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Ghafari S, Alavi SM, Khaghani S. Potentially pathogenic culturable bacteria in hemodialysis waters. BMC Microbiol 2024; 24:276. [PMID: 39054498 PMCID: PMC11270894 DOI: 10.1186/s12866-024-03430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/16/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Hemodialysis patients are at risk of acquiring healthcare-related infections due to using non-sterile water to prepare hemodialysis fluid. Therefore, microbiological control and monitoring of used water are of crucial importance. MATERIALS AND METHODS In this work, we identified bacterial populations occupying a hemodialysis water distribution system for almost a 6-month period in Ahvaz city, southwest of Iran. A total of 18 samples from three points were collected. We found high colony counts of bacteria on R2A agar. 31 bacteria with different morphological and biochemical characteristics were identified by molecular-genetic methods based on 16 S rRNA gene sequencing. Endotoxin concentrations were measured, using Endosafe® Rapid LAL Single-Test Vials. RESULTS A diverse bacterial community was identified, containing predominantly Gram-negative bacilli. The most frequently isolated genus was Sphingomonas. Five species including M. fortuitum, M. lentiflavum, M.szulgai, M. barrassiae, and M. gordonae was identified .Despite the presence of Gram-negative bacteria the endotoxin analysis of all samples revealed that their endotoxin values were below the detection limit. CONCLUSION The members of Sphingomonas genus along with Bosea and mycobacteria could be regarded as pioneers in surface colonization and biofilm creation. These bacteria with others like Pelomonas, Bradyrhizobium, staphylococcus, and Microbacterium may represent a potential health risk to patients under hemodialysis treatment.
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Affiliation(s)
- Shokouh Ghafari
- Cellular and Molecular Research Center, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Seyed Mohammad Alavi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Soheila Khaghani
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Rocha-de-Lossada C, Mazzotta C, Gabrielli F, Papa FT, Gómez-Huertas C, García-López C, Urbinati F, Rachwani-Anil R, García-Lorente M, Sánchez-González JM, Rechichi M, Rubegni G, Borroni D. Ocular Surface Microbiota in Naïve Keratoconus: A Multicenter Validation Study. J Clin Med 2023; 12:6354. [PMID: 37834997 PMCID: PMC10573816 DOI: 10.3390/jcm12196354] [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: 09/10/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of Ophthalmology, the mNGS 16S rRNA sequencing method of studying the microbiota and ocular microbiome is gaining more and more weight in the scientific community. This study aims to characterize the ocular microbiota of patients diagnosed with keratoconus who have not undergone any prior surgical treatment using the mNGS 16S rRNA sequencing method. Samples of naïve keratoconus patients were collected with an eNAT with 1 mL of Liquid Amies Medium (Copan Brescia, Italy), and DNA was extracted and analyzed with 16S NGS. The microbiota analysis showed a relative abundance of microorganisms at the phylum level in each sample collected from 38 patients with KC and 167 healthy controls. A comparison between healthy control and keratoconus samples identified two genera unique to keratoconus, Pelomonas and Ralstonia. Our findings suggest that alterations in the microbiota may play a role in the complex scenario of KC development.
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Affiliation(s)
- Carlos Rocha-de-Lossada
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
- Ophthalmology Department, QVision, Vithas Almería, 04120 Almeria, Spain
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | - Cosimo Mazzotta
- Siena Crosslinking Center, 53100 Siena, Italy;
- Departmental Ophthalmology Unit, USL Toscana Sud Est l, 53100 Siena, Italy
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Federico Gabrielli
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Filomena Tiziana Papa
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Carmen Gómez-Huertas
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Celia García-López
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Facundo Urbinati
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - María García-Lorente
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - Miguel Rechichi
- Centro Polispecialistico Mediterraneo, 88050 Sellia Marina, Italy;
| | - Giovanni Rubegni
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Davide Borroni
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
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3
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Pylephlebitis: A Systematic Review on Etiology, Diagnosis, and Treatment of Infective Portal Vein Thrombosis. Diagnostics (Basel) 2023; 13:diagnostics13030429. [PMID: 36766534 PMCID: PMC9914785 DOI: 10.3390/diagnostics13030429] [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: 11/13/2022] [Revised: 12/20/2022] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Pylephlebitis, defined as infective thrombophlebitis of the portal vein, is a rare condition with an incidence of 0.37-2.7 cases per 100,000 person-years, which can virtually complicate any intra-abdominal or pelvic infections that develop within areas drained by the portal venous circulation. The current systematic review aimed to investigate the etiology behind pylephlebitis in terms of pathogens involved and causative infective processes, and to report the most common symptoms at clinical presentation. We included 220 individuals derived from published cases between 1971 and 2022. Of these, 155 (70.5%) were male with a median age of 50 years. There were 27 (12.3%) patients under 18 years of age, 6 (2.7%) individuals younger than one year, and the youngest reported case was only 20 days old. The most frequently reported symptoms on admission were fever (75.5%) and abdominal pain (66.4%), with diverticulitis (26.5%) and acute appendicitis (22%) being the two most common causes. Pylephlebitis was caused by a single pathogen in 94 (42.8%) cases and polymicrobial in 60 (27.2%) cases. However, the responsible pathogen was not identified or not reported in 30% of the included patients. The most frequently isolated bacteria were Escherichia coli (25%), Bacteroides spp. (17%), and Streptococcus spp. (15%). The treatment of pylephlebitis consists initially of broad-spectrum antibiotics that should be tailored upon bacterial identification and continued for at least four to six weeks after symptom presentation. There is no recommendation for prescribing anticoagulants to all patients with pylephlebitis. However, they should be administered in patients with thrombosis progression on repeat imaging or persistent fever despite proper antibiotic therapy to increase the rates of thrombus resolution or decrease the overall mortality, which is approximately 14%.
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Huggins LG, Koehler AV, Gasser RB, Traub RJ. Advanced approaches for the diagnosis and chemoprevention of canine vector-borne pathogens and parasites-Implications for the Asia-Pacific region and beyond. ADVANCES IN PARASITOLOGY 2023; 120:1-85. [PMID: 36948727 DOI: 10.1016/bs.apar.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Vector-borne pathogens (VBPs) of canines are a diverse range of infectious agents, including viruses, bacteria, protozoa and multicellular parasites, that are pernicious and potentially lethal to their hosts. Dogs across the globe are afflicted by canine VBPs, but the range of different ectoparasites and the VBPs that they transmit predominate in tropical regions. Countries within the Asia-Pacific have had limited prior research dedicated to exploring the epidemiology of canine VBPs, whilst the few studies that have been conducted show VBP prevalence to be high, with significant impacts on dog health. Moreover, such impacts are not restricted to dogs, as some canine VBPs are zoonotic. We reviewed the status of canine VBPs in the Asia-Pacific, with particular focus on nations in the tropics, whilst also investigating the history of VBP diagnosis and examining recent progress in the field, including advanced molecular methods, such as next-generation sequencing (NGS). These tools are rapidly changing the way parasites are detected and discovered, demonstrating a sensitivity equal to, or exceeding that of, conventional molecular diagnostics. We also provide a background to the armoury of chemopreventive products available for protecting dogs from VBP. Here, field-based research within high VBP pressure environments has underscored the importance of ectoparasiticide mode of action on their overall efficacy. The future of canine VBP diagnosis and prevention at a global level is also explored, highlighting how evolving portable sequencing technologies may permit diagnosis at point-of-care, whilst further research into chemopreventives will be essential if VBP transmission is to be effectively controlled.
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Affiliation(s)
- Lucas G Huggins
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia.
| | - Anson V Koehler
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Rebecca J Traub
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
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5
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Li Y, Zhao L, Wang J, Qi P, Yang Z, Zou X, Peng F, Li S. A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis. PeerJ 2023; 11:e15325. [PMID: 37197582 PMCID: PMC10184654 DOI: 10.7717/peerj.15325] [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: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5-100 copies/reaction for each standard strain, and the detection range was 20-200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.
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Affiliation(s)
- Yun Li
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - LuJie Zhao
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Jingye Wang
- Department of Pathology, Weifang Maternal and Child Health Care Hospital, Weifang, China
| | - Peipei Qi
- The Third Department of Neurology Weifang People’s Hospital, Weifang, China
| | - Zhongfa Yang
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Xiangyu Zou
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Fujun Peng
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
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Infection prevention requirements for the medical care of immunosuppressed patients: recommendations of the Commission for Hospital Hygiene and Infection Prevention (KRINKO) at the Robert Koch Institute. GMS HYGIENE AND INFECTION CONTROL 2022; 17:Doc07. [PMID: 35707229 PMCID: PMC9174886 DOI: 10.3205/dgkh000410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In Germany, guidelines for hygiene in hospitals are given in form of recommendations by the Commission for Hospital Hygiene and Infection Prevention (Kommission für Krankenhaushygiene und Infektionsprävention, "KRINKO"). The KRINKO and its voluntary work are legitimized by the mandate according to § 23 of the Infection Protection Act (Infektionsschutzgesetz, "IfSG"). The original German version of this document was published in February 2021 and has now been made available to the international professional public in English. The guideline provides recommendations on infection prevention and control for immunocompromised individuals in health care facilities. This recommendation addresses not only measures related to direct medical care of immunocompromised patients, but also management aspects such as surveillance, screening, antibiotic stewardship, and technical/structural aspects such as patient rooms, air quality, and special measures during renovations.
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7
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Song Y, Neff M, Gyarmati P. Challenges and advances in the diagnosis of bloodstream infection. Future Microbiol 2022; 17:311-314. [PMID: 35172600 DOI: 10.2217/fmb-2021-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yajing Song
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
| | - Michael Neff
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
| | - Peter Gyarmati
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
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8
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Horiba K, Torii Y, Okumura T, Takeuchi S, Suzuki T, Kawada JI, Muramatsu H, Takahashi Y, Ogi T, Ito Y. Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases. Open Forum Infect Dis 2021; 8:ofab223. [PMID: 34859110 PMCID: PMC8634086 DOI: 10.1093/ofid/ofab223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Background Febrile neutropenia (FN) is a frequent complication in immunocompromised patients. However, causative microorganisms are detected in only 10% of patients. This study aimed to detect the microorganisms that cause FN using next-generation sequencing (NGS) to identify the genome derived from pathogenic microorganisms in the bloodstream. Here, we implemented a metagenomic approach to comprehensively analyze microorganisms present in clinical samples from patients with FN. Methods FN is defined as a neutrophil count <500 cells/µL and fever ≥37.5°C. Plasma/serum samples of 112 pediatric patients with FN and 10 patients with neutropenia without fever (NE) were sequenced by NGS and analyzed by a metagenomic pipeline, PATHDET. Results The putative pathogens were detected by NGS in 5 of 10 FN patients with positive blood culture results, 15 of 87 FN patients (17%) with negative blood culture results, and 3 of 8 NE patients. Several bacteria that were common in the oral, skin, and gut flora were commonly detected in blood samples, suggesting translocation of the human microbiota to the bloodstream in the setting of neutropenia. The cluster analysis of the microbiota in blood samples using NGS demonstrated that the representative bacteria of each cluster were mostly consistent with the pathogens in each patient. Conclusions NGS technique has great potential for detecting causative pathogens in patients with FN. Cluster analysis, which extracts characteristic microorganisms from a complex microbial population, may be effective to detect pathogens in minute quantities of microbiota, such as those from the bloodstream.
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Affiliation(s)
- Kazuhiro Horiba
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Correspondence: Yoshinori Ito, MD, PhD, Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466–8550, Japan ()
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Mitchell KF, Yarbrough ML, Burnham CAD. More than Just Contaminants: Frequency and Characterization of Polymicrobial Blood Cultures from a Central Clinical Microbiology Laboratory Serving a Large Healthcare System. J Appl Lab Med 2021; 6:1433-1440. [PMID: 34164681 DOI: 10.1093/jalm/jfab052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Polymicrobial blood stream infection is often considered uncommon, and corresponding cultures may be assumed to represent contamination. Here we characterized the prevalence and epidemiology of these cultures submitted to a central clinical microbiology laboratory. METHODS Blood cultures from 2017 to 2018 (n = 104 547) were evaluated. Polymicrobial blood cultures were defined by the presence of more than one organism in a blood culture set (set = one aerobic and one anaerobic bottle). Data were stratified by patient location and characteristics of the microbiota detected. RESULTS Of all blood culture sets, 14 600 (14.0%) were positive. Among these, 1651 sets (11.3% of positive cultures; 1.6% of total cultures) were polymicrobial. Most cultures (85.2%) grew two microorganisms; the greatest number of microorganisms in a culture was 6. The most common microorganism pairs were (a) two coagulase-negative staphylococci (CoNS), (b) Corynebacterium and CoNS, and (c) S. aureus and CoNS. Microorganisms in polymicrobial cultures represented microbiota from skin (46.1%), the gastrointestinal (GI) tract (33.9%), strict anaerobes (1.4%), and "other" microorganisms (18.6%). Most cultures with GI microbiota originated from an adult academic medical center compared to community or pediatric settings (40.5% of polymicrobial cultures vs 27.2% and 25.8%, P < 0.0001). Within the academic medical center, patients in an intensive care unit (ICU) or who had bone marrow transplants (BMT) had more cultures suggestive of GI microbiota compared to those from the emergency department (ED) (50.8% and 52.8% vs 31.2%, P < 0.0001). CONCLUSIONS Polymicrobial blood cultures are common in a variety of healthcare settings and the recovered microorganisms can be clinically relevant.
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Affiliation(s)
- Kaitlin F Mitchell
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Melanie L Yarbrough
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
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Yang J, Li Z, Liu Y, Guo S. Tracking bacterial DNA patterns in septic progression using 16s rRNA gene amplicon sequencing analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2021; 14:753-767. [PMID: 34239678 PMCID: PMC8255196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/23/2021] [Indexed: 06/13/2023]
Abstract
Bloodstream infections remain prevalent in intensive care units, leading to a public health challenge worldwide. Routine diagnosis is mainly based on blood culture, but the technique is limited by its time-consuming process and relatively low sensitivity. Emerging molecular diagnostic tools, such as 16S metagenomics, have been developed for detecting bacteria in the blood samples of septic patients. Using a collection of 168 blood samples from 96 septic patients, 16S metagenomics method followed by bioinformatics were applied to study bacterial alterations during the pathogenesis of sepsis. Significant taxonomic variations were found between the two survival groups at different therapeutic time points through sequential 16S metagenomics research. The results on the third day during the treatment course were notably distinct among the studied groups. 16S metagenomics approach can bring novel genetic insight about microbiological fluctuations during septic progression, which may be utilized as a complementary prognostic application. Further etiologic and pathophysiologic explorations are needed to fully explain the linkage between clinical outcomes and genetic changes.
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Affiliation(s)
- Jie Yang
- Department of Emergency, Beijing Chaoyang Hospital, Capital Medical UniversityNo. 8 Worker’s Stadium South Road, Chaoyang District, Beijing, China
- Department of Emergency, Beijing Shunyi District HospitalNo. 3 Guangming South Street, Shunyi District, Beijing, China
| | - Zhuo Li
- Department of Emergency, Beijing Chaoyang Hospital, Capital Medical UniversityNo. 8 Worker’s Stadium South Road, Chaoyang District, Beijing, China
| | - Yanan Liu
- Department of Emergency, Beijing Chaoyang Hospital, Capital Medical UniversityNo. 8 Worker’s Stadium South Road, Chaoyang District, Beijing, China
- Department of Emergency, Cilil Aviation General HospitalNo. 1 Gaojingjia Road, Chaoyang District, Beijing, China
| | - Shubin Guo
- Department of Emergency, Beijing Chaoyang Hospital, Capital Medical UniversityNo. 8 Worker’s Stadium South Road, Chaoyang District, Beijing, China
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Benamu E, Gajurel K, Anderson JN, Lieb T, Gomez CA, Seng H, Aquino R, Hollemon D, Hong DK, Blauwkamp TA, Kertesz M, Blair L, Bollyky PL, Medeiros BC, Coutre S, Zompi S, Montoya JG, Deresinski S. Plasma Microbial Cell-free DNA Next Generation Sequencing in the Diagnosis and Management of Febrile Neutropenia. Clin Infect Dis 2021; 74:1659-1668. [PMID: 33870413 PMCID: PMC9070798 DOI: 10.1093/cid/ciab324] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 11/14/2022] Open
Abstract
Background Standard testing fails to identify a pathogen in most patients with febrile neutropenia (FN). We evaluated the ability of the Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies of FN and its impact on antimicrobial management. Methods This prospective study (ClinicalTrials.gov; NCT02912117) enrolled and analyzed 55 patients with FN. Up to 5 blood samples were collected per subject within 24 hours of fever onset (T1) and every 2 to 3 days. KT results were compared with blood culture (BC) and standard microbiological testing (SMT) results. Results Positive agreement was defined as KT identification of ≥1 isolate also detected by BC. At T1, positive and negative agreement were 90% (9/10) and 31% (14/45), respectively; 61% of KT detections were polymicrobial. Clinical adjudication by 3 independent infectious diseases specialists categorized Karius results as: unlikely to cause FN (N = 0); definite (N = 12): KT identified ≥1 organism also found by SMT within 7 days; probable (N = 19): KT result was compatible with a clinical diagnosis; possible (N = 10): KT result was consistent with infection but not considered a common cause of FN. Definite, probable, and possible cases were deemed true positives. Following adjudication, KT sensitivity and specificity were 85% (41/48) and 100% (14/14), respectively. Calculated time to diagnosis was generally shorter with KT (87%). Adjudicators determined real-time KT results could have allowed early optimization of antimicrobials in 47% of patients, by addition of antibacterials (20%) (mostly against anaerobes [12.7%]), antivirals (14.5%), and/or antifungals (3.6%); and antimicrobial narrowing in 27.3% of cases. Clinical Trials Registration NCT02912117 Conclusion KT shows promise in the diagnosis and treatment optimization of FN.
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Affiliation(s)
- Esther Benamu
- School of Medicine, Division of Infectious Diseases, University of Colorado Denver, Aurora, CO, USA
| | - Kiran Gajurel
- Division of Infectious Diseases, Carolinas Medical Center, Atrium Health, Charlotte, NC, USA
| | - Jill N Anderson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tullia Lieb
- Hematopoietic Malignancies Unit Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Carlos A Gomez
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Hon Seng
- Cytovale, Inc, San Francisco, CA, USA
| | | | | | | | | | | | | | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bruno C Medeiros
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven Coutre
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jose G Montoya
- The Dr. Jack S. Remington Laboratory for Specialty Diagnostics at the Palo Alto Medical Foundation, Palo Alto, CA, USA
| | - Stan Deresinski
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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12
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Direct DNA Sequencing-Based Analysis of Microbiota Associated with Hematological Malignancies in the Eastern Province of Saudi Arabia. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4202019. [PMID: 33623780 PMCID: PMC7875615 DOI: 10.1155/2021/4202019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/25/2021] [Indexed: 12/02/2022]
Abstract
Introduction Bloodstream infections (BSI) among patients with hematological malignancies (HM) could predispose them to higher morbidity and mortality for various underlying conditions. Several microorganisms, either pathogenic or opportunistic normal human flora, could cause severe bacteremia and septicemia. While conventional methods have their own limitations, molecular methods such as next-generation sequencing (NGS) can detect these blood infections with more reliability, specificity, and sensitivity, in addition to information on microbial population landscape. Methodology. Blood samples from HM patients (n = 50) and volunteer blood donor control individuals with no HM (n = 50) were subjected to 16S rRNA gene amplification using standard PCR protocols. A metagenomic library was prepared, and NGS was run on a MiSeq (Illumina) sequencer. Sequence reads were analyzed using MiSeq Reporter, and microbial taxa were aligned using the Green Genes library. Results 82% of the patients showed BSI with Gram-negative bacteria as the most predominant group. E. coli comprised a major chunk of the bacterial population (19.51%), followed by K. pneumoniae (17.07%). The CoNS and Viridans Streptococci groups are 17.07% and 14.63%, respectively. Other major species were S. aureus (9.75%), P. aeruginosa (7.31%), A. baumannii (4.87%), E. cloacae (4.87%), and P. mirabilis (4.87%). 34.14% of the cases among patients showed a Gram-positive infection, while 14.63% showed polymicrobial infections. Conclusion Most of the BSI in patients were characterized by polymicrobial infections, unlike the control samples. Molecular methods like NGS showed robust, fast, and specific identification of infectious agents in BSI in HM, indicating the possibility of its application in routine follow-up of such patients for infections.
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13
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Anforderungen an die Infektionsprävention bei der medizinischen Versorgung von immunsupprimierten Patienten. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2021; 64:232-264. [PMID: 33394069 PMCID: PMC7780910 DOI: 10.1007/s00103-020-03265-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Emery DC, Cerajewska TL, Seong J, Davies M, Paterson A, Allen-Birt SJ, West NX. Comparison of Blood Bacterial Communities in Periodontal Health and Periodontal Disease. Front Cell Infect Microbiol 2021; 10:577485. [PMID: 33469518 PMCID: PMC7813997 DOI: 10.3389/fcimb.2020.577485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
The use of Next Generation Sequencing (NGS) techniques has generated a wide variety of blood microbiome data. Due to the large variation in bacterial DNA profiles between studies and the likely high concentrations of cell-free bacterial DNA in the blood, it is still not clear how such microbiome data relates to viable microbiota. For these reasons much remains to be understood about the true nature of any possible healthy blood microbiota and of bacteraemic events associated with disease. The gut, reproductive tracts, skin, and oral cavity are all likely sources of blood-borne bacteria. Oral bacteria, especially those associated with periodontal diseases, are also commonly associated with cardiovascular diseases such as infective endocarditis, and also have been linked to rheumatoid arthritis and Alzheimer's disease. Periodontal treatment, dental probing, and toothbrushing have been shown to cause transient bacteraemia and oral bacteria from the phyla Firmicutes (e.g. Streptococci) and Bacteroidetes (e.g. Porphyromonas) are found in cardiovascular lesions (CVD). Many studies of blood bacterial DNA content however, find Proteobacteria DNA to be the dominant microbiome component, suggesting a gut origin. Most studies of this type use total DNA extracted from either whole blood or blood fractions, such as buffy coat. Here, using a method that purifies DNA from intact bacterial cells only, we examined blood donated by those with active, severe periodontitis and periodontally healthy controls and show that 43-52% of bacterial species in blood are classified as oral. Firmicutes, consisting largely of members of the Streptococcus mitis group and Staphylococcus epidermidis, were predominant at 63.5% of all bacterial sequences detected in periodontal health and, little changed at 66.7% in periodontitis. Compared to studies using total DNA Proteobacteria were found here at relatively low levels in blood at 13.3% in periodontitis and 17.6% in health. This study reveals significant phylogenetic differences in blood bacterial population profiles when comparing periodontal health to periodontal disease cohorts.
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Affiliation(s)
- David C. Emery
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Tanya L. Cerajewska
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Joon Seong
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Maria Davies
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Alex Paterson
- University of Bristol Genomics Facility, School of Biological Sciences, Bristol, United Kingdom
| | - Shelley J. Allen-Birt
- Bristol Medical School, Translational Health Sciences, Learning & Research, Southmead Hospital, Bristol, United Kingdom
| | - Nicola X. West
- Periodontology, Bristol Dental School, University of Bristol, Bristol, United Kingdom
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15
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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16
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Song Y, Gyarmati P. Microbiota changes in a pediatric acute lymphocytic leukemia mouse model. Microbiologyopen 2019; 9:e982. [PMID: 31884727 PMCID: PMC7066458 DOI: 10.1002/mbo3.982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Hematological malignancies are the most common type of pediatric cancers, and acute lymphocytic leukemia (ALL) is the most frequently occurring hematological malignancy during childhood. A major cause of mortality in leukemia is bloodstream infection (BSI). The aim of the current study was to explore the gut microbiota in ALL and its potential functional alterations. High-throughput sequencing was used to characterize the bacterial and fungal microbiota in feces and their predicted functional characteristics in a xenotransplant pediatric ALL mouse model. Our work shows that gut microbiota significantly changes in leukemia, which may result in functional alterations. This study may provide potential therapeutic or preventive strategies of BSI in ALL.
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Affiliation(s)
- Yajing Song
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Peter Gyarmati
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
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17
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Huggins LG, Koehler AV, Ng-Nguyen D, Wilcox S, Schunack B, Inpankaew T, Traub RJ. Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand. Parasit Vectors 2019; 12:394. [PMID: 31395073 PMCID: PMC6686542 DOI: 10.1186/s13071-019-3651-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Globally, bacterial vector-borne disease (VBD) exerts a large toll on dogs in terms of morbidity and mortality but nowhere is this more pronounced than in the tropics. Tropical environments permit a burgeoning diversity and abundance of ectoparasites some of which can transmit an extensive range of infectious agents, including bacteria, amongst others. Although some of these vector-borne bacteria are responsible for both animal and human diseases in the tropics, there is a scarcity of epidemiological investigation into these pathogens' prevalence. The situation is further exacerbated by frequent canine co-infection, complicating symptomatology that regular diagnostic techniques may miss or be unable to fully characterise. Such limitations draw attention to the need to develop screening tools capable of detecting a wide range of pathogens from a host simultaneously. RESULTS Here, we detail the employment of a next-generation sequencing (NGS) metabarcoding methodology to screen for the spectrum of bacterial VBD that are infecting semi-domesticated dogs across temple communities in Bangkok, Thailand. Our NGS detection protocol was able to find high levels of Ehrlichia canis, Mycoplasma haemocanis and Anaplasma platys infection rates as well as less common pathogens, such as "Candidatus Mycoplasma haematoparvum", Mycoplasma turicensis and Bartonella spp. We also compared our high-throughput approach to conventional endpoint PCR methods, demonstrating an improved detection ability for some bacterial infections, such as A. platys but a reduced ability to detect Rickettsia. CONCLUSIONS Our methodology demonstrated great strength at detecting coinfections of vector-borne bacteria and rare pathogens that are seldom screened for in canines in the tropics, highlighting its advantages over traditional diagnostics to better characterise bacterial pathogens in environments where there is a dearth of research.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052 Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052 Australia
| | - Dinh Ng-Nguyen
- Faculty of Animal Sciences and Veterinary Medicine, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000 Vietnam
| | - Stephen Wilcox
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia
| | | | - Tawin Inpankaew
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900 Thailand
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052 Australia
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18
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Stinson LF, Boyce MC, Payne MS, Keelan JA. The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Front Microbiol 2019; 10:1124. [PMID: 31231319 PMCID: PMC6558212 DOI: 10.3389/fmicb.2019.01124] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/03/2019] [Indexed: 01/12/2023] Open
Abstract
The human microbiome includes trillions of bacteria, many of which play a vital role in host physiology. Numerous studies have now detected bacterial DNA in first-pass meconium and amniotic fluid samples, suggesting that the human microbiome may commence in utero. However, these data have remained contentious due to underlying contamination issues. Here, we have used a previously described method for reducing contamination in microbiome workflows to determine if there is a fetal bacterial microbiome beyond the level of background contamination. We recruited 50 women undergoing non-emergency cesarean section deliveries with no evidence of intra-uterine infection and collected first-pass meconium and amniotic fluid samples. Full-length 16S rRNA gene sequencing was performed using PacBio SMRT cell technology, to allow high resolution profiling of the fetal gut and amniotic fluid bacterial microbiomes. Levels of inflammatory cytokines were measured in amniotic fluid, and levels of immunomodulatory short chain fatty acids (SCFAs) were quantified in meconium. All meconium samples and most amniotic fluid samples (36/43) contained bacterial DNA. The meconium microbiome was dominated by reads that mapped to Pelomonas puraquae. Aside from this species, the meconium microbiome was remarkably heterogeneous between patients. The amniotic fluid microbiome was more diverse and contained mainly reads that mapped to typical skin commensals, including Propionibacterium acnes and Staphylococcus spp. All meconium samples contained acetate and propionate, at ratios similar to those previously reported in infants. P. puraquae reads were inversely correlated with meconium propionate levels. Amniotic fluid cytokine levels were associated with the amniotic fluid microbiome. Our results demonstrate that bacterial DNA and SCFAs are present in utero, and have the potential to influence the developing fetal immune system.
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Affiliation(s)
- Lisa F Stinson
- Division of Obstetrics and Gynaecology, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mary C Boyce
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Perth, WA, Australia
| | - Matthew S Payne
- Division of Obstetrics and Gynaecology, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Jeffrey A Keelan
- Division of Obstetrics and Gynaecology, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia
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19
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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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20
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Greninger AL, Naccache SN. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 2018; 3:643-653. [PMID: 31639732 DOI: 10.1373/jalm.2018.026120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today. CONTENT Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation. SUMMARY Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.
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Affiliation(s)
| | - Samia N Naccache
- Department of Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
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21
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Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen. J Clin Med 2018; 7:jcm7100346. [PMID: 30322074 PMCID: PMC6210133 DOI: 10.3390/jcm7100346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022] Open
Abstract
Background: The purpose of this study was to profile the bacterium in the ascites and blood of patients with acute surgical abdomen by metagenome analysis. Methods: A total of 97 patients with acute surgical abdomen were included in this study. Accompanied with the standard culture procedures, ascites and blood samples were collected for metagenome analysis to measure the relative abundance of bacteria among groups of patients and between blood and ascites. Results: Metagenomic analysis identified 107 bacterial taxa from the ascites of patients. A principal component analysis (PCA) could separate the bacteria of ascites into roughly three groups: peptic ulcer, perforated or non-perforated appendicitis, and a group which included cholecystitis, small bowel lesion, and colon perforation. Significant correlation between the bacteria of blood and ascites was found in nine bacterial taxa both in blood and ascites with more than 500 sequence reads. However, the PCA failed to separate the variation in the bacteria of blood into different groups of patients, and the bacteria of metagenomic analysis is only partly in accordance with those isolated from a conventional culture method. Conclusion: This study indicated that the metagenome analysis can provide limited information regarding the bacteria in the ascites and blood of patients with acute surgical abdomen.
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Watanabe N, Kryukov K, Nakagawa S, Takeuchi JS, Takeshita M, Kirimura Y, Mitsuhashi S, Ishihara T, Aoki H, Inokuchi S, Imanishi T, Inoue S. Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis. PLoS One 2018; 13:e0202049. [PMID: 30110400 PMCID: PMC6093674 DOI: 10.1371/journal.pone.0202049] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/26/2018] [Indexed: 02/01/2023] Open
Abstract
Prompt identification of causative pathogenic bacteria is imperative for the treatment of patients suffering from infectious diseases, including sepsis and pneumonia. However, current culture-based methodologies have several drawbacks including their limitation of use to culturable bacterial species. To circumvent these problems, we attempted to detect bacterial DNA in blood using next-generation DNA sequencing (NGS) technology. We conducted metagenomic and 16S ribosomal RNA (rRNA) gene amplicon sequencing of DNA extracted from bacteria-spiked blood using an Ion Personal Genome Machine. NGS data was analyzed using our in-house pipeline Genome Search Toolkit and database GenomeSync. The metagenomic sequencing analysis successfully detected three gram-positive and three gram-negative bacteria spiked in the blood, which was associated with a significant portion of non-bacterial reads, even though human blood cells were separated by low-speed centrifugation prior to DNA extraction. Sequencing analysis of seven variable regions of the 16S rRNA gene amplicon also successfully detected all six bacteria spiked in the blood. The methodology using 16S rRNA gene amplicon analysis was verified using DNA from the blood of six patients with sepsis and four healthy volunteers with potential pathogenic bacteria in the blood being identified at the species level. These findings suggest that our system will be a potential platform for practical diagnosis in the future.
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Affiliation(s)
- Nobuo Watanabe
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
- Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa, Japan
| | - Junko S. Takeuchi
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Meiko Takeshita
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Yukiko Kirimura
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Satomi Mitsuhashi
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Toru Ishihara
- Department of General Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Hiromichi Aoki
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Sadaki Inokuchi
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
- * E-mail:
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Rutanga JP, Van Puyvelde S, Heroes AS, Muvunyi CM, Jacobs J, Deborggraeve S. 16S metagenomics for diagnosis of bloodstream infections: opportunities and pitfalls. Expert Rev Mol Diagn 2018; 18:749-759. [PMID: 29985081 DOI: 10.1080/14737159.2018.1498786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Bacterial bloodstream infections (BSI) form a large public health threat worldwide. Current routine diagnosis is based on blood culture (BC) but this technique suffers from limited sensitivity. Molecular diagnostic tools have been developed for identification of bacteria in the blood of BSI patients. 16S metagenomics is an open-ended technique that can detect simultaneously all bacteria in a given sample based on PCR amplification of the 16S ribosomal RNA gene (rDNA) followed by sequencing of the PCR amplicons and taxonomic labeling of the sequence reads at genus or species level. Areas covered: Here we review the studies that have used 16S metagenomics for the identification of bacteria in human blood samples. We also discuss the potential added value of 16S metagenomics in the diagnosis of BSI, challenges as well as future directions for implementation in clinical settings. Expert commentary: 16S metagenomics has the potential to complement conventional BC; however, the technique currently suffers from several technical limitations jeopardizing implementation in routine clinical microbiology laboratories. Further studies are required to assess the cost-efficiency and clinical impact of 16S metagenomics in comparison to BC which remains the gold standard diagnostic method for BSI.
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Affiliation(s)
- Jean Pierre Rutanga
- a College of Science and Technology , University of Rwanda , Kigali , Rwanda.,b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium
| | - Sandra Van Puyvelde
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium.,c Wellcome Trust Sanger Institute , Hinxton , United Kingdom
| | - Anne-Sophie Heroes
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Claude Mambo Muvunyi
- f College of Medicine and Health Sciences , University of Rwanda , Kigali , Rwanda
| | - Jan Jacobs
- d Department of Microbiology and Immunology , KU Leuven , Leuven , Belgium.,e Department of Clinical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
| | - Stijn Deborggraeve
- b Department of Biomedical Sciences , Institute of Tropical Medicine , Antwerp , Belgium
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24
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Peker N, Couto N, Sinha B, Rossen JW. Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches. Clin Microbiol Infect 2018; 24:944-955. [PMID: 29787889 DOI: 10.1016/j.cmi.2018.05.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2018] [Accepted: 05/12/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Bloodstream infections are a major cause of death with increasing incidence and severity. Blood cultures are still the reference standard for microbiological diagnosis, but are rather slow. Molecular methods can be used as add-on complementary assays. They can be useful to speed up microbial identification and to predict antimicrobial susceptibility, applied to direct blood samples or positive blood cultures. AIM To review recent developments in molecular-based diagnostic platforms used for the identification of bloodstream infections, with a focus on assays performed directly on blood samples and positive blood cultures. SOURCES Peer reviewed articles, conference abstracts, and manufacturers' websites. CONTENT We give an update on recent developments of molecular methods in diagnosing BSIs. We first describe the currently available molecular methods to be used for positive blood cultures including: a) in situ hybridization-based methods; b) DNA-microarray-based hybridization technology; c) nucleic acid amplification-based methods; and d) combined methods. Subsequently, molecular methods applied directly to whole blood samples are discussed, including the use of nucleic acid amplification-based methods, T2 magnetic resonance-based methods, and metagenomics for diagnosing BSIs. IMPLICATIONS Advances in molecular-based methods complementary to conventional blood culture diagnostics and antimicrobial stewardship programmes may optimize infection management by allowing rapid identification of pathogens and relevant antimicrobial resistance genes. Rapid diagnosis of the causing microorganism and relevant resistance determinants is important for early administration and modification of appropriate antimicrobial therapy. Ultimately, this may lead to improved quality and cost-effectiveness of health care, as well as reduced antimicrobial resistance selection.
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Affiliation(s)
- N Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - N Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - B Sinha
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands.
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25
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Linder LA, Gerdy C, Jo Y, Wilson A. Changes in Central Line-Associated Bloodstream Infection Rates Among Children With Immune Compromised Conditions: An 11-Year Review. J Pediatr Oncol Nurs 2018; 35:382-391. [PMID: 29665727 DOI: 10.1177/1043454218767885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This article describes changes in central line-associated bloodstream infection (CLABSI) rates among common causative organisms over an 11-year period on a pediatric inpatient unit prior to and following CLABSI reduction strategies. The setting for this descriptive cohort design study was a 32-bed inpatient unit in a tertiary pediatric hospital serving children with immune compromised conditions, including cancer and recipients of hematopoietic stem cell and solid organ transplants. Between January 2006 and December 2016, 265 CLABSIs involving 189 patients were reported. Data were organized into three time periods: 5-year preintervention baseline (2006-2010), implementation of maintenance care bundles (2011-2012), and addition of formalized supportive care practices to the maintenance care bundles (2013-2016). Organisms were categorized into four groups based on the National Health Safety Network organism list. Time-by-class Poisson regression models evaluated changes in CLABSI rates. Characteristics of patients who developed CLABSIs were unchanged. Infections occurred most frequently among patients with hematologic malignancies and neutropenia. Significant log rate decreases in CLABSI rates were observed with the implementation of maintenance care bundles plus enhanced supportive cares compared to preintervention baseline for the following organisms: (1) common commensal organisms (-1.05, p = .005), (2) mucosal barrier injury (MBI) organisms common to the mouth (-.708, p = .007), and (3) other noncommensal/non-MBI pathogens (-.77, p = .005). Rates were unchanged for MBI organisms common to the lower gastrointestinal tract. Central line maintenance care bundles and formalized supportive care practices resulted in sustained decreased CLABSI rates. Additional interventions are needed to reduce CLABSIs involving MBI-associated organisms common to the lower gastrointestinal tract.
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Affiliation(s)
- Lauri A Linder
- 1 University of Utah, Salt Lake City, UT, USA.,2 Primary Children's Hospital, Salt Lake City, UT, USA
| | - Cheryl Gerdy
- 2 Primary Children's Hospital, Salt Lake City, UT, USA
| | - Yeonjung Jo
- 1 University of Utah, Salt Lake City, UT, USA
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26
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Af Sandeberg M, Johansson E, Wettergren L, Björk O, Hertting O, Nilsson A. Antibiotic use during infectious episodes in the first 6 months of anticancer treatment-A Swedish cohort study of children aged 7-16 years. Pediatr Blood Cancer 2017; 64. [PMID: 28074531 DOI: 10.1002/pbc.26397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022]
Abstract
BACKGROUND Children undergoing cancer therapy are at risk for infectious complications that require hospitalization and antimicrobial therapy. Host factors such as age and underlying disease may predict the risk of severe infections in these children. To describe the increased morbidity due to infections in children with cancer, we characterized the antibiotic use during the infectious complications in a national cohort of children 7-16 years of age with cancer. PROCEDURE Data on infectious complications were prospectively collected from the medical records of all newly diagnosed children with cancer, aged 7-16 years, in Sweden between 2004 and 2006. An episode of infection was defined as a period of time when oral or intravenous antimicrobial treatment was prescribed because of symptoms of infection. RESULTS A total of 230 infectious episodes occurred in 80 of the 101 patients. Pathogens were isolated in 15% of the blood cultures that showed a predominance of Gram-positive bacteria. Intravenous broad-spectrum antibiotics with cephalosporins and carbapenems were mostly used as single drugs but also in combination with aminoglycosides and glycopeptide. The median treatment length varied between 6 and 11 days depending on cancer diagnosis. CONCLUSION Our data demonstrate that infectious complications contribute significantly to morbidity in children with cancer aged 7-16 years. At the time of this survey, antibiotic prescription patterns varied and cephalosporins and carbapenems were mostly used. With increasing antibiotic resistance, a more stringent antibiotic stewardship with less use of cephalosporins and carbapenems should be encouraged for children with cancer. Data on prescription patterns should be incorporated as a quality measurement in pediatric cancer care.
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Affiliation(s)
- M Af Sandeberg
- Department of Women's and Children's Health, Childhood Cancer Research Unit, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - E Johansson
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - L Wettergren
- Department of Neurobiology, Care Sciences and Society, Division of Nursing, Karolinska Institutet, Stockholm, Sweden
| | - O Björk
- Department of Women's and Children's Health, Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska Institutet, Stockholm, Sweden
| | - O Hertting
- Pediatric Infectious Disease Unit, Astrid Lindgren Children's Hospital, Stockholm, Sweden
| | - A Nilsson
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska Institutet, Stockholm, Sweden
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27
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Branton WG, Lu JQ, Surette MG, Holt RA, Lind J, Laman JD, Power C. Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis. Sci Rep 2016; 6:37344. [PMID: 27892518 PMCID: PMC5125007 DOI: 10.1038/srep37344] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/26/2016] [Indexed: 12/14/2022] Open
Abstract
Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200–1,400 bacterial genomes/cm3 and low bacterial rRNA:rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients’ WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients’ WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms.
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Affiliation(s)
- W G Branton
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada
| | - J Q Lu
- Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Psychiatry, University of Alberta, Edmonton AB Canada
| | - M G Surette
- Department of Medicine, McMaster University, Hamilton ON Canada
| | - R A Holt
- Genome Sciences Centre, Vancouver BC, Canada
| | - J Lind
- Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
| | - J D Laman
- Multiple Sclerosis Centre, University of Alberta, Edmonton AB Canada
| | - C Power
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
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28
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Gyarmati P, Kjellander C, Aust C, Song Y, Öhrmalm L, Giske CG. Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia. Sci Rep 2016; 6:23532. [PMID: 26996149 PMCID: PMC4800731 DOI: 10.1038/srep23532] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/08/2016] [Indexed: 01/05/2023] Open
Abstract
Leukemic patients are often immunocompromised due to underlying conditions, comorbidities and the effects of chemotherapy, and thus at risk for developing systemic infections. Bloodstream infection (BSI) is a severe complication in neutropenic patients, and is associated with increased mortality. BSI is routinely diagnosed with blood culture, which only detects culturable pathogens. We analyzed 27 blood samples from 9 patients with acute leukemia and suspected BSI at different time points of their antimicrobial treatment using shotgun metagenomics sequencing in order to detect unculturable and non-bacterial pathogens. Our findings confirm the presence of bacterial, fungal and viral pathogens alongside antimicrobial resistance genes. Decreased white blood cell (WBC) counts were associated with the presence of microbial DNA, and was inversely proportional to the number of sequencing reads. This study could indicate the use of high-throughput sequencing for personalized antimicrobial treatments in BSIs.
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Affiliation(s)
- P Gyarmati
- Karolinska Institutet, Department of Laboratory Medicine, Alfred Nobels Allé 8, Stockholm, 17177 Sweden.,Karolinska University Hospital, Department of Clinical Microbiology L2:02, Stockholm, 17176 Sweden
| | - C Kjellander
- Karolinska Institutet, Department of Medicine, Division of Hematology, Stockholm, 17176 Sweden
| | - C Aust
- Karolinska Institutet, Department of Medicine, Solna, Infectious Diseases Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 17176 Sweden
| | - Y Song
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, 17176 Sweden
| | - L Öhrmalm
- Karolinska Institutet, Department of Medicine, Solna, Infectious Diseases Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 17176 Sweden
| | - C G Giske
- Karolinska Institutet, Department of Laboratory Medicine, Alfred Nobels Allé 8, Stockholm, 17177 Sweden.,Karolinska University Hospital, Department of Clinical Microbiology L2:02, Stockholm, 17176 Sweden
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Decuypere S, Meehan CJ, Van Puyvelde S, De Block T, Maltha J, Palpouguini L, Tahita M, Tinto H, Jacobs J, Deborggraeve S. Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach. PLoS Negl Trop Dis 2016; 10:e0004470. [PMID: 26927306 PMCID: PMC4771206 DOI: 10.1371/journal.pntd.0004470] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/27/2016] [Indexed: 01/17/2023] Open
Abstract
Background Bacterial bloodstream infection (bBSI) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI. Methodology/Principal Findings The proof-of-concept was delivered in 75 children (median age 15 months) with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3–V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046). Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030). Conclusions/Significance Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination. Bacterial bloodstream infection (bBSI) is one of the biggest causes of mortality in critically ill patients and standard diagnosis is still done by blood culture methods. Parallel deep sequencing of the 16S ribosomal RNA genes (16S metagenomics) is a new and rapidly evolving research field for profiling bacterial communities. We designed a 16S metagenomics approach for the identification of bacteria in the blood of patients with a bBSI, and evaluated its performance in 75 children with severe febrile illness in Burkina Faso. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recently recovered from acute malaria are at increased risk of presenting polymicrobial bloodstream infection, which was in itself a significant risk for non-survival. This proof-of-concept study shows that 16S metagenomics is a powerful approach to diagnose and understand bBSI but also that appropriate control samples are crucial for correct data interpretation.
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Affiliation(s)
- Saskia Decuypere
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Conor J. Meehan
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
| | - Sandra Van Puyvelde
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
| | - Tessa De Block
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
| | - Jessica Maltha
- Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
- Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | | | - Marc Tahita
- Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Halidou Tinto
- Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Jan Jacobs
- Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
- Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| | - Stijn Deborggraeve
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium
- * E-mail:
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30
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Kell DB, Kenny LC. A Dormant Microbial Component in the Development of Preeclampsia. Front Med (Lausanne) 2016; 3:60. [PMID: 27965958 PMCID: PMC5126693 DOI: 10.3389/fmed.2016.00060] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022] Open
Abstract
Preeclampsia (PE) is a complex, multisystem disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused. We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is, in fact, microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, and urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of "preeclampsia" that we assessed has, in fact, also been shown to be raised in response to infection. An infectious component to PE fulfills the Bradford Hill criteria for ascribing a disease to an environmental cause and suggests a number of treatments, some of which have, in fact, been shown to be successful. PE was classically referred to as endotoxemia or toxemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the etiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, Manchester, UK
- The Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, Manchester, UK
- *Correspondence: Douglas B. Kell,
| | - Louise C. Kenny
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), University College Cork, Cork, Ireland
- Department of Obstetrics and Gynecology, University College Cork, Cork, Ireland
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