1
|
Miringu G, Musyoki A, Muriithi B, Wandera E, Waithiru D, Odoyo E, Shoji H, Menza N, Ichinose Y. Development of two multiplex PCR assays for rapid detection of eleven Gram-negative bacteria in children with septicemia. Trop Med Health 2024; 52:40. [PMID: 38840209 DOI: 10.1186/s41182-024-00606-3] [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: 02/26/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
AIM This study aimed to develop a multiplex PCR assay for simultaneous detection of major Gram-negative etiologies of septicemia and evaluate its performance. METHODS Multiplex PCR (mPCR) assays were developed targeting 11 bacterial strains. Species-specific primers were confirmed using known clinical isolates and standard strains. Gradient PCR was performed on each primer against its target bacterial gene to determine its optimal amplification condition. The minimum detectable DNA concentration of the two assays was evaluated by adjusting bacterial DNA concentration to 100 ng/μL and, tenfold serially diluting it up to 10 pg/μL with DNAse-free water. The diagnostic accuracy of mPCR assays was established by subjecting the assays to 60 clinical blood samples. RESULTS Two mPCR assays were developed. Optimal primer annealing temperature of 55 °C was established and utilized in the final amplification conditions. The assays detected all targeted bacteria, with a 100 pg minimum detectable DNA concentration. Pathogens were not detected directly from whole blood, but after 4 h and 8 h of incubation, 41% (5/12) and 100% (12/12) of the bacteria were detected in culture fluids, respectively. The assays also identified Salmonella spp. and Klebsiella pneumoniae co-infections and extra pathogens (1 E. coli and 2 K. pneumoniae) compared with culture. The sensitivity and specificity of the mPCR were 100.0% (71.7-100.0) and 98.0% (90.7-99.0), respectively. The area under the ROC curve was 1.00 (1.00-1.00). CONCLUSIONS The mPCR assays demonstrated substantial potential as a rapid tool for septicemia diagnosis alongside the traditional blood culture method. Notably, it was able to identify additional isolates, detect co-infections, and efficiently detect low bacterial DNA loads with high sensitivity, implying its value in enhancing efficiency of diagnosis of septicemia.
Collapse
Affiliation(s)
- Gabriel Miringu
- Kenya Medical Research Institute, Institute of Tropical Medicine, Nagasaki University, Nairobi, 19993-00202, Kenya.
- Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya.
| | - Abednego Musyoki
- Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya
| | - Betty Muriithi
- Kenya Medical Research Institute, Institute of Tropical Medicine, Nagasaki University, Nairobi, 19993-00202, Kenya
| | - Ernest Wandera
- Kenya Medical Research Institute, Institute of Tropical Medicine, Nagasaki University, Nairobi, 19993-00202, Kenya
- Center for Virus Research, KEMRI, Nairobi, Kenya
| | - Dan Waithiru
- Center for Microbiology Research, KEMRI, Nairobi, Kenya
| | - Erick Odoyo
- United States Army Medical Research Unit, KEMRI, Nairobi, Kenya
| | | | - Nelson Menza
- Department of Medical Laboratory Sciences, Kenyatta University, Nairobi, Kenya
| | - Yoshio Ichinose
- Kenya Medical Research Institute, Institute of Tropical Medicine, Nagasaki University, Nairobi, 19993-00202, Kenya
| |
Collapse
|
2
|
Jiang S, Zhao D, Wang C, Liu X, Yang Q, Bao X, Dong T, Li G, Gu Y, Ye Y, Sun B, Xu S, Zhou X, Fan L, Tang L. Clinical evaluation of droplet digital PCR in the early identification of suspected sepsis patients in the emergency department: a prospective observational study. Front Cell Infect Microbiol 2024; 14:1358801. [PMID: 38895732 PMCID: PMC11183271 DOI: 10.3389/fcimb.2024.1358801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024] Open
Abstract
Background Rapid and accurate diagnosis of the causative agents is essential for clinical management of bloodstream infections (BSIs) that might induce sepsis/septic shock. A considerable number of suspected sepsis patients initially enter the health-care system through an emergency department (ED), hence it is vital to establish an early strategy to recognize sepsis and initiate prompt care in ED. This study aimed to evaluate the diagnostic performance and clinical value of droplet digital PCR (ddPCR) assay in suspected sepsis patients in the ED. Methods This was a prospective single-centered observational study including patients admitted to the ED from 25 October 2022 to 3 June 2023 with suspected BSIs screened by Modified Shapiro Score (MSS) score. The comparison between ddPCR and blood culture (BC) was performed to evaluate the diagnostic performance of ddPCR for BSIs. Meanwhile, correlative analysis between ddPCR and the inflammatory and prognostic-related biomarkers were conducted to explore the relevance. Further, the health economic evaluation of the ddPCR was analyzed. Results 258 samples from 228 patients, with BC and ddPCR performed simultaneously, were included in this study. We found that ddPCR results were positive in 48.13% (103 of 214) of episodes, with identification of 132 pathogens. In contrast, BC only detected 18 positives, 88.89% of which were identified by ddPCR. When considering culture-proven BSIs, ddPCR shows an overall sensitivity of 88.89% and specificity of 55.61%, the optimal diagnostic power for quantifying BSI through ddPCR is achieved with a copy cutoff of 155.5. We further found that ddPCR exhibited a high accuracy especially in liver abscess patients. Among all the identified virus by ddPCR, EBV has a substantially higher positive rate with a link to immunosuppression. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity as well as prognosis. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs. Conclusions The multiplexed ddPCR delivers precise and quantitative load data on the causal pathogen, offers the ability to monitor the patient's condition and may serve as early warning of sepsis in time-urgent clinical situations as ED. Importance Early detection and effective administration of antibiotics are essential to improve clinical outcomes for those with life-threatening infection in the emergency department. ddPCR, an emerging tool for rapid and sensitive pathogen identification used as a precise bedside test, has developed to address the current challenges of BSI diagnosis and precise treatment. It characterizes sensitivity, specificity, reproducibility, and absolute quantifications without a standard curve. ddPCR can detect causative pathogens and related resistance genes in patients with suspected BSIs within a span of three hours. In addition, it can identify polymicrobial BSIs and dynamically monitor changes in pathogenic microorganisms in the blood and can be used to evaluate antibiotic efficacy and survival prognosis. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.
Collapse
Affiliation(s)
- Sen Jiang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Dongyang Zhao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Chunxue Wang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiandong Liu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Qian Yang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaowei Bao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Tiancao Dong
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Gen Li
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Gu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Yangqin Ye
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingke Sun
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Shumin Xu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui Zhou
- School of Medicine, Tongji University, Shanghai, China
- Research Center for Translational Medicine, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Lieying Fan
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| |
Collapse
|
3
|
Jones JD, Proffitt KM, Ramsey JM, Almberg ES, Anderson NJ. Reproductive Fate of Brucellosis-Seropositive Elk (Cervus canadensis): Implications for Disease Transmission Risk. J Wildl Dis 2024; 60:52-63. [PMID: 37889938 DOI: 10.7589/jwd-d-22-00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/25/2023] [Indexed: 10/29/2023]
Abstract
Brucellosis is a disease caused by the bacterium Brucella abortus that infects elk (Cervus canadensis) and cattle (Bos taurus). There is the potential for transmission from wildlife to livestock through contact with infected material shed during abortions or live births. To understand the impact of exposure on pregnancy rates we captured 30-100 elk per year from 2011 through 2020, testing their blood for serologic exposure to B. abortus. Predicted pregnancy rates for seropositive animals were 9.6% lower in prime-age (2.5-15.5 yr; 85%, 95% confidence interval [CI]: 74-91%) and 37.7% lower in old (>15.5 yr; 43%, 95% CI: 19-71%) elk as compared with seronegative animals. To understand the risk of seropositive elk shedding B. abortus bacteria and the effects of exposure on elk reproductive performance, we conducted a 5-yr longitudinal study monitoring 30 seropositive elk. We estimated the annual probability of a seropositive elk having an abortion as 0.06 (95% CI: 0.02-0.15). We detected B. abortus at three abortions and two live births, using a combination of culture and PCR testing. The predicted probability of a pregnant seropositive elk shedding B. abortus during an abortion or live birth was 0.08 (95% CI: 0.04-0.19). To understand what proportion of seropositive elk harbored live B. abortus bacteria in their tissues, we euthanized seropositive elk at the end of 5 yr of monitoring and sampled tissues for B. abortus. Assuming perfect detection, the predicted probability of a seropositive elk having B. abortus in at least one tissue was 0.18 (95% CI: 0.06-0.43). The transmission risk seropositive elk pose is mitigated by decreased pregnancy rates, low probability of abortion events, low probability of shedding at live birth events, and reasonably low probability of B. abortus in tissues.
Collapse
Affiliation(s)
- Jennifer D Jones
- Montana Department of Fish, Wildlife & Parks, 1400 South 19th Avenue, Bozeman, Montana 59718, USA
| | - Kelly M Proffitt
- Montana Department of Fish, Wildlife & Parks, 1400 South 19th Avenue, Bozeman, Montana 59718, USA
| | - Jennifer M Ramsey
- Montana Department of Fish, Wildlife & Parks, 1400 South 19th Avenue, Bozeman, Montana 59718, USA
| | - Emily S Almberg
- Montana Department of Fish, Wildlife & Parks, 1400 South 19th Avenue, Bozeman, Montana 59718, USA
| | - Neil J Anderson
- Montana Department of Fish, Wildlife & Parks, 490 North Meridian Road, Kalispell, Montana 59901, USA
| |
Collapse
|
4
|
Zhang B, Li M, Liu Y, Zhang B, Liu Z, Chen X, Huo J, Han Y. The diagnostic value of blood sample NGS in patients with early periprosthetic joint infection after total hip arthroplasty. Int Wound J 2023; 20:961-970. [PMID: 36054590 PMCID: PMC10030938 DOI: 10.1111/iwj.13943] [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: 07/26/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
The diagnostic value of next-generation sequencing (NGS) of blood samples from patients with periprosthetic joint infection (PJI) after total hip arthroplasty (THA) was evaluated by comparing it with drainage fluid NGS and bacterial culture. The study was designed as a retrospective diagnostic test. Thirty-six infected patients were diagnosed with PJI according to the Musculoskeletal Infection Society (MSIS) criteria and 57 volunteers were included in our study. NGS and bacterial culture were chosen to detect PJI after THA. Blood samples and drainage fluid were collected for NGS, and the drainage fluid, which was collected at the same time as the NGS drainage fluid sample, was used for bacterial culture. The primary outcomes of interest were sensitivity, specificity, and accuracy. In the infection group, 31 patients showed positive results by blood sample NGS, 33 patients showed positive results by drainage fluid NGS, and 17 patients showed positive bacterial culture results. In the control group, the results of 2 blood sample NGS, 16 drainage fluid NGS, and 3 bacterial cultures were positive. The sensitivity, specificity, and accuracy of the blood sample were 0.86, 0.96, and 0.92, respectively. The sensitivity, specificity, and accuracy of the drainage fluid samples were 0.92, 0.72, and 0.80, respectively. The sensitivity, specificity, and accuracy of bacterial culture were 0.47, 0.95, and 0.79, respectively. The study demonstrated that both the sensitivity and specificity of NGS were higher than those of bacterial culture, regardless of the kind of sample. Compared with drainage fluid NGS, the sensitivity of blood sample NGS was slightly lower (0.86 vs 0.92), but blood sample NGS showed higher specificity (0.96 vs 0.72). In total, the diagnostic value of blood sample NGS was superior to that of drainage fluid NGS and bacterial culture. The majority of infected patients could be identified by blood sample NGS. Moreover, because of its high specificity, blood sample NGS can not only detect infectious bacteria but also distinguish infectious from non-infectious bacteria, which is dramatically different from using drainage fluid NGS.
Collapse
Affiliation(s)
- Bingshi Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Mengnan Li
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yawei Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Binquan Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Zeming Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Xiao Chen
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Jia Huo
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| |
Collapse
|
5
|
Safir F, Vu N, Tadesse LF, Firouzi K, Banaei N, Jeffrey SS, Saleh AAE, Khuri-Yakub B(P, Dionne JA. Combining Acoustic Bioprinting with AI-Assisted Raman Spectroscopy for High-Throughput Identification of Bacteria in Blood. NANO LETTERS 2023; 23:2065-2073. [PMID: 36856600 PMCID: PMC10037319 DOI: 10.1021/acs.nanolett.2c03015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Identifying pathogens in complex samples such as blood, urine, and wastewater is critical to detect infection and inform optimal treatment. Surface-enhanced Raman spectroscopy (SERS) and machine learning (ML) can distinguish among multiple pathogen species, but processing complex fluid samples to sensitively and specifically detect pathogens remains an outstanding challenge. Here, we develop an acoustic bioprinter to digitize samples into millions of droplets, each containing just a few cells, which are identified with SERS and ML. We demonstrate rapid printing of 2 pL droplets from solutions containing S. epidermidis, E. coli, and blood; when they are mixed with gold nanorods (GNRs), SERS enhancements of up to 1500× are achieved.We then train a ML model and achieve ≥99% classification accuracy from cellularly pure samples and ≥87% accuracy from cellularly mixed samples. We also obtain ≥90% accuracy from droplets with pathogen:blood cell ratios <1. Our combined bioprinting and SERS platform could accelerate rapid, sensitive pathogen detection in clinical, environmental, and industrial settings.
Collapse
Affiliation(s)
- Fareeha Safir
- *Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Nhat Vu
- Pumpkinseed
Technologies, Inc., Palo Alto, California 94306, United States
| | - Loza F. Tadesse
- Department
of Bioengineering, Stanford University School
of Medicine and School of Engineering, Stanford, California 94305, United States
| | - Kamyar Firouzi
- E.
L. Ginzton Laboratory, Stanford University, Stanford, California 94305, United States
| | - Niaz Banaei
- Department
of Pathology, Stanford University School
of Medicine, Stanford, 94305 California, United
States
- Clinical
Microbiology Laboratory, Stanford Health Care, Palo Alto, California 94304, United States
- Department
of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Stefanie S. Jeffrey
- Department
of Surgery, Stanford University School of
Medicine, Stanford, California 94305, United States
| | - Amr. A. E. Saleh
- Department
of Engineering Mathematics and Physics, Cairo University, Cairo 12613, Egypt
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Butrus (Pierre)
T. Khuri-Yakub
- E.
L. Ginzton Laboratory, Stanford University, Stanford, California 94305, United States
- Department
of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Jennifer A. Dionne
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
- Department
of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, California 94035, United States
| |
Collapse
|
6
|
Lai ZX, Wu CC, Huang NT. A Microfluidic Platform with an Embedded Miniaturized Electrochemical Sensor for On-Chip Plasma Extraction Followed by In Situ High-Sensitivity C-Reactive Protein (hs-CRP) Detection. BIOSENSORS 2022; 12:1163. [PMID: 36551130 PMCID: PMC9775575 DOI: 10.3390/bios12121163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Blood testing is a clinical diagnostic tool to evaluate physiological conditions, the immune system response, or the presence of infection from whole blood samples. Although conventional blood testing can provide rich biological information, it usually requires complicated and tedious whole blood processing steps operated by benchtop instruments and well-experienced technicians, limiting its usage in point-of-care (POC) settings. To address the above problems, we propose a microfluidic platform for on-chip plasma extraction directly from whole blood and in situ biomarker detection. Herein, we chose C-reactive protein (CRP) as the target biomarker, which can be used to predict fatal cardiovascular disease (CVD) events such as heart attacks and strokes. To achieve a rapid, undiluted, and high-purity on-chip plasma extraction, we combined two whole blood processing methods: (1) anti-D immunoglobulin-assisted sedimentation, and (2) membrane filtration. To perform in situ CRP detection, we fabricated a three-dimensional (3D) microchannel with an embedded electrochemical (EC) sensor, which has a modular design to attach the blood collector and buffer reservoir with standard Luer connectors. As a proof of concept, we first confirmed that the dual plasma extraction design achieved the same purity level as the standard centrifugation method with smaller sample (100 µL of plasma extracted from 400 µL of whole blood) and time (7 min) requirements. Next, we validated the functionalization protocol of the EC sensor, followed by evaluating the detection of CRP spiked in plasma and whole blood. Our microfluidic platform performed on-chip plasma extraction directly from whole blood and in situ CRP detection at a 0.1-10 μg/mL concentration range, covering the CVD risk evaluation level of the high-sensitivity CRP (hs-CRP) test. Based on the above features, we believe that this platform constitutes a flexible way to integrate the processing of complex samples with accurate biomarker detection in a sample-to-answer POC platform, which can be applied in CVD risk monitoring under critical clinical situations.
Collapse
Affiliation(s)
- Zhi-Xuan Lai
- Graduation Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chien Wu
- Graduation Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Nien-Tsu Huang
- Graduation Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
7
|
Ngo H, Mbadugha UJ, Cepeda F, Surani S, Udeani G. Clinical and Economic Impact of Rapid Blood Pathogen Identification Via Verigene. Cureus 2022; 14:e30366. [PMID: 36407168 DOI: 10.7759/cureus.30366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
|
8
|
Su H, Jiang ZH, Chiou SF, Shiea J, Wu DC, Tseng SP, Jain SH, Chang CY, Lu PL. Rapid Characterization of Bacterial Lipids with Ambient Ionization Mass Spectrometry for Species Differentiation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092772. [PMID: 35566120 PMCID: PMC9104219 DOI: 10.3390/molecules27092772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022]
Abstract
Ambient ionization mass spectrometry (AIMS) is both labor and time saving and has been proven to be useful for the rapid delineation of trace organic and biological compounds with minimal sample pretreatment. Herein, an analytical platform of probe sampling combined with a thermal desorption–electrospray ionization/mass spectrometry (TD-ESI/MS) and multivariate statistical analysis was developed to rapidly differentiate bacterial species based on the differences in their lipid profiles. For comparison, protein fingerprinting was also performed with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) to distinguish these bacterial species. Ten bacterial species, including five Gram-negative and five Gram-positive bacteria, were cultured, and the lipids in the colonies were characterized with TD-ESI/MS. As sample pretreatment was unnecessary, the analysis of the lipids in a bacterial colony growing on a Petri dish was completed within 1 min. The TD-ESI/MS results were further performed by principal component analysis (PCA) and hierarchical cluster analysis (HCA) to assist the classification of the bacteria, and a low relative standard deviation (5.2%) of the total ion current was obtained from repeated analyses of the lipids in a single bacterial colony. The PCA and HCA results indicated that different bacterial species were successfully distinguished by the differences in their lipid profiles as validated by the differences in their protein profiles recorded from the MALDI-TOF analysis. In addition, real-time monitoring of the changes in the specific lipids of a colony with growth time was also achieved with probe sampling and TD-ESI/MS. The developed analytical platform is promising as a useful diagnostic tool by which to rapidly distinguish bacterial species in clinical practice.
Collapse
Affiliation(s)
- Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Zong-Han Jiang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Shu-Fen Chiou
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung 804201, Taiwan;
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Correspondence: (J.S.); (P.-L.L.)
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
- Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Shu-Huei Jain
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
| | - Chung-Yu Chang
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Po-Liang Lu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- College of Medicine, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- Correspondence: (J.S.); (P.-L.L.)
| |
Collapse
|
9
|
A diagnostic platform for rapid, simultaneous quantification of procalcitonin and C-reactive protein in human serum. EBioMedicine 2022; 76:103867. [PMID: 35149284 PMCID: PMC8841998 DOI: 10.1016/j.ebiom.2022.103867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 01/08/2023] Open
Abstract
Background Early and accurate determination of bacterial infections as a potential cause for a patient's systemic inflammatory response is required for timely administration of appropriate treatment and antibiotic stewardship. Procalcitonin (PCT) and C-reactive protein (CRP) have both been used as biomarkers to infer bacterial infections, particularly in the context of sepsis. There is an urgent need to develop a platform for simultaneous quantification of PCT and CRP, to enable the potential use of these biomarkers at the point-of-care. Methods A multiplexed lateral flow assay (LFA) and a fluorescence optical reader were developed. Assay performance was validated by testing spiked antigens in the buffer, followed by a validation study comparing results with conventional assays (Roche Cobas e411 Elecsys PCT and Siemens ADVIA XPT CRP) in 25 archived remnant human serum samples. Findings A linear regression correlation of 0·97 (P < 0·01) was observed for PCT, and a correlation of 0·95 (P < 0·01) was observed for CRP using direct patient samples. We also validated our platform's ability to accurately quantify high-dose CRP in the hook effect range where excess unlabeled analytes occupy binding sites at test lines. Interpretation A fluorescence reader-based duplex LFA for simultaneous quantification of PCT and CRP was developed and successfully validated with clinical samples. The rapid, portable, and low-cost nature of the platform offers potential for differentiation of bacterial and viral infections in emergency and low-resource settings at the point-of-care. Funding NIH/NIBIB Award 1R01EB021331, and Academic Venture Fund from the Atkinson Center for a Sustainable Future at Cornell University.
Collapse
|
10
|
Kavipriya D, Prakash SS, Dhandapani S, Rajshekar D, Sastry AS. Evaluation of the Performance of Direct Susceptibility Test by VITEK-2 from Positively Flagged Blood Culture Broth for Gram-Negative Bacilli. J Lab Physicians 2022; 13:374-379. [PMID: 34975259 PMCID: PMC8714412 DOI: 10.1055/s-0041-1732489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background
Timely initiation of antimicrobial therapy in patients with blood stream infection is absolutely necessary to reduce mortality and morbidity. Most clinical microbiology laboratories use conventional methods for identification and antimicrobial susceptibility testing (AST) that involve biochemical methods for identification followed by AST by disk diffusion. The aim of the current study is to assess the various errors associated with direct susceptibility testing done from blood culture broth using automated AST system-Vitek-2 compact compared with the reference method of AST done from bacterial colonies.
Materials and Methods
The study was conducted in a tertiary care public sector 2,200-bedded hospital in South India for a period of 6 months. The study involved positively flagged blood culture bottles that yielded single morphotype of Gram-negative organism by Gram stain. A total of 120 bacterial isolates were collected that consisted of consecutively obtained first 60 isolates of Enterobacteriaceae family (30
Escherichia coli
and 30
Klebsiella pneumoniae
) and consecutively obtained first 60 nonfermenters (30
Pseudomonas aeruginosa
and 30
Acinetobacter baumannii).
Vitek-2 AST was done from these 120 blood culture broth, following the protocol by Biomerieux, and results were obtained. Then, Vitek-2 was done from colonies (reference method) using appropriate panel for Enterobacteriaceae and nonfermenters, and results were obtained. Both the results were compared.
Results
Nonfermenters showed a better categorical agreement of 97.6%, as compared to Enterobacteriaceae, which showed 97%. Among Enterobacteriaceae, both
E. coli
and
K. pneumoniae
showed categorical agreement of 97% each.
Conclusion
The procedure of AST directly from blood culture broth represents a simple and effective technique that can reduce the turnaround time by 24 hours, which in turn benefits the clinician in appropriate utilization of antimicrobials for better patient care.
Collapse
Affiliation(s)
- D Kavipriya
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Suman Susan Prakash
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Sarumathi Dhandapani
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Deepashree Rajshekar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Apurba Sankar Sastry
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| |
Collapse
|
11
|
Singhal C, Bruno JG, Kaushal A, Sharma TK. Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections. ACS APPLIED BIO MATERIALS 2021; 4:3962-3984. [PMID: 35006817 DOI: 10.1021/acsabm.0c01358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.
Collapse
Affiliation(s)
- Chaitali Singhal
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - John G Bruno
- Nanohmics, Inc., Austin, Texas 78741, United States
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram, Haryana 122413, India
| | - Tarun K Sharma
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| |
Collapse
|
12
|
Źródłowski T, Sobońska J, Salamon D, McFarlane IM, Ziętkiewicz M, Gosiewski T. Classical Microbiological Diagnostics of Bacteremia: Are the Negative Results Really Negative? What is the Laboratory Result Telling Us About the "Gold Standard"? Microorganisms 2020; 8:microorganisms8030346. [PMID: 32121353 PMCID: PMC7143506 DOI: 10.3390/microorganisms8030346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022] Open
Abstract
Standard blood cultures require at least 24–120 h to be reported as preliminary positive. The objective of this study was to compare the reliability of Gram staining and fluorescent in-situ hybridization (FISH) for detecting bacteria in otherwise negative blood culture bottles. Ninety-six sets were taken from patients with a diagnosis of sepsis. Six incomplete blood culture sets and eight blood cultures sets demonstrating positive growth were excluded. We performed Gram stain and FISH on 82 sets taken from post-operative septic patients: 82 negative aerobic blood cultures, 82 anaerobic blood cultures, and 82 blood samples, as well as 57 blood samples taken from healthy volunteers. From the eighty-two blood sets analyzed from the septic patients, Gram stain visualized bacteria in 62.2% of blood samples, 35.4% of the negative aerobic bottles, and in 31.7% of the negative anaerobic bottles. Utilizing FISH, we detected bacteria in 75.6%, 56.1%, and 64.6% respectively. Among the blood samples from healthy volunteers, FISH detected bacteria in 64.9%, while Gram stain detected bacteria in only 38.6%. The time needed to obtain the study results using Gram stain was 1 h, for FISH 4 h, and for the culture method, considering the duration of growth, 5 days. Gram stain and FISH allow quick detection of bacteria in the blood taken directly from a patient. Finding phagocytosed bacteria, which were also detected among healthy individuals, confirms the hypothesis that blood microbiome exists.
Collapse
Affiliation(s)
- Tomasz Źródłowski
- Thoracic Anesthesia and Respiratory Intensive Care Unit, John Paul II Hospital, 31- 202 Kraków, Poland;
- Department of Internal Medicine, St. John’s Episcopal Hospital, Far Rockaway, NY 11691, USA
| | - Joanna Sobońska
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Dominika Salamon
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Isabel M. McFarlane
- Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Mirosław Ziętkiewicz
- Thoracic Anesthesia and Respiratory Intensive Care Unit, John Paul II Hospital, 31- 202 Kraków, Poland;
- Department of Anesthesiology and Intensive Care, Faculty of Medicine, Jagiellonian University Medical College, 31-501 Krakow, Poland
- Correspondence: (M.Z.); (T.G.)
| | - Tomasz Gosiewski
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
- Correspondence: (M.Z.); (T.G.)
| |
Collapse
|
13
|
Development of a combined RLEP/16S rRNA (RT) qPCR assay for the detection of viable M. leprae from nasal swab samples. BMC Infect Dis 2019; 19:753. [PMID: 31462296 PMCID: PMC6714382 DOI: 10.1186/s12879-019-4349-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/01/2019] [Indexed: 12/29/2022] Open
Abstract
Background Leprosy continues to be a health problem in endemic areas. More than 200,000 new cases of leprosy per year suggest that transmission of the disease is still ongoing, presumably as airborne infection through nasal droplets. Late diagnosis supports continued transmission and increases the individual risk for functional disabilities. Laboratory tools are considered beneficial to facilitate early detection and clinical assessment of cases. The aim of this study was to validate molecular tools allowing detection, quantification and assessment of viability of M. leprae from nasal swab samples which are easy to obtain without the need of any invasive procedures. Methods Validation of two real-time PCRs detecting M. leprae DNA (RLEP qPCR) and RNA (16S rRNA RT qPCR) was conducted on “must not detect”/“must detect” samples and 160 pre-treatment nasal swab samples from 20 clinically diagnosed multibacillary (MB) leprosy patients from Togo. Results Both assays were 100% M. leprae specific and showed analytical sensitivities of three templates each. Out of 20 clinically diagnosed MB leprosy patients, 15 (75.0%) had a positive RLEP qPCR result from nasal swab samples. The 16S rRNA RT qPCR detected viable bacilli in nasal swab samples of ten out of these 15 RLEP positive patients (66.7%). Conclusion The combined RLEP/16S rRNA (RT) qPCR assay provides a sensitive and specific tool to determine the bacterial load and viability of M. leprae from nasal swab samples and is applicable for early diagnosis, monitoring treatment response and investigating the role of nasal carriage of M. leprae in human-to-human transmission through aerosol infection. Electronic supplementary material The online version of this article (10.1186/s12879-019-4349-9) contains supplementary material, which is available to authorized users.
Collapse
|
14
|
Źródłowski TW, Jurkiewicz-Badacz D, Sroka-Oleksiak A, Salamon D, Bulanda M, Gosiewski T. Comparison of PCR, Fluorescent in Situ Hybridization and Blood Cultures for Detection of Bacteremia in Children and Adolescents During Antibiotic Therapy. Pol J Microbiol 2019; 67:479-486. [PMID: 30550234 PMCID: PMC7256870 DOI: 10.21307/pjm-2018-056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2018] [Indexed: 02/02/2023] Open
Abstract
The gold standard in microbiological diagnostics of bacteremia is a blood culture in automated systems. This method may take several days and has low sensitivity. New screening methods that could quickly reveal the presence of bacteria would be extremely useful. The objective of this study was to estimate the effectiveness of these methods with respect to blood cultures in the context of antibiotic therapy. Blood samples from 92 children with sepsis were analyzed. Blood cultures were carried out in standard automated systems. Subsequently, FISH (Fluorescent In-Situ Hybridization) and nested multiplex-real-time-PCR (PCR) were performed. Blood cultures, FISH and PCR yielded positive results in 18%, 39.1%, and 71.7% of samples, respectively. Significant differences were found between the results obtained through culture before and after induction of antibiotherapy: 25.5% vs. 9.7%. There was no significant difference in FISH and PCR results in relation to antibiotics. The three methods employed demonstrated significant differences in detecting bacteria effectively. Time to obtain test results for FISH and PCR averaged 4–5 hours. FISH and PCR allow to detect bacteria in blood without prior culture. These methods had high sensitivity for the detection of bacteremia regardless of antibiotherapy. They provide more timely results as compared to automated blood culture, and may be useful as rapid screening tests in sepsis.
Collapse
Affiliation(s)
- Tomasz W Źródłowski
- Thoracic Anesthesia and Respiratory Intensive Care Unit, John Paul II Hospital , Cracow , Poland
| | | | - Agnieszka Sroka-Oleksiak
- Chair of Microbiology, Department of Molecular Medical Microbiology, Faculty of Medicine, Jagiellonian University Medical College , Cracow , Poland.,Department of Mycology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College , Czysta 18; 31-121 Krakow , Poland
| | - Dominika Salamon
- Chair of Microbiology, Department of Molecular Medical Microbiology, Faculty of Medicine, Jagiellonian University Medical College , Cracow , Poland
| | - Małgorzata Bulanda
- Chair of Microbiology, Department of Epidemiology of Infection, Faculty of Medicine, Jagiellonian University Medical College , Cracow , Poland
| | - Tomasz Gosiewski
- Chair of Microbiology, Department of Molecular Medical Microbiology, Faculty of Medicine, Jagiellonian University Medical College , Cracow , Poland
| |
Collapse
|
15
|
Lorenz B, Rösch P, Popp J. Isolation matters-processing blood for Raman microspectroscopic identification of bacteria. Anal Bioanal Chem 2019; 411:5445-5454. [PMID: 31152224 DOI: 10.1007/s00216-019-01918-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022]
Abstract
Bacteremia with its high mortality is a frequent case in clinical health care. Further, bacteremia includes the considerable risk of progressing to a sepsis. Even in case of survival, sepsis still entails diminished quality of life for the survivors and high indirect cost for the society. The crucial factor in sepsis is time. Therefore, timely description of adequate antibiotics is vital to reduce mortality and improve quality of life after survival. Despite that, the current gold standard of clinical bacteria diagnostic is based on cultivation of bacteria, which requires an average of 13-h cultivation. Consequently, there is a necessity for culture free identification methods without sacrificing the range of bacteria strains which can be identified. Raman microspectroscopy in general requires only single bacteria cells and has proven to offer high identification accuracies. However, the prerequisite for Raman microspectroscopy is a suitable isolation strategy to obtain single unharmed bacteria cells free from matrix. Moreover, in blood, bacteria are outnumbered by billions of blood cells. In this study, we present an isolation strategy to recover single bacteria cells from blood and evaluate their suitability for Raman microspectroscopic identification. Graphical abstract.
Collapse
Affiliation(s)
- Björn Lorenz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany. .,InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743, Jena, Germany.
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743, Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, 07745, Jena, Germany
| |
Collapse
|
16
|
Srivastava S, Singh PK, Vatsalya V, Karch RC. Developments in the Diagnostic Techniques of Infectious Diseases: Rural and Urban Prospective. ACTA ACUST UNITED AC 2018; 8:121-138. [PMID: 30197838 PMCID: PMC6124492 DOI: 10.4236/aid.2018.83012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Objectives: Diagnostics is the first step for the treatment and eradication of infectious microbial diseases. Due to ever evolving pathogens and emerging new diseases, there is an urgent need to identify suitable diagnostic techniques for better management of each disease. The success rate of specific diagnostic technique in any population depends on various factors including type of the microbial pathogen, availability of resources, technical expertise, disease severity and degree of epidemic of disease in the area. One of the important tasks of the policy makers is to identify and implement suitable diagnostic techniques for specific regions based on their specific requirements. In this review we have discussed various techniques available in the literature and their suitability for the target population based on above mentioned criteria. Methods: Diagnostic techniques evaluation of well documented representative microbial diseases; Tuberculosis (bacterial), Malaria (parasitic) and HIV (viral) were included in the study. Identification and collection of information and data was performed focusing on the diagnostic techniques used from the scientific publications from Pubmed, Science Access, Scopus, EMBASE and several regional databases. WHO and CDC database for Tuberculosis, Malaria and HIV were also included. These techniques were compared with respect to the financial resource availability, expertise and management, functional capacity, pathogen virulence and degree of epidemic in the population. Results and Conclusion: In case of Tuberculosis, ELISA and colorimetric techniques are successful in rural and urban communities with 80% – 90% sensitivity. Genotyping and SNP analysis are useful in drug resistant strains. Parasitic disease Malaria also follows the same trend with diagnostic techniques like RDTs being common in both population with fast results and around 90% sensitivity. STD disease like HIV however shows slight different trends due to urgent need of interference in rural epidemics of the disease. Rapid and sensitive immunotechniques like dipsticks and agglutination with almost 100% sensitivity are used in both rural and urban areas. For the confirmation further tests are done like protein Western and NAAT. Advance techniques could be the option for higher epidemic area, drug resistance and disease research, while rapid techniques would be suitable for low income areas and POC facilities. Therefore, suitability of the diagnostic techniques for better management depends not only on the financial resources and assessment skills of a community but sometimes on the disease itself. We have further discussed the technological improvements for specific settings (rural/urban) based on the past research for better management of diseases, which could be implemented for the understanding of understudied and newly emerging diseases.
Collapse
Affiliation(s)
- Shweta Srivastava
- University of Louisville School of Medicine, Louisville, USA.,College of Arts and Sciences American University, Washington DC, USA
| | | | - Vatsalya Vatsalya
- University of Louisville School of Medicine, Louisville, USA.,College of Arts and Sciences American University, Washington DC, USA
| | - Robert C Karch
- College of Arts and Sciences American University, Washington DC, USA
| |
Collapse
|
17
|
Zhao JJ, Lou XL, Chen HW, Zhu FT, Hou YQ. Diagnostic value of decoy receptor 3 combined with procalcitonin and soluble urokinase-type plasminogen activator receptor for sepsis. Cell Mol Biol Lett 2018; 23:22. [PMID: 29760745 PMCID: PMC5941621 DOI: 10.1186/s11658-018-0087-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
The levels of decoy receptor 3 (DcR3), soluble urokinase type plasminogen activator receptor (suPAR) and procalcitonin (PCT) are significantly increased in sepsis. We investigated the diagnostic value of DcR3 combined with suPAR and PCT in sepsis. Patients with sepsis, non-infectious systemic inflammatory response comprehensive syndrome (SIRS) and healthy controls were recruited according to the diagnostic standard. We measured DcR3, suPAR, PCT, interleukin-6 (IL-6) and C-reactive protein (CRP), and the diagnostic value was evaluated by receiver operating characteristics (ROC) curves. In our analysis, serum DcR3, suPAR and PCT levels of the sepsis group were significantly higher than those of the SIRS and control groups. However, IL-6, CRP and WBC showed no significant difference between the SIRS group and the sepsis group. The serum DcR3 level was positively correlated with the serum suPAR level (r = 0.37, p = 0.0022) and PCT level (r = 0.37, p = 0.0021). Using DcR3, suPAR and PCT to distinguish SIRS from sepsis, the area under the curve (AUC) values were 0.892, 0.778 and 0.692. When DcR3, suPAR and PCT combined were used for diagnosis of sepsis, the AUC was 0.933, at a cut-off point of 0.342. This combination improved the sensitivity and specificity of diagnosis of sepsis, suggesting that use of the combination of three indexes enhanced the efficiency of sepsis diagnosis.
Collapse
Affiliation(s)
- Jing-Jing Zhao
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, 201600 China
| | - Xiao-Li Lou
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, 201600 China
| | - Hong-Wei Chen
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, 201600 China
| | - Feng-Ting Zhu
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, 201600 China
| | - Yan-Qiang Hou
- Department of Central Laboratory, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, 201600 China
| |
Collapse
|
18
|
Jha AK, Hittalmani SK. Septic Shock in Low-Cardiac-Output Patients With Heart and Lung Transplantation: Diagnosis and Management Dilemma. J Cardiothorac Vasc Anesth 2017; 31:1389-1396. [PMID: 28094175 DOI: 10.1053/j.jvca.2016.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Ajay Kumar Jha
- Department of Cardiac Anesthesiology (Heart-Lung Transplantation), Global Health City, Chennai, India.
| | | |
Collapse
|
19
|
Curtoni A, Cipriani R, Marra ES, Barbui AM, Cavallo R, Costa C. Rapid Identification of Microorganisms from Positive Blood Culture by MALDI-TOF MS After Short-Term Incubation on Solid Medium. Curr Microbiol 2016; 74:97-102. [PMID: 27858149 DOI: 10.1007/s00284-016-1161-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/08/2016] [Indexed: 11/28/2022]
Abstract
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms. Unfortunately, its direct application to positive blood culture is still lacking standardized procedures. In this study, we evaluated an easy- and rapid-to-perform protocol for MALDI-TOF MS direct identification of microorganisms from positive blood culture after a short-term incubation on solid medium. This protocol was used to evaluate direct identification of microorganisms from 162 positive monomicrobial blood cultures; at different incubation times (3, 5, 24 h), MALDI-TOF MS assay was performed from the growing microorganism patina. Overall, MALDI-TOF MS concordance with conventional methods at species level was 60.5, 80.2, and 93.8% at 3, 5, and 24 h, respectively. Considering only bacteria, the identification performances at species level were 64.1, 85.0, and 94.1% at 3, 5, and 24 h, respectively. This protocol applied to a commercially available MS typing system may represent, a fast and powerful diagnostic tool for pathogen direct identification and for a promptly and pathogen-driven antimicrobial therapy in selected cases.
Collapse
Affiliation(s)
- Antonio Curtoni
- Microbiology and Virology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy.
| | - Raffaella Cipriani
- Microbiology and Virology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Elisa Simona Marra
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Anna Maria Barbui
- Microbiology and Virology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| |
Collapse
|
20
|
Miglio A, Stefanetti V, Antognoni MT, Cappelli K, Capomaccio S, Coletti M, Passamonti F. Stored Canine Whole Blood Units: What is the Real Risk of Bacterial Contamination? J Vet Intern Med 2016; 30:1830-1837. [PMID: 27734567 PMCID: PMC5115181 DOI: 10.1111/jvim.14593] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/16/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
Background Bacterial contamination of whole blood (WB) units can result in transfusion‐transmitted infection, but the extent of the risk has not been established and may be underestimated in veterinary medicine. Objectives To detect, quantify, and identify bacterial microorganisms in 49 canine WB units during their shelf life. Animals Forty‐nine healthy adult dogs. Methods Forty‐nine WB units were included in the study. Immediately after collection, 8 sterile samples from the tube segment line of each unit were aseptically collected and tested for bacterial contamination on days 0, 1, 7, 14, 21, 28, 35, and 42 of storage. A qPCR assay was performed on days 0, 21, and 35 to identify and quantify any bacterial DNA. Results On bacterial culture, 47/49 blood units were negative at all time points tested, 1 unit was positive for Enterococcus spp. on days 0 and 1, and 1 was positive for Escherichia coli on day 35. On qPCR assay, 26 of 49 blood units were positive on at least 1 time point and the bacterial loads of the sequences detected (Propionobacterium spp., Corynebacterium spp., Caulobacter spp., Pseudomonas spp., Enterococcus spp., Serratia spp., and Leucobacter spp.) were <80 genome equivalents (GE)/μL. Conclusions and Clinical Importance Most of the organisms detected were common bacteria, not usually implicated in septic transfusion reactions. The very low number of GE detected constitutes an acceptable risk of bacterial contamination, indicating that WB units have a good sanitary shelf life during commercial storage.
Collapse
Affiliation(s)
- A Miglio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - V Stefanetti
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - M T Antognoni
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - K Cappelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - S Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - M Coletti
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - F Passamonti
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| |
Collapse
|
21
|
Hauptmann M, Schaible UE. Linking microbiota and respiratory disease. FEBS Lett 2016; 590:3721-3738. [PMID: 27637588 DOI: 10.1002/1873-3468.12421] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions.
Collapse
Affiliation(s)
- Matthias Hauptmann
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany.,German Centre for Infection Research, TTU-TB, Borstel, Germany
| |
Collapse
|
22
|
Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis. J Microbiol Methods 2016; 127:197-202. [DOI: 10.1016/j.mimet.2016.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 11/22/2022]
|
23
|
Gupta MD, Kaur H, Ray P, Gautam V, Puri GD. Ribosomal RNA-based panbacterial polymerase chain reaction for rapid diagnosis of septicaemia in Intensive Care Unit patients. Indian J Med Microbiol 2016; 34:219-21. [PMID: 27080778 DOI: 10.4103/0255-0857.180351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Early diagnosis and treatment of sepsis by appropriate antibiotics is of utmost importance. Therefore, we evaluated 16S rRNA panbacterial polymerase chain reaction (PCR) for rapid diagnosis of sepsis in 49 adult patients in Intensive Care Units (ICUs) and compared it with an automated blood culture. 8 ml of 10 ml blood collected was inoculated into BACTEC® aerobic bottle and the remaining 2 ml was used for DNA extraction and PCR. 109 of 115 (93%) episodes of suspected sepsis showed concordant results between automated culture and PCR. Six episodes were positive by PCR only. Panbacterial PCR reduces turnaround time with rapid differentiation between systemic inflammatory response syndrome and sepsis.
Collapse
Affiliation(s)
| | | | | | - Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Vardakas KZ, Anifantaki FI, Trigkidis KK, Falagas ME. Rapid molecular diagnostic tests in patients with bacteremia: evaluation of their impact on decision making and clinical outcomes. Eur J Clin Microbiol Infect Dis 2015; 34:2149-60. [PMID: 26329038 DOI: 10.1007/s10096-015-2466-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/29/2015] [Indexed: 02/04/2023]
Abstract
We performed a systematic review of the data regarding rapid diagnostic tests and their advantages or limitations on patients' clinical outcomes. The PubMed and Scopus databases were searched independently by two reviewers. Mortality was the primary outcome. Most studies compared rapid tests with blood cultures. Although not observed in all studies, only studies comparing rapid tests in conjunction with antimicrobial stewardship programs (ASPs) showed a mortality benefit. A reduction in hospital or intensive care unit (ICU) length of stay was also observed in almost all studies when the rapid tests, with or without ASPs, were used. Finally, treatment decisions were taken earlier in the rapid test groups. Despite a faster treatment decision, a clear mortality benefit was not seen when rapid tests were used. It is crucial to differentiate the influence of rapid tests from that of ASPs and clarify the actual effect of each factor separately.
Collapse
Affiliation(s)
- K Z Vardakas
- Alfa Institute of Biomedical Sciences (AIBS), 9 Neapoleos Street, 151 23, Marousi, Athens, Greece.,Department of Internal Medicine-Infectious Diseases, Iaso General Hospital, Athens, Greece
| | - F I Anifantaki
- Alfa Institute of Biomedical Sciences (AIBS), 9 Neapoleos Street, 151 23, Marousi, Athens, Greece
| | - K K Trigkidis
- Alfa Institute of Biomedical Sciences (AIBS), 9 Neapoleos Street, 151 23, Marousi, Athens, Greece
| | - M E Falagas
- Alfa Institute of Biomedical Sciences (AIBS), 9 Neapoleos Street, 151 23, Marousi, Athens, Greece. .,Department of Internal Medicine-Infectious Diseases, Iaso General Hospital, Athens, Greece. .,Department of Medicine, Tufts University School of Medicine, Boston, MA, USA.
| |
Collapse
|
26
|
16S rRNA Gene Sequence-Based Identification of Bacteria in Automatically Incubated Blood Culture Materials from Tropical Sub-Saharan Africa. PLoS One 2015; 10:e0135923. [PMID: 26270631 PMCID: PMC4535881 DOI: 10.1371/journal.pone.0135923] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The quality of microbiological diagnostic procedures depends on pre-analytic conditions. We compared the results of 16S rRNA gene PCR and sequencing from automatically incubated blood culture materials from tropical Ghana with the results of cultural growth after automated incubation. METHODS Real-time 16S rRNA gene PCR and subsequent sequencing were applied to 1500 retained blood culture samples of Ghanaian patients admitted to a hospital with an unknown febrile illness after enrichment by automated culture. RESULTS Out of all 1500 samples, 191 were culture-positive and 98 isolates were considered etiologically relevant. Out of the 191 culture-positive samples, 16S rRNA gene PCR and sequencing led to concordant results in 65 cases at species level and an additional 62 cases at genus level. PCR was positive in further 360 out of 1309 culture-negative samples, sequencing results of which suggested etiologically relevant pathogen detections in 62 instances, detections of uncertain relevance in 50 instances, and DNA contamination due to sample preparation in 248 instances. In two instances, PCR failed to detect contaminants from the skin flora that were culturally detectable. Pre-analytical errors caused many Enterobacteriaceae to be missed by culture. CONCLUSIONS Potentially correctable pre-analytical conditions and not the fastidious nature of the bacteria caused most of the discrepancies. Although 16S rRNA gene PCR and sequencing in addition to culture led to an increase in detections of presumably etiologically relevant blood culture pathogens, the application of this procedure to samples from the tropics was hampered by a high contamination rate. Careful interpretation of diagnostic results is required.
Collapse
|
27
|
Arabestani MR, Rastiany S, Kazemi S, Mousavi SM. Conventional, molecular methods and biomarkers molecules in detection of septicemia. Adv Biomed Res 2015; 4:120. [PMID: 26261822 PMCID: PMC4513309 DOI: 10.4103/2277-9175.158027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/18/2014] [Indexed: 11/13/2022] Open
Abstract
Sepsis is a leading cause of morbidity and mortality in hospitalized patients worldwide and based on studies, 30–40% of all cases of severe sepsis and septic shock results from the blood stream infections (BSIs). Identifying of the disease, performing laboratory tests, and consequently treatment are factors that required for optimum management of BSIs. In addition, applying precise and immediate identification of the etiologic agent is a prerequisite for specific antibiotic therapy of pathogen and thereby decreasing mortality rates. The diagnosis of sepsis is difficult because clinical signs of sepsis often overlap with other noninfectious cases of systemic inflammation. BSIs are usually diagnosed by performing a series of techniques such as blood cultures, polymerase chain reaction-based methods, and biomarkers of sepsis. Extremely time-consuming even to take up to several days is a major limitation of conventional methods. In addition, yielding false-negative results due to fastidious and slow-growing microorganisms and also in case of antibiotic pretreated samples are other limitations. In comparison, molecular methods are capable of examining a blood sample obtained from suspicious patient with BSI and gave the all required information to prescribing antimicrobial therapy for detected bacterial or fungal infections immediately. Because of an emergency of sepsis, new methods are being developed. In this review, we discussed about the most important sepsis diagnostic methods and numbered the advantage and disadvantage of the methods in detail.
Collapse
Affiliation(s)
- Mohammad Reza Arabestani
- Brucellosis Research Center, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran ; Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sahar Rastiany
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sima Kazemi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Masoud Mousavi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| |
Collapse
|
28
|
Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
Collapse
Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | |
Collapse
|
29
|
Boardman AK, Campbell J, Wirz H, Sharon A, Sauer-Budge AF. Rapid microbial sample preparation from blood using a novel concentration device. PLoS One 2015; 10:e0116837. [PMID: 25675242 PMCID: PMC4326418 DOI: 10.1371/journal.pone.0116837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1–100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms’ viability, giving a 30‑μL final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40–50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA)to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample.
Collapse
Affiliation(s)
- Anna K. Boardman
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts, United States of America
| | - Jennifer Campbell
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts, United States of America
| | - Holger Wirz
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts, United States of America
| | - Andre Sharon
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts, United States of America
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Alexis F. Sauer-Budge
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
30
|
Chun K, Syndergaard C, Damas C, Trubey R, Mukindaraj A, Qian S, Jin X, Breslow S, Niemz A. Sepsis Pathogen Identification. ACTA ACUST UNITED AC 2015; 20:539-61. [PMID: 25631157 DOI: 10.1177/2211068214567345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/29/2022]
Abstract
Sepsis is a rapidly progressing, severe inflammatory response to infection, causing more than 200,000 deaths per year. Rapid, specific pathogen identification is important to guide sepsis treatment. In this review, we describe and compare currently available commercial products for sepsis diagnosis and pathogen identification, based on microbiological, molecular, and mass spectrometric technologies. Microbiological techniques, the current "gold standard" in sepsis pathogen identification, include blood culture followed by subculturing and pathogen identification via biochemical or microscopic means. These methods have been automated but nevertheless require several days to generate results. Alternative technologies, including highly multiplexed PCR-based methods and mass spectrometric approaches, can decrease the required turnaround time. Matrix-assisted laser-desorption ionization time-of-flight-based systems have recently become an attractive option to rapidly identify a broad spectrum of sepsis pathogens with good sensitivity and specificity. Effectively integrating rapid sepsis pathogen identification into the hospital workflow can improve patient outcomes and can reduce the length of hospitalization and cost per patient.
Collapse
Affiliation(s)
- Katy Chun
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Chas Syndergaard
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Carlos Damas
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Richard Trubey
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Shenyu Qian
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Xin Jin
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Scott Breslow
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| |
Collapse
|
31
|
Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
32
|
Sitnik R, Marra AR, Petroni RC, Ramos OPS, Martino MDV, Pasternak J, Santos OFPD, Mangueira CLP, Pinho JRR. SeptiFast for diagnosis of sepsis in severely ill patients from a Brazilian hospital. ACTA ACUST UNITED AC 2014; 12:191-6. [PMID: 25003925 PMCID: PMC4891162 DOI: 10.1590/s1679-45082014ao2932] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/01/2013] [Indexed: 11/25/2022]
Abstract
Objective To test and validate a multiplex real-time polymerase chain reaction method for bloodstream infections, as well as to compare the results with conventional blood culture. Methods A total of 114 consecutive patients with clinical evidence of sepsis were submitted to blood culture and LightCycler™ SeptiFast tests. Results More positive specimens (23; 20.2%) were detected using the LightCycler™ SeptiFast than the blood culture (17; 14.9%), with an agreement of 86.8%. Discordant results were seen in four patients positive only to blood culture, ten positive only to LightCycler™ SeptiFast and one to different pathogens found by each test. Infections with microorganisms detected only using blood culture reassured the need to perform both tests. The mean time to results for blood culture was 5 days for negative and 3.5 days for positive results. LightCycler™ SeptiFast results were achieved in less than 8 hours. Conclusion LightCycler™ SeptiFast showed a high potential as a test to be carried out concomitantly with blood culture for sepsis diagnosis in severely ill patients. This test allowed a faster diagnosis of bacterial and fungal infections that helped to reduce hospital stay and to control the use of antibiotics. LightCycler™ SeptiFast can also eventually detect microorganism and infections that are hardly detected by blood culture, especially Candida non-albicans infections.
Collapse
Affiliation(s)
- Roberta Sitnik
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Southern TR, VanSchooneveld TC, Bannister DL, Brown TL, Crismon AS, Buss SN, Iwen PC, Fey PD. Implementation and performance of the BioFire FilmArray® Blood Culture Identification panel with antimicrobial treatment recommendations for bloodstream infections at a midwestern academic tertiary hospital. Diagn Microbiol Infect Dis 2014; 81:96-101. [PMID: 25488272 DOI: 10.1016/j.diagmicrobio.2014.11.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/28/2014] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
Abstract
The FilmArray® Blood Culture Identification (BCID) panel was recently implemented at a midwestern academic tertiary care hospital to provide rapid identification (ID) of common pathogens from positive blood cultures. This study evaluated the clinical performance of the BCID panel compared to culture-based ID methods. One hundred thirty-eight monomicrobial and 8 polymicrobial blood cultures were evaluated during the 30-day study resulting in the ID of 152 total organisms by culture with 115 organisms correctly identified using the BCID panel. The BCID panel had sensitivities of 80.4% (115/152) for all organisms identified during the study and 94.6% (115/122) when considering only on-panel organisms. BCID panel specificity was 100%. Implementation of the BCID panel was coupled with the development of empiric therapy recommendations for bloodstream infections by the antimicrobial stewardship team. Based on this study, the FilmArray® BCID panel is a rapid and reliable test for the detection of common bloodstream pathogens, and therapeutic decisions can be based upon panel results.
Collapse
Affiliation(s)
- Timothy R Southern
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Nebraska Public Health Laboratory, Omaha, NE, USA.
| | - Trevor C VanSchooneveld
- Division of Infectious Disease, Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dianna L Bannister
- Clinical Microbiology Laboratory, The Nebraska Medical Center, Omaha, NE, USA
| | - TeAnne L Brown
- Clinical Microbiology Laboratory, The Nebraska Medical Center, Omaha, NE, USA
| | - Amy S Crismon
- Clinical Microbiology Laboratory, The Nebraska Medical Center, Omaha, NE, USA
| | - Sarah N Buss
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Nebraska Public Health Laboratory, Omaha, NE, USA
| | - Peter C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Nebraska Public Health Laboratory, Omaha, NE, USA
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
34
|
Song Y, Giske CG, Gille-Johnson P, Emanuelsson O, Lundeberg J, Gyarmati P. Nuclease-assisted suppression of human DNA background in sepsis. PLoS One 2014; 9:e103610. [PMID: 25076135 PMCID: PMC4116218 DOI: 10.1371/journal.pone.0103610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/29/2014] [Indexed: 11/18/2022] Open
Abstract
Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.
Collapse
Affiliation(s)
- Yajing Song
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Christian G. Giske
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
| | - Patrik Gille-Johnson
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Emanuelsson
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Joakim Lundeberg
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Peter Gyarmati
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
35
|
Gosiewski T, Jurkiewicz-Badacz D, Sroka A, Brzychczy-Włoch M, Bulanda M. A novel, nested, multiplex, real-time PCR for detection of bacteria and fungi in blood. BMC Microbiol 2014; 14:144. [PMID: 24893651 PMCID: PMC4049433 DOI: 10.1186/1471-2180-14-144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022] Open
Abstract
Background The study describes the application of the PCR method for the simultaneous detection of DNA of Gram-negative bacteria, Gram-positive bacteria, yeast fungi and filamentous fungi in blood and, thus, a whole range of microbial etiological agents that may cause sepsis. Material for the study was sterile blood inoculated with four species of microorganisms (Escherichia coli, Staphylococcus aureus, Candida albicans and Aspergillus fumigatus) and blood collected from patients with clinical symptoms of sepsis. The developed method is based on nested-multiplex real-time PCR . Results Analysis of the obtained data shows that sensitivity of nested-multiplex real-time PCR remained at the level of 101 CFU/ml for each of the four studied species of microorganisms and the percentage of positive results of the examined blood samples from the patients was 70% and 19% for the microbiological culture method. The designed primers correctly typed the studied species as belonging to the groups of Gram-positive bacteria, Gram-negative bacteria, yeast fungi, or filamentous fungi. Conclusions Results obtained by us indicated that the designed PCR methods: (1) allow to detect bacteria in whole blood samples, (2) are much more sensitive than culture method, (3) allow differentiation of the main groups of microorganisms within a few hours.
Collapse
Affiliation(s)
- Tomasz Gosiewski
- Department of Bacteriology, Microbial Ecology and Parasitology, Chair of Microbiology Jagiellonian University Medical College, Czysta 18 Str, 31-121 Kraków, Poland.
| | | | | | | | | |
Collapse
|
36
|
Loonen AJM, Wolffs PFG, Bruggeman CA, van den Brule AJC. Developments for improved diagnosis of bacterial bloodstream infections. Eur J Clin Microbiol Infect Dis 2014; 33:1687-702. [PMID: 24848132 DOI: 10.1007/s10096-014-2153-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 12/26/2022]
Abstract
Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.
Collapse
Affiliation(s)
- A J M Loonen
- Laboratory for Molecular Diagnostics, Department of Medical Microbiology and Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | | | | | | |
Collapse
|
37
|
Evaluation of three rapid diagnostic methods for direct identification of microorganisms in positive blood cultures. J Clin Microbiol 2014; 52:2521-9. [PMID: 24808235 DOI: 10.1128/jcm.00529-14] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The identification of organisms from positive blood cultures generally takes several days. However, recently developed rapid diagnostic methods offer the potential for organism identification within only a few hours of blood culture positivity. In this study, we evaluated the performance of three commercial methods to rapidly identify organisms directly from positive blood cultures: QuickFISH (AdvanDx, Wolburn, MA), Verigene Gram-Positive Blood Culture (BC-GP; Nanosphere, Northbrook, IL), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with Sepsityper processing (Bruker Daltonics, Billerica, MA). A total of 159 blood cultures (VersaTREK Trek Diagnostic Systems, Cleveland, OH) positive for Gram-positive and Gram-negative bacteria as well as yeast were analyzed with QuickFISH and MALDI-TOF MS. In all, 102 blood cultures were analyzed using the BC-GP assay. For monomicrobial cultures, we observed 98.0% concordance with routine methods for both QuickFISH (143/146) and the BC-GP assay (93/95). MALDI-TOF MS demonstrated 80.1% (117/146) and 87.7% (128/146) concordance with routine methods to the genus and species levels, respectively. None of the methods tested were capable of consistently identifying polymicrobial cultures in their entirety or reliably differentiating Streptococcus pneumoniae from viridans streptococci. Nevertheless, the methods evaluated in this study are convenient and accurate for the most commonly encountered pathogens and have the potential to dramatically reduce turnaround time for the provision of results to the treating physician.
Collapse
|
38
|
Improving the diagnosis of bloodstream infections: PCR coupled with mass spectrometry. BIOMED RESEARCH INTERNATIONAL 2014; 2014:501214. [PMID: 24818144 PMCID: PMC4000954 DOI: 10.1155/2014/501214] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/27/2014] [Indexed: 12/22/2022]
Abstract
The reference method for the diagnosis of bloodstream infections is blood culture followed by biochemical identification and antibiotic susceptibility testing of the isolated pathogen. This process requires 48 to 72 hours. The rapid administration of the most appropriate antimicrobial treatment is crucial for the survival of septic patients; therefore, a rapid method that enables diagnosis directly from analysis of a blood sample without culture is needed. A recently developed platform that couples broad-range PCR amplification of pathogen DNA with electrospray ionization mass spectrometry (PCR/ESI-MS) has the ability to identify virtually any microorganism from direct clinical specimens. To date, two clinical evaluations of the PCR/ESI-MS technology for the diagnosis of bloodstream infections from whole blood have been published. Here we discuss them and describe recent improvements that result in an enhanced sensitivity. Other commercially available assays for the molecular diagnosis of bloodstream infections from whole blood are also reviewed. The use of highly sensitive molecular diagnostic methods in combination with conventional procedures could substantially improve the management of septic patients.
Collapse
|
39
|
Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
Collapse
|
40
|
Soleimani E, Honarmand H, Nikokar I, Falakian Z. Comparing the Accuracy Rate of Two Different Universal Primers in Enteric Pathogen Diagnosis in Blood. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2014. [DOI: 10.17795/ijep15595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
41
|
Schmitz RPH, Keller PM, Baier M, Hagel S, Pletz MW, Brunkhorst FM. Quality of blood culture testing - a survey in intensive care units and microbiological laboratories across four European countries. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2013; 17:R248. [PMID: 24144084 PMCID: PMC4056044 DOI: 10.1186/cc13074] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/25/2013] [Indexed: 12/29/2022]
Abstract
Introduction Blood culture (BC) testing before initiation of antimicrobial therapy is recommended as a standard of care in international sepsis guidelines and has been shown to reduce intensive care unit (ICU) stay, antibiotic use, and costs in hospitalized patients. Whereas microbiological laboratory practice has been highly standardized, shortfalls in the preanalytic procedures in the ICU (that is indication, time-to-incubation, blood volume and numbers of BC sets) have a significant effect on the diagnostic yield. The objective of this study was to gain insights into current practices regarding BC testing in intensive care units. Methods Qualitative survey, data collection by 138 semi-structured telephone interviews in four European countries (Italy, UK, France and Germany) between September and November 2009 in 79 clinical microbiology laboratories (LABs) and 59 ICUs. Results Whereas BC testing is expected to remain the gold standard for sepsis diagnostics in all countries, there are substantial differences regarding preanalytic procedures. The decision to launch BC testing is carried out by physicians vs. ICU nurses in the UK in 92 vs. 8%, in France in 75 vs. 25%, in Italy in 88 vs. 12% and in Germany in 92 vs. 8%. Physicians vs. nurses collect BCs in the UK in 77 vs. 23%, in France in 0 vs. 100%, in Italy in 6 vs. 94% and in Germany in 54 vs. 46%. The mean time from blood collection to incubation in the UK is 2 h, in France 3 h, in Italy 4 h, but 20 h in German remote LABs (2 h in in-house LABs), due to the large number of remote nonresident microbiological laboratories in Germany. There were major differences between the perception of the quality of BC testing between ICUs and LABs. Among German ICU respondents, 62% reported that they have no problems with BC testing, 15% reported time constraints, 15% cost pressure, and only 8% too long time to incubation. However, the corresponding LABs of these German ICUs reported too many false positive results due to preanalytical contaminations (49%), insufficient numbers of incoming BC sets (47%), long transportation time (41%) or cost pressure (18%). Conclusions There are considerable differences in the quality of BC testing across European countries. In Germany, time to incubation is a considerable problem due to the increasing number of remote LABs. This is a major issue of concern to physicians aiming to implement sepsis guidelines in the ICUs.
Collapse
|
42
|
Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L. Proteomics boosts translational and clinical microbiology. J Proteomics 2013; 97:69-87. [PMID: 24145144 DOI: 10.1016/j.jprot.2013.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/28/2013] [Accepted: 10/09/2013] [Indexed: 01/17/2023]
Abstract
The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
Collapse
Affiliation(s)
- F Del Chierico
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Petrucca
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Via di Grottarossa 1035, 00185 Rome, Italy
| | - P Vernocchi
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - G Bracaglia
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - E Fiscarelli
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - P Bernaschi
- Unit of Microbiology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - M Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Urbani
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - L Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
| |
Collapse
|
43
|
Zweitzig DR, Riccardello NM, Morrison J, Rubino J, Axelband J, Jeanmonod R, Sodowich BI, Kopnitsky MJ, O’Hara SM. Measurement of microbial DNA polymerase activity enables detection and growth monitoring of microbes from clinical blood cultures. PLoS One 2013; 8:e78488. [PMID: 24155986 PMCID: PMC3796490 DOI: 10.1371/journal.pone.0078488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Surveillance of bloodstream infections (BSI) is a high priority within the hospital setting. Broth-based blood cultures are the current gold standard for detecting BSI, however they can require lengthy incubation periods prior to detection of positive samples. We set out to demonstrate the feasibility of using enzymatic template generation and amplification (ETGA)-mediated measurement of DNA polymerase activity to detect microbes from clinical blood cultures. In addition to routine-collected hospital blood cultures, one parallel aerobic blood culture was collected and immediately refrigerated until being transported for ETGA analysis. After refrigeration holding and transport, parallel-collected cultures were placed into a BACTEC incubator and ETGA time-course analysis was performed. Of the 308 clinical blood cultures received, 22 were BACTEC positive, and thus were initially selected for ETGA time course analysis. The ETGA assay detected microbial growth in all 22 parallel-positive blood cultures in less time than a BACTEC incubator and also yielded genomic DNA for qPCR-based organism identification. In summary, feasibility of detecting microbes from clinical blood culture samples using the ETGA blood culture assay was demonstrated. Additional studies are being considered towards development of clinically beneficial versions of this methodology.
Collapse
Affiliation(s)
- Daniel R. Zweitzig
- Research and Development, ZEUS Scientific, Raritan, New Jersey, United States of America
- * E-mail:
| | - Nichol M. Riccardello
- Research and Development, ZEUS Scientific, Raritan, New Jersey, United States of America
| | - John Morrison
- St. Luke’s University Health Network, Bethlehem, Pennsylvania, United States of America
| | - Jason Rubino
- St. Luke’s University Health Network, Bethlehem, Pennsylvania, United States of America
| | - Jennifer Axelband
- St. Luke’s University Health Network, Bethlehem, Pennsylvania, United States of America
| | - Rebecca Jeanmonod
- St. Luke’s University Health Network, Bethlehem, Pennsylvania, United States of America
| | - Bruce I. Sodowich
- Research and Development, ZEUS Scientific, Raritan, New Jersey, United States of America
| | - Mark J. Kopnitsky
- Research and Development, ZEUS Scientific, Raritan, New Jersey, United States of America
| | - S. Mark O’Hara
- Research and Development, ZEUS Scientific, Raritan, New Jersey, United States of America
| |
Collapse
|
44
|
Molecular detection of culture-confirmed bacterial bloodstream infections with limited enrichment time. J Clin Microbiol 2013; 51:3720-5. [PMID: 23985915 DOI: 10.1128/jcm.01981-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and pyrosequencing protocols, the molecular approach yielded results in 11.8 ± 2.9 h compared to means of 27.9 ± 13.6 h to obtain the Gram stain results and 81.6 ± 24.0 h to generate the final culture-based identification. The molecular approach enabled accurate detection of most bacteria present in incubating blood culture bottles on average about 16 h sooner than Gram stain results became available and approximately 3 days sooner than the phenotypic identification was entered in the Laboratory Information System. If implemented, this more rapid molecular approach could minimize the number of doses of unnecessary or ineffective antibiotics administered to patients.
Collapse
|
45
|
Abstract
In patients with suspected sepsis, rapid and accurate diagnosis of the causative infectious agent is critical. Although clinicians often use empiric antimicrobial therapy until the blood cultures are available to potentially adjust treatment, this approach is often not optimum for patient care. Recently, several commercial molecular multiplex technologies have shown promise for fast and comprehensive diagnosis of microorganisms and their antimicrobial resistance signatures. While one class of multiplex technologies is directed at improving the speed and diagnostic information obtained from positive blood cultures, the other identifies the causative microorganisms directly from clinical blood samples. This review provides an overview of these molecular technologies and describes their performance capabilities compared to standard blood cultures and in some cases to each other. We discuss the current clinical impact, limitations, and likely futures advances these multiplex technologies may have in guiding the management of patients with sepsis.
Collapse
Affiliation(s)
- Evan E. Lebovitz
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Peter D. Burbelo
- Clinical Dental Research Core, Clinical Center, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| |
Collapse
|
46
|
Khanam F, Sheikh A, Sayeed MA, Bhuiyan MS, Choudhury FK, Salma U, Pervin S, Sultana T, Ahmed D, Goswami D, Hossain ML, Mamun KZ, Charles RC, Brooks WA, Calderwood SB, Cravioto A, Ryan ET, Qadri F. Evaluation of a typhoid/paratyphoid diagnostic assay (TPTest) detecting anti-Salmonella IgA in secretions of peripheral blood lymphocytes in patients in Dhaka, Bangladesh. PLoS Negl Trop Dis 2013; 7:e2316. [PMID: 23951368 PMCID: PMC3708850 DOI: 10.1371/journal.pntd.0002316] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 06/03/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Rapid and reliable diagnostic assays for enteric (typhoid and paratyphoid) fever are urgently needed. We report the characterization of novel approach utilizing lymphocyte secretions, for diagnosing patients with enteric fever by the TPTest procedure. METHODOLOGY TPTest detects Salmonella-specific IgA responses in lymphocyte culture supernatant. We utilized TPTest in patients with suspected enteric fever, patients with other illnesses, and healthy controls. We also evaluated simplified modifications of TPTest for adaptation in laboratories with limited facilities and equipment. PRINCIPAL FINDINGS TPTest was positive in 39 (27 typhoid and 12 paratyphoid A) patients confirmed by blood culture and was negative in 74 healthy individuals. Among 32 individuals with other illnesses, 29 were negative by TPTest. Of 204 individuals with suspected enteric fever who were negative by blood culture, 44 were positive by TPTest and the patients were clinically indistinguishable from patients with confirmed bacteremia, except they were more likely to be under 5 years of age. We evaluated simplifications in TPTest, including showing that lymphocytes could be recovered using lysis buffer or buffy coat method as opposed to centrifugation, that incubation of cells at 37°C did not require supplemental CO2, and that results were available for majority of samples within 24 hours. Positive results by TPTest are transient and revert to negative during convalescence, supporting use of the test in endemic areas. The results can also be read using immunodot blot approach as opposed to ELISA. Since no true gold standard currently exists, we used a number of definitions of true positives and negatives. TPTest had sensitivity of 100% compared to blood culture, and specificity that ranged from 78-97% (73-100, 95% CI), depending on definition of true negative. CONCLUSION The TPTest is useful for identification of patients with enteric fever in an endemic area, and additional development of simplified TPTest is warranted.
Collapse
Affiliation(s)
- Farhana Khanam
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Alaullah Sheikh
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Abu Sayeed
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Saruar Bhuiyan
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Feroza Kaneez Choudhury
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Umme Salma
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Shahnaz Pervin
- Department of Microbiology, Dhaka Medical College and Hospital (DMCH), Dhaka, Bangladesh
| | - Tania Sultana
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Doli Goswami
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Lokman Hossain
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - K. Z. Mamun
- Department of Microbiology, Dhaka Medical College and Hospital (DMCH), Dhaka, Bangladesh
| | - Richelle C. Charles
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. Abdullah Brooks
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Edward T. Ryan
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
- * E-mail:
| |
Collapse
|
47
|
Laakso S, Mäki M. Assessment of a semi-automated protocol for multiplex analysis of sepsis-causing bacteria with spiked whole blood samples. Microbiologyopen 2013; 2:284-92. [PMID: 23417871 PMCID: PMC3633352 DOI: 10.1002/mbo3.69] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 01/01/2013] [Accepted: 01/07/2013] [Indexed: 11/28/2022] Open
Abstract
Sepsis is associated with high morbidity and mortality rates worldwide. Rapid and reliable diagnostic methods are needed for efficient and evidence-based treatment of septic patients. Recently, new molecular tools have emerged to complement the conventional culture-based diagnostic methods. In this study, we used spiked whole blood samples to evaluate together two ready-to-use molecular solutions for the detection of sepsis-causing bacteria. We spiked whole blood with bacterial species relevant in sepsis and extracted bacterial DNA with the NorDiag Arrow device, using the SelectNA Blood pathogen DNA isolation kit. DNA extracts were analyzed by the polymerase chain reaction (PCR)- and microarray-based Prove-it™ Bone and Joint assay, resulting in correctly identified bacterial species with detection limits of 11-600 colony-forming unit/mL (CFU/mL). To understand the recovery losses of bacterial DNA during the sample preparation step and the capability of the PCR- and microarray-based platform to respond to the sensitivity requirements, we also determined the analytical sensitivity of the PCR and microarray platform to be 1-21 genome equivalents for the tested bacterial species. In addition, the inclusivity of the Prove-it™ Bone and Joint assay was demonstrated with methicillin-resistant Staphylococcus aureus (MRSA) clones carrying SCCmec types I, II, IV, or V and a nontypable SCCmec type. The proof-of-concept for accurate multiplex pathogen and antibacterial resistance marker detection from spiked whole blood samples was demonstrated by the selective bacterial DNA extraction method combined with the high-throughput PCR- and microarray-based platform. Further investigations are needed to study the promising potential of the concept for sensitive, semi-automated identification of sepsis-causing pathogens directly from whole blood.
Collapse
|
48
|
Schreiber J, Nierhaus A, Braune SA, de Heer G, Kluge S. Comparison of three different commercial PCR assays for the detection of pathogens in critically ill sepsis patients. Med Klin Intensivmed Notfmed 2013; 108:311-8. [PMID: 23516029 DOI: 10.1007/s00063-013-0227-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 01/16/2013] [Accepted: 02/03/2013] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The high mortality rate associated with sepsis necessitates a timely identification of the causative organism in order to optimize antimicrobial therapy. PCR assays are increasingly being used for this purpose. The aim of this study was to compare three commercially available PCR systems for the diagnosis of systemic infections. PATIENTS AND METHODS In a prospective observational study, a broad-range (SepsiTest®; Molzym, Bremen, Germany) and two multiplex PCR assays (VYOO®; SIRS-Lab, Jena, Germany and LightCycler® SeptiFast; Roche, Mannheim, Germany) were compared to blood cultures with respect to the clinical course of 50 critically ill patients with sepsis, severe sepsis or septic shock. RESULTS Pathogens were detected by PCR in 12 % (SepsiTest®), 10 % (VYOO®) and 14 % (LightCycler® SeptiFast) of samples and in 26 % by blood culture. Negative results were obtained using all four methods in 32 samples (64 %) and 3 (6 %) samples were positive in all tests. Upon consideration of additional diagnostic findings and the clinical course, eight (16 %) of the positive blood culture results were deemed clinically relevant. All three PCR assays could also identify the causative organism (or a specific gene thereof) in three of these eight positive blood cultures, whereas for five of the eight, all three PCR assays were negative. In one patient with a negative blood culture, the SepsiTest®, VYOO® and LightCycler® SeptiFast assays were positive for Streptococcus species. The PCR assays appeared to be less susceptible than blood cultures to false-positive results arising from contamination with coagulase-negative staphylococcal organisms. CONCLUSION There was some variability between the three PCR assays tested and the corresponding blood cultures with regards to the type of pathogen detected. The three PCR assays appeared to be less susceptible to false-positive results than blood cultures.
Collapse
Affiliation(s)
- J Schreiber
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.
| | | | | | | | | |
Collapse
|
49
|
Zweitzig DR, Sodowich BI, Riccardello NM, O'Hara SM. Feasibility of a novel approach for rapid detection of simulated bloodstream infections via enzymatic template generation and amplification (ETGA)-mediated measurement of microbial DNA Polymerase activity. J Mol Diagn 2013; 15:319-30. [PMID: 23499338 DOI: 10.1016/j.jmoldx.2012.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 11/12/2012] [Accepted: 12/20/2012] [Indexed: 01/18/2023] Open
Abstract
Bloodstream infections (BSIs) caused by bacteria and fungi are associated with significant morbidity and mortality. Currently, blood culture is the gold standard for confirming a suspected BSI, but has the drawback of lengthy time-to-detection (TTD) required for indicating the presence of microbes. Detection of conserved microbial nucleic acid sequences within blood culture samples via PCR has been demonstrated to offer potential for reducing the TTD of BSI; however, these approaches have various other limitations. We report a novel approach toward rapid detection of microbes from simulated BSI via differential hematopoietic cell lysis followed by enzymatic template generation and amplification (ETGA)-mediated measurement of microbial DNA polymerase extension activity. The differential cell lysis procedure effectively reduced the level of detectable DNA polymerase extension activity associated with human-derived hematopoietic cells present in blood culture samples taken from healthy donors. After treatment with the differential cell lysis procedure, the ETGA assay detected a panel of clinically prevalent bacteria and Candida albicans from spiked blood culture samples. The ETGA blood culture method also reduced by threefold the TTD required for simulated BSI, compared with a continuous-monitoring blood culture instrument. In summary, these findings demonstrate the feasibility of an innovative approach toward a rapid, sensitive, and universal screen for microbes within blood culture samples. Potential for clinical application and automation are also addressed.
Collapse
Affiliation(s)
- Daniel R Zweitzig
- Research and Development, ZEUS Scientific, Inc., Branchburg, NJ, USA
| | | | | | | |
Collapse
|
50
|
Weigel KM, Jones KL, Do JS, Melton Witt J, Chung JH, Valcke C, Cangelosi GA. Molecular viability testing of bacterial pathogens from a complex human sample matrix. PLoS One 2013; 8:e54886. [PMID: 23365682 PMCID: PMC3554692 DOI: 10.1371/journal.pone.0054886] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022] Open
Abstract
Assays for bacterial ribosomal RNA precursors (pre-rRNA) have been shown to distinguish viable from inactivated bacterial cells in drinking water samples. Because the synthesis of pre-rRNA is rapidly induced by nutritional stimulation, viable bacteria can be distinguished from inactivated cells and free nucleic acids by measuring the production of species-specific pre-rRNA in samples that have been briefly stimulated with nutrients. Here, pre-rRNA analysis was applied to bacteria from serum, a human sample matrix. In contrast to drinking water, serum is rich in nutrients that might be expected to mask the effects of nutritional stimulation. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays were used to detect pre-rRNA of four bacterial species: Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, and the Mycobacterium tuberculosis complex. These species were chosen for their clinical significance and phylogenetic diversity (Proteobacteria, Firmicutes, and Actinobacteria). To maximize resolving power, pre-rRNA was normalized to genomic DNA of each pathogen. When viable cells were shifted from serum to bacteriological culture medium, rapid replenishment of pre-rRNA was always observed. Cells of P. aeruginosa that were inactivated in the presence of serum exhibited no pre-rRNA response to nutritional stimulation, despite strong genomic DNA signals in these samples. When semi-automated methods were used, pre-rRNA analysis detected viable A. baumannii cells in serum at densities of ≤100 CFU/mL in <5.5 hours. Originally developed for rapid microbiological analysis of drinking water, ratiometric pre-rRNA analysis can also assess the viability of bacterial cells derived from human specimens, without requiring bacteriological culture.
Collapse
Affiliation(s)
- Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kelly L. Jones
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julie S. Do
- AttoDx, Inc., Seattle, Washington, United States of America
| | - Jody Melton Witt
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Christian Valcke
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|