1
|
Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
Collapse
Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
| |
Collapse
|
2
|
Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
Collapse
Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
| |
Collapse
|
3
|
Evaluation of a commercial microbial enrichment kit used prior DNA extraction to improve the molecular detection of vector-borne pathogens from naturally infected dogs. J Microbiol Methods 2021; 188:106163. [PMID: 33581169 DOI: 10.1016/j.mimet.2021.106163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/28/2023]
Abstract
Accurate detection of vector-borne pathogens (VBPs) is extremely important as the number of reported cases in humans and animals continues to rise in the US and abroad. Validated PCR assays are currently the cornerstone of molecular diagnostics and can achieve excellent analytical sensitivity and specificity. However, the detection of pathogens at low parasitemia still presents a challenge for VBP diagnosis, especially given the very low volume of specimens tested by molecular methods. The objective of this study is to determine if a commercially available microbial enrichment kit, used prior DNA extraction, is capable of expanding the overall microbial community and increasing detectable levels of VBPs in canine blood samples through host DNA depletion. This study used EDTA-whole blood samples from dogs naturally infected with varying parasitemia levels of either Anaplasma phagocytophilum, Babesia gibsoni, or Ehrlichia ewingii. For two VBPs, EDTA-blood samples were diluted to determine the effect of microbial concentration at low parasitemia. Paired EDTA-blood samples from each dog were subjected to traditional, automated DNA extraction with or without the microbial concentrating kit (MolYsis®) prior to DNA extraction. Relative amounts of pathogen DNA in paired samples were determined by real-time PCR and Next-Generation Sequencing targeting conserved regions of 16S rRNA (for bacteria) and 18S rRNA (for protozoa). Results from the three molecular methods suggest that the microbial concentrating kit did not improve the detection of VBPs, although significantly reduced the presence of host DNA. Alternative methods for VBP enrichment in clinical samples prior to molecular testing should continue to be investigated, as it may significantly improve clinical sensitivity and reduce the number of false-negative results.
Collapse
|
4
|
Rubiola S, Chiesa F, Dalmasso A, Di Ciccio P, Civera T. Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth. Front Microbiol 2020; 11:1983. [PMID: 32983010 PMCID: PMC7479305 DOI: 10.3389/fmicb.2020.01983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
Over the past decades, antimicrobial resistance (AMR) has been recognized as one of the most serious threats to public health. Although originally considered a problem to human health, the emerging crisis of AMR requires a "One Health" approach, considering human, animal, and environmental reservoirs. In this regard, the extensive use of antibiotics in the livestock production systems to treat mastitis and other bacterial diseases can lead to the presence of AMR genes in bacteria that contaminate or naturally occur in milk and dairy products, thereby introducing them into the food chain. The recent development of high-throughput next-generation sequencing (NGS) technologies is improving the fast characterization of microbial communities and their functional capabilities. In this context, whole metagenome sequencing (WMS), also called shotgun metagenomic sequencing, allows the generation of a vast amount of data which can be interrogated to generate the desired evidence, including the resistome. However, the amount of host DNA poses a major challenge to metagenome analysis. Given the current absence of literature concerning the application of WMS on milk to detect the presence of AMR genes, in the present study, we evaluated the effect of different sequencing depths, host DNA depletion methods and matrices to characterize the resistome of a milk production environment. WMS was conducted on three aliquots of bulk tank milk and three aliquots of the in-line milk filter collected from a single dairy farm; a fourth aliquot of milk and milk filter was bioinformatically subsampled. Two commercially available host DNA depletion methods were applied, and metagenomic DNA was sequenced to two different sequencing depth. Milk filters proved to be the most suitable matrices to evaluate the presence of AMR genes; besides, the pre-extraction host DNA depletion method was the most efficient approach to remove host reads. To our knowledge, this is the first study to evaluate the limitations posed by the host DNA in investigating the milk resistome with a WMS approach, confirming the circulation of AMR genes in the milk production environment.
Collapse
Affiliation(s)
| | - Francesco Chiesa
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | | | | | | |
Collapse
|
5
|
Microfluidic-Based Bacteria Isolation from Whole Blood for Diagnostics of Blood Stream Infection. Methods Mol Biol 2018; 1547:175-186. [PMID: 28044296 DOI: 10.1007/978-1-4939-6734-6_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Bacterial blood stream infection (BSI) potentially leads to life-threatening clinical conditions and medical emergencies such as severe sepsis, septic shock, and multi organ failure syndrome. Blood culturing is currently the gold standard for the identification of microorganisms and, although it has been automated over the decade, the process still requires 24-72 h to complete. This long turnaround time, especially for the identification of antimicrobial resistance, is driving the development of rapid molecular diagnostic methods. Rapid detection of microbial pathogens in blood related to bloodstream infections will allow the clinician to decide on or adjust the antimicrobial therapy potentially reducing the morbidity, mortality, and economic burden associated with BSI. For molecular-based methods, there is a lot to gain from an improved and straightforward method for isolation of bacteria from whole blood for downstream processing.We describe a microfluidic-based sample-preparation approach that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.
Collapse
|
6
|
Dalla-Costa LM, Morello LG, Conte D, Pereira LA, Palmeiro JK, Ambrosio A, Cardozo D, Krieger MA, Raboni SM. Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR. J Microbiol Methods 2017; 140:61-66. [PMID: 28669799 DOI: 10.1016/j.mimet.2017.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/16/2022]
Abstract
Sepsis is the leading cause of death in intensive care units (ICUs) worldwide and its diagnosis remains a challenge. Blood culturing is the gold standard technique for blood stream infection (BSI) identification. Molecular tests to detect pathogens in whole blood enable early use of antimicrobials and affect clinical outcomes. Here, using real-time PCR, we evaluated DNA extraction using seven manual and three automated commercially available systems with whole blood samples artificially contaminated with Escherichia coli, Staphylococcus aureus, and Candida albicans, microorganisms commonly associated with BSI. Overall, the commercial kits evaluated presented several technical limitations including long turnaround time and low DNA yield and purity. The performance of the kits was comparable for detection of high microorganism loads (106CFU/mL). However, the detection of lower concentrations was variable, despite the addition of pre-processing treatment to kits without such steps. Of the evaluated kits, the UMD-Universal CE IVD kit generated a higher quantity of DNA with greater nucleic acid purity and afforded the detection of the lowest microbial load in the samples. The inclusion of pre-processing steps with the kit seems to be critical for the detection of microorganism DNA directly from whole blood. In conclusion, future application of molecular techniques will require overcoming major challenges such as the detection of low levels of microorganism nucleic acids amidst the large quantity of human DNA present in samples or differences in the cellular structures of etiological agents that can also prevent high-quality DNA yields.
Collapse
Affiliation(s)
- Libera M Dalla-Costa
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Laboratory of Bacteriology, Universidade Federal do Paraná, Rua Padre Camargo, 280, - 80060-240, Curitiba, Brazil; Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632, - 80250-200, Curitiba, Brazil
| | - Luis G Morello
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Laboratory of Functional Genomics, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Rua Professor Algacyr Munhoz Mader, 3775, - 81310-020, Curitiba, Brazil
| | - Danieli Conte
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil
| | - Luciane A Pereira
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil
| | - Jussara K Palmeiro
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Laboratory of Bacteriology, Universidade Federal do Paraná, Rua Padre Camargo, 280, - 80060-240, Curitiba, Brazil
| | - Altair Ambrosio
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Laboratory of Bacteriology, Universidade Federal do Paraná, Rua Padre Camargo, 280, - 80060-240, Curitiba, Brazil
| | - Dayane Cardozo
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil
| | - Marco A Krieger
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Laboratory of Functional Genomics, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Rua Professor Algacyr Munhoz Mader, 3775, - 81310-020, Curitiba, Brazil.
| | - Sonia M Raboni
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader, 3775, - 81925-610, Curitiba, Brazil; Infectious Disease Division, Universidade Federal do Paraná, Rua Gen. Carneiro, 181, - 80060-900, Curitiba, Brazil.
| |
Collapse
|
7
|
Brennecke J, Kraut S, Zwadlo K, Gandi SK, Pritchard D, Templeton K, Bachmann T. High-yield extraction of Escherichia coli RNA from human whole blood. J Med Microbiol 2017; 66:301-311. [PMID: 28126043 DOI: 10.1099/jmm.0.000439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Studies of bacterial transcriptomics during bloodstream infections are limited to-date because unbiased extraction of bacterial mRNA from whole blood in sufficient quantity and quality has proved challenging. Problems include the high excess of human cells, the presence of PCR inhibitors and the short intrinsic half-life of bacterial mRNA. This study aims to provide a framework for the choice of the most suitable sample preparation method. METHODOLOGY Escherichia coli cells were spiked into human whole blood and the bacterial gene expression was stabilized with RNAprotect either immediately or after lysis of the red blood cells with Triton X-100, saponin, ammonium chloride or the commercial MolYsis buffer CM. RNA yield, purity and integrity were assessed by absorbance measurements at 260 and 280 nm, real-time PCR and capillary electrophoresis. RESULTS For low cell numbers, the best mRNA yields were obtained by adding the commercial RNAprotect reagent directly to the sample without prior lyses of the human blood cells. Using this protocol, significant amounts of human RNA were co-purified, however, this had a beneficial impact on the yields of bacterial mRNA. Among the tested lysis agents, Triton X-100 was the most effective and reduced the human RNA background by three to four orders of magnitude. CONCLUSION For most applications, lysis of the human blood cells is not required. However, co-purified human RNA may interfere with some downstream processes such as RNA sequencing. In this case, blood cell lysis with Triton X-100 is desirable.
Collapse
Affiliation(s)
- Johannes Brennecke
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
| | - Simone Kraut
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK.,AG Aus- und Weiterbildung, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Klara Zwadlo
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK.,AG Aus- und Weiterbildung, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Senthil Kumar Gandi
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - Till Bachmann
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
8
|
Comparison between a chimeric lysin ClyH and other enzymes for extracting DNA to detect methicillin resistant Staphylococcus aureus by quantitative PCR. World J Microbiol Biotechnol 2015; 32:1. [PMID: 26596268 DOI: 10.1007/s11274-015-1971-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/14/2015] [Indexed: 02/01/2023]
Abstract
Extracting DNA from Staphylococcus aureus cells is important for detecting MRSA by PCR. However, S. aureus cells are known to be difficult to disrupt due to their compact cell walls. Here, we systematically studied the efficiency of a highly active lysin ClyH for extracting DNA of S. aureus in comparison with commonly used enzymes, such as lysostaphin and achromopeptidase (ACP), and its compatibility in quantitative PCR (qPCR) detection of MRSA. qPCR analysis of S. aureus specific gene femB showed that ClyH was much faster than lysostaphin, ACP and lysozyme for releasing DNA. Five minutes disruption with ClyH at room temperature was enough to release all the DNA from S. aureus. Analysis of the spiked nasal swabs by a dual qPCR assay of the β-lactam resistance mecA gene and the staphylococcal cassette chromosome (SCCmec)-open reading frame X (orfX) junction (SCCmec-orfX) after ClyH lysis showed 100% sensitivity and specificity to the commercial BD GeneOhm™ MRSA test with ACP lysis, but the lysis time was reduced from 20 min by ACP to 5 min by ClyH. Our research shows that ClyH could be a better option than the currently used enzymes for DNA extraction from S. aureus, which can provide simpler and faster PCR detection of MRSA.
Collapse
|
9
|
Direct Screening of Blood by PCR and Pyrosequencing for a 16S rRNA Gene Target from Emergency Department and Intensive Care Unit Patients Being Evaluated for Bloodstream Infection. J Clin Microbiol 2015; 54:99-105. [PMID: 26511737 DOI: 10.1128/jcm.02394-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/22/2015] [Indexed: 11/20/2022] Open
Abstract
Here we compared the results of PCR/pyrosequencing to those of culture for detecting bacteria directly from blood. DNA was extracted from 1,130 blood samples from 913 patients suspected of bacteremia (enrollment criteria were physician-ordered blood culture and complete blood count [CBC]), and 102 controls (healthy blood donors). Real-time PCR assays for beta-globin and Universal 16S rRNA gene targets were performed on all 1,232 extracts. Specimens identified by Universal 16S rRNA gene PCR/pyrosequencing as containing staphylococci, streptococci, or enteric Gram-negative rods had target-specific PCR/pyrosequencing performed. Amplifiable beta-globin (melting temperature [Tm], 87.2°C ± 0.2°C) occurred in 99.1% (1,120/1,130) of patient extracts and 100% (102/102) of controls. Concordance between PCR/pyrosequencing and culture was 96.9% (1,085/1,120) for Universal 16S rRNA gene targets, with positivity rates of 9.4% (105/1,120) and 11.3% (126/1,120), respectively. Bacteria cultured included staphylococci (59/126, 46.8%), Gram-negative rods (34/126, 27%), streptococci (32/126, 25.4%), and a Gram-positive rod (1/126, 0.8%). All controls screened negative by PCR/pyrosequencing. Clinical performance characteristics (95% confidence interval [CI]) for Universal 16S rRNA gene PCR/pyrosequencing included sensitivity of 77.8% (69.5 to 84.7), specificity of 99.3% (98.6 to 99.7), positive predictive value (PPV) of 93.3% (86.8 to 97.3), and negative predictive value (NPV) of 97.2% (96.0 to 98.2). Bacteria were accurately identified in 77.8% (98/126) of culture-confirmed sepsis samples with Universal 16S PCR/pyrosequencing and in 76.4% (96/126) with follow-up target-specific PCR/pyrosequencing. The initial PCR/pyrosequencing took ∼5.5 h to complete or ∼7.5 h when including target-specific PCR/pyrosequencing compared to 27.9 ± 13.6 h for Gram stain or 81.6 ± 24.0 h for phenotypic identification. In summary, this molecular approach detected the causative bacteria in over three-quarters of all culture-confirmed cases of bacteremia directly from blood in significantly less time than standard culture but cannot be used to rule out infection.
Collapse
|
10
|
Stedtfeld RD, Liu YC, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomed Microdevices 2015; 17:89. [PMID: 26260693 PMCID: PMC4531140 DOI: 10.1007/s10544-015-9994-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A microfluidic card is described for simultaneous and rapid genetic detection of multiple microbial pathogens. The hydrophobic surface of native acrylic and a novel microfluidic mechanism termed "airlock" were used to dispense sample into a series of 64 reaction wells without the use of valves, external pumping peripherals, multiple layers, or vacuum assistance. This airlock mechanism was tested with dilutions of whole human blood, saliva, and urine, along with mock samples of varying viscosities and surface tensions. Samples spiked with genomic DNA (gDNA) or crude lysates from clinical bacterial isolates were tested with loop mediated isothermal amplification assays (LAMP) designed to target virulence and antibiotic resistance genes. Reactions were monitored in real time using the Gene-Z, which is a portable smartphone-driven system. Samples loaded correctly into the microfluidic card in 99.3% of instances. Amplification results confirmed no carryover of pre-dispensed primer between wells during sample loading, and no observable diffusion between adjacent wells during the 60 to 90 min isothermal reaction. Sensitivity was comparable between LAMP reactions tested within the microfluidic card and in conventional vials. Tests demonstrate that the airlock card works with various sample types, manufacturing techniques, and can potentially be used in many point-of-care diagnostics applications.
Collapse
Affiliation(s)
- Robert D. Stedtfeld
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Yen-Cheng Liu
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Tiffany M. Stedtfeld
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Tanja Kostic
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
- />Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Maggie Kronlein
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
| | - Onnop Srivannavit
- />Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 USA
| | - Walid T. Khalife
- />Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912 USA
| | - James M. Tiedje
- />The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
- />Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
| | - Erdogan Gulari
- />Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mary Hughes
- />Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824 USA
| | - Brett Etchebarne
- />Department of Osteopathic Medical Specialties, Section of Emergency Medicine, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824 USA
| | - Syed A. Hashsham
- />Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824 USA
- />The Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| |
Collapse
|
11
|
Bwanga F, Disqué C, Lorenz MG, Allerheiligen V, Worodria W, Luyombya A, Najjingo I, Weizenegger M. Higher blood volumes improve the sensitivity of direct PCR diagnosis of blood stream tuberculosis among HIV-positive patients: an observation study. BMC Infect Dis 2015; 15:48. [PMID: 25656799 PMCID: PMC4326319 DOI: 10.1186/s12879-015-0785-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 01/27/2015] [Indexed: 12/14/2022] Open
Abstract
Background Blood stream tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB) is common among HIV-positive patients, turning rapidly fatal unless detected and treated promptly. Blood culture is currently the standard test for the detection of MTB in whole blood but results take weeks; patients deteriorate markedly and often die before a diagnosis of blood stream TB is made. Rapid molecular tests on whole blood, with potential for same day diagnosis of blood stream TB usually show low sensitivity due to the problem of insufficient MTB DNA template when extraction is performed directly on low blood volumes. This study assessed the influence of blood volume on the sensitivity of a HyBeacon PCR assay-the FluoroType® MTB (Hain Lifescience, Nehren, Germany) on direct detection of MTB in whole blood. Methods Prospective recruitment of HIV-positive patients with clinical suspicion of blood stream TB but not on anti-TB or HIV drug treatment was done. Venous blood samples were collected and DNA extracted using the MolYsis (Molzym, Bremen, Germany) methods; for study A, from duplicate 1 ml (42 patients) and for study B (31 patients) from 9 ml EDTA blood samples. The FluoroType® MTB PCR assay targeting an IS6110 sequence was performed and results compared with blood culture. Results The diagnostic sensitivity and specificity of the FluoroType® MTB PCR in study A was 33% and 97%, respectively. Corresponding values in study B were 71% and 96%, respectively. In both studies, one case each of blood culture-negative blood stream TB was detected with the FluoroType® MTB PCR assay. The median time to positivity of blood culture was 20.1 (range 12–32) for study A and 19.9 days (range 15–30) for study B. Conclusion Larger blood volumes (9 ml) improved and gave acceptable sensitivity of direct PCR diagnosis of blood stream TB.
Collapse
Affiliation(s)
- Freddie Bwanga
- Makerere University College of Health Sciences, Kampala, Uganda. .,MBN Clinical Laboratories, Kampala, Uganda.
| | | | | | | | - William Worodria
- Makerere University College of Health Sciences, Kampala, Uganda.
| | | | | | - Michael Weizenegger
- Medizinisches Versorgungszentrum Labor Dr. Limbach und Kollegen, Heidelberg, Germany.
| |
Collapse
|
12
|
Abstract
One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fulbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. This technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.In this chapter, I give my personal account of the development of Pyrosequencing(®)-beginning on a winter day in 1986, when I first envisioned the method-until today, nearly 30 years later.
Collapse
Affiliation(s)
- Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, Roslagstullsbacken 21, AlbaNova, SE-106 91, Stockholm, Sweden,
| |
Collapse
|