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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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Wang H, Zhong Y, Ma L. Leukaemia Infection Diagnosis and Intestinal Flora Disorder. Curr Mol Med 2021; 22:2-7. [PMID: 33653248 DOI: 10.2174/1566524021666210302144720] [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: 11/01/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 11/22/2022]
Abstract
Leukaemia is the most common malignant tumor in childhood and can be cured by chemotherapy. Infection is an important cause of treatment-related death and treatment failure in childhood leukaemia. Recent studies have shown that the correlation between the occurrence of leukaemia infection and the intestinal flora has attracted more and more attention. Intestinal flora can affect the body's physiological defense and immune function. When intestinal microflora disorder occurs, metabolites/microorganisms related to intestinal flora alterations and even likely the associated morpho-functional alteration of the epithelial barrier may be promising diagnostic biomarkers for the early diagnosis of leukaemia infection. This review will focus on the interaction between leukaemia infection and intestinal flora, and the influence of intestinal flora in the occurrence and development of leukaemia infection.
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Affiliation(s)
- Hongwu Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen. China
| | - Yong Zhong
- Department of paediatrics, The Southeast General Hospital of Dongguan, Dongguan. China
| | - Lian Ma
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen. China
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Burch TR, Spencer SK, Borchardt SS, Larson RA, Borchardt MA. Fate of Manure-Borne Pathogens during Anaerobic Digestion and Solids Separation. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:336-344. [PMID: 29634802 PMCID: PMC7166490 DOI: 10.2134/jeq2017.07.0285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Anaerobic digestion can inactivate zoonotic pathogens present in cattle manure, which reduces transmission of these pathogens from farms to humans through the environment. However, the variability of inactivation across farms and over time is unknown because most studies have examined pathogen inactivation under ideal laboratory conditions or have focused on only one or two full-scale digesters at a time. In contrast, we sampled seven full-scale digesters treating cattle manure in Wisconsin for 9 mo on a biweekly basis ( = 118 pairs of influent and effluent samples) and used real-time quantitative polymerase chain reaction to analyze these samples for 19 different microbial genetic markers. Overall, inactivation of pathogens and fecal indicators was highly variable. When aggregated across digester and season, log-removal values for several representative microorganisms-bovine , -like CowM3, and bovine polyomavirus-were 0.78 ± 0.34, 0.70 ± 0.50, and 0.53 ± 0.58, respectively (mean ± SD). These log-removal values were up to two times lower than expected based on the scientific literature. Thus, our study indicates that full-scale anaerobic digestion of cattle manure requires optimization with regard to pathogen inactivation. Future studies should focus on identifying the potential causes of this suboptimal performance (e.g., overloading, poor mixing, poor temperature control). Our study also examined the fate of pathogens during manure separation and found that the majority of microbes we detected ended up in the liquid fraction of separated manure. This finding has important implications for the transmission of zoonotic pathogens through the environment to humans.
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Affiliation(s)
| | | | - Spencer S. Borchardt
- Wisconsin Water Science Center, USGS2615 Yellowstone Dr.MarshfieldWI54449
- Present address:
Kimley Horn and Associates2550 University Ave. W. Suite 238NSaint PaulMN55114
| | - Rebecca A. Larson
- Dep. of Biological Systems EngineeringUniv. of Wisconsin–Madison460 Henry Mall, Room 232EMadisonWI53706
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Felt JR, Yurkovich C, Garshott DM, Kamat D, Farooqi A, Fribley AM, Callaghan MU, Hebert K. The Utility of Real-Time Quantitative Polymerase Chain Reaction Genotype Detection in the Diagnosis of Urinary Tract Infections in Children. Clin Pediatr (Phila) 2017; 56:912-919. [PMID: 28436231 DOI: 10.1177/0009922817706144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Urinary tract infections (UTIs) are the most common serious bacterial infection in children with significant morbidity with delayed diagnosis. Polymerase chain reaction (PCR) is very accurate in detecting bacteria and widely available, but has never been evaluated to detect UTIs in children. To assess the utility of PCR as a rapid diagnostic tool, we conducted a prospective cohort study of 193 urine samples from children younger than 36 months undergoing evaluation for UTI in the emergency department over a 10-month period. A quantification cycle (Cq) threshold of 26.15 identified all Escherichia coli positive samples with sensitivity and specificity of 100% and 99.5%, respectively (95% CI = 71.5%-100% and 97.9%-99.5%, respectively). A Cq threshold of 19.03 identified E coli infections >100 000 colony forming units/mL with sensitivity and specificity of 100% (95% CI = 72.2%-100% and 98.6%-100%, respectively). PCR is very accurate in diagnosing E coli UTIs in young children and could be useful as a rapid diagnostic tool.
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Affiliation(s)
- Jon R Felt
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Chelsey Yurkovich
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Deepak Kamat
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Ahmad Farooqi
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | - Andrew M Fribley
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
| | | | - Katherine Hebert
- 1 Children's Hospital of Michigan, Wayne State University, Detroit, MI, USA
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Wang HY, Kim S, Kim J, Park SD, Kim HY, Uh Y, Lee H. Comparison of multiplex real-time PCR and PCR-reverse blot hybridization assay for the direct and rapid detection of bacteria and antibiotic resistance determinants in positive culture bottles. J Med Microbiol 2016; 65:962-974. [DOI: 10.1099/jmm.0.000319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hye-Young Wang
- Optipharm M&D, Inc., Wonju Eco Environmental Technology Center, Wonju, Gangwon, 26493, South Korea
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
| | - Jungho Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
| | - Soon Deok Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Hyo Youl Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Gangwon, 26426, South Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Gangwon, 26493, South Korea
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Molecular Diagnosis of Urinary Tract Infections by Semi-Quantitative Detection of Uropathogens in a Routine Clinical Hospital Setting. PLoS One 2016; 11:e0150755. [PMID: 26954694 PMCID: PMC4783162 DOI: 10.1371/journal.pone.0150755] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/17/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The objective of our study was the development of a semi-quantitative real-time PCR to detect uropathogens. Two multiplex PCR reactions were designed to detect Escherichia coli, Klebsiella spp., Enterobacter spp., Citrobacter spp., Proteus mirabilis, Enterococcus faecalis, and Pseudomonas aeruginosa. 16S based PCR was performed in parallel to detect Gram-positive and Gram-negative bacteria. Firstly to identify non-targeted agents of infection in the same urine specimen, and secondly to quantify background flora. The method was evaluated in comparison with standard bacterial culture, and a commercial PCR kit for detection of uropathogens. FINDINGS Analysis with a known panel of 116 clinical isolates yielded a PCR specificity of 100%. Analysis of urine specimens from 211 patients revealed a high correlation of PCR Cq values with both culture positivity and quantity. Concordance between PCR and culture was 98% when both methods yielded results. PCR was found to be more sensitive than culture. With a cut-off Cq value of 33, the negative predictive value of PCR was 94%. The 16S PCR confirmed most results. One specimen was positive by 16S PCR suggesting another cause of infection not detected by the specific PCR assays. CONCLUSION We conclude that it is feasible to detect and identify uropathogens by multiplex real-time PCR assay.
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Habets MN, Cremers AJH, Bos MP, Savelkoul P, Eleveld MJ, Meis JF, Hermans PWM, Melchers WJ, de Jonge MI, Diavatopoulos DA. A novel quantitative PCR assay for the detection of Streptococcus pneumoniae using the competence regulator gene target comX. J Med Microbiol 2015; 65:129-136. [PMID: 26628261 DOI: 10.1099/jmm.0.000204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pneumoniae is responsible for an estimated 1.6 million deaths worldwide every year. While rapid detection and timely treatment with appropriate antibiotics is preferred, this is often difficult due to the amount of time that detection with blood cultures takes. In this study, a novel quantitative PCR assay for the detection of Streptococcus pneumoniae was developed. To identify novel targets, we analysed the pneumococcal genome for unique, repetitive DNA sequences. This approach identified comX, which is conserved and present in duplicate copies in Streptococcus pneumoniae but not in other bacterial species. Comparison with lytA, the current 'gold standard' for detection by quantitative PCR, demonstrated an analytic specificity of 100% for both assays on a panel of 10 pneumococcal and 18 non-pneumococcal isolates, but a reduction of 3.5 quantitation cycle values (± 0.23 sem), resulting in an increased analytical detection rate of comX. We validated our assay on DNA extracted from the serum of 30 bacteraemic patients who were blood culture positive for Streptococcus pneumoniae and 51 serum samples that were culture positive for other bacteria. This resulted in a similar clinical sensitivity between the comX and lytA assays (47%) and in a diagnostic specificity of 98.2 and 100% for the lytA and comX assays, respectively. In conclusion, we have developed a novel quantitative PCR assay with increased analytical sensitivity for the detection of Streptococcus pneumoniae, which may be used to develop a rapid bedside test for the direct detection of Streptococcus pneumoniae in clinical specimens.
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Affiliation(s)
- Marrit N Habets
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amelieke J H Cremers
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Paul Savelkoul
- Microbiome, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, VU University Medical Center, The Netherlands
- Department of Medical Microbiology, Maastricht University Medical Center, The Netherlands
| | - Marc J Eleveld
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter W M Hermans
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dimitri A Diavatopoulos
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Impact of same-day antibiotic susceptibility testing on time to appropriate antibiotic treatment of patients with bacteraemia: a randomised controlled trial. Eur J Clin Microbiol Infect Dis 2014; 34:831-8. [PMID: 25527447 DOI: 10.1007/s10096-014-2299-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/07/2014] [Indexed: 10/24/2022]
Abstract
Inadequate therapy in bloodstream infections is suggested to be associated with higher mortality. We evaluated the reduction in inappropriate antibiotic therapy using rapid identification and antibiotic susceptibility testing (FAST) compared to standard of care (SOC) testing in patients with bloodstream infections. The FAST method used polymerase chain reaction (PCR) for identification and to detect growth in the presence or absence of antibiotics after only 6 h. For SOC testing, the BD Phoenix system was used. Patients with blood cultures growing Staphylococcus, Streptococcus or Enterococcus species or Gram-negative rods were randomised for FAST or SOC tests. A total of 129 patients were randomised for FAST and 121 patients for the SOC group. At the time SOC results became available, 78 patients in the FAST group could have been switched to more appropriate therapy. Although FAST results were highly accurate (agreement with SOC was 94%), they were only implemented in a minority (16) of patients. However, significantly fewer patients in the FAST group used inappropriate therapy at the time of SOC results (p = 0.025). The time to results in the FAST group was reduced by 15.6 h (p < 0.001). In the patients switched after FAST, this was done after a mean of 42.3 h compared to 61.4 h in those switched after SOC tests (p < 0.001). In bacteraemic patients, FAST resulted in significantly more patients using appropriate antibiotic therapy at the time SOC results were available and 15.6 h earlier than SOC tests. However, the implementation of FAST results was not optimal and no benefit on clinical outcome was shown.
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Park SD, Lee G, Wang HY, Park M, Kim S, Kim H, Kim J, Kim YK, Kim HY, Lee H, Uh Y, Kim JB. Evaluation of PCR-reverse blot hybridization assay, REBA Sepsis-ID test, for simultaneous identification of bacterial pathogens and mecA and van genes from blood culture bottles. Ann Lab Med 2014; 34:446-55. [PMID: 25368820 PMCID: PMC4215418 DOI: 10.3343/alm.2014.34.6.446] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/13/2014] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
Background The aim of this study was to evaluate a newly developed PCR-based reverse blot hybridization assay (PCR-REBA), REBA Sepsis-ID (M&D, Wonju, Korea), to rapidly detect the presence of bacteremia and antimicrobial resistance gene in blood culture samples. Methods One thousand four hundred consecutive blood culture samples from patients with a delta neutrophil index greater than 2.7% were selected from March to July in 2013. Three hundred positive and 1,100 negative for bacterial growth in blood culture bottles samples were tested by conventional and real-time PCR-REBA, respectively. Results The overall agreement between the conventional identification test and the REBA Sepsis-ID test was 95.3% (286/300). Agreement for gram-positive bacteria, gram-negative bacteria, fungi, and polymicrobials was 94.5% (190/201), 97.3% (71/73), 100% (14/14), and 91.7% (11/12), respectively. The detection rate of the mecA gene from methicillin-resistant Staphylococcus isolates was 97.8% (90/92). The vanA gene was detected in one blood culture sample from which vancomycin-resistant Enterococcus was isolated. When the cycle threshold for real-time PCR was defined as 30.0, 2.4% (26/1,100) of negative blood culture samples tested positive by real-time PCR. Conclusions The REBA Sepsis-ID test is capable of simultaneously and quickly detecting both causative agents and antimicrobial resistance genes, such as mecA and van, in blood culture positive samples.
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Affiliation(s)
- Soon Deok Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Gyusang Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Hye-Young Wang
- M&D, Inc., Wonju Eco Environmental Technology Center, Wonju, Korea
| | - Min Park
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Sunghyun Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Hyunjung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Jungho Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Young Keun Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyo Youl Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jong Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
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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.
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Affiliation(s)
- A J M Loonen
- Laboratory for Molecular Diagnostics, Department of Medical Microbiology and Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
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12
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Lupetti A, Barnini S, Dodi C, Menconi M, Favre C, Giagnoni M, Florio W, Nibbering PH, Campa M. New rapid methods cannot replace the current method to diagnose bloodstream infections. J Med Microbiol 2014; 63:767-769. [PMID: 24554742 DOI: 10.1099/jmm.0.069161-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno 35-39, 56127 Pisa, Italy
| | - Simona Barnini
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno 35-39, 56127 Pisa, Italy
| | - Carlotta Dodi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno 35-39, 56127 Pisa, Italy
| | - Mariacristina Menconi
- U.O. Oncoematologia Pediatrica con Trapianto di Cellule Staminali Ematopoietiche, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Claudio Favre
- U.O. Oncoematologia Pediatrica con Trapianto di Cellule Staminali Ematopoietiche, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Marco Giagnoni
- Grandi Ustioni, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno 35-39, 56127 Pisa, Italy
| | - Peter H Nibbering
- Center for Infectious Diseases, Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Mario Campa
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno 35-39, 56127 Pisa, Italy
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13
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Hansen WLJ, van der Donk CFM, Bruggeman CA, Stobberingh EE, Wolffs PFG. A real-time PCR-based semi-quantitative breakpoint to aid in molecular identification of urinary tract infections. PLoS One 2013; 8:e61439. [PMID: 23626685 PMCID: PMC3634083 DOI: 10.1371/journal.pone.0061439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 03/13/2013] [Indexed: 11/18/2022] Open
Abstract
This study presents a novel approach to aid in diagnosis of urinary tract infections (UTIs). A real-time PCR assay was used to screen for culture-positive urinary specimens and to identify the causative uropathogen. Semi-quantitative breakpoints were used to screen for significant bacteriuria (presence of ≥ 10(5) CFU/ml of uropathogens) or low-level bacteriuria (containing between 10(3) and 10(4) CFU/ml of uropathogens). The 16S rDNA-based assay could identify the most prevalent uropathogens using probes for Escherichia coli, Pseudomonas species, Pseudomonas aeruginosa, Staphylococcus species, Staphylococcus aureus, Enterococcus species and Streptococcus species. 330 urinary specimens were analysed and results were compared with conventional urine culture. Using a PCR Ct value of 25 as semi-quantitative breakpoint for significant bacteriuria resulted in a sensitivity and specificity of 97% and 80%, respectively. In 78% of the samples with monomicrobial infections the assay contained probes to detect the bacteria present in the urine specimens and 99% of these uropathogens was correctly identified. Concluding, this proof-of-concept approach demonstrates that the assay can distinguish bacteriuria from no bacteriuria as well as detect the involved uropathogen within 4 hours after sampling, allowing adequate therapy decisions within the same day as well as drastically reduce consequent urine culturing.
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Affiliation(s)
- Wendy L. J. Hansen
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christina F. M. van der Donk
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Cathrien A. Bruggeman
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ellen E. Stobberingh
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Petra F. G. Wolffs
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
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PCR-reverse blot hybridization assay for screening and identification of pathogens in sepsis. J Clin Microbiol 2013; 51:1451-7. [PMID: 23447637 DOI: 10.1128/jcm.01665-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate identification of the pathogens involved in bloodstream infections is crucial for the prompt initiation of appropriate therapy, as this can decrease morbidity and mortality rates. A PCR-reverse blot hybridization assay for sepsis, the reverse blot hybridization assay (REBA) Sepsis-ID test, was developed; it uses pan-probes to distinguish Gram-positive and -negative bacteria and fungi. In addition, the assay was designed to identify bacteria and fungi using six genus-specific and 13 species-specific probes; it uses additional probes for antibiotic resistance genes, i.e., the mecA gene of methicillin-resistant Staphylococcus aureus (MRSA) and the vanA and vanB genes of vancomycin-resistant enterococci (VRE). The REBA Sepsis-ID test successfully identified clinical isolates and blood culture samples as containing Gram-positive bacteria, Gram-negative bacteria, or fungi. The results matched those obtained with conventional microbiological methods. For the REBA Sepsis-ID test, of the 115 blood culture samples tested, 47 (40.8%) and 49 (42.6%) samples were identified to the species and genus levels, respectively, and the remaining 19 samples (16.5%), which included five Gram-positive rods, were identified as Gram-positive bacteria, Gram-negative bacteria, or fungi. The antibiotic resistances of the MRSA and VRE strains were identified using both conventional microbiological methods and the REBA Sepsis-ID test. In conclusion, the REBA Sepsis-ID test developed for this study is a fast and reliable test for the identification of Gram-positive bacteria, Gram-negative bacteria, fungi, and antibiotic resistance genes (including mecA for MRSA and the vanA and vanB genes for VRE) in bloodstream infections.
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Abstract
INTRODUCTION Current management of sepsis relies on the early detection and early administration of antimicrobials. This requires detection of pathogens earlier than conventional blood cultures and recognition of the immune status of the host earlier than the conventional biomarkers. This can be achieved by molecular techniques. AREAS COVERED Molecular diagnosis of pathogens is based on either rapid detection of pathogens grown in blood cultures or direct use of whole blood and blood products. Molecular diagnosis of the constellation of activations and inhibitions of pathways implicated in cellular processes can be achieved by gene profiling of a large array of genes. EXPERT OPINION Molecular microbial diagnosis enables rapid identification and precedes results obtained by conventional culture methods. Its role can be proved more useful in sepsis caused by specific microorganisms such as fungi performed by PMA-FISH and MALDI-TOF MS. Molecular techniques using blood aim for rapid pathogen identification. However, the provided information regarding the antimicrobial susceptibility of the pathogen is limited. Gene profiling in sepsis provides individualized information for the activation or inhibition of pathways of a variety of cellular processes. The transcriptome information is difficult to interpret in everyday clinical practice particularly on how information translates to patient needs.
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Affiliation(s)
- Antigone Kotsaki
- University of Athens, Medical School, 4th Department of Internal Medicine , Athens , Greece
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Beuving J, Verbon A, Gronthoud FA, Stobberingh EE, Wolffs PFG. Antibiotic susceptibility testing of grown blood cultures by combining culture and real-time polymerase chain reaction is rapid and effective. PLoS One 2011; 6:e27689. [PMID: 22194790 PMCID: PMC3237415 DOI: 10.1371/journal.pone.0027689] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/21/2011] [Indexed: 11/19/2022] Open
Abstract
Background Early administration of appropriate antibiotic therapy in bacteraemia patients dramatically reduces mortality. A new method for RApid Molecular Antibiotic Susceptibility Testing (RAMAST) that can be applied directly to positive blood cultures was developed and evaluated. Methodology/Principal Findings Growth curves and antibiotic susceptibility of blood culture isolates (Staphylococcus aureus, enterococci and (facultative) aerobic Gram-negative rods) were determined by incubating diluted blood cultures with and without antibiotics, followed by a quantitative universal 16S PCR to detect the presence or absence of growth. Testing 114 positive blood cultures, RAMAST showed an agreement with microbroth dilution of 96.7% for Gram-negative rods, with a minor error (false-susceptibility with a intermediate resistant strain) rate of 1.9%, a major error (false resistance) rate of 0.8% and a very major error (false susceptibility) rate of 0.6%. Agreement for S.aureus was 97.9%, with a very major error rate of 2.1%. Enterococcus species showed 95.0% agreement, with a major error rate of 5.0%. These agreements are comparable with those of the Phoenix system. Starting from a positive blood culture, the test was completed within 9 hours. Conclusions/Significance This new rapid method for antibiotic susceptibility testing can potentially provide accurate results for most relevant bacteria commonly isolated from positive blood cultures in less time than routine methods.
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Affiliation(s)
- Judith Beuving
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Firza A. Gronthoud
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ellen E. Stobberingh
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Petra F. G. Wolffs
- Department of Medical Microbiology, Care And Public Health Research Institute (CAPHRI), Maastricht University Medical Center, Maastricht, The Netherlands
- * E-mail:
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Gherardi G, Angeletti S, Panitti M, Pompilio A, Di Bonaventura G, Crea F, Avola A, Fico L, Palazzo C, Sapia GF, Visaggio D, Dicuonzo G. Comparative evaluation of the Vitek-2 Compact and Phoenix systems for rapid identification and antibiotic susceptibility testing directly from blood cultures of Gram-negative and Gram-positive isolates. Diagn Microbiol Infect Dis 2011; 72:20-31. [PMID: 22030102 DOI: 10.1016/j.diagmicrobio.2011.09.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/08/2011] [Accepted: 09/10/2011] [Indexed: 11/30/2022]
Abstract
We performed a comparative evaluation of the Vitek-2 Compact and Phoenix systems for direct identification and antimicrobial susceptibility testing (AST) from positive blood culture bottles in comparison to the standard methods. Overall, 139 monomicrobial blood cultures, comprising 91 Gram-negative and 48 Gram-positive isolates, were studied. Altogether, 100% and 92.3% of the Gram-negative isolates and 75% and 43.75% of the Gram-positive isolates showed concordant identification between the direct and the standard methods with Vitek and Phoenix, respectively. AST categorical agreements of 98.7% and 99% in Gram-negative and of 96.2% and 99.5% in Gram-positive isolates with Vitek and Phoenix, respectively, were observed. In conclusion, direct inoculation procedures for Gram-negative isolates showed an excellent performance with both automated systems, while for identification of Gram-positive isolates they proved to be less reliable, although Vitek provided acceptable results. This approach contributes to reducing the turnaround time to result of blood cultures, with a positive impact on patient care.
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Affiliation(s)
- Giovanni Gherardi
- Centro Integrato di Ricerche, Laboratory of Clinical Microbiology, University Campus Bio-medico, 00128 Rome, Italy.
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Sanvicens N, Pascual N, Fernández-Argüelles MT, Adrián J, Costa-Fernández JM, Sánchez-Baeza F, Sanz-Medel A, Marco MP. Quantum dot-based array for sensitive detection of Escherichia coli. Anal Bioanal Chem 2011; 399:2755-62. [PMID: 21249344 DOI: 10.1007/s00216-010-4624-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/07/2010] [Accepted: 12/17/2010] [Indexed: 10/18/2022]
Abstract
A fluorescent quantum dot-based antibody array, used in sandwich format, has been developed to detect Escherichia coli O157:H7. Numerous parameters such as solid support, optimal concentration of immunoreagents, blocking reagents, and assay time were optimized for array construction. Quantum dot-conjugated anti-IgG was used as the detecting system. The array allows the detection of E. coli O157:H7 at concentrations below 10 CFU mL(-1) without sample enrichment, exhibiting an increase of three orders of magnitude in the limit of detection compared to ELISA. The interference caused by Gram (+) and Gram (-) bacteria was negligible at low concentrations of bacteria.
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Affiliation(s)
- Nuria Sanvicens
- Applied Molecular Receptors Group, Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research, Barcelona, Spain
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