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Mikita K, Tajima M, Haque A, Kato Y, Iwata S, Suzuki K, Hasegawa N, Yano H, Matsumoto T. Development of a Simple Method to Detect the Carbapenemase-Producing Genes blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM Using a LAMP Method with Lateral Flow DNA Chromatography. Diagnostics (Basel) 2024; 14:1027. [PMID: 38786325 PMCID: PMC11119924 DOI: 10.3390/diagnostics14101027] [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: 04/22/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Infections by carbapenemase-producing Enterobacterales constitute a global public health threat. The rapid and efficient diagnosis of Enterobacterales infection is critical for prompt treatment and infection control, especially in hospital settings. We developed a novel loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography to identify five major groups of carbapenemase-producing genes (blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM). This method uses DNA-DNA hybridization-based detection in which LAMP products can be easily visualized as colored lines. No specific technical expertise, expensive equipment, or special facilities are required for this method, allowing its broad application. Here, 73 bacteria collections including strains with carbapenemase-producing genes were tested. Compared to sequencing results, LAMP DNA chromatography for five carbapenemase-producing genes had a sensitivity and specificity of 100% and >97%, respectively. This newly developed method can be a valuable rapid diagnostic test to guide appropriate treatments and infection control measures, especially in resource-limited settings.
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Affiliation(s)
- Kei Mikita
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Moe Tajima
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Anwarul Haque
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
| | - Yasuyuki Kato
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
| | - Satoshi Iwata
- Department of Microbiology, Tokyo Medical University, Tokyo 160-8402, Japan;
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo 173-8606, Japan;
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo 160-8582, Japan; (M.T.); (N.H.)
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara 634-8522, Japan;
| | - Tetsuya Matsumoto
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Narita 286-8520, Japan; (A.H.); (Y.K.); (T.M.)
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Carbapenem resistance determinants in Klebsiella pneumoniae strains isolated from blood cultures-comparative analysis of molecular and phenotypic methods. REV ROMANA MED LAB 2022. [DOI: 10.2478/rrlm-2022-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Introduction: This study provides data on carbapenemases identified in carbapenem-resistant Klebsiella pneumoniae (CR-KP) isolated from blood-cultures by the multiplex molecular method.
Material and method: Between October 2016 and September 2017, 47 non-duplicate Klebsiella pneumoniae (KP) were isolated from blood cultures, from hospitalized patients in the Regional Institute of Gastroenterology and Hepathology, Cluj-Napoca, Romania. Identification and antimicrobial susceptibility tests (AST) were performed by Vitek 2 Compact. The combination disks test (CDT) was used for phenotypic analysis and the LightCycler® Multiplex DNA assay was used to detect and identify the carbapenemases by the LightCycler®z 480 Instrument. The following targets were chosen: blaKPC, blaNDM, blaGES, blaIMP and blaOXA-48 genes and the Cobas® 4800 software variant 2.2.0 was used for the results interpretation.
Results: Taking into consideration the meropenem minimum inhibitory concentration (MIC), 29 KP were susceptible and 18 were not-susceptible (MIC≥0.5 µg ml-1). In the CR-KP group, the CDT identified OXA-48 (10/18) and KPC (7/18) producers. One isolate showed a noninterpretable profile. The multiplex molecular analyses confirmed the carbapenemases production as: 9 CR-KP were KPC and OXA-48 co-producers, 8 were OXA-48 and one was KPC producing strains. In CR-KP group, we found a significant correlation between the CDT and RT-PCR tests results, concerning KPC (p = 0.671). Eight phenotypic results were confirmed by molecular Light-Cycler® Multiplex DNA assay. For CR-KP co-producers (KPC and OXA-48), the CDT could indicate only one carbapenem-hydrolyzing enzyme.
Conclusion: This study highlights the CR-KP co-producers (OXA-48 and KPC). OXA-48-like is more frequently encountered in our area than other carbapenemases.
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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Poirier AC, Kuang D, Siedler BS, Borah K, Mehat JW, Liu J, Tai C, Wang X, van Vliet AHM, Ma W, Jenkins DR, Clark J, La Ragione RM, Qu J, McFadden J. Development of Loop-Mediated Isothermal Amplification Rapid Diagnostic Assays for the Detection of Klebsiella pneumoniae and Carbapenemase Genes in Clinical Samples. Front Mol Biosci 2022; 8:794961. [PMID: 35223985 PMCID: PMC8864245 DOI: 10.3389/fmolb.2021.794961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
Klebsiella pneumoniae is an important pathogenic bacterium commonly associated with human healthcare and community-acquired infections. In recent years, K. pneumoniae has become a significant threat to global public and veterinary health, because of its high rates of antimicrobial resistance (AMR). Early diagnosis of K. pneumoniae infection and detection of any associated AMR would help to accelerate directed therapy and reduce the risk of the emergence of multidrug-resistant isolates. In this study, we identified three target genes (yhaI, epsL, and xcpW) common to K. pneumoniae isolates from both China and Europe and designed loop-mediated isothermal amplification (LAMP) assays for the detection of K. pneumoniae in clinical samples. We also designed LAMP assays for the detection of five AMR genes commonly associated with K. pneumoniae. The LAMP assays were validated on a total of 319 type reference strains and clinical isolates of diverse genetic backgrounds, in addition to 40 clinical human sputum samples, and were shown to be reliable, highly specific, and sensitive. For the K. pneumoniae-specific LAMP assay, the calculated sensitivity, specificity, and positive and negative predictive values (comparison with culture and matrix-assisted laser desorption/ionization-time of flight mass spectrometry) were all 100% on clinical isolates and, respectively, of 100%, 91%, and 90%, and 100% when tested on clinical sputum samples, while being significantly faster than the reference methods. For the bla KPC and other carbapenemases' LAMP assays, the concordance between the LAMP results and the references methods (susceptibility tests) was 100%, on both pure cultures (n = 125) and clinical samples (n = 18). In conclusion, we developed highly sensitive and specific LAMP assays for the clinical identification of K. pneumoniae and detection of carbapenem resistance.
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Affiliation(s)
- Aurore C. Poirier
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Dai Kuang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, School of Medicine, Institute of Respiratory Diseases, Shanghai Jiao Tong University, Shanghai, China
| | - Bianca S. Siedler
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Khushboo Borah
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Jai W. Mehat
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Centre for Microbial Genomics and Animal Microbiome Research, Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Wang
- Department of Critical Care Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Arnoud H. M. van Vliet
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Centre for Microbial Genomics and Animal Microbiome Research, Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - David R. Jenkins
- Department of Medical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - John Clark
- Department of Medical Microbiology, Epsom and St Helier University Hospitals NHS Trust, Carshalton, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, School of Medicine, Institute of Respiratory Diseases, Shanghai Jiao Tong University, Shanghai, China
| | - Johnjoe McFadden
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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Comparative Evaluation of Phenotypic Synergy Tests versus RESIST-4 O.K.N.V. and NG Test Carba 5 Lateral Flow Immunoassays for the Detection and Differentiation of Carbapenemases in Enterobacterales and Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0108021. [PMID: 35107384 PMCID: PMC8809327 DOI: 10.1128/spectrum.01080-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spread of carbapenem-resistant Pseudomonas aeruginosa and carbapenemase-producing Enterobacterales (CPE) has dramatically impacted morbidity and mortality. COVID-19 pandemic has favored the selection of these microorganisms because of the excessive and prolonged use of broad-spectrum antibiotics and the outbreaks related to patient transfer between hospitals and inadequate personal protective equipment. Therefore, early CPE detection is considered essential for their control. We aimed to compare conventional phenotypic synergy tests and two lateral flow immunoassays for detecting carbapenemases in Enterobacterales and P. aeruginosa. We analyzed 100 carbapenem-resistant Gram-negative bacilli isolates, 80 Enterobacterales, and 20 P. aeruginosa (86 isolates producing KPC, NDM, OXA-48, IMP, and VIM carbapenemases and 14 non-carbapenemase-producing isolates). We performed a modified Hodge test, boronic acid and ethylenediaminetetraacetic acid (EDTA) synergy tests, and two lateral flow immunoassays: RESIST-4 O.K.N.V. (Coris Bioconcept) and NG Test Carba 5 (NG Biotech). In total, 76 KPC, seven VIM, one NDM, one OXA-48, and one isolate coproducing KPC + NDM enzymes were included. The concordance of different methods estimated by the Kappa index was 0.432 (standard error: 0.117), thus showing a high variability with the synergy tests with boronic acid and EDTA and reporting 16 false negatives that were detected by the two immunochromatographic methods. Co-production was only detected using immunoassays. Conventional phenotypic synergy tests with boronic acid and EDTA for detecting carbapenemases are suboptimal, and their routine use should be reconsidered. These tests depend on the degree of enzyme expression and the distance between disks. Lateral flow immunoassay tests are a rapid and cost-effective tool to detect and differentiate carbapenemases, improving clinical outcomes through targeted therapy and promoting infection prevention measures. IMPORTANCE Infections due to multidrug-resistant pathogens are a growing problem worldwide. The production of carbapenemases in Pseudomonas aeruginosa and Enterobacterales cause a high impact on the mortality of infected patients. Therefore, it is of great importance to have methods that allow the early detection of these multi-resistant microorganisms, achieving the confirmation of the type of carbapenemase present, with high sensitivity and specificity, with the aim of improving epidemiological control, dissemination, the clinical course to through targeted antibiotic therapy and promoting infection control in hospitals.
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Feng W, Niu S, Chang Y, Jia X, Huang S, Yang P. Design of Rapid Detection System for Five Major Carbapenemase Families ( bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48-Like) by Colorimetric Loop-Mediated Isothermal Amplification. Infect Drug Resist 2021; 14:1865-1874. [PMID: 34079297 PMCID: PMC8164214 DOI: 10.2147/idr.s301757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/07/2021] [Indexed: 01/16/2023] Open
Abstract
Purpose Carbapenemase-producing Enterobacteriaceae (CPE) infection constitutes a public health threat. Timely and efficient diagnosis is of paramount importance for prompt and effective therapy. In order to quickly and comprehensively detect the five major families of carbapenemases (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48-like), colorimetric loop-mediated isothermal amplification (LAMP) was employed. Materials and Methods Five sets of LAMP primers were designed, each of which can, respectively, amplify all the carbapenemase subtypes described in this work. Twenty whole genome sequencing-verified-“standard strains”, including 1 blaNDM-1, 1 blaNDM-5, 1 blaNDM-6, 1 blaNDM-7, 2 blaIMP-4, 1 blaIMP-8, 2 blaKPC-2, 1 blaKPC-3, 1 blaKPC-4, 1 blaKPC-5, 1 blaKPC-6, 1 blaKPC-7, 1 blaOXA-48 and 1 blaOXA-181 carrier, and 1 blaVIM and blaOXA-244, 1 blaKPC-2 and blaIMP-4, 1 blaKPC-2 and blaVIM-1 and 1 blaKPC-2 and blaNDM-1-co-carriers, were used to establish a 25-microliter visual LAMP reaction system (kept at 65°C for 30 minutes in water bath). Color change from bright pink to yellow indicated positive amplification. In addition, 126 pre-verified clinical carbapenem-resistant Enterobacteriaceae (CRE) isolates, including 65 CPE (23 blaNDM, 2 blaOXA-48-like, 1 blaKPC and blaVIM, 2 blaIMP, and 37 blaKPC carriers) and 61 non-CPE, were also detected. Results With the lowest detection limit of 10 colony forming units (CFU) per reaction for LAMP and 103 CFU per reaction for PCR, the LAMP system demonstrated dramatically higher sensitivity while retaining the same specificity. Furthermore, we demonstrated concordant results between the two methods for the 126 clinical isolates. Conclusion Therefore, LAMP could be used for rapid identification of the five major carbapenemase gene families in routine clinical laboratories.
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Affiliation(s)
- Wenjuan Feng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Siqiang Niu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yanbin Chang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaojiong Jia
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shifeng Huang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Ping Yang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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7
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Patidar N, Vyas N, Sharma S, Sharma B. Phenotypic Detection of Carbapenemase Production in Carbapenem-Resistant Enterobacteriaceae by Modified Hodge Test and Modified Strip Carba NP Test. J Lab Physicians 2021; 13:14-21. [PMID: 34054236 PMCID: PMC8154340 DOI: 10.1055/s-0041-1723859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Objective
Carbapenems are last resort antibiotics for multidrug-resistant
Enterobacteriaceae
. However, resistance to carbapenem is increasing at an alarming rate worldwide leading to major therapeutic failures and increased mortality rate. Early and effective detection of carbapenemase producing carbapenem-resistant
Enterobacteriaceae
(CRE) is therefore key to control dissemination of carbapenem resistance in nosocomial as well as community-acquired infection. The aim of present study was to evaluate efficacy of Modified strip Carba NP (CNP) test against Modified Hodge test (MHT) for early detection of carbapenemase producing
Enterobacteriaceae
(CPE).
Material and MethodsEnterobacteriaceae
isolated from various clinical samples were screened for carbapenem resistance. A total of 107 CRE were subjected to MHT and Modified strip CNP test for the detection of CPE.
Statistical Analysis
It was done on Statistical Package for the Social Sciences (SPSS) software, IBM India; version V26. Nonparametric test chi-square and
Z
-test were used to analyze the results within a 95% level of confidence.
Results
Out of 107 CRE, 94 (88%) were phenotypically confirmed as carbapenemase producer by Modified strip CNP test and 46 (43%) were confirmed by Modified Hodge Test (MHT). Thirty-eight (36%) isolates showed carbapenemase production by both MHT and CNP test, 56 isolates (52%) were CNP test positive but MHT negative, eight (7%) isolates were MHT positive but CNP test negative and five (5%) isolates were both MHT and CNP test negative. There is statistically significant difference in efficiency of Modified CNP test and MHT (
p
< 0.05).
Conclusion
Modified strip CNP test is simple and inexpensive test which is easy to perform and interpret and gives rapid results in less than 5 minutes. It has high degree of sensitivity and specificity. Modified strip CNP test shows significantly higher detection capacity for carbapenemase producers as compared with MHT.
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Affiliation(s)
- Nisha Patidar
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Nitya Vyas
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Shanoo Sharma
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Babita Sharma
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
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Jasuja JK, Zimmermann S, Burckhardt I. Applicability and performance of EUCAST's rapid antimicrobial susceptibility testing (RAST) on primarily sterile body fluids in blood culture bottles in laboratory routine with total lab automation. Eur J Clin Microbiol Infect Dis 2021; 40:1217-1225. [PMID: 33438162 PMCID: PMC8139921 DOI: 10.1007/s10096-020-04146-6] [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: 08/25/2020] [Accepted: 12/28/2020] [Indexed: 11/06/2022]
Abstract
Optimisation of microbiological diagnostics in primarily sterile body fluids is required. Our objective was to apply EUCAST’s RAST on primarily sterile body fluids in blood culture bottles with total lab automation (TLA) and to compare results to our reference method Vitek2 in order to report susceptibility results earlier. Positive blood culture bottles (BACTEC™ Aerobic/Anaerobic/PEDS) inoculated with primarily sterile body fluids were semi-automatically subcultured onto Columbia 5% SB agar, chocolate agar, MacConkey agar, Schaedler/KV agar and Mueller-Hinton agar. On latter, cefoxitin, ampicillin, vancomycin, piperacillin/tazobactam, meropenem and ciprofloxacin were added. After 6 h, subcultures and RAST were imaged and MALDI-TOF MS was performed. Zone sizes were digitally measured and interpreted following RAST breakpoints for blood cultures. MIC values were determined using Vitek2 panels. During a 1-year period, 197 Staphylococcus aureus, 91 Enterococcus spp., 38 Escherichia coli, 11 Klebsiella pneumoniae and 8 Pseudomonas aeruginosa were found. Categorical agreement between RAST and MIC was 96.5%. Comparison showed no very major errors, 2/7 (28.6%) and 1/7 (14.3%) of major errors for P. aeruginosa and meropenem and ciprofloxacin, 1/9 (11.1%) for K. pneumoniae and ciprofloxacin, 4/69 (7.0%) and 3/43 (5.8%) for Enterococcus spp. and vancomycin and ampicillin, respectively. Minor errors for P. aeruginosa and meropenem (1/8; 12.8%) and for E. coli and ciprofloxacin (2/29; 6.5%) were found. 30/550 RAST measurements were within area of technical uncertainty. RAST is applicable and performs well for primarily sterile body fluids in blood culture bottles, partially better than blood-based RAST. Official EUCAST evaluation is needed.
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Affiliation(s)
- Jasmin Kaur Jasuja
- Department for Infectious Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
| | - Stefan Zimmermann
- Department for Infectious Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Irene Burckhardt
- Department for Infectious Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
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Cooper AL, Carter C, McLeod H, Wright M, Sritharan P, Tamber S, Wong A, Carrillo CD, Blais BW. Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Cassandra Carter
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Hana McLeod
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Marie Wright
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Prithika Sritharan
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Catherine D. Carrillo
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
| | - Burton W. Blais
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Accuracy and applicability of different phenotypic methods for carbapenemase detection in Enterobacteriaceae: A systematic review and meta-analysis. J Glob Antimicrob Resist 2020; 21:138-147. [DOI: 10.1016/j.jgar.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 11/23/2022] Open
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Katongole P, Bulwadda Kisawuzi D, Kyobe Bbosa H, Patrick Kateete D, Florence Najjuka C. Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda. F1000Res 2019. [DOI: 10.12688/f1000research.20930.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Uropathogenic Escherichia coli (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community-acquired and 30-50% of all hospital-acquired UTIs. E. coli strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified E. coli strains into eight phylogenetic groups using the quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of UPEC strains in Uganda using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. Methods: In this cross-sectional study, 140 stored uropathogenic E. coli isolates from the Clinical Microbiology Laboratory, Department of Medical Microbiology, College of Health Sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Phenotypic detection of extended-spectrum beta-lactamase, AmpC and carbapenemases was done according to CLSI guidelines and Laboratory SOPs. Results: Phylogenetic group B2 (40%) was the most predominant, followed by A (6.23%), clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was trimethoprim-sulphamethoxazole (90.71%) and the least was imipenem (1.43%). In total, 73.57% of isolates were multi-drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). Conclusions: Our findings showed the high prevalence of MDR E. coli isolates, with the dominance of phylogenetic group B2. About 9% of E. coli isolates belonged to the newly described phylogroups C, E, F, and clade I and II.
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Messaoudi A, Haenni M, Bouallègue O, Saras E, Chatre P, Chaouch C, Boujâafar N, Mansour W, Madec JY. Dynamics and molecular features of OXA-48-like-producing Klebsiella pneumoniae lineages in a Tunisian hospital. J Glob Antimicrob Resist 2019; 20:87-93. [PMID: 31306816 DOI: 10.1016/j.jgar.2019.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/18/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES The aim of this study was to elucidate the molecular features of genes, plasmids and clones of OXA-48-like producingKlebsiella pneumoniae isolates recovered in Sahloul Hospital (Sousse, Tunisia) in the period 2012-2014. METHODS In vitro antimicrobial susceptibility testing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and PCR-based replicon typing (PBRT) were performed. Extended-spectrum β-lactamase (ESBL) and carbapenemases genes were detected by PCR and sequencing. The clonality of isolates was assessed by PFGE and multilocus sequence typing (MLST). RESULTS Klebsiella pneumoniae accounted for 26.8% (1095/4083) of clinical Enterobacterales isolates identified during 2012-2014, of which 21.9% (240/1095) were resistant to carbapenems, mostly harbouring blaOXA-48-like genes (196/240; 81.7%). Plasmid analysis showed that blaOXA-204 and blaOXA-48 were mostly carried by IncA/C and IncL plasmids, respectively. The current data highlight the dominance of two ST101 and ST147 lineages spreading OXA-48 and OXA-204, respectively, through successive clonal spreads at this hospital. In addition, a large diversity of other K. pneumoniae lineages was also identified, such as ST15, ST36 and ST525 spreading OXA-48 as well as ST340, ST2032, ST301, ST199 and ST1561 spreading OXA-48 or OXA-204, constituting a reservoir of possible dominant clones in the future. CONCLUSION This study reports the full molecular characterisation of carbapenem resistance in K. pneumoniae and the predominance of a few clones responsible for the dissemination of OXA-48 and OXA-204 enzymes in a Tunisian hospital.
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Affiliation(s)
- Aziza Messaoudi
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia
| | - Marisa Haenni
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Olfa Bouallègue
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Medicine Ibn Al Jazzar Sousse, University of Sousse, Sousse, Tunisia
| | - Estelle Saras
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pierre Chatre
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Cherifa Chaouch
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Noureddine Boujâafar
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Wejdene Mansour
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Medicine Ibn Al Jazzar Sousse, University of Sousse, Sousse, Tunisia; Laboratory of Metabolic Biophysics and Applied Pharmacology (LR12ES02), Department of Biophysics, Faculty of Medicine Ibn El Jazzar Sousse, University of Sousse, Sousse, Tunisia.
| | - Jean-Yves Madec
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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Guzel M, Afsar Y, Akdogan D, Moncheva P, Hristova P, Erdem G. Evaluation of metallo-beta-lactamase production in multiple antibiotic-resistant Pseudomonas spp. and Acinetobacter baumannii strains. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1500146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Mustafa Guzel
- Microbiology Laboratory, Private Maltepe Medical Center, Istanbul, Turkey
| | - Yusuf Afsar
- Microbiology Laboratory, Ağrı State Hospital, Ağrı, Turkey
| | - Dogan Akdogan
- Microbiology Laboratory, 29 Mayıs State Hospital, Ankara, Turkey
| | - Penka Moncheva
- Department of Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Petya Hristova
- Department of Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Gul Erdem
- Department of Medical Microbiology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey
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Hojabri Z, Arab M, Darabi N, Kia NS, Lopes BS, Pajand O. Evaluation of the commercial combined disk test and minimum inhibitory concentration (MIC) determination for detection of carbapenemase producers among Gram-negative bacilli isolated in a region with high prevalence of blaOXA-48 and blaNDM. Int Microbiol 2018; 22:81-89. [DOI: 10.1007/s10123-018-0030-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/13/2018] [Accepted: 08/19/2018] [Indexed: 12/01/2022]
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Freystätter C, Radtke C, Ihra G, Thalhammer F, Fochtmann-Frana A. Sepsis caused by multidrug-resistant klebsiella pneumoniae infection in a 23-year-old burn patient: case report and literature review. ANNALS OF BURNS AND FIRE DISASTERS 2018; 31:113-117. [PMID: 30374262 PMCID: PMC6199020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Septic complications are a major problem in burn care. Infections caused by multidrug-resistant (MDR) Klebsiella pneumoniae strains represent a growing threat. In particular, Romania has seen rapidly increasing rates of MDR Klebsiella pneumoniae isolates in recent years. The PubMed database was searched with the terms 'Klebsiella pneumoniae', 'multiple drug resistant', 'enterobacteria', 'infection', 'sepsis or septicaemia or blood stream infection', 'surveillance', 'diagnose', 'burn', 'intensive care unit' and 'Romania or Europe'. In addition, the case of a burn patient who suffered from sepsis caused by MDR Klebsiella pneumoniae and who was treated at our burn intensive care unit (ICU) was reviewed. The 23-year-old male was initially treated in Romania, but after 48 hours he was transferred to our burn ICU. Initially, the treatment course was appropriate and sufficient wound healing was achieved by day 27. However, the patient's condition deteriorated rapidly on day 28 and blood culture analysis showed growth of MDR Klebsiella pneumoniae. Despite intensive medical therapy, the patient died as a result of multiple organ failure (MOF) on day 44. Sepsis caused by MDR Klebsiella pneumoniae represents an enormous therapeutic challenge. Burn patients who are transferred from Southeast Europe would likely benefit from an intensified screening for MDR pathogens.
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Affiliation(s)
- C. Freystätter
- Alexandra Fochtmann-Frana
Clinical Division of Plastic and Reconstructive Surgery, Department of Surgery, Medical University of ViennaWaehringer Guertel 18-20, A-1090, ViennaAustria+43 1 40400 69800+43 1 40400 69820
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Hamzaoui Z, Ocampo-Sosa A, Fernandez Martinez M, Landolsi S, Ferjani S, Maamar E, Saidani M, Slim A, Martinez-Martinez L, Boutiba-Ben Boubaker I. Role of association of OmpK35 and OmpK36 alteration and bla ESBL and/or bla AmpC genes in conferring carbapenem resistance among non-carbapenemase-producing Klebsiella pneumoniae. Int J Antimicrob Agents 2018; 52:898-905. [PMID: 29621592 DOI: 10.1016/j.ijantimicag.2018.03.020] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/01/2018] [Accepted: 03/28/2018] [Indexed: 12/16/2022]
Abstract
In Klebsiella pneumoniae, loss of the two major outer membrane porins (OMPs) OmpK35 and OmpK36 confers resistance to carbapenems in strains producing extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC-type β-lactamases. This study investigated mechanisms responsible for carbapenem resistance in non-carbapenemase-producing K. pneumoniae (NCPK). All carbapenem-resistant Enterobacteriaceae (CRE) at Charles Nicolle Hospital (Tunis, Tunisia) were collected over a 6-year period (2010-2015). Among the 334 CRE strains collected, 44 (13.2%) were NCPK. MIC ranges for ertapenem, imipenem and meropenem were 1 to >32 mg/L, 0.125-8 mg/L and 0.125-32 mg/L, respectively. All strains showed a multidrug-resistant (MDR) phenotype and were negative for carbapenemase activity. None of the carbapenemase genes searched for were found. ESBL production was confirmed in all isolates except one [CTX-M-15 (n = 39) and SHV-5 (n = 4)]. Three isolates produce DHA-1 (associated with CTX-M-15 in two strains). Molecular fingerprints grouped the 44 NCPK isolates into seven clusters. In seven representative strains of these clusters, SDS-PAGE results showed that four isolates lacked the OmpK35 porin, one isolate lacked OmpK36 and two isolates lacked both OmpK35 and OmpK36. Sequencing of the corresponding porin genes showed amino acid insertions and deletions leading to early termination of translation, point mutations in the promoter region, or insertion sequences disrupting the gene coding sequence. Loss or deficiency of OMPs, coupled with ESBL and/or AmpC production, plays an important role in conferring carbapenem resistance in K. pneumoniae. Dissemination of these MDR bacteria in our hospital may create serious therapeutic problems in the future.
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Affiliation(s)
- Zaineb Hamzaoui
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia.
| | - Alain Ocampo-Sosa
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander 39008, Spain
| | - Marta Fernandez Martinez
- Service of Microbiology, University Hospital Marqués de Valdecilla-IDIVAL, Santander 39008, Spain
| | - Sarrah Landolsi
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia
| | - Elaa Maamar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia
| | - Mabrouka Saidani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Amine Slim
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
| | - Luis Martinez-Martinez
- Clinical Unit of Microbiology, University Hospital Reina Sofía, Córdoba, Spain; Department of Microbiology, University of Córdoba, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Ilhem Boutiba-Ben Boubaker
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09 Research Laboratory 'Antimicrobial resistance', 1007 Tunis, Tunisia; Charles Nicolle Hospital, Laboratory of Microbiology, 1006 Tunis, Tunisia
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Fröding I, Vondracek M, Giske CG. Rapid EUCAST disc diffusion testing of MDR Escherichia coli and Klebsiella pneumoniae: inhibition zones for extended-spectrum cephalosporins can be reliably read after 6 h of incubation. J Antimicrob Chemother 2017; 72:1094-1102. [PMID: 27999046 DOI: 10.1093/jac/dkw515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/02/2016] [Indexed: 01/20/2023] Open
Abstract
Objectives The need for rapid antibiotic susceptibility testing increases with escalating levels of antimicrobial resistance in Enterobacteriaceae. Our objective was to evaluate the accuracy of reading EUCAST disc diffusion, ROSCO ESBL and carbapenemase detection kits and the Mast Carbapenemase Activity Test (CAT-ID) disc, after 6 h of incubation. Methods We used a collection of 128 isolates of Escherichia coli and Klebsiella pneumoniae with a wide variety of resistance mechanisms. Inhibition zones read from digital photo images with the BD Kiestra™ Total Lab Automation System after 6 h of incubation were compared with standard reading, after 18 h, of the same Mueller-Hinton agar plates. Results For WT isolates, zones were generally smaller at 6 h than at 18 h. Cefotaxime had excellent categorical agreement of 99%, despite the high number of challenge isolates. However, for some other antimicrobials, hetero-resistant subpopulations were commonly invisible at 6 h, which resulted in an unacceptable number of errors when using standard EUCAST breakpoints. Accurate ESBL detection was possible at 6 h for isolates lacking other β-lactamases. Carbapenemase detection was not reliable after 6 h. Conclusions Inhibition zone reading at 6 h is an accurate method for susceptibility testing of extended-spectrum cephalosporins for Enterobacteriaceae. For other antimicrobials, 6 h reading can be used for preliminary reports of clearly resistant or susceptible isolates, preferably with application of adjusted breakpoints including an area of uncertainty between susceptible and resistant values.
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Affiliation(s)
- Inga Fröding
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Vondracek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Aguirre-Quiñonero A, Martínez-Martínez L. Non-molecular detection of carbapenemases in Enterobacteriaceae clinical isolates. J Infect Chemother 2017; 23:1-11. [DOI: 10.1016/j.jiac.2016.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 01/11/2023]
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Ribeiro PCS, Monteiro AS, Marques SG, Monteiro SG, Monteiro-Neto V, Coqueiro MMM, Marques ACG, de Jesus Gomes Turri R, Santos SG, Bomfim MRQ. Phenotypic and molecular detection of the bla KPC gene in clinical isolates from inpatients at hospitals in São Luis, MA, Brazil. BMC Infect Dis 2016; 16:737. [PMID: 27927163 PMCID: PMC5142414 DOI: 10.1186/s12879-016-2072-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/28/2016] [Indexed: 11/10/2022] Open
Abstract
Background Bacteria that produce Klebsiella pneumoniae carbapenemases (KPCs) are resistant to broad-spectrum β-lactam antibiotics. The objective of this study was to phenotypically and genotypically characterize the antibiotic susceptibility to carbapenems of 297 isolates recovered from clinical samples obtained from inpatients at 16 hospitals in São Luis (Maranhão, Brazil). Methods The study was conducted using phenotypic tests and molecular methods, including polymerase chain reaction (PCR), sequencing and enterobacterial repetitive intergenic consensus (ERIC)-PCR. The nonparametric chi-square test of independence was used to evaluate the associations between the bacterial blaKPC gene and the modified Hodge test, and the chi-square adherence test was used to assess the frequency of carbapenemases and their association with the blaKPC gene. Results The most frequently isolated species were Acinetobacter baumannii (n = 128; 43.0%), K. pneumoniae (n = 75; 25.2%), and Pseudomonas aeruginosa (n = 42; 14.1%). Susceptibility assays showed that polymixin B was active against 89.3% of the bacterial isolates. The Acinetobacter spp. and K. pneumoniae strains were susceptible to amikacin and tigecycline, and Pseudomonas spp. were sensitive to gentamicin and amikacin. Among the 297 isolates, 100 (33.7%) were positive for the blaKPC gene, including non-fermentative bacteria (A. baumannii) and Enterobacteriaceae species. Among the isolates positive for the blaKPC gene, K. pneumoniae isolates had the highest positivity rate of 60.0%. The blaKPC gene variants detected included KPC-2, which was found in all isolates belonging to species of the Enterobacteriaceae family. KPC-2 and KPC-3 were observed in A. baumannii isolates. Importantly, the blaKPC gene was also detected in three Raoultella isolates and one isolate of the Pantoea genus. ERIC-PCR patterns showed a high level of genetic diversity among the bacterial isolates; it was capable of distinguishing 34 clones among 100 strains that were positive for blaKPC and were circulating in 11 of the surveyed hospitals. Conclusions The high frequency of the blaKPC gene and the high degree of clonal diversity among microorganisms isolated from patients from different hospitals in São Luis suggest the need to improve the quality of health care to reduce the incidence of infections and the emergence of carbapenem resistance in these bacteria as well as other Gram-negative pathogens.
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Affiliation(s)
- Patricia Cristina Saldanha Ribeiro
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil
| | - Andrea Souza Monteiro
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil
| | - Sirlei Garcia Marques
- Hospital Universitário da Universidade Federal do Maranhão, Rua Barão de Itapari, 227, Centro, São Luís, Maranhão, Brazil
| | - Sílvio Gomes Monteiro
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil
| | - Valério Monteiro-Neto
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil
| | - Martina Márcia Melo Coqueiro
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil
| | - Ana Cláudia Garcia Marques
- Programa de Pós-Graduação em Saúde do Adulto e da Criança-UFMA, Universidade Federal do Maranhão, Av. dos Portugueses, 1966 - Bacanga, São Luis, Maranhão, Brazil
| | - Rosimary de Jesus Gomes Turri
- Departamento de Farmácia, Universidade Federal do Maranhão, Av. dos Portugueses, 1966 - Bacanga, São Luis, Maranhão, Brazil
| | - Simone Gonçalves Santos
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, Brazil
| | - Maria Rosa Quaresma Bomfim
- Programa de Pós-Graduação em Biologia Parasitária, Universidade CEUMA, Rua Josué Montello, No. 1, Renascença II, São Luís, Maranhão, CEP 65075-120, Brazil.
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Frasson I, Bettanello S, De Canale E, Richter SN, Palù G. Serotype epidemiology and multidrug resistance patterns of Salmonella enterica infecting humans in Italy. Gut Pathog 2016; 8:26. [PMID: 27252785 PMCID: PMC4888612 DOI: 10.1186/s13099-016-0110-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/19/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Salmonella enterica is the zoonotic agent most frequently responsible for foodborne infections in humans worldwide. In this work the presence of S. enterica was investigated in 734 unique enteropathogenic isolates collected from human patients between 2011 and 2012. RESULTS All Salmonella spp. isolates were subjected to serotyping and antimicrobial susceptibility testing. Isolates displaying phenotypes and antimicrobial susceptibility profiles different from the reference strains were genotipically characterized. Several plasmid-embedded resistance determinants were identified and characterized. Non-typhoidal serotypes were most frequently diagnosed; monophasic Salmonella typhimurium 1,4 [5],12:i- and S. typhimurium represented the most prevalent serovars. Five isolates displayed phenotypes with extremely reduced susceptibility to antimicrobials: we detected multidrug resistance elements belonging to Ambler class A and class C in two non-typhoidal S. enterica serovars, i.e. Rissen and monophasic S. typhimurium 1,4 [5],12:i-, and in one typhoidal serovar, i.e., Paratyphi B. These resistance determinants have been so far almost exclusively associated with non-Salmonella members of the Enterobacteriaceae family. Alarmingly, two colistin resistant Salmonella enteritidis were also found. CONCLUSIONS This work draws the attention to the still low, but rising, percentage of multidrug resistant Salmonella isolates infecting humans in Italy. Our results suggest that prompt monitoring of Salmonella serovar dissemination and resistance to antimicrobials is highly required.
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Affiliation(s)
- Ilaria Frasson
- />Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
| | - Sabrina Bettanello
- />Microbiology and Virology Unit, Padua Teaching Hospital, via Giustiniani 2, 35121 Padua, Italy
| | - Ettore De Canale
- />Microbiology and Virology Unit, Padua Teaching Hospital, via Giustiniani 2, 35121 Padua, Italy
| | - Sara N. Richter
- />Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
- />Microbiology and Virology Unit, Padua Teaching Hospital, via Giustiniani 2, 35121 Padua, Italy
| | - Giorgio Palù
- />Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy
- />Microbiology and Virology Unit, Padua Teaching Hospital, via Giustiniani 2, 35121 Padua, Italy
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Bajaj P, Singh NS, Virdi JS. Escherichia coli β-Lactamases: What Really Matters. Front Microbiol 2016; 7:417. [PMID: 27065978 PMCID: PMC4811930 DOI: 10.3389/fmicb.2016.00417] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/14/2016] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.
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Affiliation(s)
- Priyanka Bajaj
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
| | - Nambram S Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
| | - Jugsharan S Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
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Iman FEG, Marwa AM, Doaa AY. Phenotypic and genotypic methods for detection of metallo beta lactamases among carbapenem resistant Enterobacteriaceae clinical isolates in Alexandria Main University Hospital. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajmr2015.7821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Takayama Y, Adachi Y, Nihonyanagi S, Okamoto R. Modified Hodge test using Mueller–Hinton agar supplemented with cloxacillin improves screening for carbapenemase-producing clinical isolates of Enterobacteriaceae. J Med Microbiol 2015; 64:774-777. [DOI: 10.1099/jmm.0.000068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yoko Takayama
- Department of Infection Control and Prevention, Kitasato University Hospital, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0375, Japan
- Department of Infection Control and Infectious Diseases, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Yuzuru Adachi
- Laboratory Department, Kitasato University Hospital, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0375, Japan
| | - Shin Nihonyanagi
- Laboratory Department, Kitasato University Hospital, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0375, Japan
| | - Ryoichi Okamoto
- Department of Microbiology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
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Stoesser N, Sheppard AE, Shakya M, Sthapit B, Thorson S, Giess A, Kelly D, Pollard AJ, Peto TEA, Walker AS, Crook DW. Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing. J Antimicrob Chemother 2015; 70:1008-15. [PMID: 25558071 PMCID: PMC4356206 DOI: 10.1093/jac/dku521] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES There are limited data on Enterobacter cloacae outbreaks and fewer describing these in association with NDM-1. With whole-genome sequencing, we tested the hypothesis that a cluster of 16 E. cloacae bacteraemia cases in a Nepali neonatal unit represented a single clonal outbreak, using a wider set of epidemiologically unrelated clinical E. cloacae isolates for comparison. METHODS Forty-three isolates were analysed, including 23 E. cloacae and 3 Citrobacter sp. isolates obtained from blood cultures from 16 neonates over a 3 month period. These were compared with two contemporaneous community-associated drug-resistant isolates from adults, a unit soap dispenser isolate and a set of historical invasive isolates (n=14) from the same geographical locality. RESULTS There were two clear neonatal outbreaks and one isolated case in the unit. One outbreak was associated with an NDM-1 plasmid also identified in a historical community-associated strain. The smaller, second outbreak was likely associated with a contaminated soap dispenser. The two community-acquired adult cases and three sets of historical hospital-associated neonatal isolates represented four additional genetic clusters. CONCLUSIONS E. cloacae infections in this context represent several different transmission networks, operating at the community/hospital and host strain/plasmid levels. Wide sampling frames and high-resolution typing methods are needed to describe the complex molecular epidemiology of E. cloacae outbreaks, which is not appropriately reflected by routine susceptibility phenotypes. Soap dispensers may represent a reservoir for E. cloacae and bacterial strains and plasmids may persist in hospitals and in the community for long periods, sporadically being involved in outbreaks of disease.
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Affiliation(s)
- N Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - A E Sheppard
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - M Shakya
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - B Sthapit
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - S Thorson
- Department of Paediatrics, Patan Hospital, Kathmandu, Nepal
| | - A Giess
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - D Kelly
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - A J Pollard
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - T E A Peto
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - A S Walker
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
| | - D W Crook
- NIHR Biomedical Research Centre, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, UK
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