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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [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: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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2
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Kissler SM, Oliveira Roster KI, Petherbridge R, Mehrotra A, Barnett ML, Grad YH. Drivers of Geographic Patterns in Outpatient Antibiotic Prescribing in the United States. Clin Infect Dis 2024:ciae111. [PMID: 38509670 DOI: 10.1093/cid/ciae111] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Indexed: 03/22/2024] Open
Abstract
In a retrospective, ecological analysis of US medical claims, visit rates explained more of the geographic variation in outpatient antibiotic prescribing rates than per-visit prescribing. Efforts to reduce antibiotic use may benefit from addressing the factors that drive higher rates of outpatient visits, in addition to continued focus on stewardship.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kirstin I Oliveira Roster
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ateev Mehrotra
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael L Barnett
- Department of Health Policy and Management, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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3
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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. bioRxiv 2023:2023.03.19.532758. [PMID: 36993299 PMCID: PMC10055259 DOI: 10.1101/2023.03.19.532758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally-encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 64 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Siân V. Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lucy M. McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Maximillian G. Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Eleanor A. Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alice C. Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Boston University, Boston, MA 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Oluremi J. Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E. Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jillian S. Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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4
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Foy BH, Petherbridge R, Roth M, Mow C, Patel HR, Patel CH, Ho SN, Lam E, Karczewski KJ, Tozzo V, Higgins JM. Hematologic setpoints are a stable and patient-specific deep phenotype. medRxiv 2023:2023.09.26.23296146. [PMID: 37808854 PMCID: PMC10557837 DOI: 10.1101/2023.09.26.23296146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The complete blood count is an important screening tool for healthy adults and is the most commonly ordered test at periodic physical exams. However, results are usually interpreted relative to one-size-fits-all reference intervals, undermining the goal of precision medicine to tailor medical care to the needs of individual patients based on their unique characteristics. Here we show that standard complete blood count indices in healthy adults have robust homeostatic setpoints that are patient-specific and stable, with the typical healthy adult's set of 9 blood count setpoints distinguishable from 98% of others, and with these differences persisting for decades. These setpoints reflect a deep physiologic phenotype, enabling improved detection of both acquired and genetic determinants of hematologic regulation, including discovery of multiple novel loci via GWAS analyses. Patient-specific reference intervals derived from setpoints enable more accurate personalized risk assessment, and the setpoints themselves are significantly correlated with mortality risk, providing new opportunities to enhance patient-specific screening and early intervention. This study shows complete blood count setpoints are sufficiently stable and patient-specific to help realize the promise of precision medicine for healthy adults.
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Affiliation(s)
- Brody H Foy
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Rachel Petherbridge
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Maxwell Roth
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Mow
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Enterprise Research IS, Boston, MA, USA
| | - Hasmukh R Patel
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Chhaya H Patel
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Samantha N Ho
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Evie Lam
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Veronica Tozzo
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - John M Higgins
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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