1
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Campos-Madueno EI, Aldeia C, Perreten V, Sendi P, Moser AI, Endimiani A. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. Front Microbiol 2023; 14:1236208. [PMID: 37720151 PMCID: PMC10501143 DOI: 10.3389/fmicb.2023.1236208] [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: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.
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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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2
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Flint A, Cooper A, Rao M, Weedmark K, Carrillo C, Tamber S. Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood. Front Microbiol 2023; 14:1188872. [PMID: 37520363 PMCID: PMC10373929 DOI: 10.3389/fmicb.2023.1188872] [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: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.
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Affiliation(s)
- Annika Flint
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Ashley Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mary Rao
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Catherine Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
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3
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Lumbreras-Iglesias P, Sabater C, Fernández Moreno A, López de Ugarriza P, Fernández-Verdugo A, Margolles A, Rodicio MR, Bernal T, Fernández J. Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia. Microorganisms 2023; 11:microorganisms11020402. [PMID: 36838367 PMCID: PMC9964539 DOI: 10.3390/microorganisms11020402] [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: 12/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Patients diagnosed with acute leukemia (AL) have a weakened immune system. Infections acquired by these patients are cause for concern and especially worrisome when Gram-negative multidrug-resistant (MDR) bacteria are involved, as they are difficult to treat, especially in the case of ESBL- and/or carbapenemase-producing Enterobacterales. Culture-based approaches have been relied on over the past decades as the method of choice for the early detection of gut colonization by MDR Gram-negative bacteria. However, various studies have indicated its limited sensitivity, underlining the need for new screening procedures in onco-hematological patients. Here, we evaluated a shotgun metagenomics approach to detect ESBL- and/or carbapenemase-producing Enterobacterales in the gut of 28 patients who had recovered from AL, which were previously colonized by these bacteria but cured at the time of sampling, as judged by culture-based methods. No ESBL or carbapenemase determinants were detected among the many resistance genes found by the metagenomics approach, supporting that patients were truly decolonized, with considerable consequences for their future clinical management. Due to the relatively low number of patients available for the present investigation, further studies should be conducted to support the utility and applicability of metagenomics for the routine screening of MDR bacteria in onco-hematological patients.
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Affiliation(s)
- Pilar Lumbreras-Iglesias
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
| | - Carlos Sabater
- Dairy Research Institute of Asturias (IPLA), Spanish National Research Council (CSIC), 33300 Villaviciosa, Spain
- MicroHealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ainhoa Fernández Moreno
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), 33011 Oviedo, Spain
| | - Paula López de Ugarriza
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), 33011 Oviedo, Spain
| | - Ana Fernández-Verdugo
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
| | - Abelardo Margolles
- Dairy Research Institute of Asturias (IPLA), Spanish National Research Council (CSIC), 33300 Villaviciosa, Spain
- MicroHealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - María Rosario Rodicio
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Department of Functional Biology, Microbiology Area, University of Oviedo, 33006 Oviedo, Spain
| | - Teresa Bernal
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto de Oncología del Principado de Asturias (IUOPA), 33011 Oviedo, Spain
| | - Javier Fernández
- Traslational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Department of Clinical Microbiology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 28029 Madrid, Spain
- Correspondence:
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Dewayani A, Afrida Fauzia K, Alfaray RI, Waskito LA, Doohan D, Rejeki PS, Alshawsh MA, Rezkitha YAA, Yamaoka Y, Miftahussurur M. Gastric microbiome changes in relation with Helicobacter pylori resistance. PLoS One 2023; 18:e0284958. [PMID: 37200323 DOI: 10.1371/journal.pone.0284958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/12/2023] [Indexed: 05/20/2023] Open
Abstract
INTRODUCTION Inadequate antimicrobial treatment has led to multidrug-resistant (MDR) bacteria, including Helicobacter pylori (H. pylori), which one of the notable pathogens in the stomach. Antibiotic-induced changes in the microbiota can negatively affect the host. This study aimed to determine the influence of H. pylori resistance on the diversity and abundance of the stomach microbiome. METHODS Bacterial DNA was extracted from biopsy samples of patients presenting dyspepsia symptoms with H. pylori positive from cultures and histology. DNA was amplified from the V3-V4 regions of the 16S rRNA gene. In-vitro E-test was used to detect antibiotic resistance. Microbiome community analysis was conducted through α-diversity, β-diversity, and relative abundance. RESULTS Sixty-nine H. pylori positive samples were eligible after quality filtering. Following resistance status to five antibiotics, samples were classified into 24 sensitive, 24 single resistance, 16 double resistance, 5 triple resistance. Samples were mostly resistant to metronidazole (73.33%; 33/45). Comparation of four groups displayed significantly elevated α-diversity parameters under the multidrug resistance condition (all P <0.05). A notable change was observed in triple-resistant compared to sensitive (P <0.05) and double-resistant (P <0.05) groups. Differences in β-diversity by UniFrac and Jaccard were not significant in terms of the resistance (P = 0.113 and P = 0.275, respectively). In the triple-resistant group, the relative abundance of Helicobacter genera was lower, whereas that of Streptococcus increased. Moreover, the linear discriminant analysis effect size (LEfSe) was associated with the presence of Corynebacterium and Saccharimonadales in the single-resistant group and Pseudomonas and Cloacibacterium in the triple-resistant group. CONCLUSION Our results suggest that the resistant samples showed a higher trend of diversity and evenness than the sensitive samples. The abundance of H. pylori in the triple-resistant samples decreased with increasing cohabitation of pathogenic bacteria, which may support antimicrobial resistance. However, antibiotic susceptibility determined by the E-test may not completely represent the resistance status.
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Affiliation(s)
- Astri Dewayani
- Oita University Faculty of Medicine, Department of Infectious Disease Control, Yufu, Oita, Japan
- Faculty of Medicine, Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
| | - Kartika Afrida Fauzia
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
- Oita University Faculty of Medicine, Department of Environmental and Preventive Medicine, Yufu, Oita, Japan
- Faculty of Medicine, Department of Public Health and Preventive Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Ricky Indra Alfaray
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
- Oita University Faculty of Medicine, Department of Environmental and Preventive Medicine, Yufu, Oita, Japan
| | - Langgeng Agung Waskito
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
- Faculty of Medicine, Department of Medical Physiology and Biochemistry, Universitas Airlangga, Surabaya, Indonesia
| | - Dalla Doohan
- Faculty of Medicine, Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
| | - Purwo Sri Rejeki
- Faculty of Medicine, Department of Medical Physiology and Biochemistry, Universitas Airlangga, Surabaya, Indonesia
| | - Mohammed Abdullah Alshawsh
- Faculty of Medicine, Department of Pharmacology, Universiti Malaya, Kuala Lumpur, Malaysia
- Faculty of Medicine, School of Clinical Sciences, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Yudith Annisa Ayu Rezkitha
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
- Faculty of Medicine, Department of Internal Medicine, University of Muhammadiyah Surabaya, Surabaya, Indonesia
| | - Yoshio Yamaoka
- Oita University Faculty of Medicine, Department of Environmental and Preventive Medicine, Yufu, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, United States of America
- Research Center for Global and Local Infectious Diseases, Oita University, Yufu, Oita, Japan
- Faculty of Medicine, Department of Internal Medicine, Division of Gastroentero-Hepatology, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Muhammad Miftahussurur
- Institute of Tropical Disease, Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, Indonesia
- Faculty of Medicine, Department of Internal Medicine, Division of Gastroentero-Hepatology, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
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5
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. THE ISME JOURNAL 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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6
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Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022; 13:761873. [PMID: 35464955 PMCID: PMC9020828 DOI: 10.3389/fmicb.2022.761873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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Affiliation(s)
- Claudie Lamoureux
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Laure Surgers
- GHU AP-HP Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Vincent Fihman
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France
| | - Guillaume Gricourt
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Melissa N'Debi
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Camille Gomart
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Guilhem Royer
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Nathalie Launay
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jeanne-Marie Le Glaunec
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Charlotte Wemmert
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Giulia La Martire
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Geoffrey Rossi
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jean-Michel Pawlotsky
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Christophe Rodriguez
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France.,NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Paul-Louis Woerther
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France.,Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
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7
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Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021; 11:694756. [PMID: 34568089 PMCID: PMC8458627 DOI: 10.3389/fcimb.2021.694756] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.
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Affiliation(s)
- Yan Zheng
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Xiaojian Qiu
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
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8
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Langdon A, Schwartz DJ, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CAD, Dubberke ER, Dantas G. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med 2021; 13:28. [PMID: 33593430 PMCID: PMC7888090 DOI: 10.1186/s13073-021-00843-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI. METHODS An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms. RESULTS Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted. CONCLUSIONS Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others. TRIAL REGISTRATION ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.
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Affiliation(s)
- Amy Langdon
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Christopher Bulow
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly A. Reske
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | | | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Erik R. Dubberke
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
| | - for the CDC Prevention Epicenter Program
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Rebiotix, Inc., Minneapolis, MN USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
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Obermeier MM, Wicaksono WA, Taffner J, Bergna A, Poehlein A, Cernava T, Lindstaedt S, Lovric M, Müller Bogotá CA, Berg G. Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance. ISME JOURNAL 2020; 15:921-937. [PMID: 33177608 PMCID: PMC8027415 DOI: 10.1038/s41396-020-00822-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022]
Abstract
The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.
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Affiliation(s)
- Melanie Maria Obermeier
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Alessandro Bergna
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstrasse 8, 37077, Göttingen, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Stefanie Lindstaedt
- Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, 8010, Graz, Austria
| | - Mario Lovric
- Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, 8010, Graz, Austria
| | - Christina Andrea Müller Bogotá
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria. .,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
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10
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Metagenomic study focusing on antibiotic resistance genes from the sediments of River Yamuna. Gene 2020; 758:144951. [DOI: 10.1016/j.gene.2020.144951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/26/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
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11
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Badia P, Andersen H, Haslam D, Nelson AS, Pate AR, Golkari S, Teusink-Cross A, Flesch L, Bedel A, Hickey V, Kramer K, Lane A, Davies SM, Thikkurissy S, Dandoy CE. Improving Oral Health and Modulating the Oral Microbiome to Reduce Bloodstream Infections from Oral Organisms in Pediatric and Young Adult Hematopoietic Stem Cell Transplantation Recipients: A Randomized Controlled Trial. Biol Blood Marrow Transplant 2020; 26:1704-1710. [PMID: 32505810 PMCID: PMC11168732 DOI: 10.1016/j.bbmt.2020.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 12/22/2022]
Abstract
Bloodstream infections (BSIs) from oral organisms are a significant cause of morbidity and mortality in hematopoietic stem cell transplantation (HSCT) recipients. There are no proven strategies to decrease BSIs from oral organisms. The aim of this study was to evaluate the impact of daily xylitol wipes in improving oral health, decreasing BSI from oral organisms, and modulating the oral microbiome in pediatric HSCT recipients. This was a single-center 1:1 randomized controlled trial in pediatric HSCT recipients age >2 years. Age-matched healthy children were enrolled to compare the oral microbiome. The oral hygiene standard of care (SOC) group continued to receive the standard oral hygiene regimen. The xylitol group received daily oral xylitol wipes (with .7 g xylitol) in addition to the SOC. The intervention started from the beginning of the transplantation chemotherapy regimen and extended to 28 days following transplantation. The primary outcome was oral health at interval time points, and secondary outcomes included BSIs from oral organisms in the first 30 days following transplantation, oral microbiome abundance, and diversity and oral pathogenic organism abundance. The study was closed early due to efficacy after an interim analysis of the first 30 HSCT recipients was performed (SOC group, n = 16; xylitol group, n = 14). The xylitol group had a significantly lower rate of gingivitis at days 7, 14, and 28 following transplantation (P = .031, .0039, and .0005, respectively); oral plaque at days 7 and 14 (P = .045 and .0023, respectively); and oral ulcers >10 mm at day 14 (P = .049) compared with the SOC group. The xylitol group had no BSI from oral organisms compared with the SOC group, which had 4 (P = .04). The xylitol group had significantly lower abundance of potential BSI pathogens, such as Staphylococcus aureus (P = .036), Klebsiella pneumoniae (P = .033), and Streptococcus spp (P = .011) at the day after transplantation compared with the SOC group. Healthy children and young adults had significantly increased oral microbiome diversity compared with all HSCT recipients (P < .001). The addition of xylitol to standard oral care significantly improves oral health, decreases BSI from oral organisms, and decreases the abundance of pathogenic oral organisms in pediatric and young adult HSCT recipients.
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Affiliation(s)
- Priscila Badia
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona.
| | - Heidi Andersen
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David Haslam
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Adam S Nelson
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Abigail R Pate
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sara Golkari
- Division of Pediatric Dentistry, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ashley Teusink-Cross
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Laura Flesch
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ashely Bedel
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Victoria Hickey
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kathi Kramer
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Adam Lane
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Stella M Davies
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sarat Thikkurissy
- Division of Pediatric Dentistry, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Christopher E Dandoy
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
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12
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Peto L, Fawcett NJ, Crook DW, Peto TEA, Llewelyn MJ, Walker AS. Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae. PLoS One 2019; 14:e0222831. [PMID: 31703058 PMCID: PMC6839868 DOI: 10.1371/journal.pone.0222831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/07/2019] [Indexed: 01/02/2023] Open
Abstract
Metagenomic sequencing of fecal DNA can usefully characterise an individual's intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.
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Affiliation(s)
- Leon Peto
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
- * E-mail:
| | - Nicola J. Fawcett
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Derrick W. Crook
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
- National Infection Service, Public Health England, Colindale, London, England, United Kingdom
| | - Tim E. A. Peto
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Martin J. Llewelyn
- Department of Global Health and Infection, Brighton and Sussex Medical School, Falmer, Sussex, England, United Kingdom
- Department of Microbiology and Infection, Brighton and Sussex University Hospitals NHS Trust, Brighton, England, United Kingdom
| | - A. Sarah Walker
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
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13
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Han D, Li Z, Li R, Tan P, Zhang R, Li J. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol 2019; 45:668-685. [PMID: 31691607 DOI: 10.1080/1040841x.2019.1681933] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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14
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15
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16
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Barraud O, Peyre M, Couvé-Deacon E, Chainier D, Bahans C, Guigonis V, Ploy MC, Bedu A, Garnier F. Antibiotic Resistance Acquisition in the First Week of Life. Front Microbiol 2018; 9:1467. [PMID: 30022973 PMCID: PMC6039568 DOI: 10.3389/fmicb.2018.01467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives: The fetus is considered sterile but recent studies have suggested that gut colonization could start before birth. Scarce data are available for the acquisition of resistant Gram-negative bacteria (GNB) during the first days of life. Several studies have shown that integrons play a major role in antibiotic resistance acquisition. In this work, we studied the dynamics of human intestinal acquisition of GNB and integrons during the first days of life. Methods: Meconium was collected at birth and a stool sample before hospital discharge (days 2 or 3) on 185 term neonates. GNB were searched by culture on each sample and class 1, 2, and 3 integrons from each GNB or directly from samples. Eight risk factors for integron and GNB acquisition were studied. Results: We isolated 228 GNB, 46 from meconium and the remainder from stools. No link was found between GNB isolation and antibiotic exposure during delivery, but antibiotic exposure during labor significantly selected blaTEM-positive amoxicillin-resistant Enterobacteria. Two-thirds of GNB were antibiotic-susceptible and most of the resistant isolates were acquired after birth. Integrons were detected in 18 of the 228 GNB isolates from 3 meconium and 20 stools. Antibiotic administration during delivery and vaginal carriage of Streptococcus agalactiae appeared as risk factors for integron acquisition. Conclusion: Gram-negative bacteria and integrons are mostly acquired after birth during the first days of life even if for some term neonates, meconium was not sterile. Antibiotic administration during delivery is a major risk for integron acquisition and for selection of amoxicillin-resistant Enterobacteria.
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Affiliation(s)
- Olivier Barraud
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Marianne Peyre
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France
| | | | - Delphine Chainier
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Claire Bahans
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Vincent Guigonis
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Marie-Cécile Ploy
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Antoine Bedu
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Fabien Garnier
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
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17
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The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis. mSphere 2018; 3:3/3/e00104-18. [PMID: 29875143 PMCID: PMC5990886 DOI: 10.1128/msphere.00104-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
Preterm infants face health problems likely related to microbial exposures, including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from that of healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from 32 preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found that both the preterm infant microbiome and the metabolome were personalized and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangle the health consequences of the preterm infant microbiome. The assembly and development of the gut microbiome in infants have important consequences for immediate and long-term health. Preterm infants represent an abnormal case for bacterial colonization because of early exposure to bacteria and frequent use of antibiotics. To better understand the assembly of the gut microbiota in preterm infants, fecal samples were collected from 32 very low birth weight preterm infants over the first 6 weeks of life. Infant health outcomes included health, late-onset sepsis, and necrotizing enterocolitis (NEC). We characterized bacterial compositions by 16S rRNA gene sequencing and metabolomes by untargeted gas chromatography-mass spectrometry. Preterm infant fecal samples lacked beneficial Bifidobacterium spp. and were dominated by Enterobacteriaceae, Enterococcus, and Staphylococcus organisms due to nearly uniform antibiotic administration. Most of the variance between the microbial community compositions could be attributed to the baby from which the sample derived (permutational multivariate analysis of variance [PERMANOVA] R2 = 0.48, P < 0.001), while clinical status (health, NEC, or late-onset sepsis) and overlapping times in the neonatal intensive care unit (NICU) did not explain a significant amount of variation in bacterial composition. Fecal metabolomes were also found to be unique to the individual (PERMANOVA R2 = 0.43, P < 0.001) and weakly associated with bacterial composition (Mantel statistic r = 0.23 ± 0.05, P < 0.05). No measured metabolites were found to be associated with necrotizing enterocolitis, late-onset sepsis, or a healthy outcome. Overall, preterm infant gut microbial communities were personalized and reflected antibiotic usage. IMPORTANCE Preterm infants face health problems likely related to microbial exposures, including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from that of healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from 32 preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found that both the preterm infant microbiome and the metabolome were personalized and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangle the health consequences of the preterm infant microbiome.
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18
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Jose S, Abhyankar MM, Mukherjee A, Xue J, Andersen H, Haslam DB, Madan R. Leptin receptor q223r polymorphism influences neutrophil mobilization after Clostridium difficile infection. Mucosal Immunol 2018; 11:947-957. [PMID: 29363668 PMCID: PMC5976520 DOI: 10.1038/mi.2017.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/11/2017] [Indexed: 02/04/2023]
Abstract
Clostridium difficile is the leading cause of nosocomial infections in the United States. Clinical disease outcomes after C. difficile infection (CDI) are dependent on intensity of host inflammatory responses. Specifically, peak peripheral white blood cell (WBC) count >20 × 109 l-1 is an indicator of adverse outcomes in CDI patients, and is associated with higher 30-day mortality. We show that homozygosity for a common single nucleotide polymorphism (Q to R mutation in leptin receptor that is present in up to 50% of people), significantly increases the risk of having peak peripheral WBC count >20 × 109 l-1 (odds ratio=5.41; P=0.0023) in CDI patients. In a murine model of CDI, we demonstrate that mice homozygous for the same single nucleotide polymorphism (RR mice) have more blood and tissue leukocytes (specifically neutrophils), exaggerated tissue inflammation, and higher mortality as compared with control mice, despite similar pathogen burden. Further, we show that neutrophilia in RR mice is mediated by gut microbiota-directed expression of CXC chemokine receptor 2 (CXCR2), which promotes the release of neutrophils from bone marrow reservoir. Overall these studies provide novel mechanistic insights into the role of human genetic polymorphisms and gut microbiota in regulating the fundamental biological process of CDI-induced neutrophilia.
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Affiliation(s)
- Shinsmon Jose
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Mayuresh M. Abhyankar
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Anindita Mukherjee
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Jianli Xue
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Heidi Andersen
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - David B. Haslam
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rajat Madan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA,Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45267, USA,Correspondence:
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19
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Häsler R, Kautz C, Rehman A, Podschun R, Gassling V, Brzoska P, Sherlock J, Gräsner JT, Hoppenstedt G, Schubert S, Ferlinz A, Lieb W, Laudes M, Heinsen FA, Scholz J, Harmsen D, Franke A, Eisend S, Kunze T, Fickenscher H, Ott S, Rosenstiel P, Schreiber S. The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany. MICROBIOME 2018; 6:37. [PMID: 29458422 PMCID: PMC5819293 DOI: 10.1186/s40168-018-0414-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/24/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Multidrug-resistant bacteria represent a substantial global burden for human health, potentially fuelled by migration waves: in 2015, 476,649 refugees applied for asylum in Germany mostly as a result of the Syrian crisis. In Arabic countries, multiresistant bacteria cause significant problems for healthcare systems. Currently, no data exist describing antibiotic resistances in healthy refugees. Here, we assess the microbial landscape and presence of antibiotic resistance genes (ARGs) in refugees and German controls. To achieve this, a systematic study was conducted in 500 consecutive refugees, mainly from Syria, Iraq, and Afghanistan and 100 German controls. Stool samples were subjected to PCR-based quantification of 42 most relevant ARGs, 16S ribosomal RNA gene sequencing-based microbiota analysis, and culture-based validation of multidrug-resistant microorganisms. RESULTS The fecal microbiota of refugees is substantially different from that of resident Germans. Three categories of resistance profiles were found: (i) ARGs independent of geographic origin of individuals comprising BIL/LAT/CMA, ErmB, and mefE; (ii) vanB with a high prevalence in Germany; and (iii) ARGs showing substantially increased prevalences in refugees comprising CTX-M group 1, SHV, vanC1, OXA-1, and QnrB. The majority of refugees carried five or more ARGs while the majority of German controls carried three or less ARGs, although the observed ARGs occurred independent of signatures of potential pathogens. CONCLUSIONS Our results, for the first time, assess antibiotic resistance genes in refugees and demonstrate a substantially increased prevalence for most resistances compared to German controls. The antibiotic resistome in refugees may thus require particular attention in the healthcare system of host countries.
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Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Christian Kautz
- Pharmaceutical Institute, Department of Clinical Pharmacy, Christian Albrecht University of Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Rainer Podschun
- Institute of Infection Medicine, Christian Albrecht University of Kiel, Kiel, Germany
| | - Volker Gassling
- Department of Oral and Maxillofacial Surgery, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Pius Brzoska
- Thermo Fisher Scientific, San Francisco, CA, USA
| | - Jon Sherlock
- Thermo Fisher Scientific, San Francisco, CA, USA
| | - Jan-Thorsten Gräsner
- Department of Anaesthesia and Intensive Care Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Gesine Hoppenstedt
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Sabine Schubert
- Institute of Infection Medicine, Christian Albrecht University of Kiel, Kiel, Germany
| | - Astrid Ferlinz
- Thermo Fisher Scientific, Life Technologies GmbH, Darmstadt, Germany
| | - Wolfgang Lieb
- POPGEN Biobank and Institute of Epidemiology, Christian Albrecht University of Kiel, Kiel, Germany
| | - Matthias Laudes
- POPGEN Biobank and Institute of Epidemiology, Christian Albrecht University of Kiel, Kiel, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Jens Scholz
- Department of Anaesthesia and Intensive Care Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University Hospital Münster, Münster, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Swantje Eisend
- Department of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Thomas Kunze
- Pharmaceutical Institute, Department of Clinical Pharmacy, Christian Albrecht University of Kiel, Kiel, Germany
| | - Helmut Fickenscher
- Institute of Infection Medicine, Christian Albrecht University of Kiel, Kiel, Germany
| | - Stephan Ott
- Department of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian Albrecht University of Kiel, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
- Department of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
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Abstract
PURPOSE OF REVIEW With the advent of novel massively parallel sequencing technologies and bioinformatic processing capabilities, clinical applications of metagenomic studies are rapidly being integrated into medicine. Through this paper, we hope to introduce this powerful new tool to clinicians caring for children. RECENT FINDINGS Very few studies have looked at metagenomic applications in children. The ability to perform these types of massive sequencing projects was not possible as little as 7 years ago. SUMMARY Metagenomics is defined as the study of all genetic material within a given sample. Novel sequencing and analysis approaches allow for unbiased assays to identify pathogens missed by targeted sequencing and culture methods. Although not widely available yet, metagenomic studies have been used to diagnose pediatric infections, identify resistance genes in clinical samples, and characterize outbreaks. Although cost and turnaround time have limited its application in clinical laboratories to date, novel platforms and increasing comfort with these techniques continue to push diagnostic metagenomics into clinical pediatric medicine. Much work in this field is yet to be done. That being said, we feel that pediatric clinicians will be using metagenomic techniques in the care of children with increasing frequency in the near future.
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21
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Araos R, Montgomery V, Ugalde JA, Snyder GM, D’Agata EMC. Microbial Disruption Indices to Detect Colonization With Multidrug-Resistant Organisms. Infect Control Hosp Epidemiol 2017; 38:1312-1318. [PMID: 28899445 PMCID: PMC6262892 DOI: 10.1017/ice.2017.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To characterize the microbial disruption indices of hospitalized patients to predict colonization with multidrug-resistant organisms (MDROs). DESIGN A cross-sectional survey of the fecal microbiome was conducted in a tertiary referral, acute-care hospital in Boston, Massachusetts. PARTICIPANTS The study population consisted of adult patients hospitalized in general medical/surgical wards. METHODS Rectal swabs were obtained from patients within 48 hours of hospital admission and screened for MDRO colonization using conventional culture techniques. The V4 region of the 16S rRNA gene was sequenced to assess the fecal microbiome. Microbial diversity and composition, as well as the functional potential of the microbial communities present in fecal samples, were compared between patients with and without MDRO colonization. RESULTS A total of 44 patients were included in the study, of whom 11 (25%) were colonized with at least 1 MDRO. Reduced microbial diversity and high abundance of metabolic pathways associated with multidrug-resistance mechanisms characterized the fecal microbiome of patients colonized with MDRO at hospital admission. CONCLUSIONS Our data suggest that microbial disruption indices may be key to predicting MDRO colonization and could provide novel infection control approaches. Infect Control Hosp Epidemiol 2017;38:1312-1318.
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Affiliation(s)
- Rafael Araos
- Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Veronica Montgomery
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Juan A. Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Graham M. Snyder
- Department of Medicine, Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA
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22
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Thomas M, Webb M, Ghimire S, Blair A, Olson K, Fenske GJ, Fonder AT, Christopher-Hennings J, Brake D, Scaria J. Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle. Sci Rep 2017; 7:12257. [PMID: 28947833 PMCID: PMC5612972 DOI: 10.1038/s41598-017-12481-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 01/28/2023] Open
Abstract
In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.
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Affiliation(s)
- Milton Thomas
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Megan Webb
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Amanda Blair
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Kenneth Olson
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Gavin John Fenske
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Alex Thomas Fonder
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Jane Christopher-Hennings
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Derek Brake
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA. .,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA.
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23
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Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms. Proc Natl Acad Sci U S A 2017; 114:10467-10472. [PMID: 28900004 DOI: 10.1073/pnas.1710235114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of multidrug-resistant organisms (MDROs) across global healthcare networks poses a serious threat to hospitalized individuals. Strategies to limit the emergence and spread of MDROs include oversight to decrease selective pressure for MDROs by promoting appropriate antibiotic use via antibiotic stewardship programs. However, restricting the use of one antibiotic often requires a compensatory increase in the use of other antibiotics, which in turn selects for the emergence of different MDRO species. Further, the downstream effects of antibiotic treatment decisions may also be influenced by functional interactions among different MDRO species, with the potential clinical implications of such interactions remaining largely unexplored. Here, we attempt to decipher the influence network between antibiotic treatment, MDRO colonization, and infection by leveraging active surveillance and antibiotic treatment data for 234 nursing home residents. Our analysis revealed a complex network of interactions: antibiotic use was a risk factor for primary MDRO colonization, which in turn increased the likelihood of colonization and infection by other MDROs. When we focused on the risk of catheter-associated urinary tract infections (CAUTI) caused by Escherichia coli, Enterococcus, and Staphylococcus aureus we observed that cocolonization with specific pairs of MDROs increased the risk of CAUTI, signifying the involvement of microbial interactions in CAUTI pathogenesis. In summary, our work demonstrates the existence of an underappreciated healthcare-associated ecosystem and strongly suggests that effective control of overall MDRO burden will require stewardship interventions that take into account both primary and secondary impacts of antibiotic treatments.
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24
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Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: The Next Culture-Independent Game Changer. Front Microbiol 2017; 8:1069. [PMID: 28725217 PMCID: PMC5495826 DOI: 10.3389/fmicb.2017.01069] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/29/2017] [Indexed: 02/01/2023] Open
Abstract
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other 'omics' disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.
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Affiliation(s)
- Jessica D. Forbes
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
- Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
| | - Aleisha Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
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25
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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