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Liu Y, Wang R, Yuan Y, Zhao C, Wang Q, Wang Y, Zhang X, Wang B. Comparison of targeted next-generation sequencing and traditional microbial culture in the diagnosis of pulmonary infections. Diagn Microbiol Infect Dis 2024; 110:116534. [PMID: 39276718 DOI: 10.1016/j.diagmicrobio.2024.116534] [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: 05/31/2024] [Revised: 08/14/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
This study investigated the diagnostic potential of targeted next-generation sequencing (tNGS) for pulmonary infections. The positivity rate of tNGS was significantly higher than that of traditional microbial culture (92.6 % vs 25.2 %, χ2 = 378.272, P < 0.001). The proportion of two or more species of pathogens detected using tNGS exceeded that detected using microbial culture (χ2 = 337.283, P < 0.001). There were inconsistencies between the results of the tNGS antibiotic resistance gene and the drug susceptibility test resistance phenotype. The tNGS technique demonstrates rapid and effective capabilities in identifying bacteria, fungi, viruses, and specific pathogens, with a detection sensitivity that surpasses that of conventional culture methodologies. Microbial drug resistance genotypes detected by tNGS cannot accurately predict drug resistance phenotypes and require further improvement or integration with traditional microbial culture to establish a foundation for effective clinical treatment.
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Affiliation(s)
- Yongyan Liu
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang 464300, PR China; Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Ruijie Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Youhua Yuan
- Department of Clinical Microbiology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, and People's Hospital of Henan University, Weiwu Road 5, Zhengzhou, Henan 450003, PR China
| | - Chen Zhao
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang 464300, PR China
| | - Qian Wang
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang 464300, PR China
| | - Yujie Wang
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang 464300, PR China
| | - Xi Zhang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Baoya Wang
- Department of Clinical Microbiology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, and People's Hospital of Henan University, Weiwu Road 5, Zhengzhou, Henan 450003, PR China.
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Zhang X, Ye J, Wang L, Zhang L, Wang L, Jin H. Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia. Infect Drug Resist 2024; 17:3659-3667. [PMID: 39205800 PMCID: PMC11352510 DOI: 10.2147/idr.s475861] [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: 04/27/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China. Patients and Methods From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People's Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared. Results The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time. Conclusion Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.
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Affiliation(s)
- Xiyue Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Jian Ye
- Department of Respiratory Medicine, Zhejiang Hospital, Hangzhou, People’s Republic of China
| | - Limin Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liuhai Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liusheng Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Hualiang Jin
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
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Herman EK, Lacoste SR, Freeman CN, Otto SJG, McCarthy EL, Links MG, Stothard P, Waldner CL. Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle. Front Microbiol 2024; 15:1386319. [PMID: 38779502 PMCID: PMC11110911 DOI: 10.3389/fmicb.2024.1386319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples. Methods This pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing. Results Non-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads. Discussion By increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.
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Affiliation(s)
- Emily K. Herman
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stacey R. Lacoste
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - E. Luke McCarthy
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew G. Links
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Stothard
- Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Zhao M, Zhang Y, Chen L, Yan X, Xu T, Fu M, Han Y, Zhang Y, Zhang B, Cao J, Lin J, Shen D, Li S, Zhu C, Zhao W. Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario. Front Cell Infect Microbiol 2024; 14:1330788. [PMID: 38352054 PMCID: PMC10861792 DOI: 10.3389/fcimb.2024.1330788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Infectious diseases are major causes of morbidity and mortality worldwide, necessitating the rapid identification and accurate diagnosis of pathogens. While unbiased metagenomic next-generation sequencing (mNGS) has been extensively utilized in clinical pathogen identification and scientific microbiome detection, there is limited research about the application of nanopore platform-based mNGS in the diagnostic performance of various infectious fluid samples. Methods In this study, we collected 297 suspected infectious fluids from 10 clinical centers and detected them with conventional microbiology culture and nanopore platform-based mNGS. The objective was to assess detective and diagnostic performance of nanopore-sequencing technology (NST) in real-world scenarios. Results Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts. For samples collected from initially sterile body sites, the detected microorganisms were highly suspected pathogens, and the negative predictive agreements were relatively higher than those in the microbial-colonized sites, particularly with 100% in abscess and 95.7% in cerebrospinal fluid. Furthermore, consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii. Discussion Rapid NST is a promising clinical tool to supplement gold-standard culture, and it has the potential improve patient prognosis and facilitate clinical treatment of infectious diseases.
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Affiliation(s)
- Manna Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yongyang Zhang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Li Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xuebing Yan
- Department of Infectious Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tianmin Xu
- Department of Infectious Diseases, The Third People’s Hospital of Changzhou, Changzhou, Jiangsu, China
| | - Maoying Fu
- Infectious Diseases Department, Kunshan First People’s Hospital, Kunshan, Jiangsu, China
| | - Yangguang Han
- Department of Infectious Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ying Zhang
- Department of Infection Medicine, The Fifth People’s Hospital of Wuxi, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Bin Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Juan Cao
- Emergency Department, Shanghai Shibei Hospital, Shanghai, China
| | - Jing Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dan Shen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Shuo Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
- Medical Department, Nanjing Dian Diagnostics Group Co., Ltd., Nanjing, Jiangsu, China
| | - Chuanlong Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weifeng Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Coșeriu RL, Mare AD, Toma F, Vintilă C, Ciurea CN, Togănel RO, Cighir A, Simion A, Man A. Uncovering the Resistance Mechanisms in Extended-Drug-Resistant Pseudomonas aeruginosa Clinical Isolates: Insights from Gene Expression and Phenotypic Tests. Microorganisms 2023; 11:2211. [PMID: 37764055 PMCID: PMC10535578 DOI: 10.3390/microorganisms11092211] [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: 07/20/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: The purpose of the study was to describe the activity of mex efflux pumps in Multidrug-Resistant (MDR) clinical isolates of Pseudomonas aeruginosa and to compare the carbapenem-resistance identification tests with PCR; (2) Methods: Sixty MDR P. aeruginosa were analyzed for detection of carbapenemase by disk diffusion inhibitory method, carbapenem inactivation method and Modified Hodge Test. Endpoint PCR was used to detect 7 carbapenemase genes (blaKPC, blaOXA48-like, blaNDM, blaGES-2, blaSPM, blaIMP, blaVIM) and mcr-1 for colistin resistance. The expression of mexA, mexB, mexC, mexE and mexX genes corresponding to the four main efflux pumps was also evaluated; (3) Results: From the tested strains, 71.66% presented at least one carbapenemase gene, with blaGES-2 as the most occurring gene (63.3%). Compared with the PCR, the accuracy of phenotypic tests did not exceed 25% for P. aeruginosa. The efflux pump genes were present in all strains except one. In 85% of the isolates, an overactivity of mexA, mexB and mostly mexC was detected. Previous treatment with ceftriaxone increased the activity of mexC by more than 160 times; (4) Conclusions: In our MDR P. aeruginosa clinical isolates, the carbapenem resistance is not accurately detected by phenotypic tests, due to the overexpression of mex efflux pumps and in a lesser amount, due to carbapenemase production.
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Affiliation(s)
- Răzvan Lucian Coșeriu
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania
| | - Anca Delia Mare
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
| | - Felicia Toma
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
| | - Camelia Vintilă
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania
| | - Cristina Nicoleta Ciurea
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
| | - Radu Ovidiu Togănel
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania
| | - Anca Cighir
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania
| | - Anastasia Simion
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania
| | - Adrian Man
- Department of Microbiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology Târgu Mureș, 540142 Târgu Mures, Romania; (R.L.C.); (F.T.); (C.V.); (C.N.C.); (R.O.T.); (A.C.); (A.S.); (A.M.)
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Alnimr A. Antimicrobial Resistance in Ventilator-Associated Pneumonia: Predictive Microbiology and Evidence-Based Therapy. Infect Dis Ther 2023:10.1007/s40121-023-00820-2. [PMID: 37273072 DOI: 10.1007/s40121-023-00820-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023] Open
Abstract
Ventilator-associated pneumonia (VAP) is a serious intensive care unit (ICU)-related infection in mechanically ventilated patients that is frequent, as more than half of antibiotics prescriptions in ICU are due to VAP. Various risk factors and diagnostic criteria for VAP have been referred to in different settings. The estimated attributable mortality of VAP can go up to 50%, which is higher in cases of antimicrobial-resistant VAP. When the diagnosis of pneumonia in a mechanically ventilated patient is made, initiation of effective antimicrobial therapy must be prompt. Microbiological diagnosis of VAP is required to optimize timely therapy since effective early treatment is fundamental for better outcomes, with controversy continuing regarding optimal sampling and testing. Understanding the role of antimicrobial resistance in the context of VAP is crucial in the era of continuously evolving antimicrobial-resistant clones that represent an urgent threat to global health. This review is focused on the risk factors for antimicrobial resistance in adult VAP and its novel microbiological tools. It aims to summarize the current evidence-based knowledge about the mechanisms of resistance in VAP caused by multidrug-resistant bacteria in clinical settings with focus on Gram-negative pathogens. It highlights the evidence-based antimicrobial management and prevention of drug-resistant VAP. It also addresses emerging concepts related to predictive microbiology in VAP and sheds lights on VAP in the context of coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Amani Alnimr
- Department of Microbiology, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia.
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Li J, Zhang L, Yang X, Wang P, Feng L, Guo E, Chen Y. Diagnostic Significance of Targeted Next-Generation Sequencing in Central Nervous System Infections in Neurosurgery of Pediatrics. Infect Drug Resist 2023; 16:2227-2236. [PMID: 37090034 PMCID: PMC10115197 DOI: 10.2147/idr.s404277] [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: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023] Open
Abstract
Background Cerebrospinal fluid (CSF) pathogen culture suffers from the drawbacks of prolonged cycle time and a low positivity rate in diagnosing intracranial infections in children. This study aims to investigate the diagnostic potential of targeted next-generation sequencing (tNGS) in pediatric neurosurgery for central nervous system (CNS) infections. Methods A retrospective study was conducted on children under 14 with suspected intracranial infections following craniocerebral trauma or surgery between November 2018 and August 2020. Routine, biochemical, smear, and pathogen culture tests were performed on CSF during treatment. The main parameters of CSF analysis encompassed white blood cells (WBC, ×106/L) count, percentage of multinucleated cells (%), protein levels (g/L), glucose concentration (GLU, mmol/L), chloride levels (mmol/L), and pressure (mmH2O). The outcomes of tNGS were assessed through the Receiver Operating Characteristic (ROC) curve and pertinent diagnostic parameters. Results Among the 35 included pediatric patients, 22 were clinically diagnosed with CNS infection in neurosurgery, tNGS was confirmed in 18 cases. The sensitivity and specificity of tNGS were 81.8% and 76.9%, respectively, while the traditional method of CSF cultures and smears exhibited a sensitivity of 13.6% and a specificity of 100%. ROC curve analysis indicated an area under the curve (AUC) of 0.794 for tNGS and 0.568 for the CSF cultures and smears. CSF analysis indicated that the two groups exhibited statistically significant differences in terms of WBC count [330.0 (110.00-2639.75) vs 14.00 (4.50-26.50), P<0.001] and percentage of multinuclear cells (%) [87.50 (39.75-90.00) vs 0 (0-10.00), P<0.001]. However, the remaining parameters did not statistically significant differences between the groups (all P>0.05). Conclusion tNGS demonstrates a high degree of diagnostic accuracy when detecting infections within the CNS of pediatric neurosurgery patients. tNGS can effectively establish for diagnosing CNS infections by detecting pathogenic microorganisms and their corresponding virulence and/or resistance genes within the test samples.
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Affiliation(s)
- Jihong Li
- Department of Laboratory Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Lili Zhang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Xiaohui Yang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Pan Wang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Lijie Feng
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Erkun Guo
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
| | - Yuan Chen
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People’s Republic of China
- Correspondence: Yuan Chen, Department of Pediatrics, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, 050000, Hebei, People’s Republic of China, Tel +86-311-66002936, Email
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