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Stevens DA, Beierschmitt C, Mahesula S, Corley MR, Salogiannis J, Tsu BV, Cao B, Ryan AP, Hakozawki H, Reck-Peterson SL, Daugherty MD. Antiviral function and viral antagonism of the rapidly evolving dynein activating adaptor NINL. eLife 2022; 11:e81606. [PMID: 36222652 PMCID: PMC9651953 DOI: 10.7554/elife.81606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses interact with the intracellular transport machinery to promote viral replication. Such host-virus interactions can drive host gene adaptation, leaving signatures of pathogen-driven evolution in host genomes. Here, we leverage these genetic signatures to identify the dynein activating adaptor, ninein-like (NINL), as a critical component in the antiviral innate immune response and as a target of viral antagonism. Unique among genes encoding components of active dynein complexes, NINL has evolved under recurrent positive (diversifying) selection, particularly in its carboxy-terminal cargo-binding region. Consistent with a role for NINL in host immunity, we demonstrate that NINL knockout cells exhibit an impaired response to interferon, resulting in increased permissiveness to viral replication. Moreover, we show that proteases encoded by diverse picornaviruses and coronaviruses cleave and disrupt NINL function in a host- and virus-specific manner. Our work reveals the importance of NINL in the antiviral response and the utility of using signatures of host-virus genetic conflicts to uncover new components of antiviral immunity and targets of viral antagonism.
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Affiliation(s)
- Donté Alexander Stevens
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
| | | | - Swetha Mahesula
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Miles R Corley
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
| | - John Salogiannis
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
| | - Brian V Tsu
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
| | - Bryant Cao
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
| | - Andrew P Ryan
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
| | - Hiroyuki Hakozawki
- Nikon Imaging Center at UC San Diego, University of California, San DiegoSan DiegoUnited States
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cell and Developmental Biology, University of California, San DiegoLa JollaUnited States
| | - Matthew D Daugherty
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
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Abstract
In response to viral predation, bacteria have evolved a wide range of defense mechanisms, which rely mostly on proteins acting at the cellular level. Here, we show that aminoglycosides, a well-known class of antibiotics produced by Streptomyces, are potent inhibitors of phage infection in widely divergent bacterial hosts. We demonstrate that aminoglycosides block an early step of the viral life cycle, prior to genome replication. Phage inhibition was also achieved using supernatants from natural aminoglycoside producers, indicating a broad physiological significance of the antiviral properties of aminoglycosides. Strikingly, we show that acetylation of the aminoglycoside antibiotic apramycin abolishes its antibacterial effect but retains its antiviral properties. Altogether, our study expands the knowledge of aminoglycoside functions, suggesting that aminoglycosides not only are used by their producers as toxic molecules against their bacterial competitors but also could provide protection against the threat of phage predation at the community level. IMPORTANCE Predation by phages is a major driver of bacterial evolution. As a result, elucidating antiphage strategies is crucial from both fundamental and therapeutic standpoints. While protein-mediated defense mechanisms, like restriction-modification systems or CRISPR/Cas, have been extensively studied, much less is known about the potential antiphage activity of small molecules. Focusing on the model bacteria Escherichia coli and Streptomyces venezuelae, our findings revealed significant antiphage properties of aminoglycosides, a major class of translation-targeting antibiotics produced by Streptomyces. Further, we demonstrate that supernatants from natural aminoglycoside producers protect bacteria from phage propagation, highlighting the physiological relevance of this inhibition. Suppression of phage infection by aminoglycosides did not result from the indirect inhibition of bacterial translation, suggesting a direct interaction between aminoglycosides and phage components. This work highlights the molecular versatility of aminoglycosides, which have evolved to efficiently block protein synthesis in bacterial competitors and provide protection against phages.
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Yacouba A, Olowo-Okere A, Yunusa I. Repurposing of antibiotics for clinical management of COVID-19: a narrative review. Ann Clin Microbiol Antimicrob 2021; 20:37. [PMID: 34020659 PMCID: PMC8139224 DOI: 10.1186/s12941-021-00444-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 05/11/2021] [Indexed: 12/22/2022] Open
Abstract
Background Drug repurposing otherwise known as drug repositioning or drug re-profiling is a time-tested approach in drug discovery through which new medical uses are being established for already known drugs. Antibiotics are among the pharmacological agents being investigated for potential anti-SARS-COV-2 activities. The antibiotics are used either to resolve bacterial infections co-existing with COVID-19 infections or exploitation of their potential antiviral activities. Herein, we aimed to review the various antibiotics that have been repositioned for the management of COVID-19. Methods This literature review was conducted from a methodical search on PubMed and Web of Science regarding antibiotics used in patients with COVID-19 up to July 5, 2020. Results Macrolide and specifically azithromycin is the most common antibiotic used in the clinical management of COVID-19. The other antibiotics used in COVID-19 includes teicoplanin, clarithromycin, doxycycline, tetracyclines, levofloxacin, moxifloxacin, ciprofloxacin, and cefuroxime. In patients with COVID-19, antibiotics are used for their immune-modulating, anti-inflammatory, and antiviral properties. The precise antiviral mechanism of most of these antibiotics has not been determined. Moreover, the use of some of these antibiotics against SARS-CoV-2 infection remains highly controversial and not widely accepted. Conclusion The heavy use of antibiotics during the COVID-19 pandemic would likely worsen antibiotic resistance crisis. Consequently, antibiotic stewardship should be strengthened in order to prevent the impacts of COVID-19 on the antibiotic resistance crisis.
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Affiliation(s)
- Abdourahamane Yacouba
- Faculté des Sciences de la Santé, Université Abdou Moumouni, P.M.B. 10896, Niamey, Niger.
| | - Ahmed Olowo-Okere
- Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria
| | - Ismaeel Yunusa
- Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina College of Pharmacy, Columbia, SC, USA
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Yang M, Yang Y, He Q, Zhu P, Liu M, Xu J, Zhao M. Intestinal Microbiota-A Promising Target for Antiviral Therapy? Front Immunol 2021; 12:676232. [PMID: 34054866 PMCID: PMC8149780 DOI: 10.3389/fimmu.2021.676232] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota is thought to be an important biological barrier against enteric pathogens. Its depletion, however, also has curative effects against some viral infections, suggesting that different components of the intestinal microbiota can play both promoting and inhibitory roles depending on the type of viral infection. The two primary mechanisms by which the microbiota facilitates or inhibits viral invasion involve participation in the innate and adaptive immune responses and direct or indirect interaction with the virus, during which the abundance and composition of the intestinal microbiota might be changed by the virus. Oral administration of probiotics, faecal microbiota transplantation (FMT), and antibiotics are major therapeutic strategies for regulating intestinal microbiota balance. However, these three methods have shown limited curative effects in clinical trials. Therefore, the intestinal microbiota might represent a new and promising supplementary antiviral therapeutic target, and more efficient and safer methods for regulating the microbiota require deeper investigation. This review summarizes the latest research on the relationship among the intestinal microbiota, anti-viral immunity and viruses and the most commonly used methods for regulating the intestinal microbiota with the goal of providing new insight into the antiviral effects of the gut microbiota.
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Affiliation(s)
- Mengling Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yang Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingnan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Mengqi Liu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jiahao Xu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
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Nishimoto A, Wohlgemuth N, Rosch J, Schultz-Cherry S, Cortez V, Rowe HM. Transkingdom Interactions Important for the Pathogenesis of Human Viruses. J Infect Dis 2020; 223:S201-S208. [PMID: 33330907 DOI: 10.1093/infdis/jiaa735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The bacterial, fungal, and helminthic species that comprise the microbiome of the mammalian host have profound effects on health and disease. Pathogenic viruses must contend with the microbiome during infection and likely have evolved to exploit or evade the microbiome. Both direct interactions between the virions and the microbiota and immunomodulation and tissue remodeling caused by the microbiome alter viral pathogenesis in either host- or virus-beneficial ways. Recent insights from in vitro and murine models of viral pathogenesis have highlighted synergistic and antagonistic, direct and indirect interactions between the microbiome and pathogenic viruses. This review will focus on the transkingdom interactions between human gastrointestinal and respiratory viruses and the constituent microbiome of those tissues.
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Affiliation(s)
- Andrew Nishimoto
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jason Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Valerie Cortez
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hannah M Rowe
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Woods Acevedo MA, Pfeiffer JK. Microbiota-independent antiviral effects of antibiotics on poliovirus and coxsackievirus. Virology 2020; 546:20-24. [PMID: 32452414 PMCID: PMC7253499 DOI: 10.1016/j.virol.2020.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 01/14/2023]
Abstract
Coxsackieviruses primarily infect the gastrointestinal tract of humans, but they can disseminate systemically and cause severe disease. Using antibiotic treatment regimens to deplete intestinal microbes in mice, several groups have shown that bacteria promote oral infection with a variety of enteric viruses. However, it is unknown whether antibiotics have microbiota-independent antiviral effects for enteric viruses or whether antibiotics influence extra-intestinal, systemic infection. Here, we examined the effects of antibiotics on systemic enteric virus infection by performing intraperitoneal injections of either coxsackievirus B3 (CVB3) or poliovirus followed by quantification of viral titers. We found that antibiotic treatment reduced systemic infection for both viruses. Interestingly, antibiotics reduced CVB3 titers in germ-free mice, suggesting that antibiotic treatment alters CVB3 infection through a microbiota-independent mechanism. Overall, these data provide further evidence that antibiotics can have noncanonical effects on viral infection.
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Affiliation(s)
- Mikal A Woods Acevedo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Robinson CM, Woods Acevedo MA, McCune BT, Pfeiffer JK. Related Enteric Viruses Have Different Requirements for Host Microbiota in Mice. J Virol 2019; 93:e01339-19. [PMID: 31511379 PMCID: PMC6854509 DOI: 10.1128/jvi.01339-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 08/30/2019] [Indexed: 01/01/2023] Open
Abstract
Accumulating evidence suggests that intestinal bacteria promote enteric virus infection in mice. For example, previous work demonstrated that antibiotic treatment of mice prior to oral infection with poliovirus reduced viral replication and pathogenesis. Here, we examined the effect of antibiotic treatment on infection with coxsackievirus B3 (CVB3), a picornavirus closely related to poliovirus. We treated mice with a mixture of five antibiotics to deplete host microbiota and examined CVB3 replication and pathogenesis following oral inoculation. We found that, as seen with poliovirus, CVB3 shedding and pathogenesis were reduced in antibiotic-treated mice. While treatment with just two antibiotics, vancomycin and ampicillin, was sufficient to reduce CVB3 replication and pathogenesis, this treatment had no effect on poliovirus. The quantity and composition of bacterial communities were altered by treatment with the five-antibiotic cocktail and by treatment with vancomycin and ampicillin. To determine whether more-subtle changes in bacterial populations impact viral replication, we examined viral infection in mice treated with milder antibiotic regimens. Mice treated with one-tenth the standard concentration of the normal antibiotic cocktail supported replication of poliovirus but not CVB3. Importantly, a single dose of one antibiotic, streptomycin, was sufficient to reduce CVB3 shedding and pathogenesis while having no effect on poliovirus shedding and pathogenesis. Overall, replication and pathogenesis of CVB3 are more sensitive to antibiotic treatment than poliovirus, indicating that closely related viruses may differ with respect to their reliance on microbiota.IMPORTANCE Recent data indicate that intestinal bacteria promote intestinal infection of several enteric viruses. Here, we show that coxsackievirus, an enteric virus in the picornavirus family, also relies on microbiota for intestinal replication and pathogenesis. Relatively minor depletion of the microbiota was sufficient to decrease coxsackievirus infection, while poliovirus infection was unaffected. Surprisingly, a single dose of one antibiotic was sufficient to reduce coxsackievirus infection. Therefore, these data indicate that closely related viruses may differ with respect to their reliance on microbiota.
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Affiliation(s)
- Christopher M Robinson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Mikal A Woods Acevedo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Broc T McCune
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Eskew AM, Stout MJ, Bedrick BS, Riley JK, Omurtag KR, Jimenez PT, Odem RR, Ratts VS, Keller SL, Jungheim ES, Wylie KM. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study. BJOG 2019; 127:208-216. [PMID: 31529767 DOI: 10.1111/1471-0528.15951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The objective of this study was to use high-throughput sequencing to describe the vaginal eukaryotic DNA virome in patients undergoing in vitro fertilisation (IVF) to examine associations between the vaginal virome, antibiotic exposure and IVF outcomes. DESIGN Prospective exploratory study. SETTING Single academic fertility centre. POPULATION Subfertile women age 18-43 years undergoing their first IVF cycle with a fresh embryo transfer. METHODS The primary exposure was prophylactic azithromycin or no azithromycin before IVF. A mid-vaginal swab was obtained at the time of embryo transfer for virome analysis. MAIN OUTCOME MEASURES The primary outcomes compared between exposure groups were characteristics of vaginal virome and clinical pregnancy rates. Secondary outcomes were virome associations with number of oocytes retrieved, number of blastocysts and implantation rate. RESULTS Twenty-six women contributed a vaginal swab before embryo transfer. There were no significant differences in IVF outcomes between azithromycin groups. There was no association between viral diversity and clinical pregnancy overall. A higher diversity of herpesviruses and α-papillomaviruses was observed in samples from the azithromycin-treated group compared with the no azithromycin group (P = 0.04). In women that received azithromycin, viral diversity was higher in the group that did not achieve clinical pregnancy compared with those who did (P = 0.06). CONCLUSIONS We demonstrate that the vaginal eukaryotic virome in women undergoing IVF is associated with antibiotic exposure. Additionally, we demonstrate an inverse trend between viral diversity and pregnancy, with a higher number of viruses detected associated with failure to achieve clinical pregnancy in the azithromycin group. TWEETABLE ABSTRACT Higher viral diversity is associated with prophylactic antibiotic exposure in subfertile women undergoing IVF.
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Affiliation(s)
- A M Eskew
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - M J Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University in St Louis, St Louis, MO, USA
| | - B S Bedrick
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - J K Riley
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - K R Omurtag
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - P T Jimenez
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - R R Odem
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - V S Ratts
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - S L Keller
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - E S Jungheim
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - K M Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St Louis, St Louis, MO, USA.,McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
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