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Pakbin B, Didban A, Brück WM, Alizadeh M. Phylogenetic analysis and antibiotic resistance of Shigella sonnei isolates. FEMS Microbiol Lett 2022; 369:6575538. [PMID: 35482608 DOI: 10.1093/femsle/fnac042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Shigellosis is one of the most important gastric infections caused by different species of Shigella and has been regarded as a serious threat to public health. Lineage/sublineage profile of S. sonnei is strongly associated with the antibiotic resistance and population structure of this pathogen. In this study, we determined the phylogeny and antibiotic resistance profiles of S. sonnei strains, isolated from 1246 stool and 580 food samples, using multiplex PCR-HRMA genotyping and Kirby-Bauer disk diffusion methods, respectively. A total of 64 S. sonnei strains were isolated (13 food and 51 clinical isolates). Multiplex PCR-HMR assay was able to differentiate the lineages II and III, and sublineages IIIb and IIIc strains successfully considering the definite melting curves and temperatures. Lineage I and sublineage IIIa strain were not isolated in this study. We also demonstrated that most of the S. sonnei strains isolated from both food and clinical samples clustered within the lineage III and sublineage IIIc. Resistance against trimethoprim-sulfamethoxazole, tetracycline, chloramphenicol and streptomycin antibiotics were the most prevalent phenotypes among the S. sonnei lineage III and sublineage IIIc strains.
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Affiliation(s)
- Babak Pakbin
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland.,Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., PO Box: 34185-754, Qazvin, Iran.,Medical Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin 34197-59811, Iran
| | - Abdollah Didban
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., PO Box: 34185-754, Qazvin, Iran
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland
| | - Mehdi Alizadeh
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., PO Box: 34185-754, Qazvin, Iran
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Simultaneous differential detection of canine blood parasites: Multiplex high-resolution melting analysis (mHRM). Ticks Tick Borne Dis 2020; 11:101370. [PMID: 31924501 DOI: 10.1016/j.ttbdis.2020.101370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/28/2019] [Accepted: 01/02/2020] [Indexed: 11/21/2022]
Abstract
Recently, the incidence of canine infection by the tick-borne parasites Babesia spp., Hepatozoon canis, Ehrlichia canis and Anaplasma platys has been increasing globally. We have developed a multiplex high-resolution melting analysis (mHRM) technique to reduce the time demands and costs associated with detecting haemoparasites in canine blood, while increasing the degree of reliability of this method of analysis. We have designed primers that are specific for protozoans (B. vogeli and H. canis) and Rickettsia-like bacteria (E. canis and A. platys) based on the 18S or 16S rDNA sequences, respectively. Two primer pairs (Protz18S-C and Bact16S-A) were found to be suitable for detecting these agents since their melting temperatures (Tm) exhibited discernible differences among the four haemoparasites, A. platys, B. vogeli, E. canis and H. canis (83.10 °C, 82.41 °C, 80.37 °C and 78.56 °C, respectively). The sequences acquired from these PCR products were >94 % identical to those of A. platys, B. vogeli, E. canis and H. canis in GenBank. The limit of detection (LOD) for B. vogeli, E. canis and A. platys was 103 copies/μl, while the LOD for H. canis was 104 copies/μl. Of the 68 dogs tested, 28 (41 %) were infected with these agents. The most commonly occurring infection involved E. canis, followed by B. vogeli, A. platys and H. canis, with infection percentages of 26 %, 13 %, 7 % and 6 %, respectively. These results demonstrate that mHRM can serve as a rapid, economical and reliable tool for the detection of parasitic diseases in canine blood for diagnosis and epidemiology.
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
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A Novel Multiplex HRM Assay to Detect Clopidogrel Resistance. Sci Rep 2017; 7:16021. [PMID: 29167499 PMCID: PMC5700108 DOI: 10.1038/s41598-017-16310-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/10/2017] [Indexed: 12/25/2022] Open
Abstract
Clopidogrel is an antiplatelet medicine used to prevent blood clots in patients who have had a heart attack, stroke, or other symptoms. Variability in the clinical response to clopidogrel treatment has been attributed to genetic factors. In particular, five SNPs of rs4244285, rs4986893, rs12248560, rs662 and rs1045642 have been associated with resistance to clopidogrel therapy in Chinese population. This work involves the development of a multiplex high-resolution melting (HRM) assay to genotype all five of these loci in 2 tubes. Amplicons corresponding to distinct SNPs in a common tube were designed with the aid of uMelt prediction software to have different melting temperatures Tm by addition of a GC-rich tail to the 5' end of the certain primers. Two kinds of commercial methods, Digital Fluorescence Molecular Hybridization (DFMH) and Sanger sequencing, were used as a control. Three hundred sixteen DFMH pretested samples from consecutive acute coronary syndrome patients were used for a blinded study of multiplex HRM. The sensitivity of HRM was 100% and the specificity was 99.93% reflecting detection of variants other than the known resistance SNPs. Multiplex HRM is an effective closed-tube, highly accurate, fast, and inexpensive method for genotyping the 5 clopidogrel resistance associated SNPs.
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Sváb D, Bálint B, Vásárhelyi B, Maróti G, Tóth I. Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain. Front Cell Infect Microbiol 2017; 7:229. [PMID: 28611956 PMCID: PMC5447701 DOI: 10.3389/fcimb.2017.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/17/2017] [Indexed: 01/26/2023] Open
Abstract
Shigella strains are important agents of bacillary dysentery, and in recent years Shigella sonnei has emerged as the leading cause of shigellosis in industrialized and rapidly developing countries. More recently, several S. sonnei and Shigella flexneri strains producing Shiga toxin (Stx) have been reported from sporadic cases and from an outbreak in America. In the present study we aimed to shed light on the evolution of a recently identified Shiga toxin producing S. sonnei (STSS) isolated in Europe. Here we report the first completely assembled whole genome sequence of a multidrug resistant (MDR) Stx-producing S. sonnei (STSS) clinical strain and reveal its phylogenetic relations. STSS 75/02 proved to be resistant to ampicillin, streptomycin, tetracycline, chloramphenicol, thrimetoprim, and sulfomethoxazol. The genome of STSS 75/02 contains a 4,891,717 nt chromosome and seven plasmids including the 214 kb invasion plasmid (pInv) harboring type III secretion system genes and associated effectors. The chromosome harbors 23 prophage regions including the Stx1 converting prophage. The genome carries all virulence determinants necessary for an enteroinvasive lifestyle, as well as the Stx1 encoding gene cluster within an earlier described inducible converting prophage. In silico SNP genotyping of the assembled genome as well as 438 complete or draft S. sonnei genomes downloaded from NCBI GenBank revealed that S. sonnei 75/02 belongs to the more recently diverged global MDR lineage (IIIc). Targeted screening of 1131 next-generation sequencing projects taken from NCBI Short Read Archive of confirms that only a few S. sonnei isolates are Stx positive. Our results suggest that the acquisition of Stx phages could have occurred in different environments as independent events and that multiple horizontal transfers are responsible for the appearance of Stx phages in S. sonnei strains.
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Affiliation(s)
- Domonkos Sváb
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of SciencesBudapest, Hungary
| | | | | | - Gergely Maróti
- Biological Research Centre, Institute of Biochemistry, Hungarian Academy of SciencesSzeged, Hungary
| | - István Tóth
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of SciencesBudapest, Hungary
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High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli. Antimicrob Agents Chemother 2017; 61:AAC.00265-17. [PMID: 28416542 PMCID: PMC5444143 DOI: 10.1128/aac.00265-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/07/2017] [Indexed: 02/05/2023] Open
Abstract
Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification.
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Chiou CS, Izumiya H, Kawamura M, Liao YS, Su YS, Wu HH, Chen WC, Lo YC. The worldwide spread of ciprofloxacin-resistant Shigella sonnei among HIV-infected men who have sex with men, Taiwan. Clin Microbiol Infect 2016; 22:383.e11-383.e16. [DOI: 10.1016/j.cmi.2015.12.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 12/25/2015] [Accepted: 12/31/2015] [Indexed: 10/22/2022]
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Ison SA, Delannoy S, Bugarel M, Nagaraja TG, Renter DG, den Bakker HC, Nightingale KK, Fach P, Loneragan GH. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique. Appl Environ Microbiol 2016; 82:640-9. [PMID: 26567298 PMCID: PMC4711113 DOI: 10.1128/aem.03182-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.
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Affiliation(s)
- Sarah A Ison
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Sabine Delannoy
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Marie Bugarel
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - David G Renter
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Henk C den Bakker
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Kendra K Nightingale
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Patrick Fach
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Guy H Loneragan
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
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