1
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Hamami E, Huo W, Hernandez-Bird J, Castaneda A, Bai J, Syal S, Ortiz-Marquez JC, van Opijnen T, Geisinger E, Isberg RR. Identification of Determinants that Allow Maintenance of High-Level Fluoroquinolone Resistance in Acinetobacter baumannii. bioRxiv 2024:2023.10.03.560562. [PMID: 38645180 PMCID: PMC11030222 DOI: 10.1101/2023.10.03.560562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Acinetobacter baumannii is associated with multidrug resistant (MDR) infections in healthcare settings, with fluoroquinolones such as ciprofloxacin being currently ineffective. Clinical isolates largely harbor mutations in the GyrA and TopoIV fluoroquinolone targets, as well as mutations that increase expression of drug resistance-nodulation-division (RND) efflux pumps. Factors critical for maintaining fitness levels of pump overproducers are uncharacterized despite their prevalence in clinical isolates. We here identify proteins that contribute to the fitness of FQR strains overexpressing three known RND systems using high-density insertion mutagenesis. Overproduction of the AdeFGH efflux pump caused hypersensitization to defects in outer membrane homeostatic regulation, including lesions that reduced LOS biosynthesis and blocked production of the major A. baumannii porin. In contrast, AdeAB pump overproduction, which does not affect the outer membrane pump component, was relatively tolerant to loss of these functions, consistent with outer membrane protein overproduction being the primary disruptive component. Surprisingly, overproduction of proton-transporting efflux pumps had little impact on cytosolic pH, consistent with a compensatory response to pump activity. The most striking transcriptional changes were associated with AdeFGH pump overproduction, resulting in activation of the phenylacetate (PAA) degradation regulon. Disruption of the PAA pathway resulted in cytosolic acidification and defective expression of genes involved in protection from peroxide stress. These results indicate that the RND outer membrane protein overproduction is compensated by cytoplasmic buffering and maintenance of outer membrane integrity in A. baumannii to facilitate fitness of FQR isolates.
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Affiliation(s)
- Efrat Hamami
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Juan Hernandez-Bird
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | | | - Jinna Bai
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Sapna Syal
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Juan C Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, MA 02135 USA
- Innovation Laboratory, Broad Institute, Cambridge, MA 02412, USA
| | - Tim van Opijnen
- Innovation Laboratory, Broad Institute, Cambridge, MA 02412, USA
| | - Edward Geisinger
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
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2
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Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM. RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genet 2024; 20:e1011188. [PMID: 38442125 PMCID: PMC10942264 DOI: 10.1371/journal.pgen.1011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.
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Affiliation(s)
- Indu Warrier
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ariana Perry
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Sara M. Hubbell
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Matthew Eichelman
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Boston Children’s Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M. Meyer
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
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3
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Malley K, Pham Q, Loynd C, Huang Z, van Opijnen T, Chatterjee A. Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angew Chem Int Ed Engl 2024; 63:e202316428. [PMID: 38279536 PMCID: PMC10922736 DOI: 10.1002/anie.202316428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/28/2024]
Abstract
Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel L Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Kaitlin Malley
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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4
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Dao TH, Echlin H, McKnight A, Marr ES, Junker J, Jia Q, Hayden R, van Opijnen T, Isberg RR, Cooper VS, Rosch JW. Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones. mBio 2024; 15:e0282823. [PMID: 38193698 PMCID: PMC10865975 DOI: 10.1128/mbio.02828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Streptococcus pneumoniae is a major human pathogen of global health concern and the rapid emergence of antibiotic resistance poses a serious public health problem worldwide. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage and has remained rare. Our data indicate that deleterious fitness costs in the mammalian host constrain the emergence of fluoroquinolone resistance both by de novo mutation and recombination. S. pneumoniae was able to circumvent such deleterious fitness costs via the development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, resulting in a fitness benefit during infection of mice treated with fluoroquinolones. These data suggest that the emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes are an important contributor to the evasion of antibiotic-mediated killing.IMPORTANCEThe increasing prevalence of antibiotic resistant bacteria is a major global health concern. While many species have the potential to develop antibiotic resistance, understanding the barriers to resistance emergence in the clinic remains poorly understood. A prime example of this is fluroquinolone resistance in Streptococcus pneumoniae, whereby, despite continued utilization, resistance to this class of antibiotic remains rare. In this study, we found that the predominant pathways for developing resistance to this antibiotic class severely compromised the infectious capacity of the pneumococcus, providing a key impediment for the emergence of resistance. Using in vivo models of experimental evolution, we found that S. pneumoniae responds to repeated fluoroquinolone exposure by modulating key metabolic pathways involved in the generation of redox molecules, which leads to antibiotic treatment failure in the absence of appreciable shifts in resistance levels. These data underscore the complex pathways available to pathogens to evade antibiotic mediating killing via antibiotic tolerance.
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Affiliation(s)
- Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Abigail McKnight
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Enolia S. Marr
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Julia Junker
- Nationales Referenzzentrum für Streptokokken Abteilung Medizinische Mikrobiologie, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ralph R. Isberg
- Deptartment of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Vaughn S. Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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5
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Price SL, Thibault D, Garrison TM, Brady A, Guo H, Kehl‐Fie TE, Garneau‐Tsodikova S, Perry RD, van Opijnen T, Lawrenz MB. Droplet Tn-Seq identifies the primary secretion mechanism for yersiniabactin in Yersinia pestis. EMBO Rep 2023; 24:e57369. [PMID: 37501563 PMCID: PMC10561177 DOI: 10.15252/embr.202357369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Nutritional immunity includes sequestration of transition metals from invading pathogens. Yersinia pestis overcomes nutritional immunity by secreting yersiniabactin to acquire iron and zinc during infection. While the mechanisms for yersiniabactin synthesis and import are well-defined, those responsible for yersiniabactin secretion are unknown. Identification of this mechanism has been difficult because conventional mutagenesis approaches are unable to inhibit trans-complementation by secreted factors between mutants. To overcome this obstacle, we utilized a technique called droplet Tn-seq (dTn-seq), which uses microfluidics to isolate individual transposon mutants in oil droplets, eliminating trans-complementation between bacteria. Using this approach, we first demonstrated the applicability of dTn-seq to identify genes with secreted functions. We then applied dTn-seq to identify an AcrAB efflux system as required for growth in metal-limited conditions. Finally, we showed this efflux system is the primary yersiniabactin secretion mechanism and required for virulence during bubonic and pneumonic plague. Together, these studies have revealed the yersiniabactin secretion mechanism that has eluded researchers for over 30 years and identified a potential therapeutic target for bacteria that use yersiniabactin for metal acquisition.
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Affiliation(s)
- Sarah L Price
- Department of Microbiology and ImmunologyUniversity of LouisvilleLouisvilleKYUSA
| | | | - Taylor M Garrison
- Department of Microbiology and ImmunologyUniversity of LouisvilleLouisvilleKYUSA
| | - Amanda Brady
- Department of Microbiology and ImmunologyUniversity of LouisvilleLouisvilleKYUSA
| | - Haixun Guo
- Center for Predictive Medicine for Biodefense and Emerging Infectious DiseasesUniversity of LouisvilleLouisvilleKYUSA
- Department of RadiologyUniversity of LouisvilleLouisvilleKYUSA
| | - Thomas E Kehl‐Fie
- Department of MicrobiologyUniversity of Illinois Urbana‐ChampaignChampaignILUSA
- Carl R Woese Institute for Genomic BiologyUrbanaILUSA
| | | | - Robert D Perry
- Department of Microbiology, Immunology and Molecular GeneticsUniversity of KentuckyLexingtonKYUSA
| | | | - Matthew B Lawrenz
- Department of Microbiology and ImmunologyUniversity of LouisvilleLouisvilleKYUSA
- Center for Predictive Medicine for Biodefense and Emerging Infectious DiseasesUniversity of LouisvilleLouisvilleKYUSA
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6
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Bai J, Raustad N, Denoncourt J, van Opijnen T, Geisinger E. Genome-wide phage susceptibility analysis in Acinetobacter baumannii reveals capsule modulation strategies that determine phage infectivity. PLoS Pathog 2023; 19:e1010928. [PMID: 37289824 DOI: 10.1371/journal.ppat.1010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Phage have gained renewed interest as an adjunctive treatment for life-threatening infections with the resistant nosocomial pathogen Acinetobacter baumannii. Our understanding of how A. baumannii defends against phage remains limited, although this information could lead to improved antimicrobial therapies. To address this problem, we identified genome-wide determinants of phage susceptibility in A. baumannii using Tn-seq. These studies focused on the lytic phage Loki, which targets Acinetobacter by unknown mechanisms. We identified 41 candidate loci that increase susceptibility to Loki when disrupted, and 10 that decrease susceptibility. Combined with spontaneous resistance mapping, our results support the model that Loki uses the K3 capsule as an essential receptor, and that capsule modulation provides A. baumannii with strategies to control vulnerability to phage. A key center of this control is transcriptional regulation of capsule synthesis and phage virulence by the global regulator BfmRS. Mutations hyperactivating BfmRS simultaneously increase capsule levels, Loki adsorption, Loki replication, and host killing, while BfmRS-inactivating mutations have the opposite effect, reducing capsule and blocking Loki infection. We identified novel BfmRS-activating mutations, including knockouts of a T2 RNase protein and the disulfide formation enzyme DsbA, that hypersensitize bacteria to phage challenge. We further found that mutation of a glycosyltransferase known to alter capsule structure and bacterial virulence can also cause complete phage resistance. Finally, additional factors including lipooligosaccharide and Lon protease act independently of capsule modulation to interfere with Loki infection. This work demonstrates that regulatory and structural modulation of capsule, known to alter A. baumannii virulence, is also a major determinant of susceptibility to phage.
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Affiliation(s)
- Jinna Bai
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Nicole Raustad
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jason Denoncourt
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, CISID, Cambridge, Massachusetts, United States of America
| | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
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7
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Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Veening JW, van Opijnen T. CRISPRi-TnSeq: A genome-wide high-throughput tool for bacterial essential-nonessential genetic interaction mapping. bioRxiv 2023:2023.05.31.543074. [PMID: 37398100 PMCID: PMC10312587 DOI: 10.1101/2023.05.31.543074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Genetic interaction networks can help identify functional connections between genes and pathways, which can be leveraged to establish (new) gene function, drug targets, and fill pathway gaps. Since there is no optimal tool that can map genetic interactions across many different bacterial strains and species, we develop CRISPRi-TnSeq, a genome-wide tool that maps genetic interactions between essential genes and nonessential genes through the knockdown of a targeted essential gene (CRISPRi) and the simultaneous knockout of individual nonessential genes (Tn-Seq). CRISPRi-TnSeq thereby identifies, on a genome-wide scale, synthetic and suppressor-type relationships between essential and nonessential genes, enabling the construction of essential-nonessential genetic interaction networks. To develop and optimize CRISPRi-TnSeq, CRISPRi strains were obtained for 13 essential genes in Streptococcus pneumoniae, involved in different biological processes including metabolism, DNA replication, transcription, cell division and cell envelope synthesis. Transposon-mutant libraries were constructed in each strain enabling screening of ∼24,000 gene-gene pairs, which led to the identification of 1,334 genetic interactions, including 754 negative and 580 positive genetic interactions. Through extensive network analyses and validation experiments we identify a set of 17 pleiotropic genes, of which a subset tentatively functions as genetic capacitors, dampening phenotypic outcomes and protecting against perturbations. Furthermore, we focus on the relationships between cell wall synthesis, integrity and cell division and highlight: 1) how essential gene knockdown can be compensated by rerouting flux through nonessential genes in a pathway; 2) the existence of a delicate balance between Z-ring formation and localization, and septal and peripheral peptidoglycan (PG) synthesis to successfully accomplish cell division; 3) the control of c-di-AMP over intracellular K + and turgor, and thereby modulation of the cell wall synthesis machinery; 4) the dynamic nature of cell wall protein CozEb and its effect on PG synthesis, cell shape morphology and envelope integrity; 5) functional dependency between chromosome decatenation and segregation, and the critical link with cell division, and cell wall synthesis. Overall, we show that CRISPRi-TnSeq uncovers genetic interactions between closely functionally linked genes and pathways, as well as disparate genes and pathways, highlighting pathway dependencies and valuable leads for gene function. Importantly, since both CRISPRi and Tn-Seq are widely used tools, CRISPRi-TnSeq should be relatively easy to implement to construct genetic interaction networks across many different microbial strains and species.
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8
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Cao X, Malley K, Huang Z, Pasha M, Anthony J, van Opijnen T, Chatterjee A. Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells. Nat Methods 2023; 20:95-103. [PMID: 36550276 PMCID: PMC9855281 DOI: 10.1038/s41592-022-01706-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Site-specific incorporation of unnatural amino acids (Uaas) in living cells relies on engineered aminoacyl-transfer RNA synthetase-tRNA pairs borrowed from a distant domain of life. Such heterologous suppressor tRNAs often have poor intrinsic activity, presumably due to suboptimal interaction with a non-native translation system. This limitation can be addressed in Escherichia coli using directed evolution. However, no suitable selection system is currently available to do the same in mammalian cells. Here we report virus-assisted directed evolution of tRNAs (VADER) in mammalian cells, which uses a double-sieve selection scheme to facilitate single-step enrichment of active yet orthogonal tRNA mutants from naive libraries. Using VADER we developed improved mutants of Methanosarcina mazei pyrrolysyl-tRNA, as well as a bacterial tyrosyl-tRNA. We also show that the higher activity of the most efficient mutant pyrrolysyl-tRNA is specific for mammalian cells, alluding to an improved interaction with the unique mammalian translation apparatus.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | | | - Rachel L Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Kaitlin Malley
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Muhammad Pasha
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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9
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Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Rep 2022; 41:111835. [PMID: 36516783 PMCID: PMC9850807 DOI: 10.1016/j.celrep.2022.111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.
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Affiliation(s)
- Andrew T. Nishimoto
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, MA 02467, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Lead contact,Correspondence:
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10
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Rosconi F, Rudmann E, Li J, Surujon D, Anthony J, Frank M, Jones DS, Rock C, Rosch JW, Johnston CD, van Opijnen T. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nat Microbiol 2022; 7:1580-1592. [PMID: 36097170 PMCID: PMC9519441 DOI: 10.1038/s41564-022-01208-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.
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Affiliation(s)
| | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jien Li
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Matthew Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Leshchiner D, Rosconi F, Sundaresh B, Rudmann E, Ramirez LMN, Nishimoto AT, Wood SJ, Jana B, Buján N, Li K, Gao J, Frank M, Reeve SM, Lee RE, Rock CO, Rosch JW, van Opijnen T. A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance. Nat Commun 2022; 13:3165. [PMID: 35672367 PMCID: PMC9174251 DOI: 10.1038/s41467-022-30967-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Detailed knowledge on how bacteria evade antibiotics and eventually develop resistance could open avenues for novel therapeutics and diagnostics. It is thereby key to develop a comprehensive genome-wide understanding of how bacteria process antibiotic stress, and how modulation of the involved processes affects their ability to overcome said stress. Here we undertake a comprehensive genetic analysis of how the human pathogen Streptococcus pneumoniae responds to 20 antibiotics. We build a genome-wide atlas of drug susceptibility determinants and generated a genetic interaction network that connects cellular processes and genes of unknown function, which we show can be used as therapeutic targets. Pathway analysis reveals a genome-wide atlas of cellular processes that can make a bacterium less susceptible, and often tolerant, in an antibiotic specific manner. Importantly, modulation of these processes confers fitness benefits during active infections under antibiotic selection. Moreover, screening of sequenced clinical isolates demonstrates that mutations in genes that decrease antibiotic sensitivity and increase tolerance readily evolve and are frequently associated with resistant strains, indicating such mutations could be harbingers for the emergence of antibiotic resistance.
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Affiliation(s)
| | - Federico Rosconi
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Andrew T Nishimoto
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen J Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Bimal Jana
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Noemí Buján
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Kaicheng Li
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Matthew Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephanie M Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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12
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Huo W, Busch LM, Hernandez-Bird J, Hamami E, Marshall CW, Geisinger E, Cooper VS, van Opijnen T, Rosch JW, Isberg RR. Immunosuppression broadens evolutionary pathways to drug resistance and treatment failure during Acinetobacter baumannii pneumonia in mice. Nat Microbiol 2022; 7:796-809. [PMID: 35618774 PMCID: PMC9159950 DOI: 10.1038/s41564-022-01126-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/20/2022] [Indexed: 01/02/2023]
Abstract
Acinetobacter baumannii is increasingly refractory to antibiotic treatment in healthcare settings. As is true of most human pathogens, the genetic path to antimicrobial resistance (AMR) and the role that the immune system plays in modulating AMR during disease are poorly understood. Here we reproduced several routes to fluoroquinolone resistance, performing evolution experiments using sequential lung infections in mice that are replete with or depleted of neutrophils, providing two key insights into the evolution of drug resistance. First, neutropenic hosts acted as reservoirs for the accumulation of drug resistance during drug treatment. Selection for variants with altered drug sensitivity profiles arose readily in the absence of neutrophils, while immunocompetent animals restricted the appearance of these variants. Secondly, antibiotic treatment failure in the immunocompromised host was shown to occur without clinically defined resistance, an unexpected result that provides a model for how antibiotic failure occurs clinically in the absence of AMR. The genetic mechanism underlying both these results is initiated by mutations activating the drug egress pump regulator AdeL, which drives persistence in the presence of antibiotic. Therefore, antibiotic persistence mutations present a two-pronged risk during disease, causing drug treatment failure in the immunocompromised host while simultaneously increasing the emergence of high-level AMR.
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Affiliation(s)
- Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Lindsay M Busch
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Juan Hernandez-Bird
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Efrat Hamami
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | | | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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13
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Alvarez-Manzo HS, Davidson RK, Van Cauwelaert de Wyels J, Cotten KL, Nguyen BH, Xiao M, Zhu Z, Anthony J, van Opijnen T, Davis KM. Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications. PLoS Pathog 2022; 18:e1010556. [PMID: 35576231 PMCID: PMC9135342 DOI: 10.1371/journal.ppat.1010556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/26/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Antibiotic tolerance is typically associated with a phenotypic change within a bacterial population, resulting in a transient decrease in antibiotic susceptibility that can contribute to treatment failure and recurrent infections. Although tolerant cells may emerge prior to treatment, the stress of prolonged antibiotic exposure can also promote tolerance. Here, we sought to determine how Yersinia pseudotuberculosis responds to doxycycline exposure, to then verify if these gene expression changes could promote doxycycline tolerance in culture and in our mouse model of infection. Only four genes were differentially regulated in response to a physiologically-relevant dose of doxycycline: osmB and ompF were upregulated, tusB and cnfy were downregulated; differential expression also occurred during doxycycline treatment in the mouse. ompF, tusB and cnfy were also differentially regulated in response to chloramphenicol, indicating these could be general responses to ribosomal inhibition. cnfy has previously been associated with persistence and was not a major focus here. We found deletion of the OmpF porin resulted in increased antibiotic accumulation, suggesting expression may promote diffusion of doxycycline out of the cell, while OsmB lipoprotein had a minor impact on antibiotic permeability. Overexpression of tusB significantly impaired bacterial survival in culture and in the mouse, suggesting that tRNA modification by tusB, and the resulting impacts on translational machinery, promotes survival during treatment with an antibiotic classically viewed as bacteriostatic. We believe this may be the first observation of bactericidal activity of doxycycline under physiological conditions, which was revealed by reversing tusB downregulation.
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Affiliation(s)
- Hector S. Alvarez-Manzo
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert K. Davidson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jasper Van Cauwelaert de Wyels
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine L. Cotten
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Benjamin H. Nguyen
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Melody Xiao
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Jon Anthony
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kimberly Michele Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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14
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Stevens EJ, Morse DJ, Bonini D, Duggan S, Brignoli T, Recker M, Lees JA, Croucher NJ, Bentley S, Wilson DJ, Earle SG, Dixon R, Nobbs A, Jenkinson H, van Opijnen T, Thibault D, Wilkinson OJ, Dillingham MS, Carlile S, McLoughlin RM, Massey RC. Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae. Microb Genom 2022; 8:000784. [PMID: 35416147 PMCID: PMC9453066 DOI: 10.1099/mgen.0.000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis. Young children are at a particularly high risk, with an estimated 3-4 million cases of severe disease and between 300 000 and 500 000 deaths attributable to pneumococcal disease each year. The haemolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, yet despite its key role in pathogenesis, immune evasion and transmission, the regulation of Ply production is not well defined. Using a genome-wide association approach, we identified a large number of potential affectors of Ply activity, including a gene acquired horizontally on the antibiotic resistance-conferring Integrative and Conjugative Element (ICE) ICESp23FST81. This gene encodes a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like domains with potent ATP-dependent nuclease activity. We found the regulatory effect of ZomB to be specific for the ply operon, potentially mediated by its high affinity for the BOX repeats encoded therein. Using a murine model of pneumococcal colonization, we further demonstrate that a ZomB mutant strain colonizes both the upper respiratory tract and lungs at higher levels when compared to the wild-type strain. While the antibiotic resistance-conferring aspects of ICESp23FST81 are often credited with contributing to the success of the S. pneumoniae lineages that acquire it, its ability to control the expression of a major virulence factor implicated in bacterial transmission is also likely to have played an important role.
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Affiliation(s)
- Emily J Stevens
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Daniel J Morse
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Dora Bonini
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Seána Duggan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Exeter, TR10 9FE, UK.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Stephen Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Sarah G Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Robert Dixon
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Angela Nobbs
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | - Howard Jenkinson
- Bristol Dental School, University of Bristol, Bristol, BS1 2LY, UK
| | | | - Derek Thibault
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Oliver J Wilkinson
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Simon Carlile
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Rachel M McLoughlin
- Host Pathogen Interactions Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.,Schools of Microbiology and Medicine and APC Microbiome Ireland, University College Cork, Cork, Ireland
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15
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Kumar N, Rana M, Geiwitz M, Khan NI, Catalano M, Ortiz-Marquez JC, Kitadai H, Weber A, Dweik B, Ling X, van Opijnen T, Argun AA, Burch KS. Rapid, Multianalyte Detection of Opioid Metabolites in Wastewater. ACS Nano 2022; 16:3704-3714. [PMID: 35201755 PMCID: PMC9949512 DOI: 10.1021/acsnano.1c07094] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
By monitoring opioid metabolites, wastewater-based epidemiology (WBE) could be an excellent tool for real-time information on the consumption of illicit drugs. A key limitation of WBE is the reliance on costly laboratory-based techniques that require substantial infrastructure and trained personnel, resulting in long turnaround times. Here, we present an aptamer-based graphene field effect transistor (AptG-FET) platform for simultaneous detection of three different opioid metabolites. This platform provides a reliable, rapid, and inexpensive method for quantitative analysis of opioid metabolites in wastewater. The platform delivers a limit of detection 2-3 orders of magnitude lower than previous reports, but in line with the concentration range (pg/mL to ng/mL) of these opioid metabolites present in real samples. To enable multianalyte detection, we developed a facile, reproducible, and high-yield fabrication process producing 20 G-FETs with integrated side gate platinum (Pt) electrodes on a single chip. Our devices achieved the selective multianalyte detection of three different metabolites: noroxycodone (NX), 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), and norfentanyl (NF) in wastewater diluted 20× in buffer.
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Affiliation(s)
- Narendra Kumar
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Muhit Rana
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Michael Geiwitz
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Matthew Catalano
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Juan C Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Hikari Kitadai
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Andrew Weber
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Badawi Dweik
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Xi Ling
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Avni A Argun
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Kenneth S Burch
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
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16
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Sundaresh B, Xu S, Noonan B, Mansour MK, Leong JM, van Opijnen T. Host-informed therapies for the treatment of pneumococcal pneumonia. Trends Mol Med 2021; 27:971-989. [PMID: 34376327 DOI: 10.1016/j.molmed.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022]
Abstract
Over the past two decades, traditional antimicrobial strategies have lost efficacy due to a rapid rise in antibiotic resistance and limited success in developing new antibiotics. Rather than relying on therapeutics solely targeting the bacterial pathogen, therapies are emerging that simultaneously focus on host responses. Here, we describe the most promising 'host-informed therapies' (HITs) in two categories: those that aid patients with fully functional immune systems, and those that aid patients with perturbed immune processes. Using Streptococcus pneumoniae, the leading cause of bacterial pneumonia, as a case study, we show HITs as an attractive option for supplementing infection management. However, to broaden their applicability and design new strategies, targeted research and clinical trials will be essential.
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Affiliation(s)
| | - Shuying Xu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA; Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Brian Noonan
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts Medical Center, Boston, MA, USA
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - John M Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA; Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts Medical Center, Boston, MA, USA.
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA, USA; Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts Medical Center, Boston, MA, USA.
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17
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Kelly M, Cambray S, McCarthy KA, Wang W, Geisinger E, Ortiz-Marquez J, van Opijnen T, Gao J. Peptide Probes of Colistin Resistance Discovered via Chemically Enhanced Phage Display. ACS Infect Dis 2020; 6:2410-2418. [PMID: 32786283 DOI: 10.1021/acsinfecdis.0c00206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Colistin is an antibiotic of last resort used to treat infections caused by multidrug-resistant Gram-negative bacterial pathogens. The recent surge in reported cases of colistin-resistant infections urgently calls for fast and reliable diagnostic methods, which can be used for the facile detection and proper treatment of these challenging infections. A major mechanism of colistin resistance involves phosphoethanolamine (PE) modification of lipopolysaccharide (LPS), the molecular target of colistin. This LPS modification mechanism has been recently reported to be transferrable via a plasmid-carried mcr-1 gene, which is particularly concerning as it may readily confer colistin resistance to a wide array of bacterial pathogens. To develop molecular tools to allow facile detection of colistin resistance, we have herein enlisted a novel phage library that incorporates dynamic covalent warheads to recognize PE modifications on bacterial cells. Screening of this chemically modified phage library against colistin-resistant pathogens revealed a number of peptide probes that readily differentiate colistin-resistant bacterial strains from their colistin-susceptible counterparts. With a fluorophore label, these peptide probes selectively stain colistin-resistant bacteria at sub-to-low micromolar concentrations. The bacterial staining is minimally inhibited by the presence of serum proteins or even blood serum. Mechanistic studies indicate that our peptide probes bind colistin-resistant bacteria primarily by targeting PE-modified lipids. However, some species-specific features of the cell surface can also contribute to the peptides' association to bacterial cells. Further elucidation of such cell surface features may give molecular probes with improved species and strain specificity, which will enable bacterial infection diagnosis with high precision.
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Affiliation(s)
- Michael Kelly
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Samantha Cambray
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kelly A. McCarthy
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Juan Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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18
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Geisinger E, Mortman NJ, Dai Y, Cokol M, Syal S, Farinha A, Fisher DG, Tang AY, Lazinski DW, Wood S, Anthony J, van Opijnen T, Isberg RR. Antibiotic susceptibility signatures identify potential antimicrobial targets in the Acinetobacter baumannii cell envelope. Nat Commun 2020; 11:4522. [PMID: 32908144 PMCID: PMC7481262 DOI: 10.1038/s41467-020-18301-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
A unique, protective cell envelope contributes to the broad drug resistance of the nosocomial pathogen Acinetobacter baumannii. Here we use transposon insertion sequencing to identify A. baumannii mutants displaying altered susceptibility to a panel of diverse antibiotics. By examining mutants with antibiotic susceptibility profiles that parallel mutations in characterized genes, we infer the function of multiple uncharacterized envelope proteins, some of which have roles in cell division or cell elongation. Remarkably, mutations affecting a predicted cell wall hydrolase lead to alterations in lipooligosaccharide synthesis. In addition, the analysis of altered susceptibility signatures and antibiotic-induced morphology patterns allows us to predict drug synergies; for example, certain beta-lactams appear to work cooperatively due to their preferential targeting of specific cell wall assembly machineries. Our results indicate that the pathogen may be effectively inhibited by the combined targeting of multiple pathways critical for envelope growth.
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Affiliation(s)
- Edward Geisinger
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA.
| | - Nadav J Mortman
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Yunfei Dai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Murat Cokol
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sapna Syal
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Andrew Farinha
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Delaney G Fisher
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Amy Y Tang
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - David W Lazinski
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Stephen Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA.
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19
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Abstract
The goal of genomics and systems biology is to understand how complex systems of factors assemble into pathways and structures that combine to form living organisms. Great advances in understanding biological processes result from determining the function of individual genes, a process that has classically relied on characterizing single mutations. Advances in DNA sequencing has made available the complete set of genetic instructions for an astonishing and growing number of species. To understand the function of this ever-increasing number of genes, a high-throughput method was developed that in a single experiment can measure the function of genes across the genome of an organism. This occurred approximately 10 years ago, when high-throughput DNA sequencing was combined with advances in transposon-mediated mutagenesis in a method termed transposon insertion sequencing (TIS). In the subsequent years, TIS succeeded in addressing fundamental questions regarding the genes of bacteria, many of which have been shown to play central roles in bacterial infections that result in major human diseases. The field of TIS has matured and resulted in studies of hundreds of species that include significant innovations with a number of transposons. Here, we summarize a number of TIS experiments to provide an understanding of the method and explanation of approaches that are instructive when designing a study. Importantly, we emphasize critical aspects of a TIS experiment and highlight the extension and applicability of TIS into nonbacterial species such as yeast.
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Affiliation(s)
- Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Henry L Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
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20
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Zhu Z, Surujon D, Ortiz-Marquez JC, Huo W, Isberg RR, Bento J, van Opijnen T. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nat Commun 2020; 11:4365. [PMID: 32868761 PMCID: PMC7458919 DOI: 10.1038/s41467-020-18134-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.
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Affiliation(s)
- Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - José Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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21
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Clark SA, Thibault D, Shull LM, Davis KM, Aunins E, van Opijnen T, Isberg R. Topologically correct synthetic reconstruction of pathogen social behavior found during Yersinia growth in deep tissue sites. eLife 2020; 9:58106. [PMID: 32543373 PMCID: PMC7316508 DOI: 10.7554/elife.58106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022] Open
Abstract
Within deep tissue sites, extracellular bacterial pathogens often replicate in clusters that are surrounded by immune cells. Disease is modulated by interbacterial interactions as well as bacterial-host cell interactions resulting in microbial growth, phagocytic attack and secretion of host antimicrobial factors. To overcome the limited ability to manipulate these infection sites, we established a system for Yersinia pseudotuberculosis (Yptb) growth in microfluidics-driven microdroplets that regenerates microbial social behavior in tissues. Chemical generation of nitric oxide (NO) in the absence of immune cells was sufficient to reconstruct microbial social behavior, as witnessed by expression of the NO-inactivating protein Hmp on the extreme periphery of microcolonies, mimicking spatial regulation in tissues. Similarly, activated macrophages that expressed inducible NO synthase (iNOS) drove peripheral expression of Hmp, allowing regeneration of social behavior observed in tissues. These results argue that topologically correct microbial tissue growth and associated social behavior can be reconstructed in culture.
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Affiliation(s)
- Stacie A Clark
- Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States.,Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States
| | - Derek Thibault
- Department of Biology, Boston College, Boston, United States
| | - Lauren M Shull
- Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States.,Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States
| | - Kimberly M Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Emily Aunins
- Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States.,Tufts University School of Medicine, Boston, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, United States
| | - Ralph Isberg
- Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, United States.,Tufts University School of Medicine, Boston, United States
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22
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Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
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Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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23
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Kumar N, Wang W, Ortiz-Marquez JC, Catalano M, Gray M, Biglari N, Hikari K, Ling X, Gao J, van Opijnen T, Burch KS. Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs. Biosens Bioelectron 2020; 156:112123. [PMID: 32174552 DOI: 10.1016/j.bios.2020.112123] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 01/19/2023]
Abstract
The rapid increase in antibiotic resistant pathogenic bacteria has become a global threat, which besides the development of new drugs, requires rapid, cheap, scalable, and accurate diagnostics. Label free biosensors relying on electrochemical, mechanical, and mass based detection of whole bacterial cells have attempted to meet these requirements. However, the trade-off between selectivity and sensitivity of such sensors remains a key challenge. In particular, point-of-care diagnostics that are able to reduce and/or prevent unneeded antibiotic prescriptions require highly specific probes with sensitive and accurate transducers that can be miniaturized and multiplexed, and that are easy to operate and cheap. Towards achieving this goal, we present a number of advances in the use of graphene field effect transistors (G-FET) including the first use of peptide probes to electrically detect antibiotic resistant bacteria in a highly specific manner. In addition, we dramatically reduce the needed concentration for detection by employing dielectrophoresis for the first time in a G-FET, allowing us to monitor changes in the Dirac point due to individual bacterial cells. Specifically, we realized rapid binding of bacterial cells to a G-FET by electrical field guiding to the device to realize an overall 3 orders of magnitude decrease in cell-concentration enabling a single-cell detection limit, and 9-fold reduction in needed time to 5 min. Utilizing our new biosensor and procedures, we demonstrate the first selective, electrical detection of the pathogenic bacterial species Staphylococcus aureus and antibiotic resistant Acinetobacter baumannii on a single platform.
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Affiliation(s)
- Narendra Kumar
- Department of Physics, Boston College, Chestnut Hill, MA, 02467, United States
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, United States
| | | | - Matthew Catalano
- Department of Physics, Boston College, Chestnut Hill, MA, 02467, United States
| | - Mason Gray
- Department of Physics, Boston College, Chestnut Hill, MA, 02467, United States
| | - Nadia Biglari
- Department of Physics, Boston College, Chestnut Hill, MA, 02467, United States
| | - Kitadai Hikari
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Xi Ling
- Department of Chemistry, Boston University, Boston, MA, 02215, United States; Division of Materials Science and Engineering, Boston University, Boston, MA, 02214, United States; The Photonics Center, Boston University, Boston, MA, 02214, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, United States.
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, United States.
| | - Kenneth S Burch
- Department of Physics, Boston College, Chestnut Hill, MA, 02467, United States.
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24
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Abstract
BACKGROUND Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism's behavior and response in an environment. It can be daunting to manually analyze and interpret such large datasets without some programming experience. Additionally, with increasing amounts of data; management, storage and sharing challenges arise. RESULTS Here, we present ShinyOmics, a web-based application that allows rapid collaborative exploration of omics-data. By using Tn-Seq, RNA-Seq, microarray and proteomics datasets from two human pathogens, we exemplify several conclusions that can be drawn from a rich dataset. We identify a protease and several chaperone proteins upregulated under aminoglycoside stress, show that antibiotics with the same mechanism of action trigger similar transcriptomic responses, point out the dissimilarity in different omics-profiles, and overlay the transcriptional response on a metabolic network. CONCLUSIONS ShinyOmics is easy to set up and customize, and can utilize user supplied metadata. It offers several visualization and comparison options that are designed to assist in novel hypothesis generation, as well as data management, online sharing and exploration. Moreover, ShinyOmics can be used as an interactive supplement accompanying research articles or presentations.
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Affiliation(s)
- Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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25
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Thibault D, Jensen PA, Wood S, Qabar C, Clark S, Shainheit MG, Isberg RR, van Opijnen T. Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes. Nat Commun 2019; 10:5729. [PMID: 31844066 PMCID: PMC6914776 DOI: 10.1038/s41467-019-13719-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. Droplet Tn-Seq (dTn-Seq) solves this problem by microfluidics facilitated encapsulation of individual transposon mutants into growth medium-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Here we describe and validate microfluidic chip design, production, encapsulation, and dTn-Seq sample preparation. We determine that 1-3% of mutants in Streptococcus pneumoniae have a different fitness when grown in isolation and show how dTn-Seq can help identify leads for gene function, including those involved in hyper-competence, processing of alpha-1-acid glycoprotein, sensitivity against the human leukocyte elastase and microcolony formation. Additionally, we show dTn-Seq compatibility with microscopy, FACS and investigations of bacterial cell-to-cell and bacteria-host cell interactions. dTn-Seq reduces costs and retains the advantages of Tn-Seq, while expanding the method's original applicability.
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Affiliation(s)
- Derek Thibault
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Paul A Jensen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stephen Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Christine Qabar
- Department of Biological Sciences, Towson University, Towson, MD, 21252, USA
| | - Stacie Clark
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Mara G Shainheit
- Department of Biological Sciences, Towson University, Towson, MD, 21252, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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26
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Rowe HM, Karlsson E, Echlin H, Chang TC, Wang L, van Opijnen T, Pounds SB, Schultz-Cherry S, Rosch JW. Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts. Cell Host Microbe 2019; 25:884-891.e6. [PMID: 31126758 DOI: 10.1016/j.chom.2019.04.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/18/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023]
Abstract
The capacity of Streptococcus pneumoniae to successfully transmit and colonize new human hosts is a critical aspect of pneumococcal population biology and a prerequisite for invasive disease. However, the bacterial mechanisms underlying this process remain largely unknown. To identify bacterial factors required for transmission, we conducted a high-throughput genetic screen with a transposon sequencing (Tn-seq) library of a pneumococcal strain in a ferret transmission model. Key players in both metabolism and transcriptional regulation were identified as required for efficient bacterial transmission. Targeted deletion of the putative C3-degrading protease CppA, iron transporter PiaA, or competence regulatory histidine kinase ComD significantly decreased transmissibility in a mouse model, further validating the screen. Maternal vaccination with recombinant surface-exposed PiaA and CppA alone or in combination blocked transmission in offspring and were more effective than capsule-based vaccines. These data underscore the possibility of targeting pneumococcal transmission as a means of eliminating invasive disease in the population.
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Affiliation(s)
- Hannah M Rowe
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Wang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA.
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27
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Warrier I, Ram-Mohan N, Zhu Z, Hazery A, Echlin H, Rosch J, Meyer MM, van Opijnen T. The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. PLoS Pathog 2018; 14:e1007461. [PMID: 30517198 PMCID: PMC6296669 DOI: 10.1371/journal.ppat.1007461] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 12/17/2018] [Accepted: 11/07/2018] [Indexed: 11/21/2022] Open
Abstract
Efficient and highly organized regulation of transcription is fundamental to an organism’s ability to survive, proliferate, and quickly respond to its environment. Therefore, precise mapping of transcriptional units and understanding their regulation is crucial to determining how pathogenic bacteria cause disease and how they may be inhibited. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae TIGR4 by applying a combination of high-throughput RNA-sequencing techniques. We successfully map 1864 high confidence transcription termination sites (TTSs), 790 high confidence transcription start sites (TSSs) (742 primary, and 48 secondary), and 1360 low confidence TSSs (74 secondary and 1286 primary) to yield a total of 2150 TSSs. Furthermore, our study reveals a complex transcriptome wherein environment-respondent alternate transcriptional units are observed within operons stemming from internal TSSs and TTSs. Additionally, we identify many putative cis-regulatory RNA elements and riboswitches within 5’-untranslated regions (5’-UTR). By integrating TSSs and TTSs with independently collected RNA-Seq datasets from a variety of conditions, we establish the response of these regulators to changes in growth conditions and validate several of them. Furthermore, to demonstrate the importance of ribo-regulation by 5’-UTR elements for in vivo virulence, we show that the pyrR regulatory element is essential for survival, successful colonization and infection in mice suggesting that such RNA elements are potential drug targets. Importantly, we show that our approach of combining high-throughput sequencing with in vivo experiments can reconstruct a global understanding of regulation, but also pave the way for discovery of compounds that target (ribo-)regulators to mitigate virulence and antibiotic resistance. The canonical relationship between a bacterial operon and the mRNA transcript produced from the operon has become significantly more complex as numerous regulatory mechanisms that impact the stability, translational efficiency, and early termination rates for mRNA transcripts have been described. With the rise of antibiotic resistance, these mechanisms offer new potential targets for antibiotic development. In this study we used a combination of high-throughput sequencing technologies to assess genome-wide transcription start and stop sites, as well as determine condition specific global transcription patterns in the human pathogen Streptococcus pneumoniae. We find that the majority of multi-gene operons have alternative start and stop sites enabling condition specific regulation of genes within the same operon. Furthermore, we identified many putative RNA regulators that are widespread in the S. pneumoniae pan-genome. Finally, we show that separately collected RNA-Seq data enables identification of conditional triggers for regulatory RNAs, and experimentally demonstrate that our approach may be used to identify drug-able RNA targets by establishing that pyrR RNA functionality is critical for successful S. pneumoniae mouse colonization and infection. Thus, our study not only uses genome-wide high-throughput approaches to identify putative RNA regulators, but also establishes the importance of such regulators in S. pneumoniae virulence.
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Affiliation(s)
- Indu Warrier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Nikhil Ram-Mohan
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Ariana Hazery
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jason Rosch
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Michelle M. Meyer
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail: (MMM); (TvO)
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail: (MMM); (TvO)
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28
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McCarthy KA, Kelly MA, Li K, Cambray S, Hosseini AS, van Opijnen T, Gao J. Phage Display of Dynamic Covalent Binding Motifs Enables Facile Development of Targeted Antibiotics. J Am Chem Soc 2018; 140:6137-6145. [PMID: 29701966 DOI: 10.1021/jacs.8b02461] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance of bacterial pathogens poses an increasing threat to the wellbeing of our society and urgently calls for new strategies for infection diagnosis and antibiotic discovery. The antibiotic resistance problem at least partially arises from extensive use of broad-spectrum antibiotics. Ideally, for the treatment of infection, one would like to use a narrow-spectrum antibiotic that specifically targets and kills the disease-causing strain. This is particularly important considering the commensal bacterial species that are beneficial and sometimes even critical to the health of a human being. In this contribution, we describe a phage display platform that enables rapid identification of peptide probes for specific bacterial strains. The phage library described herein incorporates 2-acetylphenylboronic acid moieties to elicit dynamic covalent binding to the bacterial cell surface. Screening of the library against live bacterial cells yields submicromolar and highly specific binders for clinical strains of Staphylococcus aureus and Acinetobacter baumannii that display antibiotic resistance. We further show that the identified peptide probes can be readily converted to bactericidal agents that deliver generic toxins to kill the targeted bacterial strain with high specificity. The phage display platform described here is applicable to a wide array of bacterial strains, paving the way to facile diagnosis and development of strain-specific antibiotics.
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Affiliation(s)
- Kelly A McCarthy
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Michael A Kelly
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Kaicheng Li
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Samantha Cambray
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Azade S Hosseini
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Tim van Opijnen
- Department of Biology , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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29
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McCoy KM, Antonio ML, van Opijnen T. MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization. Bioinformatics 2018; 33:2781-2783. [PMID: 28498899 DOI: 10.1093/bioinformatics/btx320] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/10/2017] [Indexed: 02/02/2023] Open
Abstract
Motivation Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition. Results Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility. MAGenTA is a complete Tn-Seq analysis pipeline making sensitive genome-wide fitness (i.e. growth rate) analysis available for most transposons and Tn-Seq associated approaches (e.g. TraDis, HiTS, IN-Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome-wide fitness visualization. Availability and implementation MAGenTA is available at the Galaxy public ToolShed repository and all source code can be found and are freely available at https://vanopijnenlab.github.io/MAGenTA/ . Contact vanopijn@bc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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30
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Jensen PA, Zhu Z, van Opijnen T. Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Rep 2017; 20:1705-1716. [PMID: 28813680 PMCID: PMC5584877 DOI: 10.1016/j.celrep.2017.07.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/28/2017] [Accepted: 07/23/2017] [Indexed: 01/19/2023] Open
Abstract
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering.
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Affiliation(s)
- Paul A Jensen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA.
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31
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van Opijnen T, Dedrick S, Bento J. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathog 2016; 12:e1005869. [PMID: 27607357 PMCID: PMC5015961 DOI: 10.1371/journal.ppat.1005869] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022] Open
Abstract
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - Sandra Dedrick
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - José Bento
- Boston College, Computer Science Department, Massachusetts, United States of America
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32
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van Opijnen T, Lazinski DW, Camilli A. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms. Curr Protoc Microbiol 2015; 36:1E.3.1-1E.3.24. [PMID: 25641100 PMCID: PMC4696536 DOI: 10.1002/9780471729259.mc01e03s36] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobial agents and vaccines. This unit presents Tn-seq, a method that has made it possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies on the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated transposon insertion library. After library selection, changes in the frequency of each insertion mutant are determined by sequencing flanking regions en masse. These changes are used to calculate each mutant's fitness. The method was originally developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis, but has now been applied to several different microbial species.
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Affiliation(s)
- Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts
| | - David W Lazinski
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Howard Hughes Medical Institute, Boston, Massachusetts
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Howard Hughes Medical Institute, Boston, Massachusetts
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33
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Carter R, Wolf J, van Opijnen T, Muller M, Obert C, Burnham C, Mann B, Li Y, Hayden RT, Pestina T, Persons D, Camilli A, Flynn PM, Tuomanen EI, Rosch JW. Genomic analyses of pneumococci from children with sickle cell disease expose host-specific bacterial adaptations and deficits in current interventions. Cell Host Microbe 2015; 15:587-599. [PMID: 24832453 DOI: 10.1016/j.chom.2014.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/10/2014] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Sickle cell disease (SCD) patients are at high risk of contracting pneumococcal infection. To address this risk, they receive pneumococcal vaccines, and antibiotic prophylaxis and treatment. To assess the impact of SCD and these interventions on pneumococcal genetic architecture, we examined the genomes of more than 300 pneumococcal isolates from SCD patients over 20 years. Modern SCD strains retained invasive capacity but shifted away from the serotypes used in vaccines. These strains had specific genetic changes related to antibiotic resistance, capsule biosynthesis, metabolism, and metal transport. A murine SCD model coupled with Tn-seq mutagenesis identified 60 noncapsular pneumococcal genes under differential selective pressure in SCD, which correlated with aspects of SCD pathophysiology. Further, virulence determinants in the SCD context were distinct from the general population, and protective capacity of potential antigens was lost over time in SCD. This highlights the importance of understanding bacterial pathogenesis in the context of high-risk individuals.
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Affiliation(s)
- Robert Carter
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tim van Opijnen
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Martha Muller
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Caroline Obert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Corinna Burnham
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Yimei Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tamara Pestina
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Derek Persons
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Andrew Camilli
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA.,Howard Hughes Medical Institute, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Patricia M Flynn
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
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van Opijnen T, Lazinski DW, Camilli A. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms. Curr Protoc Mol Biol 2014; 106:7.16.1-7.16.24. [PMID: 24733243 PMCID: PMC4568079 DOI: 10.1002/0471142727.mb0716s106] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobial agents and vaccines. This unit presents Tn-seq, a method that has made it possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies on the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated transposon insertion library. After library selection, changes in the frequency of each insertion mutant are determined by sequencing flanking regions en masse. These changes are used to calculate each mutant's fitness. The method was originally developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis, but has now been applied to several different microbial species.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Department of Biology, Chestnut Hill, Massachusetts
| | - David W. Lazinski
- Tufts University, School of Medicine, Department of Molecular Biology & Microbiology and Howard Hughes Medical Institute, Boston, Massachusetts
| | - Andrew Camilli
- Tufts University, School of Medicine, Department of Molecular Biology & Microbiology and Howard Hughes Medical Institute, Boston, Massachusetts
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35
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Abstract
Our knowledge of gene function has increasingly lagged behind gene discovery, hindering our understanding of the genetic basis of microbial phenotypes. Recently, however, massively parallel sequencing has been combined with traditional transposon mutagenesis in techniques referred to as transposon sequencing (Tn-seq), high-throughput insertion tracking by deep sequencing (HITS), insertion sequencing (INSeq) and transposon-directed insertion site sequencing (TraDIS), making it possible to identify putative gene functions in a high-throughput manner. Here, we describe the similarities and differences of these related techniques and discuss their application to the probing of gene function and higher-order genome organization.
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Affiliation(s)
- Tim van Opijnen
- Biology Department, Boston College, 140 Commonwealth Avenue, 420 Higgins Hall, Chestnut Hill, Massachusetts 02467, USA.
| | - Andrew Camilli
- Howard Hughes Medical Institute and the Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, Massachusetts 02111, USA.
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36
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Abstract
A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We describe a high-throughput strategy based on the method Tn-seq that can be applied to any genetically manipulatable microorganism. By screening 17 in vitro and two in vivo (carriage and infection) conditions for the pathogen Streptococcus pneumoniae, we create a resource consisting of >1800 interactions that is rich in new genotype–phenotype relationships. We describe genes that are involved in differential carbon source utilization in the host, as well as genes that are involved both in virulence and in resistance against specific in vitro stresses, thereby revealing selection pressures that the pathogen experiences in vivo. We reveal the secondary response to an antibiotic, including a dual role efflux pump also involved in resistance to pH stress. Through genetic-interaction mapping and gene-expression analysis we define the mechanism of attenuation and the regulatory relationship between a two-component system and a core biosynthetic pathway specific to microorganisms. Thus, we have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae and provided a road map for similar discovery in other microorganisms.
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Affiliation(s)
- Tim van Opijnen
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI, Rosch JW. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 2012; 8:e1002788. [PMID: 22807675 PMCID: PMC3395615 DOI: 10.1371/journal.ppat.1002788] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/22/2012] [Indexed: 01/10/2023] Open
Abstract
Small noncoding RNAs (sRNAs) play important roles in gene regulation in both prokaryotes and eukaryotes. Thus far, no sRNA has been assigned a definitive role in virulence in the major human pathogen Streptococcus pneumoniae. Based on the potential coding capacity of intergenic regions, we hypothesized that the pneumococcus produces many sRNAs and that they would play an important role in pathogenesis. We describe the application of whole-genome transcriptional sequencing to systematically identify the sRNAs of Streptococcus pneumoniae. Using this approach, we have identified 89 putative sRNAs, 56 of which are newly identified. Furthermore, using targeted genetic approaches and Tn-seq transposon screening, we demonstrate that many of the identified sRNAs have important global and niche-specific roles in virulence. These data constitute the most comprehensive analysis of pneumococcal sRNAs and provide the first evidence of the extensive roles of sRNAs in pneumococcal pathogenesis. Pneumonia is a leading cause of childhood mortality worldwide, resulting in more deaths in young children than any other infectious disease. One of the leading causes of pneumonia is the human pathogen, Streptococcus pneumoniae, the causative agent of over six million infections each year in the United States. Understanding how bacterial pathogens rapidly respond to dynamic host environments is a central aspect of microbial pathogenesis. Accumulating evidence has implicated sRNAs as vital regulators in a number of important cellular processes though few have been implicated in virulence. In our investigations we have applied next-generation sequencing to define the sRNA repertoire of S. pneumoniae. In addition, we utilized both targeted genetic knockouts and transposon mutagenesis to show that a significant portion of these sRNAs play important roles at various stages of pneumococcal pathogenesis. These data represent the first example of sRNAs being involved in pneumococcal pathogenesis and greatly expand the number of sRNAs that play important roles in bacterial pathogenesis.
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Affiliation(s)
- Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Tim van Opijnen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jianmin Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Caroline Obert
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Yong-Dong Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Robert Carter
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Daniel J. McGoldrick
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Granger Ridout
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Andrew Camilli
- Howard Hughes Medical Institute and Tufts University School of Medicine, Department of Molecular Biology and Microbiology, Boston, Massachusetts, United States of America
| | - Elaine I. Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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38
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van Opijnen T, Camilli A. Genome-wide fitness and genetic interactions determined by Tn-seq, a high-throughput massively parallel sequencing method for microorganisms. Curr Protoc Microbiol 2010; Chapter 1:Unit1E.3. [PMID: 21053251 PMCID: PMC3877651 DOI: 10.1002/9780471729259.mc01e03s19] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The lagging annotation of bacterial genomes and the inherent genetic complexity of many phenotypes is hindering the discovery of new drug targets and the development of new antimicrobials and vaccines. Here we present the method Tn-seq, with which it has become possible to quantitatively determine fitness for most genes in a microorganism and to screen for quantitative genetic interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can thus direct studies in the annotation of genes and untangle complex phenotypes. The method is based on the construction of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing of the flanking regions en masse. These changes are used to calculate each mutant's fitness. The method has been developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative agent of pneumonia and meningitis; however, due to the wide activity of the Mariner transposon, Tn-seq can be applied to many different microbial species.
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Affiliation(s)
- Tim van Opijnen
- Tufts University School of Medicine, Boston, Massachusetts, USA
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39
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Abstract
Many viruses have the ability to rapidly develop resistance against antiviral drugs and escape from the host immune system. To which extent the host environment affects this adaptive potential of viruses is largely unknown. Here we show that for HIV-1, the host-cell environment is key to the adaptive potential of the virus. We performed a large-scale selection experiment with two HIV-1 strains in two different T-cell lines (MT4 and C8166). Over 110 days of culture, both virus strains adapted rapidly to the MT4 T-cell line. In contrast, when cultured on the C8166 T-cell line, the same strains did not show any increase in fitness. By sequence analyses and infections with viruses expressing either yellow or cyan fluorescent protein, we were able to show that the absence of adaptation was linked to a lower recombination rate in the C8166 T-cell line. Our findings suggest that if we can manipulate the host-cellular factors that mediate viral evolution, we may be able to significantly retard viral adaptability.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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van Opijnen T, Boerlijst MC, Berkhout B. Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments. J Virol 2006; 80:6678-85. [PMID: 16775355 PMCID: PMC1488947 DOI: 10.1128/jvi.02547-05] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A mutation's effect on fitness or phenotype may in part depend on the interaction of the mutation with the environment. The resulting phenotype or fitness is important, since it determines the adaptive potential of a species. To date, most studies have focused on alterations to protein-coding regions of the genome and their consequential fitness effects. Non-protein-coding regulatory regions have been largely neglected, although they make up a large and important part of an organism's genome. Here, we use human immunodeficiency virus type 1 as a model system to investigate fitness effects of random mutations in noncoding DNA-binding sites of the transcriptional promoter. We determined 242 fitness values for 35 viral promoter mutants with one, two, or three mutations across seven distinct cellular environments and identified that (i) all mutants have an effect in at least one cellular environment; (ii) fitness effects are highly dependent on the cellular environment; (iii) disadvantageous and advantageous mutations occur at high and similar frequencies; and (iv) epistatic effects of multiple mutations are rare. Our results underline the evolutionary potential of regulatory regions and indicate that DNA-binding sites evolve under strong selection, while at the same time, they are very plastic to environmental change.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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Abstract
Viral fitness is defined by the ability of an individual genotype to produce infectious progeny in a specific environment. For HIV the environment is never constant but rather fluctuates in time and space. For instance, environmental factors that determine viral fitness during transmission from host to host are different to the pressures from either cytotoxic T-lymphocytes (CTLs) or antiviral drugs. Consequently, viral fitness is highly dependent on the environment and the accurate determination of this value therefore depends strongly on the chosen environmental setting. This review describes how the host environment imposes selective pressures on the virus that shape its genotype and fitness. The most important environments that the virus encounters throughout its life cycle and during natural infection are discussed. In order of appearance, CTLs are discussed, followed by neutralising antibodies and antiretroviral drug treatment. It then goes on to describe receptor molecules that mediate viral entry and intracellular restriction factors, which represent selective pressures that are present directly from the start of a natural infection. It concludes by discussing the complexity of viral fitness and how an accurate measure of viral fitness eventually may, for example, contribute to the improvement of antiretroviral therapy or help in the formulation of an optimal vaccination strategy.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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42
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Lemieux AM, Paré ME, Audet B, Legault E, Lefort S, Boucher N, Landry S, van Opijnen T, Berkhout B, Naghavi MH, Tremblay MJ, Barbeau B. T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region. J Biol Chem 2004; 279:52949-60. [PMID: 15466412 DOI: 10.1074/jbc.m409896200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enhancer region in the human immunodeficiency virus type 1 (HIV-1) 5'-long terminal repeat (LTR) is very important for viral transcription. This promoter sequence binds both nuclear factor-kappaB and NFAT, two important modulators of HIV-1 gene expression. Previous studies have indicated that the enhancer regions of the different HIV-1 clade LTRs differ in their number of NF-kappaB-binding sites. In this study, we have compared the activation potential of the different HIV-1 clade and HIV-2 LTRs and assessed their interaction with NFAT and NF-kappaB. In T-cell lines and primary CD4(+) T-cells, the results showed that the HIV-1 clade E LTR (with a single NF-kappaB-binding site) was the weakest LTR regardless of the tested activators, whereas the HIV-2 LTR was the most responsive LTR. The clade E enhancer region was also demonstrated to be the weakest enhancer region in transfection experiments with luciferase reporter-based vectors. Electrophoretic mobility shift assays with extracts from activated CD4(+) T-cells indicated that, although NF-kappaB and NFAT bound all enhancers, HIV-1 clade E and HIV-2 LTR enhancers were poor binding targets for these two factors. Weak NFAT binding to clade E enhancers was also confirmed using NFAT1-expressing 293T cells in competition experiments. We have also shown the absence of interaction of NF-kappaB or NFAT with the third NF-kappaB repeat present in clade C. However, the clade C enhancer bound NFAT more efficiently than all other enhancer regions tested. Our results hence demonstrate for the first time that differences in the binding of NF-kappaB and NFAT to the enhancer regions could be responsible for some of the observed variation in HIV-1 clade LTR activation, whereas HIV-2 LTR activation seems mostly independent of these interactions.
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Affiliation(s)
- Anne-Marie Lemieux
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Pavillon CHUL, 2705 Blvd. Laurier, Sainte-Foy, Quebec G1V 4G2, Canada
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van Opijnen T, Kamoschinski J, Jeeninga RE, Berkhout B. The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication. J Virol 2004; 78:6883-90. [PMID: 15194764 PMCID: PMC421681 DOI: 10.1128/jvi.78.13.6883-6890.2004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) transcriptional promoter contains a single polymorphism in the TATA box. Most subtypes contain the sequence TATAAGC, but subtype E and some recombinant AG strains have the sequence TAAAAGC. Based on mutagenesis studies of cellular RNA polymerase II (pol II) promoters, it has been proposed that the subtype E TATA box is nonfunctional due to the T-to-A substitution at the critical position 3. By means of transcription and virus replication assays, we demonstrate that the true TATA box motif within the viral long terminal repeat (LTR) promoter starts two nucleotides further upstream. Because of this realignment, subtype E has the sequence CATAAAA and all other subtypes have the sequence CATATAA. The polymorphism therefore has shifted from position 3 to position 5 and is no longer incompatible with efficient transcription according to rules determined for cellular pol II promoters. In addition, through sensitive competition experiments, we demonstrate that the CATA box of subtypes B and E can be improved for replication by the mutations 1T and 5T, respectively. The fact that the fitness of both subtype LTRs can be increased by specific point mutations in the CATA box suggests that the transcriptional promoter of HIV-1 is fine-tuned towards a suboptimal level of replication. However, this replication rate may be optimal in the in vivo context of an infected individual.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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van Opijnen T, Jeeninga RE, Boerlijst MC, Pollakis GP, Zetterberg V, Salminen M, Berkhout B. Human immunodeficiency virus type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner. J Virol 2004; 78:3675-83. [PMID: 15016888 PMCID: PMC371093 DOI: 10.1128/jvi.78.7.3675-3683.2004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The long terminal repeat (LTR) transcriptional promoters of different human immunodeficiency virus (HIV) type 1 subtypes were inserted into the LAI molecular clone of subtype B. The viral genotypes represent seven subtypes (A, B, C, D, E, F, and G) and one circulating recombinant form (AG). We performed replication studies with this isogenic set of viruses across six cellular environments. This approach revealed strong cellular environment effects, but the method was not sensitive enough to detect small differences in the replication rate between the subtypes. By conducting pairwise competition experiments between the virus variants in six cellular environments, we could demonstrate significant differences in the replication rates of the subtypes and that LTR-determined viral fitness depends both on the host cell type and the activation state of the cell. In addition, we determined the degree of conservation of the transcription factor-binding sites (TFBS) in the different-subtype LTRs by analyzing sequences from the HIV sequence database. The sequence analyses revealed subtype-specific conservation of certain TFBS. The results indicate that one should consider the possibility of subtype-specific viral replication rates in vivo, which are strongly influenced by the host environment. We argue that the multidimensional host environment may have shaped the genetic structures of the subtype LTRs.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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