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Hernández-Neuta I, Magoulopoulou A, Pineiro F, Lisby JG, Gulberg M, Nilsson M. Highly multiplexed targeted sequencing strategy for infectious disease surveillance. BMC Biotechnol 2023; 23:31. [PMID: 37612665 PMCID: PMC10463907 DOI: 10.1186/s12896-023-00804-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs). RESULTS Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis. CONCLUSIONS Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.
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Affiliation(s)
- Iván Hernández-Neuta
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Anastasia Magoulopoulou
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Flor Pineiro
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Jan Gorm Lisby
- Department of Clinical Microbiology, Amager and Hvidovre Hospital, University of Copenhagen, Kettegaard Alle 30, Hvidovre, 2650, Denmark
| | - Mats Gulberg
- Q-linea AB, Dag Hammarskjölds Väg 52A, Uppsala, 752 37, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden.
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden.
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2
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van Thiel I, de Jonge W, van den Wijngaard R. Fungal feelings in the irritable bowel syndrome: the intestinal mycobiome and abdominal pain. Gut Microbes 2023; 15:2168992. [PMID: 36723172 PMCID: PMC9897793 DOI: 10.1080/19490976.2023.2168992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although the gut microbiota consists of bacteria, viruses, and fungi, most publications addressing the microbiota-gut-brain axis in irritable bowel syndrome (IBS) have a sole focus on bacteria. This may relate to the relatively low presence of fungi and viruses as compared to bacteria. Yet, in the field of inflammatory bowel disease research, the publication of several papers addressing the role of the intestinal mycobiome now suggested that these low numbers do not necessarily translate to irrelevance. In this review, we discuss the available clinical and preclinical IBS mycobiome data, and speculate how these recent findings may relate to earlier observations in IBS. By surveying literature from the broader mycobiome research field, we identified questions open to future IBS-oriented investigations.
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Affiliation(s)
- Iam van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Wj de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Department of General, Visceral-, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - Rm van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands,CONTACT RM van den Wijngaard Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Meibergdreef 69-71, Amsterdam1105 BK, The Netherlands
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3
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Kanokudom S, Assawakongkarat T, Akeda Y, Ratthawongjirakul P, Chuanchuen R, Chaichanawongsaroj N. Rapid detection of extended spectrum β-lactamase producing Escherichia coli isolated from fresh pork meat and pig cecum samples using multiplex recombinase polymerase amplification and lateral flow strip analysis. PLoS One 2021; 16:e0248536. [PMID: 33720963 PMCID: PMC7959403 DOI: 10.1371/journal.pone.0248536] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/27/2021] [Indexed: 12/29/2022] Open
Abstract
The emergence and dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a global health issue. Food-producing animals, including pigs, are significant reservoirs of antimicrobial resistance (AMR), which can be transmitted to humans. Thus, the rapid detection of ESBLs is required for efficient epidemiological control and treatment. In this study, multiplex recombinase polymerase amplification (RPA) combined with a single-stranded tag hybridization chromatographic printed-array strip (STH-PAS), as a lateral flow strip assay (LFA), was established for the rapid and simultaneous detection of multiple bla genes in a single reaction. Visible blue lines, indicating the presence of the blaCTX-M, blaSHV, and blaOXA genes, were observed within 10 min by the naked eye. The limit of detection of all three genes was 2.5 ng/25 μL, and no cross-reactivity with seven commensal aerobic bacteria was observed. A total of 93.9% (92/98) and 96% (48/50) of the E. coli isolates from pork meat and fecal samples, respectively, expressed an ESBL-producing phenotype. Nucleotide sequencing of the PCR amplicons showed that blaCTX-M was the most prevalent type (91.3–95.83%), of which the main form was blaCTX-M-55. The sensitivity and specificity of the RPA-LFA were 99.2% and 100%, respectively, and were in almost perfect agreement (κ = 0.949–1.000) with the results from PCR sequencing. Thus, the RPA-LFA is a promising tool for rapid and equipment-free ESBL detection and may facilitate clinical diagnosis in human and veterinary medicine, as well as AMR monitoring and surveillance.
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Affiliation(s)
- Sitthichai Kanokudom
- Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thachaporn Assawakongkarat
- Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Yukihiro Akeda
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka University, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Panan Ratthawongjirakul
- Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nuntaree Chaichanawongsaroj
- Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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Bernabeu S, Ratnam KC, Boutal H, Gonzalez C, Vogel A, Devilliers K, Plaisance M, Oueslati S, Malhotra-Kumar S, Dortet L, Fortineau N, Simon S, Volland H, Naas T. A Lateral Flow Immunoassay for the Rapid Identification of CTX-M-Producing Enterobacterales from Culture Plates and Positive Blood Cultures. Diagnostics (Basel) 2020; 10:diagnostics10100764. [PMID: 32998433 PMCID: PMC7600033 DOI: 10.3390/diagnostics10100764] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
We have developed a lateral flow immunoassay (LFIA), named NG-Test CTX-M MULTI (NG-Test), to detect group 1, 2, 8, 9, 25 CTX-M producers from agar plates and from positive blood cultures in less than 15 min. The NG-Test was validated retrospectively on 113 well-characterized enterobacterial isolates, prospectively on 102 consecutively isolated ESBL-producers from the Bicêtre hospital and on 100 consecutive blood cultures positive with a gram-negative bacilli (GNB). The NG-Test was able to detect all CTX-M producers grown on the different agar plates used in clinical microbiology laboratories. No false positive nor negative results were observed. Among the 102 consecutive ESBL isolates, three hyper mucous isolates showed an incorrect migration leading to invalid results (no control band). Using an adapted protocol, the results could be validated. The NG-Test detected 99/102 ESBLs as being CTX-Ms. Three SHV producers were not detected. Among the 100 positive blood cultures with GNB tested 10/11 ESBL-producers were detected (8 CTX-M-15, 2 CTX-M-27). One SHV-2-producing-E. cloacae was missed. The NG-Test CTX-M MULTI showed 100% sensitivity and specificity with isolates cultured on agar plates and was able to detect 98% of the ESBL-producers identified in our clinical setting either from colonies or from positive blood cultures.
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Affiliation(s)
- Sandrine Bernabeu
- Team Resist, UMR1184, School of Medicine of Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 94276 Le Kremlin-Bicêtre, France; (S.B.); (S.O.); (L.D.); (N.F.)
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
| | | | - Hervé Boutal
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Camille Gonzalez
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
| | - Anaïs Vogel
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Karine Devilliers
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Marc Plaisance
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Saoussen Oueslati
- Team Resist, UMR1184, School of Medicine of Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 94276 Le Kremlin-Bicêtre, France; (S.B.); (S.O.); (L.D.); (N.F.)
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium;
- Members of ESCMID Study Group for Antimicrobial Resistance Surveillance—ESGARS, Headquarter, 4010 Basel, Switzerland
| | - Laurent Dortet
- Team Resist, UMR1184, School of Medicine of Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 94276 Le Kremlin-Bicêtre, France; (S.B.); (S.O.); (L.D.); (N.F.)
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Nicolas Fortineau
- Team Resist, UMR1184, School of Medicine of Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 94276 Le Kremlin-Bicêtre, France; (S.B.); (S.O.); (L.D.); (N.F.)
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Stéphanie Simon
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Hervé Volland
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d’Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (H.B.); (A.V.); (K.D.); (M.P.); (S.S.); (H.V.)
| | - Thierry Naas
- Team Resist, UMR1184, School of Medicine of Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 94276 Le Kremlin-Bicêtre, France; (S.B.); (S.O.); (L.D.); (N.F.)
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France; (K.C.R.); (C.G.)
- Members of ESCMID Study Group for Antimicrobial Resistance Surveillance—ESGARS, Headquarter, 4010 Basel, Switzerland
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
- Service de Bactériologie, AP-HP, CHU de Bicêtre, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
- Correspondence: ; Tel.: +33-1-45-21-29-86
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Musa BM, Imam H, Lendel A, Abdulkadir I, Gumi HS, Aliyu MH, Habib AG. The burden of extended-spectrum β-lactamase-producing Enterobacteriaceae in Nigeria: a systematic review and meta-analysis. Trans R Soc Trop Med Hyg 2020; 114:241-248. [PMID: 31925440 DOI: 10.1093/trstmh/trz125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/18/2019] [Accepted: 11/04/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Antibiotic resistance on account of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has become a major public health concern in developing countries. The presence of ESBL-PE is associated with increased morbidity, mortality and healthcare costs. There is no active antimicrobial surveillance mechanism in Nigeria. The aim of this study is to determine a precise estimate of the burden of ESBL-PE in Nigeria. We employed Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines and searched electronic databases for suitable studies. We derived pooled prevalence estimates using random effects models and assessed trends with meta-regression. We found 208 studies, with 38 satisfying our inclusion criteria. The overall pooled prevalence of ESBL-PE in Nigeria was 34.6% (95% CI 26.8 to 42.3%) and increased at a rate of 0.22% per year (p for trend=0.837). In summary, we found the prevalence of ESBL-PE in Nigeria to be high and recommend a robust national survey to provide a more detailed picture of the epidemiology of ESBL-PE in Nigeria.
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Affiliation(s)
- Baba M Musa
- Department of Medicine, Bayero University/Aminu Kano Teaching Hospital, Kano, Nigeria. 700241
- Africa Center of Excellence of Population Health and Policy (ACEPHAP) Bayero University, Kano, Nigeria
| | - Hassana Imam
- Department of Medicine, Bayero University/Aminu Kano Teaching Hospital, Kano, Nigeria. 700241
| | - Anastasia Lendel
- Center for Medicine, Health and Society 300 Calhoun Hall, Vanderbilt University, Nashville, TN 37240, USA
| | - Isa Abdulkadir
- Department of Pediatrics, Ahmadu Bello University Teaching Hospital,Zaria, Nigeria
| | - Halima S Gumi
- North Devon District Hospital, Barnstable, EX31 1NR, UK
| | - Muktar H Aliyu
- Vanderbilt Institute for Global Health, 2525 West End Avenue, Suite 725, Nashville, Tennessee, 37203-1738, USA
| | - Abdulrazaq G Habib
- Department of Medicine, Bayero University/Aminu Kano Teaching Hospital, Kano, Nigeria. 700241
- Africa Center of Excellence of Population Health and Policy (ACEPHAP) Bayero University, Kano, Nigeria
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