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Kalu M, Jorth P, Wong-Beringer A. Comparison of phenotypic and genetic traits of ESBL-producing UPEC strains causing recurrent or single episode UTI in postmenopausal women. Ann Clin Microbiol Antimicrob 2025; 24:11. [PMID: 39920666 PMCID: PMC11806750 DOI: 10.1186/s12941-025-00779-7] [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: 11/15/2024] [Accepted: 01/22/2025] [Indexed: 02/09/2025] Open
Abstract
BACKGROUND Recurrent urinary tract infections (rUTIs) occur in over 20% of patients, with postmenopausal women (over 50 years old) carrying the highest risk for recurrence compared to younger women. Virulence factors such as type 1 fimbriae adhesin FimH, the outer membrane protease OmpT, and the secreted pore-forming toxin α-hemolysin (HlyA) have been shown to support the formation of intracellular bacterial communities (IBCs) within bladder epithelial cells (BECs), facilitating persistence. This study aims to characterize the virulence expression and intracellular persistence of ESBL-producing uropathogenic E. coli (E-UPEC) strains isolated from postmenopausal women with recurrent or single episode infections. METHODS Study strains included 72 E-UPEC strains collected from patients (36 recurrent; 36 single episode) with a confirmed UTI diagnosis and control UPEC strains (CFT073 and UTI89). Patient demographics and clinical course were collected. Presence of hlyA, ompT, and fimH genes were confirmed by colony PCR, and qRT-PCR was performed using extracted RNA from a subset of 18 strains (12 recurrent; 6 single episode) grown in Luria-Bertani media and isolated from infected BECs to characterize gene expression. Bladder cell line 5637 was infected with study strains at MOI 15 for 2 h, treated with amikacin for 2 h to remove extracellular bacteria, then lysed to enumerate intracellular CFU counts. RESULTS No differences in clinical characteristics between patient groups were observed. Overall prevalence of fimH, ompT, and hlyA was 99% (71/72), 82% (59/72), and 26% (19/72) respectively; presence of all three genes did not differ between recurrent and single-episode strains. Notably, all recurrent strains had significantly more intracellular CFUs compared to single episode strains (median 16,248 CFU/mL vs. 4,118 CFU/mL, p = 0.018). Intracellular expression ompT was significantly increased (p = 0.0312) in the recurrent group compared to LB media, while fimH was significantly decreased (p = 0.0365) in the single episode group compared to expression in LB media. CONCLUSION Our findings indicate strain-specific ability to persist inside BECs with the recurrent strains exhibiting increased ompT expression inside BECs and higher intracellular bacterial burden compared to strains causing single episode UTI. These results emphasize the potential microbial contributions to recurrence in postmenopausal women and warrant future investigations on the impact of antibiotic therapy and host response on IBC-supportive UPEC virulence.
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Affiliation(s)
- Michelle Kalu
- Department of Clinical Pharmacy, University of Southern California Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
| | - Peter Jorth
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Annie Wong-Beringer
- Department of Clinical Pharmacy, University of Southern California Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA.
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2
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Li X, Pang Y, Jiang L, Liu L, Zhou J, Jin C, Wang Q, Sun H, Li Q, Chen Z, Qin J, Mu J, Liu B, Zhang Q, Liu Y, Feng L, Wang L. Two-component system GrpP/GrpQ promotes pathogenicity of uropathogenic Escherichia coli CFT073 by upregulating type 1 fimbria. Nat Commun 2025; 16:607. [PMID: 39799152 PMCID: PMC11724981 DOI: 10.1038/s41467-025-55982-z] [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: 03/25/2024] [Accepted: 01/07/2025] [Indexed: 01/15/2025] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infections (UTIs). Invasion into bladder epithelial cells (BECs) on the bladder luminal surface via type 1 fimbria is the first critical step in UPEC infection. Although type 1 fimbria expression increases during UPEC invasion of BECs, the underlying regulatory mechanisms remain poorly understood. This study reported a previously uncharacterized two-component system (TCS) GrpP/GrpQ that directly activates type 1 fimbria expression to promote UPEC invasion and therefore pathogenicity in response to D-serine present in the host urine. grpP/grpQ mutation severely impaired UPEC invasion of BECs and decreased the bacterial burden and formation of intracellular bacterial communities in mouse bladders during acute UTI. grpP/grpQ is widely present in UPEC genomes but rarely in other E. coli genomes, suggesting that this TCS specifically contributes to UPEC evolution. This study revealed a new pathway for virulence activation in response to host cues, providing further insight into UPEC pathogenesis and a promising target for UTI treatment.
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Affiliation(s)
- Xueping Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Yu Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Lingyan Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Le Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Jiarui Zhou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Chen Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Qian Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Hongmin Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Qing Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Zhen Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Jingliang Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Jianwei Mu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Bin Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Qiyue Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Yutao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China
| | - Lu Feng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.
- Nankai International Advanced Research Institute, Nankai University Shenzhen, Shenzhen, China.
| | - Lei Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China.
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, China.
- Southwest United Graduate School, Kunming, 650092, China.
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3
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Paudel S, Severin GB, Pirani A, Snitkin ES, Mobley HLT. Multiplexed PCR to measure in situ growth rates of uropathogenic E. coli during experimental urinary tract infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.21.624689. [PMID: 39605434 PMCID: PMC11601645 DOI: 10.1101/2024.11.21.624689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Measuring bacterial growth rates in vitro is routine, however, determining growth rates during infection in host has been more challenging. Peak-to-trough ratio (PTR) is a technique for studying microbial growth dynamics, calculated using the ratio of replication origin (ori) copies to that of the terminus (ter), as originally defined by whole genome sequencing (WGS). WGS presents significant challenges in terms of expense and data analysis complexity due to the presence of host DNA in the samples. Here, we used multiplexed PCR with fluorescent probes to estimate bacterial growth rates based on the abundance of ori- and ter-adjacent loci, without the need for WGS. We establish the utility of this approach by comparing growth rates of the uropathogenic Escherichia coli (UPEC) strain HM86 by WGS (PTR) and qPCR to measure the equivalent ori:ter (O:TPCR ). We found that PTR and O:TPCR were highly correlated and that O:TPCR reliably predicted growth rates calculated by conventional methods. O:TPCR was then used to calculate the in situ E. coli growth rates in urine, bladder, and kidneys collected over the course of a week from a murine model of urinary tract infection (UTI). These analyses revealed that growth rate of UPEC strains gradually increased during the early stages of infection (0-6h), followed by a slow decrease in growth rates during later time points (1-7 days). This rapid and convenient method provides valuable insights into bacterial growth dynamics during infection and can be applied to other bacterial species in both animal models and clinical infections.
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Affiliation(s)
- Santosh Paudel
- Department of Microbiology and Immunology, and University of Michigan Medical School, Ann Arbor, USA
| | - Geoffrey B Severin
- Department of Microbiology and Immunology, and University of Michigan Medical School, Ann Arbor, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, and University of Michigan Medical School, Ann Arbor, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, and University of Michigan Medical School, Ann Arbor, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, and University of Michigan Medical School, Ann Arbor, USA
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4
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. Nat Commun 2024; 15:9466. [PMID: 39487120 PMCID: PMC11530686 DOI: 10.1038/s41467-024-53829-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 10/21/2024] [Indexed: 11/04/2024] Open
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli's broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA.
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5
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Chorro L, Ciolino T, Torres CL, Illenberger A, Aglione J, Corts P, Lypowy J, Ponce C, La Porte A, Burt D, Volberg GL, Ramaiah L, McGovern K, Hu J, Anderson AS, Silmon de Monerri NC, Kanevsky I, Donald RGK. A cynomolgus monkey E. coli urinary tract infection model confirms efficacy of new FimH vaccine candidates. Infect Immun 2024; 92:e0016924. [PMID: 39297649 PMCID: PMC11475676 DOI: 10.1128/iai.00169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/13/2024] [Indexed: 10/16/2024] Open
Abstract
The increase in urinary tract infections (UTI) caused by antibiotic-resistant Escherichia coli requires the development of new therapeutic agents and prophylactic vaccines. To evaluate the efficacy of new lead candidates, we implemented a cynomolgus macaque UTI challenge model that mimics human uncomplicated cystitis in response to transurethral challenge with a multidrug-resistant (MDR) E. coli serotype O25b ST131 isolate. E. coli fimbrial adhesin FimH and O-antigens are separately under clinical evaluation by others as vaccine candidates to prevent UTI and invasive urosepsis disease, respectively. Accordingly, we assessed the protective efficacy of three 50-µg intramuscular doses of a novel recombinant FimH antigen adjuvanted with liposomal QS21/MPLA compared with saline placebo in groups of nine animals. A third group was vaccinated with this FimH formulation in combination with 1 µg each of a four-valent mixture of serotype O1a, O2, O6, and O25b O-antigen CRM197 lattice glycoconjugates. Both vaccines elicited high levels of serum FimH IgG and adhesin blocking antibodies at the time of bacterial challenge and, for the combination group, O-antigen-specific antibodies. Following bacterial challenge, both vaccinated groups showed >200- and >700-fold reduction in bacteriuria at day 2 and day 7 post-infection compared with placebo, respectively. In parallel, both vaccines significantly reduced levels of inflammatory biomarkers IL-8 and myeloperoxidase in the urine at day 2 post-infection relative to placebo. Results provide preclinical proof-of-concept for the prevention of an MDR UTI infection by these new vaccine formulations.
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Affiliation(s)
- Laurent Chorro
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
| | - Tara Ciolino
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
| | | | | | - JohnPaul Aglione
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
| | - Paula Corts
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
| | | | | | | | - Deborah Burt
- Pfizer Drug Safety Research and Development, Groton, Connecticut, USA
| | | | - Lila Ramaiah
- Pfizer Drug Safety Research and Development, Pearl River, New York, USA
| | - Kathryn McGovern
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
| | - Jianfang Hu
- Pfizer Research Biostatistics, Collegeville, Pennsylvania, USA
| | | | | | - Isis Kanevsky
- Pfizer Vaccine Research and Development, Pearl River, New York, USA
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6
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Mobley HLT, Anderson MT, Moricz BS, Severin GB, Holmes CL, Ottosen EN, Eichler T, Gupta S, Paudel S, Sinha R, Mason S, Himpsl SD, Brown AN, Gaca M, Kiser CM, Clarke TH, Fouts DE, DiRita VJ, Bachman MA. Fitness factor genes conserved within the multi-species core genome of Gram-negative Enterobacterales species contribute to bacteremia pathogenesis. PLoS Pathog 2024; 20:e1012495. [PMID: 39178317 PMCID: PMC11376589 DOI: 10.1371/journal.ppat.1012495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 09/05/2024] [Accepted: 08/09/2024] [Indexed: 08/25/2024] Open
Abstract
There is a critical gap in knowledge about how Gram-negative bacterial pathogens, using survival strategies developed for other niches, cause lethal bacteremia. Facultative anaerobic species of the Enterobacterales order are the most common cause of Gram-negative bacteremia, including Escherichia coli, Klebsiella pneumoniae, Serratia marcescens, Citrobacter freundii, and Enterobacter hormaechei. Bacteremia often leads to sepsis, a life-threatening organ dysfunction resulting from unregulated immune responses to infection. Despite a lack of specialization for this host environment, Gram-negative pathogens cause nearly half of bacteremia cases annually. Based on our existing Tn-Seq fitness factor data from a murine model of bacteremia combined with comparative genomics of the five Enterobacterales species above, we prioritized 18 conserved fitness genes or operons for further characterization. Mutants were constructed for all genes in all five species. Each mutant was used to cochallenge C57BL/6 mice via tail vein injection along with each respective wild-type strain to determine competitive indices for each fitness gene. Five fitness factor genes, when mutated, attenuated mutants in four or five species in the spleen and liver (tatC, ruvA, gmhB, wzxE, arcA). Five additional fitness factor genes or operons were validated as outcompeted by wild-type in three, four, or five bacterial species in the spleen (xerC, prc, apaGH, atpG, aroC). Overall, 17 of 18 fitness factor mutants were attenuated in at least one species in the spleen or liver. Together, these findings allow for the development of a model of bacteremia pathogenesis that may include future targets of therapy against bloodstream infections.
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Affiliation(s)
- Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mark T Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Bridget S Moricz
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Geoffrey B Severin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Caitlyn L Holmes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Elizabeth N Ottosen
- Department of Microbiology and Molecular Genetics, Michigan State University College of Natural Sciences, East Lansing, Michigan, United States of America
| | - Tad Eichler
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Surbhi Gupta
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Santosh Paudel
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ritam Sinha
- Department of Microbiology and Molecular Genetics, Michigan State University College of Natural Sciences, East Lansing, Michigan, United States of America
| | - Sophia Mason
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Stephanie D Himpsl
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Aric N Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Margaret Gaca
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christina M Kiser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Thomas H Clarke
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Derrick E Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Victor J DiRita
- Department of Microbiology and Molecular Genetics, Michigan State University College of Natural Sciences, East Lansing, Michigan, United States of America
| | - Michael A Bachman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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7
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Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, Sacchettini J, Cai JJ, Subashchandrabose S. Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli. J Bacteriol 2024; 206:e0011224. [PMID: 38856220 PMCID: PMC11270900 DOI: 10.1128/jb.00112-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Urinary tract infections (UTIs) are a major global health problem and are caused predominantly by uropathogenic Escherichia coli (UPEC). UTIs are a leading cause of prescription antimicrobial use. Incessant increase in antimicrobial resistance in UPEC and other uropathogens poses a serious threat to the current treatment practices. Copper is an effector of nutritional immunity that impedes the growth of pathogens during infection. We hypothesized that copper would augment the toxicity of select small molecules against bacterial pathogens. We conducted a small molecule screening campaign with a library of 51,098 molecules to detect hits that inhibit a UPEC ΔtolC mutant in a copper-dependent manner. A molecule, denoted as E. coli inhibitor or ECIN, was identified as a copper-responsive inhibitor of wild-type UPEC strains. Our gene expression and metal content analysis results demonstrate that ECIN works in concert with copper to exacerbate Cu toxicity in UPEC. ECIN has a broad spectrum of activity against pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus. Subinhibitory levels of ECIN eliminate UPEC biofilm formation. Transcriptome analysis of UPEC treated with ECIN reveals induction of multiple stress response systems. Furthermore, we demonstrate that L-cysteine rescues the growth of UPEC exposed to ECIN. In summary, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC.IMPORTANCEUrinary tract infection (UTI) is a ubiquitous infectious condition affecting millions of people annually. Uropathogenic Escherichia coli (UPEC) is the predominant etiological agent of UTI. However, UTIs are becoming increasingly difficult to resolve with antimicrobials due to increased antimicrobial resistance in UPEC and other uropathogens. Here, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC. In addition to E. coli, this small molecule also inhibits pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- Braden S Hanson
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Amanuel Hailemariam
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - Yongjian Yang
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Faras Mohamed
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Dwight Baker
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James Sacchettini
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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Aitken KJ, Schröder A, Haddad A, Sidler M, Penna F, Fernandez N, Ahmed T, Marino V, Bechbache M, Jiang JX, Tolg C, Bägli DJ. Epigenetic insights to pediatric uropathology: Celebrating the fundamental biology vision of Tony Khoury. J Pediatr Urol 2024; 20 Suppl 1:S43-S57. [PMID: 38944627 DOI: 10.1016/j.jpurol.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Many pediatric urology conditions affect putatively normal tissues or appear too commonly to be based solely on specific DNA mutations. Understanding epigenetic mechanisms in pediatric urology, therefore, has many implications that can impact cell and tissue responses to settings, such as environmental and hormonal influences on urethral development, uropathogenic infections, obstructive stimuli, all of which originate externally or extracellularly. Indeed, the cell's response to external stimuli is often mediated epigenetically. In this commentary, we highlight work on the critical role that epigenetic machinery, such as DNA methyltransferases (DNMTs), Enhancer of Zeste Polycomb Repressive Complex 2 Subunit (EZH2), and others play in regulating gene expression and cellular functions in three urological contexts. DESIGN Animal and cellular constructs were used to model clinical pediatric uropathology. The hypertrophy, trabeculation, and fibrosis of the chronically obstructed bladder was explored using smooth muscle cell models employing disorganised vs. normal extracellular matrix (ECM), as well as a new animal model of chronic obstructive bladder disease (COBD) which retains its pathologic features even after bladder de-obstruction. Cell models from human and murine hypospadias or genital tubercles (GT) were used to illustrate developmental responses and epigenetic dependency of key developmental genes. Finally, using bladder urothelial and organoid culture systems, we examined activity of epigenetic machinery in response to non uropathogenic vs. uropathogenic E.coli (UPEC). DNMT and EZH2 expression and function were interrogated in these model systems. RESULTS Disordered ECM exerted a principal mitogenic and epigenetic role for on bladder smooth muscle both in vitro and in CODB in vivo. Key genes, e.g., BDNF and KCNB2 were under epigenetic regulation in actively evolving obstruction and COBD, though each condition showed distinct epigenetic responses. In models of hypospadias, estrogen strongly dysregulated WNT and Hox expression, which was normalized by epigenetic inhibition. Finally, DNA methylation machinery in the urothelium showed specific activation when challenged by uropathogenic E.coli. Similarly, UPEC induces hypermethylation and downregulation of the growth suppressor p16INK4A. Moreover, host cells exposed to UPEC produced secreted factors inducing epigenetic responses transmissible from one affected cell to another without ongoing bacterial presence. DISCUSSION Microenvironmental influences altered epigenetic activity in the three described urologic contexts. Considering that many obstructed bladders continue to display abnormal architecture and dysfunction despite relief of obstruction similar to after resection of posterior valves or BPH, the epigenetic mechanisms described highlight novel approaches for understanding the underlying smooth muscle myopathy of this crucial clinical problem. Similarly, there is evidence for an epigenetic basis of xenoestrogen on development of hypospadias, and UTI-induced pan-urothelial alteration of epigenetic marks and propensity for subsequent (recurrent) UTI. The impact of mechanical, hormonal, infectious triggers on genitourinary epigenetic machinery activity invite novel avenues for targeting epigenetic modifications associated with these non-cancer diseases in urology. This includes the use of deactivated CRISPR-based technologies for precise epigenome targeting and editing. Overall, we underscore the importance of understanding epigenetic regulation in pediatric urology for the development of innovative therapeutic and management strategies.
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Affiliation(s)
- K J Aitken
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; DIYbio Toronto, 1677 St. Clair West, Toronto, Ontario, Canada.
| | - Annette Schröder
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Urology and Pediatric Urology of the University Medical Center Mainz, Mainz, Rheinland-Pfalz, Germany
| | - Ahmed Haddad
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martin Sidler
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Frank Penna
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicolas Fernandez
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tabina Ahmed
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Human Biology Programme, University of Toronto, Toronto, Ontario, Canada
| | - Vincent Marino
- DIYbio Toronto, 1677 St. Clair West, Toronto, Ontario, Canada
| | - Matthew Bechbache
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada
| | - Jia-Xin Jiang
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Human Biology Programme, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Cornelia Tolg
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada
| | - Darius J Bägli
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Physiology, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582780. [PMID: 38463963 PMCID: PMC10925322 DOI: 10.1101/2024.02.29.582780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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10
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Kion-Crosby W, Barquist L. Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders. BIOINFORMATICS ADVANCES 2024; 4:vbae066. [PMID: 39027639 PMCID: PMC11256956 DOI: 10.1093/bioadv/vbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 05/02/2024] [Indexed: 07/20/2024]
Abstract
Summary The increasing number of publicly available bacterial gene expression data sets provides an unprecedented resource for the study of gene regulation in diverse conditions, but emphasizes the need for self-supervised methods for the automated generation of new hypotheses. One approach for inferring coordinated regulation from bacterial expression data is through neural networks known as denoising autoencoders (DAEs) which encode large datasets in a reduced bottleneck layer. We have generalized this application of DAEs to include deep networks and explore the effects of network architecture on gene set inference using deep learning. We developed a DAE-based pipeline to extract gene sets from transcriptomic data in Escherichia coli, validate our method by comparing inferred gene sets with known pathways, and have used this pipeline to explore how the choice of network architecture impacts gene set recovery. We find that increasing network depth leads the DAEs to explain gene expression in terms of fewer, more concisely defined gene sets, and that adjusting the width results in a tradeoff between generalizability and biological inference. Finally, leveraging our understanding of the impact of DAE architecture, we apply our pipeline to an independent uropathogenic E.coli dataset to identify genes uniquely induced during human colonization. Availability and implementation https://github.com/BarquistLab/DAE_architecture_exploration.
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Affiliation(s)
- Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
- Department of Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
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11
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Saenkham-Huntsinger P, Ritter M, Donati GL, Mitchell AM, Subashchandrabose S. The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli. mBio 2024; 15:e0352223. [PMID: 38470052 PMCID: PMC11005409 DOI: 10.1128/mbio.03522-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC. A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.
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Affiliation(s)
- Panatda Saenkham-Huntsinger
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Matthew Ritter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L. Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Angela M. Mitchell
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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12
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Phan MD, Schirra HJ, Nhu NTK, Peters KM, Sarkar S, Allsopp LP, Achard MES, Kappler U, Schembri MA. Combined functional genomic and metabolomic approaches identify new genes required for growth in human urine by multidrug-resistant Escherichia coli ST131. mBio 2024; 15:e0338823. [PMID: 38353545 PMCID: PMC10936160 DOI: 10.1128/mbio.03388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 03/14/2024] Open
Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, with ~400 million cases across the globe each year. Uropathogenic Escherichia coli (UPEC) is the major cause of UTI and increasingly associated with antibiotic resistance. This scenario has been worsened by the emergence and spread of pandemic UPEC sequence type 131 (ST131), a multidrug-resistant clone associated with extraordinarily high rates of infection. Here, we employed transposon-directed insertion site sequencing in combination with metabolomic profiling to identify genes and biochemical pathways required for growth and survival of the UPEC ST131 reference strain EC958 in human urine (HU). We identified 24 genes required for growth in HU, which mapped to diverse pathways involving small peptide, amino acid and nucleotide metabolism, the stringent response pathway, and lipopolysaccharide biosynthesis. We also discovered a role for UPEC resistance to fluoride during growth in HU, most likely associated with fluoridation of drinking water. Complementary nuclear magnetic resonance (NMR)-based metabolomics identified changes in a range of HU metabolites following UPEC growth, the most pronounced being L-lactate, which was utilized as a carbon source via the L-lactate dehydrogenase LldD. Using a mouse UTI model with mixed competitive infection experiments, we demonstrated a role for nucleotide metabolism and the stringent response in UPEC colonization of the mouse bladder. Together, our application of two omics technologies combined with different infection-relevant settings has uncovered new factors required for UPEC growth in HU, thus enhancing our understanding of this pivotal step in the UPEC infection pathway. IMPORTANCE Uropathogenic Escherichia coli (UPEC) cause ~80% of all urinary tract infections (UTIs), with increasing rates of antibiotic resistance presenting an urgent threat to effective treatment. To cause infection, UPEC must grow efficiently in human urine (HU), necessitating a need to understand mechanisms that promote its adaptation and survival in this nutrient-limited environment. Here, we used a combination of functional genomic and metabolomic techniques and identified roles for the metabolism of small peptides, amino acids, nucleotides, and L-lactate, as well as the stringent response pathway, lipopolysaccharide biosynthesis, and fluoride resistance, for UPEC growth in HU. We further demonstrated that pathways involving nucleotide metabolism and the stringent response are required for UPEC colonization of the mouse bladder. The UPEC genes and metabolic pathways identified in this study represent targets for the development of innovative therapeutics to prevent UPEC growth during human UTI, an urgent need given the rapidly rising rates of global antibiotic resistance.
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Affiliation(s)
- Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Horst Joachim Schirra
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M. Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Sohinee Sarkar
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Luke P. Allsopp
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maud E. S. Achard
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A. Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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13
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Méndez AAE, Argüello JM, Soncini FC, Checa SK. Scs system links copper and redox homeostasis in bacterial pathogens. J Biol Chem 2024; 300:105710. [PMID: 38309504 PMCID: PMC10907172 DOI: 10.1016/j.jbc.2024.105710] [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: 08/11/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
The bacterial envelope is an essential compartment involved in metabolism and metabolites transport, virulence, and stress defense. Its roles become more evident when homeostasis is challenged during host-pathogen interactions. In particular, the presence of free radical groups and excess copper in the periplasm causes noxious reactions, such as sulfhydryl group oxidation leading to enzymatic inactivation and protein denaturation. In response to this, canonical and accessory oxidoreductase systems are induced, performing quality control of thiol groups, and therefore contributing to restoring homeostasis and preserving survival under these conditions. Here, we examine recent advances in the characterization of the Dsb-like, Salmonella-specific Scs system. This system includes the ScsC/ScsB pair of Cu+-binding proteins with thiol-oxidoreductase activity, an alternative ScsB-partner, the membrane-linked ScsD, and a likely associated protein, ScsA, with a role in peroxide resistance. We discuss the acquisition of the scsABCD locus and its integration into a global regulatory pathway directing envelope response to Cu stress during the evolution of pathogens that also harbor the canonical Dsb systems. The evidence suggests that the canonical Dsb systems cannot satisfy the extra demands that the host-pathogen interface imposes to preserve functional thiol groups. This resulted in the acquisition of the Scs system by Salmonella. We propose that the ScsABCD complex evolved to connect Cu and redox stress responses in this pathogen as well as in other bacterial pathogens.
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Affiliation(s)
- Andrea A E Méndez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina.
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14
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Huang WS, Lee YJ, Wang L, Chen HH, Chao YJ, Cheng V, Liaw SJ. Copper affects virulence and diverse phenotypes of uropathogenic Proteus mirabilis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00044-6. [PMID: 38453541 DOI: 10.1016/j.jmii.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/18/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Copper plays a role in urinary tract infection (UTI) and urinary copper content is increased during Proteus mirabilis UTI. We therefore investigated the effect of copper on uropathogenic P. mirabilis and the underlying mechanisms, focusing on the virulence associated aspects. METHODS Mouse colonization, swarming/swimming assays, measurement of cell length, flagellin level and urease activity, adhesion/invasion assay, biofilm formation, killing by macrophages, oxidative stress susceptibility, OMPs analysis, determination of MICs and persister cell formation, RT-PCR and transcriptional reporter assay were performed. RESULTS We found that copper-supplemented mice were more resistant to be colonized in the urinary tract, together with decreased swarming/swimming, ureases activity, expression of type VI secretion system and adhesion/invasion to urothelial cells and increased killing by macrophages of P. mirabilis at a sublethal copper level. However, bacterial biofilm formation and resistance to oxidative stress were enhanced under the same copper level. Of note, the presence of copper led to increased ciprofloxacin MIC and more persister cell formation against ampicillin. In addition, the presence of copper altered the outer membrane protein profile and triggered expression of RcsB response regulator. For the first time, we unveiled the pleiotropic effects of copper on uropathogenic P. mirabilis, especially for induction of bacterial two-component signaling system regulating fitness and virulence. CONCLUSION The finding of copper-mediated virulence and fitness reinforced the importance of copper for prevention and therapeutic interventions against P. mirabilis infections. As such, this study could facilitate the copper-based strategies against UTI by P. mirabilis.
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Affiliation(s)
- Wei-Syuan Huang
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Yuan-Ju Lee
- Department of Urology, National Taiwan University Hospital, and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Lu Wang
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Hsuan-Hsuan Chen
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Yueh-Jung Chao
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Vivien Cheng
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Shwu-Jen Liaw
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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15
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Amin A, Noureen R, Iftikhar A, Hussain A, Alonazi WB, Raza HMZ, Ferheen I, Ibrahim M. Uropathogenic bacteria and deductive genomics towards antimicrobial resistance, virulence, and potential drug targets. Int Microbiol 2024; 27:325-335. [PMID: 37553507 DOI: 10.1007/s10123-023-00416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/15/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Urinary tract infections (UTIs) are among the most prevalent bacterial infections affecting people in inpatient and outpatient settings. The current study aimed to sequence the genome of uropathogenic Escherichia coli strain CUI-B1 resourced from a woman having uncomplicated cystitis and pyelonephritis. Followed by deductive genomics towards potential drug targets using E. coli strain CUI-B1, strain O25b: H4-ST131, Proteus mirabilis strain HI4320, Klebsiella pneumoniae strain 1721, and Staphylococcus saprophyticus strain ATCC 15305 uropathogenic strains. Comparative genome analysis revealed that genes related to the survival of E. coli, P. mirabilis, K. pneumoniae, and S. saprophyticus, such as genes of metal-requiring proteins, defense-associated genes, and genes associated with general physiology, were found to be highly conserved in the genomes including strain CUI-B1. However, the genes responsible for virulence and drug resistance, mainly those that are involved in bacterial secretion, fimbriae, adherence, and colonization, were found in various genomic regions and varied from one species to another or within the same species. Based on the genome sequence, virulence, and antimicrobial-resistant gene dataset, the subtractive proteomics approach revealed 22 proteins mapped to the pathogen's unique pathways and among them, entB, clbH, chuV, and ybtS were supposed to be potential drug targets and the single drug could be utilized for all above-mentioned strains. These results may provide the foundation for the optimal target for future discovery of drugs for E. coli-, P. mirabilis-, K. pneumoniae-, and S. saprophyticus-based infections and could be investigated further to employ in personalized drug development.
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Affiliation(s)
- Aaima Amin
- Medical Department, Quaid e Azam Medical College, Bahawalpur, Pakistan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Ramisha Noureen
- Medical Department, Fatima Jinnah Medical University, Lahore, Pakistan
| | - Ayesha Iftikhar
- Medical Department, Govt Khawaja Muhammad Safdar Medical Collage, Sialkot, Pakistan
| | - Annam Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, 11587, Saudi Arabia
| | | | - Ifra Ferheen
- Laboratory of Genetics of Microorganisms, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
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16
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Lu J, Liu X, Li X, Li H, Shi L, Xia X, He BL, Meyer TF, Li X, Sun H, Yang X. Copper regulates the host innate immune response against bacterial infection via activation of ALPK1 kinase. Proc Natl Acad Sci U S A 2024; 121:e2311630121. [PMID: 38232278 PMCID: PMC10823219 DOI: 10.1073/pnas.2311630121] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024] Open
Abstract
Copper is an essential trace element for the human body, and its requirement for optimistic immune functions has been recognized for decades. How copper is involved in the innate immune pathway, however, remains to be clarified. Here, we report that copper serves as a signal molecule to regulate the kinase activity of alpha-kinase 1 (ALPK1), a cytosolic pattern-recognition receptor (PRR), and therefore promotes host cell defense against bacterial infection. We show that in response to infection, host cells actively accumulate copper in the cytosol, and the accumulated cytosolic copper enhances host cell defense against evading pathogens, including intracellular and, unexpectedly, extracellular bacteria. Subsequently, we demonstrate that copper activates the innate immune pathway of host cells in an ALPK1-dependent manner. Further mechanistic studies reveal that copper binds to ALPK1 directly and is essential for the kinase activity of this cytosolic PRR. Moreover, the binding of copper to ALPK1 enhances the sensitivity of ALPK1 to the bacterial metabolite ADP-heptose and eventually prompts host cells to elicit an enhanced immune response during bacterial infection. Finally, using a zebrafish in vivo model, we show that a copper-treated host shows an increased production of proinflammatory cytokines, enhanced recruitment of phagosome cells, and promoted bacterial clearance. Our findings uncover a previously unrecognized role of copper in the modulation of host innate immune response against bacterial pathogens and advance our knowledge on the cross talk between cytosolic copper homeostasis and immune system.
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Affiliation(s)
- Jing Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Xue Liu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Department of Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Xinghua Li
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Chinese Academy of Sciences-The University of Hong Kong Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Liwa Shi
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Xin Xia
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Bai-liang He
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Thomas F. Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin10117, Germany
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht’s University of Kiel, University Hospital Schleswig Holstein, Kiel24105, Germany
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Chinese Academy of Sciences-The University of Hong Kong Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xinming Yang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai519000, China
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17
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Hossain S, Morey JR, Neville SL, Ganio K, Radin JN, Norambuena J, Boyd JM, McDevitt CA, Kehl-Fie TE. Host subversion of bacterial metallophore usage drives copper intoxication. mBio 2023; 14:e0135023. [PMID: 37737591 PMCID: PMC10653882 DOI: 10.1128/mbio.01350-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE During infection, bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes S. aureus to copper intoxication. In response to zinc starvation, S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.
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Affiliation(s)
- Saika Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jacqueline R. Morey
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jana N. Radin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Jeff M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas E. Kehl-Fie
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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18
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Kunkle DE, Skaar EP. Moving metals: How microbes deliver metal cofactors to metalloproteins. Mol Microbiol 2023; 120:547-554. [PMID: 37408317 PMCID: PMC10592388 DOI: 10.1111/mmi.15117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
First row d-block metal ions serve as vital cofactors for numerous essential enzymes and are therefore required nutrients for all forms of life. Despite this requirement, excess free transition metals are toxic. Free metal ions participate in the production of noxious reactive oxygen species and mis-metalate metalloproteins, rendering enzymes catalytically inactive. Thus, bacteria require systems to ensure metalloproteins are properly loaded with cognate metal ions to maintain protein function, while avoiding metal-mediated cellular toxicity. In this perspective we summarize the current mechanistic understanding of bacterial metallocenter maturation with specific emphasis on metallochaperones; a group of specialized proteins that both shield metal ions from inadvertent reactions and distribute them to cognate target metalloproteins. We highlight several recent advances in the field that have implicated new classes of proteins in the distribution of metal ions within bacterial proteins, while speculating on the future of the field of bacterial metallobiology.
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Affiliation(s)
- Dillon E. Kunkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Frick-Cheng AE, Shea AE, Roberts JR, Smith SN, Ohi MD, Mobley HLT. Altered motility in response to iron-limitation is regulated by lpdA in uropathogenic E. coli CFT073. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559868. [PMID: 37808639 PMCID: PMC10557643 DOI: 10.1101/2023.09.27.559868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
More than half of all women will experience a urinary tract infection (UTI) in their lifetime with most cases caused by uropathogenic Escherichia coli (UPEC). Bacterial motility enhances UPEC pathogenicity, resulting in more severe disease outcomes including kidney infection. Surprisingly, the connection between motility and iron limitation is mostly unexplored, despite the lack of free iron available in the host. Therefore, we sought to explore the potential connection between iron restriction and regulation of motility in UPEC. We cultured E. coli CFT073, a prototypical UPEC strain, in media containing an iron chelator. Under iron limitation, CFT073 had elevated fliC (flagella) promoter activity, driving motility on the leading edge of the colony. Furthermore, this iron-specific response was repressed by the addition of exogenous iron. We confirmed increased flagella expression in CFT073 by measuring fliC transcript, FliC protein, and surface-expressed flagella under iron-limited conditions. To define the regulatory mechanism, we constructed single knockouts of eight master regulators. The iron-regulated response was lost in crp, arcA, and fis mutants. Thus, we focused on the five genes regulated by all three transcription factors. Of the five genes knocked out, the iron-regulated motility response was most strongly dysregulated in an lpdA mutant, which also resulted in significantly lowered fitness in the murine model of ascending UTI. Collectively, we demonstrated that iron-mediated motility in CFT073 is regulated by lpdA , which contributes to the understanding of how uropathogens differentially regulate motility mechanisms in the iron-restricted host. Importance Urinary tract infections (UTIs) are ubiquitous and responsible for over five billion dollars in associated health care costs annually. Both iron acquisition and motility are highly studied virulence factors associated with uropathogenic E. coli (UPEC), the main causative agent of uncomplicated UTI. This work is innovative by providing mechanistic insight into the synergistic relationship between these two critical virulence properties. Here, we demonstrate that iron limitation has pleiotropic effects with consequences that extend beyond metabolism, and impact other virulence mechanisms. Indeed, targeting iron acquisition as a therapy may lead to an undesirable enhancement of UPEC pathogenesis through increased motility. It is vital to understand the full breadth of UPEC pathogenesis to adequately respond to this common infection, especially with the increase of antibiotic resistant pathogens.
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20
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Ren H, Zhong Z, Zhou S, Wei Y, Liang Y, He H, Zheng Z, Li M, He Q, Long T, Lian X, Liao X, Liu Y, Sun J. CpxA/R-Controlled Nitroreductase Expression as Target for Combinatorial Therapy against Uropathogens by Promoting Reactive Oxygen Species Generation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300938. [PMID: 37407509 PMCID: PMC10477892 DOI: 10.1002/advs.202300938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/07/2023] [Indexed: 07/07/2023]
Abstract
The antibiotic resistances emerged in uropathogens lead to accumulative treatment failure and recurrent episodes of urinary tract infection (UTI), necessitating more innovative therapeutics to curb UTI before systematic infection. In the current study, the combination of amikacin and nitrofurantoin is found to synergistically eradicate Gram-negative uropathogens in vitro and in vivo. The mechanistic analysis demonstrates that the amikacin, as an aminoglycoside, induced bacterial envelope stress by introducing mistranslated proteins, thereby constitutively activating the cpxA/R two-component system (Cpx signaling). The activation of Cpx signaling stimulates the expression of bacterial major nitroreductases (nfsA/nfsB) through soxS/marA regulons. As a result, the CpxA/R-dependent nitroreductases overexpression generates considerable quantity of lethal reactive intermediates via nitroreduction and promotes the prodrug activation of nitrofurantoin. As such, these actions together disrupt the bacterial cellular redox balance with excessively-produced reactive oxygen species (ROS) as "Domino effect", accelerating the clearance of uropathogens. Although aminoglycosides are used as proof-of-principle to elucidate the mechanism, the synergy between nitrofurantoin is generally applicable to other Cpx stimuli. To summarize, this study highlights the potential of aminoglycoside-nitrofurantoin combination to replenish the arsenal against recurrent Gram-negative uropathogens and shed light on the Cpx signaling-controlled nitroreductase as a potential target to manipulate the antibiotic susceptibility.
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Affiliation(s)
- Hao Ren
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Zixing Zhong
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Shuang Zhou
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Yiyang Wei
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Yujiao Liang
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Huiling He
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Zijian Zheng
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Mengyuan Li
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Qian He
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Tengfei Long
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Xinlei Lian
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
| | - Xiaoping Liao
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhou225009China
| | - Yahong Liu
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhou225009China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern AgricultureNational Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original BacteriaCollege of Veterinary MedicineSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Veterinary PharmaceuticsDevelopment and Safety EvaluationSouth China Agricultural UniversityGuangzhou510642China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhou225009China
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21
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Ballash GA, Diaz-Campos D, van Balen JC, Mollenkopf DF, Wittum TE. Previous Antibiotic Exposure Reshapes the Population Structure of Infecting Uropathogenic Escherichia coli Strains by Selecting for Antibiotic Resistance over Urovirulence. Microbiol Spectr 2023; 11:e0524222. [PMID: 37338386 PMCID: PMC10433818 DOI: 10.1128/spectrum.05242-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
Antibiotic therapy is the standard of care for urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC). However, previous antibiotic therapy may impart a selective pressure that influences the population structure and pathogenic potential of infecting UPEC strains. Here, we conducted a 3-year study using whole-genome-sequencing analysis and retrospective medical record review to characterize how antibiotic exposure influenced the phenotypic antibiotic resistance, acquired resistome, virulome, and population structure of 88 UTI-causing E. coli strains from dogs. A majority of UTI-associated E. coli strains were from phylogroup B2 and clustered within sequence type 372. Previous antibiotic exposure was associated with a population shift toward UPEC from phylogroups other than the typical urovirulent phylogroup B2. The specific virulence profiles within the accessory virulome that were associated with antibiotic use were elicited by the effect of antibiotics on UPEC phylogenetic structure. Among phylogroup B2, antibiotic exposure increased the quantity of genes within the resistome and the odds of developing reduced susceptibility to at least one antibiotic. Non-B2 UPEC strains harbored a more diverse and greater resistome that conferred reduced susceptibility to multiple antibiotic classes following antibiotic exposure. Collectively, these data suggest that previous antibiotic exposure establishes an environment that provides a selective edge to non-B2 UPEC strains through their diverse and abundant antibiotic resistance genes, despite their lack of urovirulence genes. Our findings highlight the necessity for judicious use of antibiotics as we uncover another mechanism by which antibiotic exposure and resistance can influence the dynamics of bacterial infectious disease. IMPORTANCE Urinary tract infections (UTIs) are one of the most common infections of dogs and humans. While antibiotic therapy is the standard of care for UTIs and other infections, antibiotic exposure may influence the pathogenic profile of subsequent infections. We used whole-genome sequencing and retrospective medical record review to characterize the effect of systemic antibiotic therapy on the resistance, virulence, and population structure of 88 UTI-causing UPEC strains isolated from dogs. Our results indicate that antibiotic exposure alters the population structure of infecting UPEC strains, providing a selective edge for non-B2 phylogroups that harbor diverse and abundant resistance gene catalogues but fewer urovirulence genes. These findings highlight how antibiotic resistance can influence pathogen infection dynamics and have clinical implications for the judicious use of antibiotics for bacterial infections.
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Affiliation(s)
- Gregory A. Ballash
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Dubraska Diaz-Campos
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Joany C. van Balen
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Dixie F. Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Thomas E. Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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22
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Hirakawa H, Takita A, Sato Y, Hiramoto S, Hashimoto Y, Ohshima N, Minamishima YA, Murakami M, Tomita H. Inactivation of ackA and pta Genes Reduces GlpT Expression and Susceptibility to Fosfomycin in Escherichia coli. Microbiol Spectr 2023; 11:e0506922. [PMID: 37199605 PMCID: PMC10269713 DOI: 10.1128/spectrum.05069-22] [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: 12/09/2022] [Accepted: 04/29/2023] [Indexed: 05/19/2023] Open
Abstract
Fosfomycin is used to treat a variety of bacterial infections, including urinary tract infections caused by Escherichia coli. In recent years, quinolone-resistant and extended-spectrum β-lactamase (ESBL)-producing bacteria have been increasing. Because fosfomycin is effective against many of these drug-resistant bacteria, the clinical importance of fosfomycin is increasing. Against this background, information on the mechanisms of resistance and the antimicrobial activity of this drug is desired to enhance the usefulness of fosfomycin therapy. In this study, we aimed to explore novel factors affecting the antimicrobial activity of fosfomycin. Here, we found that ackA and pta contribute to fosfomycin activity against E. coli. ackA and pta mutant E. coli had reduced fosfomycin uptake capacity and became less sensitive to this drug. In addition, ackA and pta mutants had decreased expression of glpT that encodes one of the fosfomycin transporters. Expression of glpT is enhanced by a nucleoid-associated protein, Fis. We found that mutations in ackA and pta also caused a decrease in fis expression. Thus, we interpret the decrease in glpT expression in ackA and pta defective strains to be due to a decrease in Fis levels in these mutants. Furthermore, ackA and pta are conserved in multidrug-resistant E. coli isolated from patients with pyelonephritis and enterohemorrhagic E. coli, and deletion of ackA and pta from these strains resulted in decreased susceptibility to fosfomycin. These results suggest that ackA and pta in E. coli contribute to fosfomycin activity and that mutation of these genes may pose a risk of reducing the effect of fosfomycin. IMPORTANCE The spread of drug-resistant bacteria is a major threat in the field of medicine. Although fosfomycin is an old type of antimicrobial agent, it has recently come back into the limelight because of its effectiveness against many drug-resistant bacteria, including quinolone-resistant and ESBL-producing bacteria. Since fosfomycin is taken up into the bacteria by GlpT and UhpT transporters, its antimicrobial activity fluctuates with changes in GlpT and UhpT function and expression. In this study, we found that inactivation of the ackA and pta genes responsible for the acetic acid metabolism system reduced GlpT expression and fosfomycin activity. In other words, this study shows a new genetic mutation that leads to fosfomycin resistance in bacteria. The results of this study will lead to further understanding of the mechanism of fosfomycin resistance and the creation of new ideas to enhance fosfomycin therapy.
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Affiliation(s)
- Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Ayako Takita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yumika Sato
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Suguru Hiramoto
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Noriyasu Ohshima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yoji A. Minamishima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masami Murakami
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
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23
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Hossain S, Morey JR, Neville SL, Ganio K, Radin JN, Norambuena J, Boyd JM, McDevitt CA, Kehl-Fie TE. Host subversion of bacterial metallophore usage drives copper intoxication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542972. [PMID: 37398167 PMCID: PMC10312489 DOI: 10.1101/2023.05.30.542972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microorganisms can acquire metal ions in metal-limited environments using small molecules called metallophores. While metals and their importers are essential, metals can also be toxic, and metallophores have limited ability to discriminate metals. The impact of the metallophore-mediated non-cognate metal uptake on bacterial metal homeostasis and pathogenesis remains to be defined. The globally significant pathogen Staphylococcus aureus uses the Cnt system to secrete the metallophore staphylopine in zinc-limited host niches. Here, we show that staphylopine and the Cnt system facilitate bacterial copper uptake, potentiating the need for copper detoxification. During in vivo infection, staphylopine usage increased S. aureus susceptibility to host-mediated copper stress, indicating that the innate immune response can harness the antimicrobial potential of altered elemental abundances in host niches. Collectively, these observations show that while the broad-spectrum metal-chelating properties of metallophores can be advantageous, the host can exploit these properties to drive metal intoxication and mediate antibacterial control. IMPORTANCE During infection bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes Staphylococcus aureus to copper intoxication. In response to zinc starvation S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.
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Affiliation(s)
- Saika Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jacqueline R Morey
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Jana N Radin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Lv Z, Xu M, Liu Y, Rønn R, Rensing C, Liu S, Gao S, Liao H, Liu YR, Chen W, Zhu YG, Huang Q, Hao X. Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3590-3601. [PMID: 36811608 DOI: 10.1021/acs.est.2c07136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (CuR) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the CuR bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.
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Affiliation(s)
- Zhenguang Lv
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Regin Rønn
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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25
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Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa. mBio 2023; 14:e0306722. [PMID: 36475772 PMCID: PMC9973009 DOI: 10.1128/mbio.03067-22] [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] [Indexed: 12/13/2022] Open
Abstract
Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias toward in vitro, fast-growing bacteria. Recent research has begun to address these gaps in knowledge by directly quantifying bacterial mRNA levels during human infection, with the goal of assessing microbial community function at the infection site. However, mRNA levels are not always predictive of protein levels, which are the primary functional units of a cell. Here, we used carefully controlled chemostat experiments to examine the relationship between mRNA and protein levels across four growth rates in the bacterial pathogen Pseudomonas aeruginosa. We found a genome-wide positive correlation between mRNA and protein abundances across all growth rates, with genes required for P. aeruginosa viability having stronger correlations than nonessential genes. We developed a statistical method to identify genes whose mRNA abundances poorly predict protein abundances and calculated an RNA-to-protein (RTP) conversion factor to improve mRNA predictions of protein levels. The application of the RTP conversion factor to publicly available transcriptome data sets was highly robust, enabling the more accurate prediction of P. aeruginosa protein levels across strains and growth conditions. Finally, the RTP conversion factor was applied to P. aeruginosa human cystic fibrosis (CF) infection transcriptomes to provide greater insights into the functionality of this bacterium in the CF lung. This study addresses a critical problem in infection microbiology by providing a framework for enhancing the functional interpretation of bacterial human infection transcriptome data. IMPORTANCE Our understanding of bacterial physiology during human infection is limited by the difficulty in assessing bacterial function at the infection site. Recent studies have begun to address this question by quantifying bacterial mRNA levels in human-derived samples using transcriptomics. One challenge for these studies is the poor predictivity of mRNA for protein levels for some genes. Here, we addressed this challenge by measuring the transcriptomes and proteomes of P. aeruginosa grown at four growth rates. Our results revealed that the growth rate does not impact the genome-wide correlation of mRNA and protein levels. We used statistical methods to identify the genes for which mRNA and protein were poorly correlated and developed an RNA-to-protein (RTP) conversion factor that improved the predictivity of protein levels across strains and growth conditions. Our results provide new insights into mRNA-protein correlations and tools to enhance our understanding of bacterial physiology from transcriptome data.
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26
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Mason S, Vornhagen J, Smith SN, Mike LA, Mobley HLT, Bachman MA. The Klebsiella pneumoniae ter Operon Enhances Stress Tolerance. Infect Immun 2023; 91:e0055922. [PMID: 36651775 PMCID: PMC9933665 DOI: 10.1128/iai.00559-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Healthcare-acquired infections are a leading cause of disease in patients that are hospitalized or in long-term-care facilities. Klebsiella pneumoniae (Kp) is a leading cause of bacteremia, pneumonia, and urinary tract infections in these settings. Previous studies have established that the ter operon, a genetic locus that confers tellurite oxide (K2TeO3) resistance, is associated with infection in colonized patients. Rather than enhancing fitness during infection, the ter operon increases Kp fitness during gut colonization; however, the biologically relevant function of this operon is unknown. First, using a murine model of urinary tract infection, we demonstrate a novel role for the ter operon protein TerC as a bladder fitness factor. To further characterize TerC, we explored a variety of functions, including resistance to metal-induced stress, resistance to radical oxygen species-induced stress, and growth on specific sugars, all of which were independent of TerC. Then, using well-defined experimental guidelines, we determined that TerC is necessary for tolerance to ofloxacin, polymyxin B, and cetylpyridinium chloride. We used an ordered transposon library constructed in a Kp strain lacking the ter operon to identify the genes that are required to resist K2TeO3-induced and polymyxin B-induced stress, which suggested that K2TeO3-induced stress is experienced at the bacterial cell envelope. Finally, we confirmed that K2TeO3 disrupts the Kp cell envelope, though these effects are independent of ter. Collectively, the results from these studies indicate a novel role for the ter operon as a stress tolerance factor, thereby explaining its role in enhancing fitness in the gut and bladder.
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Affiliation(s)
- Sophia Mason
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jay Vornhagen
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sara N. Smith
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A. Mike
- Department of Medical Microbiology & Immunology, University of Toledo, Toledo, Ohio, USA
| | - Harry L. T. Mobley
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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27
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Cho THS, Pick K, Raivio TL. Bacterial envelope stress responses: Essential adaptors and attractive targets. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119387. [PMID: 36336206 DOI: 10.1016/j.bbamcr.2022.119387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.
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Affiliation(s)
- Timothy H S Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kat Pick
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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28
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O’Boyle N, Douce GR, Farrell G, Rattray NJW, Schembri MA, Roe AJ, Connolly JPR. Distinct ecological fitness factors coordinated by a conserved Escherichia coli regulator during systemic bloodstream infection. Proc Natl Acad Sci U S A 2023; 120:e2212175120. [PMID: 36574699 PMCID: PMC9910484 DOI: 10.1073/pnas.2212175120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
The ability of bacterial pathogens to adapt to host niches is driven by the carriage and regulation of genes that benefit pathogenic lifestyles. Genes that encode virulence or fitness-enhancing factors must be regulated in response to changing host environments to allow rapid response to challenges presented by the host. Furthermore, this process can be controlled by preexisting transcription factors (TFs) that acquire new roles in tailoring regulatory networks, specifically in pathogens. However, the mechanisms underlying this process are poorly understood. The highly conserved Escherichia coli TF YhaJ exhibits distinct genome-binding dynamics and transcriptome control in pathotypes that occupy different host niches, such as uropathogenic E. coli (UPEC). Here, we report that this important regulator is required for UPEC systemic survival during murine bloodstream infection (BSI). This advantage is gained through the coordinated regulation of a small regulon comprised of both virulence and metabolic genes. YhaJ coordinates activation of both Type 1 and F1C fimbriae, as well as biosynthesis of the amino acid tryptophan, by both direct and indirect mechanisms. Deletion of yhaJ or the individual genes under its control leads to attenuated survival during BSI. Furthermore, all three systems are up-regulated in response to signals derived from serum or systemic host tissue, but not urine, suggesting a niche-specific regulatory trigger that enhances UPEC fitness via pleiotropic mechanisms. Collectively, our results identify YhaJ as a pathotype-specific regulatory aide, enhancing the expression of key genes that are collectively required for UPEC bloodstream pathogenesis.
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Affiliation(s)
- Nicky O’Boyle
- School of Microbiology, University College Cork, National University of Ireland, CorkT12 K8AF, Ireland
| | - Gillian R. Douce
- Institute of Infection, Immunity and Inflammation, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Gillian Farrell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, United Kingdom
| | - Nicholas J. W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, United Kingdom
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J. Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - James P. R. Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-TyneNE2 4HH, United Kingdom
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29
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Phenotypic Assessment of Clinical Escherichia coli Isolates as an Indicator for Uropathogenic Potential. mSystems 2022; 7:e0082722. [PMID: 36445110 PMCID: PMC9765037 DOI: 10.1128/msystems.00827-22] [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] [Indexed: 12/03/2022] Open
Abstract
For women in the United States, urinary tract infections (UTIs) are the most frequent diagnosis in emergency departments, comprising 21.3% of total visits. Uropathogenic Escherichia coli (UPEC) causes ~80% of uncomplicated UTIs. To combat this public health issue, it is vital to characterize UPEC strains as well as to differentiate them from commensal strains to reduce the overuse of antibiotics. It has been challenging to determine a consistent genetic signature that clearly distinguishes UPEC from other E. coli strains. Therefore, we examined whether phenotypic data could be predictive of uropathogenic potential. We screened 13 clinical strains of UPEC, isolated from cases of uncomplicated UTI in young otherwise healthy women, in a series of microbiological phenotypic assays using UPEC prototype strain CFT073 and nonpathogenic E. coli strain MG1655 K-12 as controls. Phenotypes included adherence, iron acquisition, biofilm formation, human serum resistance, motility, and stress resistance. By use of a well-established experimental mouse model of UTI, these data were able to predict the severity of the bacterial burden in both the urine and bladders. Multiple linear regression using three different phenotypic assays, i.e., growth in minimal medium, siderophore production, and type 1 fimbrial expression, was predictive of bladder colonization (adjusted R2 = 0.6411). Growth in ex vivo human urine, hemagglutination of red blood cells, and motility modeled urine colonization (adjusted R2 = 0.4821). These results showcase the utility of phenotypic characterization to predict the severity of infection that these strains may cause. We predict that these methods will also be applicable to other complex, genetically redundant, pathogens. IMPORTANCE Urinary tract infections are the second leading infectious disease worldwide, occurring in over half of the female population during their lifetime. Most infections are caused by uropathogenic Escherichia coli (UPEC) strains. These strains can establish a reservoir in the gut, in which they do not cause disease but, upon introduction to the urinary tract, can infect the host and elicit pathogenesis. Clinically, it would be beneficial to screen patient E. coli strains to understand their pathogenic potential, which may lead to the administration of prophylactic antibiotic treatment for those with increased risk. Others have proposed the use of PCR-based genetic screening methods to detect UPEC strains and differentiate them from other E. coli pathotypes; however, this method has not yielded a consistent uropathogenic genetic signature. Here, we used phenotypic characteristics such as growth rate, siderophore production, and expression of fimbriae to better predict uropathogenic potential.
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30
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Chan CCY, Lewis IA. Role of metabolism in uropathogenic Escherichia coli. Trends Microbiol 2022; 30:1174-1204. [PMID: 35941063 DOI: 10.1016/j.tim.2022.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is responsible for more than 75% of urinary tract infections (UTIs) and has been studied extensively to better understand the molecular underpinnings of infection and pathogenesis. Although the macromolecular adaptations UPEC employs - including the expression of virulence factors, adhesion molecules, and iron-acquisition systems - are well described, the role that metabolism plays in enabling infection is still unclear. However, a growing body of literature shows that metabolic function can have a profound impact on which strains can colonize the urinary tract. The goal of this review is to critically appraise this emerging body of literature to better understand the role that nutritional selection plays in enabling urinary tract colonization and the progression of UTIs.
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Affiliation(s)
- Carly C Y Chan
- Department of Biological Science, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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31
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Gerner RR, Hossain S, Sargun A, Siada K, Norton GJ, Zheng T, Neumann W, Nuccio SP, Nolan EM, Raffatellu M. Siderophore Immunization Restricted Colonization of Adherent-Invasive Escherichia coli and Ameliorated Experimental Colitis. mBio 2022; 13:e0218422. [PMID: 36094114 PMCID: PMC9600343 DOI: 10.1128/mbio.02184-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract and profound alterations to the gut microbiome. Adherent-invasive Escherichia coli (AIEC) is a mucosa-associated pathobiont that colonizes the gut of patients with Crohn's disease, a form of IBD. Because AIEC exacerbates gut inflammation, strategies to reduce the AIEC bloom during colitis are highly desirable. To thrive in the inflamed gut, Enterobacteriaceae acquire the essential metal nutrient iron by producing and releasing siderophores. Here, we implemented an immunization-based strategy to target the siderophores enterobactin and its glucosylated derivative salmochelin to reduce the AIEC bloom in the inflamed gut. Using chemical (dextran sulfate sodium) and genetic (Il10-/- mice) IBD mouse models, we showed that immunization with enterobactin conjugated to the mucosal adjuvant cholera toxin subunit B potently elicited mucosal and serum antibodies against these siderophores. Siderophore-immunized mice exhibited lower AIEC gut colonization, diminished AIEC association with the gut mucosa, and reduced colitis severity. Moreover, Peyer's patches and the colonic lamina propria harbored enterobactin-specific B cells that could be identified by flow cytometry. The beneficial effect of siderophore immunization was primarily B cell-dependent because immunized muMT-/- mice, which lack mature B lymphocytes, were not protected during AIEC infection. Collectively, our study identified siderophores as a potential therapeutic target to reduce AIEC colonization and its association with the gut mucosa, which ultimately may reduce colitis exacerbation. Moreover, this work provides the foundation for developing monoclonal antibodies against siderophores, which could provide a narrow-spectrum strategy to target the AIEC bloom in Crohn's disease patients. IMPORTANCE Adherent-invasive Escherichia coli (AIEC) is abnormally prevalent in patients with ileal Crohn's disease and exacerbates intestinal inflammation, but treatment strategies that selectively target AIEC are unavailable. Iron is an essential micronutrient for most living organisms, and bacterial pathogens have evolved sophisticated strategies to capture iron from the host environment. AIEC produces siderophores, small, secreted molecules with a high affinity for iron. Here, we showed that immunization to elicit antibodies against siderophores promoted a reduction of the AIEC bloom, interfered with AIEC association with the mucosa, and mitigated colitis in experimental mouse models. We also established a flow cytometry-based approach to visualize and isolate siderophore-specific B cells, a prerequisite for engineering monoclonal antibodies against these molecules. Together, this work could lead to a more selective and antibiotic-sparing strategy to target AIEC in Crohn's disease patients.
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Affiliation(s)
- Romana R. Gerner
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Suzana Hossain
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kareem Siada
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Grant J. Norton
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Tengfei Zheng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wilma Neumann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sean-Paul Nuccio
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Manuela Raffatellu
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Chiba University-University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California, USA
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32
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Sebastiampillai S, Lacasse MJ, McCusker S, Campbell T, Nitz M, Zamble DB. Using a high-throughput, whole-cell hydrogenase assay to identify potential small molecule inhibitors of [NiFe]-hydrogenase. Metallomics 2022; 14:6747159. [DOI: 10.1093/mtomcs/mfac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
Abstract
Abstract
[NiFe]-hydrogenases are used by several human pathogens to catalyze the reversible conversion between molecular hydrogen and protons and electrons. Hydrogenases provide an increased metabolic flexibility for pathogens, such as Escherichia coli and Helicobacter pylori, by allowing the use of molecular hydrogen as an energy source to promote survival in anaerobic environments. With the rise of antimicrobial resistance and the desire for novel therapeutics, the [NiFe]-hydrogenases are alluring targets. Inhibiting the nickel insertion pathway of [NiFe]-hydrogenases is attractive as this pathway is required for the generation of functional enzymes and is orthogonal to human biochemistry. In this work, nickel availability for the production and function of E. coli [NiFe]-hydrogenase was explored through immunoblot and activity assays. Whole-cell hydrogenase activities were assayed in high throughput against a small molecule library of known bioactives. Iodoquinol was identified as a potential inhibitor of the nickel biosynthetic pathway of [NiFe]-hydrogenase through a two-step screening process, but further studies with immunoblot assays showed confounding effects dependent on the cell growth phase. This study highlights the significance of considering the growth phenotype for whole-cell based assays overall and its effects on various cellular processes influenced by metal trafficking and homeostasis.
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Affiliation(s)
| | - Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
| | - Susan McCusker
- Centre for Microbial Chemical Biology , MDCL-2330, Hamilton, Ontario L8S 4K1 , Canada
| | - Tracey Campbell
- Centre for Microbial Chemical Biology , MDCL-2330, Hamilton, Ontario L8S 4K1 , Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8 , Canada
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33
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Genome-wide analysis of fitness factors in uropathogenic Escherichia coli in a pig urinary tract infection model. Microbiol Res 2022; 265:127202. [PMID: 36167007 DOI: 10.1016/j.micres.2022.127202] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/24/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is the primary cause of urinary tract infections (UTIs) in animals and humans. We applied Transposon-Directed Insertion Site sequencing (TraDIS) to determine the fitness genes in two well-characterized UPEC strains, UTI89 and CFT073, in order to identify fitness factors during UTI in a pig model. This novel animal model better reflects the course of UTI in humans than the commonly used mouse model, and facilitates the differentiation between sessile and planktonic UPEC populations. A total of 854 and 483 genes in UTI89 and CFT073, respectively, were predicted to contribute to growth in pig urine, and 1257 and 764, were scored as required for colonization of the bladder. The combined list of fitness genes for growth in urine and cystitis contained 741 (UTI89) and 439 (CFT073) genes. The essential genes for growth on LB agar media supplemented with kanamycin and the fitness factors during growth in human urine were also analyzed in CFT073. A total of 457 essential genes were identified and the pool of fitness genes for growth in human urine included 215 genes. The gene rfaG, which is involved in lipopolysaccharide biosynthesis, was included in all the fitness-gene-lists and was further confirmed to be relevant for all the conditions tested regardless of the host and the strain. Thus, this gene may represent a promising target for the development of new therapeutic strategies against UTI UPEC-associated. Besides this important observation, the study revealed strain-specific differences in gene-essentiality as well as in the fitness-gene-repertoire for growth in human urine and UTI of the pig model, and it identified novel factors required for UPEC-induced UTIs.
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Abstract
More than half of women will experience a urinary tract infection (UTI), with uropathogenic Escherichia coli (UPEC) causing ~80% of uncomplicated cases. Iron acquisition systems are essential for uropathogenesis, and UPEC strains encode highly diverse iron acquisition systems, underlining their importance. However, a recent UPEC clinical isolate, HM7, lacks this diversity and instead encodes the synthesis pathway for a sole siderophore, enterobactin. To determine if HM7 possesses unidentified iron acquisition systems, we performed RNA sequencing under iron-limiting conditions and demonstrated that the ferric citrate uptake system (fecABCDE and fecIR) was highly upregulated. Importantly, there are high levels of citrate within urine, some of which is bound to iron, and the fec system is enriched in UPEC isolates compared to fecal strains. Therefore, we hypothesized that HM7 and other similar strains use the fec system to acquire iron in the host. Deletion of both enterobactin biosynthesis and ferric citrate uptake (ΔfecA/ΔentB) abrogates use of ferric citrate as an iron source, and fecA provides an advantage in human urine in the absence of enterobactin. However, in a UTI mouse model, fecA is a fitness factor independent of enterobactin production, likely due to the action of host lipocalin-2 chelating ferrienterobactin. These findings indicate that ferric citrate uptake is used as an iron source when siderophore efficacy is limited, such as in the host during UTI. Defining these novel compensatory mechanisms and understanding the nutritional hierarchy of preferred iron sources within the urinary tract are important in the search for new approaches to combat UTI.
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35
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Fortney KR, Smith SN, van Rensburg JJ, Brothwell JA, Gardner JJ, Katz BP, Ahsan N, Duerfeldt AS, Mobley HLT, Spinola SM. CpxA Phosphatase Inhibitor Activates CpxRA and Is a Potential Treatment for Uropathogenic Escherichia coli in a Murine Model of Infection. Microbiol Spectr 2022; 10:e0243021. [PMID: 35297652 PMCID: PMC9045377 DOI: 10.1128/spectrum.02430-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
CpxRA is an envelope stress response system that is highly conserved in the Enterobacteriaceae. CpxA has kinase activity for CpxR and phosphatase activity for phospho-CpxR (CpxR-P), a transcription factor. In response to membrane stress, CpxR-P is produced and upregulates genes involved in membrane repair and downregulates genes that encode virulence factors that are trafficked across the cell membrane. Mutants that constitutively activate CpxRA in Salmonella enterica serovar Typhimurium and in uropathogenic Escherichia coli (UPEC) are attenuated in murine models. We hypothesized that pharmacologic activation of CpxR could serve as an antimicrobial/antivirulence strategy and recently showed that 2,3,4,9-tetrahydro-1H-carbazol-1-amines activate the CpxRA system by inhibiting CpxA phosphatase activity. Here, we tested the ability of a series of three CpxRA-activating compounds with increasing potency to clear UPEC stain CFT073 in a murine urinary tract infection model. We show that these compounds are well tolerated and achieve sufficient levels to activate CpxR in the kidneys, bladder, and urine. Although the first two compounds were ineffective in promoting clearance of CFT073 in the murine model, the most potent derivative, compound 26, significantly reduced bacterial recovery in the urine and trended toward reducing bacterial recovery in the bladder and kidneys, with efficacy similar to ciprofloxacin. Treatment of CFT073 cultured in human urine with compound 26 fostered accumulation of CpxR-P and decreased the expression of proteins involved in siderophore biosynthesis and binding, heme degradation, and flagellar movement. These studies suggest that chemical activation of CpxRA may present a viable strategy for treating infections due to UPEC. IMPORTANCE The increasing prevalence of urinary tract infections (UTIs) due to antibiotic-resistant uropathogenic Escherichia coli (UPEC) is a major public health concern. Bacteria contain proteins that sense their environment and have no human homologs and, thus, are attractive drug targets. CpxRA is a conserved sensing system whose function is to reduce stress in the bacterial cell membrane; activation of CpxRA reduces the expression of virulence determinants, which must cross the cell membrane to reach the bacterial surface. We previously identified a class of compounds that activate CpxRA. We show in a mouse UTI model that our most potent compound significantly reduced recovery of UPEC in the urine, trended toward reducing bacterial recovery in the bladder and kidneys, did not kill UPEC, and downregulated multiple proteins involved in UPEC virulence. Since these compounds do not act by a killing mechanism, they have potential to treat UTIs caused by antibiotic-resistant bacteria.
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Affiliation(s)
- Kate R. Fortney
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Julia J. van Rensburg
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Julie A. Brothwell
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jessi J. Gardner
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Barry P. Katz
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Biostatistics, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana, USA
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Adam S. Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Stanley M. Spinola
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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36
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Elucidation of a complete mechanical signaling and virulence activation pathway in enterohemorrhagic Escherichia coli. Cell Rep 2022; 39:110614. [PMID: 35385749 DOI: 10.1016/j.celrep.2022.110614] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 12/09/2021] [Accepted: 03/13/2022] [Indexed: 12/23/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important extracellular human pathogen. The initial adherence of EHEC to host cells is a major cue for transcriptional induction of the locus of enterocyte effacement (LEE) genes to promote colonization and pathogenesis, but the mechanism through which this adherence is sensed and the LEE is induced remains largely elusive. Here, we report a complete signal transduction pathway for this virulence activation process. In this pathway, the outer-membrane lipoprotein NlpE senses a mechanical cue generated from initial host adherence and activates the BaeSR two-component regulatory system; the response regulator BaeR then directly activates the expression of airA located on O-island-134 and encoding a LEE transcriptional activator. Disruption of this pathway severely attenuates EHEC O157:H7 virulence both in vitro and in vivo. This study provides further insights into the evolution of EHEC pathogenesis and the host-pathogen interaction.
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37
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Torres-Puig S, García V, Stærk K, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-Fresno A. “Omics” Technologies - What Have They Told Us About Uropathogenic Escherichia coli Fitness and Virulence During Urinary Tract Infection? Front Cell Infect Microbiol 2022; 12:824039. [PMID: 35237532 PMCID: PMC8882828 DOI: 10.3389/fcimb.2022.824039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infection (UTI), a widespread infectious disease of great impact on human health. This is further emphasized by the rapidly increase in antimicrobial resistance in UPEC, which compromises UTI treatment. UPEC biology is highly complex since uropathogens must adopt extracellular and intracellular lifestyles and adapt to different niches in the host. In this context, the implementation of forefront ‘omics’ technologies has provided substantial insight into the understanding of UPEC pathogenesis, which has opened the doors for new therapeutics and prophylactics discovery programs. Thus, ‘omics’ technologies applied to studies of UPEC during UTI, or in models of UTI, have revealed extensive lists of factors that are important for the ability of UPEC to cause disease. The multitude of large ‘omics’ datasets that have been generated calls for scrutinized analysis of specific factors that may be of interest for further development of novel treatment strategies. In this review, we describe main UPEC determinants involved in UTI as estimated by ‘omics’ studies, and we compare prediction of factors across the different ‘omics’ technologies, with a focus on those that have been confirmed to be relevant under UTI-related conditions. We also discuss current challenges and future perspectives regarding analysis of data to provide an overview and better understanding of UPEC mechanisms involved in pathogenesis which should assist in the selection of target sites for future prophylaxis and treatment.
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Affiliation(s)
- Sergi Torres-Puig
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Kristian Stærk
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Thomas E. Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Ana Herrero-Fresno,
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38
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Virieux-Petit M, Hammer-Dedet F, Aujoulat F, Jumas-Bilak E, Romano-Bertrand S. From Copper Tolerance to Resistance in Pseudomonas aeruginosa towards Patho-Adaptation and Hospital Success. Genes (Basel) 2022; 13:genes13020301. [PMID: 35205346 PMCID: PMC8872213 DOI: 10.3390/genes13020301] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
The hospital environment constitutes a reservoir of opportunistic pathogens responsible for healthcare-associated infections (HCAI) such as Pseudomonas aeruginosa (Pa). Pa persistence within technological niches, the increasing emergence of epidemic high-risk clones in HCAI, the epidemiological link between plumbing strains and clinical strains, make it a major nosocomial pathogen. Therefore, understanding the mechanisms of Pa adaptation to hospital water systems would be useful in preventing HCAI. This review deciphers how copper resistance contributes to Pa adaptation and persistence in a hospital environment, especially within copper water systems, and ultimately to its success as a causative agent of HCAI. Numerous factors are involved in copper homeostasis in Pa, among which active efflux conferring copper tolerance, and copper-binding proteins regulating the copper compartmentalization between periplasm and cytoplasm. The functional harmony of copper homeostasis is regulated by several transcriptional regulators. The genomic island GI-7 appeared as especially responsible for the copper resistance in Pa. Mechanisms of copper and antibiotic cross-resistance and co-resistance are also identified, with potential co-regulation processes between them. Finally, copper resistance of Pa confers selective advantages in colonizing and persisting in hospital environments but also appears as an asset at the host/pathogen interface that helps in HCAI occurrence.
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Affiliation(s)
- Maxine Virieux-Petit
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Florence Hammer-Dedet
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Fabien Aujoulat
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
| | - Sara Romano-Bertrand
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
- UMR 5151 HSM, Equipe Pathogènes Hydriques Santé et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence: ; Tel.: +33-4-11-75-94-30
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Sarshar M, Scribano D, Limongi D, Zagaglia C, Palamara AT, Ambrosi C. Adaptive strategies of uropathogenic Escherichia coli CFT073: from growth in lab media to virulence during host cell adhesion. Int Microbiol 2022; 25:481-494. [PMID: 35106679 DOI: 10.1007/s10123-022-00235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/23/2021] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
Abstract
Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic bacterium in healthcare settings is Escherichia coli. The increasing rate of antibiotic-resistant strains demands studies to understand E. coli pathogenesis to drive the development of new therapeutic approaches. This study compared the gene expression profile of selected target genes in the prototype uropathogenic E. coli (UPEC) strain CFT073 grown in Luria Bertani (LB), artificial urine (AU), and during adhesion to host bladder cells by semi-quantitative real-time PCR (RT-PCR) assays. AU effectively supported the growth of strain CFT073 as well as other E. coli strains with different lifestyles, thereby confirming the appropriateness of this medium for in vitro models. Unexpectedly, gene expression of strain CFT073 in LB and AU was quite similar; conversely, during the adhesion assay, adhesins and porins were upregulated, while key global regulators were downregulated with respect to lab media. Interestingly, fimH and papGII genes were significantly expressed in all tested conditions. Taken together, these results provide for the first time insights of the metabolic and pathogenic profile of strain CFT073 during the essential phase of host cell adhesion.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy.,Dani Di Giò Foundation-Onlus, 00193, Rome, Italy
| | - Dolores Limongi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS San Raffaele Rome, 00166, Rome, Italy
| | - Carlo Zagaglia
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore Di Sanità, 00161, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory affiliated to Institute Pasteur Italia- Cenci Bolognetti Foundation, 00185, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS San Raffaele Rome, 00166, Rome, Italy.
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40
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Yang D, Jiang F, Huang X, Li G, Cai W. Transcriptomic and Metabolomic Profiling Reveals That KguR Broadly Impacts the Physiology of Uropathogenic Escherichia coli Under in vivo Relevant Conditions. Front Microbiol 2022; 12:793391. [PMID: 34975816 PMCID: PMC8716947 DOI: 10.3389/fmicb.2021.793391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Urinary tract infections are primarily caused by uropathogenic Escherichia coli (UPEC). In contrast to the intestinal E. coli strains that reside in nutrient-rich gut environment, UPEC encounter distinct niches, for instance human urine, which is an oxygen- and nutrient-limited environment. Alpha-ketoglutarate (KG) is an abundant metabolite in renal proximal tubule cells; and previously we showed that two-component signaling system (TCS) KguS/KguR contributes to UPEC colonization of murine urinary tract by promoting the utilization of KG as a carbon source under anaerobic conditions. However, knowledge about the KguR regulon and its impact on UPEC fitness is lacking. In this work, we analyzed transcriptomic and metabolomic changes caused by kguR deletion under anaerobiosis when KG is present. Our results indicated that 620 genes were differentially expressed in the ΔkguR mutant, as compared to the wild type; of these genes, 513 genes were downregulated and 107 genes were upregulated. Genes with substantial changes in expression involve KG utilization, acid resistance, iron uptake, amino acid metabolism, capsule biosynthesis, sulfur metabolism, among others. In line with the transcriptomics data, several amino acids (glutamate, lysine, etc.) and uridine 5′-diphosphogalactose (involved in capsule biosynthesis) were significantly less abundant in the ΔkguR mutant. We then confirmed that the ΔkguR mutant, indeed, was more sensitive to acid stress than the wild type, presumably due to downregulation of genes belonging to the glutamate-dependent acid resistance system. Furthermore, using gene expression and electrophoretic mobility shift assays (EMSAs), we demonstrate that KguR autoregulates its own expression by binding to the kguSR promoter region. Lastly, we performed a genome-wide search of KguR binding sites, and this search yielded an output of at least 22 potential binding sites. Taken together, our data establish that in the presence of KG, KguR broadly impacts the physiology of UPEC under anaerobiosis. These findings greatly further our understanding of KguS/KguR system as well as UPEC pathobiology.
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Affiliation(s)
- Dawei Yang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fengwei Jiang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinxin Huang
- Technical Centre for Animal, Plant, and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Ganwu Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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41
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García V, Grønnemose RB, Torres-Puig S, Kudirkiene E, Piantelli M, Ahmed S, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-Fresno A. Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections. Microb Genom 2021; 7. [PMID: 34928200 PMCID: PMC8767336 DOI: 10.1099/mgen.0.000719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) UTI89 is a well-characterized strain, which has mainly been used to study UPEC virulence during urinary tract infection (UTI). However, little is known on UTI89 key fitness-factors during growth in lab media and during UTI. Here, we used a transposon-insertion-sequencing approach (TraDIS) to reveal the UTI89 essential-genes for in vitro growth and fitness-gene-sets for growth in Luria broth (LB) and EZ-MOPS medium without glucose, as well as for human bacteriuria and mouse cystitis. A total of 293 essential genes for growth were identified and the set of fitness-genes was shown to differ depending on the growth media. A modified, previously validated UTI murine model, with administration of glucose prior to infection was applied. Selected fitness-genes for growth in urine and mouse-bladder colonization were validated using deletion-mutants. Novel fitness-genes, such as tusA, corA and rfaG; involved in sulphur-acquisition, magnesium-uptake, and LPS-biosynthesis, were proved to be important during UTI. Moreover, rfaG was confirmed as relevant in both niches, and therefore it may represent a target for novel UTI-treatment/prevention strategies.
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Affiliation(s)
- Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Rasmus B Grønnemose
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Sergi Torres-Puig
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mateo Piantelli
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Shahana Ahmed
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Thomas E Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Jakob Møller-Jensen
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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42
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Hyre A, Casanova-Hampton K, Subashchandrabose S. Copper Homeostatic Mechanisms and Their Role in the Virulence of Escherichia coli and Salmonella enterica. EcoSal Plus 2021; 9:eESP00142020. [PMID: 34125582 PMCID: PMC8669021 DOI: 10.1128/ecosalplus.esp-0014-2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Copper is an essential micronutrient that also exerts toxic effects at high concentrations. This review summarizes the current state of knowledge on copper handling and homeostasis systems in Escherichia coli and Salmonella enterica. We describe the mechanisms by which transcriptional regulators, efflux pumps, detoxification enzymes, metallochaperones, and ancillary copper response systems orchestrate cellular response to copper stress. E. coli and S. enterica are important pathogens of humans and animals. We discuss the critical role of copper during killing of these pathogens by macrophages and in nutritional immunity at the bacterial-pathogen-host interface. In closing, we identify opportunities to advance our understanding of the biological roles of copper in these model enteric bacterial pathogens.
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Affiliation(s)
- Amanda Hyre
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Kaitlin Casanova-Hampton
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
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43
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Copper Resistance Promotes Fitness of Methicillin-Resistant Staphylococcus aureus during Urinary Tract Infection. mBio 2021; 12:e0203821. [PMID: 34488457 PMCID: PMC8546587 DOI: 10.1128/mbio.02038-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Urinary tract infection (UTI) is one of the most common infectious conditions affecting people in the United States and around the world. Our knowledge of the host-pathogen interaction during UTI caused by Gram-positive bacterial uropathogens is limited compared to that for Gram-negative pathogens. Here, we investigated whether copper and the primary copper-containing protein, ceruloplasmin, are mobilized to urine during naturally occurring UTI caused by Gram-positive uropathogens in patients. Next, we probed the role of copper resistance in the fitness of methicillin-resistant Staphylococcus aureus (MRSA) during experimental UTI in a murine model. Our findings demonstrate that urinary copper and ceruloplasmin content are elevated during UTI caused by Enterococcus faecalis, S. aureus, S. epidermidis, and S. saprophyticus. MRSA strains successfully colonize the urinary tract of female CBA mice with selective induction of inflammation in the kidneys but not the bladder. MRSA mutants lacking CopL, a copper-binding cell surface lipoprotein, and the ACME genomic region containing copL, exhibit decreased fitness in the mouse urinary tract compared to parental strains. Copper sensitivity assays, cell-associated copper and iron content, and bioavailability of iron during copper stress demonstrate that homeostasis of copper and iron is interlinked in S. aureus. Importantly, relative fitness of the MRSA mutant lacking the ACME region is further decreased in mice that receive supplemental copper compared to the parental strain. In summary, copper is mobilized to the urinary tract during UTI caused by Gram-positive pathogens, and copper resistance is a fitness factor for MRSA during UTI. IMPORTANCE Urinary tract infection (UTI) is an extremely common infectious condition affecting people throughout the world. Increasing antibiotic resistance in pathogens causing UTI threatens our ability to continue to treat patients in the clinics. Better understanding of the host-pathogen interface is critical for development of novel interventional strategies. Here, we sought to elucidate the role of copper in host-Staphylococcus aureus interaction during UTI. Our results reveal that copper is mobilized to the urine as a host response in patients with UTI. Our findings from the murine model of UTI demonstrate that copper resistance is involved in the fitness of methicillin-resistant S. aureus (MRSA) during interaction with the host. We also establish a critical link between adaptation to copper stress and iron homeostasis in S. aureus.
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44
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Zhang X, Huang D, Zhao Z, Cai X, Cai W, Li G. Bis-molybdopterin guanine dinucleotide modulates hemolysin expression under anaerobiosis and contributes to fitness in vivo in uropathogenic Escherichia coli. Mol Microbiol 2021; 116:1216-1231. [PMID: 34494331 DOI: 10.1111/mmi.14809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/05/2021] [Indexed: 01/10/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is the primary causative agent of urinary tract infections (UTIs). Successful urinary tract colonization requires appropriate expression of virulence factors in response to host environmental cues, such as limited oxygen and iron availability. Hemolysin is a pore-forming toxin, and its expression correlates with the severity of UPEC infection. Previously, we showed that hemolysin expression is enhanced under anaerobic conditions; however, the genetic basis and regulatory mechanisms involved remain undefined. Here, a transposon-based forward screen identified bis-molybdopterin guanine dinucleotide cofactor (bis-MGD) biosynthesis as an important factor for a full transcription of hemolysin under anaerobiosis but not under aerobiosis. bis-MGD positively influences hemolysin transcription via c3566-c3568, an operon immediately upstream of and cotranscribed with hlyCABD. Furthermore, suppressor mutation analysis identified the nitrogen regulator NtrC as a direct repressor of c3566-c3568-hlyCABD expression, and intact bis-MGD biosynthesis downregulated ntrC expression, thus at least partially explaining the positive role of bis-MGD in modulating hemolysin expression. Finally, bis-MGD is involved in hemolysin-mediated uroepithelial cell death and contributes to the competitive fitness of UPEC in a murine model of UTI. Collectively, our data establish that bis-MGD biosynthesis plays a crucial role in UPEC fitness in vivo, thus providing a potential target for combatting UTIs.
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Affiliation(s)
- Xinyang Zhang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dongyan Huang
- Jiangxi Engineering Research Center for Animal Health Products, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Zihui Zhao
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xuwang Cai
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ganwu Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Casanova-Hampton K, Carey A, Kassam S, Garner A, Donati GL, Thangamani S, Subashchandrabose S. A genome-wide screen reveals the involvement of enterobactin-mediated iron acquisition in Escherichia coli survival during copper stress. Metallomics 2021; 13:6355450. [PMID: 34415046 PMCID: PMC8419524 DOI: 10.1093/mtomcs/mfab052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022]
Abstract
Copper (Cu) is a key transition metal that is involved in many important biological processes in a cell. Cu is also utilized by the immune system to hamper pathogen growth during infection. However, genome-level knowledge on the mechanisms involved in adaptation to Cu stress is limited. Here, we report the results of a genome-wide reverse genetic screen for Cu-responsive phenotypes in Escherichia coli. Our screen has identified novel genes involved in adaptation to Cu stress in E. coli. We detected multiple genes involved in the biosynthesis and uptake of enterobactin, a siderophore utilized for high-affinity TonB-dependent acquisition of iron (Fe), as critical players in survival under Cu intoxication. We demonstrated the specificity of Cu-dependent killing by chelation of Cu and by genetic complementation of tonB. Notably, TonB is involved in protection from Cu in both laboratory and uropathogenic strains of E. coli. Cu stress leads to increased expression of the genes involved in Fe uptake, indicating that Fur regulon is derepressed during exposure to excess Cu. Trace element analyses revealed that Fe homeostasis is dysregulated during Cu stress. Taken together, our data supports a model in which lack of enterobactin-dependent Fe uptake leads to exacerbation of Cu toxicity, and elucidates the intricate connection between the homeostasis of Cu and Fe in a bacterial cell.
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Affiliation(s)
- Kaitlin Casanova-Hampton
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Alexis Carey
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Sarah Kassam
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Alyssa Garner
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - George L Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | - Shankar Thangamani
- Department of Pathology and Population Medicine, College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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47
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Sharma K, Thacker VV, Dhar N, Clapés Cabrer M, Dubois A, Signorino-Gelo F, Mullenders J, Knott GW, Clevers H, McKinney JD. Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model. Cell Rep 2021; 36:109351. [PMID: 34289360 DOI: 10.1016/j.celrep.2021.109351] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/26/2021] [Accepted: 06/15/2021] [Indexed: 01/24/2023] Open
Abstract
Recurrence of uropathogenic Escherichia coli (UPEC) infections has been attributed to reactivation of quiescent intracellular reservoirs (QIRs) in deep layers of the bladder wall. QIRs are thought to arise late during infection following dispersal of bacteria from intracellular bacterial communities (IBCs) in superficial umbrella cells. Here, we track the formation of QIR-like bacteria in a bladder organoid model that recapitulates the stratified uroepithelium within a volume suitable for high-resolution live-cell imaging. Bacteria injected into the organoid lumen enter umbrella-like cells and proliferate to form IBC-like bodies. In parallel, single bacteria penetrate deeper layers of the organoid wall, where they localize within or between uroepithelial cells. These "solitary" bacteria evade killing by antibiotics and neutrophils and are morphologically distinct from bacteria in IBCs. We conclude that bacteria with QIR-like properties may arise at early stages of infection, independent of IBC formation and rupture.
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Affiliation(s)
- Kunal Sharma
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Vivek V Thacker
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Neeraj Dhar
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Maria Clapés Cabrer
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anaëlle Dubois
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - François Signorino-Gelo
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jasper Mullenders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, the Netherlands
| | - Graham W Knott
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, the Netherlands
| | - John D McKinney
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland.
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48
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Desai D, Goh KGK, Sullivan MJ, Chattopadhyay D, Ulett GC. Hemolytic activity and biofilm-formation among clinical isolates of group B streptococcus causing acute urinary tract infection and asymptomatic bacteriuria. Int J Med Microbiol 2021; 311:151520. [PMID: 34273854 DOI: 10.1016/j.ijmm.2021.151520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022] Open
Abstract
Streptococcus agalactiae, also known as group B Streptococcus, is an aetiological agent of urinary tract infection (UTI) in adults, including cystitis, pyelonephritis and asymptomatic bacteriuria (ABU). Whereas ABU-causing S. agalactiae (ABSA) have been shown to grow and achieve higher culture denstity in human urine compared to uropathogenic S. agalactiae (UPSA) other phenotypic distinctions between S. agalactiae isolated from different forms of UTI are not known. Here, we define the hemolytic activities and biofilm-formation of a collection of clinical isolates of UPSA, ABSA and recurrent S. agalactiae bacteriuria (rSAB) strains to explore these phenotypes in the context of clinical history of isolates. A total of 61 UPSA, 184 ABSA, and 47 rSAB isolates were analyzed for relative hemolytic activity by spot assay on blood agar, which was validated using a erythrocyte lysis suspension assay. Biofilm formation was determined by microtiter plate assay with Lysogeny and Todd-Hewitt broths supplemented with 1% glucose to induce biofilm formation. We also used multiplex PCR to analyze isolates for the presence of genes encoding adhesive pili, which contribute to biofilm formation. Comparing the hemolytic activities of 292 isolates showed, surprisingly, that ABSA strains were significantly more likely to be highly hemolytic compared to other strains. In contrast, there were no differences between the relative abilities of strains from the different clinical history groups to form biofilms. Taken together, these findings demonstrate a propensity of S. agalactiae causing ABU to be highly hemolytic but no link between clinical history of UTI strains and ability to form biofilm.
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Affiliation(s)
- Devika Desai
- School of Pharmacy and Medical Sciences, Australia
| | - Kelvin G K Goh
- School of Pharmacy and Medical Sciences, Australia; Menzies Health Institute Queensland, Griffith University, Parklands, 4222, Australia
| | - Matthew J Sullivan
- School of Pharmacy and Medical Sciences, Australia; Menzies Health Institute Queensland, Griffith University, Parklands, 4222, Australia
| | - Debasish Chattopadhyay
- Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, AL, United States
| | - Glen C Ulett
- School of Pharmacy and Medical Sciences, Australia; Menzies Health Institute Queensland, Griffith University, Parklands, 4222, Australia; Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, AL, United States.
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49
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Prentice MB. Bacterial microcompartments and their role in pathogenicity. Curr Opin Microbiol 2021; 63:19-28. [PMID: 34107380 DOI: 10.1016/j.mib.2021.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
Catabolic bacterial microcompartments (BMC), or metabolosomes, are self-assembling structures formed by enzymes enclosed by porous protein shells. They provide a specialised environment inside bacterial cells separating a short catabolic pathway with reactive or toxic intermediates from the cytoplasm. Substrates for microcompartment metabolism like ethanolamine and 1,2-propanediol are constantly produced in the human intestine by bacterial metabolism of food or host cell components. Enteric pathogens gain a competitive advantage in the intestine by metabolising these substrates, an advantage enhanced by the host inflammatory response. They exploit the intestinal specificity of signature metabolosome substrates by adopting substrate sensors and regulators encoded by BMC operons for governance of non-metabolic processes in pathogenesis. In turn, products of microcompartment metabolism regulate the host immune system.
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Affiliation(s)
- Michael B Prentice
- Department of Pathology, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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50
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Ittensohn J, Hemberger J, Griffiths H, Keller M, Albrecht S, Miethke T. Regulation of Expression of the TIR-Containing Protein C Gene of the Uropathogenic Escherichia coli Strain CFT073. Pathogens 2021; 10:pathogens10050549. [PMID: 34062817 PMCID: PMC8147327 DOI: 10.3390/pathogens10050549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/22/2022] Open
Abstract
The uropathogenic Escherichia coli strain CFT073 causes kidney abscesses in mice Toll/interleukin-1 receptor domain-containing protein C (TcpC) dependently and the corresponding gene is present in around 40% of E. coli isolates of pyelonephritis patients. It impairs the Toll-like receptor (TLR) signaling chain and the NACHT leucin-rich repeat PYD protein 3 inflammasome (NLRP3) by binding to TLR4 and myeloid differentiation factor 88 as well as to NLRP3 and caspase-1, respectively. Overexpression of the tcpC gene stopped replication of CFT073. Overexpression of several tcpC-truncation constructs revealed a transmembrane region, while its TIR domain induced filamentous bacteria. Based on these observations, we hypothesized that tcpC expression is presumably tightly controlled. We tested two putative promoters designated P1 and P2 located at 5′ of the gene c2397 and 5′ of the tcpC gene (c2398), respectively, which may form an operon. High pH and increasing glucose concentrations stimulated a P2 reporter construct that was considerably stronger than a P1 reporter construct, while increasing FeSO4 concentrations suppressed their activity. Human urine activated P2, demonstrating that tcpC might be induced in the urinary tract of infected patients. We conclude that P2, consisting of a 240 bp region 5′ of the tcpC gene, represents the major regulator of tcpC expression.
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Affiliation(s)
- Julia Ittensohn
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Jacqueline Hemberger
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Hannah Griffiths
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Maren Keller
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Simone Albrecht
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
| | - Thomas Miethke
- Medical Faculty of Mannheim, Institute of Medical Microbiology and Hygiene, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (J.I.); (J.H.); (H.G.); (M.K.); (S.A.)
- Medical Faculty of Mannheim, Mannheim Institute for Innate Immunoscience (MI3), University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany
- Correspondence:
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