilm formation at low antibiotic concentration. Finally, we proved that the conjugation of glycopeptide antibiotics to IONPs reduced their intrinsic cytotoxicity toward a human cell line.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Federica Gamberoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Eleonora Martegani
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Ilaria Armenia
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
| | - Rosalba Gornati
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giovanni Bernardini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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Andreo-Vidal A, Binda E, Fedorenko V, Marinelli F, Yushchuk O. Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum. Antibiotics (Basel) 2021; 10:1533. [PMID: 34943745 PMCID: PMC8698665 DOI: 10.3390/antibiotics10121533] [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: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/26/2022] Open
Abstract
The spread of antimicrobial resistance (AMR) creates a challenge for global health security, rendering many previously successful classes of antibiotics useless. Unfortunately, this also includes glycopeptide antibiotics (GPAs), such as vancomycin and teicoplanin, which are currently being considered last-resort drugs. Emerging resistance towards GPAs risks limiting the clinical use of this class of antibiotics-our ultimate line of defense against multidrug-resistant (MDR) Gram-positive pathogens. But where does this resistance come from? It is widely recognized that the GPA resistance determinants-van genes-might have originated from GPA producers, such as soil-dwelling Gram-positive actinobacteria, that use them for self-protection. In the current work, we present a comprehensive bioinformatics study on the distribution and phylogeny of GPA resistance determinants within the Actinobacteria phylum. Interestingly, van-like genes (vlgs) were found distributed in different arrangements not only among GPA-producing actinobacteria but also in the non-producers: more than 10% of the screened actinobacterial genomes contained one or multiple vlgs, while less than 1% encoded for a biosynthetic gene cluster (BGC). By phylogenetic reconstructions, our results highlight the co-evolution of the different vlgs, indicating that the most diffused are the ones coding for putative VanY carboxypeptidases, which can be found alone in the genomes or associated with a vanS/R regulatory pair.
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Affiliation(s)
- Andrés Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine;
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
| | - Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.A.-V.); (E.B.); (O.Y.)
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine;
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20
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Riahi HS, Heidarieh P, Fatahi-Bafghi M. Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology. J Appl Microbiol 2021; 132:890-906. [PMID: 34469043 DOI: 10.1111/jam.15271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.
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Affiliation(s)
- Hanieh Sadat Riahi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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21
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Yushchuk O, Vior NM, Andreo-Vidal A, Berini F, Rückert C, Busche T, Binda E, Kalinowski J, Truman AW, Marinelli F. Genomic-Led Discovery of a Novel Glycopeptide Antibiotic by Nonomuraea coxensis DSM 45129. ACS Chem Biol 2021; 16:915-928. [PMID: 33913701 PMCID: PMC8291499 DOI: 10.1021/acschembio.1c00170] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Glycopeptide antibiotics
(GPAs) are last defense line drugs against
multidrug-resistant Gram-positive pathogens. Natural GPAs teicoplanin
and vancomycin, as well as semisynthetic oritavancin, telavancin,
and dalbavancin, are currently approved for clinical use. Although
these antibiotics remain efficient, emergence of novel GPA-resistant
pathogens is a question of time. Therefore, it is important to investigate
the natural variety of GPAs coming from so-called “rare”
actinobacteria. Herein we describe a novel GPA producer—Nonomuraea coxensis DSM 45129. Its de novo sequenced and completely assembled genome harbors a biosynthetic
gene cluster (BGC) similar to the dbv BGC of A40926,
the natural precursor to dalbavancin. The strain produces a novel
GPA, which we propose is an A40926 analogue lacking the carboxyl group
on the N-acylglucosamine moiety. This structural
difference correlates with the absence of dbv29—coding
for an enzyme responsible for the oxidation of the N-acylglucosamine moiety. Introduction of dbv29 into N. coxensis led to A40926 production in this strain.
Finally, we successfully applied dbv3 and dbv4 heterologous transcriptional regulators to trigger
and improve A50926 production in N. coxensis, making them prospective tools for screening other Nonomuraea spp. for GPA production. Our work highlights
genus Nonomuraea as a still untapped
source of novel GPAs.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Andres Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
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Qian X, Gunturu S, Guo J, Chai B, Cole JR, Gu J, Tiedje JM. Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. MICROBIOME 2021; 9:108. [PMID: 33990222 PMCID: PMC8122544 DOI: 10.1186/s40168-021-01047-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.
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Affiliation(s)
- Xun Qian
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jie Gu
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - James M. Tiedje
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
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23
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Secondary Metabolites of the Genus Amycolatopsis: Structures, Bioactivities and Biosynthesis. Molecules 2021; 26:molecules26071884. [PMID: 33810439 PMCID: PMC8037709 DOI: 10.3390/molecules26071884] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Actinomycetes are regarded as important sources for the generation of various bioactive secondary metabolites with rich chemical and bioactive diversities. Amycolatopsis falls under the rare actinomycete genus with the potential to produce antibiotics. In this review, all literatures were searched in the Web of Science, Google Scholar and PubMed up to March 2021. The keywords used in the search strategy were “Amycolatopsis”, “secondary metabolite”, “new or novel compound”, “bioactivity”, “biosynthetic pathway” and “derivatives”. The objective in this review is to summarize the chemical structures and biological activities of secondary metabolites from the genus Amycolatopsis. A total of 159 compounds derived from 8 known and 18 unidentified species are summarized in this paper. These secondary metabolites are mainly categorized into polyphenols, linear polyketides, macrolides, macrolactams, thiazolyl peptides, cyclic peptides, glycopeptides, amide and amino derivatives, glycoside derivatives, enediyne derivatives and sesquiterpenes. Meanwhile, they mainly showed unique antimicrobial, anti-cancer, antioxidant, anti-hyperglycemic, and enzyme inhibition activities. In addition, the biosynthetic pathways of several potent bioactive compounds and derivatives are included and the prospect of the chemical substances obtained from Amycolatopsis is also discussed to provide ideas for their implementation in the field of therapeutics and drug discovery.
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