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Lewis JD, Salipante SJ. Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests. J Clin Microbiol 2024; 62:e0024324. [PMID: 38629844 PMCID: PMC11237385 DOI: 10.1128/jcm.00243-24] [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: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.
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Affiliation(s)
- Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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2
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Long DR, Bryson-Cahn C, Waalkes A, Holmes EA, Penewit K, Tavolaro C, Bellabarba C, Zhang F, Chan JD, Fang FC, Lynch JB, Salipante SJ. Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery. Sci Transl Med 2024; 16:eadk8222. [PMID: 38598612 DOI: 10.1126/scitranslmed.adk8222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Celeste Tavolaro
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlo Bellabarba
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fangyi Zhang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jeannie D Chan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pharmacy, Harborview Medical Center, University of Washington School of Pharmacy, Seattle, WA 98104, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA
| | - John B Lynch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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3
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Microbiota of the Colonic Diverticula in the Complicated Form of Diverticulitis: A Case Report. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122129. [PMID: 36556494 PMCID: PMC9784642 DOI: 10.3390/life12122129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Intestinal microbiota appears to be implicated in the pathogenesis of diverticular disease. We present the case of a patient with diverticular colon disease complicated by a pelvic abscess. During the successful surgical treatment, two specimens were taken from the resected colon segment for the microbiota analysis: an inflamed and perforated diverticulum and a diverticulum without signs of inflammation. Culturing and 16S rRNA gene sequencing revealed significant changes in the microbial community structure and composition associated with the acute inflammation and perforation of the colonic diverticulum. The characteristics that are usually associated with the inflammatory process in the gut, namely reduced microbial diversity and richness, decreased Firmicutes-to-Bacteroidetes (F/B) ratio, depletion of butyrate-producing bacteria, and Enterobacteriaceae blooming, were more pronounced in the non-inflamed diverticulum rather than in the adjacent inflamed and perforated one. This is the first study of the intraluminal microbiota of the diverticular pockets, which is more relevant to the etiology of diverticular disease than mucosa-associated microbiota via biopsies and luminal microbiota via fecal samples.
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Kushwaha SK, Narasimhan LP, Chithananthan C, Marathe SA. Clustered regularly interspaced short palindromic repeats-Cas system: diversity and regulation in Enterobacteriaceae. Future Microbiol 2022; 17:1249-1267. [PMID: 36006039 DOI: 10.2217/fmb-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Insights into the arms race between bacteria and invading mobile genetic elements have revealed the intricacies of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system and the counter-defenses of bacteriophages. Incredible spacer diversity but significant spacer conservation among species/subspecies dictates the specificity of the CRISPR-Cas system. Researchers have exploited this feature to type/subtype the bacterial strains, devise targeted antimicrobials and regulate gene expression. This review focuses on the nuances of the CRISPR-Cas systems in Enterobacteriaceae that predominantly harbor type I-E and I-F CRISPR systems. We discuss the systems' regulation by the global regulators, H-NS, LeuO, LRP, cAMP receptor protein and other regulators in response to environmental stress. We further discuss the regulation of noncanonical functions like DNA repair pathways, biofilm formation, quorum sensing and virulence by the CRISPR-Cas system. The review comprehends multiple facets of the CRISPR-Cas system in Enterobacteriaceae including its diverse attributes, association with genetic features, regulation and gene regulatory mechanisms.
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Affiliation(s)
- Simran K Kushwaha
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Lakshmi P Narasimhan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Chandrananthi Chithananthan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Sandhya A Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
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Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
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Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
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Kortekangas E, Fan YM, Chaima D, Lehto KM, Malamba-Banda C, Matchado A, Chingwanda C, Liu Z, Ashorn U, Cheung YB, Dewey KG, Maleta K, Ashorn P. Associations between Gut Microbiota and Intestinal Inflammation, Permeability and Damage in Young Malawian Children. J Trop Pediatr 2022; 68:6527323. [PMID: 35149871 PMCID: PMC8846364 DOI: 10.1093/tropej/fmac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Environmental enteric dysfunction (EED) is common in low- and middle-income countries and associated with childhood undernutrition. The composition of gut microbiota has been implicated in the pathogenesis of EED. Our aim was to assess the associations between gut microbiota and EED biomarkers in rural Malawian children. We hypothesized that there would be an inverse association between microbiota maturity and diversity and fecal concentrations of EED biomarkers. METHODS We used data from fecal samples collected at 6, 18 and 30 months from 611 children who were followed up during a nutrition intervention trial. The primary time point for analysis was 18 months. Microbiota data were obtained through 16S rRNA sequencing and variables included microbiota maturity and diversity, phylogenetic dissimilarity and relative abundances of individual taxa. EED biomarkers included calprotectin (marker of inflammation), alpha-1 antitrypsin (intestinal permeability) and REG1B (intestinal damage). RESULTS There was an inverse association between microbiota maturity and diversity and fecal concentrations of all 3 EED biomarkers at 18 months (p≤0.001). The results were similar at 30 months, while at 6 months inverse associations were found only with calprotectin and alpha-1 antitrypsin concentrations. At 18 months, EED biomarkers were not associated with phylogenetic dissimilarity, but at 6 and 30 months several associations were observed. Individual taxa predicting EED biomarker concentrations at 18 months included several Bifidobacterium and Enterobacteriaceae taxa as well as potentially displaced oral taxa. CONCLUSIONS Our findings support the hypothesis of an inverse association between microbiota maturity and diversity and EED in rural Malawian children.
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Affiliation(s)
- Emma Kortekangas
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland,Correspondence: Emma Kortekangas, Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Global Health, Tampere University, Arvo Ylpön katu 34, Arvo building, Tampere 33014, Finland. Tel: +358-3-355-111. Fax +358-3-213-4473. E-mail <>
| | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - David Chaima
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Kirsi-Maarit Lehto
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Chikondi Malamba-Banda
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Andrew Matchado
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi,Department of Nutrition and Institute for Global Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Chilungamo Chingwanda
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Zhifei Liu
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland
| | - Yin Bun Cheung
- Program in Health Services & Systems Research and Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kathryn G Dewey
- Department of Nutrition and Institute for Global Nutrition, University of California Davis, Davis, CA 95616, USA
| | - Kenneth Maleta
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere 33014, Finland,Department of Pediatrics, Tampere University Hospital, Tampere 33520, Finland
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Hernandez-Alonso E, Barreault S, Augusto LA, Jatteau P, Villet M, Tissieres P, Doucet-Populaire F, Bourgeois-Nicolaos N. dnaJ: a New Approach to Identify Species within the Genus Enterobacter. Microbiol Spectr 2021; 9:e0124221. [PMID: 34937187 PMCID: PMC8694106 DOI: 10.1128/spectrum.01242-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/19/2021] [Indexed: 01/19/2023] Open
Abstract
The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI). We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type-strain library and the SeqScape software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research. IMPORTANCE We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF.
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Affiliation(s)
- Enrique Hernandez-Alonso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Simon Barreault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris-Saclay, Bicêtre Hospital, Paris, France
| | - Luis A. Augusto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pierre Jatteau
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Millie Villet
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Pierre Tissieres
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris-Saclay, Bicêtre Hospital, Paris, France
- FHU Sepsis, AP-HP/Université Paris-Saclay/Inserm, Le Kremlin-Bicêtre, France
| | - Florence Doucet-Populaire
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Nadege Bourgeois-Nicolaos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
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Daisley BA, Reid G. BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities. mSystems 2021; 6:e00082-21. [PMID: 33824193 PMCID: PMC8546966 DOI: 10.1128/msystems.00082-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 01/04/2023] Open
Abstract
High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to "bxid" placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species-two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors.IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on "in-house" reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.
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Affiliation(s)
- Brendan A Daisley
- Department of Microbiology & Immunology, The University of Western Ontario, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
| | - Gregor Reid
- Department of Microbiology & Immunology, The University of Western Ontario, London, Ontario, Canada
- Canadian Centre for Human Microbiome and Probiotics Research, London, Ontario, Canada
- Department of Surgery, Schulich School of Medicine, London, Ontario, Canada
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Wastewaters, with or without Hospital Contribution, Harbour MDR, Carbapenemase-Producing, but Not Hypervirulent Klebsiella pneumoniae. Antibiotics (Basel) 2021; 10:antibiotics10040361. [PMID: 33805405 PMCID: PMC8065489 DOI: 10.3390/antibiotics10040361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae (CPKP) isolated from influent (I) and effluent (E) of two wastewater treatment plants, with (S1) or without (S2) hospital contribution, were investigated. The strains belonged to the Kp1 phylogroup, their highest frequency being observed in S1, followed by S2. The phenotypic and genotypic hypervirulence tests were negative for all the strains tested. At least one carbapenemase gene (CRG), belonging to the blaKPC, blaOXA-48, blaNDM and blaVIM families, was observed in 63% of CPKP, and more than half co-harboured two to four CRGs, in different combinations. Only five CRG variants were observed, regardless of wastewater type: blaKPC-2, blaNDM-1, blaNDM-6, blaVIM-2, and blaOXA-48. Sequence types ST258, ST101 and ST744 were common for both S1 and S2, while ST147, ST525 and ST2502 were found only in S1 and ST418 only in S2. The strains tested were multi-drug resistant (MDR), all being resistant to beta-lactams, cephalosporins, carbapenems, monobactams and fluoroquinolones, followed by various resistance profiles to aminoglycosides, trimethoprim-sulphamethoxazole, tigecycline, chloramphenicol and tetracycline. After principal component analysis, the isolates in S1 and S2 groups did not cluster independently, confirming that the antibiotic susceptibility patterns and gene-type profiles were both similar in the K. pneumoniae investigated, regardless of hospital contribution to the wastewater type.
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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The Changing Face of the Family Enterobacteriaceae (Order: " Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes. Clin Microbiol Rev 2021; 34:34/2/e00174-20. [PMID: 33627443 DOI: 10.1128/cmr.00174-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.
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Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. J Clin Microbiol 2020; 58:JCM.01605-20. [PMID: 33028602 DOI: 10.1128/jcm.01605-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
The broad-range detection and identification of bacterial DNA from clinical specimens are a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false-negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acids. Here, we describe an alternative, next-generation sequencing approach for the broad range detection of bacterial DNA using broad-range 16S rRNA gene hybrid capture ("16S Capture"). The method is able to deconvolute multiple bacterial species present in a specimen, is compatible with highly fragmented templates, and can be readily implemented when the overwhelming majority of nucleic acids in a specimen derive from the human host. We find that this approach is sensitive to detecting as few as 17 Staphylococcus aureus genomes from a background of 100 ng of human DNA, providing 19- to 189-fold greater sensitivity for identifying bacterial sequences than standard shotgun metagenomic sequencing, and is able to successfully recover organisms from across the eubacterial tree of life. Application of 16S Capture to a proof-of-principle case series demonstrated its ability to identify bacterial species that were consistent with histological evidence of infection, even when diagnosis could not be established using conventional broad range bacterial detection assays. 16S Capture provides a novel means for the efficient and sensitive detection of bacteria embedded in human tissues and for specimens containing highly fragmented template DNA.
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Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country. Diagnostics (Basel) 2020; 10:diagnostics10100816. [PMID: 33066371 PMCID: PMC7602188 DOI: 10.3390/diagnostics10100816] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.
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Lieberman JA, Naureckas Li C, Lamb GS, Kane DA, Stewart MK, Mamedov RA, Cookson BT, Salipante SJ. Case Report: Comparison of Plasma Metagenomics to Bacterial PCR in a Case of Prosthetic Valve Endocarditis. Front Pediatr 2020; 8:575674. [PMID: 33489996 PMCID: PMC7819283 DOI: 10.3389/fped.2020.575674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular assays for infectious diseases have emerged as important clinical decision-making tools. Unbiased, metagenomic next-generation sequencing is a novel approach holding promise to detect pathogens missed by conventional modalities and to deconvolute admixed nucleic acid sequences from polymicrobial infections in order to identify constituent pathogens. Recent studies have raised concerns about the clinical impact of metagenomics assays and whether their expense is justified. Here, we report a case of polyclonal Streptococcus cristatus endocarditis in a 14-year-old woman with a history of Tetralogy of Fallot. Three sets of admission blood cultures and a commercial plasma metagenomics assay were negative for pathogens, despite persistent vegetations observed on the valve during a later procedure. Multiple strains of Streptococcus cristatus were identified from the explanted valve by amplicon-based 16S rRNA sequencing, confirming the patient had received appropriate antibiotic therapy. This case highlights limitations in the use and interpretation of clinical metagenomics for infectious disease diagnosis and indicates that the clinical yield of these tools may depend upon infection type and anatomic location.
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Affiliation(s)
- Joshua A Lieberman
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Caitlin Naureckas Li
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - Gabriella S Lamb
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - David A Kane
- Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Mary K Stewart
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Ruslan A Mamedov
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Brad T Cookson
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States.,Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
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