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Husna A, Rahman MM, Badruzzaman ATM, Sikder MH, Islam MR, Rahman MT, Alam J, Ashour HM. Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities. Biomedicines 2023; 11:2937. [PMID: 38001938 PMCID: PMC10669213 DOI: 10.3390/biomedicines11112937] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 11/26/2023] Open
Abstract
The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.
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Affiliation(s)
- Asmaul Husna
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town 350, Miaoli County, Taiwan
| | - Md. Masudur Rahman
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- ABEx Bio-Research Center, East Azampur, Dhaka 1230, Bangladesh
| | - A. T. M. Badruzzaman
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town 350, Miaoli County, Taiwan
| | - Mahmudul Hasan Sikder
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mohammad Rafiqul Islam
- Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka 1215, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka 1349, Bangladesh
| | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL 33701, USA
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Wang S, Wang S, Tang Y, Peng G, Hao T, Wu X, Wei J, Qiu X, Zhou D, Zhu S, Li Y, Wu S. Detection of Klebsiella pneumonia DNA and ESBL positive strains by PCR-based CRISPR-LbCas12a system. Front Microbiol 2023; 14:1128261. [PMID: 36846807 PMCID: PMC9948084 DOI: 10.3389/fmicb.2023.1128261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
INTRODUCTION Klebsiella pneumonia (K. pneumonia) is a Gram-negative bacterium that opportunistically causes nosocomial infections in the lung, bloodstream, and urinary tract. Extended-spectrum β-Lactamases (ESBLs)-expressed K. pneumonia strains are widely reported to cause antibiotic resistance and therapy failure. Therefore, early identification of K. pneumonia, especially ESBL-positive strains, is essential in preventing severe infections. However, clinical detection of K. pneumonia requires a time-consuming process in agar disk diffusion. Nucleic acid detection, like qPCR, is precise but requires expensive equipment. Recent research reveals that collateral cleavage activity of CRISPR-LbCas12a has been applied in nucleic acid detection, and the unique testing model can accommodate various testing models. METHODS This study established a system that combined PCR with CRISPR-LbCas12a targeting the K. pneumoniae system. Additionally, this study summarized the antibiotic-resistant information of the past five years' K. pneumoniae clinic cases in Luohu Hospital and found that the ESBL-positive strains were growing. This study then designs a crRNA that targets SHV to detect ESBL-resistant K. pneumoniae. This work is to detect K. pneumoniae and ESBL-positive strains' nucleic acid using CRISPR-Cas12 technology. We compared PCR-LbCas12 workflow with PCR and qPCR techniques. RESULTS AND DISCUSSION This system showed excellent detection specificity and sensitivity in both bench work and clinical samples. Due to its advantages, its application can meet different detection requirements in health centers where qPCR is not accessible. The antibiotic-resistant information is valuable for further research.
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Affiliation(s)
- Shang Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shan Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ying Tang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, China
| | - Guoyu Peng
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Tongyu Hao
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Xincheng Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jiehong Wei
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Xinying Qiu
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Dewang Zhou
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Shimao Zhu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- *Correspondence: Yuqing Li, ; Song Wu,
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
- *Correspondence: Yuqing Li, ; Song Wu,
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AbiGhosn J, AlAsmar M, Abboud E, Bailey BA, Haddad N. The Effect of Infection Precautions on Extended-Spectrum Beta-Lactamase Enterobacteriaceae Colonization Among Nurses in Three Beirut Hospitals. Cureus 2022; 14:e23849. [PMID: 35530839 PMCID: PMC9071177 DOI: 10.7759/cureus.23849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background and objective Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) are rapidly emerging worldwide. This study aimed to assess the effect of contact precaution (CP) on ESBL-PE-colonization rates among nurses in three hospitals in Beirut, Lebanon, where ESBL is endemic, in order to define the risk factors for colonization. Accordingly, the ongoing use of CP to prevent ESBL-PE transmission to healthy nurses was evaluated. Methods This cross-sectional study was conducted in three hospitals. Hospital 1 required CP, Hospital 2 had recently stopped CP, and Hospital 3 had stopped it three years previously. Questionnaires and stool-collection containers were distributed to all patient care nurses in those three hospitals. The Returned samples were tested using the agar dilution technique. Results A total of 269 out of 733 nurses volunteered to participate; 140 met the inclusion criteria (no recent hospitalization, antibiotic use, or known ESBL-PE colonization) and provided samples. Among them, 15% were ESBL-positive. Compared to nurses from Hospital 3, nurses from Hospital 1 were 59% less likely to be colonized, while nurses from Hospital 2 were 62% more likely to be colonized. Conclusion In hospitals where CP is in place for ESBL-positive patients, ESBL-PE prevalence in nursing staff was significantly lower. Additionally, a work experience of two to four years increased the odds of ESBL-PE colonization in comparison with longer nursing experience. CP may be a justifiable means of protection against ESBL-PE transmission to healthy nurses. The risk factors for colonization were discontinuation of CP and a shorter clinical work experience.
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Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases. Antibiotics (Basel) 2021; 10:antibiotics10091140. [PMID: 34572722 PMCID: PMC8465816 DOI: 10.3390/antibiotics10091140] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.
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Extended Spectrum Beta-Lactamase (ESBL) Produced by Gram-Negative Bacteria in Trinidad and Tobago. Int J Microbiol 2021; 2021:5582755. [PMID: 34475957 PMCID: PMC8408010 DOI: 10.1155/2021/5582755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Gram-negative bacterial infections are a global health problem. The production of beta-lactamase is still the most vital factor leading to beta-lactam resistance. In Trinidad and Tobago, extended spectrum beta-lactamase (ESBL) production has been detected and reported mainly in the isolates of Klebsiella pneumoniae and Escherichia coli and constitutes a public health emergency that causes high morbidity and mortality in some patients. In this literature review, the authors cover vast information on ESBL frequency and laboratory detection using both conventional and molecular methods from clinical data. The aim is to make the reader reflect on how the actual knowledge can be used for rapid detection and understanding of the spread of antimicrobial resistance problems stemming from ESBL production among common Gram-negative organisms in the health care system.
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Molecular Epidemiology of Third-Generation-Cephalosporin-Resistant Enterobacteriaceae in Southeast Queensland, Australia. Antimicrob Agents Chemother 2021; 65:AAC.00130-21. [PMID: 33781999 DOI: 10.1128/aac.00130-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/10/2021] [Indexed: 01/23/2023] Open
Abstract
Third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae represent a major threat to human health. Here, we captured 288 3GC-R Enterobacteriaceae clinical isolates from 264 patients presenting at a regional Australian hospital over a 14-month period. In addition to routine mass spectrometry and antibiotic sensitivity testing, isolates were examined using rapid (∼40-min) real-time PCR assays targeting the most common extended-spectrum β-lactamases (ESBLs; bla CTX-M-1 and bla CTX-M-9 groups, plus bla TEM, bla SHV, and an internal 16S rRNA gene control). AmpC CMY β-lactamase (bla CMY) prevalence was also examined. Escherichia coli (80.2%) and Klebsiella pneumoniae (17.0%) were dominant, with Klebsiella oxytoca, Klebsiella aerogenes, and Enterobacter cloacae infrequently identified. Ceftriaxone and cefoxitin resistance were identified in 97.0% and 24.5% of E. coli and K. pneumoniae isolates, respectively. Consistent with global findings in Enterobacteriaceae, most (98.3%) isolates harbored at least one β-lactamase gene, with 144 (50%) harboring bla CTX-M-1 group, 92 (31.9%) harboring bla CTX-M-9 group, 48 (16.7%) harboring bla SHV, 133 (46.2%) harboring bla TEM, and 34 (11.8%) harboring bla CMY genes. A subset of isolates (n = 98) were subjected to whole-genome sequencing (WGS) to identify the presence of cryptic resistance determinants and to verify genotyping accuracy. WGS of β-lactamase-negative or carbapenem-resistant isolates identified uncommon ESBL and carbapenemase genes, including bla NDM and bla IMP, and confirmed all PCR-positive genotypes. We demonstrate that our PCR assays enable the rapid and cost-effective identification of ESBLs in the hospital setting, which has important infection control and therapeutic implications.
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Poline J, Postaire M, Parize P, Pilmis B, Bille E, Zahar JR, Frange P, Cohen JF, Lortholary O, Toubiana J. Stewardship program on carbapenem prescriptions in a tertiary hospital for adults and children in France: a cohort study. Eur J Clin Microbiol Infect Dis 2021; 40:1039-1048. [PMID: 33389261 PMCID: PMC7778866 DOI: 10.1007/s10096-020-04103-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 01/31/2023]
Abstract
Antimicrobial stewardship programs aim at reducing the overuse of broad-spectrum antibiotics such as carbapenems, but their impact remains unclear. We compared the use of carbapenems between paediatric and adult subjects admitted to a French tertiary hospital and described the intervention of an antibiotic stewardship team (AST). As part of AST routine activity, all adult and paediatric patients receiving carbapenems are identified in real time using a computer-generated alert system and reviewed by the AST. Data associated with carbapenem prescriptions were extracted for 2 years (2014-2015) and were compared between paediatric and adult wards. Prescription appropriateness (i.e. no clinically suitable narrower spectrum alternative to carbapenem for de-escalation) and AST intervention were analysed. In total, 775 carbapenem prescriptions for 291 children and 262 adults were included. Most patients (95%) had a comordity and 52% had known recent carriage of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBLE). Most carbapenem prescriptions came from intensive care units (n = 269, 35%) and were initiated for urinary tract (n = 200, 27%), sepsis (n = 181, 25%), and lung (n = 153, 21%) infections. Carbapenems were initiated empirically in 537 (70%) cases, and an organism was isolated in 523 (67%) cases. Among the isolated organisms, 47% (n = 246) were ESBLE and 90% (n = 468) were susceptible to carbapenems, but an alternative existed in 61% (n = 320) of cases according to antibiotic susceptibility testing. Among prescriptions reviewed by the AST, 39% (n = 255) were considered non-appropriate and led to either antibiotic discontinuation (n = 47, 7%) or de-escalation (n = 208, 32%). Non-appropriate prescriptions were more frequent in paediatric wards (p = 0.01) and in microbiologically documented infections (p = 0.013), and less observed in immunocompromised patients (p = 0.009) or with a known ESBLE carriage (p < 0.001). Tailored stewardship programs are essential to better control carbapenem use and subsequent antimicrobial resistance.
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Affiliation(s)
- Julie Poline
- Department of General Paediatrics and Paediatric Infectious Diseases, Hôpital Necker–Enfants Malades, APHP, Université de Paris, 149 rue de Sèvres, 75015 Paris, France ,Department of Gut Inflammation, Center for Research on Inflammation CRI, INSERM 1149, Université de Paris, 75006 Paris, France
| | - Martine Postaire
- Department of Pharmacy, Hôpital Necker–Enfants Malades, APHP, Université de Paris, Paris, France
| | - Perrine Parize
- Department of Infectious Diseases and Tropical Medicine, Necker Enfants-Malades Hospital, Necker-Pasteur Infectious Diseases Center, Université de Paris, IHU Imagine, Paris, France
| | - Benoit Pilmis
- Department of Infectious Diseases and Tropical Medicine, Necker Enfants-Malades Hospital, Necker-Pasteur Infectious Diseases Center, Université de Paris, IHU Imagine, Paris, France
| | - Emmanuelle Bille
- Department of Microbiology, Necker Enfants-Malades Hospital, APHP, Université de Paris, Paris, France
| | - Jean Ralph Zahar
- Department of Microbiology, Necker Enfants-Malades Hospital, APHP, Université de Paris, Paris, France ,Infection Control Unit, IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Pierre Frange
- Department of Microbiology, Necker Enfants-Malades Hospital, APHP, Université de Paris, Paris, France
| | - Jérémie F. Cohen
- Department of General Paediatrics and Paediatric Infectious Diseases, Hôpital Necker–Enfants Malades, APHP, Université de Paris, 149 rue de Sèvres, 75015 Paris, France
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Necker Enfants-Malades Hospital, Necker-Pasteur Infectious Diseases Center, Université de Paris, IHU Imagine, Paris, France
| | - Julie Toubiana
- Department of General Paediatrics and Paediatric Infectious Diseases, Hôpital Necker–Enfants Malades, APHP, Université de Paris, 149 rue de Sèvres, 75015 Paris, France ,Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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Vock I, Aguilar-Bultet L, Egli A, Tamma PD, Tschudin-Sutter S. Independent, external validation of clinical prediction rules for the identification of extended-spectrum β-lactamase-producing Enterobacterales, University Hospital Basel, Switzerland, January 2010 to December 2016. ACTA ACUST UNITED AC 2020; 25. [PMID: 32643598 PMCID: PMC7346366 DOI: 10.2807/1560-7917.es.2020.25.26.1900317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Algorithms for predicting infection with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) on hospital admission or in patients with bacteraemia have been proposed, aiming to optimise empiric treatment decisions. Aim We sought to confirm external validity and transferability of two published prediction models as well as their integral components. Methods We performed a retrospective case–control study at University Hospital Basel, Switzerland. Consecutive patients with ESBL-producing Escherichia coli or Klebsiella pneumoniae isolated from blood samples between 1 January 2010 and 31 December 2016 were included. For each case, three non-ESBL-producing controls matching for date of detection and bacterial species were identified. The main outcome measure was the ability to accurately predict infection with ESBL-PE by measures of discrimination and calibration. Results Overall, 376 patients (94 patients, 282 controls) were analysed. Performance measures for prediction of ESBL-PE infection of both prediction models indicate adequate measures of calibration, but poor discrimination (area under receiver-operating curve: 0.627 and 0.651). History of ESBL-PE colonisation or infection was the single most predictive independent risk factor for ESBL-PE infection with high specificity (97%), low sensitivity (34%) and balanced positive and negative predictive values (80% and 82%). Conclusions Applying published prediction models to institutions these were not derived from, may result in substantial misclassification of patients considered as being at risk, potentially leading to wrong allocation of antibiotic treatment, negatively affecting patient outcomes and overall resistance rates in the long term. Future prediction models need to address differences in local epidemiology by allowing for customisation according to different settings.
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Affiliation(s)
- Isabelle Vock
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Lisandra Aguilar-Bultet
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Pranita D Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sarah Tschudin-Sutter
- Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
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Lei JE, Wang Q, Lin Y, Li F, Ma C, He Y, Xu JR. Rapid detection of extended-spectrum β-Lactamases producers in Enterobacteriaceae using a calorimetry approach. J Appl Microbiol 2020; 130:1523-1530. [PMID: 32890446 DOI: 10.1111/jam.14841] [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: 04/30/2020] [Revised: 08/04/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022]
Abstract
AIM To design and assess a novel protocol that employs isothermal titration calorimetry (ITC) for rapid detection of extended-spectrum β-lactamase (ESBL)-producers in clinical pathogens. METHODS AND RESULTS A total of 69 clinical Enterobacteriaceae isolates were examined in the new ESBL-ITC test by examining the heat profiles associated with enzyme hydrolysis of different substrates (imipenem, cefotaxime and clavulanic acid). The presence of β-lactamase genes in the bacteria tested was confirmed by PCR and DNA sequencing. Comparative analysis between ESBL-ITC and conventional minimum inhibitory concentrations (MIC)/combined disk method (CDM) showed high agreement between the two assays. However, the ESBL-ITC test had a remarkable advantage of providing testing result within 1 h, in comparison to the 32-48 h required by MIC/CDM. CONCLUSIONS The ESBL-ITC test developed in this work offers a new option for rapid and accurate detection of ESBL-producers. SIGNIFICANCE AND IMPACT OF THE STUDY Timely detection of ESBL-producers is vital to guide the decision-making process in clinical treatment as well as in hospital-infection control. The new ESBL-ITC test provides a rapid phenotypic assay that can be further adapted for clinical diagnosis of ESBL-producing pathogens.
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Affiliation(s)
- J-E Lei
- Department of Microbiology and Immunology, School of Basic Medical Science of Xi'anJiaotong University Health Science Center, Key Laboratory of Environmental and Genes Related to Disease, Ministry of Education, Xi'an, China.,Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Q Wang
- College of Chemistry and Materials Science, Key Laboratory of Synthetic and Natural Functional Molecule, Ministry of Education, Northwest University, Xi'an, Shaanxi, China
| | - Y Lin
- Scion (New Zealand Forest Research Institute), Rotorua, New Zealand
| | - F Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - C Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Y He
- College of Chemistry and Materials Science, Key Laboratory of Synthetic and Natural Functional Molecule, Ministry of Education, Northwest University, Xi'an, Shaanxi, China
| | - J-R Xu
- Department of Microbiology and Immunology, School of Basic Medical Science of Xi'anJiaotong University Health Science Center, Key Laboratory of Environmental and Genes Related to Disease, Ministry of Education, Xi'an, China
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The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020; 34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
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Tsai HP, Yeh CS, Lin IT, Ko WC, Wang JR. Increasing Cytomegalovirus Detection Rate from Respiratory Tract Specimens by a New Laboratory-Developed Automated Molecular Diagnostic Test. Microorganisms 2020; 8:microorganisms8071063. [PMID: 32708818 PMCID: PMC7409230 DOI: 10.3390/microorganisms8071063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lots of automated molecular methods for detecting cytomegalovirus (CMV) DNA in the blood are available, but seldom for various clinical specimens. This study was designed to establish a highly sensitive automated assay to detect CMV DNA in non-blood specimens. We designed a new QMT assay using QIAGEN artus CMV RG polymerase chain reaction (Q-CMV PCR) kit applied on the BD MAX system and compared with the other assays, including an RGQ assay (LabTurbo auto-extraction combined Q-CMV PCR kit on Rotor-Gene-Q instrument), and in-house PCR assay. A total of 1067 various clinical samples, including 426 plasma, 293 respiratory tract specimens (RTS), 127 stool, 101 cerebral spinal fluid, 90 vitreous humours were analysed. Examining CMV DNA in simultaneous specimens of the same immunocompromised patient with respiratory symptoms, the detection rate of RTS (93.6%, 88/94) was significant higher than plasma (65.9%, 62/94). The positive rates for plasma samples with a low CMV viral load (<137 IU/mL) and diagnostic sensitivity of QMT, RGQ, and in-house assays were 65% and 99.1%, 45% and 100%, 5% and 65.5%, respectively. The QMT assay performs better, with shorter operational and turnaround time than the other assays, enabling the effective and early detection of CMV infection in various clinical specimens, particularly for RTS.
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Affiliation(s)
- Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Correspondence: (H.-P.T.); (J.-R.W.); Tel.: +886-6-2353535 (ext. 2653) (H.-P.T.); Fax: +886-6-2094937 (H.-P.T.); Tel./Fax: +886-6-2760695 (J.-R.W.)
| | - Chun-Sheng Yeh
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
| | - I-Ting Lin
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
| | - Wen-Chien Ko
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 704, Taiwan
- Correspondence: (H.-P.T.); (J.-R.W.); Tel.: +886-6-2353535 (ext. 2653) (H.-P.T.); Fax: +886-6-2094937 (H.-P.T.); Tel./Fax: +886-6-2760695 (J.-R.W.)
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Performance of the Check-Direct ESBL Screen for BD MAX TM for detection of asymptomatic faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae. J Glob Antimicrob Resist 2020; 22:408-413. [PMID: 32348901 DOI: 10.1016/j.jgar.2020.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Accurte diagnostic methods are crucial for the detection of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Besides culture-based gold-standard methods, new molecular gene detection tests are reaching the market. The aim of this study was to investigate the performance of the direct quantitative PCR (qPCR)-based methods Check-Direct ESBL and CPE Screen for BD MAXTM in relation to traditional culture-based methods for detection of ESBL-E faecal carriage. METHODS Faecal samples were collected from healthy adult volunteers. Samples were cultured on chromogenic ESBL agar plates and were screened for ESBL-producing Escherichia coli and Klebsiella pneumoniae. Confirmed ESBL- and AmpC-producing isolates were further analysed using whole-genome sequencing. In addition, faecal samples were analysed using Check-Direct ESBL and CPE Screen for BD MAXTM and the results were compared with the gold-standard culture-based method. RESULTS Of 176 faecal samples examined, 11 (6.3%) grew ESBL-producing E. coli or K. pneumoniae isolates. Among 173 analysed samples, Check-Direct ESBL Screen for BD MAXTM detected 22 (12.7%) ESBL-positive samples. No carbapenemase-producing isolates were detected. Two culture-positive samples remained negative with Check-Direct ESBL Screen for BD MAXTM. Culture-negative but qPCR-positive discrepancy was observed in 12 samples (6.9%). Altogether, concordant results were obtained for 158 samples (91.3%; 9 positive and 149 negative). CONCLUSION Check-Direct ESBL Screen for BD MAXTM is a fast screening method for ESBL carriage. However, several discrepant results were observed, which hinders interpretation. More clinical samples should be tested in combination with culture to evaluate the true benefits of this method.
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Mojica MF, De La Cadena E, Correa A, Appel TM, Pallares CJ, Villegas MV. Evaluation of Allplex™ Entero-DR assay for detection of antimicrobial resistance determinants from bacterial cultures. BMC Res Notes 2020; 13:154. [PMID: 32178721 PMCID: PMC7075001 DOI: 10.1186/s13104-020-04997-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/05/2020] [Indexed: 12/18/2022] Open
Abstract
Objective To evaluate the sensitivity and specificity of the Allplex™ Entero-DR, a quantitative PCR-based method, for the detection of β-lactamase-encoding genes and vancomycin-resistance determinants in 156 previously characterized Gram-negative bacilli and Enterococcus spp. from bacterial cultures. Result The method had 100% sensitivity and between 92 and 100% of specificity for identifying blaKPC, blaVIM, blaIMP, blaNDM, blaOXA-48-like, blaCTX-M and vanA. In nine isolates, unspecific amplifications were detected. The Ct of these false positives was above 33. The Ct of the correctly identified bla and van genes did not surpass 28 and 30, respectively. None of the clinical isolates included as negative controls yielded any amplification. Therefore, the Allplex™ Entero-DR assay is a highly accurate test for the detection of important antibiotic resistance determinants. With this assay, reliable results can be obtained within 3 h. However, according to our data, samples with Ct values greater than 33 should be considered with caution.
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Affiliation(s)
- María Fernanda Mojica
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Ak. 9 #131a-02, Bogotá, DC, Colombia.,Infectious Diseases Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Elsa De La Cadena
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Ak. 9 #131a-02, Bogotá, DC, Colombia.
| | - Adriana Correa
- Universidad Santiago de Cali, Cali, Colombia.,Centro Médico Imbanaco, Cali, Colombia
| | - Tobias Manuel Appel
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Ak. 9 #131a-02, Bogotá, DC, Colombia
| | - Christian José Pallares
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Ak. 9 #131a-02, Bogotá, DC, Colombia.,Centro Médico Imbanaco, Cali, Colombia
| | - María Virginia Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Ak. 9 #131a-02, Bogotá, DC, Colombia.,Centro Médico Imbanaco, Cali, Colombia
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Prospective evaluation of the Amplidiag® CarbaR+VRE assay for direct screening of carbapenemase producing gram-negative bacilli from rectal swabs. Diagn Microbiol Infect Dis 2019; 95:114890. [DOI: 10.1016/j.diagmicrobio.2019.114890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 07/10/2019] [Indexed: 11/22/2022]
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Pereckaite L, Tatarunas V, Giedraitiene A. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings. J Microbiol Methods 2018; 152:154-164. [PMID: 30063958 DOI: 10.1016/j.mimet.2018.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 11/17/2022]
Abstract
The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.
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Affiliation(s)
- Laura Pereckaite
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vacis Tatarunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Agne Giedraitiene
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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van den Bijllaardt W, Janssens MM, Buiting AG, Muller AE, Mouton JW, Verweij JJ. Extended-spectrum β-lactamase (ESBL) polymerase chain reaction assay on rectal swabs and enrichment broth for detection of ESBL carriage. J Hosp Infect 2017; 98:264-269. [PMID: 29080706 DOI: 10.1016/j.jhin.2017.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Extended-spectrum β-lactamase (ESBL) screening and contact precautions on patients at high risk for ESBL carriage are considered important infection control measures. Since contact precautions are costly and may negatively impact patient care, rapid exclusion of ESBL carriage and therefore earlier discontinuation of contact precautions are desired. AIM In the present study, the performance of an ESBL polymerase chain reaction (PCR) targeting blaCTX-M genes was evaluated as a screening assay for ESBL carriage. METHODS Two methods were assessed: PCR performed directly on rectal swabs and PCR on enrichment broth after incubation overnight. The reference standard was culture of ESBL-producing Enterobacteriaceae on selective agar after overnight enrichment and confirmation by the combination disc diffusion method. Microarray was used for discrepancy analysis. A secondary analysis was performed to evaluate the added value of including a blaSHV target in the PCR. FINDINGS A total of 551 rectal swabs from 385 patients were included, of which 28 (5%) were ESBL positive in culture. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 86%, 98%, 67%, and 99%, respectively, for PCR directly on swabs, and 96%, 98%, 75%, and 100%, respectively, for PCR on enrichment broth. Adding a blaSHV target to the assay resulted in a lower PPV without increasing the sensitivity and NPV. CONCLUSION Screening for ESBL by PCR directly on rectal swabs has a high negative predictive value, is up to 48h faster than traditional culture and therefore facilitates earlier discontinuation of contact precautions, thereby improving patient care and saving valuable resources in the hospital.
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Affiliation(s)
- W van den Bijllaardt
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.
| | - M M Janssens
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - A G Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - A E Muller
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands; Department of Medical Microbiology, Haaglanden Medical Centre, The Hague, The Netherlands
| | - J W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - J J Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
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