1
|
Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix KA. A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues. Arch Microbiol 2024; 206:248. [PMID: 38713383 PMCID: PMC11076400 DOI: 10.1007/s00203-024-03985-7] [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: 03/13/2024] [Accepted: 04/28/2024] [Indexed: 05/08/2024]
Abstract
Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.
Collapse
Affiliation(s)
- Kenny Yeo
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
| | - James Connell
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - George Bouras
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Eric Smith
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - William Murphy
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - John-Charles Hodge
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Suren Krishnan
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Otolaryngology, Head and Neck Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Rowan Valentine
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Alkis James Psaltis
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Sarah Vreugde
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia
| | - Kevin Aaron Fenix
- Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia.
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.
| |
Collapse
|
2
|
Didouh N, Khadidja M, Campos C, Sampaio-Maia B, Boumediene MB, Araujo R. Assessment of biofilm, enzyme production and antibiotic susceptibility of bacteria from milk pre- and post-pasteurization pipelines in Algeria. Int J Food Microbiol 2023; 407:110389. [PMID: 37708608 DOI: 10.1016/j.ijfoodmicro.2023.110389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Bacterial biofilm is a major concern of dairy industry due to its association with milk contamination and its derived products. Algerian pasteurized milk shelf-life does not exceed one day, which may reflect the high level of contamination of this product and presence of extracellular enzymes such as lipases and proteases. This work aimed to investigate the microbial biodiversity in milk-processing surfaces of a dairy plant in Algeria. Therefore, stainless steel cylinders were placed in piping system of the dairy system before and after pasteurization of the milk, being removed after 7 days, for biofilm maturation and microorganism isolation and identification by mass spectrometry. Fifty-nine Gram-positive isolates were identified, namely Bacillus altitudinis, Bacillus cereus, Bacillus pumilus, Bacillus subtilis, Bacillus weithenstephanensis, Enterococcus casseliflavus, Enterococcus faecium, and Staphylococcus epidermidis. In addition, twenty-four Gram-negative isolates were identified, namely Acinetobacter schindleri Enterobacter cloacae, Enterobacter xiangfangensis, Leclercia adecarboxylata, and Raoultella ornithinolytica. Bacterial isolates showed ability for production of extracellular enzymes, being 49 % capable of both proteolytic and lipolytic activities. Milk isolates were tested for the ability to form biofilms on stainless steel. The cell numbers recovered on plate count agar plates from stainless steel biofilms ranged from 3.52 to 6.92 log10 CFU/cm2, being the maximum number detected for Enterococcus casseliflavus. Bacterial isolates showed intermediate and/or resistant profiles to multiple antibiotics. Resistance to amoxicillin, cefoxitin and/or erythromycin was commonly found among the bacterial isolates.
Collapse
Affiliation(s)
- Nassima Didouh
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria
| | - Medjahdi Khadidja
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria; Université Hassiba Benbouali Chlef, Algeria
| | - Carla Campos
- Instituto Português de Oncologia (IPO) do Porto Francisco Gentil, Porto, Portugal
| | - Benedita Sampaio-Maia
- Nephrology & Infectious Diseases R&D Group, INEB - Instituto de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
| | - Moussa Boudjemaa Boumediene
- Université Abou Bekr Belkaid Tlemcen, Algeria; Laboratoire de Microbiologie Appliqué à l'Agroalimentaire au Biomédical et à l'Environnement, 13000 Tlemcen, Algeria
| | - Ricardo Araujo
- Nephrology & Infectious Diseases R&D Group, INEB - Instituto de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
| |
Collapse
|
3
|
López-Plaza B, Gil Á, Menéndez-Rey A, Bensadon-Naeder L, Hummel T, Feliú-Batlle J, Palma-Milla S. Effect of Regular Consumption of a Miraculin-Based Food Supplement on Taste Perception and Nutritional Status in Malnourished Cancer Patients: A Triple-Blind, Randomized, Placebo-Controlled Clinical Trial-CLINMIR Pilot Protocol. Nutrients 2023; 15:4639. [PMID: 37960292 PMCID: PMC10648678 DOI: 10.3390/nu15214639] [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: 10/02/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Taste disorders are common among cancer patients undergoing chemotherapy, with a prevalence ranging from 20% to 86%, persisting throughout treatment. This condition leads to reduced food consumption, increasing the risk of malnutrition. Malnutrition is associated not only with worse treatment efficacy and poor disease prognosis but also with reduced functional status and quality of life. The fruit of Synsepalum dulcificum (Daniell), commonly known as miracle berry or miracle fruit, contains miraculin, a taste-modifying protein with profound effects on taste perception. The CLINMIR Protocol is a triple-blind, randomized, placebo-controlled clinical trial designed to evaluate the regular consumption of a food supplement containing a miraculin-based novel food, dried miracle berry (DMB), on the taste perception (measured through electrogustometry) and nutritional status (evaluated through the GLIM Criteria) of malnourished cancer patients under active antineoplastic treatment. To this end, a pilot study was designed with 30 randomized patients divided into three study arms (150 mg DMB + 150 mg freeze-dried strawberries, 300 mg DMB, or placebo) for three months. Throughout the five main visits, an exhaustive assessment of different parameters susceptible to improvement through regular consumption of the miraculin-based food supplement will be conducted, including electrical and chemical taste perception, smell perception, nutritional and morphofunctional assessment, diet, quality of life, the fatty acid profile of erythrocytes, levels of inflammatory and cancer-associated cytokines, oxidative stress, antioxidant defense system, plasma metabolomics, and saliva and stool microbiota. The primary anticipated result is that malnourished cancer patients with taste distortion who consume the miraculin-based food supplement will report an improvement in food taste perception. This improvement translates into increased food intake, thereby ameliorating their nutritional status and mitigating associated risks. Additionally, the study aims to pinpoint the optimal dosage that provides maximal benefits. The protocol adheres to the SPIRIT 2013 Statement, which provides evidence-based recommendations and is widely endorsed as an international standard for trial protocols. The clinical trial protocol has been registered at the platform for Clinical Trials (NCT05486260).
Collapse
Affiliation(s)
- Bricia López-Plaza
- Nutrition Research Group, La Paz University Hospital Institute for Health Research (IdiPAZ), 28046 Madrid, Spain;
- Medicine Department, Faculty of Medicine, Complutense University of Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Armilla, 18016 Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | | | - Thomas Hummel
- Smell & Taste Clinic, Department of Otorhinolaryngology, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany;
| | - Jaime Feliú-Batlle
- Oncology Department, Hospital La Paz Institute for Health Research—IdiPAZ, Hospital Universitario La Paz, 28029 Madrid, Spain;
- CIBERONC (CIBER Cancer), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Medicine Department, Faculty of Medicine, Autonomous University of Madrid, Arzobispo Morcillo 4, 28029 Madrid, Spain;
| | - Samara Palma-Milla
- Medicine Department, Faculty of Medicine, Autonomous University of Madrid, Arzobispo Morcillo 4, 28029 Madrid, Spain;
- Nutrition Department, Hospital University La Paz, 28046 Madrid, Spain
| |
Collapse
|
4
|
Nabeshima K, Asakura S, Iwata R, Honjo H, Haga A, Goka K, Onuma M. Sequencing methods for HA and NA genes of avian influenza viruses from wild bird feces using Oxford Nanopore sequencing. Comp Immunol Microbiol Infect Dis 2023; 102:102076. [PMID: 37804607 DOI: 10.1016/j.cimid.2023.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
We developed a method to determine the sequences of hemagglutinin (HA) and neuraminidase (NA) from RNA extracted directly from wild bird fecal samples, using Nanopore Flongle. We determined the nucleotide sequences and subtypes of HA and NA in 16 and 15 samples respectively, using Flongle. The results of HA and NA subtyping determined by the conventional method were consistent with their subtypes determined by our method, thereby the applicability of this method in the identification of HA and NA subtypes. In addition, the homology between the HA fragments in this and the Sanger methods ranged from 98.5 % to 100 %. Compared with conventional PCR with the Sanger method, this method can easily determine HA and NA subtypes and sequences directly from the fecal samples. It is easier to implement and has lower running costs (USD100$) than other NGS-based methods, making it a useful tool for avian influenza surveillance in wild birds.
Collapse
Affiliation(s)
- Kei Nabeshima
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shingo Asakura
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan; Animal Research Center of Hokkaido Research Organization, 5-39 Shintoku, Hokkaido, 081-0038, Japan
| | - Ritsuko Iwata
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hisako Honjo
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Atsushi Haga
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Koichi Goka
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Manabu Onuma
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
| |
Collapse
|
5
|
Oehler JB, Wright H, Stark Z, Mallett AJ, Schmitz U. The application of long-read sequencing in clinical settings. Hum Genomics 2023; 17:73. [PMID: 37553611 PMCID: PMC10410870 DOI: 10.1186/s40246-023-00522-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, thereby providing a valuable tool for precision medicine. In the third-generation sequencing duopoly, Oxford Nanopore Technologies and Pacific Biosciences work towards increasing the accuracy, throughput, and portability of long-read sequencing methods while trying to keep costs low. These trades have made long-read sequencing an attractive tool for use in research and clinical settings. This article provides an overview of current clinical applications and limitations of long-read sequencing and explores its potential for point-of-care testing and health care in remote settings.
Collapse
Affiliation(s)
- Josephine B Oehler
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
| | - Helen Wright
- Nursing and Midwifery, College of Healthcare Sciences, James Cook University, Townsville, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
| | - Andrew J Mallett
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Ulf Schmitz
- Biomedical Sciences and Molecular Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Townsville, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
- Computational BioMedicine Lab Centenary Institute, The University of Sydney, Camperdown, Australia.
- Faculty of Medicine & Health, The University of Sydney, Camperdown, Australia.
| |
Collapse
|
6
|
Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [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: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
Collapse
Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
7
|
Szoboszlay M, Schramm L, Pinzauti D, Scerri J, Sandionigi A, Biazzo M. Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms 2023; 11:microorganisms11030804. [PMID: 36985377 PMCID: PMC10059749 DOI: 10.3390/microorganisms11030804] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.
Collapse
Affiliation(s)
| | | | | | | | - Anna Sandionigi
- Department of Informatics, Systems and Communication, University of Milan Bicocca, 20126 Milan, Italy
| | | |
Collapse
|
8
|
Viehweger A, Marquet M, Hölzer M, Dietze N, Pletz MW, Brandt C. Nanopore-based enrichment of antimicrobial resistance genes - a case-based study. GIGABYTE 2023; 2023:gigabyte75. [PMID: 36949817 PMCID: PMC10027057 DOI: 10.46471/gigabyte.75] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment ("adaptive") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compared its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then modelled the influence of several variables on the enrichment results and predicted the large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we showed how all relevant resistance genes are detected using adaptive sequencing on a miniature ("Flongle") flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.
Collapse
Affiliation(s)
- Adrian Viehweger
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
- Corresponding author. E-mail:
| | - Mike Marquet
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Martin Hölzer
- MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Nadine Dietze
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| |
Collapse
|
9
|
Kopanczyk R, Lester J, Long MT, Kossbiel BJ, Hess AS, Rozycki A, Nunley DR, Habib A, Taylor A, Awad H, Bhatt AM. The Future of Cardiothoracic Surgical Critical Care Medicine as a Medical Science: A Call to Action. MEDICINA (KAUNAS, LITHUANIA) 2022; 59:47. [PMID: 36676669 PMCID: PMC9867461 DOI: 10.3390/medicina59010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Cardiothoracic surgical critical care medicine (CT-CCM) is a medical discipline centered on the perioperative care of diverse groups of patients. With an aging demographic and an increase in burden of chronic diseases the utilization of cardiothoracic surgical critical care units is likely to escalate in the coming decades. Given these projections, it is important to assess the state of cardiothoracic surgical intensive care, to develop goals and objectives for the future, and to identify knowledge gaps in need of scientific inquiry. This two-part review concentrates on CT-CCM as its own subspeciality of critical care and cardiothoracic surgery and provides aspirational goals for its practitioners and scientists. In part one, a list of guiding principles and a call-to-action agenda geared towards growth and promotion of CT-CCM are offered. In part two, an evaluation of selected scientific data is performed, identifying gaps in CT-CCM knowledge, and recommending direction to future scientific endeavors.
Collapse
Affiliation(s)
- Rafal Kopanczyk
- Department of Anesthesiology, Division of Critical Care, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jesse Lester
- Department of Anesthesiology, Division of Critical Care, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Micah T. Long
- Department of Anesthesiology, University of Wisconsin Hospitals & Clinics, Madison, WI 53792, USA
| | - Briana J. Kossbiel
- Department of Anesthesiology, Division of Critical Care, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Aaron S. Hess
- Department of Anesthesiology and Pathology & Laboratory Medicine, University of Wisconsin Hospitals & Clinics, Madison, WI 53792, USA
| | - Alan Rozycki
- Department of Pharmacology, The Ohio State Wexner Medical Center, Columbus, OH 43210, USA
| | - David R. Nunley
- Department of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Alim Habib
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Ashley Taylor
- Department of Anesthesiology, Division of Critical Care, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Hamdy Awad
- Department of Anesthesiology, Division of Cardiothoracic and Vascular Anesthesia, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Amar M. Bhatt
- Department of Anesthesiology, Division of Critical Care, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| |
Collapse
|
10
|
Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11101364. [PMID: 36290022 PMCID: PMC9598329 DOI: 10.3390/antibiotics11101364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3′)-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates.
Collapse
|
11
|
Hare D, Meaney C, Powell J, Slevin B, O' Brien B, Power L, O' Connell N, De Gascun C, Dunne C, Stapleton P. Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing. J Hosp Infect 2022; 126:1-9. [PMID: 35562074 PMCID: PMC9088210 DOI: 10.1016/j.jhin.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 01/11/2023]
Abstract
AIM To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.
Collapse
Affiliation(s)
- D. Hare
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland,UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland,Corresponding author. Address: Department of Clinical Microbiology University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - C. Meaney
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - J. Powell
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - B. Slevin
- Department of Infection, Prevention and Control, University Hospital Limerick, Limerick, Ireland
| | - B. O' Brien
- Department of Infection, Prevention and Control, University Hospital Limerick, Limerick, Ireland
| | - L. Power
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - N.H. O' Connell
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland,Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - C.F. De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - C.P. Dunne
- School of Medicine, University of Limerick, Limerick, Ireland,Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - P.J. Stapleton
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland
| |
Collapse
|
12
|
Whittle E, Yonkus JA, Jeraldo P, Alva-Ruiz R, Nelson H, Kendrick ML, Grys TE, Patel R, Truty MJ, Chia N. Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. mSphere 2022; 7:e0096421. [PMID: 35171692 PMCID: PMC8849348 DOI: 10.1128/msphere.00964-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery. IMPORTANCE Surgical site infections (SSI) are a significant burden to patients and health care systems. They increase mortality rates, length of hospital stays, and associated health care costs. To reduce the risk of SSI, surgical patients are administered broad-spectrum antibiotics that are later adapted to target microbial species detected at the site of surgical incision. Use of broad-spectrum antibiotics can be harmful to the patient. We wanted to develop a rapid method of detecting microbial species and their antimicrobial resistance phenotypes. We developed a method of detecting microbial species and predicting resistance phenotypes using Nanopore sequencing. Results generated using Nanopore sequencing were similar to current methods of detection but were obtained in a significantly shorter amount of time. This suggests that Nanopore sequencing could be used to tailor antibiotics in surgical patients and reduce use of broad-spectrum antibiotics.
Collapse
Affiliation(s)
- Emma Whittle
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Jennifer A. Yonkus
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Roberto Alva-Ruiz
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Heidi Nelson
- Division of Research and Optimal Patient Care, Cancer Programs, American College of Surgeonsgrid.417954.a, Chicago, Illinois, USA
| | - Michael L. Kendrick
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Phoenix, Arizona, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Mark J. Truty
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Nicholas Chia
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| |
Collapse
|
13
|
Emerging tools for understanding the human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:29-51. [DOI: 10.1016/bs.pmbts.2022.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
14
|
Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis. WATER 2021. [DOI: 10.3390/w13243551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.
Collapse
|