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Kapoor DA, Holton MR, Hafron J, Aljundi R, Zwaans B, Hollander M. Comparison of Polymerase Chain Reaction and Urine Culture in the Evaluation of Patients with Complex Urinary Tract Infections. BIOLOGY 2024; 13:257. [PMID: 38666869 PMCID: PMC11048588 DOI: 10.3390/biology13040257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
To compare organism identification using polymerase chain reaction (PCR) and urine culture (UC) in patients with complex urinary tract infections (cUTIs), we reviewed the results of 3395 patients seen during 2022 with cUTI who underwent concomitant PCR and UC testing. We compared the overall positivity rates as well as the ability of each test to identify fastidious organisms (FOs) and the presence of polymicrobial infections (PMOs) and conducted concordance analysis between the tests. PCR detected 36.4% more organisms than UC and was 20 and nearly 36 times more likely to detect PMOs and FOs, respectively. PCR identified 90.6% of organisms found in UC, whereas UC identified 40.7% of organisms found in PCR testing. We found that 62.4% of organisms found in PCR were not found in urine culture, while UC found 9.4% of organisms not identified in polymerase chain reaction. All these differences were statistically significant (p < 0.05). Although we found that PCR was superior to UC in overall pathogen detection, and detection of both PMOs and FOs, both identified potentially pathogenic organisms not found in the corresponding test. Our data strongly suggest that the evaluation of patients with cUTI is best accomplished using PCR in conjunction with UC.
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Affiliation(s)
| | | | - Jason Hafron
- Michigan Institute of Urology, St. Clair Shores, MI 48081, USA; (J.H.); (R.A.); (M.H.)
| | - Rima Aljundi
- Michigan Institute of Urology, St. Clair Shores, MI 48081, USA; (J.H.); (R.A.); (M.H.)
| | - Bernadette Zwaans
- Corewell Health William Beaumont University Hospital, Royal Oak, MI 48073, USA;
| | - Mitchell Hollander
- Michigan Institute of Urology, St. Clair Shores, MI 48081, USA; (J.H.); (R.A.); (M.H.)
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2
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Chi W, Wang S, Liu T, Jiang W, Ding L, Miao Y, Yang F, Zhang J, Ji D, Xiao Z, Zhu H, Wu Y, Bao Z, Zhao H, Wang S. A rapid and high-throughput multiplex genetic detection assay for detection, semi-quantification and virulence genotyping of Helicobacter pylori in non-invasive oral samples. Front Cell Infect Microbiol 2023; 13:1267288. [PMID: 37842005 PMCID: PMC10570550 DOI: 10.3389/fcimb.2023.1267288] [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: 07/26/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Aim This study established a high-throughput multiplex genetic detection assay (HMGA) for rapid identification, semi-quantification and virulence analysis of Helicobacter pylori directly from the clinical non-invasive oral samples. Methods The gastric mucosa and oral samples were collected from 242 patients in Shanghai from 2021 to 2022. All the samples were detected by routine clinical tests for H. pylori and Sanger sequenced for inconsistent results. A new multiplex PCR assay providing results within 4 hours was designed and optimized involving fluorescent dye-labeled specific primers targeted 16S rRNA gene, semi-quantitative gene ureC and 10 virulence genes of H. pylori. Semi-quantification was carried out by simulating the serial 10-fold dilutions of positive oral samples, and the H. pylori loads in different clinical samples were further compared. The mixed plasmids of virulence genes vacA s1, vacA m1 and vacA m2 were used to evaluate the performance on different genotypes. The consistency of 10 virulence genes in gastric mucosa, saliva, mouthwash and dental plaque of H. pylori-positive patients was compared. Results The non-invasive HMGA was highly specific for detection of all 12 targets of H. pylori and human internal reference gene β-globin, and the sensitivity to all target genes could reach 10 copies/μL. Compared with routine clinical tests and sequencing, non-invasive HMGA has a high level (>0.98) of sensitivity, specificity, accuracy, PPV, NPV and kappa coefficient for direct detection of H. pylori in oral samples. Moreover, by detecting peak area levels of ureC, it was confirmed that the H. pylori loads in gastric mucosa were significantly higher than those of the three kinds of oral samples (p<0.05). We also found that 45.0% (91/202) of patients had different H. pylori virulence genes in different oral samples. The concordance of positive detection rates of each virulence gene between saliva and gastric mucosa was more than 78% (p<0.05). Conclusion The non-invasive HMGA proved to be a reliable method for the rapid H. pylori identification, semi-quantification and detection of 10 virulence genes directly in oral samples, providing a new idea for non-invasive detection of H. pylori.
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Affiliation(s)
- Wenjing Chi
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Su Wang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Tao Liu
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Wenrong Jiang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Li Ding
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Yingxin Miao
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Feng Yang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Danian Ji
- Department of Endoscopy, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Zili Xiao
- Department of Endoscopy, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Haowei Zhu
- Department of Research and Development, Ningbo HEALTH Gene Technologies Co., Ltd, Ningbo, China
| | - Yong Wu
- Department of Research and Development, Ningbo HEALTH Gene Technologies Co., Ltd, Ningbo, China
| | - Zhijun Bao
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
- Department of Gerontology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Shiwen Wang
- Department of Laboratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
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Hao X, Cognetti M, Patel C, Jean-Charles N, Tumati A, Burch-Smith R, Holton M, Kapoor DA. The Essential Role of PCR and PCR Panel Size in Comparison with Urine Culture in Identification of Polymicrobial and Fastidious Organisms in Patients with Complicated Urinary Tract Infections. Int J Mol Sci 2023; 24:14269. [PMID: 37762570 PMCID: PMC10531650 DOI: 10.3390/ijms241814269] [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: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Complicated urinary tract infections (cUTIs) are difficult to treat, consume substantial resources, and cause increased patient morbidity. Data suggest that cUTI may be caused by polymicrobial and fastidious organisms (PMOs and FOs, respectively); as such, urine culture (UC) may be an unreliable diagnostic tool for detecting cUTIs. We sought to determine the utility of PCR testing for patients presumed to have a cUTI and determine the impact of PCR panel size on organism detection. We reviewed 36,586 specimens from patients with presumptive cUTIs who received both UC and PCR testing. Overall positivity rate for PCR and UC was 52.3% and 33.9%, respectively (p < 0.01). PCR detected more PMO and FO than UC (PMO: 46.2% vs. 3.6%; FO: 31.3% vs. 0.7%, respectively, both p < 0.01). Line-item concordance showed that PCR detected 90.2% of organisms identified by UC whereas UC discovered 31.9% of organisms detected by PCR (p < 0.01). Organism detection increased with expansion in PCR panel size from 5-25 organisms (p < 0.01). Our data show that overall positivity rate and the detection of individual organisms, PMO and FO are significantly with PCR testing and that these advantages are ideally realized with a PCR panel size of 25 or greater.
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Affiliation(s)
- Xingpei Hao
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Marcus Cognetti
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Chiraag Patel
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Nathalie Jean-Charles
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Arun Tumati
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Rhonda Burch-Smith
- P4 Diagnostix, Pine Brook, NJ 07058, USA; (M.C.); (C.P.); (N.J.-C.); (A.T.); (R.B.-S.)
| | - Mara Holton
- Anne Arundel Urology, Annapolis, MD 21401, USA;
| | - Deepak A. Kapoor
- Solaris Health Holdings, LLC, Fort Lauderdale, FL 33394, USA
- The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Tao J, Liu D, Xiong J, Shan W, Dou L, Zhai W, Wang Y, Shen J, Wen K. MC-PRPA-HLFIA Cascade Detection System for Point-of-Care Testing Pan-Drug-Resistant Genes in Urinary Tract Infection Samples. Int J Mol Sci 2023; 24:ijms24076784. [PMID: 37047757 PMCID: PMC10095522 DOI: 10.3390/ijms24076784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/21/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Recently, urinary tract infection (UTI) triggered by bacteria carrying pan-drug-resistant genes, including carbapenem resistance gene blaNDM and blaKPC, colistin resistance gene mcr-1, and tet(X) for tigecycline resistance, have been reported, posing a serious challenge to the treatment of clinical UTI. Therefore, point-of-care (POC) detection of these genes in UTI samples without the need for pre-culturing is urgently needed. Based on PEG 200-enhanced recombinase polymerase amplification (RPA) and a refined Chelex-100 lysis method with HRP-catalyzed lateral flow immunoassay (LFIA), we developed an MCL-PRPA-HLFIA cascade assay system for detecting these genes in UTI samples. The refined Chelex-100 lysis method extracts target DNA from UTI samples in 20 min without high-speed centrifugation or pre-incubation of urine samples. Following optimization, the cascade detection system achieved an LOD of 102 CFU/mL with satisfactory specificity and could detect these genes in both simulated and actual UTI samples. It takes less than an hour to complete the process without the use of high-speed centrifuges or other specialized equipment, such as PCR amplifiers. The MCL-PRPA-HLFIA cascade assay system provides new ideas for the construction of rapid detection methods for pan-drug-resistant genes in clinical UTI samples and provides the necessary medication guidance for UTI treatment.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Wenchong Shan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
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Zhaoyang S, Guowei S, Jing P, Yundong Z, Xinhua L, Muyun W, Xiaowei M, Lixin L, Xiaoying C. Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. Front Immunol 2022; 13:1016440. [PMID: 36458015 PMCID: PMC9705594 DOI: 10.3389/fimmu.2022.1016440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. The present study is the first to evaluate the clinical characteristics of the host DNA-removed mNGS technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. METHODS 46 swab specimens collected from COVID-19 patients were assayed by two approved commercial RT-qPCR kits and mNGS. The evolutionary tree of SARS-CoV-2 was plotted using FigTree directly from one sample. The workflow of removing the host and retaining the host was compared to investigate the influence of host DNA removal on the performances of mNGS. Functional enrichment analysis of DEGs and xCell score were used to explore the characteristics of host local immune signaling. RESULTS The detection rate of mNGS achieved 92.9% (26/28) for 28 samples with a Ct value ≤ 35 and 81.1% (30/37) for all 46 samples. The genome coverage of SARS-CoV-2 could reach up to 98.9% when the Ct value is about 20 in swab samples. Removing the host could enhance the sensitivity of mNGS for detecting SARS-CoV-2 from the swab sample but does not affect the species abundance of microbes RNA. Improving the sequencing depth did not show a positive effect on improving the detection sensitivity of SARS-CoV-2. Cell type enrichment scores found multiple immune cell types were differentially expressed between patients with high and low viral load. CONCLUSIONS The host DNA-removed mNGS has great potential utility and superior performance on comprehensive identification of SARS-CoV-2 and rapid traceability, revealing the microbiome's transcriptional profiles and host immune responses.
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Affiliation(s)
- Sun Zhaoyang
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Guowei
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Pan Jing
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Zhou Yundong
- Shanghai Medical Innovation Fusion Biomedical Research Center, Shanghai, China
| | - Lu Xinhua
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Muyun
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ma Xiaowei
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Lixin
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, China
| | - Chen Xiaoying
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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David S, Munteanu RE, Tițoiu AM, Petcu IC, Cernat IC, Leancu C, Gheorghiu M, Gheorghiu E. Direct, Rapid Detection of Pathogens from Urine Samples. MATERIALS (BASEL, SWITZERLAND) 2022; 15:ma15217640. [PMID: 36363232 PMCID: PMC9656601 DOI: 10.3390/ma15217640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 06/02/2023]
Abstract
The problem of rapidly detecting pathogens directly from clinical samples poses significant analytical challenges. Addressing this issue in relation to urinary tract infections, we propose an effective protocol and related immunomagnetic test kits enabling versatile screening for the presence of pathogenic bacteria in unprocessed urine samples. To achieve this, the components of a typical immunomagnetic separation protocol were optimized towards the sensitive assessment of the aggregates formed out of immunomagnetically tagged target pathogens collected from clinical samples. Specifically, a dedicated immunomagnetic material was developed via the functionalization of standardized, micron-sized magnetic beads with generic antibodies against gram-specific bacterial constituents with mannan binding lectin. As such, we demonstrate efficient procedures for achieving the enhanced, specific, and pathogen-mediated cluster formation of these tailored affinity-coated magnetic beads in complex samples. We further show how cluster analysis, in conjunction with the use of nonspecific, inexpensive fluorescent dye, allows for a straightforward optical assessment of the bacterial load directly from urine samples. The optimized sensing protocol and related kits provide, in less than 60 min, qualitative (positive/negative) information on the bacterial load with 85% specificity and 96% sensitivity, which is appropriate to empower clinical microscopy with a new analytic dimension. The procedure is prone to automation, can be conveniently used in clinical microbiology laboratories and, since it preserves the viability of the captured bacteria, can be interfaced with downstream analyses and antimicrobial susceptibility testing. Moreover, the study emphasizes a suite of practical validation assays that are useful for bringing the tool-box of immunomagnetic materials outside the academic laboratory and into real-life applications.
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Affiliation(s)
- Sorin David
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
| | - Raluca-Elena Munteanu
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania
| | - Ana-Maria Tițoiu
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
| | - Ionela-Cristina Petcu
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
| | - Ioana-Cristina Cernat
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
| | - Corina Leancu
- Laboratoarele SynLab, Bld. Tudor Vladimirescu nr.29, 050881 Bucharest, Romania
| | - Mihaela Gheorghiu
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania
| | - Eugen Gheorghiu
- International Centre of Biodynamics, Intrarea Portocalelor 1B, 060101 Bucharest, Romania
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania
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Molecular Diagnostic Methods Versus Conventional Urine Culture for Diagnosis and Treatment of Urinary Tract Infection: A Systematic Review and Meta-analysis. EUR UROL SUPPL 2022; 44:113-124. [PMID: 36093322 PMCID: PMC9459428 DOI: 10.1016/j.euros.2022.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Context Objective Evidence acquisition Evidence synthesis Conclusions Patient summary
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Datar R, Orenga S, Pogorelcnik R, Rochas O, Simner PJ, van Belkum A. Recent Advances in Rapid Antimicrobial Susceptibility Testing. Clin Chem 2021; 68:91-98. [DOI: 10.1093/clinchem/hvab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer.
Content
Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other “omic” methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance.
Summary
We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.
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Affiliation(s)
- Rucha Datar
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | - Sylvain Orenga
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | | | - Olivier Rochas
- bioMérieux, Corporate Business Development, Marcy l'Etoile, France
| | - Patricia J Simner
- Department of Pathology, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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