Osong Public Health and Research Perspectives

Original Articles

Development of a Two Triplex Real-Time Polymerase Chain Reaction for Rapid Detection of Six Carbapenemase Genes in Enterobacteriaceae: Ji Ae Choi, Song Mee Bae, Jung Wook Kim, Kwang Jun Lee; Osong Public Health Res Perspect. 2020;11(1):53-59. Published online February 28, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.1.08

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Objectives

Carbapenem resistance is a serious clinical and public health threat. Carbapenemase can confer carbapenem resistance, and most carbapenemase genes are plasmid encoded so resistance can easily spread. In this study, we aimed to develop a novel system based on the TaqMan platform for the rapid detection of 6 clinically prevalent carbapenemase genes: Klebsiella pneumoniae carbapenemase, New Delhi metallo-β-lactamase, oxacillinase, imipenem-hydrolyzing, Verona integron-encoded metallo-β-lactamase, and Guiana extended-spectrum β-lactamase.

Methods

The triplex assay was verified by testing genomic DNA of 6 carbapenemase-producing Klebsiella pneumoniae. It was validated with a blinded panel of 310 Enterobacteriaceae isolates, including 225 carbapenemase-producers and 85 non-producers, by direct colony triplex real-time polymerase chain reaction (PCR). The real-time PCR was performed using the ABI 7500 fast instrument (Applied Biosystems, CA, USA) and specific primers for each carbapenemase target were designed to include modified peptide-nucleic acid oligonucleotides.

Results

No amplification was detected among the negative samples. The result showed 100% concordance with the genotypes previously identified. The entire assay, including DNA extraction and real-time PCR, was completed within 2 hours.

Conclusion

The newly developed triplex real-time PCR assay was useful for the rapid, accurate and simultaneous detection of 6 carbapenemase genes in Enterobacteriaceae, suggesting its potential to allow an early decision on the appropriate treatment, management, and prevention of the spread of resistant infections in hospitals.

Citations

Citations to this article as recorded by

Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods
Ena Gupta, Juhi Saxena, Sanni Kumar, Umang Sharma, Saundarya Rastogi, Vijay Kumar Srivastava, Sanket Kaushik, Anupam Jyoti
Diagnostics.2023; 13(2): 277. CrossRef

Rapid Molecular Approach for Simultaneous Detection of Salmonella spp., Shigella spp., and Vibrio cholera: Reza Ranjbar, Ali Naghoni, Davoud Afshar, Farhad Nikkhahi, Mohsen Mohammadi; Osong Public Health Res Perspect. 2016;7(6):373-377. Published online December 31, 2016; DOI: https://doi.org/10.1016/j.phrp.2016.10.002

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Abstract PDF

Objectives
Gastrointestinal tract infection is still one of the serious public health problems in many geographic areas and is endemic in most countries including Iran. Early detection of the gastrointestinal tract pathogens can be extremely important. The aim of the current study was to apply a shortened time-multiplex polymerase chain reaction (PCR) for rapid and simultaneous detection of Salmonella spp., Shigella spp., and Vibrio cholera.
Methods
The standard and clinical strains of Salmonella spp., Shigella spp., and V. cholerae were used in the assay. Multiplex PCR was performed and optimized based on amplification of invA, putative integrase, and ompW genes for detecting Salmonella spp., Shigella spp., and V. cholerae, respectively. The specificity of the assay was evaluated by testing 12 different bacterial species.
Results
Only Salmonella spp., Shigella spp., and V. cholerae strains had positive results when subjected to the assay using multiplex PCR. The assay showed a high sensitivity, and no amplification products were observed in multiplex PCR with any of the other microorganisms.
Conclusion
Our study indicated that the invA, putative integrase, and ompW-based multiplex PCR assay appears to be an efficient method for rapid and simultaneous detection of Salmonella spp., Shigella spp., and V. cholerae.

Citations

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Development and Validation of an Efficient Multiplex PCR Assay for Simultaneous Detection of Six Common Foodborne Pathogens and Hygiene Indicators
Natharin Ngamwongsatit, Soraya Chaturongakul, Ratchaneewan Aunpad
Foodborne Pathogens and Disease.2023; 20(6): 222. CrossRef
Rapid and multiplexed quantification of Salmonella, Escherichia coli O157:H7, and Shigella flexneri in ground beef using flow cytometry
Ziquan Wang, Qian Xu, Siyuan Liu, Yingying Liu, Ying Gao, Meng Wang, Ling Zhang, Haiyan Chang, Qiang Wei, Zhiwei Sui
Talanta.2022; 238: 123005. CrossRef
Development of multiplex real-time quantitative PCR for simultaneous detection of Chlamydia trachomatis, Mycoplasma hominis, Ureaplasma urealyticum, and Mycoplasma genitalium in infertile women
Sara Sadeqi, Farhad Nikkhahi, Amir Javadi, Sonia Eskandarion, Seyed Mahmoud Amin Marashi
Indian Journal of Medical Microbiology.2022; 40(2): 231. CrossRef
Multiple fluorescent saltatory rolling circle amplification (SRCA) for simultaneous and sensitive detection of Salmonella spp. and Shigella spp. in food
Wei Guo, Qian Yang, Jie Liu, Xiuling Chen, Yunzhe Zhang, Wei Zhang
LWT.2022; 168: 113875. CrossRef
Campylobacter Species in the Middle East
Daryoush Babazadeh, Reza Ranjbar
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Mohammad Lukman Yahaya, Nor Dyana Zakaria, Rahmah Noordin, Khairunisak Abdul Razak
Biotechnology and Applied Biochemistry.2021; 68(5): 1095. CrossRef
Ultrasensitive pathogen detection with a rolling circle amplification-empowered multiplex electrochemical DNA sensor
Cheryl S.Y. Yeap, Thanyarat Chaibun, Su Yin Lee, Bin Zhao, Yuan Jan, Chan La-o-vorakiat, Werasak Surareungchai, Shiping Song, Benchaporn Lertanantawong
Chemical Communications.2021; 57(91): 12155. CrossRef
Taqman hydrolysis probe application for Escherichia coli, Salmonella enterica, and Vibrio cholerae detection in surface and drinking water
Ahmed K. A. El-Sayed, Mohamed I. Abou-Dobara, Camelia A. Abdel-Malak, Amira A. E. El-Badaly
Journal of Water, Sanitation and Hygiene for Devel.2019; 9(3): 492. CrossRef
Pathways of healthcare and antibiotics use following reported gastrointestinal illness: a cross-sectional study in rural Anhui, China
Xing Rong Shen, Maomao Xie, Jing Chai, Rui Feng, Jing Cheng, Rong Liu, Paul Kadetz, DeBin Wang
BMJ Open.2019; 9(8): e030986. CrossRef
DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab
Reza Ranjbar, Payam Behzadi, Ali Najafi, Raheleh Roudi
The Open Microbiology Journal.2017; 11(1): 330. CrossRef

Comparison of Three Different Methods for Detection of IL28 rs12979860 Polymorphisms as a Predictor of Treatment Outcome in Patients with Hepatitis C Virus: Abolfazl Fateh, Mohammadreza Aghasadeghi, Seyed D. Siadat, Farzam Vaziri, Farzin Sadeghi, Roohollah Fateh, Hossein Keyvani, Alireza H. Tasbiti, Shamsi Yari, Angila Ataei-Pirkooh, Seyed H. Monavari; Osong Public Health Res Perspect. 2016;7(2):83-89. Published online April 30, 2016; DOI: https://doi.org/10.1016/j.phrp.2015.11.004

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Abstract PDF

Objectives
This study aimed to evaluate the specificity, sensitivity, cost, and turn-around time of three methods of gene polymorphism analysis and to study the relationship between IL28B rs12979860 and SVR rate to pegIFN-α/RVB therapy among patients with chronic hepatitis C.
Methods
A total of 100 samples from chronic hepatitis C patients were analyzed in parallel using the three methods: direct sequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system (ARMS)-PCR.
Results
The different profiles for IL28B rs12979860 alleles (CC, CT, and TT) obtained with PCR-RFLP, ARMS-PCR, and direct sequencing were consistent among the three methods. Prevalence of rs12979860 genotypes CC, CT and TT in HCV genotype 1a was 10(19.6%), 35(68.6%), and six (11.8%), respectively, and in HCV genotype 31, it was 13(26.5%), 31(63.3%), and five (10.2%), respectively. No significant difference was seen between rs12979860 genotype and HCV genotype (p = 0.710).
Conclusion
Screening by ARMS – PCR SNOP detection represents the most efficient and reliable method to determine HCV polymorphisms in routine clinical practice.

Citations

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Pegah Namdar Aligoodarzi, Golale Rostami, Seyed Reza Kazemi Nezhad, Mohammad Hamid
Iranian Biomedical Journal.2023; 27(1): 46. CrossRef
Expression of TRIM56 gene in SARS-CoV-2 variants and its relationship with progression of COVID-19
Rezvan Tavakoli, Pooneh Rahimi, Mojtaba Hamidi-Fard, Sana Eybpoosh, Delaram Doroud, Iraj Ahmadi, Enayat Anvari, Mohammadreza Aghasadeghi, Abolfazl Fateh
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Ellen Hochleitner Souza Kindermann, Karoline Rodrigues Campos, Adele Caterino-de-Araujo
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Hamed Hosseinalizadeh, Ammar Ebrahimi, Ahmad Tavakoli, Seyed Hamidreza Monavari
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Ehsan Alborzi, Ahmad Tavakoli, Seyed Jalal Kiani, Saied Ghorbani, Davod Javanmard, Milad Sabaei, Maryam Fatemipour, Seyed Hamidreza Monavari
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Mohsen Moghoofei, Sohrab Najafipour, Shayan Mostafaei , Ahmad Tavakoli , Farah Bokharaei-Salim , Saied Ghorbani, Davod Javanmard, Hadi Ghaffari , Seyed Hamidreza Monavari
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Amir Hossein Nafari, Ahmad Ayadi, Zahra Noormohamadi, Fatemeh Sakhaee, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
Infection, Genetics and Evolution.2020; 79: 104144. CrossRef
Polymerase Chain Reaction Assay Using the Restriction Fragment Length Polymorphism Technique in the Detection of Prosthetic Joint Infections: A Multi-Centered Study
Ataollah Moshirabadi, Mohammad Razi, Peyman Arasteh, Mohammad Mahdi Sarzaeem, Saman Ghaffari, Saied Aminiafshar, Kami Hosseinian Khosroshahy, Fatemeh Maryam Sheikholeslami
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One-Step ARMS-PCR for the Detection of SNPs—Using the Example of the PADI4 Gene
Ehnert, Linnemann, Braun, Botsch, Leibiger, Hemmann, Nussler
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Epstein–Barr virus and risk of breast cancer: a systematic review and meta-analysis
Mohammad Farahmand, Seyed Hamidreza Monavari, Zabihollah Shoja, Hadi Ghaffari, Mehdi Tavakoli, Ahmad Tavakoli
Future Oncology.2019; 15(24): 2873. CrossRef
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Eyal Shteyer, Louis Shekhtman, Tal Zinger, Sheri Harari, Inna Gafanovich, Dana Wolf, Hefziba Ivgi, Rima Barsuk, Ilana Dery, Daniela Armoni, Mila Rivkin, Rahul Pipalia, Michal Cohen Eliav, Yizhak Skorochod, Gabriel S. Breuer, Ran Tur-kaspa, Yonit Weil Wien
PLOS ONE.2019; 14(1): e0210173. CrossRef
Correlation of CD81 and SCARB1 polymorphisms on virological responses in Iranian patients with chronic hepatitis C virus genotype 1
Milad Nafari, Shiva Irani, Farzam Vaziri, Safoora Gharibzadeh, Fatemeh Sakhaee, Mohammad Khazeni, Naser Kalhor, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
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First detection of human hepegivirus-1 (HHpgV-1) in Iranian patients with hemophilia
Yazdan Bijvand, Mohammad Reza Aghasadeghi, Fatemeh Sakhaee, Parviz Pakzad, Farzam Vaziri, Alireza Azizi Saraji, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
Scientific Reports.2018;[Epub] CrossRef
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Setareh Mobasheri, Nazanin Irani, Abbas Akhavan Sepahi, Fatemeh Sakhaee, Fatemeh Rahimi Jamnani, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
Gene.2018; 676: 95. CrossRef
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Hend Ibrahim Shousha, Abubakr Hussein Awad, Dalia Abdelhamid Omran, Mayada Mohamed Elnegouly, Mahasen Mabrouk
Japanese Journal of Infectious Diseases.2018; 71(1): 51. CrossRef
IL28B rs12980275 and HLA rs4273729 genotypes as a powerful predictor factor for rapid, early, and sustained virologic response in patients with chronic hepatitis C
Parvaneh Sedighimehr, Shiva Irani, Fatemeh Sakhaee, Farzam Vaziri, Mohammadreza Aghasadeghi, Seyed Mehdi Sadat, Fatemeh Rahimi Jamnani, Abolfazl Fateh, Seyed Davar Siadat
Archives of Virology.2017; 162(1): 181. CrossRef
Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C)
Wai-Ying Fong, Chi-Chun Ho, Wing-Tat Poon
Diagnostics.2017; 7(2): 27. CrossRef
Effect of IL15 rs10833 and SCARB1 rs10846744 on virologic responses in chronic hepatitis C patients treated with pegylated interferon-α and ribavirin
Sahar Sadeghi, Mehdi Davari, Esmaeil Asli, Safoora Gharibzadeh, Farzam Vaziri, Fatemeh Rahimi Jamnani, Abolfazl Fateh, Seyed Davar Siadat
Gene.2017; 630: 28. CrossRef
High platelet count and high probability of CALR detection in myeloproliferative neoplasms
Reza Shirzad, Zari Tahan-nejad, Javad Mohamadi-asl, Mohammad Seghatoleslami, Ahmad Ahmadzadeh, Amal Saki Malehi, Najmaldin Saki
Comparative Clinical Pathology.2017; 26(1): 25. CrossRef
A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C
Seyed Hamidreza Monavari, Roohollah Fateh, Farzam Vaziri, Fatemeh Rahimi Jamnani, Enayat Anvari, Farzin Sadeghi, Parviz Afrough, Ava Behrouzi, Fatemeh Sakhaee, Sepideh Meidaninikjeh, Hamidreza Mollaie, Alireza Hadizadeh Tasbiti, Shamsi Yari, Maryam Sadegh
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EGFR rs11506105 and IFNL3 SNPs but not rs8099917 are strongly associated with treatment responses in Iranian patients with chronic hepatitis C
M Asnavandi, M Zargar, F Vaziri, F R Jamnani, S Gharibzadeh, A Fateh, S D Siadat
Genes & Immunity.2017; 18(3): 144. CrossRef
Genetic Variation in Interleukin-28B and Response to Peg-IFNα-2a/RBV Combination Therapy in Patients with Hepatitis C Virus Infection
Farah Bokharaei-Salim, Mostafa Salehi-Vaziri, Farzin Sadeghi, Khadijeh Khanaliha, Maryam Esghaei, Seyed Hamidreza Monavari, Seyed Moayed Alavian, Shahin Fakhim, Hossein Keyvani
Jundishapur Journal of Microbiology.2016;[Epub] CrossRef

TEM and SHV Genes in Klebsiella pneumoniae Isolated from Cockroaches and Their Antimicrobial Resistance Pattern: Abbas Doosti, Mohammad Pourabbas, Asghar Arshi, Mohammad Chehelgerdi, Hamidreza Kabiri; Osong Public Health Res Perspect. 2015;6(1):3-8. Published online February 28, 2015; DOI: https://doi.org/10.1016/j.phrp.2014.10.011

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Abstract PDF

Objectives
Klebsiella pneumoniae is a gram-negative rod bacterium, a known cause of community-acquired bacterial pneumonia and is an important hospital-acquired pathogen that causes severe morbidity and mortality. The aim of this study was to identify the TEM and SHV genes in K. pneumoniae isolated from cockroaches obtained from hospitals.
Methods
In this study, 250 cockroaches were collected from different hospitals in the province of Chaharmahal Va Bakhtiari, which is located in southwest Iran. The samples were examined for the presence of K. pneumoniae by plating onto a combination of culture media, and the antimicrobial susceptibility patterns of isolated K. pneumoniae from samples were evaluated using the disk diffusion test. In addition, from the culture, genomic bacterial DNA was extracted, and sequence-specific targets (TEM and SHV genes) were amplified using the polymerase chain reaction (PCR) method.
Results
Out of 250 cockroach samples collected from various hospitals, 179 samples (71.60%) were positive for K. pneumoniae. PCR reaction was performed using specific oligonucleotide primers (TEM-F, TEM-R and SHV-F, SHV-R) for the amplification of each gene, and amplified products were visualized on 1% agarose gel electrophoresis. Of all the specimens amplified by PCR in this research, 32 samples (17.87%) were positive for TEM and 15 samples (8.37%) were positive for SHV.
Conclusion
Detection of TEM and SHV genes using molecular methods and their pattern of antimicrobial resistance can provide useful information about the epidemiology of and risk factors associated with K. pneumoniae infection.

Citations

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Novel adjuvant nano-vaccine induced immune response against Acinetobacter baumannii
Tohid Piri-Gharaghie, Abbas Doosti, Seyed Abbas Mirzaei
AMB Express.2023;[Epub] CrossRef
Virulence factors, antibiotic resistance patterns, and molecular types of clinical isolates of Klebsiella Pneumoniae
Mitra Ahmadi, Reza Ranjbar, Payam Behzadi, Taher Mohammadian
Expert Review of Anti-infective Therapy.2022; 20(3): 463. CrossRef
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Kashaf Junaid, Hasan Ejaz, Sonia Younas, Awadh Alanazi, Humaira Yasmeen, Abdul Rehman
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First Report of Extended-Spectrum β-Lactamase ( bla CTX-M1 ) and Colistin Resistance Gene mcr-1 in E. coli of Lineage ST648 from Cockroaches in Tunisia
Sarrah Landolsi, Rachid Selmi, Linda Hadjadj, Asma Ben Haj Yahia, Kaouther Ben Romdhane, Lilia Messadi, Jean Marc Rolain, Courtney J. Robinson
Microbiology Spectrum.2022;[Epub] CrossRef
Phenotypic and genotypic detection of extended spectrum beta lactamase enzyme in Klebsiella pneumoniae
Aso Bakr Mohammed, Khanda Abdullateef Anwar, Monica Cartelle Gestal
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Virulence factors and antibiotic resistance properties of Streptococcus species isolated from hospital cockroaches
Mohammad Chehelgerdi, Reza Ranjbar
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Sheida Beiranvand, Abbas Doosti, Seyed Abbas Mirzaei
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Molecular epidemiology of Carbapenem-resistant Klebsiella pneumoniae in a paediatric hospital in China
Bingjie Wang, Fen Pan, Chun Wang, Wantong Zhao, Yan Sun, Tiandong Zhang, Yingying Shi, Hong Zhang
International Journal of Infectious Diseases.2020; 93: 311. CrossRef
Fecal Carriage and Molecular Epidemiology of Carbapenem-Resistant Enterobacteriaceae from Inpatient Children in a Pediatric Hospital of Shanghai

Qi Xu, Fen Pan, Yan Sun, Chun Wang, Yingying Shi, Tiandong Zhang, Fangyuan Yu, Hong Zhang
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Hassan Nasirian, Michael Rust
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Lotfi Loucif, Djamila Gacemi-Kirane, Zineb Cherak, Naima Chamlal, Nadia Grainat, Jean-Marc Rolain
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Multiplex Real-time Polymerase Chain Reaction Assays for Simultaneous Detection of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus: Jie Yeun Park, Semi Jeon, Jun Young Kim, Misun Park, Seonghan Kim; Osong Public Health Res Perspect. 2013;4(3):133-139. Published online June 30, 2013; DOI: https://doi.org/10.1016/j.phrp.2013.04.004

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Abstract PDF

Objectives
A multiplex real-time polymerase chain reaction (RT-PCR) method was developed for the identification of three Vibrio species: Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus.
Methods
Specific primers and probes targeting the hlyA, tlh, and vvhA genes were selected and used for multiplex real-time PCR to confirm the identification of V. cholerae, V. parahaemolyticus, and V. vulnificus, respectively. This method was applied to screen Vibrio species from environmental samples and combining it with a culture-based method, its effectiveness was evaluated in comparison with culture-based methods alone.
Results
Specific PCR fragments were obtained from isolates belonging to the target species, indicating a high specificity of this multiplex real-time PCR. No cross-reactivity with the assay was observed between the tested bacteria. The sensitivity of the multiplex real-time PCR was found to have a lower limit of 10⁴ colony-forming units/reaction for all three Vibrio species. The combination strategy raised the isolation ratio of all three Vibrio species 1.26- to 2.75-fold.
Conclusion
This assay provides a rapid, sensitive, and specific technique to detect these three Vibrio species in the environment.

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A Comparison of Subtyping Methods for Differentiating Salmonella enterica Serovar Enteritidis Isolates Obtained from Food and Human Sources: Ji-Yeon Hyeon, Jung-Whan Chon, Jun-Ho Park, Moo-Sang Kim, Young-Hee Oh, In-Soo Choi, Kun-Ho Seo; Osong Public Health Res Perspect. 2013;4(1):27-33. Published online February 28, 2013; DOI: https://doi.org/10.1016/j.phrp.2012.12.005

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Abstract PDF

Purpose: To evaluate the abilities of these subtyping methods, we distinguished Salmonella Enteritidis (S. Enteritidis) isolated from food products and human clinical samples between 2009 and 2010 in Seoul using five subtyping methods.
Methods
We determined the subtypes of 20 S. Enteritidis isolates from food and human sources using phage typing, antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multi-locus sequence typing (MLST).
Results
A total of 20 tested isolates were differentiated into six antimicrobial susceptibility patterns, three different phage types, four different PFGE profiles, seven rep-PCR patterns, and one MLST type. Food isolates were considerably more susceptible to antibiotics than human isolates. We were best able to discriminate among S. Enteritidis isolates using rep-PCR, and obtained the highest Simpson’s diversity index of 0.82, whereas other methods produced indices that were less than 0.71. PFGE pattern appeared to be more related to antimicrobial resistance and phage types of S. Enteritidis isolates than rep-PCR. MLST revealed identical alleles in all isolates at all seven loci examined, indicating no resolution.
Conclusion
The results of this study suggest that rep-PCR provided the best discriminatory power for phenotypically similar S. Enteritidis isolates of food and human origins, whereas the discriminatory ability of MLST may be problematic because of the high sequence conservation of the targeted genes.

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Article

Multiplex Real-Time Polymerase Chain Reaction-Based Method for the Rapid Detection of gyrA and parC Mutations in Quinolone-Resistant Escherichia coli and Shigella spp.: Junyoung Kim, Semi Jeon, Hyungjun Kim, Misun Park, Soobok Kim, Seonghan Kim; Osong Public Health Res Perspect. 2012;3(2):113-117. Published online June 30, 2012; DOI: https://doi.org/10.1016/j.phrp.2012.04.004

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15 Download
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Abstract PDF

Two real-time polymerase chain reaction assays were developed to detect mutations in codons 83 and 87 in gyrA and in codons 80 and 91 in parC, the main sites that causes quinolone resistance in pathogenic Escherichia coli and Shigella spp. isolates. These assays can be employed as a useful method for controlling infections caused by quinolone-resistant E coli and Shigella isolates.

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