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Saini V, Como J, Abdulmassih R, Min Z, Bhanot N. Utility of Direct Specimen Sequencing in Addition to Conventional Testing in Management of Infections in an Urban Referral Health Center. J Appl Lab Med 2023; 8:559-567. [PMID: 36759952 DOI: 10.1093/jalm/jfac144] [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: 08/05/2022] [Accepted: 12/06/2022] [Indexed: 02/11/2023]
Abstract
BACKGROUND Direct specimen sequencing (DSS) offers the promise of enhanced pathogen detection and disease diagnosis. METHODS A single healthcare network, retrospective chart review over a 3-year period was completed for all cases in which DSS was submitted, in addition to conventional testing (CT) for workup of an infectious disease. We sought to compare results (concordance and discordance) from these 2 techniques in order to evaluate any additional yield from DSS over CT. Additionally, we calculated mean turnaround time (TAT) and average cost for obtaining DSS on all specimens. RESULTS A total of 23 patients' specimens were sent for DSS. DSS and CT concordance occurred in 91% (21/23) of cases. DSS testing was able to identify specific pathogens in 17.4% (4/23) of patients, out of which 4% (1/23) were discordant. The respective mean TAT and total cost per specimen for DSS were 6 days and $821.52 (range $573-$1590), respectively. CONCLUSIONS In our limited cohort of patients, there was significant concordance between the 2 testing modalities primarily due to negative tests. DSS did not provide significant additional yield in the infectious diagnosis in our cohort compared to CT. Short TAT may provide advantage in the detection of fastidious organisms, but high cost remains a limitation. Larger sample size may reveal a clinically meaningful difference.
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Affiliation(s)
- Vikram Saini
- Allegheny Health Network, Pittsburgh, PA, United States
| | - James Como
- Allegheny Health Network, Pittsburgh, PA, United States
| | | | - Zaw Min
- Allegheny Health Network, Pittsburgh, PA, United States
| | - Nitin Bhanot
- Allegheny Health Network, Pittsburgh, PA, United States
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Lu H, Ma L, Zhang H, Feng L, Yu Y, Zhao Y, Li L, Zhou Y, Song L, Li W, Zhao J, Liu L. The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases. Infect Drug Resist 2022; 15:6115-6128. [PMID: 36277249 PMCID: PMC9586124 DOI: 10.2147/idr.s370964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging. Methods From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed. Results Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains. Conclusion In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.
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Affiliation(s)
- Hongzhi Lu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Ma
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Hong Zhang
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Feng
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Ying Yu
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yihan Zhao
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Li
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Yujiao Zhou
- Department of Infectious Diseases, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China
| | - Li Song
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd, Shanghai, 201204, People’s Republic of China,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, People’s Republic of China
| | - Lanxiang Liu
- Medical Imaging Center, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, 066000, People’s Republic of China,Correspondence: Lanxiang Liu, Department of Medical Imaging Center, First Hospital of Qinhuangdao, 258 Wenhua Road, Qinhuangdao, 066000, Hebei, People’s Republic of China, Email
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Idelevich EA, Reischl U, Becker K. New Microbiological Techniques in the Diagnosis of Bloodstream Infections. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 115:822-832. [PMID: 30678752 DOI: 10.3238/arztebl.2018.0822] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/04/2017] [Accepted: 10/12/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment. METHODS This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience. RESULTS A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS. CONCLUSION The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.
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Abstract
Microbiological diagnostic procedures have changed rapidly in recent years. This is especially true in the field of molecular diagnostics. Classical culture-based techniques are still the gold standard in many areas; however, they are already complemented by automated and also molecular techniques to guarantee faster and better quality results. The most commonly used techniques include real-time polymerase chain reaction (RT-PCR) based systems and nucleic acid hybridization. These procedures are used most powerfully from direct patient samples or in assays to detect the presence of nonculturable or fastidious organisms. Further techniques such as DNA sequencing are not yet used routinely for urological samples and can be considered experimental. However, in conjunction with dropping prices and further technical developments, these techniques promise to be used much more in the near future. Regarding bacterial identification from culture, mass spectrometry (MALDI-TOF MS) has become the technique of choice in recent years especially in Europe. It has tremendously shortened the time to result. This is now going to be extended to antibiotic susceptibility testing. This is of paramount importance in view of ever rising antimicrobial resistance rates. Techniques described in this review offer a faster and better microbiological diagnosis. Such continuous improvements are critical especially in times of cost pressure and rising antimicrobial resistance rates. It is in our interest to provide the best possible care for patients and in this regard a good and effective communication between the laboratory and the clinician is of vital importance.
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Affiliation(s)
- S Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.
| | - A Wieser
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.,Abteilung für Infektions- und Tropenmedizin der LMU, Leopoldstrasse 5, 80802, München, Deutschland.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort München, München, Deutschland
| | - G Bonkat
- alta uro AG, Centralbahnplatz 6, 4051, Basel, Schweiz
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Shi W, Li J, Zhou H, Gao GF. Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1317-1330. [PMID: 29270793 PMCID: PMC7088571 DOI: 10.1007/s11427-017-9211-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/01/2017] [Indexed: 02/06/2023]
Abstract
In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome (SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and mortality. In addition, several emerging and re-emerging viral pathogens have also been imported into China from travelers, e.g. the Middle East respiratory syndrome (MERS) coronavirus and Zika virus (ZIKV). Herein, we review these emerging viral pathogens in China and focus on how surveillance by pathogen genomics has been employed to discover and annotate novel pathogenic agents, identify natural reservoirs, monitor the transmission events and delineate their evolution and adaption to the human host. We also highlight the application of genomic sequencing in the recent Ebola epidemics in Western Africa. In summary, genomic sequencing has become a standard research tool in the field of emerging infectious diseases which has been proven invaluable in containing these viral infections and reducing burden of disease in humans and animals. Genomic surveillance of pathogenic agents will serve as a key epidemiological and research tool in the modern era of precision infectious diseases and in the future studies of virosphere.
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Affiliation(s)
- Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China.
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Friedman JM, Cornel MC, Goldenberg AJ, Lister KJ, Sénécal K, Vears DF. Genomic newborn screening: public health policy considerations and recommendations. BMC Med Genomics 2017; 10:9. [PMID: 28222731 PMCID: PMC5320805 DOI: 10.1186/s12920-017-0247-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is possible today. METHODS The Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Working Group reviewed current understanding and concerns regarding the use of genomic technologies for population-based newborn screening and developed, by consensus, eight recommendations for clinicians, clinical laboratory scientists, and policy makers. RESULTS Before genome-wide sequencing can be implemented in newborn screening programs, its clinical utility and cost-effectiveness must be demonstrated, and the ability to distinguish disease-causing and benign variants of all genes screened must be established. In addition, each jurisdiction needs to resolve ethical and policy issues regarding the disclosure of incidental or secondary findings to families and ownership, appropriate storage and sharing of genomic data. CONCLUSION The best interests of children should be the basis for all decisions regarding the implementation of genomic newborn screening.
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Affiliation(s)
- Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Child & Family Research Institute, Vancouver, Canada
| | - Martina C. Cornel
- Section Clinical Genetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, Holland
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, Holland
| | - Aaron J. Goldenberg
- The Center for Genetic Research Ethics and Law, Department of Bioethics, Case Western Reserve University, Cleveland, OH USA
| | - Karla J. Lister
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, Australia
| | - Karine Sénécal
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Canada
| | - Danya F. Vears
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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7
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Giorgio F, Ierardi E, Sorrentino C, Principi M, Barone M, Losurdo G, Iannone A, Giangaspero A, Monno R, Di Leo A. Helicobacter pylori DNA isolation in the stool: an essential pre-requisite for bacterial noninvasive molecular analysis. Scand J Gastroenterol 2016; 51:1429-1432. [PMID: 27687850 DOI: 10.1080/00365521.2016.1216592] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Real-time polymerase chain reaction (RT-PCR) is a widely used technique for bacterial and viral infection diagnosis. Herein, we report our preliminary experience in retrieving H. pylori genetic sequences in stools and analyzing genotypic clarithromycin resistance by RT-PCR (noninvasive), with the aim of comparing this procedure with that performed on biopsy samples (invasive). MATERIALS AND METHODS After 'in vitro' demonstration of H. pylori DNA detection from pure and stool-mixed bacteria, 52 consecutive patients at the first diagnosis of infection were investigated. DNA was extracted from biopsy tissue and stool samples (THD® Fecal Test, Italy). RT-PCR was performed to detect 23S rRNA encoding bacterial subunit gene and search A2143G, A2142C, A2142G point mutations for clarithromycin resistance assessment. RESULTS RT-PCR showed H. pylori positive DNA in all infected patients with full concordance between tissue and stool detection (100%). We found A2143G mutation in 10 (19.2%), A2142G in 4 (7.7%) and A2142C in 5 (9.6%) patients; there was a full agreement between biopsy and fecal samples. A2143G was found in all the four A2142G positive cases and in three out of the five A2142C positive strains. Overall clarithromycin resistance rate in our series was 23%. CONCLUSIONS Despite the need of confirmation on large sample, stool RT-PCR analysis could represent a feasible tool to detect H. pylori DNA sequences and antibiotic resistance point mutations. As compared to tissue molecular analysis, this technique is noninvasive, with potential advantages such as improvement of patient compliance, reduction of diagnostic procedure time/cost and improvement of therapeutic outcome.
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Affiliation(s)
- Floriana Giorgio
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Enzo Ierardi
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Claudia Sorrentino
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Mariabeatrice Principi
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Michele Barone
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Giuseppe Losurdo
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Andrea Iannone
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Antonio Giangaspero
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
| | - Rosa Monno
- b Section of Microbiology, Department of Basic Medical Science, Neuroscience and Sense Organs , University of Bari , Bari , Italy
| | - Alfredo Di Leo
- a Section of Gastroenterology, Department of Emergency and Organ Transplantation , University of Bari , Bari , Italy
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Engstrom-Melnyk J, Rodriguez PL, Peraud O, Hein RC. Clinical Applications of Quantitative Real-Time PCR in Virology. METHODS IN MICROBIOLOGY 2015; 42:161-197. [PMID: 38620180 PMCID: PMC7148891 DOI: 10.1016/bs.mim.2015.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats.
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Affiliation(s)
- Julia Engstrom-Melnyk
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Pedro L Rodriguez
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Olivier Peraud
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Raymond C Hein
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
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Abstract
Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable. This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.
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Affiliation(s)
- N Khardori
- Department of Internal Medicine, Division of Infectious Disease, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
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Akbari S, Oshaghi MA, Hashemi-Aghdam SS, Hajikhani S, Oshaghi G, Shirazi MH. Aerobic Bacterial Community of American Cockroach Periplaneta americana,a Step toward Finding Suitable Paratransgenesis Candidates. J Arthropod Borne Dis 2015; 9:35-48. [PMID: 26114142 PMCID: PMC4478416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/16/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cockroaches mechanically spread pathogenic agents, however, little is known about their gut microbiota. Identification of midgut microbial community helps targeting novel biological control strategies such as paratransgenesis. Here the bacterial microbiota of Periplaneta americana midgut, were identified and evaluated for finding proper paratransgenesis candidate. METHODS Midgut of specimens were dissected and cultivated in different media. The bacterial isolates were then identified using the phenotypic and 16S-rRNA sequencing methods. RESULTS The analytical profile index (API) kit showed presence of 11 bacterial species including: Escherichia coli, Shigella flexineri, Citrobacter freundii, E. vulneris, Enterobacter cloacae, Yersinia pseudotuberculosis, Y. intermedia, Leclericia adecarboxylata, Klebsiella oxytoca, K. planticola, and Rahnella aquatilis in the cockroach midguts. The first three species are potentially symbiotic whereas others are transient. The conventional plating method revealed presence of only four isolates of Salmonella, E. coli, and Proteus which in three cases mismatched with API and 16S-rRNA genotyping. The API correctly identified the four isolates as Shigella flexneri, Citrobacter freundii, and E. coli (n= 2). 16S-rRNA sequence analysis confirmed the API results; however the C. freundii sequence was identical with C. murliniae indicating lack of genetic variation in the gene between these two closely related species. CONCLUSION A low number of potentially symbiotic bacteria were found in the American cockroach midguts. Among them Enterobacter cloacae is a potential candidate for paratransgenesis approach whereas other bacteria are pathogens and are not useful for the approach. Data analysis showed that identification levels increase from the conventional to API and to genotyping respectively.
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Affiliation(s)
- Sanaz Akbari
- Department of Microbiology, Islamic Azad University, Damghan Branch, Damghan, Iran
| | - Mohammad Ali Oshaghi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sara Hajikhani
- Department of Pathology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Oshaghi
- Department of Nutrition, National Nutrition and Food Technology Research Institute (NNFTRI), Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hasan Shirazi
- Department of Pathology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics 2014; 15:918. [PMID: 25336203 PMCID: PMC4218995 DOI: 10.1186/1471-2164-15-918] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/06/2014] [Indexed: 12/04/2022] Open
Abstract
Background Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis. Results Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results. Conclusion CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, George Washington University, Washington DC 20037, USA.
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Niehues T. The febrile child: diagnosis and treatment. DEUTSCHES ARZTEBLATT INTERNATIONAL 2014; 110:764-73; quiz 774. [PMID: 24290365 DOI: 10.3238/arztebl.2013.0764] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND Fever accounts for 70% of all consultations with pediatricians and family physicians. Fever without an identifiable cause (<7 days' duration) and fever of unknown origin (FUO, ≥ 7 days' duration) are particularly challenging clinical situations. METHOD This article is based on a selective literature search for publications containing the term "pediatric fever management," with special attention to meta-analyses and systematic reviews. RESULTS The mainstay of diagnosis is physical examination by a physician who is experienced in the care of children and adolescents. The frequency of severe bacterial infection (SBI) is about 10% in neonates, 5% in babies aged up to 3 months, and 0.5% to 1% in older infants and toddlers. The mortality of SBI in neonates is about 10%. Both the degree of the parents' and the physician's concern are important warning signs for SBI. Clinical signs of SBI include cyanosis, tachypnea, poor peripheral perfusion, petechiae, and a rectal temperature above 40°C. Antipyretic drugs should only be used in special, selected situations. More than 40% of cases of FUO are due to infection; in more than 30% of cases, the cause is never determined. CONCLUSION Aspects of central importance include the repeated physical examination of the patient, and parent counseling and education of medical and nursing staff pertaining to the warning signs for SBI. Research is needed in the areas of diagnostic testing and the development of new vaccines.
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Affiliation(s)
- Tim Niehues
- Centre for Pediatric and Adolescent Medicine, HELIOS Klinikum Krefeld
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Willemsen I, Hille L, Vrolijk A, Bergmans A, Kluytmans J. Evaluation of a commercial real-time PCR for the detection of extended spectrum β-lactamase genes. J Med Microbiol 2014; 63:540-543. [DOI: 10.1099/jmm.0.070110-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the performance of a real-time PCR for the detection of extended spectrum β-lactamase genes in Enterobacteriaceae (Check-MDR ESBL PCR). Results from micro-arrays were considered as the gold standard. An analysis on 489 isolates resulted in a sensitivity of 98.9 % and a specificity of 100 % for the PCR.
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Affiliation(s)
- Ina Willemsen
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Linda Hille
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Angela Vrolijk
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Anneke Bergmans
- Department for Microbiology and Infection Control, Saint Fransiscus Hospital, Roosendaal, The Netherlands
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Jan Kluytmans
- Department for Microbiology and Infection Control, VUmc Medical Center, Amsterdam, The Netherlands
- Department for Microbiology and Infection Control, Saint Fransiscus Hospital, Roosendaal, The Netherlands
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
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Poirel L, Bonnin RA, Nordmann P. Rapid identification of antibiotic-resistant bacteria: how could new diagnostic tests halt potential endemics? Expert Rev Mol Diagn 2013; 13:409-11. [PMID: 23782246 DOI: 10.1586/erm.13.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Bustin S. Transparency of reporting in molecular diagnostics. Int J Mol Sci 2013; 14:15878-84. [PMID: 23903047 PMCID: PMC3759891 DOI: 10.3390/ijms140815878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 12/12/2022] Open
Affiliation(s)
- Stephen Bustin
- Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK; E-Mail: ; Tel.: +44-0-845-196-4845
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Diagnosis of ventilator-associated pneumonia: controversies and working toward a gold standard. Curr Opin Infect Dis 2013; 26:140-50. [PMID: 23411419 DOI: 10.1097/qco.0b013e32835ebbd0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PURPOSE OF REVIEW The aim is to discuss the clinical, microbiologic, and radiological criteria used in the diagnosis of ventilator-associated pneumonia (VAP), distinguish between ventilator-associated tracheobronchitis (VAT) and VAP, and reconcile the proposed Centers for Disease Control surveillance criteria with clinical practice. RECENT FINDINGS Numerous ventilator-associated complications (VACs), including VAP and VAT, may occur in critically ill, intubated patients. A variety of definitions for identifying VAP have been proposed, but there is no diagnostic gold standard. The proposed surveillance definition will identify infectious and noninfectious VAC, including VAP and VAT, but this definition may be inadequate for clinical practice. SUMMARY The clinical characteristics of VAP and VAT are similar and include fever, leukocytosis, and purulent sputum. An infiltrate on chest radiograph is consistent with VAP but lacks diagnostic precision, so it is not a criterion in the proposed surveillance definition and should be interpreted cautiously by clinicians. Microbiologically, quantitative and semiquantitative endotracheal aspirate cultures may be employed to diagnose VAP and VAT. Positive bronchoalveolar lavage and protected specimen brush cultures are useful only for the diagnosis of VAP. Experts should collaborate to develop consensus definitions for VAP and VAT that can be applied in practice.
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