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Sass TH, Lovett ST. The DNA damage response of Escherichia coli, revisited: Differential gene expression after replication inhibition. Proc Natl Acad Sci U S A 2024; 121:e2407832121. [PMID: 38935560 PMCID: PMC11228462 DOI: 10.1073/pnas.2407832121] [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: 04/19/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
In 1967, in this journal, Evelyn Witkin proposed the existence of a coordinated DNA damage response in Escherichia coli, which later came to be called the "SOS response." We revisited this response using the replication inhibitor azidothymidine (AZT) and RNA-Seq analysis and identified several features. We confirm the induction of classic Save our ship (SOS) loci and identify several genes, including many of the pyrimidine pathway, that have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. We show that the transcription factor "stringent starvation protein" SspA is as important as LexA in the regulation of AZT-induced genes and that the genes activated by SspA change dramatically after AZT exposure. Our experiments identify additional LexA-independent DNA damage inducible genes, including 22 small RNA genes, some of which appear to activated by SspA. Motility and chemotaxis genes are strongly down-regulated by AZT, possibly as a result of one of more of the small RNAs or other transcription factors such as AppY and GadE, whose expression is elevated by AZT. Genes controlling the iron siderophore, enterobactin, and iron homeostasis are also strongly induced, independent of LexA. We confirm that IraD antiadaptor protein is induced independent of LexA and that a second antiadaptor, IraM is likewise strongly AZT-inducible, independent of LexA, suggesting that RpoS stabilization via these antiadaptor proteins is an integral part of replication stress tolerance.
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Affiliation(s)
- Thalia H Sass
- Department of Biology, Brandeis University, Waltham, MA 02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA 02454-9110
| | - Susan T Lovett
- Department of Biology, Brandeis University, Waltham, MA 02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA 02454-9110
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2
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Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 PMCID: PMC11237771 DOI: 10.1128/mbio.00504-24] [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: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
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Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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3
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Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
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Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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4
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Stanton IC, Tipper HJ, Chau K, Klümper U, Subirats J, Murray AK. Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:623-636. [PMID: 36416260 DOI: 10.1002/etc.5498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universitӓt Dresden, Dresden, Germany
| | - Jessica Subirats
- Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Aimee K Murray
- College of Medicine and Health, University of Exeter, Cornwall, UK
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5
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Chowdhury AR, Mukherjee D, Chatterjee R, Chakravortty D. Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay. Mol Microbiol 2024; 121:213-229. [PMID: 38071466 DOI: 10.1111/mmi.15209] [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: 07/31/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.
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Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Debapriya Mukherjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Ritika Chatterjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
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6
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Wu D, Liang S, Du X, Xiao J, Feng H, Ren Z, Yang X, Yang X. Effects of fecal microbiota transplantation and fecal virome transplantation on LPS-induced intestinal injury in broilers. Poult Sci 2024; 103:103316. [PMID: 38128454 PMCID: PMC10776634 DOI: 10.1016/j.psj.2023.103316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/12/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
The interesting roles and efficiencies of fecal microbiota transplantation (FMT) have attracted considerable attention and have been gradually evidenced in specific animal models. While the growing evidence that bacteriophages play roles in FMT efficacy has attracted considerable interest. In this study, we aimed to explore the effects of FMT and fecal virome transplantation (FVT) in improving inflammatory damage and ileal microbiota disorder in broilers. A total of 224 Arbor Acres broilers were selected at 1-day-old and randomly divided into the following 4 groups, with 56 broilers in each group: the CON group (the negative control group, sterile physiological saline injection + sterile phosphate-buffered saline (PBS) solution gavage), LPS group (the positive control group, lipopolysaccharide (LPS) injection + sterile PBS solution gavage), LPS + FMT group (LPS injection + FMT solution gavage), LPS + FVT group (LPS injection + FVT solution gavage). The results showed that: LPS injection significantly upregulated the mRNA expression levels of IFN-γ (P < 0.05) and IL-8 (P < 0.001) in ileal mucosa of broilers at 11th day of age (D11), while LPS + FMT and LPS + FVT did not; LPS injection significantly upregulated the mRNA expression of ZO-1 in ileal mucosa at D11 (P < 0.01), while LPS + FMT and LPS + FVT did not; at D11, compare to CON group, LPS injection and LPS + FMT significantly increased the relative abundance of virulence factor Rab2 interacting conserved protein A-related genes in broiler ileum contents (P < 0.05), while LPS + FVT had no significant difference with CON group (P > 0.05); at D11, LPS injection significantly downregulated the biosynthesis of antibiotics pathway (P < 0.05) in the ileal contents, while LPS + FVT did not. In conclusion, both FMT and FVT could promote the recovery of inflammation caused by LPS. Furthermore, FVT had shown less disadvantage stimulation on the broilers and could reduce the risk of transmission of pathogenic genes, compared to FMT.
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Affiliation(s)
- Dengyu Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Saisai Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaoqian Du
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jinhao Xiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hongyu Feng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhouzheng Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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7
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Tashjian TF, Zeinert RD, Eyles SJ, Chien P. Proteomic survey of the DNA damage response in Caulobacter crescentus. J Bacteriol 2023; 205:e0020623. [PMID: 37730540 PMCID: PMC10601758 DOI: 10.1128/jb.00206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 09/22/2023] Open
Abstract
The bacterial DNA damage response is a critical, coordinated response to endogenous and exogenous sources of DNA damage. Response dynamics are dependent on coordinated synthesis and loss of relevant proteins. While much is known about its global transcriptional control, changes in protein abundance that occur upon DNA damage are less well characterized at the system level. Here, we perform a proteome-wide survey of the DNA damage response in Caulobacter crescentus. We find that while most protein abundance changes upon DNA damage are readily explained by changes in transcription, there are exceptions. The survey also allowed us to identify the novel DNA damage response factor, YaaA, which has been overlooked by previously published, transcription-focused studies. A similar survey in a ∆lon strain was performed to explore lon's role in DNA damage survival. The ∆lon strain had a smaller dynamic range of protein abundance changes in general upon DNA damage compared to the wild-type strain. This system-wide change to the dynamics of the response may explain this strain's sensitivity to DNA damage. Our proteome survey of the DNA damage response provides additional insight into the complex regulation of stress response and nominates a novel response factor that was overlooked in prior studies. IMPORTANCE The DNA damage response helps bacteria to react to and potentially survive DNA damage. The mutagenesis induced during this stress response contributes to the development of antibiotic resistance. Understanding how bacteria coordinate their response to DNA damage could help us to combat this growing threat to human health. While the transcriptional regulation of the bacterial DNA damage response has been characterized, this study is the first to our knowledge to assess the proteomic response to DNA damage in Caulobacter.
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Affiliation(s)
- Tommy F. Tashjian
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Rilee D. Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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8
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Thabet MA, Penadés JR, Haag AF. The ClpX protease is essential for inactivating the CI master repressor and completing prophage induction in Staphylococcus aureus. Nat Commun 2023; 14:6599. [PMID: 37852980 PMCID: PMC10584840 DOI: 10.1038/s41467-023-42413-0] [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: 09/22/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
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Affiliation(s)
- Mohammed A Thabet
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK
- Department of Biology, Faculty of Science, Al-Baha University, Al-Baha city, Al Aqiq, 65779, Kingdom of Saudi Arabia
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Andreas F Haag
- School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, UK.
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
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9
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Hu J, Wu Y, Kang L, Liu Y, Ye H, Wang R, Zhao J, Zhang G, Li X, Wang J, Han D. Dietary D-xylose promotes intestinal health by inducing phage production in Escherichia coli. NPJ Biofilms Microbiomes 2023; 9:79. [PMID: 37821428 PMCID: PMC10567762 DOI: 10.1038/s41522-023-00445-w] [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: 05/03/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023] Open
Abstract
Elimination of specific enteropathogenic microorganisms is critical to gut health. However, the complexity of the gut community makes it challenging to target specific bacterial organisms. Accumulating evidence suggests that various foods can change the abundance of intestinal bacteria by modulating prophage induction. By using pathogenic Escherichia coli (E. coli) ATCC 25922 as a model in this research, we explored the potential of dietary modulation of prophage induction and subsequent bacterial survival. Among a panel of sugars tested in vitro, D-xylose was shown to efficiently induce prophages in E. coli ATCC 25922, which depends, in part, upon the production of D-lactic acid. In an enteric mouse model, prophage induction was found to be further enhanced in response to propionic acid. Dietary D-xylose increased the proportion of Clostridia which converted D-lactic acid to propionic acid. Intestinal propionic acid levels were diminished, following either oral gavage with the dehydrogenase gene (ldhA)-deficient E. coli ATCC 25922 or depletion of intestinal Clostridia by administration of streptomycin. D-Xylose metabolism and exposure to propionic acid triggered E. coli ATCC 25922 SOS response that promoted prophage induction. E. coli ATCC 25922 mutant of RecA, a key component of SOS system, exhibited decreased phage production. These findings suggest the potential of using dietary components that can induce prophages as antimicrobial alternatives for disease control and prevention by targeted elimination of harmful gut bacteria.
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Affiliation(s)
- Jie Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yifan Wu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Luyuan Kang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yisi Liu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Ye
- Department of Animal Sciences, Wageningen University & Research, NL-6700, AH, Wageningen, the Netherlands
| | - Ran Wang
- Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinbiao Zhao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Xilong Li
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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10
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Wu D, Zhang C, Liu Y, Yao J, Yang X, Wu S, Du J, Yang X. Beyond faecal microbiota transplantation, the non-negligible role of faecal virome or bacteriophage transplantation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:893-908. [PMID: 36890066 DOI: 10.1016/j.jmii.2023.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/09/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
Intestinal microbiota, which contains bacteria, archaea, fungi, protists, and viruses including bacteriophages, is symbiotic and evolves together with humans. The balanced intestinal microbiota plays indispensable roles in maintaining and regulating host metabolism and health. Dysbiosis has been associated with not only intestinal diseases but other diseases such as neurology disorders and cancers. Faecal microbiota transplantation (FMT) or faecal virome or bacteriophage transplantation (FVT or FBT), transfers faecal bacteria or viruses, with a focus on bacteriophage, from one healthy individual to another individual (normally unhealthy condition), and aims to restore the balanced gut microbiota and assist in subduing diseases. In this review, we summarized the applications of FMT and FVT in clinical settings, discussed the advantages and challenges of FMT and FVT currently and proposed several considerations prospectively. We further provided our understanding of why FMT and FVT have their limitations and raised the possible future development strategy of FMT and FVT.
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Affiliation(s)
- Dengyu Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Juan Du
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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11
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Fang Y, Yang G, Wu X, Qin B, Xie Y, Zhuang L. Sub-MIC antibiotics affect microbial ferrihydrite reduction by extracellular membrane vesicles. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131876. [PMID: 37379597 DOI: 10.1016/j.jhazmat.2023.131876] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Environmental concentrations of antibiotics, usually below MIC, have significant biological effects on bacterial cells. Sub-MIC antibiotics exposure induces bacteria to produce outer membrane vesicles (OMVs). Recently, OMVs is discovered as a novel pathway for dissimilatory iron reducing bacteria (DIRB) to mediate extracellular electron transfer (EET). Whether and how the antibiotic-induced OMVs modulate iron oxides reduction by DIRB have not been studied. This study showed the sub-MIC antibiotics (ampicillin or ciprofloxacin) increased OMVs secretion in Geobacter sulfurreducens, and the antibiotic-induced OMVs contained more redox active cytochromes facilitating iron oxides reduction, especially for the ciprofloxacin-induced OMVs. Deduced from a combination of electron microscopy and proteomic analysis, the influence of ciprofloxacin on SOS response triggered prophage induction and led to the formation of outer-inner membrane vesicles (OIMVs) in, which was a first report in Geobacter species. While ampicillin disrupting cell membrane integrity resulted in more formation of classic OMVs from outer membrane blebbing. The results indicated that the different structure and composition of vesicles were responsible for the antibiotic-dependent regulation on iron oxides reduction. This newly identified regulation on EET-mediated redox reactions by sub-MIC antibiotics expands our knowledge about the impact of antibiotics on microbial processes or "non-target" organisms.
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Affiliation(s)
- Yanlun Fang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Xian Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Baoli Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yiqiao Xie
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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12
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Liu YJ, Yang HY, Hu YY, Li ZH, Yin H, He YT, Zhong KQ, Yuan L, Zheng X, Sheng GP. Face mask derived micro(nano)plastics and organic compounds potentially induce threat to aquatic ecosystem security revealed by toxicogenomics-based assay. WATER RESEARCH 2023; 242:120251. [PMID: 37356160 DOI: 10.1016/j.watres.2023.120251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Micro(nano)plastics widely detected in aquatic environments have caused serious threat to water quality security. However, as a potential important source of micro(nano)plastics in surface water during the COVID-19 pandemic, the ecological risks of face mask waste to aquatic environments remain poorly understood. Herein, we comprehensively characterized the micro(nano)plastics and organic compounds released from four daily used face masks in aqueous environments and further evaluated their potential impacts on aquatic ecosystem safety by quantitative genotoxicity assay. Results from spectroscopy and high-resolution mass spectrum showed that plastic microfibers/particles (∼11%-83%) and leachable organic compounds (∼15%-87%) were dominantly emitted pollutants, which were significantly higher than nanoplastics (< ∼5%) based on mass of carbon. Additionally, a toxicogenomics approach using green fluorescence protein-fused whole-cell array revealed that membrane stress was the primary response upon the exposure to micro(nano)plastics, whereas the emitted organic chemicals were mainly responsible for DNA damage involving most of the DNA repair pathways (e.g., base/nucleotide excision repair, mismatch repair, double-strand break repair), implying their severe threat to membrane structure and DNA replication of microorganisms. Therefore, the persistent release of discarded face masks derived pollutants might exacerbate water quality and even adversely affect aquatic microbial functions. These findings would contribute to unraveling the potential effects of face mask waste on aquatic ecosystem security and highlight the necessity for more developed management regulations in face mask disposal.
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Affiliation(s)
- Yan-Jun Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - He-Yun Yang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Yan-Yun Hu
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Zheng-Hao Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Hao Yin
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Yun-Tian He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Keng-Qiang Zhong
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Li Yuan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xing Zheng
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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13
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Singh S, Verma T, Khamari B, Bulagonda EP, Nandi D, Umapathy S. Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains. Anal Chem 2023. [PMID: 37463121 DOI: 10.1021/acs.analchem.3c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm-1) and proteins (640 and 1662 cm-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm-1) and the lipid band (1445 cm-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, Karnataka, India
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14
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Zhang C, Wang C, Zhao X, Hakizimana I. Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163142. [PMID: 36996977 DOI: 10.1016/j.scitotenv.2023.163142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 05/13/2023]
Abstract
The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.
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Affiliation(s)
- Cong Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Xin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Israel Hakizimana
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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15
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Yan X, Liu W, Wen S, Wang L, Zhu L, Wang J, Kim YM, Wang J. Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action. J Environ Sci (China) 2023; 127:399-409. [PMID: 36522071 DOI: 10.1016/j.jes.2022.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 06/17/2023]
Abstract
As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10-5, which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.
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Affiliation(s)
- Xiaojing Yan
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Wenwen Liu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Shengfang Wen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Lanjun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Lusheng Zhu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Korea
| | - Jinhua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, China.
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16
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Crane JK, Catanzaro MN. Role of Extracellular DNA in Bacterial Response to SOS-Inducing Drugs. Antibiotics (Basel) 2023; 12:antibiotics12040649. [PMID: 37107011 PMCID: PMC10135224 DOI: 10.3390/antibiotics12040649] [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: 12/31/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
The SOS response is a conserved stress response pathway that is triggered by DNA damage in the bacterial cell. Activation of this pathway can, in turn, cause the rapid appearance of new mutations, sometimes called hypermutation. We compared the ability of various SOS-inducing drugs to trigger the expression of RecA, cause hypermutation, and produce elongation of bacteria. During this study, we discovered that these SOS phenotypes were accompanied by the release of large amounts of DNA into the extracellular medium. The release of DNA was accompanied by a form of bacterial aggregation in which the bacteria became tightly enmeshed in DNA. We hypothesize that DNA release triggered by SOS-inducing drugs could promote the horizontal transfer of antibiotic resistance genes by transformation or by conjugation.
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Affiliation(s)
- John K Crane
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Marissa N Catanzaro
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
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17
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [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: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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18
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Ledger EVK, Lau K, Tate EW, Edwards AM. XerC Is Required for the Repair of Antibiotic- and Immune-Mediated DNA Damage in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0120622. [PMID: 36802166 PMCID: PMC10019262 DOI: 10.1128/aac.01206-22] [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] [Indexed: 02/23/2023] Open
Abstract
To survive in the host environment, pathogenic bacteria need to be able to repair DNA damage caused by both antibiotics and the immune system. The SOS response is a key bacterial pathway to repair DNA double-strand breaks and may therefore be a good target for novel therapeutics to sensitize bacteria to antibiotics and the immune response. However, the genes required for the SOS response in Staphylococcus aureus have not been fully established. Therefore, we carried out a screen of mutants involved in various DNA repair pathways to understand which were required for induction of the SOS response. This led to the identification of 16 genes that may play a role in SOS response induction and, of these, 3 that affected the susceptibility of S. aureus to ciprofloxacin. Further characterization revealed that, in addition to ciprofloxacin, loss of the tyrosine recombinase XerC increased the susceptibility of S. aureus to various classes of antibiotics, as well as to host immune defenses. Therefore, the inhibition of XerC may be a viable therapeutic approach to sensitize S. aureus to both antibiotics and the immune response.
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Affiliation(s)
- Elizabeth V. K. Ledger
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Katie Lau
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Andrew M. Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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19
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Zhou H, Yang X, Yang Y, Niu Y, Li J, Fu X, Wang S, Xue B, Li C, Zhao C, Zhang X, Shen Z, Wang J, Qiu Z. Docosahexaenoic acid inhibits pheromone-responsive-plasmid-mediated conjugative transfer of antibiotic resistance genes in Enterococcus faecalis. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130390. [PMID: 36423456 DOI: 10.1016/j.jhazmat.2022.130390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
The rapid spread of antibiotic-resistance genes (ARGs) in Enterococcus faecalis (E. faecalis) poses a great challenge to human health and ecological and environmental safety. Therefore, it is important to control the spread of ARGs. In this study, we observed that the addition of 5 μg/mL docosahexaenoic acid (DHA) reduced the conjugative transfer of pCF10 plasmid by more than 95% in E. faecalis. DHA disturbed the pheromone transport by inhibiting the mRNA levels of the prgZ gene, causing the iCF10 pheromone to accumulate in the donor bacteria and bond to the PrgX receptor to form an inhibitory phase, which resulted in the down-regulation of the expression of genes related to conjugative transfer, inhibiting biofilm formation, reducing bacterial adhesion and thus inhibiting conjugative transfer. Collectively, DHA exhibited an admirable inhibitory effect on the transfer of ARGs in E. faecalis. This study provided a technical option to control the transfer of ARGs.
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Affiliation(s)
- Hongrui Zhou
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Xiaobo Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Yutong Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Yuanyuan Niu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Shanghai Ocean University, Shanghai 201306, China
| | - Jing Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xinyue Fu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Shanghai Ocean University, Shanghai 201306, China
| | - Shang Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Bin Xue
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chenyu Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chen Zhao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Xi Zhang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Zhiqiang Shen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Jingfeng Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Zhigang Qiu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
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20
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Disarm The Bacteria: What Temperate Phages Can Do. Curr Issues Mol Biol 2023; 45:1149-1167. [PMID: 36826021 PMCID: PMC9955262 DOI: 10.3390/cimb45020076] [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: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.
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21
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RecA inactivation as a strategy to reverse the heteroresistance phenomenon in clinical isolates of Escherichia coli. Int J Antimicrob Agents 2023; 61:106721. [PMID: 36642235 DOI: 10.1016/j.ijantimicag.2023.106721] [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: 07/15/2022] [Revised: 11/25/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
RecA inhibition could be an important strategy to combat antimicrobial resistance because of its key role in the SOS response, DNA repair and homologous recombination contributing to bacterial survival. This study evaluated the impact of RecA inactivation on heteroresistance in clinical isolates of Escherichia coli and their corresponding recA-deficient isogenic strains to multiple classes of antimicrobial agents. A high frequency (>30%) of heteroresistance was observed in this collection of clinical isolates. Deletion of the recA gene led to a marked reduction in heteroresistant subpopulations, especially against quinolones or β-lactams. The molecular basis of heteroresistance was associated with an increase in copy number of plasmid-borne resistance genes (blaTEM-1B) or tandem gene amplifications (qnrA1). Of note, in the absence of the recA gene, the increase in copy number of resistance genes was suppressed. This makes the recA gene a promising target for combating heteroresistance.
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22
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Liu Z, Xue Y, Yang C, Li B, Zhang Y. Rapid identification and drug resistance screening of respiratory pathogens based on single-cell Raman spectroscopy. Front Microbiol 2023; 14:1065173. [PMID: 36778844 PMCID: PMC9909742 DOI: 10.3389/fmicb.2023.1065173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Respiratory infections rank fourth in the global economic burden of disease. Lower respiratory tract infections are the leading cause of death in low-income countries. The rapid identification of pathogens causing lower respiratory tract infections to help guide the use of antibiotics can reduce the mortality of patients with lower respiratory tract infections. Single-cell Raman spectroscopy is a "whole biological fingerprint" technique that can be used to identify microbial samples. It has the advantages of no marking and fast and non-destructive testing. In this study, single-cell Raman spectroscopy was used to collect spectral data of six respiratory tract pathogen isolates. The T-distributed stochastic neighbor embedding (t-SNE) isolation analysis algorithm was used to compare the differences between the six respiratory tract pathogens. The eXtreme Gradient Boosting (XGBoost) algorithm was used to establish a Raman phenotype database model. The classification accuracy of the isolated samples was 93-100%, and the classification accuracy of the clinical samples was more than 80%. Combined with heavy water labeling technology, the drug resistance of respiratory tract pathogens was determined. The study showed that single-cell Raman spectroscopy-D2O (SCRS-D2O) labeling could rapidly identify the drug resistance of respiratory tract pathogens within 2 h.
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Affiliation(s)
- Ziyu Liu
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,School of Life Science, Jilin University, Changchun, China
| | - Ying Xue
- HOOKE Instruments Ltd., Changchun, China
| | - Chun Yang
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bei Li
- HOOKE Instruments Ltd., Changchun, China,The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences (CAS), Changchun, China
| | - Ying Zhang
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,*Correspondence: Ying Zhang ✉
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23
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Guo N, Liu M, Yang Z, Wu D, Chen F, Wang J, Zhu Z, Wang L. The synergistic mechanism of β-lactam antibiotic removal between ammonia-oxidizing microorganisms and heterotrophs. ENVIRONMENTAL RESEARCH 2023; 216:114419. [PMID: 36174754 DOI: 10.1016/j.envres.2022.114419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Nitrifying system is an effective strategy to remove numerous antibiotics, however, the contribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and heterotrophs for antibiotic removal are still unclear. In this study, the mechanism of β-lactam antibiotic (cefalexin, CFX) removal was studied in a nitrifying sludge system. Results showed that CFX was synergistically removed by AOB (Nitrosomonas, played a major role) and AOA (Candidatus_Nitrososphaera) through ammonia monooxygenase-mediated co-metabolism, and by heterotrophs (Pseudofulvimonas, Hydrogenophaga, RB41, Thauera, UTCFX1, Plasticicumulans, Phaeodactylibacter) through antibiotic resistance genes (ARGs)-encoded β-lactamases-mediated hydrolysis. Regardless of increased archaeal and heterotrophic CFX removal with the upregulation of amoA in AOA and ARGs, the system exhibited poorer CFX removal performance at 10 mg/L, mainly due to the inhibition of AOB. This study provides new reference for the important roles of heterotrophs and ARGs, opening the possibilities for the application of ARGs in antibiotic biodegradation.
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Affiliation(s)
- Ning Guo
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China; Resources and Environment Innovation Institute, Shandong Jianzhu University, Jinan, 250101, China
| | - Mengmeng Liu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Zhuhui Yang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Daoji Wu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China; Resources and Environment Innovation Institute, Shandong Jianzhu University, Jinan, 250101, China
| | - Feiyong Chen
- Resources and Environment Innovation Institute, Shandong Jianzhu University, Jinan, 250101, China
| | - Jinhe Wang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China; Resources and Environment Innovation Institute, Shandong Jianzhu University, Jinan, 250101, China
| | - Zhaoliang Zhu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China.
| | - Lin Wang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China; Resources and Environment Innovation Institute, Shandong Jianzhu University, Jinan, 250101, China.
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24
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Ding P, Lu J, Wang Y, Schembri MA, Guo J. Antidepressants promote the spread of antibiotic resistance via horizontally conjugative gene transfer. Environ Microbiol 2022; 24:5261-5276. [PMID: 36054646 DOI: 10.1111/1462-2920.16165] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 01/07/2023]
Abstract
Antibiotic resistance is a global concern threatening public health. Horizontal gene transfer (HGT) between bacterial species contributes greatly to the dissemination of antibiotic resistance. Conjugation is one of the major HGT pathways responsible for the spread of antibiotic resistance genes (ARGs). Antidepressant drugs are commonly prescribed antipsychotics for major depressive disorders and are frequently detected in aquatic environments. However, little is known about how antidepressants stress bacteria and whether such effect can promote conjugation. Here, we report that commonly prescribed antidepressants, sertraline, duloxetine, fluoxetine, and bupropion, can promote the conjugative transfer of plasmid-borne multidrug resistance genes carried by environmentally and clinically relevant plasmids. Noteworthy, the transfer of plasmids across bacterial genera is significantly enhanced by antidepressants at clinically relevant concentrations. We also reveal the underlying mechanisms of enhanced conjugative transfer by employing flow cytometric analysis, genome-wide RNA sequencing and proteomic analysis. Antidepressants induce the production of reactive oxygen species and the SOS response, increase cell membrane permeability, and upregulate the expression of conjugation relevant genes. Given the contribution of HGT in the dissemination of ARGs, our findings highlight the importance of prudent prescription of antidepressants and to the potential connection between antidepressants and increasing antibiotic resistance.
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Affiliation(s)
- Pengbo Ding
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland, Australia
| | - Ji Lu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland, Australia
| | - Yue Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland, Australia
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25
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Okoye CO, Nyaruaba R, Ita RE, Okon SU, Addey CI, Ebido CC, Opabunmi AO, Okeke ES, Chukwudozie KI. Antibiotic resistance in the aquatic environment: Analytical techniques and interactive impact of emerging contaminants. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 96:103995. [PMID: 36210048 DOI: 10.1016/j.etap.2022.103995] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic pollution is becoming an increasingly severe threat globally. Antibiotics have emerged as a new class of environmental pollutants due to their expanding usage and indiscriminate application in animal husbandry as growth boosters. Contamination of aquatic ecosystems by antibiotics can have a variety of negative impacts on the microbial flora of these water bodies, as well as lead to the development and spread of antibiotic-resistant genes. Various strategies for removing antibiotics from aqueous systems and environments have been developed. Many of these approaches, however, are constrained by their high operating costs and the generation of secondary pollutants. This review aims to summarize research on the distribution and effects of antibiotics in aquatic environments, their interaction with other emerging contaminants, and their remediation strategy. The ecological risks associated with antibiotics in aquatic ecosystems and the need for more effective monitoring and detection system are also highlighted.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | - Raphael Nyaruaba
- Center for Biosafety Megascience, Wuhan Institute of Virology, CAS, Wuhan, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Richard Ekeng Ita
- Department of Biological Sciences Ritman University, Ikot Ekpene, Akwa Ibom State, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | - Samuel Ukpong Okon
- Department of Marine Science, Akwa Ibom State University, Mkpat Enin, P.M.B. 1167, Nigeria; Department of Ocean Engineering, Ocean College, Zhejiang University, Zhoushan 316021, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Charles Izuma Addey
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China; Organization of African Academic Doctor, Nairobi, Kenya
| | - Chike C Ebido
- Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, 212013, PR China; Organization of African Academic Doctor, Nairobi, Kenya.
| | - Kingsley Ikechukwu Chukwudozie
- Department of Microbiology, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Organization of African Academic Doctor, Nairobi, Kenya; Department of Clinical Medicine, School of Medicine, Jiangsu University 212013, PR China.
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26
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Singh S, Verma T, Nandi D, Umapathy S. Herbicides 2,4-Dichlorophenoxy Acetic Acid and Glyphosate Induce Distinct Biochemical Changes in E. coli during Phenotypic Antibiotic Resistance: A Raman Spectroscopic Study. J Phys Chem B 2022; 126:8140-8154. [PMID: 36205931 DOI: 10.1021/acs.jpcb.2c04151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antibiotic resistance is a major global health concern. The increased use of herbicides may lead to multiple antibiotic resistance in bacteria. Conventional techniques for diagnosing antibiotic resistance are laborious, time-intensive, expensive, and lack information about antibiotic susceptibility. On the other hand, Raman spectroscopy is a rapid, label-free, noninvasive alternative to traditional techniques to detect antibiotic resistance. In this study, two popular herbicides 2,4-dichlorophenoxy acetic acid (2,4-D) and N-(phosphonomethyl)glycine (glyphosate) were used to study their effects on the emergence of antibiotic resistance. The Escherichia coli wild-type (WT) MG1655 strain and two isogenic mutants, Δlon and ΔacrB, were used together with Raman spectroscopy. The WT E. coli is sensitive to antibiotics, but exposure to both herbicides induces antibiotic resistance. Using an excitation wavelength of 785 nm, the intensity ratios (e.g., I740/I785, I740/I1003, I1480/I1445, I2934/I2868, and I2934/I2845) were identified as biomarkers to study the induction of antibiotic resistance in bacteria but not NaCl-mediated stress. Using an excitation wavelength of 633 nm, the peak intensity at 740 cm-1 assigned to cytochrome bd decreases under antibiotic stress but increases upon exposure to both herbicides and antibiotics, indicating the development of resistance. Thus, this study can be applied to monitor antibiotic resistance using Raman spectroscopy.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India.,Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India.,Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
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27
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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28
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Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [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: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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29
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Metzger M, Hacobian A, Karner L, Krausgruber L, Grillari J, Dungel P. Resistance of Bacteria toward 475 nm Blue Light Exposure and the Possible Role of the SOS Response. Life (Basel) 2022; 12:1499. [PMID: 36294934 PMCID: PMC9605056 DOI: 10.3390/life12101499] [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] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2023] Open
Abstract
The increase in antibiotic resistance represents a major global challenge for our health systems and calls for alternative treatment options, such as antimicrobial light-based therapies. Blue light has shown promising results regarding the inactivation of a variety of microorganisms; however, most often, antimicrobial blue light (aBL) therapy is performed using wavelengths close to the UV range. Here we investigated whether inactivation was possible using blue light with a wavelength of 475 nm. Both Gram-positive and -negative bacterial strains were treated with blue light with fluences of 7.5-45 J/cm2. Interestingly, only some bacterial strains were susceptible to 475 nm blue light, which was associated with the lack of RecA, i.e., a fully functional DNA repair mechanism. We demonstrated that the insertion of the gene recA reduced the susceptibility of otherwise responsive bacterial strains, indicating a protective mechanism conveyed by the bacterial SOS response. However, mitigating this pathway via three known RecA inhibiting molecules (ZnAc, curcumin, and Fe(III)-PcTs) did not result in an increase in bactericidal action. Nonetheless, creating synergistic effects by combining a multitarget therapy, such as aBL, with an RecA targeting treatment could be a promising strategy to overcome the dilemma of antibiotic resistance in the future.
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Affiliation(s)
- Magdalena Metzger
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Ara Hacobian
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Lisa Karner
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Leonie Krausgruber
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Johannes Grillari
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Peter Dungel
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
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30
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da Luz BSR, de Rezende Rodovalho V, Nicolas A, Chabelskaya S, Jardin J, Briard-Bion V, Le Loir Y, de Carvalho Azevedo VA, Guédon É. Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles. Microorganisms 2022; 10:microorganisms10091808. [PMID: 36144410 PMCID: PMC9506334 DOI: 10.3390/microorganisms10091808] [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: 07/26/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus, a major opportunistic pathogen in humans, produces extracellular vesicles (EVs) that are involved in cellular communication, the delivery of virulence factors, and modulation of the host immune system response. However, to date, the impact of culture conditions on the physicochemical and functional properties of S. aureus EVs is still largely unexplored. Here, we use a proteomic approach to provide a complete protein characterization of S. aureus HG003, a NCTC8325 derivative strain and its derived EVs under four growth conditions: early- and late-stationary growth phases, and in the absence and presence of a sub-inhibitory concentration of vancomycin. The HG003 EV protein composition in terms of subcellular localization, COG and KEGG categories, as well as their relative abundance are modulated by the environment and differs from that of whole-cell (WC). Moreover, the environmental conditions that were tested had a more pronounced impact on the EV protein composition when compared to the WC, supporting the existence of mechanisms for the selective packing of EV cargo. This study provides the first general picture of the impact of different growth conditions in the proteome of S. aureus EVs and its producing-cells and paves the way for future studies to understand better S. aureus EV production, composition, and roles.
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Affiliation(s)
- Brenda Silva Rosa da Luz
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinícius de Rezende Rodovalho
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Svetlana Chabelskaya
- BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, Inserm 1230, University of Rennes 1, 35000 Rennes, France
| | | | | | - Yves Le Loir
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Éric Guédon
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Correspondence:
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31
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Gao P, Wei Y, Wan RE, Wong KW, Iu HTV, Tai SSC, Li Y, Yam HCB, Halebeedu Prakash P, Chen JHK, Ho PL, Yuen KY, Davies J, Kao RYT. Subinhibitory Concentrations of Antibiotics Exacerbate Staphylococcal Infection by Inducing Bacterial Virulence. Microbiol Spectr 2022; 10:e0064022. [PMID: 35758685 PMCID: PMC9431598 DOI: 10.1128/spectrum.00640-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/17/2022] [Indexed: 01/24/2023] Open
Abstract
Antibiotics are widely used for the treatment of bacterial infections. However, injudicious use of antibiotics based on an empirical method may lead to the emergence of resistant strains. Despite appropriate administration of antibiotics, their concentrations may remain subinhibitory in the body, due to individual variations in tissue distribution and metabolism rates. This may promote bacterial virulence and complicate the treatment strategies. To investigate whether the administration of certain classes of antibiotics will induce bacterial virulence and worsen the infection under in vivo conditions. Different classes of antibiotics were tested in vitro for their ability to induce virulence in a methicillin-resistant S. aureus strain Mu3 and clinical isolates. Antibiotic-induced pathogenicity was assessed in vivo using mouse peritonitis and bacteremia models. In vitro, β-lactam antibiotics and tetracyclines induced the expression of multiple surface-associated virulence factors as well as the secretion of toxins. In peritonitis and bacteremia models, mice infected with MRSA and treated with ampicillin, ceftazidime, or tetracycline showed enhanced bacterial pathogenicity. The release of induced virulence factors in vivo was confirmed in a histological examination. Subinhibitory concentrations of antibiotics belonging to β-lactam and tetracycline aggravated infection by inducing staphylococcal virulence in vivo. Thus, when antibiotics are required, it is preferable to employ combination therapy and to initiate the appropriate treatment plan, following diagnosis. Our findings emphasize the risks associated with antibiotic-based therapy and underline the need for alternative therapeutic options. IMPORTANCE Antibiotics are widely applied to treat infectious diseases. Empirically treatment with incorrect antibiotics, or even correct antibiotics always falls into subinhibitory concentrations, due to dosing, distribution, or secretion. In this study, we have systematically evaluated in vitro virulence induction effect of antibiotics and in vivo exacerbated infection. The major highlight of this work is to prove the β-lactam and tetracyclines antibiotics exacerbated disease is due to their induction effect on staphylococcal virulence. This phenomenon is common and suggests that if β-lactam antibiotics remain the first line of defense during empirical therapy, we either need to increase patient reliability or the treatment approach may improve in the future when paired with anti-virulence drugs.
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Affiliation(s)
- Peng Gao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yuanxin Wei
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rachel Evelyn Wan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ka Wing Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ho Ting Venice Iu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Sherlock Shing Chiu Tai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yongli Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hin Cheung Bill Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Pradeep Halebeedu Prakash
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Jonathan Hon Kwan Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Pak Leung Ho
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases and the Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kwok Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Microbiology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases and the Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Julian Davies
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Yi Tsun Kao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases and the Research Centre of Infection and Immunology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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32
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Hussan JR, Irwin SG, Mathews B, Swift S, Williams DL, Cornish J. Optimal dose of lactoferrin reduces the resilience of in vitro Staphylococcus aureus colonies. PLoS One 2022; 17:e0273088. [PMID: 35960734 PMCID: PMC9374217 DOI: 10.1371/journal.pone.0273088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/02/2022] [Indexed: 11/19/2022] Open
Abstract
The rise in antibiotic resistance has stimulated research into adjuvants that can improve the efficacy of broad-spectrum antibiotics. Lactoferrin is a candidate adjuvant; it is a multifunctional iron-binding protein with antimicrobial properties. It is known to show dose-dependent antimicrobial activity against Staphylococcus aureus through iron sequestration and repression of β–lactamase expression. However, S. aureus can extract iron from lactoferrin through siderophores for their growth, which confounds the resolution of lactoferrin’s method of action. We measured the minimum inhibitory concentration (MIC) for a range of lactoferrin/ β–lactam antibiotic dose combinations and observed that at low doses (< 0.39 μM), lactoferrin contributes to increased S. aureus growth, but at higher doses (> 6.25 μM), iron-depleted native lactoferrin reduced bacterial growth and reduced the MIC of the β-lactam-antibiotic cefazolin. This differential behaviour points to a bacterial population response to the lactoferrin/ β–lactam dose combination. Here, with the aid of a mathematical model, we show that lactoferrin stratifies the bacterial population, and the resulting population heterogeneity is at the basis of the dose dependent response seen. Further, lactoferrin disables a sub-population from β-lactam-induced production of β-lactamase, which when sufficiently large reduces the population’s ability to recover after being treated by an antibiotic. Our analysis shows that an optimal dose of lactoferrin acts as a suitable adjuvant to eliminate S. aureus colonies using β-lactams, but sub-inhibitory doses of lactoferrin reduces the efficacy of β-lactams.
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Affiliation(s)
- Jagir R. Hussan
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
- * E-mail:
| | - Stuart G. Irwin
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Brya Mathews
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Dustin L. Williams
- Department of Microbiology and Immunology, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Jillian Cornish
- Department of Medicine, University of Auckland, Auckland, NZ
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Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration. THE ISME JOURNAL 2022; 16:1993-2001. [PMID: 35577916 PMCID: PMC9296650 DOI: 10.1038/s41396-022-01249-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/08/2022]
Abstract
Vibrio cholerae, the bacterial pathogen responsible for the diarrheal disease cholera, resides in the aquatic environment between outbreaks. For bacteria, genetic variation by lateral gene transfer (LGT) is important for survival and adaptation. In the aquatic environment, V. cholerae is predominantly found in biofilms associated with chitinous organisms or with chitin "rain". Chitin induces competency in V. cholerae, which can lead to LGT. In the environment, V. cholerae is also subjected to predation pressure by protist. Here we investigated whether protozoal predation affected LGT using the integron as a model. Integrons facilitate the integration of mobile DNA (gene cassettes) into the bacterial chromosome. We report that protozoal predation enhances transformation of a gene cassette by as much as 405-fold. We show that oxidative radicals produced in the protozoal phagosome induces the universal SOS response, which in turn upregulates the integron-integrase, the recombinase that facilitates cassette integration. Additionally, we show that during predation, V. cholerae requires the type VI secretion system to acquire the gene cassette from Escherichia coli. These results show that protozoal predation enhances LGT thus producing genetic variants that may have increased capacity to survive grazing. Additionally, the conditions in the food vacuole may make it a "hot spot" for LGT by accumulating diverse bacteria and inducing the SOS response helping drive genetic diversification and evolution.
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
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Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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Abstract
Mechanisms of evolution and evolution of antibiotic resistance are both fundamental and world health problems. Stress-induced mutagenesis defines mechanisms of mutagenesis upregulated by stress responses, which drive adaptation when cells are maladapted to their environments—when stressed. Work in mutagenesis induced by antibiotics had produced tantalizing clues but not coherent mechanisms. We review recent advances in antibiotic-induced mutagenesis that integrate how reactive oxygen species (ROS), the SOS and general stress responses, and multichromosome cells orchestrate a stress response-induced switch from high-fidelity to mutagenic repair of DNA breaks. Moreover, while sibling cells stay stable, a mutable “gambler” cell subpopulation is induced by differentially generated ROS, which signal the general stress response. We discuss other evolvable subpopulations and consider diverse evolution-promoting molecules as potential targets for drugs to slow evolution of antibiotic resistance, cross-resistance, and immune evasion. An FDA-approved drug exemplifies “stealth” evolution-slowing drugs that avoid selecting resistance to themselves or antibiotics.
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Blanco-Picazo P, Gómez-Gómez C, Tormo M, Ramos-Barbero MD, Rodríguez-Rubio L, Muniesa M. Prevalence of bacterial genes in the phage fraction of food viromes. Food Res Int 2022; 156:111342. [DOI: 10.1016/j.foodres.2022.111342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/04/2022]
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Shalon N, Relman DA, Yaffe E. Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors. Genome Res 2022; 32:986-1003. [PMID: 35414589 PMCID: PMC9104695 DOI: 10.1101/gr.275894.121] [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: 06/15/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called 'dominant' graph cycles. In the implementation we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.
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Azithromycin can induce SOS response and horizontal gene transfer of SXT element in Vibrio cholerae. Mol Biol Rep 2022; 49:4737-4748. [DOI: 10.1007/s11033-022-07323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Wintachai P, Phaonakrop N, Roytrakul S, Naknaen A, Pomwised R, Voravuthikunchai SP, Surachat K, Smith DR. Enhanced antibacterial effect of a novel Friunavirus phage vWU2001 in combination with colistin against carbapenem-resistant Acinetobacter baumannii. Sci Rep 2022; 12:2633. [PMID: 35173237 PMCID: PMC8850435 DOI: 10.1038/s41598-022-06582-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022] Open
Abstract
The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has been increasingly reported, leading to greater challenges in treating infections. With the development of phage therapy and phage-antibiotic combinations, it is promising to improve the treatment of bacterial infections. In the present study, a novel vB_AbaP_WU2001 (vWU2001) phage-specific CRAB with a genome of 40,792 bp was isolated. Genomic analysis disclosed that it belongs to the Autographiviridae family of the order Caudovirales. Phage vWU2001 had a broad host range with a high adsorption rate, short latent period, large burst size and good stability. The phage could reduce preformed biofilms and inhibit biofilm formation. The combination of phage vWU2001 and colistin had significantly higher bacterial growth inhibition activity than that of phage, or colistin alone. The efficacy of the combined treatment was also evaluated in Galleria mellonella. Evaluation of its therapeutic potential showed that the combination of phage and colistin resulted in a significantly greater increase in G. mellonella survival and in bacterial clearance, as compared with that of phage or colistin alone, indicating that the combination was synergistic against CRAB. The results demonstrated that phage vWU2001 has the potential to be developed as an antibacterial agent.
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Affiliation(s)
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ampapan Naknaen
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.,Center of Antimicrobial Biomaterial Innovation-Southeast Asia and Natural Product Research Center of Excellence, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Phuttamonthon, Nakhon Pathom, 73170, Thailand
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Li H, Song R, Wang Y, Zhong R, Wang T, Jia H, Zhu L. Environmental free radicals efficiently inhibit the conjugative transfer of antibiotic resistance by altering cellular metabolism and plasmid transfer. WATER RESEARCH 2022; 209:117946. [PMID: 34923439 DOI: 10.1016/j.watres.2021.117946] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/07/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Spread of antibiotic-resistant genes (ARGs) is a global public safety issue and inhibition their transfer is imperative. In this study, a novel strategy using environmental free radical exposure was developed to inhibit conjugative transfer of ARGs (RP4 plasmid) in aqueous solutions. Long-time free radical (·OH, 1O2, and O2·-) exposure significantly suppressed the conjugative transfer frequency of ARGs between Escherichia coli (E. coli) strains, and ·OH was more likely to attack ARG, thereby inhibiting the conjugate transfer frequency, compared to 1O2 and O2·-. Compared with the control, the conjugative transfer frequency significantly decreased from 4.08 × 10-5 to 1.2 × 10-8 after 10 min free radical exposure, confirming that the transfer and proliferation of ARGs were well inhibited. Correspondingly, the number of transconjugant significantly decreased by 61.7% after 10 min free radical exposure. Significant reductions in reactive oxygen species levels (ROS content and enzyme levels) and DNA damage-induced responses in the donor strains were observed after 10 min free radical exposure. Concurrently, intercellular contact was also weakened via inhibiting the synthesis of polysaccharides in extracellular polymeric substances. Moreover, the expressions of plasmid transfer genes were down-regulated after 10 min exposure due to the shortage of adenosine-triphosphate supply. This study firstly disclosed the underneath mechanisms for depressing ARGs transfer and dissemination via environmental free radical exposure.
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Affiliation(s)
- Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ruiying Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Rongwei Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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Regulation of Heterogenous LexA Expression in Staphylococcus aureus by an Antisense RNA Originating from Transcriptional Read-Through upon Natural Mispairings in the sbrB Intrinsic Terminator. Int J Mol Sci 2022; 23:ijms23010576. [PMID: 35009002 PMCID: PMC8745188 DOI: 10.3390/ijms23010576] [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: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the lexA antisense RNA (lexA-asRNA) is generated by a TRE on the intrinsic terminator (TTsbrB) of the sbrB gene, which is located downstream of lexA, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TTsbrB structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TTsbrB prevented lexA-asRNA transcription. The level of lexA-asRNA directly correlated with cellular stress since the expressions of sbrB and lexA-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TTsbrB, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among S. aureus strains.
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Hu J, Ye H, Wang S, Wang J, Han D. Prophage Activation in the Intestine: Insights Into Functions and Possible Applications. Front Microbiol 2021; 12:785634. [PMID: 34966370 PMCID: PMC8710666 DOI: 10.3389/fmicb.2021.785634] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/25/2021] [Indexed: 01/20/2023] Open
Abstract
Prophage activation in intestinal environments has been frequently reported to affect host adaptability, pathogen virulence, gut bacterial community composition, and intestinal health. Prophage activation is mostly caused by various stimulators, such as diet, antibiotics, some bacterial metabolites, gastrointestinal transit, inflammatory environment, oxidative stress, and quorum sensing. Moreover, with advancements in biotechnology and the deepening cognition of prophages, prophage activation regulation therapy is currently applied to the treatment of some bacterial intestinal diseases such as Shiga toxin-producing Escherichia coli infection. This review aims to make headway on prophage induction in the intestine, in order to make a better understanding of dynamic changes of prophages, effects of prophage activation on physiological characteristics of bacteria and intestinal health, and subsequently provide guidance on prophage activation regulation therapy.
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Affiliation(s)
| | | | | | | | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Liu G, Thomsen LE, Olsen JE. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J Antimicrob Chemother 2021; 77:556-567. [PMID: 34894259 DOI: 10.1093/jac/dkab450] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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Liu S, Zhao Y, Hayes A, Hon K, Zhang G, Bennett C, Hu H, Finnie J, Morales S, Shearwin L, Psaltis AJ, Shearwin K, Wormald P, Vreugde S. Overcoming bacteriophage insensitivity in Staphylococcus aureus using clindamycin and azithromycinat subinhibitory concentrations. Allergy 2021; 76:3446-3458. [PMID: 33930199 DOI: 10.1111/all.14883] [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: 11/27/2020] [Revised: 03/02/2021] [Accepted: 03/18/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Staphylococcus aureus is a pathogen of major concern in both acute infections and chronic conditions such as chronic rhinosinusitis (CRS). Bacteriophage (phage) therapy has recently regained interest for its potential to treat infections caused by antibiotic resistant strains including Methicillin Resistant Staphylococcus aureus (MRSA). However, bacteria can adapt and become resistant to phages. The aim of this study is to determine the potential for antibiotics to overcome phage resistance. METHODS The susceptibility of S. aureus clinical isolates (CIs) to phages J-Sa36, Sa83 and Sa87 alone or in combination with protein synthesis inhibitor (PSI) antibiotics clindamycin, azithromycin and erythromycin was assessed using plaque spot assays, minimum inhibitory concentration (MIC) assays, double layer spot assays and resazurin assays. The safety and efficacy of subinhibitory PSI antibiotics in combination with phage was tested in a Sprague Dawley rat model of sinusitis infected with a phage resistant S. aureus CI. RESULTS All three antibiotics at subinhibitory concentrations showed synergy when combined with all 3 phages against S. aureus CIs in planktonic and biofilm form and could sensitize phage-resistant S. aureus to promote phage infection. The combination of topical subinhibitory clindamycin or azithromycin and phage was safe and could eradicate S. aureus sinonasal biofilms in vivo. CONCLUSION Subinhibitory concentrations of PSI antibiotics could sensitize phage-resistant S. aureus and MRSA strains to phages in vitro and in vivo. This data supports the potential use of phage-PSI antibiotic combination therapies, in particular for difficult-to-treat infections with phage-resistant S. aureus and MRSA strains.
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Affiliation(s)
- Sha Liu
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Yin Zhao
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
- Department of Otolaryngology, Head and Neck Surgery The Second Hospital of Jilin University Changchun China
| | - Andrew Hayes
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Karen Hon
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Guimin Zhang
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
- Department of Otolaryngology‐Head and Neck Surgery Tianjin First Center Hospital Tianjin China
| | - Catherine Bennett
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Hua Hu
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
- Department of Otolaryngology, Head and Neck Surgery Shanghai General Hospital Shanghai Jiaotong University Shanghai China
| | - John Finnie
- Discipline of Anatomy and Pathology Adelaide Medical School University of Adelaide Adelaide SA Australia
| | | | - Linda Shearwin
- Department of Molecular and Biomedical Science Adelaide University Adelaide SA Australia
| | - Alkis J. Psaltis
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Keith Shearwin
- Department of Molecular and Biomedical Science Adelaide University Adelaide SA Australia
| | - Peter‐John Wormald
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
| | - Sarah Vreugde
- Department of Surgery‐Otolaryngology Head and Neck Surgery Basil Hetzel Institute for Translational Health Research Central Adelaide Local Health Network Woodville South SA Australia
- Adelaide Medical School The University of Adelaide Adelaide SA Australia
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed.
Part 4: β-Lactams: amoxicillin and penicillin V. EFSA J 2021; 19:e06855. [PMID: 34729084 PMCID: PMC8547409 DOI: 10.2903/j.efsa.2021.6855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for amoxicillin, whilst for penicillin V no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.
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Li H, Song R, Wang Y, Zhong R, Zhang Y, Zhou J, Wang T, Jia H, Zhu L. Inhibited conjugative transfer of antibiotic resistance genes in antibiotic resistant bacteria by surface plasma. WATER RESEARCH 2021; 204:117630. [PMID: 34536683 DOI: 10.1016/j.watres.2021.117630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistant bacteria (ARB) and resistance genes (ARGs) are emerging environmental pollutants with strong pathogenicity. In this study, surface plasma was developed to inactivate the donor ARB with Escherichia coli (AR E. coli) as a model, eliminate ARGs, and inhibit conjugative transfer of ARGs in water, highlighting the influences of concomitant inorganic ions. Surface plasma oxidation significantly inactivated AR E. coli, eliminated ARGs, and inhibited conjugative transfer of ARGs, and the presence of NO3-, Cu2+, and Fe2+ all promoted these processes, and SO42- did not have distinct effect. Approximately 4.5log AR E. coli was inactivated within 10 min treatment, and it increased to 7.4log AR E. coli after adding Fe2+. Integrons intI1 decreased by 3.10log (without Fe2+) and 4.43log (adding Fe2+); the addition of Fe2+ in the surface plasma induced 99.8% decline in the conjugative transfer frequency. The inhibition effects on the conjugative transfer of ARGs were mainly attributed to the reduced reactive oxygen species levels, decreased DNA damage-induced response, decreased intercellular contact, and down-regulated expression of plasmid transfer genes. This study disclosed underlying mechanisms for inhibiting ARGs transfer, and supplied a prospective technique for ARGs control.
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Affiliation(s)
- Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ruiying Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Rongwei Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ying Zhang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jian Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
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Sulaiman JE, Long L, Wu L, Qian PY, Lam H. Comparative proteomic investigation of multiple methicillin-resistant Staphylococcus aureus strains generated through adaptive laboratory evolution. iScience 2021; 24:102950. [PMID: 34458699 PMCID: PMC8377494 DOI: 10.1016/j.isci.2021.102950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 06/14/2021] [Accepted: 08/02/2021] [Indexed: 12/16/2022] Open
Abstract
Recent discoveries indicate that tolerance and resistance could rapidly evolve in bacterial populations under intermittent antibiotic treatment. In the present study, we applied antibiotic combinations in laboratory experiments to generate novel methicillin-resistant Staphylococcus aureus strains with distinct phenotypes (tolerance, resistance, and suppressed tolerance), and compared their proteome profiles to uncover the adaptation mechanisms. While the tolerant strains have very different proteomes than the susceptible ancestral strain, the resistant strain largely resembles the ancestral in terms of their proteomes. Our proteomics data and other assays support the connection between the detected mutations to the observed phenotypes, confirming the general understanding of tolerance and resistance mechanisms. While resistance directly counteracts the action mechanism of the antibiotic, tolerance involves complex substantial changes in the cells' biological process to achieve survival advantages. Overall, this study provides insights into the existence of diverse evolutionary pathways for tolerance and resistance development under different treatment scenarios.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lexin Long
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Long Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
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48
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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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49
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Fosfomycin and nitrofurantoin: classic antibiotics and perspectives. J Antibiot (Tokyo) 2021; 74:547-558. [PMID: 34244614 DOI: 10.1038/s41429-021-00444-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
Antibiotics are essential molecules for the treatment and prophylaxis of many infectious diseases. However, drugs that combat microbial infections can become a human health threat due to their high and often indiscriminate consumption, considered one of the factors of antimicrobial resistance (AMR) emergence. The AMR crisis, the decrease in new drug development by the pharmaceutical industry, and reduced economic incentives for research have all reduced the options for treating infections, and new strategies are necessary, including the return of some traditional but "forgotten" antibiotics. However, prescriptions for these older drugs including nitrofurantoin and oral fosfomycin, have been based on the results of pioneer studies, and the limited knowledge generated 50-70 years ago may not be enough. To avoid harming patients and further increasing multidrug resistance, systematic evaluation is required, mainly for the drugs prescribed for community-acquired infections, such as urinary tract infections (UTI). Therefore, this review has the objective of reporting the use of two classic drugs from the nitrofuran and phosphonic acid classes for UTI control nowadays. Furthermore, we also explore new approaches used for these antibiotics, including new combination regimes for spectral amplification, and the prospects for reducing bacterial resistance in the fight against bacteria responsible for UTI.
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50
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Bikel S, López-Leal G, Cornejo-Granados F, Gallardo-Becerra L, García-López R, Sánchez F, Equihua-Medina E, Ochoa-Romo JP, López-Contreras BE, Canizales-Quinteros S, Hernández-Reyna A, Mendoza-Vargas A, Ochoa-Leyva A. Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome. iScience 2021; 24:102900. [PMID: 34409269 PMCID: PMC8361208 DOI: 10.1016/j.isci.2021.102900] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/01/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales. Notably, phage richness and diversity of individuals with O and OMS tended to increase, while the VLP abundance remained the same among all groups. Of the 4,611 phage contigs composing the phageome, 48 contigs were highly prevalent in ≥80% of individuals, suggesting high inter-individual phage diversity. The abundance of several contigs correlated with gut bacterial taxa; and with anthropometric and biochemical parameters altered in O and OMS. To our knowledge, this gut phageome represents one of the largest datasets and suggests disease-specific phage alterations.
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Affiliation(s)
- Shirley Bikel
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Gamaliel López-Leal
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Fernanda Cornejo-Granados
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Luigui Gallardo-Becerra
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Rodrigo García-López
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Filiberto Sánchez
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Edgar Equihua-Medina
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Juan Pablo Ochoa-Romo
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Blanca Estela López-Contreras
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Abigail Hernández-Reyna
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | | | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
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