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Calvo M, Migliorisi G, Maugeri G, Bongiorno D, Bonomo C, Nicitra E, Scalia G, Stefani S. The molecular detection of carbapenem markers with a two-levels amplification screening protocol: epidemiological and resistome insights. Front Microbiol 2024; 15:1346442. [PMID: 38585692 PMCID: PMC10996853 DOI: 10.3389/fmicb.2024.1346442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 04/09/2024] Open
Abstract
Objectives Carbapenem-resistance is a challenging healthcare concern and require specific stewardship programs. Monitoring workflows include the identification from surveillance samples, such as rectal swabs. Although culture assays represent the gold standard, data report a significant effectiveness in detecting carbapenemases genes directly from rectal swabs. The aim of this study was to evaluate the REALQUALITY Carba-Screen kit (AB ANALITICA, Padova, Italy) in detecting carbapenemases genes directly from rectal swabs, also comparing its effectiveness to culture assays results. A next-generation sequencing (NGS) was performed to investigate the positive samples about resistance markers and sequence type (ST). Methods A number of 136 rectal swabs were collected from the University Hospital Policlinico of Catania critical wards. The samples simultaneously underwent culture and molecular assays (REALQUALITY Carba-Screen kit). The molecular method included two-steps. The first step (1 h and 6 min) rapidly excluded negative samples, while the second one (1 h and 6 min) included only positive samples for a resistance confirmation. All the positive culture samples underwent NGS analysis. Results Statistical evaluations demonstrated high sensitivity (100%) and detection rates (92.6%) for the REALQUALITY Carba-Screen kit, which mostly correlated to the standard workflow. All the culture positive results matched the positive molecular results, which were mainly confirmed by the NGS resistome analysis. The identified ST appeared to be diversified and different from the clinically significative strains of the same setting, furnishing interesting epidemiological evidence. Conclusion The molecular detection allowed a coordinate approach in a high-prevalence multi-drug-resistance area. The rapid identification with a multi-step procedure accelerated the infection control procedures, while the preliminary negative results reduced the overtreatment episodes. The molecular method efficacy was confirmed through the NGS. In conclusion, the molecular screening could initially lead to a more conservative approach, which may be reevaluated after a culture result about the microorganisms' identification and susceptibility profile.
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Affiliation(s)
- Maddalena Calvo
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-San Marco”, Catania, Italy
| | - Giuseppe Migliorisi
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-San Marco”, Catania, Italy
| | - Gaetano Maugeri
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-San Marco”, Catania, Italy
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Carmelo Bonomo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Emanuele Nicitra
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Guido Scalia
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-San Marco”, Catania, Italy
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Stefania Stefani
- U.O.C. Laboratory Analysis Unit, A.O.U. “Policlinico-San Marco”, Catania, Italy
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
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Fasciana T, Antonelli A, Bianco G, Lombardo D, Codda G, Roscetto E, Perez M, Lipari D, Arrigo I, Galia E, Tricoli MR, Calvo M, Niccolai C, Morecchiato F, Errico G, Stefani S, Cavallo R, Marchese A, Catania MR, Ambretti S, Rossolini GM, Pantosti A, Palamara AT, Sabbatucci M, Serra N, Giammanco A. Multicenter study on the prevalence of colonization due to carbapenem-resistant Enterobacterales strains before and during the first year of COVID-19, Italy 2018-2020. Front Public Health 2023; 11:1270924. [PMID: 38186699 PMCID: PMC10771343 DOI: 10.3389/fpubh.2023.1270924] [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: 08/01/2023] [Accepted: 11/07/2023] [Indexed: 01/09/2024] Open
Abstract
Background Among multidrug-resistant (MDR) bacteria able to threaten human health, carbapenem-resistant Enterobacterales (CRE) have become a major public health threat globally. National and international guidelines point out the importance of active routine surveillance policies to prevent CRE transmission. Therefore, defining lines of intervention and strategies capable of containing and controlling the spread of CRE is considered determinant. CRE screening is one of the main actions to curb transmission and control outbreaks, outlining the presence and also the prevalence and types of carbapenemase enzymes circulating locally. Objective The purpose of this study was to outline the epidemiology of CRE colonization in Italy, detecting CRE-colonized patients at admission and during hospitalization, before and during the first year of COVID-19. Materials and methods A total of 11,063 patients admitted to seven different hospitals (Bologna, Catania, Florence, Genoa, Naples, Palermo, and Turin) in Intensive Care Units (ICU) and other wards (non-ICU) located in the North, Center, and South of Italy were enrolled and screened for CRE carriage at admission (T0) and during the first 3 weeks of hospitalization (T1-T3). The study spanned two periods, before (September 2018-Septemeber 2019, I observational period) and during the COVID-19 pandemic (October 2019-September 2020, II observational period). Results Overall, the prevalence of CRE-colonized patients at admission in ICU or in other ward, ranged from 3.9 to 11.5%, while a percentage from 5.1 to 15.5% of patients acquired CRE during hospital stay. There were large differences between the I and II period of study according to the different geographical areas and enrolling centers. Overall, comparison of prevalence of CRE-positive patients showed a significant increased trend between I and II observational periods both in ICU and non-ICU wards, mostly in the Southern participating centers. KPC-producing Klebsiella pneumoniae was the most frequent CRE species-carbapenemase combination reported in this study. In particular, the presence of KPC-producing K. pneumoniae was reported in period I during hospitalization in all the CRE-positive patients enrolled in ICU in Turin (North Italy), while in period II at admission in all the CRE-positive patients enrolled in ICU in Catania and in 58.3% of non-ICU CRE-positive patients in Naples (both centers in South Italy). Conclusion The prevalence of CRE in Italy highly increased during the COVID-19 pandemic, mostly in the Southern hospital centers. KPC-producing K. pneumoniae was the most frequent colonizing CRE species reported. The results of our study confirmed the crucial value of active surveillance as well as the importance of multicenter studies representing diverse geographical areas even in endemic countries. Differences in CRE colonization prevalence among centers suggest the need for diversified and center-specific interventions as well as for strengthening efforts in infection prevention and control practices and policies.
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Affiliation(s)
- Teresa Fasciana
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gabriele Bianco
- University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Donatella Lombardo
- Unit of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giulia Codda
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genova, Italy
| | - Emanuela Roscetto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Marianna Perez
- Department of Biomedical and Biotechnological Sciences, University Hospital Policlinico Rodolico San Marco, Catania, Italy
| | - Dario Lipari
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
| | - Ignazio Arrigo
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
| | - Elena Galia
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
| | - Maria Rita Tricoli
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
| | - Maddalena Calvo
- Department of Biomedical and Biotechnological Sciences, University Hospital Policlinico Rodolico San Marco, Catania, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giulia Errico
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University Hospital Policlinico Rodolico San Marco, Catania, Italy
| | - Rossana Cavallo
- University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genova, Italy
- Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Maria Rosaria Catania
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simone Ambretti
- Unit of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Michela Sabbatucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- Directorate General for Health Prevention, Ministry of Health, Rome, Italy
| | - Nicola Serra
- Department of Public Health, University Hospital Federico II, Naples, Italy
| | - Anna Giammanco
- Department of Health Promotion, Maternal and Child Health, Internal Medicine and Medical Specialies “G. D’Alessandro”, University of Palermo, Palermo, Italy
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Ljubović AD, Granov Ð, Husić E, Gačanović D, Halković J, lab.ing AČ, Kotorić Keser Š, Loga Zec S. Prevalence of extended-spectrum β-lactamase and carbapenem-resistant Klebsiella pneumoniae in clinical samples. Saudi Med J 2023; 44:801-807. [PMID: 37582566 PMCID: PMC10425626 DOI: 10.15537/smj.2023.44.8.20230237] [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: 05/17/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
OBJECTIVES To assess the prevalence of these resistant strains in the overall isolates of Klebsiella pneumoniae (K. pneumoniae) in hospital settings. METHODS This retrospective study was conducted from November 2020 to November 2021. The identification and antibiotic susceptibility testing were performed using standard laboratory methods according to the EUCAST standards. The detection of ESBL and carbapenemase production was performed using phenotypic methods such as E-test, combined-disk test with various inhibitors (ROSCO Diagnostica A/S), chromogenic medium for the detection of ESBL/carbapenemase-producing Enterobacteriaceae (CPE) isolates, and the VITEK 2 Compact system (BioMerieux). RESULTS 944 isolates of K. pneumoniae were detected in various clinical specimens. Among these, ESBL-producing strains were detected in 349/944 (37%), whereas carbapenem- resistant strains in 188/944 (20%) of the isolates. The remaining isolates (407/944 [43%]) belonged to the wild type. ESBL isolates were the most common in wound swabs (138 [39.5%]), whereas CRKP isolates in screening samples (110 [58.5%]). The majority of ESBL isolates were detected in surgical departments (105 [30.1%]), whereas CRKP isolates in adult intensive care unit departments (79 [42.%]). CONCLUSION Our results show an increasing frequency of CRKP strains. This presents a significant issue in terms of infection prevention and control in hospital settings.
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Affiliation(s)
- Amela Dedeić Ljubović
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Ðana Granov
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Erna Husić
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Džemilja Gačanović
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Jasmina Halković
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Azra Čamdžić lab.ing
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Šejla Kotorić Keser
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Svjetlana Loga Zec
- From the Unit of Clinical Microbiology, Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
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4
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Baraka K, Abozahra R, Haggag MM, Abdelhamid SM. Genotyping and molecular investigation of plasmid-mediated carbapenem resistant clinical Klebsiella pneumoniae isolates in Egypt. AIMS Microbiol 2023; 9:228-244. [PMID: 37091821 PMCID: PMC10113168 DOI: 10.3934/microbiol.2023014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Klebsiella pneumoniae is a multidrug-resistant nosocomial pathogen. Carbapenem resistance is mediated mainly by enzymes carried on transmissible plasmids causing their dissemination among other members of Enterobacteriaceae. This study aimed to molecularly detect carbapenem resistance genes in K. pneumoniae clinical isolates, genotype them using ERIC-PCR, and investigate plasmid transformation of resistant genes by using ERIC-PCR and sequencing. Methods Antimicrobial resistance of sixty carbapenem-resistant K. pneumoniae strains was evaluated by using the disc diffusion method. Five carbapenemases' genes were amplified by conventional PCR. Genotyping was performed using ERIC-PCR. Gene transformation was performed for the five genes to sensitive isolates. Wild and transformed isolates were genetically investigated using ERIC-PCR and sequencing. Results Carbapenem resistance in our isolates was associated with high resistance to all tested antibiotics. The 60 K. pneumoniae isolates were divided into 6 resistor types. The prevalence of KPC, IMP, VIM, NDM, and OXA-48 genes were 17%, 63%, 93%, 85% and 100%, respectively. Dendrogram analysis showed 57 distinct patterns, arranged in three clusters. The five genes were transformed successfully into sensitive isolates. ERIC profiles of wild and transformed isolates showed cluster A contained all the wild isolates, and cluster B contained all transformed isolates. Genetic sequences of the 5 genes reflected high genetic similarity with the GenBank reference genes before plasmid transformation; however, a distinguishable decrease of genetic similarity was observed after transformation. Conclusion Plasmid-mediated carbapenem resistance in K. pneumoniae and its dissemination among different strains is a real threat to public health.
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Affiliation(s)
- Kholoud Baraka
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, El Behira, Egypt
- * Correspondence: ; Tel: +21006878989
| | - Rania Abozahra
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, El Behira, Egypt
| | - Marwa Mohammed Haggag
- Microbiology and Immunology Department, Faculty of Pharmacy, Sinai University, Arish Campus, Sinai, Egypt
| | - Sarah M Abdelhamid
- Microbiology and Immunology Department, Faculty of Pharmacy, Damanhour University, El Behira, Egypt
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5
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Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal. Antibiotics (Basel) 2022; 11:antibiotics11111613. [PMID: 36421258 PMCID: PMC9686965 DOI: 10.3390/antibiotics11111613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
While antibiotic resistance is rising to dangerously high levels, resistance mechanisms are spreading globally among diverse bacterial species. The emergence of antibiotic-resistant Klebsiella pneumoniae, mainly due to the production of antibiotic-inactivating enzymes, is currently responsible for most treatment failures, threatening the effectiveness of classes of antibiotics used for decades. This study assessed the presence of genetic determinants of β-lactam resistance in 102 multi-drug resistant (MDR) K. pneumoniae isolates from patients admitted to two central hospitals in northern Portugal from 2010 to 2020. Antimicrobial susceptibility testing revealed a high rate (>90%) of resistance to most β-lactam antibiotics, except for carbapenems and cephamycins, which showed antimicrobial susceptibility rates in the range of 23.5−34.3% and 40.2−68.6%, respectively. A diverse pool of β-lactam resistance genetic determinants, including carbapenemases- (i.e., blaKPC-like and blaOXA-48-like), extended-spectrum β-lactamases (ESBL; i.e., blaTEM-like, blaCTX-M-like and blaSHV-like), and AmpC β-lactamases-coding genes (i.e., blaCMY-2-like and blaDHA-like) were found in most K. pneumoniae isolates. blaKPC-like (72.5%) and ESBL genes (37.3−74.5%) were the most detected, with approximately 80% of K. pneumoniae isolates presenting two or more resistance genes. As the optimal treatment of β-lactamase-producing K. pneumoniae infections remains problematic, the high co-occurrence of multiple β-lactam resistance genes must be seen as a serious warning of the problem of antimicrobial resistance.
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Jubair N, Rajagopal M, Chinnappan S, Abdullah NB, Fatima A. Review on the Antibacterial Mechanism of Plant-Derived Compounds against Multidrug-Resistant Bacteria (MDR). EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:3663315. [PMID: 34447454 PMCID: PMC8384518 DOI: 10.1155/2021/3663315] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/27/2021] [Accepted: 07/24/2021] [Indexed: 02/06/2023]
Abstract
Microbial resistance has progressed rapidly and is becoming the leading cause of death globally. The spread of antibiotic-resistant microorganisms has been a significant threat to the successful therapy against microbial infections. Scientists have become more concerned about the possibility of a return to the pre-antibiotic era. Thus, searching for alternatives to fight microorganisms has become a necessity. Some bacteria are naturally resistant to antibiotics, while others acquire resistance mainly by the misuse of antibiotics and the emergence of new resistant variants through mutation. Since ancient times, plants represent the leading source of drugs and alternative medicine for fighting against diseases. Plants are rich sources of valuable secondary metabolites, such as alkaloids, quinones, tannins, terpenoids, flavonoids, and polyphenols. Many studies focus on plant secondary metabolites as a potential source for antibiotic discovery. They have the required structural properties and can act by different mechanisms. This review analyses the antibiotic resistance strategies produced by multidrug-resistant bacteria and explores the phytochemicals from different classes with documented antimicrobial action against resistant bacteria, either alone or in combination with traditional antibiotics.
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Affiliation(s)
- Najwan Jubair
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Mogana Rajagopal
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Sasikala Chinnappan
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | | | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul, Turkey
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7
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Holma T, Antikainen J, Haiko J. Evaluation of three molecular carbapenemase tests: Eazyplex SuperBug complete B, Novodiag CarbaR+, and Amplidiag CarbaR+MCR. J Microbiol Methods 2020; 180:106105. [PMID: 33217483 DOI: 10.1016/j.mimet.2020.106105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Carbapenemase-producing Gram-negative bacilli, i.e., Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter, are of increased concern for the public health around the world. There is urgent need for rapid and accurate tests in order to provide correct treatment and to prevent bacterial spread in healthcare settings. METHODS The aim of this study was to evaluate three commercial multiplex carbapenemase tests with CE-IVD marking: Eazyplex SuperBug complete B (AmplexDiagnostics), Novodiag CarbaR+ (Mobidiag), and Amplidiag CarbaR+MCR (Mobidiag). All these tests recognize KPC, NDM, OXA-48/181 group, VIM, OXA-23 group, and OXA-24/40 group, and Novodiag CarbaR+ and Amplidiag CarbaR+MCR additionally recognize IMP, OXA-51 group (with promoter located within ISAbaI), OXA-58 group, and MCR, and Amplidiag CarbaR+MCR further recognizes GES (carbapenemase-type only). RESULTS The sensitivities and specificities of these tests with bacterial isolates were 100%. The sensitivity directly from clinical samples was 100%, but the specificity was lower, which is simply explained by the higher sensitivity of the molecular methods compared with culture method. CONCLUSIONS Overall, these CE-IVD marked tests provide a good alternative in the detection of carbapenemase-producing organisms.
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Affiliation(s)
- Tanja Holma
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland
| | - Jenni Antikainen
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland
| | - Johanna Haiko
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland.
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8
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Jin X, Zhang H, Wu S, Qin X, Jia P, Tenover FC, Tang YW, Li M, Hu F, Yang Q, Yu Y. Multicenter Evaluation of Xpert Carba-R Assay for Detection and Identification of the Carbapenemase Genes in Rectal Swabs and Clinical Isolates. J Mol Diagn 2020; 23:111-119. [PMID: 33212263 DOI: 10.1016/j.jmoldx.2020.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid detection of carbapenemase-producing organisms is clinically desirable for hospital infection control and antibiotic stewardship. In this multicenter study, the Xpert Carba-R assay was evaluated for detection of the five carbapenemase genes (blaKPC, blaNDM, blaIMP, blaOXA-48, and blaVIM) in 2404 nonduplicate rectal swabs of admitted inpatients and 521 Gram-negative isolates from four tertiary hospitals in China, compared with the reference growth-based method with DNA sequence analysis of colonies. All suspected false-positive results in rectal swabs were resolved by supplementary sequencing from broth cultures. A total of 197 blaKPC, 171 blaNDM, 142 blaIMP, 6 blaVIM, and 5 blaOXA-48 genes were detected by Xpert Carba-R in 417 rectal swabs, with overall positive and negative percentage agreements ranging from 94.5% to 100% and from 94.8% to 99.9%, respectively. Notably, 17.5% (263/1500) of inpatients had rectal colonization with carbapenem-nonsusceptible organisms detected in intensive care units, and 63.1% (166/263) were Xpert Carba-R positive. Among the 469 carbapenem-nonsusceptible and 52 carbapenem-susceptible isolates examined, 373 were Enterobacteriaceae, 55 were Pseudomonas aeruginosa, and 93 were Acinetobacter baumannii. Compared with the reference isolate sequencing, overall positive and negative percentage agreements were 99.7% and 98.0%, respectively. The intra-assay and interassay coefficient of variability values were both <2%. Thus, we show that Xpert Carba-R assay provides good reproducibility and reliable results for detection and differentiation of five carbapenemase genes in both rectal swabs and clinical isolates.
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Affiliation(s)
- Xi Jin
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haomin Zhang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Shi Wu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Xiaohua Qin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fred C Tenover
- Department of Medical Affairs, Cepheid, Sunnyvale, California
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Rapid detection of antimicrobial resistance markers with Allplex™ Entero-DR assay directly from positive blood culture bottles. Eur J Clin Microbiol Infect Dis 2020; 40:801-806. [PMID: 33099709 DOI: 10.1007/s10096-020-04082-5] [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: 06/23/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
A method for rapid detection of one extended-spectrum β-lactamase (ESBL) and five carbapenemase-encoding genes as well as vancomycin resistance markers directly from blood cultures using the Allplex™ Entero-DR assay (Seegene, Seoul, South Korea) is presented. Altogether 28 previously well-characterized resistant Gram-negative bacilli and Enterococcus spp., and 142 clinical blood cultures containing Gram-negative bacilli or Gram-positive cocci were analyzed. The method had 100% sensitivity and specificity for detecting blaOXA-48-like, blaKPC, blaVIM, blaIMP, blaNDM, blaCTX-M, vanA, and vanB. The lowest detectable amount of viable cells in blood culture samples were 5.39·104 CFU/mL, 6.66·104 CFU/mL, 5.13·103 CFU/mL, 6.09·104 CFU/mL, 6.66·104 CFU/mL, 6.66·104 CFU/mL, 3.12·104 CFU/mL, and 5.34·104 CFU/mL for the blaKPC, blaOXA-48-like, blaVIM, blaIMP, blaNDM, blaCTX-M, vanA, and vanB, respectively. The results were available within 90 min from signal positive blood cultures, as no separate DNA extraction steps were needed, and the assay showed no interference from blood or culture media used allowing reliable and simplified detection of the resistance markers.
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Yan L, Sun J, Xu X, Huang S. Epidemiology and risk factors of rectal colonization of carbapenemase-producing Enterobacteriaceae among high-risk patients from ICU and HSCT wards in a university hospital. Antimicrob Resist Infect Control 2020; 9:155. [PMID: 32967718 PMCID: PMC7513325 DOI: 10.1186/s13756-020-00816-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Nosocomial carbapenemase-producing Enterobacterieceae (CPE) infections constitute a major global health concern and are associated with increased morbidity and mortality. Rectal colonization with CPE is a risk factor for bacterial translocation leading to subsequent endogenous CPE infections. This prospective observational study was aimed to investigate the prevalence and epidemiology of rectal colonization of CPE, the carbapenemase genotypes, and to identify the independent risk factors for the acquisition of CPE colonization in high-risk patients from ICU and HSCT wards in a university hospital in China. Methods In a prospective cohort study, 150 fecal samples from rectal swabs were consecutively obtained for inpatients from the intensive care unit (ICU) and hematopoietic stem cell transplantation (HSCT) wards from November 2018 to May 2019, and screening test for CPE was conducted by using prepared in-house trypsin soybean broth (TSB) selective media and MacConkey agar. Antimicrobial susceptibility was determined by the broth microdilution method and carbapenemase genes were characterized by both the GeneXpert Carba-R and PCR for blaKPC, blaNDM, blaIMP, blaVIM and blaOXA. Multi-locus sequence typing (MLST) was employed to characterize the genetic relationships among the carbapenemase-producing K. Pneumonia (CPKP) isolates. In order to further investigate the risk factors and clinical outcomes of CPE colonization, a prospective case-control study was also performed. Results Twenty-six suspected CPE strains, including 17 Klebsiella pneumoniae, 6 Escherichia coli, 1 Citrobacter freundii, 1 Enterobacter Kobe, and 1 Raoultella ornithinolytica, were identified in 25 non-duplicated rectal swab samples from 25 patients, with a carriage rate of 16.67% (25/150). Through GeneXpert Carba-R and subsequent PCR and sequencing, all the suspected CPE isolates were identified to be positive for the carbapenemase genes, of which 17 were blaKPC-carriers, and another 9 were blaNDM-producers. MLST designated all the CPKP isolates to be ST11 clone. Multivariate analysis indicated that urinary system diseases, operation of bronchoscopy, and combined use of antibiotics were independent risk factors for acquiring CPE colonization in high-risk patients from the ICU and HSCT wards. Conclusions This study revealed a high prevalence of rectal CPE colonization in high-risk patients from ICU and HSCT wards, and a predominant colonization of the KPC-producing K. pneumoniae clone ST11. Stricter infection control measures are urgently needed to limit the dissemination of CPE strains, especially in patients who were afflicted by urinary system diseases, have underwent bronchoscopy, and were previously exposed to combined antibiotic use.
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Affiliation(s)
- Li Yan
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, No.1 Friendship Road, Yuzhong District, Chongqing, 400016, China.
| | - Jide Sun
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, No.1 Friendship Road, Yuzhong District, Chongqing, 400016, China
| | - Xiuyu Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, No.1 Friendship Road, Yuzhong District, Chongqing, 400016, China
| | - Shifeng Huang
- Department of Laboratory Medicine, the First Affiliated Hospital of Chongqing Medical University, No.1 Friendship Road, Yuzhong District, Chongqing, 400016, China.
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Park CE. Clinical Laboratory Aspect of Carbapenem-Resistant Enterobacteriaceae. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.1.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Chang-Eun Park
- Department of Biomedical Laboratory ScienceㆍMolecular Diagnostics Research Institute, Namseoul University, Cheonan, Korea
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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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