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Fisher CR, Masters TL, Johnson S, Greenwood-Quaintance KE, Chia N, Abdel MP, Patel R. Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions. Int J Med Microbiol 2024; 315:151620. [PMID: 38579524 DOI: 10.1016/j.ijmm.2024.151620] [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: 08/22/2023] [Revised: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Staphylococcus epidermidis is part of the commensal microbiota of the skin and mucous membranes, though it can also act as a pathogen in certain scenarios, causing a range of infections, including periprosthetic joint infection (PJI). Transcriptomic profiling may provide insights into mechanisms by which S. epidermidis adapts while in a pathogenic compared to a commensal state. Here, a total RNA-sequencing approach was used to profile and compare the transcriptomes of 19 paired PJI-associated S. epidermidis samples from an in vivo clinical source and grown in in vitro laboratory culture. Genomic comparison of PJI-associated and publicly available commensal-state isolates were also compared. Of the 1919 total transcripts found, 145 were from differentially expressed genes (DEGs) when comparing in vivo or in vitro samples. Forty-two transcripts were upregulated and 103 downregulated in in vivo samples. Of note, metal sequestration-associated genes, specifically those related to staphylopine activity (cntA, cntK, cntL, and cntM), were upregulated in a subset of clinical in vivo compared to laboratory grown in vitro samples. About 70% of the total transcripts and almost 50% of the DEGs identified have not yet been annotated. There were no significant genomic differences between known commensal and PJI-associated S. epidermidis isolates, suggesting that differential genomics may not play a role in S. epidermidis pathogenicity. In conclusion, this study provides insights into phenotypic alterations employed by S epidermidis to adapt to infective and non-infected microenvironments, potentially informing future therapeutic targets for related infections.
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Affiliation(s)
- Cody R Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thao L Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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2
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Tan J, Wu L, Zhan L, Sheng M, Tang Z, Xu J, Ma H. Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections. Front Cell Infect Microbiol 2024; 14:1356804. [PMID: 38500507 PMCID: PMC10945027 DOI: 10.3389/fcimb.2024.1356804] [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: 12/16/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Objective This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients. Methods This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed. Results The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types. Conclusion mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.
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Affiliation(s)
- Jun Tan
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Lingxiao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Zhan
- Department of Neurology, People’s Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Minkui Sheng
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Zhongxin Tang
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haijun Ma
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
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Kim M, Parrish RC, Shah VS, Ross M, Cormier J, Baig A, Huang CY, Brenner L, Neuringer I, Whiteson K, Harris JK, Willis AD, Lai PS. Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies. RESEARCH SQUARE 2024:rs.3.rs-3638876. [PMID: 38343829 PMCID: PMC10854296 DOI: 10.21203/rs.3.rs-3638876/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Most respiratory microbiome studies have focused on amplicon rather than metagenomics sequencing due to high host DNA content. We evaluated efficacy of five host DNA depletion methods on previously frozen human bronchoalveolar lavage (BAL), nasal swabs, and sputum prior to metagenomic sequencing. Results Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum and BAL samples had 94.1%, 99.2%, and 99.7% host-reads. The effect of host depletion differed by sample type. Most treatment methods increased microbial reads, species richness and predicted functional richness; the increase in species and predicted functional richness was mediated by higher effective sequencing depth. For BAL and nasal samples, most methods did not change Morisita-Horn dissimilarity suggesting limited bias introduced by host depletion. Conclusions Metagenomics sequencing without host depletion will underestimate microbial diversity of most respiratory samples due to shallow effective sequencing depth and is not recommended. Optimal host depletion methods vary by sample type.
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Affiliation(s)
- Minsik Kim
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
| | - Raymond C Parrish
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Viral S Shah
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Matthew Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine
| | - Juwan Cormier
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine
| | - Aribah Baig
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; College of Science, Northeastern University
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Laura Brenner
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
| | - Isabel Neuringer
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Katrine Whiteson
- Department of Molecular Biology & Biochemistry, University of California
| | - J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus
| | - Amy D Willis
- Department of Biostatistics, University of Washington School of Public Health
| | - Peggy S Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
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Abdelrazek S, Bush E, Oliver C, Liu H, Sharma P, Johnson MA, Donegan MA, Almeida RPP, Nita M, Vinatzer BA. A Survey of Xylella fastidiosa in the U.S. State of Virginia Reveals Wide Distribution of Both Subspecies fastidiosa and multiplex in Grapevine. PHYTOPATHOLOGY 2024; 114:35-46. [PMID: 37530473 DOI: 10.1094/phyto-06-23-0212-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Global travel and trade in combination with climate change are expanding the geographic distribution of plant pathogens. The bacterium Xylella fastidiosa is a prime example. Native to the Americas, it has spread to Europe, Asia, and the Middle East. To assess the risk that pathogen introductions pose to crops in newly invaded areas, it is key to survey their diversity, host range, and disease incidence in relation to climatic conditions where they are already present. We performed a survey of X. fastidiosa in grapevine in Virginia using a combination of quantitative PCR, multilocus sequencing, and metagenomics. We also analyzed samples from deciduous trees with leaf scorch symptoms. X. fastidiosa subspecies fastidiosa was identified in grapevines in all regions of the state, even in Northern Virginia, where the temperature was below -9°C for 10 days per year on average in the years preceding sampling. Unexpectedly, we also found for the first time grapevine samples infected with X. fastidiosa subspecies multiplex (Xfm). The Xfm lineage found in grapevines had been previously isolated from blueberries in the Southeastern United States and was distinct from that found in deciduous trees in Virginia. The obtained results will be important for risk assessment of X. fastidiosa introductions in other parts of the world.
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Affiliation(s)
- Sahar Abdelrazek
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Elizabeth Bush
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Charlotte Oliver
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA 22602
| | - Haijie Liu
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Parul Sharma
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061
| | - Marcela A Johnson
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061
| | - Monica A Donegan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720
| | - Mizuho Nita
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA 22602
| | - Boris A Vinatzer
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
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Flurin L, Fisher CR, Wolf MJ, Pritt BS, DeSimone DC, Patel R. Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis. Open Forum Infect Dis 2023; 10:ofad546. [PMID: 38075017 PMCID: PMC10709542 DOI: 10.1093/ofid/ofad546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023] Open
Abstract
Background Shotgun and targeted metagenomic sequencing have been shown in separate studies to be potentially useful for culture-free pathogen identification in blood and/or plasma of patients with infective endocarditis (IE). However, the 2 approaches have not been directly compared. The aim of this study was to compare shotgun metagenomic sequencing with targeted metagenomic sequencing (tMGS) for organism identification in blood or plasma of patients with IE. Methods Patients with possible or definite IE were prospectively enrolled from October 2020 to July 2021. Shotgun metagenomic sequencing was performed with the Karius test, which uses microbial cell-free DNA (mcfDNA) sequencing to detect, identify, and quantitate DNA-based pathogens in plasma. tMGS was performed using a 16S ribosomal RNA (rRNA) polymerase chain reaction assay targeting the V1 to V3 regions of the 16S rRNA gene. Results were compared using the McNemar test of paired proportions. Results Samples from 34 patients were investigated. The Karius test was positive in 24/34 (71%), including 3/6 (50%) with blood culture-negative endocarditis (BCNE), which was not significantly different from the positivity rate of tMGS (P = .41). Results of the Karius test were concordant with tMGS in 75% of cases. The Karius test detected 2 cases of methicillin-resistant Staphylococcus aureus among the 7 S. aureus detections, in accordance with results of phenotypic susceptibility testing. The combination of blood cultures, the Karius test, and tMGS found a potential causative pathogen in 33/34 (97%), including 5/6 with BCNE. Conclusions The Karius test and tMGS yielded comparable detection rates; however, beyond organism identification, the Karius test generated potentially useful antibiotic resistance data.
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Affiliation(s)
- Laure Flurin
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Cody R Fisher
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel C DeSimone
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Divisions of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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Cheng WY, Liu WX, Ding Y, Wang G, Shi Y, Chu ESH, Wong S, Sung JJY, Yu J. High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1195-1205. [PMID: 36174929 PMCID: PMC11082407 DOI: 10.1016/j.gpb.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.
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Affiliation(s)
- Wing Yin Cheng
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Wei-Xin Liu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Yanqiang Ding
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Guoping Wang
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Yu Shi
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Eagle S H Chu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Sunny Wong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Joseph J Y Sung
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China; Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore 639798, Singapore
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China.
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7
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Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Lahner E, Pivetta G, Turroni F, Ventura M, Milani C. Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses. MICROBIOME RESEARCH REPORTS 2023; 3:4. [PMID: 38455080 PMCID: PMC10917613 DOI: 10.20517/mrr.2023.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024]
Abstract
Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host's DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Edith Lahner
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Giulia Pivetta
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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Sturm L, Hirose M, Stolz L, Schultheiss M, Zoldan K, Reincke M, Huber JP, Kaeser R, Boettler T, Thimme R, Albert E, Busch H, Künstner A, Bettinger D. Proton pump inhibitor treatment aggravates bacterial translocation in patients with advanced cirrhosis and portal hypertension. mBio 2023; 14:e0049223. [PMID: 37623323 PMCID: PMC10653923 DOI: 10.1128/mbio.00492-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE Long-term prescription of proton pump inhibitors (PPIs) in patients with cirrhosis is common practice. However, in recent years, several observational studies have reported increased complications and negative prognostic effects of PPI treatment in these patients. Judging the significance of these associations is complicated by the fact that a plausible underlying pathomechanism has not been identified so far. In the present study, we address this important issue by investigating the impact of PPI treatment on subclinical bacterial translocation from the gut into the blood stream in patients with advanced cirrhosis and portal hypertension. Indeed, we report significantly aggravated bacterial translocation in cirrhosis patients receiving PPI treatment. This finding is highly relevant, as bacterial translocation is known to promote the development of complications and impair prognosis in patients with cirrhosis. Hence, the present study could establish a plausible link between PPI treatment and adverse effects in cirrhosis.
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Affiliation(s)
- Lukas Sturm
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Misa Hirose
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | - Laura Stolz
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Michael Schultheiss
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Zoldan
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Marlene Reincke
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Jan Patrick Huber
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Rafael Kaeser
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
- IMM-PACT-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
| | - Elisabeth Albert
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | - Hauke Busch
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Axel Künstner
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Dominik Bettinger
- Department of Medicine II, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
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Hantouly AT, Alzobi O, Toubasi AA, Zikria B, Al Dosari MAA, Ahmed G. Higher sensitivity and accuracy of synovial next-generation sequencing in comparison to culture in diagnosing periprosthetic joint infection: a systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc 2023; 31:3672-3683. [PMID: 36244018 PMCID: PMC10435641 DOI: 10.1007/s00167-022-07196-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/02/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE The purpose of this meta-analysis was to compare the diagnostic parameters of synovial next-generation sequencing (NGS) and cultures in diagnosing periprosthetic joint infections (PJI). METHODS PubMed, Web of Science, Cochrane, and Google Scholar were searched from inception until 8 Jan 2022 for literature investigating the role of NGS in comparison to culture in the diagnosis of PJI. The studies were included if they investigated the diagnostic value of culture and NGS in diagnosing PJIs against the Musculoskeletal Infection Society (MSIS) criteria. Diagnostic parameters, such as sensitivity, specificity, positive predictive value, negative predictive value, positive-likelihood ratio, negative-likelihood ratio, accuracy, and area under the curve (AUC), were calculated for the included studies to evaluate the performance of NGS in comparison to culture in PJI diagnosis. RESULTS The total number of the included patients was 341 from seven articles. The pooled sensitivity, specificity, and diagnostic odds ratio of NGS were 94% (95% CI 91-97%), 89% (95% CI 82-95%), and 138.5 (95% CI 49.1-390.5), respectively. NGS has positive- and negative-likelihood ratios of 7.9 (95% CI 3.99-15.6) and 0.1 (95% CI 0.0-0.1), respectively. On the other hand, the pooled sensitivity, specificity, and diagnostic odds ratio of culture were 70% (95% CI 61-79%), 94% (95% CI 88-98%), and 28.0 (95% CI 12.6-62.2), respectively. The SROC curve for NGS showed that the accuracy (AUC) was 91.9%, and that the positive and negative predictive values were 8.6 (95% CI 5.0-19.5) and 0.1 (95% CI 0.0-0.1), respectively. While, culture SROC curve demonstrated that the accuracy (AUC) was 80.5% and the positive- and negative-likelihood ratio were 12.1 (95% CI 4.5-49.6) and 0.3 (95% CI 0.2-0.4). CONCLUSIONS NGS has a potential role in diagnosing hip and knee PJIs due to its high sensitivity, specificity, and accuracy. However, the sensitivity and specificity reported by the studies varied according to the time of synovial sampling (preoperative, postoperative, or mixed).
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Affiliation(s)
- Ashraf T Hantouly
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar
| | - Osama Alzobi
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar
| | | | - Bashir Zikria
- Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | | | - Ghalib Ahmed
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar.
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10
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Marchukov D, Li J, Juillerat P, Misselwitz B, Yilmaz B. Benchmarking microbial DNA enrichment protocols from human intestinal biopsies. Front Genet 2023; 14:1184473. [PMID: 37180976 PMCID: PMC10169731 DOI: 10.3389/fgene.2023.1184473] [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: 03/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Shotgun metagenomic sequencing is a powerful tool for studying bacterial communities in their natural habitats or sites of infection, without the need for cultivation. However, low microbial signals in metagenomic sequencing can be overwhelmed by host DNA contamination, resulting in decreased sensitivity for microbial read detection. Several commercial kits and other methods have been developed to enrich bacterial sequences; however, these assays have not been tested extensively for human intestinal tissues yet. Therefore, the objective of this study was to assess the effectiveness of various wet-lab and software-based approaches for depleting host DNA from microbiome samples. Four different microbiome DNA enrichment methods, namely the NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit, and Zymo HostZERO microbial DNA kit, were evaluated, along with a software-controlled adaptive sampling (AS) approach by Oxford Nanopore Technologies (ONT) providing microbial signal enrichment by aborting unwanted host DNA sequencing. The NEBNext and QIAamp kits proved to be effective in shotgun metagenomic sequencing studies, as they efficiently reduced host DNA contamination, resulting in 24% and 28% bacterial DNA sequences, respectively, compared to <1% in the AllPrep controls. Additional optimization steps using further detergents and bead-beating steps improved the efficacy of less efficient protocols but not of the QIAamp kit. In contrast, ONT AS increased the overall number of bacterial reads resulting in a better bacterial metagenomic assembly with more bacterial contigs with greater completeness compared to non-AS approaches. Additionally, AS also allowed for the recovery of antimicrobial resistance markers and the identification of plasmids, demonstrating the potential utility of AS for targeted sequencing of microbial signals in complex samples with high amounts of host DNA. However, ONT AS resulted in relevant shifts in the observed bacterial abundance, including 2 to 5 times more Escherichia coli reads. Furthermore, a modest enrichment of Bacteroides fragilis and Bacteroides thetaiotaomicron was also observed with AS. Overall, this study provides insight into the efficacy and limitations of various methods for reducing host DNA contamination in human intestinal samples to improve the utility of metagenomic sequencing.
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Affiliation(s)
- Dmitrij Marchukov
- University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Jiaqi Li
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
- Crohn’s and Colitis Center, Gastroenterologie Beaulieu, Lausanne, Switzerland
| | - Benjamin Misselwitz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
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11
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Koh WLC, Poh SE, Lee CK, Chan THM, Yan G, Kong KW, Lau L, Lee WYT, Cheng C, Hoon S, Seow Y. Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms. Bioengineering (Basel) 2023; 10:bioengineering10050520. [PMID: 37237590 DOI: 10.3390/bioengineering10050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder widespread deployment. Separate preparations of DNA and RNA also increases costs. In this study, we developed a rapid unbiased metagenomics next-generation sequencing (mNGS) workflow with a human background depletion method (HostEL) and a combined DNA/RNA library preparation kit (AmpRE) to address this issue. We enriched and detected bacterial and fungal standards spiked in plasma at physiological levels with low-depth sequencing (<1 million reads) for analytical validation. Clinical validation also showed 93% of plasma samples agreed with the clinical diagnostic test results when the diagnostic qPCR had a Ct < 33. The effect of different sequencing times was evaluated with the 19 h iSeq 100 paired end run, a more clinically palatable simulated iSeq 100 truncated run and the rapid 7 h MiniSeq platform. Our results demonstrate the ability to detect both DNA and RNA pathogens with low-depth sequencing and that iSeq 100 and MiniSeq platforms are compatible with unbiased low-depth metagenomics identification with the HostEL and AmpRE workflow.
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Affiliation(s)
- Winston Lian Chye Koh
- Bioinformatic Institute, A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore
| | - Si En Poh
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Tim Hon Man Chan
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Gabriel Yan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Division of Microbiology, Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Kiat Whye Kong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Lalita Lau
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | | | - Clark Cheng
- Paths Diagnostics Pte Limited, Singapore 349317, Singapore
| | - Shawn Hoon
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Yiqi Seow
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
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12
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Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiol 2023; 110:104162. [DOI: 10.1016/j.fm.2022.104162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022]
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13
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Zhang B, Li M, Liu Y, Zhang B, Liu Z, Chen X, Huo J, Han Y. The diagnostic value of blood sample NGS in patients with early periprosthetic joint infection after total hip arthroplasty. Int Wound J 2023; 20:961-970. [PMID: 36054590 PMCID: PMC10030938 DOI: 10.1111/iwj.13943] [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: 07/26/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
The diagnostic value of next-generation sequencing (NGS) of blood samples from patients with periprosthetic joint infection (PJI) after total hip arthroplasty (THA) was evaluated by comparing it with drainage fluid NGS and bacterial culture. The study was designed as a retrospective diagnostic test. Thirty-six infected patients were diagnosed with PJI according to the Musculoskeletal Infection Society (MSIS) criteria and 57 volunteers were included in our study. NGS and bacterial culture were chosen to detect PJI after THA. Blood samples and drainage fluid were collected for NGS, and the drainage fluid, which was collected at the same time as the NGS drainage fluid sample, was used for bacterial culture. The primary outcomes of interest were sensitivity, specificity, and accuracy. In the infection group, 31 patients showed positive results by blood sample NGS, 33 patients showed positive results by drainage fluid NGS, and 17 patients showed positive bacterial culture results. In the control group, the results of 2 blood sample NGS, 16 drainage fluid NGS, and 3 bacterial cultures were positive. The sensitivity, specificity, and accuracy of the blood sample were 0.86, 0.96, and 0.92, respectively. The sensitivity, specificity, and accuracy of the drainage fluid samples were 0.92, 0.72, and 0.80, respectively. The sensitivity, specificity, and accuracy of bacterial culture were 0.47, 0.95, and 0.79, respectively. The study demonstrated that both the sensitivity and specificity of NGS were higher than those of bacterial culture, regardless of the kind of sample. Compared with drainage fluid NGS, the sensitivity of blood sample NGS was slightly lower (0.86 vs 0.92), but blood sample NGS showed higher specificity (0.96 vs 0.72). In total, the diagnostic value of blood sample NGS was superior to that of drainage fluid NGS and bacterial culture. The majority of infected patients could be identified by blood sample NGS. Moreover, because of its high specificity, blood sample NGS can not only detect infectious bacteria but also distinguish infectious from non-infectious bacteria, which is dramatically different from using drainage fluid NGS.
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Affiliation(s)
- Bingshi Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Mengnan Li
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yawei Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Binquan Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Zeming Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Xiao Chen
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Jia Huo
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
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14
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Parker K, Wood H, Russell JA, Yarmosh D, Shteyman A, Bagnoli J, Knight B, Aspinwall JR, Jacobs J, Werking K, Winegar R. Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications. Trop Med Infect Dis 2023; 8:tropicalmed8020121. [PMID: 36828537 PMCID: PMC9966482 DOI: 10.3390/tropicalmed8020121] [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: 01/07/2023] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted by clinical microbiology laboratories due in part to the absence of standardized workflows. Here, we describe a sample-to-answer workflow called PanGIA (Pan-Genomics for Infectious Agents) that includes simplified, standardized wet-lab procedures and data analysis with an easy-to-use bioinformatics tool. PanGIA is an end-to-end, multi-use workflow that can be used for pathogen detection and related applications, such as biosurveillance and biothreat detection. We performed a comprehensive survey and assessment of current, commercially available wet-lab technologies and open-source bioinformatics tools for each workflow component. The workflow includes total nucleic acid extraction from clinical human whole blood and environmental microbial forensic swabs as sample inputs, host nucleic acid depletion, dual DNA and RNA library preparation, shotgun sequencing on an Illumina MiSeq, and sequencing data analysis. The PanGIA workflow can be completed within 24 h and is currently compatible with bacteria and viruses. Here, we present data from the development and application of the clinical and environmental workflows, enabling the specific detection of pathogens associated with bloodstream infections and environmental biosurveillance, without the need for targeted assay development.
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Affiliation(s)
- Kyle Parker
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
- Correspondence: (K.P.); (R.W.)
| | - Hillary Wood
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | | | - David Yarmosh
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Alan Shteyman
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - John Bagnoli
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Brittany Knight
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Jacob R. Aspinwall
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Jonathan Jacobs
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Kristine Werking
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Richard Winegar
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
- Correspondence: (K.P.); (R.W.)
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15
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Chang Y, Jiang K, Zhang L, Yang F, Huang J. Application of next-generation sequencing technology in the detection of pathogenic bacteria of the periprosthetic joint infection after arthroplasty. Int Wound J 2023. [PMID: 36647902 DOI: 10.1111/iwj.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
To investigate the application value of next-generation sequencing (NGS) technology in the detection of pathogenic bacteria in the periprosthetic joint infection after arthroplasty. Twenty-two cases of patients with joint infection after arthroplasty in our hospital from March 2020 to March 2021 were selected, with 11 cases of knee and 11 cases of hip, including 8 cases of male and 14 cases of female, and an average age of 63.55 ± 13.11 years old (range from 28 to 85). Microbiological culture results of synovial fluid and periprosthetic joint tissue and NGS results of periprosthetic joint tissue were collected. The detection rate of NGS and microbiological culture were calculated and statistically analysed by paired χ2 test. Among the 22 patients with joint infection after arthroplasty, the positive rate of NGS was 90.91% (20/22), whereas the positive rate of bacterial culture was 50.00% (11/22). Paired chi-square test showed a statistically significant difference in the detection rate between the two groups (P = .0029). In the detection of pathogenic microorganism, NGS detected 12 kinds of bacteria, Staphylococcus aureus in 3 patients, Staphylococcus epidermidis in 5 cases, Streptococcus 1 case, Streptococcus dysgalactiae 1 case, Xanthomonas campestris 3 cases, Escherichia coli 2 cases, Bacillus cereus 2 cases, Klebsiella pneumoniae 1 case, Finegoldia magna 1 case, Corynebacterium klopensteriella in 1 case, Brucella 1 case, and Aspergillus flavus 1 case. Bacterial culture detected 6 kinds of bacteria, included 5 cases of Staphylococcus epidermis (including 3 cases of Methicillin-resistant coagulase-negative Staphylococcus, (MRSCoN)), 2 cases of Staphylococcus aureus (both Methicillin-resistant Staphylococcus aureus, (MRSA)), 1 case of Klebsiella pneumoniae, 1 case of Staphylococcus hominis (MRSCoN), 1 case of G+ bacillus, and 1 case of Brucella. Compared with bacterial culture, NGS technology has some advantages in the detection efficiency, detection rate, and comprehensiveness, which might be greater diagnostic value in the joint fluid of infection after arthroplasty.
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Affiliation(s)
- Yu Chang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Kai Jiang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Lixin Zhang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Fang Yang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jing Huang
- Department of Clinical Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
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16
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Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
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Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
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17
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Lazarevic V, Gaïa N, Girard M, Mauffrey F, Ruppé E, Schrenzel J. Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing. ISME COMMUNICATIONS 2022; 2:122. [PMID: 37938717 PMCID: PMC9792467 DOI: 10.1038/s43705-022-00208-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 10/28/2023]
Abstract
Before implementing metagenomic next-generation sequencing (mNGS) in the routine diagnostic laboratory, several challenges need to be resolved. To address strengths and limitations of mNGS in bacterial detection and quantification in samples with overwhelming host DNA abundance, we used the pig muscle tissue spiked with a home-made bacterial mock community, consisting of four species from different phyla. From the spiked tissue, we extracted DNA using: (i) a procedure based on mechanical/chemical lysis (no bacterial DNA enrichment); (ii) the Ultra-Deep Microbiome Prep (Molzym) kit for bacterial DNA enrichment; and (iii) the same enrichment kit but replacing the original proteinase K treatment for tissue solubilization by a collagenases/thermolysin digestion and cell filtration. Following mNGS, we determined bacterial: 'host' read ratios and taxonomic abundance profiles. We calculated the load of each mock-community member by combining its read counts with read counts and microscopically-determined cell counts of other co-spiked bacteria. In unenriched samples, bacterial quantification and taxonomic profiling were fairly accurate but at the expense of the sensitivity of detection. The removal of 'host' DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Florian Mauffrey
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Etienne Ruppé
- Université Sorbonne Paris Nord and INSERM UMR1137 IAME, Université de Paris Cité, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
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18
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Rajar P, Dhariwal A, Salvadori G, Junges R, Åmdal HA, Berild D, Fugelseth D, Saugstad OD, Lausten-Thomsen U, Greisen G, Haaland K, Petersen FC. Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies. Front Microbiol 2022; 13:1038120. [PMID: 36620054 PMCID: PMC9811202 DOI: 10.3389/fmicb.2022.1038120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Methods Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. Results The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness. Discussion Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.
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Affiliation(s)
- Polona Rajar
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway,Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, Oslo University, Oslo, Norway
| | - Drude Fugelseth
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, Oslo University, Oslo, Norway
| | | | - Ulrik Lausten-Thomsen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Gorm Greisen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kirsti Haaland
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway
| | - Fernanda Cristina Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway,*Correspondence: Fernanda Cristina Petersen,
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19
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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20
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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21
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Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022; 10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism. RESULTS A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes. CONCLUSIONS These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.
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Affiliation(s)
- Joseph B Kelly
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany.
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - David E Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Jun Siong Low
- Institute of Microbiology,ETH Zürich, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama City, Republic of Panama
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22
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Qu C, Chen Y, Ouyang Y, Huang W, Liu F, Yan L, Lu R, Zeng Y, Liu Z. Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis. Front Neurol 2022; 13:989280. [PMID: 36203993 PMCID: PMC9530978 DOI: 10.3389/fneur.2022.989280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Objective It is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis. Methods Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation. Results A total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70–82%, I2 = 39.69%) and specificity was 96% (95% CI: 93–98%, I2 = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88–0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p > 0.05). Conclusion Overall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application. Study registration number INPLASY202120002
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Affiliation(s)
- Chunrun Qu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuzhen Ouyang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Weicheng Huang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Luzhe Yan
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruoyu Lu
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Zeng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yu Zeng
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Zhixiong Liu
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23
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Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. mSphere 2022; 7:e0000922. [PMID: 35491834 PMCID: PMC9241506 DOI: 10.1128/msphere.00009-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Syphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogen
Treponema pallidum
subspecies
pallidum
. Primary syphilis typically presents as single or multiple mucocutaneous lesions and, if left untreated, can progress through multiple stages with various clinical manifestations.
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Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
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Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
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25
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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26
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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27
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Albloshi AMK, Alqumber MAA. Infective endocarditis: Role of molecular techniques in early diagnosis. Saudi J Biol Sci 2021; 28:6844-6852. [PMID: 34866984 PMCID: PMC8626217 DOI: 10.1016/j.sjbs.2021.07.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
Infective endocarditis (IE), a heart valve infection primarily caused by bacteria such as streptococci or staphylococci, causes significant morbidity and mortality. Despite the long-term use of broad-spectrum antimicrobials, the infection is often difficult to manage. The latest diagnostic modalities for IE are discussed in this study. Blood culture use in pathogen identification can lead to loss of precious time as well as generation of false negative reports. The first steps in diagnosis are blood cultures and echocardiography, but molecular techniques can be extremely useful and may be used for an accurate and early diagnosis.
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Affiliation(s)
| | - Mohammed A A Alqumber
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia
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28
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Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory: A Step Forward, but Not an End-All. J Mol Diagn 2021; 23:1415-1421. [PMID: 34756275 DOI: 10.1016/j.jmoldx.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
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29
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Cho H, Masters T, Greenwood‐Quaintance KE, Johnson S, Jeraldo PR, Chia N, Pu M, Abdel MP, Patel R. Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection. Microbiologyopen 2021; 10:e1256. [PMID: 34964296 PMCID: PMC8678771 DOI: 10.1002/mbo3.1256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 11/08/2022] Open
Abstract
Although Streptococcus agalactiae periprosthetic joint infection (PJI) is not as prevalent as staphylococcal PJI, invasive S. agalactiae infection is not uncommon. Here, RNA-seq was used to perform transcriptomic analysis of S. agalactiae PJI using fluid derived from sonication of explanted arthroplasties of subjects with S. agalactiae PJI, with results compared to those of S. agalactiae strain NEM316 grown in vitro. A total of 227 genes with outlier expression were found (164 upregulated and 63 downregulated) between PJI sonicate fluid and in vitro conditions. Functional enrichment analysis showed genes involved in mobilome and inorganic ion transport and metabolism to be most enriched. Genes involved in nickel, copper, and zinc transport, were upregulated. Among known virulence factors, cyl operon genes, encoding β-hemolysin/cytolysin, were consistently highly expressed in PJI versus in vitro. The data presented provide insight into S. agalactiae PJI pathogenesis and may be a resource for identification of novel PJI therapeutics or vaccines against invasive S. agalactiae infections.
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Affiliation(s)
- Hye‐Kyung Cho
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Thao Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | | | - Stephen Johnson
- Department of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - Patricio R. Jeraldo
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Nicholas Chia
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Meng Pu
- Department of Medicine, Division of Gastroenterology and HepatologyMayo ClinicRochesterMinnesotaUSA
| | - Matthew P. Abdel
- Department of Orthopedic SurgeryMayo ClinicRochesterMinnesotaUSA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
- Division of Infectious Diseases, Department of MedicineMayo ClinicRochesterMinnesotaUSA
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30
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Gan M, Wu B, Yan G, Li G, Sun L, Lu G, Zhou W. Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens. BMC Genomics 2021; 22:732. [PMID: 34627155 PMCID: PMC8501638 DOI: 10.1186/s12864-021-08023-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background Enzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing machine, which enabled effective enrichment of microbial sequences. However, few studies have compared the enzyme-based host depletion and nanopore adaptive sequencing for microbial enrichment efficiency. Results To compare the host depletion and microbial enrichment efficiency of enzyme-based and adaptive sequencing methods, the present study collected clinical samples from eight children with respiratory tract infections. The same respiratory samples were subjected to standard methods, adaptive sequencing methods, enzyme-based host depletion methods, and the combination of adaptive sequencing and enzyme-based host depletion methods. We compared the host depletion efficiency, microbial enrichment efficiency, and pathogenic microorganisms detected between the four methods. We found that adaptive sequencing, enzyme-based host depletion and the combined methods significantly enriched the microbial sequences and significantly increased the diversity of microorganisms (p value < 0.001 for each method compared to standard). The highest microbial enrichment efficiency was achieved using the combined method. Compared to the standard method, the combined method increased the microbial reads by a median of 113.41-fold (interquartile range 23.32–327.72, maximum 1812), and the number of genera by a median of 70-fold (interquartile range 56.75–86.75, maximum 164). The combined method detected 6 pathogens in 4 samples with a median read of 547, compared to 5 pathogens in 4 samples with a median read of 4 using the standard method. Conclusion The combined method is an effective, easy-to-run method for enriching microbial sequences in clinical metagenomics from sputum and bronchoalveolar lavage fluid samples and may improve the sensitivity of clinical metagenomics for other host-derived clinical samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08023-0.
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Affiliation(s)
- Mingyu Gan
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gangfeng Yan
- Department of Pediatric Emergency and Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Gang Li
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Li Sun
- Department of Rheumatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoping Lu
- Department of Pediatric Emergency and Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Wenhao Zhou
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China. .,Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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31
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Piantadosi A, Mukerji SS, Ye S, Leone MJ, Freimark LM, Park D, Adams G, Lemieux J, Kanjilal S, Solomon IH, Ahmed AA, Goldstein R, Ganesh V, Ostrem B, Cummins KC, Thon JM, Kinsella CM, Rosenberg E, Frosch MP, Goldberg MB, Cho TA, Sabeti P. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis. mBio 2021; 12:e0114321. [PMID: 34465023 PMCID: PMC8406231 DOI: 10.1128/mbio.01143-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/21/2023] Open
Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
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Affiliation(s)
- Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Michael J. Leone
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lisa M. Freimark
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Lemieux
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isaac H. Solomon
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Asim A. Ahmed
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Children’s Hospital, Boston, Massachusetts, USA
| | - Robert Goldstein
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Vijay Ganesh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Bridget Ostrem
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kaelyn C. Cummins
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jesse M. Thon
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Cormac M. Kinsella
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tracey A. Cho
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- University of Iowa, Department of Neurology, Iowa City, Iowa, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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32
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Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
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33
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Benny PA, Al-Akwaa FM, Dirkx C, Schlueter RJ, Wolfgruber TK, Chern IY, Hoops S, Knights D, Garmire LX. Placentas delivered by pre-pregnant obese women have reduced abundance and diversity in the microbiome. FASEB J 2021; 35:e21524. [PMID: 33742690 PMCID: PMC8251846 DOI: 10.1096/fj.202002184rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. We examined the microbiome recovered from placentas in a multi‐ethnic maternal pre‐pregnant obesity cohort, through an optimized microbiome protocol to enrich low bacterial biomass samples. We found that the microbiomes recovered from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. Microbiome richness also decreases from the maternal side to the fetal side, demonstrating heterogeneity by geolocation within the placenta. In summary, our study shows that the microbiomes recovered from the placentas are associated with pre‐pregnancy obesity. Importance Maternal pre‐pregnancy obesity may have an impact on both maternal and fetal health. The placenta is an important organ at the interface of the mother and fetus, and supplies nutrients to the fetus. We report that the microbiomes enriched from the placentas of obese pre‐pregnant mothers are less abundant and less diverse when compared to those from mothers of normal pre‐pregnancy weight. More over, the microbiomes also vary by geolocation within the placenta.
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Affiliation(s)
- Paula A Benny
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Fadhl M Al-Akwaa
- Department of Computational Medicine and Bioinformatics, North Campus Research Complex, University of Michigan, Ann Arbor, MI, USA
| | - Corbin Dirkx
- University of Minnesota Genomics Center, University of Minnesota- Twin Cities, Minneapolis, MN, USA
| | - Ryan J Schlueter
- Department of Obstetrics and Gynaecology, University of Hawaii, Honolulu, HI, USA
| | - Thomas K Wolfgruber
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ingrid Y Chern
- Department of Obstetrics and Gynaecology, University of Hawaii, Honolulu, HI, USA
| | - Suzie Hoops
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, North Campus Research Complex, University of Michigan, Ann Arbor, MI, USA
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34
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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [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] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
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35
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Campana S, Busch K, Hentschel U, Muyzer G, de Goeij JM. DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM). Environ Microbiol 2021; 23:4489-4504. [PMID: 34159693 PMCID: PMC8453545 DOI: 10.1111/1462-2920.15642] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022]
Abstract
Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12 C) and labelled (13 C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.
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Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Kathrin Busch
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Ute Hentschel
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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36
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Bruggeling CE, Garza DR, Achouiti S, Mes W, Dutilh BE, Boleij A. Optimized bacterial DNA isolation method for microbiome analysis of human tissues. Microbiologyopen 2021; 10:e1191. [PMID: 34180607 PMCID: PMC8208965 DOI: 10.1002/mbo3.1191] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, the presence of host DNA in tissue isolates has hampered the analysis of host‐associated bacteria. Here, we present a DNA isolation protocol for tissue, optimized on biopsies from resected human colons (~2–5 mm in size), which includes reduction of human DNA without distortion of relative bacterial abundance at the phylum level. We evaluated which concentrations of Triton and saponin lyse human cells and leave bacterial cells intact, in combination with DNAse treatment to deplete released human DNA. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5‐fold enrichment of bacterial DNA while preserving the relative abundance of Firmicutes, Bacteroidetes, γ‐Proteobacteria, and Actinobacteria assessed by qPCR. Our optimized protocol was validated in the setting of two large clinical studies on 521 in vivo acquired colon biopsies of 226 patients using shotgun metagenomics. The resulting bacterial profiles exhibited alpha and beta diversities that are similar to the diversities found by 16S rRNA amplicon sequencing. A direct comparison between shotgun metagenomics and 16S rRNA amplicon sequencing of 15 forceps tissue biopsies showed similar bacterial profiles and a similar Shannon diversity index between the sequencing methods. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of all bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.
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Affiliation(s)
- Carlijn E Bruggeling
- Department of Pathology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Daniel R Garza
- Radboud Institute for Molecular Life Sciences (RIMLS), Center for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Bacteriology, Rega Institute, Leuven, Belgium
| | - Soumia Achouiti
- Department of Pathology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Wouter Mes
- Department of Animal Ecology & Physiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, The Netherlands.,Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, The Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences (RIMLS), Center for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Annemarie Boleij
- Department of Pathology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands
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37
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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid. mSystems 2021; 6:e0061921. [PMID: 34128697 PMCID: PMC8574158 DOI: 10.1128/msystems.00619-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. The focus of this study is on gathering the primary material, in this case, DNA. We used bovine milk as a model to (i) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk, (ii) evaluate host DNA depletion methods for use with milk, and (iii) develop and evaluate a selective lysis-propidium monoazide (PMA)-based protocol for host DNA depletion in milk. Our results suggest that magnetically based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting the finding that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety, where the detection of Gram-negative pathogens and hygiene indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host. IMPORTANCE Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around 1,000 times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods for the ability to detect specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
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38
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Le Masters T, Johnson S, Jeraldo PR, Greenwood-Quaintance KE, Cunningham SA, Abdel MP, Chia N, Patel R. Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions. J Mol Diagn 2021; 23:986-999. [PMID: 34098085 DOI: 10.1016/j.jmoldx.2021.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Abstract
Transcriptomic analysis can provide insight as to how Staphylococcus aureus adapts to the environmental niche of periprosthetic joint infection (PJI), a challenging clinical infection. Here, in vivo RNA expression of eight S. aureus PJIs was compared with expression of the corresponding isolates in planktonic culture using a total RNA-sequencing approach. Expression varied among isolates, with a common trend showing increased expression of several ica-independent biofilm formation genes, including sdr, fnb, ebpS, and aaa; genes encoding enzymes and toxins, including coa, nuc, hlb, and hlgA/B/C; and genes facilitating acquisition of iron via the iron-binding molecule siderophore B (snb) and heme consumption protein (isd) pathways in PJI. Several antimicrobial resistance determinants were detected; although their presence correlated with phenotypic susceptibility of the associated isolates, no difference in expression between in vivo and in vitro conditions was identified.
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Affiliation(s)
- Thao Le Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patricio R Jeraldo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
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39
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Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, Schöler A, Niedermeier S, Bleuel R, Zink A, Neuhaus K, Schloter M, Biedermann T, Köberle M. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. MICROBIOME 2021; 9:123. [PMID: 34039428 PMCID: PMC8157445 DOI: 10.1186/s40168-021-01067-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/01/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. RESULTS We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias. CONCLUSIONS The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.
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Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Ilias Lagkouvardos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), HCMR, Heraklion, Greece
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Oluwaseun Ayodeji Ishola
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- DKFZ German Cancer Research Center, Berlin, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rachela Bleuel
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Alexander Zink
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany.
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
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Filkins LM, Bryson AL, Miller SA, Mitchell SL. Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations. Clin Chem 2021; 66:1381-1395. [PMID: 33141913 DOI: 10.1093/clinchem/hvaa183] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next generation sequencing (mNGS) is becoming increasingly available for pathogen detection directly from clinical specimens. These tests use target-independent, shotgun sequencing to detect potentially unlimited organisms. The promise of this methodology to aid infection diagnosis is demonstrated through early case reports and clinical studies. However, the optimal role of mNGS in clinical microbiology remains uncertain. CONTENT We reviewed studies reporting clinical use of mNGS for pathogen detection from various specimen types, including cerebrospinal fluid, plasma, lower respiratory specimens, and others. Published clinical study data were critically evaluated and summarized to identify promising clinical indications for mNGS-based testing, to assess the clinical impact of mNGS for each indication, and to recognize test limitations. Based on these clinical studies, early testing recommendations are made to guide clinical utilization of mNGS for pathogen detection. Finally, current barriers to routine clinical laboratory implementation of mNGS tests are highlighted. SUMMARY The promise of direct-from-specimen mNGS to enable challenging infection diagnoses has been demonstrated through early clinical studies of patients with meningitis or encephalitis, invasive fungal infections, community acquired pneumonia, and other clinical indications. However, the proportion of patient cases with positive clinical impact due to mNGS testing is low in published studies and the cost of testing is high, emphasizing the importance of improving our understanding of 'when to test' and for which patients mNGS testing is appropriate.
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Affiliation(s)
- Laura M Filkins
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, VA
| | - Steve A Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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He R, Wang Q, Wang J, Tang J, Shen H, Zhang X. Better choice of the type of specimen used for untargeted metagenomic sequencing in the diagnosis of periprosthetic joint infections. Bone Joint J 2021; 103-B:923-930. [PMID: 33934659 DOI: 10.1302/0301-620x.103b5.bjj-2020-0745.r1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AIMS As a proven and comprehensive molecular technique, metagenomic next-generation sequencing (mNGS) has shown its potential in the diagnosis of pathogens in patients with periprosthetic joint infection (PJI), using a single type of specimen. However, the optimal use of mNGS in the management of PJI has not been explored. In this study, we evaluated the diagnostic value of mNGS using three types of specimen with the aim of achieving a better choice of specimen for mNGS in these patients. METHODS In this prospective study, 177 specimens were collected from 59 revision arthroplasties, including periprosthetic tissues, synovial fluid, and prosthetic sonicate fluid. Each specimen was divided into two, one for mNGS and one for culture. The criteria of the Musculoskeletal Infection Society were used to define PJI (40 cases) and aseptic failure (19 cases). RESULTS The sensitivity and specificity of mNGS in the diagnosis of PJI were 95% and 94.7%, respectively, for all types of specimen. The sensitivity and specificity were 65% and 100%, respectively, for periprosthetic tissues, 87.5% and 94.7%, respectively, for synovial fluid, and 92.5% and 94.7%, respectively, for prosthetic sonicate fluid. The mNGS of prosthetic sonicate fluid outperformed that for other types of specimen in the rates of detection of pathogens (84.6%), sequencing reads (> ten-fold) and the rate of genome coverage (> five-fold). CONCLUSION mNGS could serve as an accurate diagnostic tool in the detection of pathogens in patients with a PJI using three types of specimen. Due to its superior perfomance in identifying a pathogen, mNGS of prosthetic sonicate fluid provides the most value and may partly replace traditional tests such as bacteriological culture in these patients. Cite this article: Bone Joint J 2021;103-B(5):923-930.
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Affiliation(s)
- Renke He
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaojie Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Tang
- Clinical Laboratory, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hao Shen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xianlong Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Grützke J, Gwida M, Deneke C, Brendebach H, Projahn M, Schattschneider A, Hofreuter D, El-Ashker M, Malorny B, Al Dahouk S. Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen. Microb Genom 2021; 7. [PMID: 33945456 PMCID: PMC8209726 DOI: 10.1099/mgen.0.000552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metagenomics is a valuable diagnostic tool for enhancing microbial food safety because (i) it enables the untargeted detection of pathogens, (ii) it is fast since primary isolation of micro-organisms is not required, and (iii) it has high discriminatory power allowing for a detailed molecular characterization of pathogens. For shotgun metagenomics, total nucleic acids (NAs) are isolated from complex samples such as foodstuff. Along with microbial NAs, high amounts of matrix NAs are extracted that might outcompete microbial NAs during next-generation sequencing and compromise sensitivity for the detection of low abundance micro-organisms. Sensitive laboratory methods are indispensable for detecting highly pathogenic foodborne bacteria like Brucella spp., because a low infectious dose is sufficient to cause human disease through the consumption of contaminated dairy or meat products. In our study, we applied shotgun metagenomic sequencing for the identification and characterization of Brucella spp. in artificially and naturally contaminated raw milk from various ruminant species. With the depletion of eukaryotic cells prior to DNA extraction, Brucella was detectable at 10 bacterial cells ml−1, while at the same time microbiological culture and isolation of the fastidious bacteria commonly failed. Moreover, we were able to retrieve the genotype of a Brucella isolate from a metagenomic dataset, indicating the potential of metagenomics for outbreak investigations using SNPs and core-genome multilocus sequence typing (cgMLST). To improve diagnostic applications, we developed a new bioinformatics approach for strain prediction based on SNPs to identify the correct species and define a certain strain with only low numbers of genus-specific reads per sample. This pipeline turned out to be more sensitive and specific than Mash Screen. In raw milk samples, we simultaneously detected numerous other zoonotic pathogens, antimicrobial resistance genes and virulence factors. Our study showed that metagenomics is a highly sensitive tool for biological risk assessment of foodstuffs, particularly when pathogen isolation is hazardous or challenging.
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Affiliation(s)
- Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mayada Gwida
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Michaela Projahn
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Dirk Hofreuter
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maged El-Ashker
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Department of Internal Medicine III, RWTH Aachen University Hospital, Aachen, Germany
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Sam SS, Rogers R, Gillani FS, Tsongalis GJ, Kraft CS, Caliendo AM. Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients. J Mol Diagn 2021; 23:719-731. [PMID: 33706010 PMCID: PMC8279015 DOI: 10.1016/j.jmoldx.2021.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
Viral infections are major causes of morbidity and mortality in solid-organ and hematopoietic stem cell transplant recipients. This study evaluated the performance of the Galileo Pathogen Solution metagenomics Next-Generation sequencing assay to detect and quantify 11 DNA viruses (cytomegalovirus, Epstein-Barr virus, BK virus, human adenovirus, JC virus, herpes simplex virus 1 and 2, varicella zoster virus, human herpesvirus 6A and 6B, and parvovirus B19) and to qualitatively detect torque teno virus. DNA extracted from 47 plasma samples of viremic transplant recipients were subjected to DNA library preparation with pathogen enrichment/human background depletion, sequencing, and automated data analysis. The viral loads were determined with the Galileo assay using a standard curve generated from a calibration panel. All of the samples tested had a 100% agreement with the real-time quantitative PCR (qPCR) assays in detecting the primary virus targets and the majority of the quantified samples had a viral load difference within 0.46 log10 IU/mL or copies/mL. The mean difference for cytomegalovirus between the Galileo and qPCR assays was 0.21 log10 IU/mL (SD, ±0.43 log10 IU/mL). The mean difference for BK virus between the Galileo and qPCR assays was 0.17 log10 cp/mL (SD, ±0.67 log10 cp/mL). Additionally, 75 co-infections were detected in 31 samples by the Galileo assay. The study findings show that the Galileo assay can simultaneously detect and quantify multiple viruses in transplant recipients with results that are comparable with standard-of-care qPCR assays.
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Affiliation(s)
- Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island.
| | - Ralph Rogers
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Fizza S Gillani
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Angela M Caliendo
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
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Yin H, Xu D, Wang D. Diagnostic value of next-generation sequencing to detect periprosthetic joint infection. BMC Musculoskelet Disord 2021; 22:252. [PMID: 33676477 PMCID: PMC7937267 DOI: 10.1186/s12891-021-04116-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background We herein compared the diagnostic value of next-generation sequencing (NGS), bacterial culture, and serological biomarkers to detect periprosthetic joint infection (PJI) after joint replacement. Methods According to the diagnostic criteria of the Musculoskeletal Infection Society, 35 patients who underwent joint revision surgery were divided into infection (15 cases) and non-infection (20 cases) groups, and were routinely examined preoperatively for erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), and D-dimer levels. All patients underwent arthrocentesis preoperatively. Synovial fluid was used for white blood cell count, white blood cell classification, bacterial culture, and NGS. Furthermore, we calculated the area under the curve (AUC) of the receiver operating characteristic curve (ROC) for ESR, CRP, PCT, IL-6, and D-dimer. Data were assessed by comparing diagnostic accuracy, sensitivity, and specificity. Results Fourteen patients showed positive results by NGS and seven showed positive bacterial culture results in the infection group; further, 18 showed negative results by NGS in the non-infection group. The AUC of ESR, D-dimer, CRP, IL-6, and PCT was 0.667, 0.572, 0.827, 0.767, and 0.808, respectively. The accuracy of NGS, bacterial culture, CRP, IL-6, and PCT was 0.91, 0.74, 0.77, 0.74, and 0.83, respectively. When comparing NGS with CRP, IL-6, PCT, and bacterial culture, differences in overall test results and those in sensitivity were statistically significant, and compared with CRP, differences in specificity were also statistically significant. In comparison with IL-6, PCT, and bacterial culture, the specificity of NGS was statistically insignificant. Conclusions Our results indicated that NGS had higher accuracy and sensitivity than the bacterial culture method and commonly used serological biomarkers for diagnosing PJI.
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Affiliation(s)
- Han Yin
- Department of Orthopaedics, Liaocheng People's Hospital and Liaocheng Clinical School of Taishan Medical University, No. 67, Dongchang Road, Liaocheng, Shandong, China
| | - Duliang Xu
- Department of Orthopaedics, Liaocheng People's Hospital and Liaocheng Clinical School of Taishan Medical University, No. 67, Dongchang Road, Liaocheng, Shandong, China
| | - Dawei Wang
- Department of Orthopaedics, Liaocheng People's Hospital and Liaocheng Clinical School of Taishan Medical University, No. 67, Dongchang Road, Liaocheng, Shandong, China.
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Evaluation of a commercial microbial enrichment kit used prior DNA extraction to improve the molecular detection of vector-borne pathogens from naturally infected dogs. J Microbiol Methods 2021; 188:106163. [PMID: 33581169 DOI: 10.1016/j.mimet.2021.106163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/28/2023]
Abstract
Accurate detection of vector-borne pathogens (VBPs) is extremely important as the number of reported cases in humans and animals continues to rise in the US and abroad. Validated PCR assays are currently the cornerstone of molecular diagnostics and can achieve excellent analytical sensitivity and specificity. However, the detection of pathogens at low parasitemia still presents a challenge for VBP diagnosis, especially given the very low volume of specimens tested by molecular methods. The objective of this study is to determine if a commercially available microbial enrichment kit, used prior DNA extraction, is capable of expanding the overall microbial community and increasing detectable levels of VBPs in canine blood samples through host DNA depletion. This study used EDTA-whole blood samples from dogs naturally infected with varying parasitemia levels of either Anaplasma phagocytophilum, Babesia gibsoni, or Ehrlichia ewingii. For two VBPs, EDTA-blood samples were diluted to determine the effect of microbial concentration at low parasitemia. Paired EDTA-blood samples from each dog were subjected to traditional, automated DNA extraction with or without the microbial concentrating kit (MolYsis®) prior to DNA extraction. Relative amounts of pathogen DNA in paired samples were determined by real-time PCR and Next-Generation Sequencing targeting conserved regions of 16S rRNA (for bacteria) and 18S rRNA (for protozoa). Results from the three molecular methods suggest that the microbial concentrating kit did not improve the detection of VBPs, although significantly reduced the presence of host DNA. Alternative methods for VBP enrichment in clinical samples prior to molecular testing should continue to be investigated, as it may significantly improve clinical sensitivity and reduce the number of false-negative results.
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W. Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics. Med Mycol 2021; 58:650-660. [PMID: 31758176 DOI: 10.1093/mmy/myz109] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/26/2019] [Accepted: 11/19/2019] [Indexed: 11/14/2022] Open
Abstract
The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a life-threatening fungal disease caused by P. jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P. jirovecii cannot be cultured readily in vitro. P. jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Yiheng Hu
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Lana Pasic
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Menuk Jayawardena
- Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Indira Basu
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Wendy McKinney
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Arthur J Morris
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Eric Stone
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ANU-CSIRO Centre for Genomics, Metabolomics and Bioinformatics, Canberra, ACT, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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Emery DC, Cerajewska TL, Seong J, Davies M, Paterson A, Allen-Birt SJ, West NX. Comparison of Blood Bacterial Communities in Periodontal Health and Periodontal Disease. Front Cell Infect Microbiol 2021; 10:577485. [PMID: 33469518 PMCID: PMC7813997 DOI: 10.3389/fcimb.2020.577485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
The use of Next Generation Sequencing (NGS) techniques has generated a wide variety of blood microbiome data. Due to the large variation in bacterial DNA profiles between studies and the likely high concentrations of cell-free bacterial DNA in the blood, it is still not clear how such microbiome data relates to viable microbiota. For these reasons much remains to be understood about the true nature of any possible healthy blood microbiota and of bacteraemic events associated with disease. The gut, reproductive tracts, skin, and oral cavity are all likely sources of blood-borne bacteria. Oral bacteria, especially those associated with periodontal diseases, are also commonly associated with cardiovascular diseases such as infective endocarditis, and also have been linked to rheumatoid arthritis and Alzheimer’s disease. Periodontal treatment, dental probing, and toothbrushing have been shown to cause transient bacteraemia and oral bacteria from the phyla Firmicutes (e.g. Streptococci) and Bacteroidetes (e.g. Porphyromonas) are found in cardiovascular lesions (CVD). Many studies of blood bacterial DNA content however, find Proteobacteria DNA to be the dominant microbiome component, suggesting a gut origin. Most studies of this type use total DNA extracted from either whole blood or blood fractions, such as buffy coat. Here, using a method that purifies DNA from intact bacterial cells only, we examined blood donated by those with active, severe periodontitis and periodontally healthy controls and show that 43–52% of bacterial species in blood are classified as oral. Firmicutes, consisting largely of members of the Streptococcus mitis group and Staphylococcus epidermidis, were predominant at 63.5% of all bacterial sequences detected in periodontal health and, little changed at 66.7% in periodontitis. Compared to studies using total DNA Proteobacteria were found here at relatively low levels in blood at 13.3% in periodontitis and 17.6% in health. This study reveals significant phylogenetic differences in blood bacterial population profiles when comparing periodontal health to periodontal disease cohorts.
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Affiliation(s)
- David C Emery
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Tanya L Cerajewska
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Joon Seong
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Maria Davies
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Alex Paterson
- University of Bristol Genomics Facility, School of Biological Sciences, Bristol, United Kingdom
| | - Shelley J Allen-Birt
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Nicola X West
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
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Yap M, Feehily C, Walsh CJ, Fenelon M, Murphy EF, McAuliffe FM, van Sinderen D, O'Toole PW, O'Sullivan O, Cotter PD. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome. Sci Rep 2020; 10:21665. [PMID: 33303873 PMCID: PMC7728742 DOI: 10.1038/s41598-020-78773-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mark Fenelon
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Fionnuala M McAuliffe
- APC Microbiome Ireland, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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