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Zong W, Friedman ES, Allu SR, Firrman J, Tu V, Daniel SG, Bittinger K, Liu L, Vinogradov SA, Wu GD. Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome. Gut Microbes 2024; 16:2361493. [PMID: 38958039 PMCID: PMC11225921 DOI: 10.1080/19490976.2024.2361493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
The juxtaposition of well-oxygenated intestinal colonic tissue with an anerobic luminal environment supports a fundamentally important relationship that is altered in the setting of intestinal injury, a process likely to be relevant to diseases such as inflammatory bowel disease. Herein, using two-color phosphorometry to non-invasively quantify both intestinal tissue and luminal oxygenation in real time, we show that intestinal injury induced by DSS colitis reduces intestinal tissue oxygenation in a spatially defined manner and increases the flux of oxygen from the tissue into the gut lumen. By characterizing the composition of the microbiome in both DSS colitis-affected gut and in a bioreactor containing a stable human fecal community exposed to microaerobic conditions, we provide evidence that the increased flux of oxygen into the gut lumen augments glycan degrading bacterial taxa rich in glycoside hydrolases which are known to inhabit gut mucosal surface. Continued disruption of the intestinal mucus barrier through such a mechanism may play a role in the perpetuation of the intestinal inflammatory process.
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Affiliation(s)
- Wenjing Zong
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Elliot S. Friedman
- Department of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Srinivasa Rao Allu
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA ,USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Sergei A. Vinogradov
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D. Wu
- Department of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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2
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Tubiana J, Xiang Y, Fan L, Wolfson HJ, Chen K, Schneidman-Duhovny D, Shi Y. Reduced B cell antigenicity of Omicron lowers host serologic response. Cell Rep 2022; 41:111512. [PMID: 36223774 PMCID: PMC9515332 DOI: 10.1016/j.celrep.2022.111512] [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: 06/07/2022] [Revised: 08/10/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 Omicron variant evades most neutralizing vaccine-induced antibodies and is associated with lower antibody titers upon breakthrough infections than previous variants. However, the mechanism remains unclear. Here, we find using a geometric deep-learning model that Omicron's extensively mutated receptor binding site (RBS) features reduced antigenicity compared with previous variants. Mice immunization experiments with different recombinant receptor binding domain (RBD) variants confirm that the serological response to Omicron is drastically attenuated and less potent. Analyses of serum cross-reactivity and competitive ELISA reveal a reduction in antibody response across both variable and conserved RBD epitopes. Computational modeling confirms that the RBS has a potential for further antigenicity reduction while retaining efficient receptor binding. Finally, we find a similar trend of antigenicity reduction over decades for hCoV229E, a common cold coronavirus. Thus, our study explains the reduced antibody titers associated with Omicron infection and reveals a possible trajectory of future viral evolution.
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Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Yufei Xiang
- Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Fan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Haim J Wolfson
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel.
| | - Yi Shi
- Center for Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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3
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Emelianova AG, Petrova NV, Fremez C, Fontanié M, Tarasov SА, Epstein ОI. Therapeutic potential of highly diluted antibodies in antibiotic-resistant infection. Eur J Pharm Sci 2022; 173:106161. [DOI: 10.1016/j.ejps.2022.106161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/02/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
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4
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Tubiana J, Xiang Y, Fan L, Wolfson HJ, Chen K, Schneidman-Duhovny D, Shi Y. Reduced antigenicity of Omicron lowers host serologic response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.15.480546. [PMID: 35194608 PMCID: PMC8863144 DOI: 10.1101/2022.02.15.480546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2 Omicron variant of concern (VOC) contains fifteen mutations on the receptor binding domain (RBD), evading most neutralizing antibodies from vaccinated sera. Emerging evidence suggests that Omicron breakthrough cases are associated with substantially lower antibody titers than other VOC cases. However, the mechanism remains unclear. Here, using a novel geometric deep-learning model, we discovered that the antigenic profile of Omicron RBD is distinct from the prior VOCs, featuring reduced antigenicity in its remodeled receptor binding sites (RBS). To substantiate our deep-learning prediction, we immunized mice with different recombinant RBD variants and found that the Omicron's extensive mutations can lead to a drastically attenuated serologic response with limited neutralizing activity in vivo , while the T cell response remains potent. Analyses of serum cross-reactivity and competitive ELISA with epitope-specific nanobodies revealed that the antibody response to Omicron was reduced across RBD epitopes, including both the variable RBS and epitopes without any known VOC mutations. Moreover, computational modeling confirmed that the RBS is highly versatile with a capacity to further decrease antigenicity while retaining efficient receptor binding. Longitudinal analysis showed that this evolutionary trend of decrease in antigenicity was also found in hCoV229E, a common cold coronavirus that has been circulating in humans for decades. Thus, our study provided unprecedented insights into the reduced antibody titers associated with Omicron infection, revealed a possible trajectory of future viral evolution and may inform the vaccine development against future outbreaks.
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Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, USA
- Current address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, USA
| | - Li Fan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, USA
| | - Haim J. Wolfson
- Blavatnik School of Computer Science, Tel Aviv University, Israel
| | - Kong Chen
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, USA
| | | | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, USA
- Current address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, USA
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5
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Dey J, Mahapatra SR, Lata S, Patro S, Misra N, Suar M. Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia. Expert Rev Vaccines 2022; 21:569-587. [PMID: 34932430 DOI: 10.1080/14760584.2022.2021882] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Klebsiella pneumoniae is an emerging human pathogen causing neonatal lung disease, catheter-associated infections, and nosocomial outbreaks with high fatality rates. Capsular polysaccharide (CPS) protein plays a major determinant in virulence and is considered as a promising target for vaccine development. RESEARCH DESIGN AND METHODS In this study, we used immunoinformatic approaches to design a multi-peptide vaccine against K. pneumonia. The epitopes were selected through several immune filters, such as antigenicity, conservancy, nontoxicity, non-allergenicity, binding affinity to HLA alleles, overlapping epitopes, and peptides having common epitopes. RESULTS Finally, a construct comprising 2 B-Cell, 8 CTL, 2 HTL epitopes, along with adjuvant, linkers was designed. Peptide-HLA interaction analysis showed strong binding of these epitopes with several common HLA molecules. The in silico immune simulation and population coverage analysis of the vaccine showed its potential to evoke strong immune responses.. Further, the interaction between vaccine and immune was evaluated by docking and simulation, revealing high affinity and complex stability. Codon adaptation and in silico cloning revealed higher expression of vaccine in E. coli K12 expression system. CONCLUSIONS Conclusively, the findings of the present study suggest that the designed novel multi-epitopic vaccine holds potential for further experimental validation against the pathogen.
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Affiliation(s)
- Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India
| | - S Lata
- Kalinga Institute of Dental Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | - Shubhransu Patro
- Kalinga Institute of Medical Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India
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6
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Muruganandah V, Kupz A. Immune responses to bacterial lung infections and their implications for vaccination. Int Immunol 2021; 34:231-248. [PMID: 34850883 DOI: 10.1093/intimm/dxab109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/28/2021] [Indexed: 11/14/2022] Open
Abstract
The pulmonary immune system plays a vital role in protecting the delicate structures of gaseous exchange against invasion from bacterial pathogens. With antimicrobial resistance becoming an increasing concern, finding novel strategies to develop vaccines against bacterial lung diseases remains a top priority. In order to do so, a continued expansion of our understanding of the pulmonary immune response is warranted. Whilst some aspects are well characterised, emerging paradigms such as the importance of innate cells and inducible immune structures in mediating protection provide avenues of potential to rethink our approach to vaccine development. In this review, we aim to provide a broad overview of both the innate and adaptive immune mechanisms in place to protect the pulmonary tissue from invading bacterial organisms. We use specific examples from several infection models and human studies to depict the varying functions of the pulmonary immune system that may be manipulated in future vaccine development. Particular emphasis has been placed on emerging themes that are less reviewed and underappreciated in vaccine development studies.
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Affiliation(s)
- Visai Muruganandah
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Andreas Kupz
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
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7
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Balaska A, Polonyfi K, Rigatou A, Miliotis G, Margaroni M, Daikos GL, Drogari-Apiranthitou M. Induction of innate immune responses by KPC-producing Klebsiella pneumoniae of the pandemic sequence type 258-clade I. Access Microbiol 2021; 3:000275. [PMID: 35018322 PMCID: PMC8742589 DOI: 10.1099/acmi.0.000275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae
-carbapenemase-producing
K. pneumoniae
(KPC) sequence-type 258 (ST258) has emerged as an important human pathogen throughout the world. Although lacking known virulence factors, it is associated with significant morbidity and high mortality rates. The pathogenicity of KPC
K. pneumoniae
ST258 strains has not been fully elucidated yet. We sought to investigate the interactions of the KPC
K. pneumoniae
ST258-clade I with different components of innate immunity. Human serum was used to evaluate the serum bactericidal activity and the J774A.1 murine (BALB/c mice) macrophage cell-line was used to examine phagocytosis, mRNA expression and production of the pro-inflammatory cytokines IL-1β, TNF-α and IL-6. L-78, a KPC-producing
K. pneumoniae
ST258-clade I strain was used as representative of the strains circulating in Greek hospitals.
K. pneumoniae
ATCC 43816, a virulent K2 strain, was used for comparison. Strain L-78 was susceptible to human serum and rapidly phagocytosed by J774A.1 cells, in contrast to the virulent K2 strain, which was serum-resistant and slowly phagocytosed. Stimulation of the J774A.1 cells with the L-78 strain induced production of IL-1β at concentration levels significantly higher compared to K2, whereas production of TNF-α and IL-6 levels were comparable by the two strains. L-78 was able to induce IL-1β mRNA and NLRP3 mRNA expression. Our findings indicate that
K. pneumoniae
ST258-clade I is serum sensitive, rapidly phagocytosed and is capable of eliciting adequate innate immune response in terms of production of pro-inflammatory cytokines.
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Affiliation(s)
- Asimina Balaska
- Hellenic National Public Health Organization (EODY), Athens, Greece
| | - Katerina Polonyfi
- First Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasia Rigatou
- First Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Miliotis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Maritsa Margaroni
- Immunology of Infectious Diseases Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - George L. Daikos
- First Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Drogari-Apiranthitou
- Infectious Diseases Research Laboratory, 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, General University Hospital “Attikon”, Athens, Greece
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8
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Bekeredjian-Ding I. Challenges for Clinical Development of Vaccines for Prevention of Hospital-Acquired Bacterial Infections. Front Immunol 2020; 11:1755. [PMID: 32849627 PMCID: PMC7419648 DOI: 10.3389/fimmu.2020.01755] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing antibiotic resistance in bacteria causing endogenous infections has entailed a need for innovative approaches to therapy and prophylaxis of these infections and raised a new interest in vaccines for prevention of colonization and infection by typically antibiotic resistant pathogens. Nevertheless, there has been a long history of failures in late stage clinical development of this type of vaccines, which remains not fully understood. This article provides an overview on present and past vaccine developments targeting nosocomial bacterial pathogens; it further highlights the specific challenges associated with demonstrating clinical efficacy of these vaccines and the facts to be considered in future study designs. Notably, these vaccines are mainly applied to subjects with preexistent immunity to the target pathogen, transient or chronic immunosuppression and ill-defined microbiome status. Unpredictable attack rates and changing epidemiology as well as highly variable genetic and immunological strain characteristics complicate the development. In views of the clinical need, re-thinking of the study designs and expectations seems warranted: first of all, vaccine development needs to be footed on a clear rationale for choosing the immunological mechanism of action and the optimal time point for vaccination, e.g., (1) prevention (or reduction) of colonization vs. prevention of infection and (2) boosting of a preexistent immune response vs. altering the quality of the immune response. Furthermore, there are different, probably redundant, immunological and microbiological defense mechanisms that provide protection from infection. Their interplay is not well-understood but as a consequence their effect might superimpose vaccine-mediated resolution of infection and lead to failure to demonstrate efficacy. This implies that improved characterization of patient subpopulations within the trial population should be obtained by pro- and retrospective analyses of trial data on subject level. Statistical and systems biology approaches could help to define immune and microbiological biomarkers that discern populations that benefit from vaccination from those where vaccines might not be effective.
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Affiliation(s)
- Isabelle Bekeredjian-Ding
- Division of Microbiology, Langen, Germany.,Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
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9
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Cheng W, Wang H, Zhang J, Bai G, Han W, Chen J, Cui N. Lymphocyte subset counts as diagnostic and prognostic markers for carbapenem-resistant Enterobacteriaceae (CRE) infection in critically ill patients. Int J Infect Dis 2020; 96:315-322. [PMID: 32389844 DOI: 10.1016/j.ijid.2020.04.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/07/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES This study investigated the use of lymphocyte subset counts as diagnostic and prognostic markers for carbapenem-resistant Enterobacteriaceae (CRE) infection. METHODS We assessed the lymphocyte subset populations and other clinical parameters of septic patients upon intensive care unit (ICU) admission, and evaluated their potential impact on CRE infection diagnosis and outcome. RESULTS Among 373 septic patients, 51 were diagnosed with CRE infection. The 28-day mortality was significantly higher in CRE than non-CRE patients (35.3% vs 14.9%). The T lymphocyte count and CD4+CD28+ T cell count were both independent risk factors for CRE infection, with the latter had the best diagnostic ability (AUC: 0.908; p < 0.0001). Lower CD4+CD28+ T cell counts were associated with higher likelihoods of CRE infection. The CRE incidence and 28-day mortality of CRE-infected patients could be predicted using cutoff values of 242 (sensitivity: 83.9%; specificity: 87.5%) and 58.5 (sensitivity: 100%; specificity: 61.1%) CD4+CD28+ T cells/μl at ICU admission, respectively. CONCLUSIONS Septic patients with CRE infection had higher 28-day mortality. Given that the CD4+CD28+ T cell count was significantly lower in CRE than non-CRE septic patients and a lower cell count was significantly associated with higher 28-day mortality, CD4+CD28+ T cell counts may be useful markers for early diagnosis of CRE infection and outcome prediction.
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Affiliation(s)
- Wei Cheng
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Hao Wang
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Jiahui Zhang
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Guangxu Bai
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Wen Han
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Jianwei Chen
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China
| | - Na Cui
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing 100730, China.
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10
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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11
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Dar HA, Zaheer T, Shehroz M, Ullah N, Naz K, Muhammad SA, Zhang T, Ali A. Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae. Vaccines (Basel) 2019; 7:E88. [PMID: 31409021 PMCID: PMC6789656 DOI: 10.3390/vaccines7030088] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.
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Affiliation(s)
- Hamza Arshad Dar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Tahreem Zaheer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Muhammad Shehroz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Nimat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
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12
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Bengoechea JA, Sa Pessoa J. Klebsiella pneumoniae infection biology: living to counteract host defences. FEMS Microbiol Rev 2019; 43:123-144. [PMID: 30452654 PMCID: PMC6435446 DOI: 10.1093/femsre/fuy043] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/16/2018] [Indexed: 12/26/2022] Open
Abstract
Klebsiella species cause a wide range of diseases including pneumonia, urinary tract infections (UTIs), bloodstream infections and sepsis. These infections are particularly a problem among neonates, elderly and immunocompromised individuals. Klebsiella is also responsible for a significant number of community-acquired infections. A defining feature of these infections is their morbidity and mortality, and the Klebsiella strains associated with them are considered hypervirulent. The increasing isolation of multidrug-resistant strains has significantly narrowed, or in some settings completely removed, the therapeutic options for the treatment of Klebsiella infections. Not surprisingly, this pathogen has then been singled out as an 'urgent threat to human health' by several organisations. This review summarises the tremendous progress that has been made to uncover the sophisticated immune evasion strategies of K. pneumoniae. The co-evolution of Klebsiella in response to the challenge of an activated immune has made Klebsiella a formidable pathogen exploiting stealth strategies and actively suppressing innate immune defences to overcome host responses to survive in the tissues. A better understanding of Klebsiella immune evasion strategies in the context of the host-pathogen interactions is pivotal to develop new therapeutics, which can be based on antagonising the anti-immune strategies of this pathogen.
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Affiliation(s)
- José A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Joana Sa Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
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13
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Riquelme SA, Ahn D, Prince A. Pseudomonas aeruginosa and Klebsiella pneumoniae Adaptation to Innate Immune Clearance Mechanisms in the Lung. J Innate Immun 2018; 10:442-454. [PMID: 29617698 PMCID: PMC6785651 DOI: 10.1159/000487515] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/02/2023] Open
Abstract
Many different species of gram-negative bacteria are associated with infection in the lung, causing exacerbations of chronic obstructive pulmonary disease, cystic fibrosis (CF), and ventilator-associated pneumonias. These airway pathogens must adapt to common host clearance mechanisms that include killing by antimicrobial peptides, antibiotics, oxidative stress, and phagocytosis by leukocytes. Bacterial adaptation to the host is often evident phenotypically, with increased extracellular polysaccharide production characteristic of some biofilm-associated organisms. Given the relatively limited repertoire of bacterial strategies to elude airway defenses, it seems likely that organisms sharing the same ecological niche might also share common strategies to persistently infect the lung. In this review, we will highlight some of the major factors responsible for the adaptation of Pseudomonas aeruginosa to the lung, addressing how growth in biofilms enables persistent infection, relevant to, but not limited to, the pathogenesis of infection in CF. In contrast, we will discuss how carbapenem-resistant Klebsiella pneumoniae evade immune clearance, an organism often associated with ventilator-associated pneumonia and health-care-acquired pneumonias, but not a typical pathogen in CF.
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Affiliation(s)
| | | | - Alice Prince
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
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