1
|
Elsayed SW, Elghaish RA, Badr E, Mouftah SF, Saif NA, Naga IS, Shata AH, Pascoe B, Sheppard SK, Elhadidy M. Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings. Ann Clin Microbiol Antimicrob 2023; 22:109. [PMID: 38098126 PMCID: PMC10722846 DOI: 10.1186/s12941-023-00659-y] [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: 06/22/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a rapidly evolving pathogen that is frequently associated with outbreaks and sustained epidemics. This study investigated the population structure, resistome, virulome, and the correlation between antimicrobial resistance determinants with phenotypic resistance profiles of 36 representative hospital-acquired MRSA isolates recovered from hospital settings in Egypt. RESULTS The community-acquired MRSA lineage, clonal complex 1 (CC1) was the most frequently detected clone, followed by three other globally disseminated clones, CC121, CC8, and CC22. Most isolates carried SCCmec type V and more than half of isolates demonstrated multi-drug resistant phenotypes. Resistance to linezolid, a last resort antibiotic for treating multidrug resistant MRSA, was observed in 11.11% of the isolates belonging to different genetic backgrounds. Virulome analysis indicated that most isolates harboured a large pool of virulence factors and toxins. Genes encoding aureolysin, gamma hemolysins, and serine proteases were the most frequently detected virulence encoding genes. CC1 was observed to have a high pool of AMR resistance determinants including cfr, qacA, and qacB genes, which are involved in linezolid and quaternary ammonium compounds resistance, as well as high content of virulence-related genes, including both of the PVL toxin genes. Molecular clock analysis revealed that CC1 had the greatest frequency of recombination (compared to mutation) among the four major clones, supporting the role of horizontal gene transfer in modulating AMR and hypervirulence in this clone. CONCLUSIONS This pilot study provided evidence on the dissemination success of CA-MRSA clone CC1 among Egyptian hospitals. Co-detection of multiple AMR and virulence genes in this lineage pose a broad public health risk, with implications for successful treatment. The results of this study, together with other surveillance studies in Egypt, should be used to develop strategies for controlling MRSA infections in Egyptian health-care settings.
Collapse
Affiliation(s)
- Salma W Elsayed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Reem A Elghaish
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Eman Badr
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
| | - Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nehal A Saif
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman S Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ahmed H Shata
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Ben Pascoe
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
| | - Mohamed Elhadidy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
| |
Collapse
|
2
|
Li J, Du Z, Wang P, Chen K, Lin S, Xu W, Zhu L. A turn-on signal biosensor for cadmium(II) based on DNAzyme and stem-loop qPCR. Anal Chim Acta 2023; 1279:341827. [PMID: 37827645 DOI: 10.1016/j.aca.2023.341827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
Cadmium is a heavy metal that is exceedingly hazardous to humans and can enter the body through tainted food or drink, causing severe harm. It is critical to develop a technology for detecting cadmium in food and water that is sensitive and accurate. One such approach, which employs nucleases, is uncommon. A cadmium(II) turn-on biosensor was successfully created in this work using repetitive cleavage of certain specific nucleases for signal conversion and sophisticated stem-loop qPCR (quantitative polymerase chain reaction) for quick signal amplification and output. The method has strong selectivity and sensitivity for precise quantification, with a detection limit of 6 nmol L-1, i.e. 0.948 g L-1, which is far lower than the 5.0 g L-1 set by the United States Environmental Protection Agency, and it also operates well in retail rice samples.
Collapse
Affiliation(s)
- Jiale Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Pengfei Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Keren Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Shenghao Lin
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| |
Collapse
|
3
|
El-Razik KAA, Arafa AA, Fouad EA, Soror AH, Abdalhamed AM, Elgioushy M. Phenotypic and genotypic characterization of erythromycin-resistant Staphylococcus aureus isolated from bovine subclinical mastitis in Egypt. Vet World 2023; 16:1562-1571. [PMID: 37621528 PMCID: PMC10446729 DOI: 10.14202/vetworld.2023.1562-1571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/14/2023] [Indexed: 08/26/2023] Open
Abstract
Background and Aim Subclinical mastitis (SCM) caused by erythromycin-resistant Staphylococcus aureus is a significant disease in lactating animals. Therefore, it is crucial to understand the genetic factors contributing to erythromycin resistance in S. aureus. This study aimed to estimate the prevalence of S. aureus in milk from subclinical mastitic cattle and buffaloes and tank milk samples as identified by probe-based real-time polymerase chain reaction (PCR) and the genotypic assessment of macrolide and erythromycin resistance profiles, as well as to analyze the phylogenetic relatedness of our local isolates of S. aureus. Materials and Methods In total, 285 milk samples were analyzed using the California mastitis test to detect SCM. Milk samples were cultured on different specific Staphylococcus media. The presence of S. aureus was confirmed by Gram staining, the catalase and coagulase tests, the detection of hemolytic activity, DNase agar testing, and biofilm activity in Congo red medium. The genotypic identification of S. aureus (nuc) was performed. The determinants of erythromycin (ermA, ermB, ermC, and ermT) and macrolide resistance (msrA) were screened in all isolates. DNA sequencing of our local isolates of S. aureus was used to analyze their phylogenetic relatedness. Moreover, histopathological examination of tissue specimens of mammary gland was performed. Results The S. aureus positivity rates were 36.4%, 48.8%, and 63.6% in cattle, buffalo, and bulk tank milk, respectively. Probe-based real-time PCR molecularly confirmed all 62 S. aureus isolates. Thirty-one isolates were subjected to PCR to create profiles of their genotypic erythromycin resistance. ermA, ermB, ermC, and ermT were present in 5 (8%), 26 (41.9%), 18 (29%), and 15 (24.1%) S. aureus isolates, respectively. Moreover, msrA was found in three (4.8%) strains. Eight PCR products were produced using standard PCR for DNA sequencing. Multiple sequence alignment, phylogenetic tree construction, and analysis of nuc in S. aureus revealed a high degree of homology (100%) with S. aureus strains isolated from milk in cases of bovine mastitis in India and Kenya. Histological analysis of udder tissues revealed extensive aggregation of mononuclear inflammatory cells in the interstitial connective tissue, primarily lymphocytes, and macrophages. Conclusion This study showed a high prevalence of erythromycin resistance in S. aureus isolates. This information is vital for controlling mastitis and the spread of resistance genes between bacterial strains and hosts. Moreover, the probe-based real-time PCR approach is helpful for the rapid screening of S. aureus isolates and the consequent efficient treatment and control of S. aureus mastitis.
Collapse
Affiliation(s)
| | - Amany A. Arafa
- Department of Microbiology and Immunology, National Research Centre, Dokki, Egypt
| | - Ehab A. Fouad
- Department of Zoonosis, National Research Centre, Dokki, Egypt
| | - Ashraf H. Soror
- Department of Animal Reproduction, National Research Centre, Dokki, Egypt
| | - Abeer M. Abdalhamed
- Department of Parasitology and Animal Diseases, National Research Centre, Dokki, Egypt
| | - Magdy Elgioushy
- Department of Animal Medicine, Faculty of Veterinary Medicine, Aswan University, Egypt
| |
Collapse
|
4
|
Wang G, Wu M, Chu LT, Chen TH. Portable microfluidic device with thermometer-like display for real-time visual quantitation of Cadmium(II) contamination in drinking water. Anal Chim Acta 2021; 1160:338444. [PMID: 33894969 DOI: 10.1016/j.aca.2021.338444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 12/20/2022]
Abstract
Cadmium (Cd2+) is a toxic metal ion widely existing in water, soil and food. Conventional water quality control heavily relies on expensive, bulky and sophisticated instrument such as spectrometry, which is time-consuming and incompatible with on-site, real-time detection. Here, a portable microfluidic device with thermometer-like visual readouts is developed for real-time quantitation of cadmium (II) contamination in drinking water. We use Cd2+-dependent DNAzyme (Cd16), which is cleaved when Cd2+ is present, creating a single strand DNA which triggers catalytic hairpin assembly (CHA) with two hairpins H1 and H2 as the building blocks. Plenty of H1H2 complex, the product after the Cd2+-mediated CHA, are generated, which can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-H1H2-PMPs" sandwich structure. To provide visual readout to quantitate the particle connection, the particle solution is loaded into a portable microfluidic chip. A magnetic separator first removes MMPs and the connected PMPs, while free PMPs can continue flowing until accumulating into a bar at the particle dam. Shown as a thermometer-like display, the accumulating length is inversely proportional to the concentration of Cd2+, enabling quantitative detection of Cd2+ by the naked eye. The proposed device exhibits a limit of detection of 11.3 nM of Cd2+, selectivity >200-fold against other metal ions, high tolerance to the interferents present in drinking water and high recovery rate in tap water. With high analytical performance without any sample preparation step, this portable device is highly promising in real-time monitoring in urban drinking water at sites.
Collapse
Affiliation(s)
- Gaobo Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Minghui Wu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Lok Ting Chu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Ting-Hsuan Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China.
| |
Collapse
|
5
|
Kumar S, Gallagher R, Bishop J, Kline E, Buser J, Lafleur L, Shah K, Lutz B, Yager P. Long-term dry storage of enzyme-based reagents for isothermal nucleic acid amplification in a porous matrix for use in point-of-care diagnostic devices. Analyst 2021; 145:6875-6886. [PMID: 32820749 DOI: 10.1039/d0an01098g] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleic acid amplification test (NAAT)-based point-of-care (POC) devices are rapidly growing for use in low-resource settings. However, key challenges are the ability to store the enzyme-based reagents in dry form in the device and the long-term stability of those reagents at elevated temperatures, especially where ambient temperatures could be as high as 45 °C. Here, we describe a set of excipients including a combination of trehalose, polyethylene glycol and dextran, and a method for using them that allows long-term dry storage of enzyme-based reagents for an isothermal strand displacement amplification (iSDA) reaction in a porous matrix. Various porous materials, including nitrocellulose, cellulose, and glass fiber, were tested. Co-dried reagents for iSDA always included those that amplified the ldh1 gene in Staphylococcus aureus (a polymerase and a nicking enzyme, 4 primers, dNTPs and a buffer). Reagents also either included a capture probe and a streptavidin-Au label required for lateral flow (LF) detection after amplification, or a fluorescent probe used for real-time detection. The reagents showed the best stability in a glass fiber matrix when stored in the presence of 10% trehalose and 2.5% dextran. The reagents were stable for over a year at ∼22 °C as determined by lateral flow detection and gel electrophoresis. The reagents also exhibited excellent stability after 360 h at 45 °C; the assay still detected as few as 10 copies of ldh1 gene target by lateral flow detection, and 50 copies with real-time fluorescence detection. These results demonstrate the potential for incorporation of amplification reagents in dry form in point-of-care devices for use in a wide range of settings.
Collapse
Affiliation(s)
- Sujatha Kumar
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, Washington, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Nurhafiza NBA, Siti Asma H, Azian H, Foo PC, Yasmin KMI, Chan YY. Distribution of sasX, qacA/B and mupA genes and determination of genetic relatedness of methicillin-resistant Staphylococcus aureus among clinical isolates and nasal swab samples from the same patients in a hospital in Malaysia. Singapore Med J 2020; 63:335-341. [PMID: 33264563 DOI: 10.11622/smedj.2020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
INTRODUCTION This study determined the distribution of sasX, qacA/B and mupA genes from methicillin-resistant Staphylococcus aureus (MRSA) isolated from clinical samples and nasal swab samples of the same patients and analysed their genetic relatedness. METHODS Polymerase chain reaction (PCR) was used to detect the presence of sasX, qacA/B and mupA genes from 47 paired MRSA isolates. A paired isolate was defined as one nasal swab (colonising) isolate and clinical isolate that caused infection in the same patient. 22 selected paired isolates were subjected to multilocus sequence typing (MLST). The genetic relatedness among the isolates and association between the putative genes with epidemic sequence types (STs) were investigated. RESULTS 7 (14.9%, n = 14) paired isolates were positive for the sasX gene. qacA/B genes were positive in 7.4% (n = 7) of the isolates, from three paired isolates and one clinical isolate whose paired colonising isolate was negative. The paired sample of three patients were positive for both genes. The mupA gene was not detected in all the isolates. MLST revealed two epidemic STs, ST22 and ST239, and a novel ST4649. sasX and qacA/B genes were found in ST239 in 29.5% (n = 13) and 13.6% (n = 6) of cases, respectively. Gene co-existence occurred in 13.6% (n = 6) of MRSA ST239 and 2.3% (n = 1) of MRSA ST4649. CONCLUSION sasX and qacA/B genes were present in the MRSA isolates, while the mupA gene was undetected. ST22 and ST239 were the major MRSA clones. The circulating MRSA genotypes conferred different virulence and resistance determinants in our healthcare settings.
Collapse
Affiliation(s)
- Nik Badrul Alam Nurhafiza
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Hassan Siti Asma
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Hospital USM, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Harun Azian
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Hospital USM, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Phiaw Chong Foo
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, Selangor, Malaysia
| | - Khairani Muhammad Ismadi Yasmin
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Hospital USM, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| |
Collapse
|
7
|
Chen X, Ma K, Yi X, Xiong L, Wang Y, Li S. The rapid and visual detection of methicillin-susceptible and methicillin-resistant Staphylococcus aureus using multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor. Antimicrob Resist Infect Control 2020; 9:111. [PMID: 32680560 PMCID: PMC7366892 DOI: 10.1186/s13756-020-00774-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Staphylococcus aureus (S. aureus), including methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA), is an eminent human pathogen that can colonize the human host and cause severe life-threatening infections. The development of a reliable, simple and rapid assay for detecting S. aureus and identifying MRSA is important for diagnosis and follow-up treatment. Methods A novel molecular diagnosis technique, named multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor (m-LAMP-LFB), was applied to detect all S. aureus species and identify MRSA. Two sets of primers were designed based on the femA gene (S. aureus-specific gene) and the mecA gene (encoding penicillin-binding protein 2a), and the multiple-LAMP products were analyzed using LFB. The m-LAMP-LFB amplification conditions, including the target DNA concentration, reaction temperature and time, were optimized. The sensitivity and specificity of the m-LAMP-LFB method were tested in the current study, and the multiple-LAMP-LFB technology was applied to detect the MSSA and MRSA strains from clinical samples. Results The S. aureus- and MRSA-specific primers based on the femA and mecA genes allowed the multiple-LAMP technology to detect S. aureus and MRSA, respectively. The multiple-LAMP conditions were optimized at 63 °C for 40 min. The full process, including genomic DNA template preparation, LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the multiple-LAMP assay for femA and mecA detection was 100 fg of genomic DNA template per reaction. The specificity of m-LAMP-LFB detection was 100 %, and no cross-reactions to non-S. aureus strains were observed. Conclusion The multiple-LAMP-LFB technique developed in the current study is a reliable, simple, rapid, specific and sensitive method to identify MSSA and MRSA infections for appropriate antibiotic therapy.
Collapse
Affiliation(s)
- Xu Chen
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China.,The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China.,Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Centre for Disease Control and Prevention, 73 Bageyan Road, Guiyang, Guizhou, 550004, P.R. China
| | - Kai Ma
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Xu Yi
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Lijuan Xiong
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Yu Wang
- Department of Clinical Laboratory Centre, The First People's Hospital of Guiyang, Guiyang, Guizhou, 55004, P.R. China
| | - Shijun Li
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Centre for Disease Control and Prevention, 73 Bageyan Road, Guiyang, Guizhou, 550004, P.R. China.
| |
Collapse
|
8
|
Kulkarni RD, Mishra MN, Mohanraj J, Chandrasekhar A, Ajantha GS, Kulkani S, Bhat S. Development of a dry-reagent mix-based polymerase chain reaction as a novel tool for the identification of Acinetobacter species and its comparison with conventional polymerase chain reaction. J Lab Physicians 2020; 10:68-72. [PMID: 29403209 PMCID: PMC5784298 DOI: 10.4103/jlp.jlp_74_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND: Nosocomial infections are often caused by multidrug-resistant bacteria and the incidence is increasing. Acinetobacter, a Gram-negative bacillus, is commonly associated with the use of intravascular catheterization and airway intubation. Polymerase chain reaction (PCR) for identification of Acinetobacter baumannii from samples has been standardized that use conventional wet-reagent mix. We have designed and optimized a dry-reagent mix for identification of Acinetobacter species by PCR. The dry-reagent mix can be stored at room temperature, has less chances of contamination, and thus can be used at point-of-care diagnosis. AIM AND OBJECTIVE: The present work was focused on comparing the sensitivity and specificity of dry-reagent PCR mix over conventional wet-reagent PCR mix for identification of Acinetobacter species. MATERIALS AND METHODS: Conventional wet-reagent mix based and dry-reagent mix based PCR were carried out for the DNA isolated from Acinetobacter species. The latter was also applied directly on bacterial growth without prior DNA extraction process. Equal numbers of bacterial isolates other than Acinetobacter species were also subjected to identification by the same protocols for determining the sensitivity and specificity of the test. RESULTS: The Acinetobacter species showed amplification of the target rpoB gene and the band was observed at 397 bp. The dry-reagent PCR mix results matched completely with the conventional wet-reagent PCR mix assay. All the non-Acinetobacter isolates were negative for the PCR. This indicates that the test is highly specific. The dry-reagent mix also contained an enzyme resistant to PCR inhibitors and capable of amplifying DNA directly from cells. CONCLUSION: Performance of dry-reagent PCR mix without the need for DNA extraction and preparation of a PCR mix proved to be more sensitive and reduce the handling error, minimizes the time, manual work, and skilled labor.
Collapse
Affiliation(s)
- Raghavendra D Kulkarni
- Department of Microbiology, SDM College of Medical Sciences and Hospital, Dharwad, India
| | - Mukti Nath Mishra
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, Karnataka, India
| | - Jeevanandam Mohanraj
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, Karnataka, India
| | - Arun Chandrasekhar
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, Karnataka, India
| | - G S Ajantha
- Department of Microbiology, SDM College of Medical Sciences and Hospital, Dharwad, India
| | - Sheetal Kulkani
- Department of Microbiology, SDM College of Medical Sciences and Hospital, Dharwad, India
| | - Shama Bhat
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, Karnataka, India
| |
Collapse
|
9
|
Mishra MN, Kulkarni RD, Mohanraj J, Nisshanthini SD, Ajantha GS, Chandrasekhar A, Kenge P, Bhat S. A novel ready-to-use dry-reagent polymerase chain reaction for detection of Escherichia coli & Shigella species. Indian J Med Res 2019; 149:671-676. [PMID: 31417036 PMCID: PMC6702690 DOI: 10.4103/ijmr.ijmr_1394_17] [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: 11/16/2022] Open
Abstract
Background & objectives: Polymerase chain reaction (PCR) has wide acceptance for rapid identification of pathogens and also for diagnosis of infectious conditions. However, because of economic and expertise constraints, a majority of small or peripheral laboratories do not use PCR. The objective of the present study was to develop a dry-reagent PCR assay as an alternative to conventional PCR to assess its applicability in routine laboratory practice using malB gene for identification of Escherichia coli as a model. Methods: A total of 184 isolates were selected for the study comprising clinical isolates of E. coli and non-E. coli including Shigella sp. and a few other control strains. The DNA was isolated from all the isolates. The isolated DNA as well as the overnight grown bacterial cultures were subjected to both conventional wet PCR and dry-reagent PCR. Results: The genomic DNA isolated from E. coli showed amplification of malB gene in both conventional wet and dry-reagent PCR and the band was observed at 491 bp. In dry-reagent PCR, the overnight grown E. coli cells also showed positive result. The non-E. coli strains other than Shigella sp. showed negative in both conventional wet and dry-reagent PCR. Shigella sp. showed positive in both conventional wet and dry-reagent PCR. Interpretation & conclusions: Considering the elimination of genomic DNA isolation step, and similar results with the conventional wet PCR, dry-reagent PCR may be a good alternative for the conventional wet PCR.
Collapse
Affiliation(s)
- Mukti Nath Mishra
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, India
| | | | - Jeevanandam Mohanraj
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, India
| | | | - G S Ajantha
- Department of Microbiology, SDM College of Medical Sciences & Hospital, Dharwad, India
| | - Arun Chandrasekhar
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, India
| | - Prachee Kenge
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, India
| | - Shama Bhat
- Department of Molecular Diagnostics, Bhat Biotech India Pvt. Ltd., Bengaluru, India
| |
Collapse
|
10
|
Galia L, Ligozzi M, Bertoncelli A, Mazzariol A. Real-time PCR assay for detection of Staphylococcus aureus, Panton-Valentine Leucocidin and Methicillin Resistance directly from clinical samples. AIMS Microbiol 2019; 5:138-146. [PMID: 31384708 PMCID: PMC6642910 DOI: 10.3934/microbiol.2019.2.138] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/26/2019] [Indexed: 02/04/2023] Open
Abstract
Rapid detection of Methicillin Resistant Staphylococcus aureus (MRSA) is an important concern for both treatment and implementation of infection control policies. The present study provides an ‘in house’ real-time PCR assay to detect directly nuc, pvl, and mecA genes. The assay is able to perform identification of MRSA, Methicillin-Sensitive S. aureus, Methicillin-Resistant Coagulase Negative Staphylococci and the Panton-Valentine leukocidin virulence gene from rectal and pharyngeal swab samples in a screening context. We found an analytical sensitivity of this current Triplex PCR assay of 514 CFU/mL. Analytical specificity was tested with different Gram-positive and Gram-negative species and yielded no false-positive PCR signal. The sensitivity and specificity of the Triplex Real Time PCR were both 100% for these targets when compared with the culture and conventional methods. This assay is readily adaptable for routine use in a microbiology laboratory, as it will enable the implementation of timely and properly guided therapy and infection control strategies.
Collapse
Affiliation(s)
- Liliana Galia
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Marco Ligozzi
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Anna Bertoncelli
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Annarita Mazzariol
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| |
Collapse
|
11
|
Luo J, Yu J, Yang H, Wei H. Parallel susceptibility testing of bacteria through culture-quantitative PCR in 96-well plates. Int J Infect Dis 2018; 70:86-92. [PMID: 29559368 DOI: 10.1016/j.ijid.2018.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/05/2018] [Accepted: 03/11/2018] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVE The methods combining culture and quantitative PCR(qPCR) offer new solutions for rapid antibiotic susceptibility testing(AST). However, the multiple steps of DNA extraction and cold storage of PCR reagents needed make them unsuitable for rapid high throughput AST. In this study, a parallel culture-qPCR method was developed to overcome above problems. METHOD In this method, bacteria culture and DNA extraction automatically and simultaneously completed through using a common PCR instrument as a controllable heating device. A lyophilized 16S rDNA targeted qPCR reagent was also developed, which was stable and could be kept at 4°C for long time and at 37°C for about two months. RESULT Testing of 36 P. aeruginosa isolates and 28 S. aureus isolates showed that the method had good agreements with the standard broth microdilution method, with an overall agreement of 97.22% (95% CI, 85.83-99.51) for P. aeruginosa and 96.43% (95% CI, 79.76-99.81) for S. aureus. This method could test 12 samples against a panel of up to 7 antibiotics simultaneously in two 96-well PCR plates within 4h, which greatly improves the testing efficiency of the culture-qPCR method. CONCLUSION With rapidness to obtain results and the capabilities for automation and multiple-sample testing, the parallel culture-qPCR method would have great potentials in clinical labs.
Collapse
Affiliation(s)
- Jun Luo
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| |
Collapse
|
12
|
A Thermostabilized, One-Step PCR Assay for Simultaneous Detection of Klebsiella pneumoniae and Haemophilus influenzae. J Trop Med 2017; 2017:7210849. [PMID: 28386286 PMCID: PMC5366220 DOI: 10.1155/2017/7210849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae and Haemophilus influenzae are two common pathogens associated with respiratory tract infections. The identification of these pathogens using conventional molecular diagnostic tests requires trained personnel, cold-chain transportation, and storage-dependance, which does not render them user-friendly. The aim of this study was to develop a thermostabilized, cold-chain-free, one-step multiplex PCR for simultaneous detection of K. pneumoniae and H. influenzae. The multiplex PCR assay was designed to amplify the php gene of K. pneumoniae (202 bp) and p6 gene of H. influenzae (582 bp). In addition, the specific primer to amplify glm gene of Helicobacter pylori (105 bp) was included as an internal amplification control. Subsequently, the designed primers and all PCR reagents were thermostabilized by lyophilization. The stability of the thermostabilized PCR was evaluated using the Q10 method. The sensitivity and specificity of performances for thermostabilized PCR were evaluated using 127 clinical isolates and were found to be 100% sensitive and specific. The thermostabilized PCR mix was found to be stable for 30 days and the Q10 accelerated stability was found to be 3.02 months. A cold-chain-free, PCR assay for easy, rapid, and simultaneous detection of K. pneumoniae and H. influenzae was successfully developed in this study.
Collapse
|
13
|
Nagaraj S, Ramlal S, Kingston J, Batra HV. Thermostabilization of indigenous multiplex polymerase chain reaction reagents for detection of enterotoxigenic Staphylococcus aureus. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 51:191-198. [PMID: 27260780 DOI: 10.1016/j.jmii.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 04/19/2016] [Accepted: 04/25/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND/PURPOSE Among DNA-based techniques, polymerase chain reaction (PCR) is the most widely accepted molecular tool for the detection of pathogens. However, the technique involves several reagents and multiple pipetting steps that often lead to error-prone results. Additionally, the reagents entail a cold-chain facility to maintain their stability during storage and transportation. The main aim of the present study was to simplify the utility of a pre-optimized multiplex PCR format that was developed to detect toxigenic strains of Staphylococcus aureus by providing stable, pre-mixed, and ready-to-use master mix in a lyophilized formulation. METHODS Master mix containing all reagents except the template was lyophilized in the presence of an excipient lyoprotectant to achieve long-term stability without altering the sensitivity, specificity and PCR performance. Bromophenol blue was also included in the master mix to reduce the risk of external contamination during gel loading. The stability of lyophilized master mix was analyzed at different temperatures. The PCR performance was also examined after exposure of master mix to notable temperature fluctuations during transportation. RESULTS The shelf-life of lyophilized master mix was estimated to be 1.5 months at ambient temperature and 6 months at 4°C. Stability was unaffected by temperature fluctuations during transportation even in cold-chain-free conditions, thus reducing the cost required for cold storage. CONCLUSION The sensitive, cost-effective, ready-to-use, and ambient temperature stable formulation could be implemented as a detection tool in food analysis and diagnostic laboratories and hospitals and for on-field application outside the laboratories, as well as for detection of toxigenic strains of S. aureus.
Collapse
Affiliation(s)
- Sowmya Nagaraj
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | - Shylaja Ramlal
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India.
| | - Joseph Kingston
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | - Harsh Vardhan Batra
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| |
Collapse
|
14
|
Liu Y, Zhang J, Ji Y. PCR-based Approaches for the Detection of Clinical Methicillin-resistant Staphylococcus aureus. Open Microbiol J 2016; 10:45-56. [PMID: 27335617 PMCID: PMC4899539 DOI: 10.2174/1874285801610010045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus is an important pathogen that can cause a variety of infections, including superficial and systematic infections, in humans and animals. The persistent emergence of multidrug resistant S. aureus, particularly methicillin-resistant S. aureus, has caused dramatically economic burden and concerns in the public health due to limited options of treatment of MRSA infections. In order to make a correct choice of treatment for physicians and understand the prevalence of MRSA, it is extremely critical to precisely and timely diagnose the pathogen that induces a specific infection of patients and to reveal the antibiotic resistant profile of the pathogen. In this review, we outlined different PCR-based approaches that have been successfully utilized for the rapid detection of S. aureus, including MRSA and MSSA, directly from various clinical specimens. The sensitivity and specificity of detections were pointed out. Both advantages and disadvantages of listed approaches were discussed. Importantly, an alternative approach is necessary to further confirm the detection results from the molecular diagnostic assays.
Collapse
Affiliation(s)
- Ying Liu
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China; Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Jiang Zhang
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Yinduo Ji
- Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| |
Collapse
|
15
|
McHugh MP, Gray SJ, Kaczmarski EB, Guiver M. Reduced turnaround time and improved diagnosis of invasive serogroup B Neisseria meningitidis and Streptococcus pneumoniae infections using a lyophilized quadruplex quantitative PCR. J Med Microbiol 2015; 64:1321-1328. [DOI: 10.1099/jmm.0.000154] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Martin P. McHugh
- Meningococcal Reference Unit, Public Health England, Manchester Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - Steve J. Gray
- Meningococcal Reference Unit, Public Health England, Manchester Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - Edward B. Kaczmarski
- Meningococcal Reference Unit, Public Health England, Manchester Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - Malcolm Guiver
- Meningococcal Reference Unit, Public Health England, Manchester Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| |
Collapse
|
16
|
Pentaplex PCR assay for detection of hemorrhagic bacteria from stool samples. J Clin Microbiol 2014; 52:3244-9. [PMID: 24958797 DOI: 10.1128/jcm.00891-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diarrheal diseases cause illness and death among children younger than 10 years in developing countries. Conventional testing for the detection of hemorrhagic bacteria takes 2 to 5 days to yield complete information on the organism and its antibiotic sensitivity pattern. Hence, in the present study, we developed a molecular-based diagnostic assay that identifies common hemorrhagic bacteria in stool samples. A set of specific primers were designed for the detection of Salmonella spp., Shigella spp., enterohemorrhagic Escherichia coli (EHEC), and Campylobacter spp., suitable for use in a one-tube PCR assay. The assay in the present study simultaneously detected five genes, namely, ompC for the Salmonella genus, virA for the Shigella genus, eaeA for EHEC, 16S rRNA for the Campylobacter genus, and hemA for an internal control. Specific primer pairs were successfully designed and simultaneously amplified the targeted genes. Validation with 20 Gram-negative and 17 Gram-positive strains yielded 100% specificity. The limit of detection of the multiplex PCR assay was 1 × 10(3) CFU at the bacterial cell level and 100 pg at the genomic DNA level. Further evaluation of the multiplex PCR with 223 bacterium-spiked stool specimens revealed 100% sensitivity and specificity. We conclude that the developed multiplex PCR assay was rapid, giving results within 4 h, which is essential for the identification of hemorrhagic bacteria, and it might be useful as an additional diagnostic tool whenever time is important in the diagnosis of hemorrhagic bacteria that cause diarrhea. In addition, the presence of an internal control in the multiplex PCR assay is important for excluding false-negative cases.
Collapse
|
17
|
Kamau E, Alemayehu S, Feghali KC, Juma DW, Blackstone GM, Marion WR, Obare P, Ogutu B, Ockenhouse CF. Sample-ready multiplex qPCR assay for detection of malaria. Malar J 2014; 13:158. [PMID: 24767409 PMCID: PMC4026594 DOI: 10.1186/1475-2875-13-158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/10/2014] [Indexed: 11/17/2022] Open
Abstract
Background Microscopy and antigen detecting rapid diagnostic tests are the diagnostic tests of choice in management of clinical malaria. However, due to their limitations, the need to utilize more sensitive methods such as real-time PCR (qPCR) is evident as more studies are now utilizing molecular methods in detection of malaria. Some of the challenges that continue to limit the widespread utilization of qPCR include lack of assay standardization, assay variability, risk of contamination, and the need for cold-chain. Lyophilization of molecular assays can overcome some of these limitations and potentially enable widespread qPCR utilization. Methods A recently published multiplex malaria qPCR assay was lyophilized by freezing drying into Sample-Ready™ format (MMSR). MMSR assay contained all the required reagents for qPCR including primers and probes, requiring only the addition of water and sample to perform qPCR. The performance of the MMSR assay was compared to the non-freeze dried, “wet” assay. Stability studies were done by maintaining the MMSR assays at four different ambient temperatures of 4°C, room temperature (RT), 37°C and 42°C over a period of 42 days, tested at seven-day intervals. Plasmodium falciparum and Plasmodium vivax DNAs were used for analysis of the MMSR assay either as single or mixed parasites, at two different concentrations. The CT values and the standard deviations (SD) were used in the analysis of the assay performance. Results The limit of detection for the MMSR assay was 0.244 parasites/μL for Plasmodium spp. (PLU) and P. falciparum (FAL) assay targets compared to “wet” assay which was 0.39 and 3.13 parasites/μL for PLU and FAL assay targets, respectively. The MMSR assay performed with high efficiencies similar to those of the “wet” assay and was stable at 37°C for 42 days, with estimated shelf-life of 5 months. When used to analyse field clinical samples, MMSR assay performed with 100% sensitivity and specificity compared to the “wet” assay. Conclusion The MMSR assay has the same robust performance characteristics as the “wet” assay and is highly stable. Availability of MMSR assay allows flexibility and provides an option in choosing assay for malaria diagnostics depending on the application, needs and budget.
Collapse
Affiliation(s)
- Edwin Kamau
- Walter Reed Army Institute of Research, Military Malaria Research Program, Malaria Vaccine Branch, 503 Robert Grant Ave, Silver Spring, Maryland, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|