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Boussina A, Langouche L, Obirieze AC, Sinha M, Mack H, Leineweber W, Aralar A, Pride DT, Coleman TP, Fraley SI. Machine learning based DNA melt curve profiling enables automated novel genotype detection. BMC Bioinformatics 2024; 25:185. [PMID: 38730317 PMCID: PMC11088152 DOI: 10.1186/s12859-024-05747-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.
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Affiliation(s)
- Aaron Boussina
- Division of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lennart Langouche
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Augustine C Obirieze
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mridu Sinha
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hannah Mack
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - William Leineweber
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - April Aralar
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Todd P Coleman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Stephanie I Fraley
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
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2
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Xu Z, Li B, Jiang Y, Huang J, Su L, Wu W, Pang Q, Li Z, Zhang J, Li X, Wang J, Cen F, Peng L, Liang J, Wang F, Liu C, Shen C, Liu Y, Yang Y. Development of a quadruple qRT-PCR assay for simultaneous identification of hypervirulent and carbapenem-resistant Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0071923. [PMID: 38059628 PMCID: PMC10783029 DOI: 10.1128/spectrum.00719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Globally, the increasing number of hypervirulent Klebsiella pneumoniae (hvKp) and carbapenem-resistant Kp (CR-Kp) infections poses a huge public health challenge with high morbidity and mortality. Worrisomely, due to the mobility of elements carrying virulence and drug-resistance genes, the increasing prevalence of CR-hvKp has also been found with an overwhelming mortality rate in recent years. However, the current detection methods for hvKp and CR-Kp have many disadvantages, such as long turnaround time, complex operation, low sensitivity, and specificity. Herein, a more sensitive, rapid, single-reaction, and multiplex quantitative real-time PCR was developed and validated to differentiate the circulating lineages of Kp with excellent performance in sensitivity and specificity, providing a useful tool for the differential diagnosis and the surveillance of the circulating Kp.
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Affiliation(s)
- Zhixiang Xu
- Savid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Baisheng Li
- Guangdong Provincial Key Laboratory of Pathogen Detection for Emerging Infectious Disease Response, Guangdong Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yushan Jiang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia Huang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lebin Su
- Zhaoqing Center for Disease Control and Prevention, Zhaoqing, Guangdong, China
| | - Weibo Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Qilin Pang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhuolin Li
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiaqi Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiaohe Li
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jun Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fulan Cen
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ling Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jinhu Liang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fuxiang Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Chang Liu
- Zhaoqing Center for Disease Control and Prevention, Zhaoqing, Guangdong, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingxia Liu
- Savid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for infectious disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong, China
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3
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Edwards T, Williams C, Teethaisong Y, Sealey J, Sasaki S, Hobbs G, Cuevas LE, Evans K, Adams ER. A highly multiplexed melt-curve assay for detecting the most prevalent carbapenemase, ESBL, and AmpC genes. Diagn Microbiol Infect Dis 2020; 97:115076. [PMID: 32521424 DOI: 10.1016/j.diagmicrobio.2020.115076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 01/12/2023]
Abstract
Resistance to third-generation cephalosporins and carbapenems in Gram-negative bacteria is chiefly mediated by beta-lactamases including extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase enzymes. Routine phenotypic detection methods do not provide timely results, and there is a lack of comprehensive molecular panels covering all important markers. An ESBL/carbapenemase high-resolution melt analysis (HRM) assay (SHV, TEM, CTX-M ESBL families, and NDM, IMP, KPC, VIM and OXA-48-like carbapenemases) and an AmpC HRM assay (16S rDNA control, FOX, MOX, ACC, EBC, CIT, and DHA) were designed and evaluated on 111 Gram-negative isolates with mixed resistance patterns. The sensitivity for carbapenemase, ESBL, and AmpC genes was 96.7% (95% confidence interval [CI]: 82.8-99.9%), 93.6% (95% CI: 85.7-97.9%), and 93.8% (95% CI: 82.8-98.7%), respectively, with a specificity of 100% (95% CI: 95.6-100%), 93.9% (95% CI: 79.8-99.3%), and 93.7% (95% CI: 84.5-98.2%). The HRM assays enable the simultaneous detection of the 14 most important ESBL, carbapenemase, and AmpC genes and could be used as a molecular surveillance tool or to hasten detection of antimicrobial resistance for treatment management.
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Affiliation(s)
- T Edwards
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - C Williams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Y Teethaisong
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - J Sealey
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - S Sasaki
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - G Hobbs
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - L E Cuevas
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - K Evans
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - E R Adams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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4
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Dehbashi S, Tahmasebi H, Alikhani MY, Keramat F, Arabestani MR. Distribution of Class B and Class A β-Lactamases in Clinical Strains of Pseudomonas aeruginosa: Comparison of Phenotypic Methods and High-Resolution Melting Analysis (HRMA) Assay. Infect Drug Resist 2020; 13:2037-2052. [PMID: 32636657 PMCID: PMC7335274 DOI: 10.2147/idr.s255292] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background There are various phenotypic methods for identifying class B and class A β-lactamase enzymes in Pseudomonas aeruginosa. The purpose of this study was to compare the sensitivity and specificity of different phenotypic methods with HRMA assay to detect β-lactamase-producing P. aeruginosa strains. Methods Eighty-eight of P. aeruginosa isolates were collected from different specimens. Conventional double-disk test (DDT) and EDTA-imipenem microbiological (EIM) were performed to detect ESBL and MBL-producing strains, respectively. Meanwhile, the Modified Hodge test and Carba-NP test were performed on all carbapenem-resistant strains. HRMA method and sensitivity and specificity of primers were determined based on the melt curve temperature range. In all comparisons, PCR was considered as the gold standard. Results Of the 402 isolates collected from different clinical specimens, 88 isolates of P. aeruginosa were identified. However, 43 strains were (48.88%) ESBL-producing, and 7 strains (7.95%) were MBL-producing. Also, using the Modified Hodge test and Carba-NP method, 11 (12.5%) and 19 (21.59%) strains were carbapenemase-producing, respectively. The results of the HRMA test revealed that genes coding for bla SHV, bla TEM, bla KPC, bla IMP, bla VIM, and bla GES were detected in 44.31%, 22.72%, 13.63%, 14.7%, 5.6%, and 2.27% of P. aeruginosa isolates. Nonetheless, for bla KPC and bla GES genes, sensitivity and specificity of the Carba-NP test were 90.47%, 94.87%, and 83.36%, 94.80%, respectively. However, sensitivity and specificity of MHT was 91.66%, 98.70%, and 77.77%, 96.42%, respectively. For bla SHV and bla TEM genes, sensitivity and specificity of DDT were 95.55%, 95.55%, and 86%, 83.50%, respectively. However, sensitivity and specificity of EMI were 77.77%, 97.59%, and 91.66%, 97.43% for bla VIM and bla IMP, respectively. Conclusion The HRMA is a powerful, accurate, closed-tube, rapid method for detecting β-lactamase genes in P. aeruginosa. The high sensitivity and specificity of this method, along with phenotypic tests, play a useful role in increasing the predictive value of clinical reports.
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Affiliation(s)
- Sanaz Dehbashi
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamed Tahmasebi
- Microbiology Department, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Yousef Alikhani
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fariba Keramat
- Brucellosis Research Center, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Reza Arabestani
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Nutrition Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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5
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One-Step Differential Detection of OXA-48-Like Variants Using High-Resolution Melting (HRM) Analysis. Antibiotics (Basel) 2020; 9:antibiotics9050256. [PMID: 32429143 PMCID: PMC7277688 DOI: 10.3390/antibiotics9050256] [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] [Received: 01/17/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 11/18/2022] Open
Abstract
OXA-48-like carbapenemase gene remains a hidden threat, as different OXA-48 variants have varying presentations of susceptibility to antibiotics that might affect the treatment decisions. Rapid detection and differentiation of OXA-48-like carbapenemase genes are critical for targeted treatment and infection control. In this study, we aimed to develop high-resolution melting (HRM) analysis for the differentiation of OXA-48 variants. HRM analysis is a post-polymerase chain reaction (post-PCR) method for identification of small variations in nucleic acid sequences based on the PCR dissociation curve. A total of 82 bacterial strains, which consisted of Enterobacteriaceae and non-Enterobacteriaceae, were collected from a tertiary teaching hospital. The sensitivity and specificity of the assay were determined, and the developed assay was evaluated using the collected isolates against conventional-sequencing method. Overall, the developed assay was able to detect isolates that harboured OXA-48 and OXA232/OXA-181 by showing two distinct peaks at 81.1 ± 0.2 °C and 82.1 ± 0.2 °C, respectively. The detection limit of the assay was 1.6 x 10−6 ng/µL for OXA-48 and 1.8 × 10−7 ng/µL for OXA-232/OXA-181. This assay showed 100% specificity when evaluated on a panel of 37 isolates comprised of different species of bacteria and yeasts. When the assay with isolates collected in the year 2016 was first evaluated, the assay showed comparable results with conventional PCR-sequencing method where 34 OXA-48 and OXA-232/OXA-181 were detected. By using HRM analysis, the presence of OXA-48-like variants could be easily identified within 3 h from the pure culture.
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6
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Sun H, Xiao G, Zhang J, Pan Z, Chen Y, Xiong F. Rapid simultaneous detection of bla oxa-23, Ade-B, int-1, and ISCR-1 in multidrug-resistant Acinetobacter baumannii using single-tube multiplex PCR and high resolution melting assay. Infect Drug Resist 2019; 12:1573-1581. [PMID: 31289445 PMCID: PMC6565808 DOI: 10.2147/idr.s207225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022] Open
Abstract
Objective: The aim of this study was to develop a multiplex PCR system for the rapid and simultaneous detection of blaoxa-23, Ade-B, int-1, and ISCR-1 genes in multidrug-resistant Acinetobacter baumannii (MDRAB) using high resolution melting (HRM) assay. Methods: Four pairs of primers were designed, and PCR amplification products were sequenced and compared with NCBI GeneBank sequences to ensure primer specificity. Multiplex PCR was performed using a dedicated HRM reagent, and melting curves and temperatures were able to distinguish the four genes. This method was subsequently used to detect these genes in 79 MDRAB isolates from the Third Affiliated Hospital of Southern Medical University in southern China. Results: Using the HRM assay, 73 out of 79 isolates were found to carry both blaoxa-23 and Ade-B, one isolate carried int-1, two isolates carried both int-1 and ISCR-1, and three isolates carried Ade-B, int-1, and ISCR-1. No isolates carried all four genes. Conclusion: Compared with traditional resistance gene detection methods–PCR and agarose gel electrophoresis-based resistance gene detection methods–the multiplex PCR and HRM assay method was simple, rapid, highly efficient, and cost-effective. Our results showed that blaoxa-23 and Ade-B were the main resistance genotypes in MDRAB.
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Affiliation(s)
- Hengbiao Sun
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, People's Republic of China
| | - Gang Xiao
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, People's Republic of China
| | - Jing Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, People's Republic of China
| | - Zuhan Pan
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, People's Republic of China
| | - Youming Chen
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, People's Republic of China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
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Fakhri O, Hartley CA, Devlin JM, Browning GF, Noormohammadi AH, Lee SW. Development and application of high-resolution melting analysis for the classification of infectious laryngotracheitis virus strains and detection of recombinant progeny. Arch Virol 2018; 164:427-438. [PMID: 30421085 PMCID: PMC6373279 DOI: 10.1007/s00705-018-4086-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
Live attenuated vaccines against infectious laryngotracheitis virus (ILTV) are widely used in the poultry industry to control disease and help prevent economic losses. Molecular epidemiological studies of currently circulating strains of ILTV within poultry flocks in Australia have demonstrated the presence of highly virulent viruses generated by genomic recombination events between vaccine strains. In this study, high-resolution melting (HRM) analysis was used to develop a tool to classify ILTV isolates and to investigate ILTV recombination. The assay was applied to plaque-purified progeny viruses generated after co-infection of chicken embryo kidney (CEK) monolayers with the A20 and Serva ILT vaccine strains and also to viruses isolated from field samples. The results showed that the HRM analysis is a suitable tool for the classification of ILTV isolates and can be used to detect recombination between ILTV vaccine strains in vitro. This method can be used to classify a broad range of ILTV strains to facilitate the classification and genotyping of ILTV and help to further understand recombination in these viruses.
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Affiliation(s)
- Omid Fakhri
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, Australia
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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8
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Smiljanic M, Kaase M, Ahmad-Nejad P, Ghebremedhin B. Comparison of in-house and commercial real time-PCR based carbapenemase gene detection methods in Enterobacteriaceae and non-fermenting gram-negative bacterial isolates. Ann Clin Microbiol Antimicrob 2017; 16:48. [PMID: 28693493 PMCID: PMC5504714 DOI: 10.1186/s12941-017-0223-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Carbapenemase-producing gram-negative bacteria are increasing globally and have been associated with outbreaks in hospital settings. Thus, the accurate detection of these bacteria in infections is mandatory for administering the adequate therapy and infection control measures. This study aimed to establish and evaluate a multiplex real-time PCR assay for the simultaneous detection of carbapenemase gene variants in gram-negative rods and to compare the performance with a commercial RT-PCR assay (Check-Direct CPE). METHODS 116 carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii isolates were genotyped for carbapenemase genes by PCR and sequencing. The defined isolates were used for the validation of the in-house RT-PCR by use of designed primer pairs and probes. RESULTS Among the carbapenem-resistant isolates the genes bla KPC, bla VIM, bla NDM or bla OXA were detected. Both RT-PCR assays detected all bla KPC, bla VIM and bla NDM in the isolates. The in-house RT-PCR detected 53 of 67 (79.0%) whereas the commercial assay detected only 29 (43.3%) of the OXA genes. The in-house sufficiently distinguished the most prevalent OXA types (23-like and 48-like) in the melting curve analysis and direct detection of the genes from positive blood culture vials. CONCLUSION The Check-Direct CPE and the in-house RT-PCR assay detected the carbapenem resistance from solid culture isolates. Moreover, the in-house assay enabled the identification of carbapenemase genes directly from positive blood-culture vials. However, we observed insufficient detection of various OXA genes in both assays. Nevertheless, the in-house RT-PCR detected the majority of the OXA type genes in Enterobacteriaceae and A. baumannii.
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Affiliation(s)
- M Smiljanic
- Center for Clinical and Translational Research, Institute for Medical Laboratory Diagnostics, HELIOS University Clinic Wuppertal; Witten/Herdecke University, Heusnerstr. 40, 42283, Wuppertal, Germany
| | - M Kaase
- Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany.,Department of Infection Control, University Medical Center Göttingen, Göttingen, Germany
| | - P Ahmad-Nejad
- Center for Clinical and Translational Research, Institute for Medical Laboratory Diagnostics, HELIOS University Clinic Wuppertal; Witten/Herdecke University, Heusnerstr. 40, 42283, Wuppertal, Germany
| | - B Ghebremedhin
- Center for Clinical and Translational Research, Institute for Medical Laboratory Diagnostics, HELIOS University Clinic Wuppertal; Witten/Herdecke University, Heusnerstr. 40, 42283, Wuppertal, Germany.
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9
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IMP-27, a Unique Metallo-β-Lactamase Identified in Geographically Distinct Isolates of Proteus mirabilis. Antimicrob Agents Chemother 2016; 60:6418-21. [PMID: 27503648 PMCID: PMC5038328 DOI: 10.1128/aac.02945-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/21/2016] [Indexed: 12/23/2022] Open
Abstract
A novel metallo-β-lactamase gene, blaIMP-27, was identified in unrelated Proteus mirabilis isolates from two geographically distinct locations in the United States. Both isolates harbor blaIMP-27 as part of the first gene cassette in a class 2 integron. Antimicrobial susceptibility testing indicated susceptibility to aztreonam, piperacillin-tazobactam, and ceftazidime but resistance to ertapenem. However, hydrolysis assays indicated that ceftazidime was a substrate for IMP-27.
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10
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Azimi L, Talebi M, Pourshafie MR, Owlia P, Rastegar Lari A. Characterization of Carbapenemases in Extensively Drug Resistance Acinetobacter baumannii in a Burn Care Center in Iran. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2015; 4:46-53. [PMID: 25815282 PMCID: PMC4359705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/22/2014] [Accepted: 01/03/2015] [Indexed: 11/11/2022]
Abstract
The emergence of multidrug resistance (MDR) and extensively drug resistance (XDR) in Acinetobacter baumannii has made an important challenge in the treatment of infections caused by this organism. The ability of carbapenemase production is one of the main mechanisms for the emergence of MDR and/or XDR in A. baumannii. The aim of this study was to detect carbapenemase producer A. baumannii. In this study, 65 imipenem resistant A. baumannii were collected from burned patients. Biochemical identification, antibiotic susceptibility test and multiplex polymerase chain reactions for the detection of carbapenemases genes were performed. The results showed that all strains carried bla OXA-51. 83%, 12.5% and 9.23% strains harbored bla OXA-23, bla VIM and bla KPC genes, respectively. None of the isolates carried bla IMP, bla OXA-48, blaNDM-1 and bla SPM-1 genes. The results of this study indicate the emergence of Klebsiella pneumoniae Carbapenemase (KPC) in A. baumannii causing nosocomial infections in burned patients which can be important for hospital infection prevention systems in Iran.
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Affiliation(s)
- Leila Azimi
- Antimicrobial Resistance Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran.
| | - Malihe Talebi
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran.
| | | | - Parviz Owlia
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran.
| | - Abdolaziz Rastegar Lari
- Antimicrobial Resistance Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran.,Corresponding author: Deparment of Microbiology, Iran University of Medical Sciences, Tehran, Iran. ,
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11
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Athamanolap P, Parekh V, Fraley SI, Agarwal V, Shin DJ, Jacobs MA, Wang TH, Yang S. Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants. PLoS One 2014; 9:e109094. [PMID: 25275518 PMCID: PMC4183555 DOI: 10.1371/journal.pone.0109094] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 09/02/2014] [Indexed: 01/04/2023] Open
Abstract
High resolution melt (HRM) is gaining considerable popularity as a simple and robust method for genotyping sequence variants. However, accurate genotyping of an unknown sample for which a large number of possible variants may exist will require an automated HRM curve identification method capable of comparing unknowns against a large cohort of known sequence variants. Herein, we describe a new method for automated HRM curve classification based on machine learning methods and learned tolerance for reaction condition deviations. We tested this method in silico through multiple cross-validations using curves generated from 9 different simulated experimental conditions to classify 92 known serotypes of Streptococcus pneumoniae and demonstrated over 99% accuracy with 8 training curves per serotype. In vitro verification of the algorithm was tested using sequence variants of a cancer-related gene and demonstrated 100% accuracy with 3 training curves per sequence variant. The machine learning algorithm enabled reliable, scalable, and automated HRM genotyping analysis with broad potential clinical and epidemiological applications.
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Affiliation(s)
- Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Vishwa Parekh
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Medicine, Baltimore, Maryland, United States of America
| | - Stephanie I. Fraley
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, Maryland, United States of America
| | - Vatsal Agarwal
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Dong J. Shin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Michael A. Jacobs
- The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Medicine, Baltimore, Maryland, United States of America
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, United States of America
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (SY); (THW)
| | - Samuel Yang
- Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, Maryland, United States of America
- * E-mail: (SY); (THW)
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12
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Whole genome mapping of the first reported case of KPC-2-positive Klebsiella pneumoniae ST258 in Nebraska. Diagn Microbiol Infect Dis 2014; 79:384-6. [PMID: 24813687 DOI: 10.1016/j.diagmicrobio.2014.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 03/31/2014] [Indexed: 11/22/2022]
Abstract
Three ertapenem-resistant Klebsiella pneumoniae carrying bla(KPC-2) were isolated from a single patient in Nebraska over a span of 5 months. A comparative analysis of the genetic relatedness of these isolates was investigated using pulsed-field gel electrophoresis, multilocus sequence typing, and whole genome mapping.
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13
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Multiplex high-resolution melting analysis as a diagnostic tool for detection of plasmid-mediated AmpC β-lactamase genes. J Clin Microbiol 2014; 52:1262-5. [PMID: 24478414 DOI: 10.1128/jcm.00214-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-resolution melting (HRM) analysis can be a diagnostic tool to evaluate the presence of resistance genes with the added bonus of discriminating sequence modifications. A real-time, multiplex PCR assay using HRM was designed for the detection of plasmid-mediated ampC genes. The specificity and sensitivity of this assay were 96% and 100%, respectively.
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14
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Fleming E, Heil EL, Hynicka LM. Treatment Strategy for a Multidrug-Resistant Klebsiella UTI. Ann Pharmacother 2013; 48:123-7. [DOI: 10.1177/1060028013509974] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objective: To describe the management strategy for a multidrug-resistant (MDR) Klebsiella urinary tract infection (UTI). Case Summary: A 69-year-old Caucasian woman with a past medical history of recurrent UTIs and a right-lung transplant presented with fever to 101.4°F, chills, malaise, and cloudy, foul-smelling urine for approximately 1 week. She was found to have a MDR Klebsiella UTI that was sensitive to tigecycline and cefepime. To further evaluate the degree of resistance Etest minimum inhibitory concentrations were requested for cefepime, amikacin, meropenem, and ertapenem. The patient received a 14-day course of amikacin, which resulted in resolution of her symptoms. One month later, the patient’s UTI symptoms returned. The urine culture again grew MDR Klebsiella, sensitive only to tigecycline. Fosfomycin was initiated and resulted in limited resolution of her symptoms. Colistin was started, however, therapy was discontinued on day 5 secondary to the development of acute kidney injury. Despite the short course of therapy, the patient’s symptoms resolved. Discussion: The case presented lends itself well to numerous discussion items that are important to consider when determining optimal treatment for MDR Gram-negative bacilli (GNBs). Susceptibility testing is an important tool for optimizing antibiotic therapy, however, automated systems may overestimate the susceptibility profile for a MDR GNB. Treatment strategies evaluated to treat MDR GNB, include combination therapy with a carbepenem and synergy using polymyxin. Conclusion: We have described the management strategy for a MDR Klebsiella UTI, the consequences of the initial management strategy, and potential strategies to manage these types of infections in future patients.
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Affiliation(s)
- Erin Fleming
- University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Emily L. Heil
- University of Maryland Medical Center, Baltimore, MD, USA
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15
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Frasson I, Biasolo MA, Bartolini A, Cavallaro A, Richter SN, Palù G. Rapid detection of blaVIM-1–37 and blaKPC1/2–12 alleles from clinical samples by multiplex PCR-based assays. Int J Antimicrob Agents 2013; 42:68-71. [DOI: 10.1016/j.ijantimicag.2013.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 10/26/2022]
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