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Sun Y, Chen F, Ma H, Wang D, Wang D, Zhang J, Jiang Z, Xia R, Tian T, Zhang W. Exploring the immune characteristions of CRKP pneumonia at single-cell level. Comput Biol Med 2024; 177:108574. [PMID: 38772102 DOI: 10.1016/j.compbiomed.2024.108574] [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: 12/14/2023] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
The immune dysregulation associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) severity was investigated through single-cell RNA sequencing (scRNA-seq) of 5 peripheral blood samples from 3 patients with moderate and severe CRKP pneumonia. Additionally, scRNA-seq datasets from two individuals with COVID-19 were included for comparative analysis. The dynamic characterization and functional properties of each immune cell type were examined by delineating the transcriptional profiles of immune cells throughout the transition from moderate to severe conditions. Overall, most immune cells in CRKP patients exhibited a robust interferon-α response and inflammatory reaction compared to healthy controls, mirroring observations in COVID-19 patients. Furthermore, cell signatures associated with NK cells, macrophages, and monocytes were identified in CRKP progression including PTPRCAP for NK cells, C1QB for macrophages, and S100A12 for both macrophages and monocytes. In summary, this study offers a comprehensive scRNA-seq resource for illustrating the dynamic immune response patterns during CRKP progression, thereby shedding light on the associations between CRKP and COVID-19.
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Affiliation(s)
- Yajiao Sun
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Fuhui Chen
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Hui Ma
- Department of Respiratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315500, China
| | - Dongjie Wang
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Dong Wang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Jingwen Zhang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhe Jiang
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Rongyao Xia
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Tian Tian
- Department of Respiratory Medicine, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wei Zhang
- Department of Respiratory Medicine, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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Chen Q, Hou K, Tang M, Ying S, Zhao X, Li G, Pan J, He X, Xia H, Li Y, Lou Z, Zhang L. Screening of potential microbial markers for lung cancer using metagenomic sequencing. Cancer Med 2022; 12:7127-7139. [PMID: 36480163 PMCID: PMC10067086 DOI: 10.1002/cam4.5513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/12/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Lung cancer is the most prevalent cancer with high mortality in China, and it is associated with the dysbiosis of the lung microbiome. This study attempted to screen for specific microorganisms as potential biomarkers for distinguishing benign lung disease from lung cancer. METHODS Bronchoalveolar lavage fluid (BALF) sample was selected in the study instead of saliva to avoid contamination with oral microorganisms, and microbial taxonomic and functional differences in BALF samples from patients with lung cancer and those with those from patients with benign lung diseases were performed based on metagenomic next-generation sequencing, for the first time, so that microorganisms other than bacteria could be included. RESULTS The results showed that the intrasample diversity of malignant samples was different from benign samples, and the microbial differences among malignant samples were smaller, with lower microbial diversity, significantly changed microbial abundance and metabolic functions. Metabolic function analysis revealed amino acid-related metabolism was more prevalent in benign samples, whereas carbohydrate-related metabolism was more prevalent in malignant samples. By LEfSe, Metastat and Random Forest analysis, we identified a series of important differential microorganisms. Importantly, the model combining five key genera plus one tumor marker (neuron-specific enolase) as indicators presented the optimal disease typing performance. CONCLUSION Thus results suggest the value of these differential microorganisms enriched in tumors in mechanism research and may be potential new targets for lung cancer therapy. More importantly, the biomarkers identified in this study can be conducive to improve the clinical diagnosis of lung cancer and have good application prospects.
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Affiliation(s)
| | - Kai Hou
- Tianjin Chest Hospital Tianjin China
- Tianjin Medical University Tianjin China
| | | | - Shuo Ying
- Tianjin Chest Hospital Tianjin China
| | | | | | | | | | - Han Xia
- Hugobiotech Co., Ltd. Beijing China
| | | | | | - Li Zhang
- Tianjin Chest Hospital Tianjin China
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Vega S, Acosta F, Landires I, Morán M, Gonzalez J, Pimentel-Peralta G, Núñez-Samudio V, Goodridge A. Phenotypic and genotypic characteristics of carbapenemase- and extended spectrum β-lactamase-producing Klebsiella pneumoniae ozaenae clinical isolates within a hospital in Panama City. Ther Adv Infect Dis 2021; 8:20499361211054918. [PMID: 34733509 PMCID: PMC8558783 DOI: 10.1177/20499361211054918] [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: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae spp ozaenae is a versatile bacterial species able to acquire antimicrobial resistance; the species presents a higher antimicrobial resistance profile compared to Klebsiella pneumoniae spp pneumoniae. Carbapenemase and extended spectrum β-lactamase (ESBL)-producing bacteria commonly arise in clinical settings where antimicrobial stewardship is limited. Our study aims to report the phenotypical and genetic characteristics of nosocomial Klebsiella pneumoniae spp ozaenae isolates associated with mortality collected from a tertiary-level hospital in Panama City. In October 2020, 11 consecutive multidrug-resistant Gram-negative isolates were recovered from secretions and blood cultures from hospitalized patients. Nearly 90% (10/11) of these patients died, and bacteria was obtained from six patients for investigation. Biochemical evaluation of the six isolates revealed the presence of multidrug-resistant Klebsiella pneumoniae spp ozaenae. Phenotypic evaluation indicated resistance to carbapenemase and EBSL. In contrast, genetic evaluation by PCR showed that only 30% (2/6) were resistant to CTX-M-1 (CTX-M group 1), whereas 60.7% (4/6) presented carbapenemase resistance genes, and 33.3% (2/6) presented New Delhi metallo-β-lactamase (NDM) resistance genes. Klebsiella pneumoniae ST258 was identified in 83.3% (5/6) of the isolates. Phylogenetic analysis using 16S revealed low homology among the six isolates. These results suggest that antibiotic resistance genes may have been incorporated into these Klebsiella pneumoniae spp ozaenae isolates within the hospital environment. We recommend strengthening the antimicrobial stewardship program and antibiotic control policy, as well as heightened infection control and prevention measures, such as ward sanitation and increased hand washing frequency.
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Affiliation(s)
- Silvio Vega
- Laboratorio Clínico, Complejo Hospitalario Metropolitano Dr. Arnulfo Arias Madrid, Caja de Seguro Social (CHMDrAAM-CSS), Panama City, Panama
| | - Fermín Acosta
- Tuberculosis Biomarker Research Unit at Centro de Biología Molecular y Celular de Enfermedades (CBCME) del Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama
| | | | - Mitchelle Morán
- Tuberculosis Biomarker Research Unit at Centro de Biología Molecular y Celular de Enfermedades (CBCME) del Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama
| | - Johanna Gonzalez
- Laboratorio Clínico, Complejo Hospitalario Metropolitano Dr. Arnulfo Arias Madrid, Caja de Seguro Social (CHMDrAAM-CSS), Panama City, Panama
| | | | | | - Amador Goodridge
- Tuberculosis Biomarker Research Unit, Centro de Biología Molecular y Celular de Enfermedades (CBCME) del Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, City of Knowledge, Panama
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Nanayakkara AK, Boucher HW, Fowler VG, Jezek A, Outterson K, Greenberg DE. Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward. CA Cancer J Clin 2021; 71:488-504. [PMID: 34546590 DOI: 10.3322/caac.21697] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infection is the second leading cause of death in patients with cancer. Loss of efficacy in antibiotics due to antibiotic resistance in bacteria is an urgent threat against the continuing success of cancer therapy. In this review, the authors focus on recent updates on the impact of antibiotic resistance in the cancer setting, particularly on the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). This review highlights the health and financial impact of antibiotic resistance in patients with cancer. Furthermore, the authors recommend measures to control the emergence of antibiotic resistance, highlighting the risk factors associated with cancer care. A lack of data in the etiology of infections, specifically in oncology patients in United States, is identified as a concern, and the authors advocate for a centralized and specialized surveillance system for patients with cancer to predict and prevent the emergence of antibiotic resistance. Finding better ways to predict, prevent, and treat antibiotic-resistant infections will have a major positive impact on the care of those with cancer.
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Affiliation(s)
- Amila K Nanayakkara
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Amanda Jezek
- Infectious Diseases Society of America, Arlington, Virginia
| | - Kevin Outterson
- CARB-X, Boston, Massachusetts
- Boston University School of Law, Boston, Massachusetts
| | - David E Greenberg
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
- Department of Microbiology, University of Texas Southwestern, Dallas, Texas
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Huo GW, Zuo R, Song Y, Chen WD, Chen WM, Chong DQ, Zhang HM, Jia SS, Chen P. Effect of antibiotic use on the efficacy of nivolumab in the treatment of advanced/metastatic non-small cell lung cancer: A meta-analysis. Open Med (Wars) 2021; 16:728-736. [PMID: 34013044 PMCID: PMC8114955 DOI: 10.1515/med-2021-0272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
This study evaluates the impact of the use of antibiotics on the effectiveness of nivolumab in the treatment of advanced/metastatic non-small cell lung cancer (NSCLC). A literature search was conducted in various electronic databases to identify studies, which evaluated the impact of antibiotic use on the survival of patients with advanced/metastatic NSCLC who have been treated with nivolumab. Six studies, comprising a total of 787 patients with 37.2% females and of age range 30–90 years, were included in the study. A lack of smoking history was reported in 14.4% of the patients. A meta-analysis was conducted in 678 and 713 patients for PFS and OS, respectively. The pooled HR was 1.95 (95% CI: 1.13–3.37, P = 0.016) for PFS and 2.70 (95% CI: 1.81–4.02, P < 0.001) for OS. Among patients exposed to antibiotics, the median PFS and OS were reduced by 1.6 months (95% CI: 1.5–1.7) and 8.8 months (95% CI: 8.5–9.1), respectively. Our study indicates that, among patients with advanced/metastatic NSCLC, the use of antibiotics with nivolumab led to a decrease in the median OS by more than 8 months. Studying the mechanism of the effect of antibiotics on the efficacy of nivolumab in patients with NSCLC should also be prioritized.
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Affiliation(s)
- Geng-Wei Huo
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Lung Cancer Diagnosis and Treatment Center, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Ran Zuo
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Lung Cancer Diagnosis and Treatment Center, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Ying Song
- Department of Pharmacy, Jining No. 1 people's Hospital, Jining 272000, Shandong, China
| | - Wei-Dong Chen
- Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Wen-Ming Chen
- Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Dao-Qun Chong
- Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Hong-Mei Zhang
- Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Sha-Sha Jia
- Department of Oncology, Jining No. 1 People's Hospital, Jining 272000, Shandong, China
| | - Peng Chen
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Lung Cancer Diagnosis and Treatment Center, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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Microbiota Biomarkers for Lung Cancer. Diagnostics (Basel) 2021; 11:diagnostics11030407. [PMID: 33673596 PMCID: PMC7997424 DOI: 10.3390/diagnostics11030407] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the number one cancer killer and its early detection can reduce mortality. Accumulating evidences suggest an etiopathogenic role of microorganisms in lung tumorigenesis. Certain bacteria are found to be associated with NSCLC. Herein we evaluated the potential use of microbiome as biomarkers for the early detection of NSCLC. We used droplet digital PCR to analyze 25 NSCLC-associated bacterial genera in 31 lung tumor and the paired noncancerous lung tissues and sputum of 17 NSCLC patients and ten cancer-free smokers. Of the bacterial genera, four had altered abundances in lung tumor tissues, while five were aberrantly abundant in sputum of NSCLC patients compared with their normal counterparts (all p < 0.05). Acidovorax and Veillonella were further developed as a panel of sputum biomarkers that could diagnose lung squamous cell carcinoma (SCC) with 80% sensitivity and 89% specificity. The use of Capnocytophaga as a sputum biomarker identified lung adenocarcinoma (AC) with 72% sensitivity and 85% specificity. The use of Acidovorax as a sputum biomarker had 63% sensitivity and 96% specificity for distinguishing between SCC and AC, the two major types of NSCLC. The sputum biomarkers were further validated for the diagnostic values in a different cohort of 69 NSCLC cases and 79 cancer-free controls. Sputum microbiome might provide noninvasive biomarkers for the early detection and classification of NSCLC.
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Yang Z, Sun Q, Chen S, Ding S, Zhang R, Zhu K. Genomic and Phenotypic Analysis of Persistent Carbapenem-Resistant Klebsiella pneumoniae Isolates from a 5-Year Hospitalized Patient. Microb Drug Resist 2020; 27:1117-1125. [PMID: 33370221 DOI: 10.1089/mdr.2020.0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emerging epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health crisis. However, the phylogenetic affiliation and pathotypic status of CRKP strains in the host colonization period under consistent antibiotic treatments are not well characterized. In this study, a 5-year tracking study was performed, in which a patient admitted to an intensive care unit was recruited and then screened for the carriage of CRKP based on microbiological culture. Nine isolates from the sputum or stool samples were acquired and subjected to real-time whole-genome sequencing, antimicrobial susceptibility testing, Galleria mellonella larval infection, and epithelial cell invasion assay. All nine isolates showed phenotypic resistance to carbapenems, quinolones, and aminoglycosides. Altogether, blaKPC-2 and 10 other antibiotic resistance genes were identified and all nine CRKP isolates exhibited low virulence with more than 38 virulence factors. All but one variant belonged to ST11 with a novel sequence type, differing at the phoE locus. The isolates shared the same plasmid replicon type, prophages, and capsular serotype (K47) with few single-nucleotide polymorphism variations, consistent with epidemiological clones. Furthermore, these CRKP isolates displayed the ability of moderate invasion of lung epithelial cells. Meanwhile, a deficiency of chromosomal type IV secretion system-related gene cluster was detected after 2 years of carriage. Our findings demonstrated that low-virulence CRKP clones could colonize in the gut and respiratory tract under multiple antibiotic stresses, suggesting the strong colonization adaptability of CRKP to the host. Ethical approval was given by The Second Affiliated Hospital of Zhejiang University, School of Medicine, (2018-039).
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Affiliation(s)
- Zhiqiang Yang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Shang Chen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuangyang Ding
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rong Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Kui Zhu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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