16S rRNA partial gene sequencing for the differentiation and molecular subtyping of Listeria species

Use of 16S rRNA partial gene sequencing within the regulatory workflow could greatly reduce the time and labor needed for confirmation and subtyping of Listeria monocytogenes. The goal of this study was to build a 16S rRNA partial gene reference library for Listeria spp. and investigate the potential for 16S rRNA molecular subtyping. A total of 86 isolates of Listeria representing L. innocua, L. seeligeri, L. welshimeri, and L. monocytogenes were obtained for use in building the custom library. Seven non-Listeria species and three additional strains of Listeria were obtained for use in exclusivity and food spiking tests. Isolates were sequenced for the partial 16S rRNA gene using the MicroSeq ID 500 Bacterial Identification Kit (Applied Biosystems). High-quality sequences were obtained for 84 of the custom library isolates and 23 unique 16S sequence types were discovered for use in molecular subtyping. All of the exclusivity strains were negative for Listeria and the three Listeria strains used in food spiking were consistently recovered and correctly identified at the species level. The spiking results also allowed for differentiation beyond the species level, as 87% of replicates for one strain and 100% of replicates for the other two strains consistently matched the same 16S type.     

Pseudomonas fluorescens group bacterial strains are responsible for repeat and sporadic postpasteurization contamination and reduced fluid milk shelf life

Postpasteurization contamination (PPC) of high temperature, short time-pasteurized fluid milk by gram-negative (GN) bacteria continues to be an issue for processors. To improve PPC control, a better understanding of PPC patterns in dairy processing facilities over time and across equipment is needed. We thus collected samples from 10 fluid milk processing facilities to (1) detect and characterize PPC patterns over time, (2) determine the efficacy of different media to detect PPC, and (3) characterize sensory defects associated with PPC. Specifically, we collected 280 samples of high temperature, short time-pasteurized milk representing different products (2%, skim, and chocolate) and different fillers over 4 samplings performed over 11 mo at each of the 10 facilities. Standard plate count (SPC) as well as total GN, coliform, and Enterobacteriaceae (EB) counts were performed upon receipt and after 7, 10, 14, 17, and 21 d of storage at 6°C. We used 16S rDNA sequencing to characterize representative bacterial isolates from (1) test days with SPC >20,000 cfu/mL and (2) all samples with presumptive GN, coliforms, or EB. Day-21 samples were also evaluated by a trained defect judging panel. By d 21, 226 samples had SPC >20,000 cfu/mL on at least 1 d of shelf life; GN bacteria were found in 132 of these 226 samples, indicating PPC. Crystal violet tetrazolium agar detected PPC with the greatest sensitivity. Spoilage due to PPC was predominantly associated with Pseudomonas (isolated from 101 of the 132 samples with PPC); coliforms and EB were found in 27 and 37 samples with spoilage due to PPC, respectively. Detection of Pseudomonas and Acinetobacter was associated with lower flavor scores; coagulated, fruity fermented, and unclean defects were more prevalent in d-21 samples with PPC. Repeat isolation of Pseudomonas fluorescens group strains with identical partial 16S rDNA sequence types was observed in 8 facilities. In several facilities, specific lines, products, or processing days were linked to repeat product contamination with Pseudomonas with identical sequence types. Our data show that PPC due to Pseudomonas remains a major challenge for fluid milk processors; the inability of coliform and EB tests to detect Pseudomonas may contribute to this. Our data also provide important initial insights into PPC patterns (e.g., line-specific contamination), supporting the importance of molecular subtyping methods for identification of PPC sources.     

Rapid detection and characterization of postpasteurization contaminants in pasteurized fluid milk

Microbial spoilage of pasteurized fluid milk is typically due to either (1) postpasteurization contamination (PPC) with psychrotolerant gram-negative bacteria (predominantly Pseudomonas) or (2) growth of psychrotolerant sporeformers (e.g., Paenibacillus) that have the ability to survive pasteurization when present as spores in raw milk, and to subsequently grow at refrigeration temperatures. While fluid milk quality has improved over the last several decades, continued reduction of PPC is hampered by the lack of rapid, sensitive, and specific methods that allow for detection of PPC in fluid milk, with fluid milk processors still often using time-consuming methods (e.g., Moseley keeping quality test). The goal of this project was to utilize a set of commercial fluid milk samples that are characterized by a mixture of samples with PPC due to psychrotolerant gram-negative bacteria and samples with presence and growth of psychrotolerant sporeforming bacteria to evaluate different approaches for rapid detection of PPC. Comprehensive microbiological shelf-life characterization of 105 pasteurized fluid milk samples obtained from 20 dairy processing plants showed that 60/105 samples reached bacterial counts >20,000 cfu/mL over the shelf-life due to PPC with gram-negative bacteria. Among these 60 samples with evidence of gram-negative PPC spoilage over the shelf-life, 100% (60/60) showed evidence of contamination with noncoliform, non-Enterobacteriaceae (EB) gram-negative bacteria (e.g., Pseudomonas), 20% (12/60) showed evidence of contamination with coliforms, and 7% (4/60) showed evidence of contamination with noncoliform EB. Among the remaining 45 samples, 28 showed levels of gram-positive bacteria above 20,000 cfu/mL and the remaining 17 samples did not exceed 20,000 cfu/mL over the shelf-life. Evaluation of the same set of 105 samples using 6 different approaches {all possible combinations of 2 different enrichment protocols (13°C or 21°C for 18 h) and 3 different plating media [crystal violet tetrazolium agar, EB Petrifilm (3M, St. Paul, MN), and Coliform Petrifilm]} showed that enrichment at 21°C for 18 h, followed by plating on crystal violet tetrazolium agar provided for the most sensitive, accelerated detection of samples that reached >20,000 cfu/mL due to PPC with psychrotolerant gram-negatives (70% sensitivity). These results show that tests still required and traditionally used in the dairy industry (e.g., coliform testing) are not suitable for monitoring for PPC. Rather, approaches that allow for detection of all gram-negative bacteria are essential for improved detection of PPC in fluid milk.     

利用16S rRNA序列鉴定分离自芽菜中的芽孢杆菌

从宜宾芽菜中分离优势菌群,选取4株芽孢杆菌,分别为B1、B2、B3、B4.对4株菌的16S rRNA基因经PCR扩增测序,将测序结果同该属内菌株的16S rRNA序列作多序列比较,并建立芽孢杆菌属的系统发育树.结合细菌形态学生理生化特性鉴定结果,结果表明菌株B1、B3为枯草芽孢杆菌,菌株B2为解淀粉芽孢杆菌,菌株B4为乙酰微小杆菌.     

单增李斯特氏菌MALDI-TOF-MS鉴定与分型研究

为建立单增李斯特氏菌的基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)快速鉴定与分型方法,实验收集37株单增李斯特氏菌分离株,应用MALDI-TOF-MS采集图谱,获取独特的蛋白质指纹图谱,汇总成标准图谱,建立单增李斯特氏菌鉴定数据库。采用单增李斯特氏菌标准菌株进行验证,表明鉴定结果的可信度很高。在数据库信息的基础上,对37株单增李斯特氏菌分离株进行聚类分型。分型结果表明,在蛋白质水平上,MALDI-TOF-MS可把37株单增李斯特氏菌分成9个型别。     

Prevalence Analysis and Molecular Characterization of Salmonella at Different Processing Steps in Broiler Slaughter Plants in South Korea

In this study, changes in the prevalence of Salmonella during the processing of broiler chicken carcasses were investigated. A total of 1040 fecal swabs and chicken carcasses samples were collected from 2 processing plants at the 4 stages of broiler processing, which included live birds in slaughter line, postevisceration/prewashing, postwashing/prechilling, and postchilling, respectively. The intraspecific biodiversity of the Salmonella isolates was determined using a DiversiLab automated repetitive sequence‐based PCR (rep‐PCR) system. In both plants, the prevalence of Salmonella increased considerably after evisceration (from 4.6% to 30.8%, P < 0.05) and decreased after washing (from 30.8% to 25.4%, P < 0.05). However, the chilling step had little effect on Salmonella prevalence (from 25.4% to 22.7%, P > 0.05). The most frequent Salmonella serovar in plant A was Infantis (35.8%), followed by Enteritidis (26.2%) and Montevideo (15.0%), while Montevideo (43.6%) and Enteritidis (35.9%) were most prevalent in plant B. A difference in the rep‐PCR banding pattern was found to be related to the processing plant origin and serovar rather than sampling point or sampling day, although there were some exceptional strains.     

2016年上海市市售肉制品中沙门菌耐药谱与分型研究

目的 研究上海市市售肉制品中沙门菌血清型、耐药谱和分子分型特征。方法 2016年1～8月在上海市所辖16个行政区,随机选择1个密集型社区,抽取1家超市或市场作为哨点,定期采集畜、禽类肉制品,按国家食品安全风险评估中心(CFSA)食源性疾病监测方案进行沙门菌分离、血清分型、抗生素定量检测与剂量评估、优势菌的分子分型。结果 606份样品包括猪、鸡、鸭、牛、羊、鹅肉制品,共分离沙门菌158株,总阳性率为26.1%,畜肉和禽肉来源分别占52.5%(83/158)和47.5%(75/158)。前5位沙门菌血清型依次为肠炎沙门菌、鼠伤寒沙门菌、德尔卑沙门菌、罗森沙门菌和印第安纳沙门菌,畜肉和禽肉来源优势菌型间差异有统计学意义(P<0.05);菌株对磺胺异噁唑耐药率最高(79.7%,126/158),对链霉素、萘啶酸、氨苄西林、四环素和氯霉素耐药率在38.0%～77.8%,多重耐药(MDR)菌株(≥3类)占77.8%(123/158),猪肉来源沙门菌对庆大霉素、链霉素、磺胺异噁唑、复方新诺明、氯霉素、四环素耐药率均高于鸡肉来源沙门菌,鸡肉来源沙门菌对头孢噻呋、头孢曲松、萘啶酸耐药率均高于猪肉来源沙门菌,差异均有统计学意义(P<0.05),32.9%(52/158)的菌株对至少6种抗生素超检测限值;肠炎沙门菌有15个分型,以1型和3型为优势型;鼠伤寒沙门菌有23个分型,具有遗传多样性特征。结论 上海市市售肉制品沙门菌暴露以猪肉和鸡肉来源为主,肉制品中多重耐药沙门菌污染严重。猪肉来源的罗森沙门菌和鸡肉来源的吉韦沙门菌是新输入性的血清型。     

应用16S rDNA全序列测序技术鉴定生鲜乳中的细菌种类

采用玻璃珠法提取生鲜乳中分离的34株细菌基因组DNA,用细菌通用引物(27f/1492r)PCR扩增16S r DNA片段并测序,与Gen Bank数据库同源序列比对,系统发育树聚类分析,并结合形态学和生理学特征确定了34株菌的种属地位。结果表明,共鉴定出16个种属。3个生鲜乳样中细菌种类及其分布特点不同。其中1号样有7种细菌,以Acinetobacter sp.(不动杆菌属)为主,2号样有6种细菌,以Klebsiella sp.(克雷贝氏杆菌属)为主,3号样有6种细菌,分布较为分散。从致病性来看,分离菌株主要为条件致病菌或腐败菌,无烈性致病菌。      

When cheese gets the blues: Pseudomonas fluorescens as the causative agent of cheese spoilage

A bacterial contamination of fresh, low-acid cheese that resulted in production of a blue fluorescent pigment on the surface of the cheese was determined to be caused by Pseudomonas fluorescens biovar IV, a gram-negative bacteria that produces a blue, nondiffusible pigment as well as the soluble pigment pyoverdin, which fluoresces under UV light. Ten isolates collected from contaminated cheese and environmental samples were initially identified as P. fluorescens using 16S rDNA sequencing, but only 8 of the isolates produced blue pigment and fluoresced under UV light when re-inoculated onto fresh, low-acid cheese. The Biolog Metabolic Fingerprint system (Biolog Inc., Hayward, CA) and the Analytical Profile Index (BioMerieux Vitek Inc., Hazelwood, MO) for nonenteric gram-negative species as well as EcoRI ribotyping did not differentiate between the isolates that produced blue color and those that did not. Pulsed field gel electrophoresis with the enzyme XbaI was able to distinguish between the isolates that produced pigment and those that did not and allowed for identification of a specific environmental site (i.e., an overhead cheese vat agitator system) as the likely source of product contamination.     

Identification of gadoid species (Pisces, Gadidae) by sequencing and PCR–RFLP analysis of mitochondrial 12S and 16S rRNA gene fragments

We applied PCR–RFLP (Polymerase Chain Reaction – Restriction Fragment Length Polymorphism) analysis to identify seven gadoid species of different biogeographical origin and commercial relevance, namely Gadus morhua (Atlantic ocean); Trisopterus minutus capelanus, Trisopterus minutus minutus, Molva elongata, Phycis blennoides, Micromesistius poutassou (Atlantic ocean and Mediterranean sea); Theragra chalcogramma (Pacific ocean). Two DNA fragments belonging to mitochondrial 12S and 16S rRNA genes of about 430 and 630 bp, respectively, were isolated by PCR amplification. Their direct sequencing showed a significant genotypic diversity among gadoid species, useful for species identification. Digestion of 16S rRNA gene PCR fragment with MvaI or Bsh1285I restriction enzymes, followed by agarose gel electrophoresis of the cleaved products, yielded specific restriction profiles that enabled direct, visual identification of the species analyzed. This PCR–RFLP method allowed a clear and rapid discrimination of the gadoid species studied.     

北京市食源性非伤寒沙门菌的分子分型和耐药性研究

目的了解北京市食源性非伤寒沙门菌的分子特征及耐药情况。方法对2004—2010年北京市食源性致病菌监测网收集的100株沙门菌进行脉冲场凝胶电泳(PFGE)分型和抗生素敏感性检测。结果 100株非伤寒沙门菌通过PFGE分型分为62个不同的带型,每个带型包含1~11株菌。抗生素敏感性结果显示,100株菌中有55株菌表现为对至少1种抗生素耐药,其中多重耐药菌株15株。菌株对各抗生素的耐药率为萘啶酸40%、四环素30%、氯霉素15%、庆大霉素10%、甲氧苄啶/磺胺甲恶唑10%、环丙沙星9%、头孢西丁1%、头孢噻肟0%。结论沙门菌PFGE带型和耐药谱均与血清型存在很高的一致性。提示北京市食源性非伤寒沙门菌的耐药情况比较严重,开展对该菌分子分型与耐药特征分析的联合监测意义重大。     

克罗诺杆菌MALDI-TOF-MS数据库的建立及应用

应用基质辅助激光解吸电离飞行时间质谱（matrix-assisted laser desorption ionisation time-of-flight mass spectrometry,MALDI-TOF-MS）技术建立了克罗诺杆菌MALDI-TOF-MS数据库,用于该菌属内种和亚种的高通 量鉴定及菌株分型。在优化培养条件、样品处理方法及确定MALDI-TOF-MS蛋白质指纹图谱采集参数的基础上, 将采集的8 种参考菌株蛋白质质谱数据通过Biotyper软件构建克罗诺杆菌的MALDI-TOF-MS数据库,再用相近肠杆 菌及该属分离株验证数据库的准确性。结果表明：应用建立的克罗诺杆菌的MALDI-TOF-MS数据库对135 株克罗 诺杆菌分离株进行分析,鉴定分值均不小于2.0,达到了种水平鉴定要求,通过聚类分析,可进一步分型。构建的 MALDI-TOF-MS数据库为克罗诺杆菌高通量鉴定与分型提供了一种新的手段。     

可降解咖啡碱菌株的筛选与鉴定

目的：筛选能够降解咖啡碱的细菌,以期在该毒素的生物脱毒中得到应用。方法：以咖啡碱作为唯一碳源和氮源进行咖啡碱降解菌株的初筛,之后将初筛的10 株菌通过液体培养基咖啡碱降解实验最终筛选出降解能力最强的1 株菌。结果：筛选出的HZ-1 菌株在48h 即可将咖啡碱完全降解,对目标菌株细胞形态、生理生化以及16SrDNA 进行鉴定,确定该菌株为Pseudomonas lutea,属于假单胞菌属。结论：利用咖啡碱作为唯一碳源和氮源从土壤中筛选出降解咖啡碱良好的菌株,为脱除咖啡碱提供了微生物菌种,填补了国内空白。     

Identification of 12 animal species meat by T-RFLP on the 12S rRNA gene

The verification of authenticity of meat products is relevant for economical, religious or public health concerning reasons. A molecular approach using terminal restriction fragment length polymorphism (T-RFLP) was developed to distinguish 12 common economically important meat species. The partial 12S rRNA gene was amplified with double-fluorescently labeled primers. The amplified fragments were digested with two endonucleases and only the terminal restriction fragment containing labeled primer was detected on capillary electrophoresis system ABI3100. AluI and Tru9I generated differently-sized terminal fragments in different species. Pig and buffalo can be separated by 3′-terminal fragment of AluI digestion. Horse, turkey, goat, sheep, deer, and cattle can be further separated by 5′-terminal fragment of Tru9I digestion. Dog and chicken, sturgeon and salmon can finally be separated by 5′-terminal fragment of AluI digestion and 3′-terminal fragment of Tru9I digestion. Our results demonstrated the potential feasibility and applicability of T-RFLP method for rapid and accurate identification of animal species.     

81株铜绿假单胞菌16S rRNA基因序列测定及系统发育学分析

采用16SrRNA基因序列分析法对2015年7~9月广东省食品检验所桶装水专项抽检中筛查所得的81株铜绿假单胞菌(Pseudomonas aeruginosa)进行复核鉴定。菌株经纯化培养后提取总DNA,采用细菌16SrRNA通用引物进行16SrRNA基因序列扩增,PCR扩增产物经2%琼脂糖凝胶电泳后,进行序列测定,序列经人工校对后用Clustal X进行比对分析,最后用MEGA5.1软件构建系统发育树。系统发育分析结果表明:81株铜绿假单胞菌与原鉴定结果一致。其中,编号24-3-QY、100-5-JM、106-3-JM菌株形成一个分支,28-1-WD单独为一支,其余77株野生菌和铜绿假单胞菌标准菌株ATCC27853聚为一群。该研究是2015年5月24日中国开始实施GB 19298—2014《食品安全国家标准包装饮用水》以来,广东省首次对水源性铜绿假单胞菌进行的研究,为下一步菌种污染朔源等研究提供依据。     

基质辅助激光解析电离-飞行时间质谱法对铜绿假单胞菌的鉴定与聚类分析

目的 建立基质辅助激光解析电离-飞行时间质谱法(matrix assisted laser desorption lonization-time of flight mass spectrometery, MALDI-TOF MS)快速鉴定和聚类分析铜绿假单胞菌(Pseudomonas aeruginosa, P. aeruginosa)。方法 将全自动微生物分析仪鉴定为P. aeruginosa的20株分离株和1株标准菌株(CICC 21636)进行MALDI-TOF MS检测。经离线微生物鉴定软件分析, 所有菌株均报告为P. aeruginosa。获取21株 P. aeruginosa的特征蛋白质指纹图谱, 建立命名为Pseudomonas aeruginosa的自建数据库, 并采用 P. aeruginosa标准菌株CICC 21636进行验证。结果 Pseudomonas aeruginosa自建数据库对P. aeruginosa的鉴定结果较设备自带数据库明显提高。而且自建数据库信息基础上, 进一步对21株P. aeruginosa进行聚类分型, 实现了对不同来源P. aeruginosa可能污染源的追溯。结论 作为一种快速、准确、高通量的全新技术手段, MALDI-TOF MS能够实现对P. aeruginosa的特异性快速鉴定, 能满足在公共安全卫生、突发食品安全事件和口岸快速通关方面对P. aeruginosa的快速鉴定需求。     

Identification of a microscopically selected microorganism in milk samples

Identification of unwanted microbial contaminants microscopically observed in food products is challenging due to their low abundance in a complex matrix, quite often containing other microorganisms. Therefore, a selective identification method was developed using laser capture microdissection in combination with direct-captured cell PCR. This procedure was validated with Geobacillus stearothermophilus and further used to identify microbial contaminants present in some industrial milk samples. The microscopically observed contaminants were identified as mainly Methylobacterium species.     

16S rRNA基因序列、生化鉴定、质谱3类方法鉴定常见微生物的结果分析

目的比较16SrRNA基因序列、生化鉴定、质谱鉴定3类实验方法分析沙门氏菌、金黄色葡萄球菌、蜡样芽孢杆菌的鉴定结果的异同。方法挑选沙门氏菌、金黄色葡萄球菌、蜡样芽孢杆菌各50株,分别进行16S rRNA基因序列测定、VITEK COMPACT 2生化鉴定、质谱鉴定3类实验,并比较3类实验的鉴定结果。结果 3类实验方法对大部分沙门氏菌鉴定在属水平,生化鉴定方法对少数血清型鉴定到种水平;对金黄色葡萄球菌均鉴定到种水平; 16SrRNA基因序列、生化方法对蜡样芽孢杆菌鉴定到属水平,质谱鉴定到种水平。结论 3类实验方法对大部分沙门氏菌、所有金黄色葡萄球菌鉴定水平相同,质谱鉴定蜡样芽孢杆菌的结果更准确,且质谱鉴定时效性更高。     

猕猴桃溃疡病菌拮抗菌筛选、鉴定及发酵条件优化

目的:从不同地区猕猴桃根际土壤中筛选拮抗猕猴桃溃疡病菌的菌株,优化其产生抑菌活性物质的发酵条件,为猕猴桃溃疡病的生物防治提供潜在的资源菌。方法:采用平板稀释法从猕猴桃根际土壤中分离获得菌株,采用抑菌圈法筛选拮抗菌;通过形态学特征、生理生化特征及16S rDNA序列分析对其进行鉴定;并采用单因素及正交试验优化培养基组分及发酵条件。结果:从土壤中共分离到288株放线菌,其中编号为NA-TXL-1的菌株对猕猴桃溃疡病菌的拮抗效果最佳,采用预防法、治疗法进行盆栽实验,发酵原液的防治效果分别为73.06%、55.62%,初步鉴定该菌株为抗生链霉菌。其最佳发酵配方和培养条件为:乳糖30 g/L、酵母粉3 g/L、NaCl 1 g/L、K_2HPO_4 0.5 g/L、MgSO_4·7H_2O 0.5 g/L、FeSO_4 0.01 g/L,种子培养基为乳糖-酵母粉培养基,接种量为2%,起始pH值为7.0,发酵原液、上清液、重悬液分别培养5、14、5 d。结论:经鉴定,拮抗菌株为Streptomyces antibioticus。在优化的发酵条件下,该菌株对猕猴桃溃疡病菌具有更好的拮抗效果。     

鲜切苦菊、生菜和紫甘蓝上假单胞菌的分离鉴定及其噬菌体的初步筛选

鲜切蔬菜是人类摄取矿物质和维生素的重要来源,假单胞菌是鲜切蔬菜上的主要腐败菌.为了控制鲜切蔬菜中假单胞菌的污染,该研究采用假单胞菌培养基和16S rRNA基因序列分析,对鲜切苦菊、生菜和紫甘蓝中的假单胞菌进行分离鉴定,筛选得到2株铜绿假单胞菌(Pseudomonas aeruginonas)、1株荧光假单胞菌(Pseu...