Foodborne

食源性
  • 文章类型: Journal Article
    食源性疾病是一个重大的公共卫生问题,尤其是在中国,它们代表了重大的食品安全挑战。目前,有必要对北京市食源性疾病的扩展流行病学模式进行全面和系统的分析。
    监测结果显示,诺如病毒和致泻性大肠杆菌(DEC)是最常见的食源性腹泻病原体。19-30岁的个体在北京食源性腹泻的风险较高,沙门氏菌感染与发烧症状有关。
    本研究分析了连续11年的监测数据,以提高对北京食源性腹泻流行病学和临床特征的认识。它旨在识别高风险人群,协助临床病原体鉴定和治疗,并支持制定量身定制的预防战略。
    UNASSIGNED: Foodborne diseases present a significant public health concern, particularly in China, where they represent a significant food safety challenge. Currently, there is a need for a thorough and systematic analysis of the extended epidemiological patterns of foodborne diseases in Beijing Municipality.
    UNASSIGNED: Monitoring results show that Norovirus and diarrheagenic Escherichia coli (DEC) are the most commonly identified foodborne diarrheal pathogens. Individuals aged 19-30 are at a higher risk of foodborne diarrhea in Beijing, with Salmonella infection being associated with fever symptoms.
    UNASSIGNED: This study analyzes 11 years of consecutive monitoring data to enhance understanding of the epidemiological and clinical features of foodborne diarrhea in Beijing. It aims to identify high-risk populations, assist in clinical pathogen identification and treatment, and support the development of tailored preventive strategies.
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  • 文章类型: Journal Article
    肺炎克雷伯菌是奶牛临床和无症状性乳腺炎的最常见原因之一,以及影响牛奶质量的牛奶和乳制品。由肺炎克雷伯菌引起的乳腺炎由于其对抗生素治疗的不良反应而甚至更为严重。这项研究的目的是检测和鉴定在利比亚生产的牛奶和乳制品中肺炎克雷伯菌的存在。
    从利比亚的不同地点随机收集了总共234个样本。使用常规培养技术检查样品中肺炎克雷伯菌的存在,包括在紫红色胆汁琼脂加4-甲基伞形酮-β-D-葡糖苷酸肉汤和CHROM琼脂中培养,随后进行聚合酶链反应鉴定和16SrRNA部分测序。
    在收集的234份牛奶和乳制品样品中,16个(6.8%)的分离株在琼脂培养基上显示出粘液样菌落,在表型上被认为是肺炎克雷伯菌。使用分子技术(16SrRNA)确认分离物的鉴定。在检查的样本中,肺炎克雷伯菌是从骆驼奶中回收的,生牛奶,生发酵乳,Maasora奶酪,意大利乳清干酪,软奶酪,全脂奶粉,婴儿配方奶粉,谷类婴儿食品,和成长公式。对16个肺炎克雷伯菌分离株中的12个进行了抗生素敏感性测试,结果显示肺炎克雷伯菌分离株对八种以上抗生素有耐药性;有趣的是,两个分离物显示产生金属β-内酰胺酶(MBL).
    K.肺炎被认为是对人类健康的危险,因为许多这些产品不符合国际和/或利比亚标准的微生物学标准。这项研究强调了肺炎克雷伯菌与原料乳之间的关系,奶酪,奶粉,和在利比亚零售的婴儿牛奶。有必要采取必要措施,以确保乳品厂生产期间的有效卫生习惯,处理,以及在市场上的分销,特别是在当地生产规模很小的情况下。
    UNASSIGNED: Klebsiella pneumoniae is one of the most common causes of clinical and asymptomatic mastitis in dairy cattle, as well as in milk and dairy products that affect milk quality. Mastitis caused by K. pneumoniae is even more serious due to its poor response to antibiotic therapy. The aim of this study was to detect and identify the presence of K. pneumoniae in milk and dairy products produced in Libya.
    UNASSIGNED: A total of 234 samples were randomly collected from various locations in Libya. Samples were examined for the presence of K. pneumoniae using conventional cultural techniques, including cultivation in violet red bile agar plus 4-methylumbelliferyl-ß-D-glucuronide broth and CHROM agar, followed by polymerase chain reaction identification and partial sequencing of 16S rRNA.
    UNASSIGNED: Of the 234 samples of milk and dairy products collected, 16 (6.8%) isolates revealed mucoid colonies on agar media that were phenotypically suggested to be K. pneumoniae. Identification of isolates was confirmed using molecular techniques (16S rRNA). Among the examined samples, K. pneumoniae was recovered from camel\'s milk, raw cow\'s milk, raw fermented milk, Maasora cheese, Ricotta cheese, soft cheese, full cream milk powder, milk powder infant formula, cereal baby food, and growing-up formula. Antibiotic susceptibility testing was performed on 12 of the 16 K. pneumoniae isolates, and the results showed that K. pneumoniae isolates were resistant to more than eight antibiotics; interestingly, two isolates showed metallo-beta-lactamase (MBL) production.
    UNASSIGNED: K. pneumoniae is considered a risk to human health because many of these products do not comply with the microbiological criteria of international and/or Libyan standards. This study emphasized the relationship between K. pneumoniae and raw milk, cheese, milk powder, and infant milk retailed in Libya. There is a need to take the necessary measures to ensure effective hygiene practices during production in dairy factories, handling, and distribution on the market, in particular at a small local production scale.
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  • 文章类型: Journal Article
    弓形虫病是由弓形虫原虫引起的食源性疾病,并通过食用生肉或未煮熟的肉传播给人类,主要是。家禽,牛肉,猪肉是秘鲁消费的主要肉类;尽管如此,豚鼠肉也被广泛食用。出于这个原因,这项研究的目的是对库斯科马兰加尼地区的家养和野生豚鼠中的弓形虫进行分子检测,秘鲁,并确定与该病原体相关的一些危险因素。从豚鼠(30只国产和30只野生)的脑组织样本中提取DNA,和PCR方案用于从弓形虫基因组中扩增内部转录间隔区(ITS-1)和529bp片段。在14只(23.3%)豚鼠中检测到弓形虫DNA。家养豚鼠的弓形虫频率为33.3%,野生豚鼠为13.3%。我们的结果表明,豚鼠是该地区人群中弓形虫感染的重要来源。
    Toxoplasmosis is a foodborne disease caused by the protozoan Toxoplasma gondii, and transmitted to humans by eating raw or undercooked meat, mainly. Poultry, beef, and pork are the main meats consumed in Peru; despite this, guinea pig meat is also widely consumed. For this reason, the objective of this study was to molecularly detect T. gondii in domestic and wild guinea pigs from the Marangani district in Cuzco, Peru, and identify some risk factors associated with this pathogen. DNA was extracted from the brain tissue samples of guinea pigs (30 domestic and 30 wild), and PCR protocols were used to amplify the internal transcribed spacer (ITS-1) region and a 529 bp fragment from the T. gondii genome. T. gondii DNA was detected in 14 (23.3%) guinea pigs. T. gondii frequency was 33.3% in domestic guinea pigs and 13.3% in wild guinea pigs. Our results demonstrated that guinea pigs represent an important source for T. gondii infection in human populations in this locality.
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  • 文章类型: Journal Article
    大肠杆菌是儿童和成人尿路感染(UTI)的主要原因。胃肠道是尿路致病性大肠杆菌的主要储库,可以从各种环境暴露中获得,包括零售肉类。在目前的研究中,我们使用一种新的统计-基因组方法来估计由食源性人畜共患大肠杆菌菌株引起的儿科UTI的比例.从儿童国家医疗中心实验室2个月至17岁的DC居民中收集大肠杆菌尿液分离株,2013-2014。在同一时期,从在整个DC的15个地点购买的零售家禽产品中收集大肠杆菌分离物。共有52个尿液和56个家禽分离株进行了全基因组测序,核心基因组系统发育分析,以及通过贝叶斯潜在类模型进行宿主起源预测,该模型结合了有关来自多个脊椎动物宿主的大肠杆菌分离株中可移动遗传元件(MGE)存在的数据。在分离物中总共鉴定了56种多位点序列类型。在尿液和家禽分离株中观察到五种序列类型-ST10,ST38,ST69,ST117和ST131。使用贝叶斯潜在类模型,我们估计,19%(10/52)的临床大肠杆菌分离株为食源性人畜共患病菌株。这些数据表明,华盛顿特区地区的大部分儿科UTI可能是由源自食用动物的大肠杆菌菌株引起的,并可能通过受污染的禽肉传播。IMPORTANCEcoli大肠杆菌UTI是沉重的公共卫生负担,可能对儿科患者产生长期的负面健康后果。大肠杆菌具有极其广泛的宿主范围,包括人类,鸡,火鸡,猪,和牛。来自食用动物的大肠杆菌是零售肉类产品的常见污染物,但对这些菌株对儿科人群的风险知之甚少。量化由食用动物源性大肠杆菌引起的儿科UTI的比例,表征最高风险菌株,并确定其主要储层物种可以提供新的干预策略,以减轻该脆弱人群的UTI负担。我们的结果表明,零售禽肉可能是儿科暴露于能够引起UTI的人畜共患大肠杆菌菌株的重要载体。为家禽接种最高风险菌株可能会减少家禽定植,禽肉污染,和下游儿科感染。
    Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children\'s National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E. coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.
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  • 文章类型: Journal Article
    在2021年7月至2021年10月期间,安大略省多家餐馆的猪肉丝产品消费与沙门氏菌的爆发有关。这次疫情涉及来自六个公共卫生单位的36名患者。牵连的切碎的猪肉产品是从未经许可的来源获得的。这是安大略省与餐厅食品接触有关的最大的婴儿沙门氏菌爆发,与调查无证食品有关的复杂性。本文旨在描述流行病学,食品安全和实验室调查,导致从有牵连的餐馆识别和清除爆发源,包括在调查与无牌食物来源有关的疫情时遇到的挑战。
    进行了流行病学和实验室分析,以确定疫情的来源。进行了食品安全调查,以确定所涉食品的来源和分布。
    全基因组测序从安大略省六个公共卫生单位的36例患者的分离株中确定了爆发菌株。7例患者(19%)住院。没有死亡报告。疫情与切碎的猪肉产品有关(即,皮或皮)由无牌肉类加工机分发,并在大多伦多地区供应东南亚融合美食的各种餐馆食用。从牵连的餐馆中取出该产品。
    历史上,未经许可来源的食品与多起大型疫情有关,并继续具有重大的公共卫生风险。疫情调查强调了无证来源的食品对公众健康的威胁,以及额外公共卫生干预措施以防止与无证来源有关的疫情的重要性。
    UNASSIGNED: An outbreak of Salmonella Infantis was associated with the consumption of shredded pork products at multiple restaurants in Ontario between July 2021 and October 2021. The outbreak involved 36 case-patients from six public health units. The implicated shredded pork products were obtained from an unlicensed source. This is the largest reported outbreak of Salmonella Infantis linked to restaurant food exposures in Ontario, with complexities related to the investigation of unlicensed foods. This article aims to describe the epidemiological, food safety and laboratory investigations that led to the identification and removal of the source of the outbreak from implicated restaurants, including the challenges encountered while investigating an outbreak related to an unlicensed source of food.
    UNASSIGNED: Epidemiological and laboratory analyses were conducted to identify the source of the outbreak. Food safety investigations were conducted to ascertain the origin and distribution of the implicated food.
    UNASSIGNED: Whole-genome sequencing identified the outbreak strain from the isolates of 36 case-patients across six public health units in Ontario. Seven case-patients (19%) were hospitalized. No deaths were reported. The outbreak was linked to shredded pork products (i.e., rinds or skins) that were distributed by an unlicensed meat processor and consumed at various restaurants that served Southeast Asian fusion cuisine concentrated in the Greater Toronto Area. The product was removed from implicated restaurants.
    UNASSIGNED: Historically, foods from unlicensed sources have been implicated in multiple large outbreaks and continue to be of significant public health risk. The outbreak investigation emphasized the threat of food from unlicensed sources to the public\'s health and the importance of additional public health interventions to prevent outbreaks linked to unlicensed sources.
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  • 文章类型: Journal Article
    棘阿米巴。,属于自由生活变形虫(FLA)组的无处不在的原生生物,被认为是其他人类感染中副作用性角膜炎或致命脑炎的病因。此外,据报道,这种寄生虫是对人类健康重要的其他微生物的宿主,例如弯曲杆菌属。或弧菌属。在其他人中。棘阿米巴作为病原体和环境吞噬细胞的这种作用增加了证实其存在于人类相关环境中的报道。作为水质指标。考虑到水和厨房环境之间的潮汐关系,以及水源中棘阿米巴的高患病率,本研究旨在建立一种基于DNA提取和实时qPCR检测棘阿米巴的快速准确方案。在抹布里。该程序已通过处理17个使用过的抹布得到验证。我们的发现证明了所使用的qPCR测定法的高灵敏度,该测定法能够从体外污染的抹布中检测到多达一个棘阿米巴。该方案准确检测出64.7%的棘阿米巴阳性样本,(在4个样品中,DNA浓度对应于1-102个变形虫)。我们的发现证明了通过有效和敏感的方法进行FLA监测的重要性,因为一种变形虫能够在与人类相关的食物环境如厨房水槽中定居,并且可能是潜在的感染源。
    Acanthamoeba spp., are ubiquitous protist which belongs to Free-Living Amoeba (FLA) group, is considered as causal agent of side-threatening keratitis or fatal encephalitis among other human infections. Besides, this parasite has been reported as host for other microorganisms important to human health such as Campylobacter spp. or Vibrio spp. among others. This role of Acanthamoeba as pathogen and environmental phagocyte has increased the reports confirming its presence in human related environments, acting as a water quality indicator. Considering the tide relationship between water and kitchen environments, and the high prevalence of Acanthamoeba in water sources, the present study aims to establish a quick and accurate protocol based on DNA extraction and a real time qPCR assay to detect Acanthamoeba spp. in dishcloths. The procedure has been validated by processing 17 used dishcloths. Our findings demonstrated the high sensitivity of the qPCR assay used which was capable of detecting up to one Acanthamoeba from an in vitro contaminated dishcloth. The protocol accurately detected 64.7% of positive samples for Acanthamoeba spp, (in 4 samples DNA concentrations corresponded to 1-102 amoebae). Our findings demonstrate the importance of FLA surveillance by efficient and sensitive methods since one amoeba is capable of colonizing human related food environments such as kitchens sinks and could be a potential source of infection.
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  • 文章类型: Journal Article
    我们描述了意大利养殖猪和野生豪猪中与疾病相关的B组链球菌。猪的发生归因于未经巴氏灭菌的牛乳乳清的传播。豪猪分离株的抗菌素耐药性表明没有常见的感染源。我们的发现扩大了B组链球菌病的已知宿主范围。
    We describe group B Streptococcus linked to disease in farmed pigs and wild porcupines in Italy. Occurrence in pigs was attributed to transmission from nonpasteurized bovine milk whey. Antimicrobial-resistance profiles in isolates from porcupines suggest no common source of infection. Our findings expand the known host range for group B Streptococcus disease.
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  • 文章类型: Journal Article
    在需要持续监测的“一个健康”背景下,在移动遗传元件(MGE)中携带抗菌素耐药性(AMR)的食源性沙门氏菌菌株的出现是一个重大的公共卫生威胁。对环丙沙星和头孢菌素的耐药性尤其令人关注。由于猪是人类食源性沙门氏菌的相关来源,我们在83个菌株的集合中研究了可传播的AMR基因和MGE,这些菌株显示了9种不同的血清变型和15种多药耐药(MDR)模式,这些模式先前是从西班牙北部常规育种系统中饲养的猪中分离出的。所有分离株都对环丙沙星敏感,三个分离株携带blaCMY-2或blaCTX-M-9基因,负责头孢噻肟耐药性。滤纸交配实验表明,携带blaCTX-M-9的两个质粒是共轭的,而携带blaCMY-2的质粒是通过转化可自我传播的。对分离物和质粒进行全基因组测序和比较分析。携带blaCMY-2的IncC质粒pSB109与牛的S中发现的相似。表明血清型和动物来源之间潜在的水平转移。携带blaCTX-M-9的IncHI2质粒在海德堡沙门氏菌中的pSH102和鼠伤寒沙门氏菌ST34中的pSTM45具有相似的主链和两个含有不同AMR和重金属基因的新型“复杂1类整合子”。我们的发现强调了测序技术对识别来自牲畜生产的接合和稳定质粒中新兴AMR区域的重要性。携带临床相关AMR基因的MGE的存在引起了公众健康问题,需要监测以减轻携带AMR基因的细菌的出现,并随后通过动物和食物传播。重要意义食源性沙门氏菌菌株在移动遗传元件(MGE)中携带抗菌素耐药性(AMR)的出现是一种健康环境下的重大公共卫生威胁。由于猪是人类食源性沙门氏菌的相关来源,在这项研究中,我们调查了83种沙门氏菌中AMR的不同方面,这些沙门氏菌显示了从常规育种系统中饲养的猪中分离出的9种不同血清变型和15种多药耐药(MDR)模式。我们的发现强调了测序技术对识别来自牲畜生产的接合和稳定质粒中新兴AMR区域的重要性。携带临床相关AMR基因的MGE的存在引起了公众健康问题,需要监测以减轻携带AMR基因的细菌的出现,并随后通过动物和食物传播。
    The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel \"complex class 1 integrons\" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.
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  • 文章类型: Journal Article
    单核细胞增生李斯特菌是一种细菌病原体,可引起危及生命的中枢神经系统(CNS)感染。虽然已经研究了单核细胞增生李斯特菌和其他病原体进入大脑的机制,对大脑内定植和复制的潜在动力学的定量理解仍然缺乏。在这项研究中,我们使用条形码单核细胞增生李斯特菌量化导致脑感染的瓶颈和传播模式。静脉(IV)接种后,多个独立的入侵事件从血液中植入了中枢神经系统的所有部分,然而,通常只有一个克隆人在大脑中占主导地位。顺序IV接种和颅内接种表明克隆具有时间优势(即,首先播种CNS),而不是空间优势(即,侵入特定的大脑区域),是克隆优势的主要驱动因素。在免疫功能低下小鼠的食源性脑感染模型中,罕见的入侵事件反而导致高度感染但单克隆的CNS。这种限制性瓶颈可能来自病原体进入血液,而不是直接从血液到大脑。总的来说,我们的研究结果为导致中枢神经系统感染的单核细胞增生李斯特菌种群动态提供了详细的定量认识,并为研究其他脑感染的动态提供了框架.
    Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.
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  • 文章类型: Journal Article
    Staka是一种传统的希腊酸奶油,主要由自发发酵的羊奶或羊奶和羊奶的混合物制成。在工业规模上,也可以使用奶油分离器和发酵剂培养物。Staka有时用面粉煮熟以吸收大部分脂肪。在这项研究中,我们采用了基于文化的技术,扩增子测序,和猎枪宏基因组学首次分析了Staka微生物组。样品以乳球菌或明串珠菌属为主。大多数其他细菌是来自链球菌和肠球菌属的乳酸菌(LAB)或来自Buttiauxella的革兰氏阴性细菌,假单胞菌,肠杆菌,大肠杆菌志贺氏菌,和哈夫尼亚属。去细菌,克鲁维酵母,或者链格孢是样本中最普遍的属,其次是其他酵母和霉菌,如酵母,青霉,曲霉菌,茎phylium,孢子孢子,或枝孢菌属。shot弹枪宏基因组学允许对乳酸乳球菌进行物种级鉴定,棉子乳球菌,嗜热链球菌,溶胆链球菌,大肠杆菌,哈夫尼亚肺泡,副链球菌,和durans肠球菌.组装的shot弹枪读段的合并,然后是单个读段的招募图分析,可以确定接近完整的宏基因组组装的基因组(MAG)。文化依赖和文化独立分析总体上是一致的,有一些明显的差异。例如,不能分离乳球菌,大概是因为他们进入了可行但不可培养的(VBNC)状态,或者是因为他们已经死亡。最后,几个实验室,Hafniaparalgivi,和假单胞菌属。分离株对口腔或其他致病性链球菌表现出抗菌活性,以及某些腐败和致病菌在食品生物保护或新的生物医学应用中确立了潜在的作用。我们的研究可能为有关手工酸液的其他研究铺平道路,以更好地了解影响其生产和质量的因素。
    Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.
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