1
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Giuliano CJ, Wei KJ, Harling FM, Waldman BS, Farringer MA, Boydston EA, Lan TCT, Thomas RW, Herneisen AL, Sanderlin AG, Coppens I, Dvorin JD, Lourido S. CRISPR-based functional profiling of the Toxoplasma gondii genome during acute murine infection. Nat Microbiol 2024:10.1038/s41564-024-01754-2. [PMID: 38977907 DOI: 10.1038/s41564-024-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/07/2024] [Indexed: 07/10/2024]
Abstract
Examining host-pathogen interactions in animals can capture aspects of infection that are obscured in cell culture. Using CRISPR-based screens, we functionally profile the entire genome of the apicomplexan parasite Toxoplasma gondii during murine infection. Barcoded gRNAs enabled bottleneck detection and mapping of population structures within parasite lineages. Over 300 genes with previously unknown roles in infection were found to modulate parasite fitness in mice. Candidates span multiple axes of host-parasite interaction. Rhoptry Apical Surface Protein 1 was characterized as a mediator of host-cell tropism that facilitates repeated invasion attempts. GTP cyclohydrolase I was also required for fitness in mice and druggable through a repurposed compound, 2,4-diamino-6-hydroxypyrimidine. This compound synergized with pyrimethamine against T. gondii and malaria-causing Plasmodium falciparum parasites. This work represents a complete survey of an apicomplexan genome during infection of an animal host and points to novel interfaces of host-parasite interaction.
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Affiliation(s)
| | - Kenneth J Wei
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | | | - Benjamin S Waldman
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | - Madeline A Farringer
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
- Biological Sciences in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Raina W Thomas
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | - Alice L Herneisen
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | | | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA, USA.
- Biology Department, MIT, Cambridge, MA, USA.
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2
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Hotinger JA, Campbell IW, Hullahalli K, Osaki A, Waldor MK. Quantification of Salmonella enterica serovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601246. [PMID: 38979326 PMCID: PMC11230369 DOI: 10.1101/2024.06.28.601246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S . Typhimurium barcoded library containing ∼55,000 unique strains distinguishable by genomic barcodes by enumerating S . Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics. Significance Statement Salmonella is a prevalent food-borne pathogen that infects hundreds of millions of people worldwide. Here, we created a highly complex barcoded Salmonella enterica serovar Typhimurium library containing ∼55,000 barcodes to further understand and quantify Salmonella population dynamics in experimental murine infection. Through comparisons of barcode abundance and frequency in different samples and following different routes of inoculation, we quantify key facets of Salmonella infection, including bottleneck sizes and dissemination patterns, and uncover hidden routes of spread that drive heterogeneity in infection outcome. These observations provide a detailed map of Salmonella infection and demonstrate the power of high-diversity barcoded libraries in deciphering microbial population dynamics.
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3
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Chevée V, Hullahalli K, Dailey KG, Güereca L, Zhang C, Waldor MK, Portnoy DA. Temporal and spatial dynamics of Listeria monocytogenes central nervous system infection in mice. Proc Natl Acad Sci U S A 2024; 121:e2320311121. [PMID: 38635627 PMCID: PMC11046682 DOI: 10.1073/pnas.2320311121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/22/2024] [Indexed: 04/20/2024] Open
Abstract
Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.
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Affiliation(s)
- Victoria Chevée
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Katherine G. Dailey
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Leslie Güereca
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Chenyu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
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4
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Wong DPGH, Good BH. Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking. Nat Commun 2024; 15:1605. [PMID: 38383538 PMCID: PMC10881964 DOI: 10.1038/s41467-024-45792-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants - most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
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Affiliation(s)
- Daniel P G H Wong
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, 94158, USA.
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5
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Ward RD, Tran JS, Banta AB, Bacon EE, Rose WE, Peters JM. Essential gene knockdowns reveal genetic vulnerabilities and antibiotic sensitivities in Acinetobacter baumannii. mBio 2024; 15:e0205123. [PMID: 38126769 PMCID: PMC10865783 DOI: 10.1128/mbio.02051-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing, they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that may explain synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.IMPORTANCEAcinetobacter baumannii is a hospital-acquired pathogen that is resistant to many common antibiotic treatments. To combat resistant A. baumannii infections, we need to identify promising therapeutic targets and effective antibiotic combinations. In this study, we comprehensively characterize the genes and pathways that are critical for A. baumannii viability. We show that genes involved in aerobic metabolism are central to A. baumannii physiology and may represent appealing drug targets. We also find antibiotic-gene interactions that may impact the efficacy of carbapenems, rifamycins, and polymyxins, providing a new window into how these antibiotics function in mono- and combination therapies. Our studies offer a useful approach for characterizing interactions between drugs and essential genes in pathogens to inform future therapies.
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Affiliation(s)
- Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jennifer S. Tran
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emily E. Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Warren E. Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Hullahalli K, Dailey KG, Hasegawa Y, Torres E, Suzuki M, Zhang H, Threadgill DW, Navarro VM, Waldor MK. Genetic and immune determinants of E. coli liver abscess formation. Proc Natl Acad Sci U S A 2023; 120:e2310053120. [PMID: 38096412 PMCID: PMC10743367 DOI: 10.1073/pnas.2310053120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Systemic infections can yield distinct outcomes in different tissues. In mice, intravenous inoculation of Escherichia coli leads to bacterial replication within liver abscesses, while other organs such as the spleen clear the pathogen. Abscesses are macroscopic necrotic regions that comprise the vast majority of the bacterial burden in the animal, yet little is known about the processes underlying their formation. Here, we characterize E. coli liver abscesses and identify host determinants of abscess susceptibility. Spatial transcriptomics revealed that liver abscesses are associated with heterogenous immune cell clusters comprised of macrophages, neutrophils, dendritic cells, innate lymphoid cells, and T-cells that surround necrotic regions of the liver. Abscess susceptibility is heightened in the C57BL lineage, particularly in C57BL/6N females. Backcross analyses demonstrated that abscess susceptibility is a polygenic trait inherited in a sex-dependent manner without direct linkage to sex chromosomes. As early as 1 d post infection, the magnitude of E. coli replication in the liver distinguishes abscess-susceptible and abscess-resistant strains of mice, suggesting that the immune pathways that regulate abscess formation are induced within hours. We characterized the early hepatic response with single-cell RNA sequencing and found that mice with reduced activation of early inflammatory responses, such as those lacking the LPS receptor TLR4 (Toll-like receptor 4), are resistant to abscess formation. Experiments with barcoded E. coli revealed that TLR4 mediates a tradeoff between abscess formation and bacterial clearance. Together, our findings define hallmarks of E. coli liver abscess formation and suggest that hyperactivation of the hepatic innate immune response drives liver abscess susceptibility.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Yuko Hasegawa
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Encarnacion Torres
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Masataka Suzuki
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Hailong Zhang
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - David W. Threadgill
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX76549
- Department of Nutrition, Texas A&M University, College Station, TX76549
| | - Victor M. Navarro
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
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7
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May DA, Taha F, Child MA, Ewald SE. How colonization bottlenecks, tissue niches, and transmission strategies shape protozoan infections. Trends Parasitol 2023; 39:1074-1086. [PMID: 37839913 DOI: 10.1016/j.pt.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Protozoan pathogens such as Plasmodium spp., Leishmania spp., Toxoplasma gondii, and Trypanosoma spp. are often associated with high-mortality, acute and chronic diseases of global health concern. For transmission and immune evasion, protozoans have evolved diverse strategies to interact with a range of host tissue environments. These interactions are linked to disease pathology, yet our understanding of the association between parasite colonization and host homeostatic disruption is limited. Recently developed techniques for cellular barcoding have the potential to uncover the biology regulating parasite transmission, dissemination, and the stability of infection. Understanding bottlenecks to infection and the in vivo tissue niches that facilitate chronic infection and spread has the potential to reveal new aspects of parasite biology.
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Affiliation(s)
- Dana A May
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Fatima Taha
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Matthew A Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Sarah E Ewald
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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8
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Hullahalli K, Dailey KG, Waldor MK. Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose. Proc Natl Acad Sci U S A 2023; 120:e2309151120. [PMID: 37669395 PMCID: PMC10500177 DOI: 10.1073/pnas.2309151120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
To cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These bottlenecks restrict the inoculum and largely determine whether pathogen exposure results in disease. Infection bottlenecks therefore quantify the effectiveness of immune barriers. Here, using a model of Escherichia coli systemic infection, we identify bottlenecks that tighten or widen with higher inoculum sizes, revealing that the efficacy of innate immune responses can increase or decrease with pathogen dose. We term this concept "dose scaling". During E. coli systemic infection, dose scaling is tissue specific, dependent on the lipopolysaccharide (LPS) receptor TLR4, and can be recapitulated by mimicking high doses with killed bacteria. Scaling therefore depends on sensing of pathogen molecules rather than interactions between the host and live bacteria. We propose that dose scaling quantitatively links innate immunity with infection bottlenecks and is a valuable framework for understanding how the inoculum size governs the outcome of pathogen exposure.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
| | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
- HHMI, Boston, MA02115
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9
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Ward RD, Tran JS, Banta AB, Bacon EE, Rose WE, Peters JM. Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551708. [PMID: 37577569 PMCID: PMC10418195 DOI: 10.1101/2023.08.02.551708] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing (Tn-seq), they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that underpin synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.
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Affiliation(s)
- Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Jennifer S Tran
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Emily E Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Warren E Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706
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10
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Quantitative dose-response analysis untangles host bottlenecks to enteric infection. Nat Commun 2023; 14:456. [PMID: 36709326 PMCID: PMC9884216 DOI: 10.1038/s41467-023-36162-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Host bottlenecks prevent many infections before the onset of disease by eliminating invading pathogens. By monitoring the diversity of a barcoded population of the diarrhea causing bacterium Citrobacter rodentium during colonization of its natural host, mice, we determine the number of cells that found the infection by establishing a replicative niche. In female mice the size of the pathogen's founding population scales with dose and is controlled by a severe yet slow-acting bottleneck. Reducing stomach acid or changing host genotype modestly relaxes the bottleneck without breaking the fractional relationship between dose and founders. In contrast, disrupting the microbiota causes the founding population to no longer scale with the size of the inoculum and allows the pathogen to infect at almost any dose, indicating that the microbiota creates the dominant bottleneck. Further, in the absence of competition with the microbiota, the diversity of the pathogen population slowly contracts as the population is overtaken by bacteria having lost the critical virulence island, the locus of enterocyte effacement (LEE). Collectively, our findings reveal that the mechanisms of protection by colonization bottlenecks are reflected in and can be generally defined by the impact of dose on the pathogen's founding population.
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11
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Aggarwal SD, Lees JA, Jacobs NT, Bee GCW, Abruzzo AR, Weiser JN. BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection. Cell Host Microbe 2023; 31:124-134.e5. [PMID: 36395758 PMCID: PMC9839470 DOI: 10.1016/j.chom.2022.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
Abstract
Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.
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Affiliation(s)
- Surya D Aggarwal
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - John A Lees
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA; European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W12 7TA, UK
| | - Nathan T Jacobs
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annie R Abruzzo
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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12
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Wincott CJ, Sritharan G, Benns HJ, May D, Gilabert-Carbajo C, Bunyan M, Fairweather AR, Alves E, Andrew I, Game L, Frickel EM, Tiengwe C, Ewald SE, Child MA. Cellular barcoding of protozoan pathogens reveals the within-host population dynamics of Toxoplasma gondii host colonization. CELL REPORTS METHODS 2022; 2:100274. [PMID: 36046624 PMCID: PMC9421581 DOI: 10.1016/j.crmeth.2022.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/20/2022] [Accepted: 07/22/2022] [Indexed: 02/09/2023]
Abstract
Cellular barcoding techniques are powerful tools to understand microbial pathogenesis. However, barcoding strategies have not been broadly applied to protozoan parasites, which have unique genomic structures and virulence strategies compared with viral and bacterial pathogens. Here, we present a CRISPR-based method to barcode protozoa, which we successfully apply to Toxoplasma gondii and Trypanosoma brucei. Using libraries of barcoded T. gondii, we evaluate shifts in the population structure from acute to chronic infection of mice. Contrary to expectation, most barcodes were present in the brain one month post-intraperitoneal infection in both inbred CBA/J and outbred Swiss mice. Although parasite cyst number and barcode diversity declined over time, barcodes representing a minor fraction of the inoculum could become a dominant population in the brain by three months post-infection. These data establish a cellular barcoding approach for protozoa and evidence that the blood-brain barrier is not a major bottleneck to colonization by T. gondii.
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Affiliation(s)
- Ceire J. Wincott
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Gayathri Sritharan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Biological Sciences, Birkbeck, University of London, Mallet Street, Bloomsbury, London WC1E 7HX, UK
| | - Henry J. Benns
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Chemistry, Imperial College London, White City Campus, London W12 0BZ, UK
| | - Dana May
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Carla Gilabert-Carbajo
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Monique Bunyan
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1BF, UK
| | - Aisling R. Fairweather
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ivan Andrew
- UKRI London Institute of Medical Sciences Genomics Laboratory, Shepherd’s Bush, London W12 0NN, UK
| | - Laurence Game
- UKRI London Institute of Medical Sciences Genomics Laboratory, Shepherd’s Bush, London W12 0NN, UK
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1BF, UK
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Calvin Tiengwe
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Sarah E. Ewald
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Matthew A. Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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13
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Fakoya B, Hullahalli K, Rubin DHF, Leitner DR, Chilengi R, Sack DA, Waldor MK. Nontoxigenic Vibrio cholerae Challenge Strains for Evaluating Vaccine Efficacy and Inferring Mechanisms of Protection. mBio 2022; 13:e0053922. [PMID: 35389261 PMCID: PMC9040834 DOI: 10.1128/mbio.00539-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 12/24/2022] Open
Abstract
Human challenge studies are instrumental for testing cholera vaccines, but these studies use outdated strains and require inpatient facilities. Here, we created next-generation isogenic Ogawa and Inaba O1 V. cholerae challenge strains (ZChol strains) derived from a contemporary Zambian clinical isolate representative of current dominant pandemic V. cholerae. Since the primary mechanism of immune protection against cholera is thought to be antibody responses that limit V. cholerae colonization and not the diarrheagenic actions of cholera toxin, these strains were rendered nontoxigenic. In infant mice, the ZChol strains did not cause diarrhea and proved to accurately gauge reduction in intestinal colonization mediated by effective vaccination. ZChol strains were also valuable as targets for measuring vibriocidal antibody responses. Using barcoded ZChol strains, we discovered that vaccination and passive immunity in the infant mouse model tightens the infection bottleneck without restricting pathogen expansion during intestinal infection. Collectively, our findings suggest that ZChol strains have the potential to enhance the safety, relevance, and scope of future cholera vaccine challenge studies and be valuable reagents for studies of immunity to cholera. IMPORTANCE Human challenge studies are a valuable method for testing the efficacy of cholera vaccines. However, challenge studies cannot be performed in countries of cholera endemicity due to safety concerns; also, contemporary pandemic Vibrio cholerae strains are not used in current challenge studies. To facilitate cholera research, we derived nontoxigenic challenge strains of both V. cholerae serotypes from a 2016 clinical isolate from Zambia and demonstrated how they can be used to gauge cholera immunity accurately and safely. These strains were also genetically barcoded, adding the potential for analyses of V. cholerae population dynamics to challenge studies. Preclinical analyses presented here suggest that these strains have the potential to enhance the safety, relevance, and scope of future cholera vaccine challenge studies and be valuable reagents for studies of immunity to cholera.
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Affiliation(s)
- Bolutife Fakoya
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
| | - Daniel H. F. Rubin
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
| | - Deborah R. Leitner
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
| | - Roma Chilengi
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - David A. Sack
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
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14
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Sit B, Fakoya B, Waldor MK. Animal models for dissecting Vibrio cholerae intestinal pathogenesis and immunity. Curr Opin Microbiol 2022; 65:1-7. [PMID: 34695646 PMCID: PMC8792189 DOI: 10.1016/j.mib.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023]
Abstract
The human diarrheal disease cholera is caused by the bacterium Vibrio cholerae. Efforts to develop animal models that closely mimic cholera to study the pathogenesis of this disease began >125 years ago. Here, we review currently used non-surgical, oral inoculation-based animal models for investigation of V. cholerae intestinal colonization and disease and highlight recent discoveries that have illuminated mechanisms of cholera pathogenesis and immunity, particularly in the area of how V. cholerae interacts with the gut microbiome to influence infection. The emergence of high-throughput tools for studies of pathogen-host interactions, along with continued advances in host genetic engineering and manipulation in animal models of V. cholerae will deepen understanding of cholera pathogenesis, uncovering knowledge important for control of this globally important bacterial pathogen.
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Affiliation(s)
- Brandon Sit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Bolutife Fakoya
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Massachusetts, USA,Howard Hughes Medical Institute, Bethesda, Maryland, USA,corresponding author: , Phone: 6175254646, Address: MCP-759, 181 Longwood Avenue, Boston, Massachusetts, USA 02115
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15
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Hullahalli K, Waldor MK. Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection. eLife 2021; 10:e70910. [PMID: 34636322 PMCID: PMC8545400 DOI: 10.7554/elife.70910] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underlie pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic Escherichia coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively, our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
| | - Matthew K Waldor
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
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