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Duff AF, Jurcisek JA, Kurbatfinski N, Chiang T, Goodman SD, Bakaletz LO, Bailey MT. Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes. NPJ Biofilms Microbiomes 2024; 10:10. [PMID: 38310144 PMCID: PMC10838340 DOI: 10.1038/s41522-024-00481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Otitis media (OM) is one of the most globally pervasive pediatric conditions. Translocation of nasopharynx-resident opportunistic pathogens like nontypeable Haemophilus influenzae (NTHi) assimilates into polymicrobial middle ear biofilms, which promote OM pathogenesis and substantially diminish antibiotic efficacy. Oral or tympanostomy tube (TT)-delivered antibiotics remain the standard of care (SOC) despite consequences including secondary infection, dysbiosis, and antimicrobial resistance. Monoclonal antibodies (mAb) against two biofilm-associated structural proteins, NTHi-specific type IV pilus PilA (anti-rsPilA) and protective tip-region epitopes of NTHi integration host factor (anti-tip-chimer), were previously shown to disrupt biofilms and restore antibiotic sensitivity in vitro. However, the additional criterion for clinical relevance includes the absence of consequential microbiome alterations. Here, nine chinchilla cohorts (n = 3/cohort) without disease were established to evaluate whether TT delivery of mAbs disrupted nasopharyngeal or fecal microbiomes relative to SOC-OM antibiotics. Cohort treatments included a 7d regimen of oral amoxicillin-clavulanate (AC) or 2d regimen of TT-delivered mAb, AC, Trimethoprim-sulfamethoxazole (TS), ofloxacin, or saline. Fecal and nasopharyngeal lavage (NPL) samples were collected before and several days post treatment (DPT) for 16S sequencing. While antibiotic-treated cohorts displayed beta-diversity shifts (PERMANOVA, P < 0.05) and reductions in alpha diversity (q < 0.20) relative to baseline, mAb antibodies failed to affect diversity, indicating maintenance of a eubiotic state. Taxonomic and longitudinal analyses showed blooms in opportunistic pathogens (ANCOM) and greater magnitudes of compositional change (P < 0.05) following broad-spectrum antibiotic but not mAb treatments. Collectively, results showed broad-spectrum antibiotics induced significant fecal and nasopharyngeal microbiome disruption regardless of delivery route. Excitingly, biofilm-targeting antibodies had little effect on fecal and nasopharyngeal microbiomes.
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Affiliation(s)
- Audrey F Duff
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Tendy Chiang
- Department of Otolaryngology at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
- Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Michael T Bailey
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
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Gallucci S. DNA at the center of mammalian innate immune recognition of bacterial biofilms. Trends Immunol 2024; 45:103-112. [PMID: 38281884 PMCID: PMC11032746 DOI: 10.1016/j.it.2023.12.004] [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: 12/08/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Historically, the study of innate immune detection of bacterial infections has focused on the recognition of pathogen-associated molecular patterns (PAMPs) from bacteria growing as single cells in planktonic phase. However, over the past two decades, studies have highlighted an adaptive advantage of bacteria: the formation of biofilms. These structures are complex fortresses that stand against a hostile environment, including antibiotics and immune responses. Extracellular DNA (eDNA) is a crucial component of the matrix of most known biofilms. In this opinion article, I propose that eDNA is a universal PAMP that the immune system uses to recognize biofilms. Outstanding questions concern the discrimination between biofilm-associated eDNA and DNA from planktonic bacteria, the innate receptors involved, and the immune response to biofilms.
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Affiliation(s)
- Stefania Gallucci
- Laboratory of Dendritic Cell Biology, Division of Innate Immunity, Department of Medicine, UMass Chan Medical School, Worcester, MA, USA.
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Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [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: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
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Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
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Kurbatfinski N, Hill PJ, Tobin N, Kramer CN, Wickham J, Goodman SD, Hall-Stoodley L, Bakaletz LO. Disruption of nontuberculous mycobacteria biofilms induces a highly vulnerable to antibiotic killing phenotype. Biofilm 2023; 6:100166. [PMID: 38078059 PMCID: PMC10698573 DOI: 10.1016/j.bioflm.2023.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 02/07/2024] Open
Abstract
Objectives Structural or mucus hypersecretory pulmonary diseases such as cystic fibrosis (CF), wherein viscous mucus accumulates and clearance functions are impaired, predispose people to lung infection by inhaled bacteria that form biofilm aggregates. Nontuberculous mycobacteria (NTM), primarily Mycobacterium abscessus and Mycobacterium avium, are the growing cause of these lung infections and are extremely challenging to treat due to antibiotic recalcitrance. Better therapeutic approaches are urgently needed. We developed a humanized monoclonal antibody (HuTipMab) directed against a biofilm structural linchpin, the bacterial DNABII proteins, that rapidly disrupts biofilms and generates highly vulnerable newly released bacteria (NRel). Methods HuTipMab's ability to recognize HupB, NTM's DNABII homologue was determined by ELISA. Relative ability of HuTipMab to disrupt biofilms formed by lab-passaged and clinical isolates of NTM was assessed by CLSM. Relative sensitivity of NTM NRel to antibiotic killing compared to when grown planktonically was evaluated by plate count. Results HuTipMab recognized HupB and significantly disrupted NTM biofilms in a time- and dose-dependent manner. Importantly, NTM NRel of lab-passaged and clinical isolates were now highly sensitive to killing by amikacin and azithromycin. Conclusions If successful, this combinatorial treatment strategy would empower existing antibiotics to more effectively kill NTM newly released from a biofilm by HuTipMab and thereby both improve clinical outcomes and perhaps decrease length of antibiotic treatment for people that are NTM culture-positive.
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Affiliation(s)
- Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Preston J. Hill
- Department of Microbial Infection and Immunity, The Ohio State University, 460 W 12 Ave., Columbus, OH, 43210, USA
| | - Noah Tobin
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Cameron N. Kramer
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Joseph Wickham
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Steven D. Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, 460 W 12 Ave., Columbus, OH, 43210, USA
| | - Lauren O. Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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Delaney DS, Liew LJ, Lye J, Atlas MD, Wong EYM. Overcoming barriers: a review on innovations in drug delivery to the middle and inner ear. Front Pharmacol 2023; 14:1207141. [PMID: 37927600 PMCID: PMC10620978 DOI: 10.3389/fphar.2023.1207141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Despite significant advances in the development of therapeutics for hearing loss, drug delivery to the middle and inner ear remains a challenge. As conventional oral or intravascular administration are ineffective due to poor bioavailability and impermeability of the blood-labyrinth-barrier, localized delivery is becoming a preferable approach for certain drugs. Even then, localized delivery to the ear precludes continual drug delivery due to the invasive and potentially traumatic procedures required to access the middle and inner ear. To address this, the preclinical development of controlled release therapeutics and drug delivery devices have greatly advanced, with some now showing promise clinically. This review will discuss the existing challenges in drug development for treating the most prevalent and damaging hearing disorders, in particular otitis media, perforation of the tympanic membrane, cholesteatoma and sensorineural hearing loss. We will then address novel developments in drug delivery that address these including novel controlled release therapeutics such as hydrogel and nanotechnology and finally, novel device delivery approaches such as microfluidic systems and cochlear prosthesis-mediated delivery. The aim of this review is to investigate how drugs can reach the middle and inner ear more efficiently and how recent innovations could be applied in aiding drug delivery in certain pathologic contexts.
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Affiliation(s)
- Derek S. Delaney
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA, Australia
- Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Lawrence J. Liew
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA, Australia
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA, Australia
| | - Joey Lye
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA, Australia
| | - Marcus D. Atlas
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA, Australia
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA, Australia
- Faculty of Health Sciences, Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Elaine Y. M. Wong
- Hearing Therapeutics, Ear Science Institute Australia, Nedlands, WA, Australia
- Centre for Ear Sciences, Medical School, The University of Western Australia, Nedlands, WA, Australia
- Faculty of Health Sciences, Curtin Medical School, Curtin University, Bentley, WA, Australia
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Wilbanks KQ, Mokrzan EM, Kesler TM, Kurbatfinski N, Goodman SD, Bakaletz LO. Nontypeable Haemophilus influenzae released from biofilm residence by monoclonal antibody directed against a biofilm matrix component display a vulnerable phenotype. Sci Rep 2023; 13:12959. [PMID: 37563215 PMCID: PMC10415356 DOI: 10.1038/s41598-023-40284-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Bacterial biofilms contribute significantly to pathogenesis, recurrence and/or chronicity of the majority of bacterial diseases due to their notable recalcitrance to clearance. Herein, we examined kinetics of the enhanced sensitivity of nontypeable Haemophilus influenzae (NTHI) newly released (NRel) from biofilm residence by a monoclonal antibody against a bacterial DNABII protein (α-DNABII) to preferential killing by a β-lactam antibiotic. This phenotype was detected within 5 min and lasted for ~ 6 h. Relative expression of genes selected due to their known involvement in sensitivity to a β-lactam showed transient up-regulated expression of penicillin binding proteins by α-DNABII NTHI NRel, whereas there was limited expression of the β-lactamase precursor. Transient down-regulated expression of mediators of oxidative stress supported similarly timed vulnerability to NADPH-oxidase sensitive intracellular killing by activated human PMNs. Further, transient up-regulated expression of the major NTHI porin aligned well with observed increased membrane permeability of α-DNABII NTHI NRel, a characteristic also shown by NRel of three additional pathogens. These data provide mechanistic insights as to the transient, yet highly vulnerable, α-DNABII NRel phenotype. This heightened understanding supports continued validation of this novel therapeutic approach designed to leverage knowledge of the α-DNABII NRel phenotype for more effective eradication of recalcitrant biofilm-related diseases.
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Affiliation(s)
- Kathryn Q Wilbanks
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Elaine M Mokrzan
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Theresa M Kesler
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.
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Kurbatfinski N, Kramer CN, Goodman SD, Bakaletz LO. ESKAPEE pathogens newly released from biofilm residence by a targeted monoclonal are sensitized to killing by traditional antibiotics. Front Microbiol 2023; 14:1202215. [PMID: 37564292 PMCID: PMC10410267 DOI: 10.3389/fmicb.2023.1202215] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction The "silent" antimicrobial resistance (AMR) pandemic is responsible for nearly five million deaths annually, with a group of seven biofilm-forming pathogens, known as the ESKAPEE pathogens, responsible for 70% of these fatalities. Biofilm-resident bacteria, as they exist within the disease site, are canonically highly resistant to antibiotics. One strategy to counter AMR and improve disease resolution involves developing methods to disrupt biofilms. These methods aim to release bacteria from the protective biofilm matrix to facilitate their killing by antibiotics or immune effectors. Several laboratories working on such strategies have demonstrated that bacteria newly released from a biofilm display a transient phenotype of significantly increased susceptibility to antibiotics. Similarly, we developed an antibody-based approach for biofilm disruption directed against the two-membered DNABII family of bacterial DNA-binding proteins, which serve as linchpins to stabilize the biofilm matrix. The incubation of biofilms with α-DNABII antibodies rapidly collapses them to induce a population of newly released bacteria (NRel). Methods In this study, we used a humanized monoclonal antibody (HuTipMab) directed against protective epitopes of a DNABII protein to determine if we could disrupt biofilms formed by the high-priority ESKAPEE pathogens as visualized by confocal laser scanning microscopy (CLSM) and COMSTAT2 analysis. Then, we demonstrated the potentiated killing of the induced NRel by seven diverse classes of traditional antibiotics by comparative plate count. Results To this end, ESKAPEE biofilms were disrupted by 50%-79% using a single tested dose and treatment period with HuTipMab. The NRel of each biofilm were significantly more sensitive to killing than their planktonically grown counterparts (heretofore, considered to be the most sensitive to antibiotic-mediated killing), even when tested at a fraction of the MIC (1/250-1/2 MIC). Moreover, the bacteria that remained within the biofilms of two representative ESKAPEE pathogens after HuTipMab disruption were also significantly more susceptible to killing by antibiotics. Discussion New data presented in this study support our continued development of a combinatorial therapy wherein HuTipMab is delivered to a patient with recalcitrant disease due to an ESKAPEE pathogen to disrupt a pathogenic biofilm, along with a co-delivered dose of an antibiotic whose ability to rapidly kill the induced NRel has been demonstrated. This novel regimen could provide a more successful clinical outcome to those with chronic, recurrent, or recalcitrant diseases, while limiting further contribution to AMR.
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Affiliation(s)
- Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Cameron N. Kramer
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Steven D. Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lauren O. Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Jonkergouw C, Beyeh NK, Osmekhina E, Leskinen K, Taimoory SM, Fedorov D, Anaya-Plaza E, Kostiainen MA, Trant JF, Ras RHA, Saavalainen P, Linder MB. Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii. Nat Commun 2023; 14:2141. [PMID: 37059703 PMCID: PMC10104825 DOI: 10.1038/s41467-023-37749-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
The limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukaryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, both in vitro and in vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.
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Affiliation(s)
- Christopher Jonkergouw
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
| | - Ngong Kodiah Beyeh
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, MI, 48309-4479, USA
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Ekaterina Osmekhina
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Katarzyna Leskinen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland
| | - S Maryamdokht Taimoory
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
- University of Michigan, Department of Chemistry, Ann Arbor, MI, USA
| | - Dmitrii Fedorov
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Eduardo Anaya-Plaza
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Mauri A Kostiainen
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - John F Trant
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
| | - Robin H A Ras
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Päivi Saavalainen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland.
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
| | - Markus B Linder
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
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Goodman SD, Bakaletz LO. Bacterial Biofilms Utilize an Underlying Extracellular DNA Matrix Structure That Can Be Targeted for Biofilm Resolution. Microorganisms 2022; 10:microorganisms10020466. [PMID: 35208922 PMCID: PMC8878592 DOI: 10.3390/microorganisms10020466] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022] Open
Abstract
Bacterial biofilms contribute significantly to the antibiotic resistance, pathogenesis, chronicity and recurrence of bacterial infections. Critical to the stability and survival of extant biofilms is the extracellular DNA (eDNA)-dependent matrix which shields the resident bacteria from hostile environments, allows a sessile metabolic state, but also encourages productive interactions with biofilm-inclusive bacteria. Given the importance of the eDNA, approaches to this area of research have been to target not just the eDNA, but also the additional constituent structural components which appear to be widespread. Chief among these is a ubiquitous two-member family of bacterial nucleoid associated proteins (the DNABII proteins) responsible for providing structural integrity to the eDNA and thereby the biofilm. Moreover, this resultant novel eDNA-rich secondary structure can also be targeted for disruption. Here, we provide an overview of both what is known about the eDNA-dependent matrix, as well as the resultant means that have resulted in biofilm resolution. Results obtained to date have been highly supportive of continued development of DNABII-targeted approaches, which is encouraging given the great global need for improved methods to medically manage, or ideally prevent biofilm-dependent infections, which remains a highly prevalent burden worldwide.
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Rogers JV, Hall VL, McOsker CC. Crumbling the Castle: Targeting DNABII Proteins for Collapsing Bacterial Biofilms as a Therapeutic Approach to Treat Disease and Combat Antimicrobial Resistance. Antibiotics (Basel) 2022; 11:104. [PMID: 35052981 PMCID: PMC8773079 DOI: 10.3390/antibiotics11010104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/02/2022] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is a concerning global threat that, if not addressed, could lead to increases in morbidity and mortality, coupled with societal and financial burdens. The emergence of AMR bacteria can be attributed, in part, to the decreased development of new antibiotics, increased misuse and overuse of existing antibiotics, and inadequate treatment options for biofilms formed during bacterial infections. Biofilms are complex microbiomes enshrouded in a self-produced extracellular polymeric substance (EPS) that is a primary defense mechanism of the resident microorganisms against antimicrobial agents and the host immune system. In addition to the physical protective EPS barrier, biofilm-resident bacteria exhibit tolerance mechanisms enabling persistence and the establishment of recurrent infections. As current antibiotics and therapeutics are becoming less effective in combating AMR, new innovative technologies are needed to address the growing AMR threat. This perspective article highlights such a product, CMTX-101, a humanized monoclonal antibody that targets a universal component of bacterial biofilms, leading to pathogen-agnostic rapid biofilm collapse and engaging three modes of action-the sensitization of bacteria to antibiotics, host immune enablement, and the suppression of site-specific tissue inflammation. CMTX-101 is a new tool used to enhance the effectiveness of existing, relatively inexpensive first-line antibiotics to fight infections while promoting antimicrobial stewardship.
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Affiliation(s)
| | | | - Charles C. McOsker
- Clarametyx Biosciences, Inc., 1275 Kinnear Rd, Columbus, OH 43212, USA; (J.V.R.); (V.L.H.)
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11
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A Humanized Monoclonal Antibody Potentiates Killing by Antibiotics of Diverse Biofilm-Forming Respiratory Tract Pathogens. Antimicrob Agents Chemother 2022; 66:e0187721. [DOI: 10.1128/aac.01877-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New strategies to treat diseases wherein biofilms contribute significantly to pathogenesis are needed as biofilm-resident bacteria are highly recalcitrant to antibiotics due to physical biofilm architecture and a canonically quiescent metabolism, among many additional attributes. We, and others, have shown that when biofilms are dispersed or disrupted, bacteria released from biofilm residence are in a distinct physiologic state that, in part, renders these bacteria highly sensitive to killing by specific antibiotics. We sought to demonstrate the breadth of ability of a recently humanized monoclonal antibody against an essential biofilm structural element (DNABII protein) to disrupt biofilms formed by respiratory tract pathogens and potentiate antibiotic-mediated killing of bacteria released from biofilm residence.
Biofilms formed by six respiratory tract pathogens were significantly disrupted by the humanized monoclonal antibody in a dose- and time-dependent manner, as corroborated by CLSM imaging. Bacteria newly released from the biofilms of 3 of 6 species were significantly more sensitive than their planktonic counterparts to killing by 2 of 3 antibiotics currently used clinically and were now also equally as sensitive to killing by the 3
rd
antibiotic. The remaining 3 pathogens were significantly more susceptible to killing by all 3 antibiotics.
A humanized monoclonal antibody directed against protective epitopes of a DNABII protein effectively released six diverse respiratory tract pathogens from biofilm residence in a phenotypic state that was now as, or significantly more, sensitive to killing by three antibiotics currently indicated for use clinically. These data support this targeted, combinatorial, species-agnostic therapy to mitigate chronic bacterial diseases.
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12
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Buzzo JR, Devaraj A, Gloag ES, Jurcisek JA, Robledo-Avila F, Kesler T, Wilbanks K, Mashburn-Warren L, Balu S, Wickham J, Novotny LA, Stoodley P, Bakaletz LO, Goodman SD. Z-form extracellular DNA is a structural component of the bacterial biofilm matrix. Cell 2021; 184:5740-5758.e17. [PMID: 34735796 DOI: 10.1016/j.cell.2021.10.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/03/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022]
Abstract
Biofilms are community architectures adopted by bacteria inclusive of a self-formed extracellular matrix that protects resident bacteria from diverse environmental stresses and, in many species, incorporates extracellular DNA (eDNA) and DNABII proteins for structural integrity throughout biofilm development. Here, we present evidence that this eDNA-based architecture relies on the rare Z-form. Z-form DNA accumulates as biofilms mature and, through stabilization by the DNABII proteins, confers structural integrity to the biofilm matrix. Indeed, substances known to drive B-DNA into Z-DNA promoted biofilm formation whereas those that drive Z-DNA into B-DNA disrupted extant biofilms. Importantly, we demonstrated that the universal bacterial DNABII family of proteins stabilizes both bacterial- and host-eDNA in the Z-form in situ. A model is proposed that incorporates the role of Z-DNA in biofilm pathogenesis, innate immune response, and immune evasion.
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Affiliation(s)
- John R Buzzo
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Aishwarya Devaraj
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Erin S Gloag
- Department of Orthopedics, Ohio State University, Columbus, OH 43210, USA
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Frank Robledo-Avila
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Theresa Kesler
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Kathryn Wilbanks
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Lauren Mashburn-Warren
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sabarathnam Balu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Joseph Wickham
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Laura A Novotny
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Paul Stoodley
- Department of Orthopedics, Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA; National Centre for Advanced Tribology at Southampton, University of Southampton, Southampton S017 1BJ, UK
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH 43210, USA.
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH 43210, USA.
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13
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da Silva RAG, Afonina I, Kline KA. Eradicating biofilm infections: an update on current and prospective approaches. Curr Opin Microbiol 2021; 63:117-125. [PMID: 34333239 DOI: 10.1016/j.mib.2021.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/13/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Biofilm formation is a multifactorial process and often a multi-species endeavour that involves complex signalling networks, chemical gradients, bacterial adhesion, and production or acquisition of matrix components. Antibiotics remain the main choice when treating bacterial biofilm-associated infections despite their intrinsic tolerance to antimicrobials, and propensity for acquisition and rapid dissemination of antimicrobial resistance within the biofilm. Eliminating hard to treat biofilm-associated infections that are antibiotic resistant will demand a holistic and multi-faceted approach, targeting multiple stages of biofilm formation, many of which are already in development. This mini review will highlight the current approaches that are employed to treat bacterial biofilm infections and discuss new approaches in development that have promise to reach clinical practice.
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Affiliation(s)
- Ronni A G da Silva
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore; Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, Singapore
| | - Irina Afonina
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore; Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore; Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
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14
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López-López N, Gil-Campillo C, Díez-Martínez R, Garmendia J. Learning from -omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives. Comput Struct Biotechnol J 2021; 19:3042-3050. [PMID: 34136102 PMCID: PMC8178019 DOI: 10.1016/j.csbj.2021.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022] Open
Abstract
Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of -omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae-host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.
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Affiliation(s)
- Nahikari López-López
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Celia Gil-Campillo
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | | | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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15
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Hatefi Oskuei R, Darvish Alipour Astaneh S, Rasooli I. A conserved region of Acinetobacter trimeric autotransporter adhesion, Ata, provokes suppression of Acinetobacter baumannii virulence. Arch Microbiol 2021; 203:3483-3493. [PMID: 33907866 DOI: 10.1007/s00203-021-02343-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 04/17/2021] [Accepted: 04/21/2021] [Indexed: 01/02/2023]
Abstract
The Acinetobacter trimeric autotransporter adhesin (Ata) is an important virulence factor. The conserved region from the genomic sequence of a 6777bp/2258 amino acid of Acinetobacter baumannii ATCC®19606™ ata was explored. A 263aa of the C-terminal of Ata (rcAta263) was expressed. The effect of rcAta263 on A. baumannii virulence was studied in a murine model. IgG and IgA were elicited and the mice groups challenged with A. baumannii showed significant survival rates from 66 to 100%. The bacterial loads were determined in the spleens, livers, and lungs of both control and test groups. The adhesion rate of A. baumannii to A549 cells in the presence of serum, cytotoxicity, mutagenicity, and biofilm disruption potential of rcAta263 were determined. Intraperitoneally challenged groups showed a significantly reduced bacterial load in the organs of the immunized mice. Intranasal challenge reduced 4 logs of bacterial CFU/g in the test group. The immunized mice sera reduced adherence of A. baumannii to A549 cells to 80%. No cytotoxic or mutagenic effect was detected. Biofilm disruption was significantly increased in the presence of immunized mice sera. Immunization with the conserved region of Ata significantly combats the virulence of A. baumannii which could be considered as a therapeutic strategy to control A. baumannii infections.
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Affiliation(s)
- Ramin Hatefi Oskuei
- Department of Biology, Shahed University, Tehran-Qom Express way, Tehran, 3319118651, Iran
| | - Shakiba Darvish Alipour Astaneh
- Department of Biotechnology, Semnan University, Central Administration of Semnan University, Campus 1, Semnan, 35131-19111, I. R. of Iran
| | - Iraj Rasooli
- Department of Biology, Shahed University, Tehran-Qom Express way, Tehran, 3319118651, Iran.
- Molecular Microbiology Research Center and Department of Biology, Shahed University, Tehran, Iran.
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16
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Kirkham LAS, Thornton RB. Targeting host-microbial interactions to develop otitis media therapies. MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Otitis media (OM; middle ear infection) is the most common reason for pre-school children to visit a doctor, be prescribed antimicrobials, or undergo surgery. Recent Cochrane reviews of clinical trials have identified that antibiotics and grommet surgery are only moderately effective in treating OM, with recurrent or persistent infection observed in one-third of children. Research efforts are focusing on developing improved therapies to treat OM and prevent disease recurrence. The recurrent nature of OM is mostly due to the persistence of bacterial pathogens within established biofilm in the middle ear. Promising novel therapies are harnessing host-microbe interactions to disrupt middle ear biofilm and permit antibiotics to work more effectively. New approaches are also being developed to prevent OM, including new vaccines and mining the host respiratory microbiome to develop novel bacterial therapies. This review describes how our improved knowledge of human and microbial interactions is driving development of OM therapies to improve health outcomes for children in Australia and worldwide.
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