食源性病原菌分型方法研究进展

目前食源性病原菌常用的分型方法主要包括血清学分型、脉冲场凝胶电泳分型、多位点序列分型、多位点可变数目串联重复序列分型等, 在食源性病原菌的监测、传染源的追踪、流行病监测等方面具有重要意义。本文就食源性病原菌常用的分型方法及其应用情况进行综述。     

多位点序列分型技术以及在乳酸菌分类鉴定中的应用

多位点序列分型(Multi-Locus Sequence Typing,MLST)技术是通过测定同种细菌管家基因(housekeeping gene)的序列,来确定等位基因的差异,进而比较分析菌株之间进化关系的一种分子分型方法。该方法在细菌生物学基础研究方面已经发挥了重要的作用,本文主要阐述MLST技术的方法和其在乳酸菌分类鉴定中的应用。     

基于VNTR技术的食用红甜菜不育系的选育

甜菜在世界糖料作物中占有重要地位,为选育提高育种效率,符合人们期望性状的优良品系,增加甜菜糖产量,分子辅助育种越来越被育种家们重视。而对于受到细胞质基因和细胞核基因控制甜菜雄性不育性的分子标记研究是近年来取得了较大突破。本实验是以食用红甜菜(工大食甜1号)为实验材料,利用数目可变的串联重复序列(VNTR)技术对其细胞质和细胞核育性类型进行鉴定,从中选育出了11株不育型甜菜。通过对其田间鉴定表明,选育的11株甜菜不育率稳定,不育率达到100%。     

食源性致病菌溯源分型技术研究进展

微生物溯源分型,是根据微生物的生化特征或基因特征,对不同来源微生物间的关系迚行分型溯源。通过对食源性致病菌的分型研究,精确分析食源性致病菌的特征,查找食源性致病菌的来源,为有效应对食品安全提供技术支持。随着分子生物学和测序技术的发展,微生物溯源分型技术获得了巨大的发展,传统的溯源分型斱法主要是表型分型和基因型分型,本文以沙门氏菌为例介绍了食源性致病菌溯源分型技术的最新研究迚展,综述了食源性致病菌分型技术中的生化分型法、血清学分型法、抗生素耐药分型法、基于蛋白质指纹图谱分型技术、脉冲场凝胶电泳技术、重复序列扩增分型技术、有规律间隔的短回文重复序列技术、核心基因组多位点序列分析分型法、基于全基因组测序的单核苷酸多态性分型法等技术,为做好食源性致病菌的监管工作提供有力参考     

单核苷酸多态性在茶树中应用的研究进展

茶树原产于中国西南地区,是一种重要的经济作物。茶叶作为中国的传统饮品,是世界上三大无酒精饮料之一。长期的自然演化及自交不亲和使得茶树的种质资源极其丰富。单核苷酸多态性(single nucleotide polymorphism,SNP)是基因组水平上单核苷酸突变引起的基因序列多样性,是继限制性酶切片段多态性(restriction fragment length polymorphism,RFLP)和简单序列重复(simple sequence repeat,SSR)的第3代分子标记,广泛存在于生物基因组中。SNP分子标记作为最重要的分子标记技术对遗传学研究有极其重要的作用。本文介绍了SNP分子标记的特征,综述了SNP在茶树中的开发检测方法,研究应用于分子标记、基因定位、关联分析等,旨在为理解和研究SNP分子标记在茶树中的研究应用提供参考。     

学生宿舍和食堂环境中克罗诺杆菌污染状况及分子分型和耐药特征分析

目的 了解徐州市某学校学生宿舍和食堂环境中克罗诺杆菌污染状况、分子分型及耐药特征,为预警食源性克罗诺杆菌病暴发提供参考.方法 采集徐州市某学校学生宿舍和食堂环境样品156份,分离并鉴定克罗诺杆菌,并利用基于O-抗原的血清分型和多位点序列分型(multilocus sequence typing,MLST)技术对分离株进...     

食源性致病菌溯源分型技术研究进展

食源性致病菌是影响食品质量与安全的主要因素。及时和准确的菌株分型数据能够快速检测暴发集群,为正在进行的感染控制和公共卫生应对活动提供信息,对于食源性疾病的预防与爆发具有重要意义。近年来各种细菌分型方法取得了巨大进展,本文对几种常见食源性致病菌溯源分型技术进行综述,包括血清分型技术、噬菌体分型技术、脉冲场凝胶电泳技术、变性梯度凝胶电泳技术、细菌基因组重复序列PCR技术（Rep-PCR）、低频限制性切割位点PCR技术（IRS-PCR）、扩增片段长度多态性技术（AFLP）、限制性片段长度多态性技术（RFLP）、多位点序列分型技术（MLST）、核心基因组多位点序列分型技术（cgMLST）、单核苷酸多态性分型技术以及基质辅助激光解析电离飞行时间质谱技术（MALDI-TOF-MS）等。针对不同技术的原理对其所适用的环境进行阐述,并对分型溯源能力进行比较分析,为流行病学中食源性致病菌监测方案提供参考依据。     

AFLP技术在食品微生物研究中的应用

随着现代分子生物学技术的发展 ,对微生物学的研究也进入到分子、基因水平。扩增片段长度多态性(AFLP)是一种基于PCR的高分辨率DNA指纹技术 ,它能检测整个微生物基因组的多态性 ,并且结果可重复、分辨率高。近些年来 ,AFLP在细菌等微生物的遗传相关性鉴定、流行病学分型等上的应用得到迅速发展。文中介绍了AFLP技术的基本原理、反应流程 ,探讨了其在食品微生物研究领域中的应用现状和前景     

金黄色葡萄球菌肠毒素与多位点序列分型分子分型研究进展

金黄色葡萄球菌是引起临床疾病、社区感染和食物中毒的常见革兰氏阳性菌;肠毒素是参与金黄色葡萄球菌引起食物中毒、猩红热、全身感染等疾病的重要毒力因子;目前已发现27种金黄色葡萄球菌肠毒素/类肠毒素,不同来源金黄色葡萄球菌携带肠毒素/类肠毒素存在差异;多位点序列分型(MLST) 是一门新兴的基于细菌多个管家基因位点差异性分析、可长期监测细菌遗传进化趋势的分子分型技术;截至2021年初MLST已建立128种细菌的分型数据库,金黄色葡萄球菌数据库中已有6583种分型,金黄色葡萄球菌ST分型存在明显的地区流行性,各地已形成独特优势克隆。目前研究表明金黄色葡萄球菌肠毒素/类肠毒素携带与MLST分型间存在一定的相关性,本文将围绕金黄色葡萄球菌肠毒素/类肠毒素、MLST分型及相关性进行综述。     

创伤弧菌16S-23S rDNA间区变形梯度凝胶电泳多态性分析

目的 建立创伤弧菌基因分型的新方法,了解创伤弧菌的分子特征.方法 应用PCR-变形梯度凝胶电泳(PCR-DGGE)技术对创伤弧菌的16S-23S rDNA间区(16S-23S rDNA intergenic spacer regions,ISR)多态性进行分析比较,结合药敏试验,以进一步验证分离菌株之间的亲缘关系.结果 ISR-PCR将创伤弧菌菌株扩增出4条约900、750、650、550 bp大小不同的条带;同时,创伤弧菌的ISR-DGGE序列表现出明显的株间差异,18株共产生了16种不同的指纹图谱;聚类分析将所有的细菌分为两大类,相似性分别为0.65和0.71;亲缘关系较近的菌株具有不同于关系较远的菌株的耐药谱,与ISR-DGGE指纹图谱分析相一致.结论 这种分子操作技术完全能够用于创伤弧菌株型的调查与鉴定,为创伤弧菌的基因分型提供了一种新的方法.     

Development and application of Multiple-Locus Variable number of tandem repeat Analysis (MLVA) to subtype a collection of Listeria monocytogenes

In this study we report the development and application of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) strategy for subtyping Listeria monocytogenes. Genome profiles of a collection of forty-five food-borne L. monocytogenes isolates were compared using MLVA. These isolates were obtained as part of an active surveillance programme of foods in the south-east region of Ireland. MLVA successfully discriminated amongst the isolates. The method was easy to perform, relatively fast and could be deployed in any molecular laboratory with basic laboratory equipment. This approach is a valuable tool, which has the capability to provide comparable results when compared with other more established typing methods, including pulsed-field gel electrophoresis (PFGE).     

Application of multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing to subtype Salmonella enterica serovar Typhimurium isolated from pig farms, pork slaughterhouses and meat producing plants in Ireland

Salmonella enterica subsp. enterica serovar Typhimurium is a common zoonotic pathogen encountered in Irish pigs and the pork industry and its characterisation using highly discriminatory typing methods is necessary for epidemiological studies, outbreak investigation and control. Multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing were applied to characterise 301 S. typhimurium isolates of porcine origin isolated from farms, slaughterhouses and pork meat producing plants in Ireland over a four-year period. 154 MLVA patterns were obtained compared to 19 phage types and 38 AMR patterns, and MLVA was particularly useful for discriminating isolates of the same phage type, e.g. DT104 and DT104b, or isolates that were Untypable or in the category of "react with phage but does not conform to a recognised phage type" (RDNC) by the phage typing method. Cluster analysis of MLVA profiles using a minimum spanning tree (MST) demonstrated two major clusters (I and II), which showed to have a clear association with phage types, cluster I associated to phage types DT104, U302 and DT120 and cluster II associated to DT193 and U288. The results of this present study showed that MLVA is highly discriminatory and permitted the identification of identical profiles among isolates obtained at different points of the pork food chain. The same MLVA profile was observed in some cases among isolates with different phage types. While this can be explained by the fact that some phage types are closely related, it also indicates that combining phage typing and MLVA enhances strain typing of S. typhimurium.     

Phenotypic Characterization and Genotypic Subtyping of Salmonella enterica Serovars Enteritidis and Gallinarum Isolated from Human and Poultry-Related Samples

This study aimed to assess the serotypes, antibiotic susceptibility, and molecular subtyping of Salmonella enterica isolated from food products and human patients with gastroenteritis. A total of 59 isolates were investigated, and the results revealed a predominance of S. Enteritidis with 57.63% (34/59) S. Gallinarum held second with 15.62% (5/32) of total food borne. While, isolates from humans showed 18.51% (5/27) of S. Typhimurium. High level of resistance to nalidixic acid was noted among food strains and 35.29% of human isolates were found to be multidrug resistant. Eight representative isolates were subtyping using three molecular approaches, ribotyping, Multilocus sequence typing (MLST) and Multiple-locus variable number tandem repeat analysis (MLVA). MLST showed three sequence types corresponding to two clonal complexes, (ST-78, CC-4) for S. Gallinarum, (ST-11, CC-4) for S. Enteritidis and (S-367, CC-37) for S. Cerro. While, MLVA generated six different profiles targeting nine loci for S. Enteritidis and S. Gallinarum.     

Multiple-locus variable number of tandem repeat analysis (MLVA) of Listeria monocytogenes directly in food samples

Listeria monocytogenes is the etiologic agent of listeriosis responsible for severe and fatal infections in humans. Listeria contamination occurs quite often in a wide range of foods due to its ubiquitous nature. Isolates need to be characterized to a strain level for accurate diagnosis of Listeria infection, epidemiological studies, investigation of outbreaks and effective prevention and control of food-borne listeriosis. The purpose of this research was to evaluate the multiple-locus variable number of tandem repeat analysis (MLVA) for sub-typing L. monocytogenes isolates in pure cultures and in food matrices. Two multiplex PCR assays were formulated to amplify six specific loci using fluorescently-labeled primers; and the amplicons were analyzed by capillary electrophoresis. The MLVA method resulted in 34 unique DNA fingerprint patterns from 46 L. monocytogenes isolates of 10 serotypes which had 29 or 30 PFGE patterns with a single restriction enzyme and 34 AFLP patterns. The MLVA patterns of the 46 isolates remained unchanged in the presence of pre-enriched food matrices including sausage, ham, chicken, milk and lettuce. The MLVA method successfully typed L. monocytogenes strains spiked in cheese, roast beef, egg salad and vegetable samples after 48 h enrichment at the initial inoculation levels of 1-5 CFU per 25 g of food or higher. The limits of detection (typing) of the MLVA method were 10³-10⁴ CFU/mL of pre-enriched food broth when evaluated using post-spiked sausage, ham, chicken, milk and lettuce samples. The MLVA method was simple, highly discriminatory, and easy to perform with portable (numerical) results. To our knowledge, this is the first report that describes the application of the MLVA method directly to food samples and demonstrates the possibility to obtain rapid and accurate subtyping results before an isolate is obtained.     

Evaluation of Fourier transform infrared (FT-IR) spectroscopy and chemometrics as a rapid approach for sub-typing Escherichia coli O157:H7 isolates

The importance of tracking outbreaks of foodborne illness and the emergence of new virulent subtypes of foodborne pathogens have created the need for rapid and reliable sub-typing methods for Escherichia coli O157:H7. Fourier transform infrared (FT-IR) spectroscopy coupled with multivariate statistical analyses was used for sub-typing 30 strains of E. coli O157:H7 that had previously been typed by multilocus variable number tandem repeat analysis (MLVA) and pulsed field gel electrophoresis (PFGE). Hierarchical cluster analysis (HCA) and canonical variate analysis (CVA) of the FT-IR spectra resulted in the clustering of the same or similar MLVA types and separation of different MLVA types of E. coli O157:H7. The developed FT-IR method showed better discriminatory power than PFGE in sub-typing E. coli O157:H7. Results also indicated the spectral relatedness between different outbreak strains. However, the grouping of some strains was not in complete agreement with the clustering based on PFGE and MLVA. Additionally, HCA of the spectra differentiated the strains into 30 sub-clusters, indicating the high specificity and suitability of the method for strain level identification. Strains were also classified (97% correct) based on the type of Shiga toxin present using CVA of the spectra. This study demonstrated that FT-IR spectroscopy is suitable for rapid (≤16 h) and economical sub-typing of E. coli O157:H7 with comparable accuracy to MLVA typing. This is the first report of using an FT-IR-based method for sub-typing E. coli O157:H7.     

Development of a multilocus variable-number of tandem repeat typing method for Listeria monocytogenes serotype 4b strains

Listeria monocytogenes serotype 4b strains have been identified as the causative agent in many human listeriosis epidemics as well as in a considerable number of sporadic cases. Due to the genetic homogeneity of serotype 4b isolates, development of rapid subtyping methods with high discriminatory power for serotype 4b isolates is required to allow for improved outbreak detection and source tracking. In this study, multilocus variable-number tandem repeat analysis (MLVA) was developed and used to characterize 60 serotype 4b isolates from various sources. All isolates were also characterized by automated EcoRI ribotyping, single enzyme pulsed-field gel electrophoresis (PFGE) with ApaI, and a multilocus sequence typing (MLST) scheme targeting six virulence and virulence-associated genes. Discriminatory power of MLVA (as determined by Simpson Index of Discrimination) was higher than the discriminatory power of any of the other three methods. MLVA markers targeted were found to be stable and did not change when three isolates were passaged daily for 70 days. Cluster analyses of MLVA, PFGE and MLST consistently grouped the same isolates into three major clusters, each of which includes one of the three major L. monocytogenes epidemic clones (i.e., ECI, ECIa and ECII). We conclude that the MLVA method described here (i) provides for more discriminatory subtyping of L. monocytogenes serotype 4b strains than the other three methods, (ii) identifies three major groups within the serotype 4b, which are consistent with the groups identified by other subtyping methods, and (iii) is easy to interpret. Use of MLVA may thus be recommended for subtyping of serotype 4b isolates, including as a secondary more discriminatory subtyping method that could be used after initial isolate characterization by PFGE or ribotyping.     

Genotyping of dairy Bacillus licheniformis isolates by high resolution melt analysis of multiple variable number tandem repeat loci

In dairy foods, the sporeformer Bacillus licheniformis can be the cause of spoilage or specification compliance issues. Currently used methods for genotyping B. licheniformis have limited discrimination with only 2 or 3 different subgroups being identified. Here, we have developed a multi-locus variable number tandem repeat analysis (MLVA) method and combined it with high resolution melt analysis (MLV-HRMA) for genotyping B. licheniformis. Five repetitive loci were identified and used as markers for genotyping 52 isolates from two milk powder processing plants and retail samples. Nineteen genotypes could be identified using both MLVA and MLV-HRMA leading to Hunter–Gaston discrimination indices (D-value) of 0.93 each. It was found that all 5 MLVA loci were stable following 10 days of sub-culturing of 8 representative isolates. All isolates were also genotyped using previously used methods including randomly amplified polymorphic DNA-PCR (RAPD) and partial rpoB sequencing. Five different RAPD profiles and 5 different partial rpoB sequence types were identified resulting in corresponding D-values of 0.6 and 0.46, respectively. Analysis of the genotypes from dairy samples revealed that dairy B. licheniformis isolates are more heterogeneous than previously thought and that this new method can potentially allow for more discriminatory tracking and monitoring of specific genotypes.     

Development of a multilocus variable number of tandem repeat typing method for Oenococcus oeni

Oenococcus oeni is responsible for the malolactic fermentation of wine. Genomic diversity has already been established in this species. In addition, winemakers usually report varying starter culture efficiency. The monitoring of indigenous and selected strains is essential for understanding strain survival and implantation during the winemaking process. In this study, we report the development of the first typing scheme for O. oeni using multiple-locus variable number of tandem repeat analysis (VNTR). The discriminatory power of 14 out of 44 tandem repeat loci in the genome of the PSU-1 strain was initially evaluated with a test collection of 18 genotypically distinct starter strains. Then five VNTR loci, which can be easily scored with the technology used here, were identified and used to genotype a collection of 236 strains, previously classified by restriction endonuclease analysis-pulsed-field gel electrophoresis (REA-PFGE) and multilocus sequence typing (MLST) into 136 REA-PFGE types or 110 MLST types. The discriminatory power of VNTR (as determined by Simpson's index of discrimination) was higher than that of the other two methods, with 201 VNTR types. The targeted VNTR markers were found to be stable and did not change for the clones of the same strain deposited in a collection at intervals of several years. Strains isolated from the different wine producing areas or the products were assigned to phylogenetic groups and were statistically linked with the VNTR profiles. Another interesting observation was that the loci were found in sequences homologous to regions encoding for membrane-anchored proteins.     

Genetically Similar Isolates of Salmonella enterica Serotype Enteritidis Persistent in China for a Long‐Term Period

Salmonella enterica serotype Enteritidis (S. Enteritidis) is an important causative agent of nontyphoidal salmonellosis in human populations. In this study, we collected 72 S. Enteritidis strains from 2004 to 2014 in Ningbo, mid‐east China. Of the 72 strains, we identified a dominant clone of 58 strains recovered from patient's feces (n = 48), blood (n = 1), pleural effusion (n = 1), chickens (n = 3), and dessert cakes (n = 5) by pulsed‐field gel electrophoresis (PFGE) and variable‐number of tandem repeat analysis (MLVA). The profile arrangements of MLVA were SE1‐SE2‐SE3‐SE5‐SE6‐SE8‐SE9: 4‐4‐3‐11‐10‐1‐3. These dominant strains were susceptible to ampicillin, chloramphenicol, tetracycline, ciprofloxacin, gentamicin, cefotaxime and trimethoprim–sulfamethoxazole, and resistant to nalidixic acid. Additionally, all isolates harboured virulence genes invA, sipA, sopE, and spvB when tested by PCR. Our results reveal that genetically similar S. Enteritidis strains which accounted for several outbreaks as well as blood infection and pleural cavity infection are prevalent in China for a long‐term period. This situation calls for further attention in the prevention and control of foodborne disease caused by Salmonella species.     

Genetic diversity of the human pathogen Vibrio vulnificus: a new phylogroup

The biotype 3 group of the human pathogen Vibrio vulnificus emerged in Israel probably as a result of genome hybridization of two bacterial populations. We performed a genomic and phylogenetic study of V. vulnificus strains isolated from the environmental niche from which this group emerged — fish aquaculture in Israel. The genetic relationships and evolutionary aspects of 188 environmental and clinical isolates of the bacterium were studied by genomic typing. Genetic relations were determined based on variation at 12 variable number tandem repeat (VNTR, also termed SSR) loci. Analysis revealed a new cluster, in addition to the main groups of biotype 1& 2 and biotype 3. Similar grouping results were obtained with three different statistical approaches. Isolates forming this new cluster presented unclear biochemical profile nevertheless were not identified as biotype 1 or biotype 3. Further examination of representative strains by multilocus sequence typing (MLST) of 10 housekeeping genes and 5 conserved hypothetical genes supported the identification of this as yet undiscovered phylogroup (phenotypically diverse), termed clade A herein. This new clonal subgroup includes environmental as well as clinical isolates. The results highlight the fish aquaculture environment, and possibly man-made ecological niches as a whole, as a source for the emergence of new pathogenic strains.