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Liu A, Liu S, Lv K, Zhu Q, Wen J, Li J, Liang C, Huang X, Gong C, Sun Q, Gu H. Rapid detection of multidrug resistance in tuberculosis using nanopore-based targeted next-generation sequencing: a multicenter, double-blind study. Front Microbiol 2024; 15:1349715. [PMID: 38495513 PMCID: PMC10940340 DOI: 10.3389/fmicb.2024.1349715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Background Resistance to anti-tuberculous drugs is a major challenge in the treatment of tuberculosis (TB). We aimed to evaluate the clinical availability of nanopore-based targeted next-generation sequencing (NanoTNGS) for the diagnosis of drug-resistant tuberculosis (DR-TB). Methods This study enrolled 253 patients with suspected DR-TB from six hospitals. The diagnostic efficacy of NanoTNGS for detecting Mycobacterium tuberculosis and its susceptibility or resistance to first- and second-line anti-tuberculosis drugs was assessed by comparing conventional phenotypic drug susceptibility testing (pDST) and Xpert MTB/RIF assays. NanoTNGS can be performed within 12 hours from DNA extraction to the result delivery. Results NanoTNGS showed a remarkable concordance rate of 99.44% (179/180) with the culture assay for identifying the Mycobacterium tuberculosis complex. The sensitivity of NanoTNGS for detecting drug resistance was 93.53% for rifampicin, 89.72% for isoniazid, 85.45% for ethambutol, 74.00% for streptomycin, and 88.89% for fluoroquinolones. Specificities ranged from 83.33% to 100% for all drugs tested. Sensitivity for rifampicin-resistant tuberculosis using NanoTNGS increased by 9.73% compared to Xpert MTB/RIF. The most common mutations were S531L (codon in E. coli) in the rpoB gene, S315T in the katG gene, and M306V in the embB gene, conferring resistance to rifampicin, isoniazid, and ethambutol, respectively. In addition, mutations in the pncA gene, potentially contributing to pyrazinamide resistance, were detected in 32 patients. Other prevalent variants, including D94G in the gyrA gene and K43R in the rpsL gene, conferred resistance to fluoroquinolones and streptomycin, respectively. Furthermore, the rv0678 R94Q mutation was detected in one sample, indicating potential resistance to bedaquiline. Conclusion NanoTNGS rapidly and accurately identifies resistance or susceptibility to anti-TB drugs, outperforming traditional methods. Clinical implementation of the technique can recognize DR-TB in time and provide guidance for choosing appropriate antituberculosis agents.
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Affiliation(s)
- Aimei Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Sang Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Kangyan Lv
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingdong Zhu
- Department of Tuberculosis, The Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jun Wen
- Department of Pulmonary Medicine, The Third People's Hospital of Guilin, Guilin, Guangxi, China
| | - Jianpeng Li
- Department of Pulmonary Medicine, The Third People's Hospital of Wuzhou, Wuzhou, Guangxi, China
| | - Chengyuan Liang
- Department of Infectious Diseases, The People's Hospital of Baise, Baise, Guangxi, China
| | - Xuegang Huang
- Department of Infectious Diseases, The First People's Hospital of Fangchenggang, Fangchenggang, Guangxi, China
| | - Chunming Gong
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingfeng Sun
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
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Buendia P, Fernandez K, Raley C, Rahnavard A, Crandall KA, Castro JG. Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics. Front Microbiol 2024; 15:1346762. [PMID: 38476940 PMCID: PMC10927822 DOI: 10.3389/fmicb.2024.1346762] [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: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA). Methods The saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received. Results Our study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis. Discussion Our results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient's salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.
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Affiliation(s)
| | | | - Castle Raley
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Ali Rahnavard
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Keith A. Crandall
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Jose Guillermo Castro
- Division of Infectious Diseases, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
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Ferguson BD. Toward Better Prediction of Postpancreatectomy Hemorrhage. JAMA Netw Open 2023; 6:e2346069. [PMID: 38055282 DOI: 10.1001/jamanetworkopen.2023.46069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
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Droogh DHM, van Dam JL, Groen JV, de Boer MGJ, van Prehn J, van Eijck CHJ, Bonsing BA, Vahrmeijer AL, Groot Koerkamp B, Mieog JSD. Prolonged antibiotics after pancreatoduodenectomy reduce abdominal infections in patients with positive bile cultures: a dual-center cohort study. HPB (Oxford) 2023; 25:1056-1064. [PMID: 37268503 DOI: 10.1016/j.hpb.2023.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/07/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Abdominal infections account for substantial morbidity after pancreatoduodenectomy. Contaminated bile is the presumed main risk factor, and prolonged antibiotic prophylaxis might prevent these complications. This study compared organ/space infection (OSIs) rates in patients receiving perioperative versus prolonged antibiotic prophylaxis after pancreatoduodenectomy. METHODS Patients undergoing pancreatoduodenectomy in two Dutch centers between 2016 and 2019 were included. Perioperative prophylaxis was compared prolonged prophylaxis (cefuroxime and metronidazole for five days). The primary outcome was an isolated OSI: an abdominal infection without concurrent anastomotic leakage. Odds ratios (OR) were adjusted for surgical approach and pancreatic duct diameter. RESULTS OSIs occurred in 137 out of 362 patients (37.8%): 93 patients with perioperative and 44 patients with prolonged prophylaxis (42.5% versus 30.8%, P = 0.025). Isolated OSIs occurred in 38 patients (10.5%): 28 patients with perioperative and 10 patients with prolonged prophylaxis (12.8% versus 7.0%, P = 0.079). Bile cultures were obtained in 198 patients (54.7%). Patients with positive bile cultures showed higher isolated OSI rates with perioperative compared to prolonged prophylaxis (18.2% versus 6.6%, OR 5.7, 95% CI: 1.3-23.9). CONCLUSION Prolonged antibiotics after pancreatoduodenectomy are associated with fewer isolated OSIs in patients with contaminated bile and warrant confirmation in a randomised controlled trial (Clinicaltrials.gov NCT0578431).
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Affiliation(s)
- Daphne H M Droogh
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jacob L van Dam
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Jesse V Groen
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mark G J de Boer
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Bert A Bonsing
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander L Vahrmeijer
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - J Sven D Mieog
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, the Netherlands
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Liu M, Li J, Tan CS. Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End. BIOSENSORS 2023; 13:598. [PMID: 37366963 DOI: 10.3390/bios13060598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.
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Affiliation(s)
- Miao Liu
- Medical College, Tianjin University, Tianjin 300072, China
| | - Junyang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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Zhang H, Wang M, Han X, Wang T, Lei Y, Rao Y, Xu P, Wang Y, Gu H. The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections. Front Microbiol 2022; 13:1065159. [PMID: 36620015 PMCID: PMC9822541 DOI: 10.3389/fmicb.2022.1065159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance. Methods This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics. Results At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla TEM (n = 29), followed by bla SHV (n = 4), bla KPC (n = 2), bla CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens. Conclusion TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.
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Affiliation(s)
- Hongying Zhang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China,*Correspondence: Hongying Zhang ✉
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ximei Han
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Ting Wang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Yanjuan Lei
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yu Rao
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Peisong Xu
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yunfei Wang
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,Graduate School, University of Science and Technology of China, Hefei, China,Hongcang Gu ✉
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Cheng H, Sun Y, Yang Q, Deng M, Yu Z, Zhu G, Qu J, Liu L, Yang L, Xia Y. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method. Brief Bioinform 2022; 23:6762743. [PMID: 36259361 DOI: 10.1093/bib/bbac453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022] Open
Abstract
Metagenomic sequencing analysis (mNGS) has been implemented as an alternative approach for pathogen diagnosis in recent years, which is independent of cultivation and is able to identify all potential antibiotic resistance genes (ARGs). However, current mNGS methods have to deal with low amounts of prokaryotic deoxyribonucleic acid (DNA) and high amounts of host DNA in clinical samples, which significantly decrease the overall microbial detection resolution. The recently released nanopore adaptive sampling (NAS) technology facilitates immediate mapping of individual nucleotides to a given reference as each molecule is sequenced. User-defined thresholds allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. We developed a metagenomics workflow for ultra-sensitive diagnosis of bacterial pathogens and ARGs from clinical samples, which is based on the efficient selective 'human host depletion' NAS sequencing, real-time species identification and species-specific resistance gene prediction. Our method increased the microbial sequence yield at least 8-fold in all 21 sequenced clinical Bronchoalveolar Lavage Fluid (BALF) samples (4.5 h from sample to result) and accurately detected the ARGs at species level. The species-level positive percent agreement between metagenomic sequencing and laboratory culturing was 100% (16/16) and negative percent agreement was 100% (5/5) in our approach. Further work is required for a more robust validation of our approach with large sample size to allow its application to other infection types.
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Affiliation(s)
- Hang Cheng
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Qing Yang
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Minggui Deng
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Zhijian Yu
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Gang Zhu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiuxin Qu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Lei Liu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
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The Notable Achievements and the Prospects of Bacterial Pathogen Genomics. Microorganisms 2022; 10:microorganisms10051040. [PMID: 35630482 PMCID: PMC9148168 DOI: 10.3390/microorganisms10051040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.
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Whittle E, Yonkus JA, Jeraldo P, Alva-Ruiz R, Nelson H, Kendrick ML, Grys TE, Patel R, Truty MJ, Chia N. Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. mSphere 2022; 7:e0096421. [PMID: 35171692 PMCID: PMC8849348 DOI: 10.1128/msphere.00964-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery. IMPORTANCE Surgical site infections (SSI) are a significant burden to patients and health care systems. They increase mortality rates, length of hospital stays, and associated health care costs. To reduce the risk of SSI, surgical patients are administered broad-spectrum antibiotics that are later adapted to target microbial species detected at the site of surgical incision. Use of broad-spectrum antibiotics can be harmful to the patient. We wanted to develop a rapid method of detecting microbial species and their antimicrobial resistance phenotypes. We developed a method of detecting microbial species and predicting resistance phenotypes using Nanopore sequencing. Results generated using Nanopore sequencing were similar to current methods of detection but were obtained in a significantly shorter amount of time. This suggests that Nanopore sequencing could be used to tailor antibiotics in surgical patients and reduce use of broad-spectrum antibiotics.
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Affiliation(s)
- Emma Whittle
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Jennifer A. Yonkus
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Roberto Alva-Ruiz
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Heidi Nelson
- Division of Research and Optimal Patient Care, Cancer Programs, American College of Surgeonsgrid.417954.a, Chicago, Illinois, USA
| | - Michael L. Kendrick
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Phoenix, Arizona, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Mark J. Truty
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Nicholas Chia
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
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