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Ghorbani A, Hashemzadeh M, Amin M, Moosavian M, Nashibi R, Mehraban Z. Occurrence of the Legionella species in the respiratory samples of patients with pneumonia symptoms from Ahvaz, Iran; first detection of Legionella cherrii. Mol Biol Rep 2021; 48:7141-7146. [PMID: 34618288 DOI: 10.1007/s11033-021-06704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND This study aimed to investigate the occurrence of Legionella species in the respiratory samples of patients with pneumonia symptoms from Ahvaz, Iran by culture and the real-time PCR of 23S-5S rRNA gene spacer region. METHODS AND RESULTS A total of 123 clinical respiratory samples including 63 pleural aspirates, 57 bronchoalveolar lavage (BAL), and 3 sputum were collected from 65 males and 58 females with pneumonia symptoms. All samples were cultured on the Modified Wadowsky-Yee (MWY) agar. The Legionella species was identified by routine bacteriological tests. The presence of the 16S-23S rRNA spacer region gene was investigated by real-time PCR. The Legionella species were differentiated by sequencing of 16S-23S rRNA gene. A total of 2 (1.6%) BAL specimens were positive for Legionella species by culture method. No Legionella spp. were identified in pleural aspirates and sputum samples by the culture method. Using real-time PCR, 9 (7.3%) samples including 6 BAL, 1 sputum, and 2 pleural aspirates were positive for legionella species. These species were detected in 3 (5.2%) females and 6 males (9.2%). The results of sequencing showed that eight species were L. pneumophila while one was L. cherrii. Also, the 2 isolates that were identified by culture method, were confirmed as L. pneumophila by sequencing. CONCLUSIONS The results showed that using the real-time PCR has a more efficacy for detecting of Legionella species in respiratory samples. Also, L. pneumophila was the most prevalent species circulating in the southwest region of Iran. So, periodic monitoring programs is recommended to prevent epidemics due to this bacterium.
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Affiliation(s)
- Atosa Ghorbani
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mansour Amin
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mojtaba Moosavian
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rohangiz Nashibi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious Diseases and Tropical Medicine Ward, Razi Teaching Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Mehraban
- Department of Pulmonology, Golestan Teaching Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Fesenko DO, Guseinov TO, Lapa SA, Kuznetsova VE, Shershov VE, Spitsyn MA, Nasedkina TV, Zasedatelev AS, Chudinov AV. Substrate Properties of New Fluorescently Labeled Deoxycytidine Triphosphates in Enzymatic Synthesis of DNA with Polymerases of Families A and B. Mol Biol 2018. [DOI: 10.1134/s0026893318030044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Zhang H, Liu X, Liu M, Gao T, Huang Y, Liu Y, Zeng W. Gene detection: An essential process to precision medicine. Biosens Bioelectron 2018; 99:625-636. [DOI: 10.1016/j.bios.2017.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/12/2017] [Indexed: 01/08/2023]
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4
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Ranjbar R, Behzadi P, Najafi A, Roudi R. DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab. Open Microbiol J 2017; 11:330-338. [PMID: 29290845 PMCID: PMC5737027 DOI: 10.2174/1874285801711010330] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/24/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Background: A rapid, accurate, flexible and reliable diagnostic method may significantly decrease the costs of diagnosis and treatment. Designing an appropriate microarray chip reduces noises and probable biases in the final result. Objective: The aim of this study was to design and construct a DNA Microarray Chip for a rapid detection and identification of 10 important bacterial agents. Method: In the present survey, 10 unique genomic regions relating to 10 pathogenic bacterial agents including Escherichia coli (E.coli), Shigella boydii, Sh.dysenteriae, Sh.flexneri, Sh.sonnei, Salmonella typhi, S.typhimurium, Brucella sp., Legionella pneumophila, and Vibrio cholera were selected for designing specific long oligo microarray probes. For this reason, the in-silico operations including utilization of the NCBI RefSeq database, Servers of PanSeq and Gview, AlleleID 7.7 and Oligo Analyzer 3.1 was done. On the other hand, the in-vitro part of the study comprised stages of robotic microarray chip probe spotting, bacterial DNAs extraction and DNA labeling, hybridization and microarray chip scanning. In wet lab section, different tools and apparatus such as Nexterion® Slide E, Qarraymini spotter, NimbleGen kit, TrayMixTM S4, and Innoscan 710 were used. Results: A DNA microarray chip including 10 long oligo microarray probes was designed and constructed for detection and identification of 10 pathogenic bacteria. Conclusion: The DNA microarray chip was capable to identify all 10 bacterial agents tested simultaneously. The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes.
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Affiliation(s)
- Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Payam Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Raheleh Roudi
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
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5
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A gyrB oligonucleotide microarray for the specific detection of pathogenic Legionella and three Legionella pneumophila subsp. Antonie van Leeuwenhoek 2017; 110:1515-1525. [PMID: 28695408 DOI: 10.1007/s10482-017-0903-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
Abstract
Among the 50 species and 70 serogroups of Legionella identified, Legionella pneumophila, comprising three subsp. (subsp. pneumophila, subsp. fraseri, and subsp. pasculleii), is recognized as the major cause of epidemic legionellosis. Rapid and reliable assays to identify pathogenic Legionella spp., and the three L. pneumophila subsp. in particular, are in great demand. In this study, we analyzed the gyrB genes of eleven Legionella spp. and subsp., comprising L. anisa, L. bozemanii, L. dumoffii, L. feeleii, L. gormanii, L. longbeachae, L. micdadei, L. waltersii, L. pneumophila subsp. pneumophila, L. pneumophila subsp. fraseri, and L. pneumophila subsp. pasculleii. We developed a rapid oligonucleotide microarray detection technique to identify accurately these common pathogenic Legionella spp. and L. pneumophila subsp. To detect multiple Legionella species with high specificity, 31 reproducible probes were designed in the array. Sixty-one strains were analyzed in total, including 37 target pathogens and 24 non-target bacterial species used to validate the microarray. The sensitivity of the detection was 1.0 ng using genomic DNA of three Legionella spp., L. anisa, L. dumoffii, and L. waltersii, or 13 CFU/100 mL using the cultured L. pneumophila subsp. pneumophila. Eight isolated strains were tested using the microarray with 100% accuracy. The data indicated that the technique is an efficient method to diagnose and detect Legionella spp. and subsp. in basic microbiology, clinical diagnosis, epidemiological surveillance, and food safety applications. In addition, a phylogenetic study based on the gyrB gene revealed the genetic relationship among the different Legionella spp. and subsp.
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6
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Dunne WM, Picot N, van Belkum A. Laboratory Tests for Legionnaire’s Disease. Infect Dis Clin North Am 2017; 31:167-178. [DOI: 10.1016/j.idc.2016.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Thaler DS. Toward a microbial Neolithic revolution in buildings. MICROBIOME 2016; 4:14. [PMID: 27021307 PMCID: PMC4810507 DOI: 10.1186/s40168-016-0157-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/11/2016] [Indexed: 05/03/2023]
Abstract
The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes but starting with the gut we continue our hundred-year project of approaching the ability to assess and cultivate benign microbiomes in our bodies. Buildings are analogous to the body and it is time to ask what it means to cultivate benign microbiomes in our built environment. A critical distinction is that we have not found, or invented, niches in buildings where healthful microbial metabolism occurs and/or could be cultivated. Key events affecting the health and healthfulness of buildings such as a hurricane leading to a flood or a burst pipe occur only rarely and unpredictably. The cause may be transient but the effects can be long lasting and, e.g., for moisture damage, cumulative. Non-invasive "building tomography" could find moisture and "sentinel microbes" could record the integral of transient growth. "Seed" microbes are metabolically inert cells able to grow when conditions allow. All microbes and their residue present actinic molecules including immunological epitopes (molecular shapes). The fascinating hygiene and microbial biodiversity hypotheses propose that a healthy immune system requires exposure to a set of microbial epitopes that is rich in diversity. A particular conjecture is that measures of the richness of diversity derived from microbiome next-generation sequencing (NGS) can be mechanistically coupled to--rather than merely correlated with some measures of--human health. These hypotheses and conjectures inspire workers and funders but an alternative is also consequent to the first Neolithic revolution: That the genetic uniformity of contemporary foods may also decrease human exposure to molecular biodiversity in a heath-relevant manner. Understanding the consequences--including the unintended consequences of the first Neolithic revolution--will inform and help us benignly implement the second--the microbial--Neolithic revolution.
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Affiliation(s)
- David S Thaler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056, Basel, Switzerland.
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8
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Fluorescence-based bioassays for the detection and evaluation of food materials. SENSORS 2015; 15:25831-67. [PMID: 26473869 PMCID: PMC4634490 DOI: 10.3390/s151025831] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.
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9
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Janczarek M, Palusińska-Szysz M. PCR method for the rapid detection and discrimination of Legionella spp. based on the amplification of pcs, pmtA, and 16S rRNA genes. J Appl Genet 2015; 57:251-61. [PMID: 26423783 DOI: 10.1007/s13353-015-0317-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/18/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
Abstract
Legionella bacteria are organisms of public health interest due to their ability to cause pneumonia (Legionnaires' disease) in susceptible humans and their ubiquitous presence in water supply systems. Rapid diagnosis of Legionnaires' disease allows the use of therapy specific for the disease. L. pneumophila serogroup 1 is the most common cause of infection acquired in community and hospital environments. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this work, simplex and duplex PCR assays with the use of new molecular markers pcs and pmtA involved in phosphatidylcholine synthesis were specified for rapid and cost-efficient identification and distinguishing Legionella species. The sets of primers developed were found to be sensitive and specific for reliable detection of Legionella belonging to the eight most clinically relevant species. Among these, four primer sets I, II, VI, and VII used for duplex-PCRs proved to have the highest identification power and reliability in the detection of the bacteria. Application of this PCR-based method should improve detection of Legionella spp. in both clinical and environmental settings and facilitate molecular typing of these organisms.
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Affiliation(s)
- Monika Janczarek
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033, Lublin, Poland
| | - Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033, Lublin, Poland.
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10
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Cao B, Tian Z, Wang S, Zhu Z, Sun Y, Feng L, Wang L. Structural comparison of O-antigen gene clusters of Legionella pneumophila and its application of a serogroup-specific multiplex PCR assay. Antonie van Leeuwenhoek 2015; 108:1405-1423. [PMID: 26415652 DOI: 10.1007/s10482-015-0594-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/21/2015] [Indexed: 01/01/2023]
Abstract
The Legionella pneumophila serogroups O1, O4, O6, O7, O10 and O13 are pathogenic strains associated with pneumonia. The surface O-antigen gene clusters of L. pneumophila serogroups O4, O6, O7, O10 and O13 were sequenced and analyzed, with the function annotated on the basis of homology to that of the genes of L. pneumophila serogroup O1 (L. pneumophila subsp. pneumophila str. Philadelphia 1). The gene locus of the six L. pneumophila serogroups contains genes of yvfE, neuABCD, pseA-like for nucleotide sugar biosynthesis, wecA for sugar transfer, and wzm as well as wzt for O-antigen processing. The detection of O-antigen genes allows the fine differentiation at species and serogroup level without the neccessity of nucleotide sequencing. The O-antigen-processing genes wzm and wzt, which were found to be distinctive for different for different serogroups, have been used as the target genes for the detection and identification of L. pneumophila strains of different O serogroups. In this report, a multiplex PCR assay based on wzm or wzt that diferentiates all the six serogroups by amplicon size was developed with the newly designed specific primer pairs for O1 and O7, and the specific primer pairs for O4, O6, O10, and O13 reported previously. The array was validated by analysis of 34 strains including 15 L. pneumophila O-standard reference strains, eight reference strains of other Legionella non-pneumophila species, six other bacterial species, and five L. pneumophila environmental isolates. The detection sensitivity was one ng genomic DNA. The accurate and sensitive assay is suitable for the identification and detection of strains of these serogroups in environmental and clinical samples.
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Affiliation(s)
- Boyang Cao
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, 300457, People's Republic of China. .,TEDA Institue of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, People's Republic of China. .,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China.
| | - Zhenyang Tian
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, 300457, People's Republic of China.,TEDA Institue of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, People's Republic of China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Suwei Wang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, 300457, People's Republic of China.,TEDA Institue of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, People's Republic of China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Zhiyan Zhu
- Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Yamin Sun
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Lu Feng
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, 300457, People's Republic of China.,TEDA Institue of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, People's Republic of China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Lei Wang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, 300457, People's Republic of China. .,TEDA Institue of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, People's Republic of China. .,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, People's Republic of China.
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