Comparison of methods for detection of Erysipelothrix spp. and their distribution in some Australasian seafoods

For many years, Erysipelothrix rhusiopathiae has been known to be the causative agent of the occupationally related infection erysipeloid. A survey of the distribution of Erysipelothrix spp. in 19 Australasian seafoods was conducted, and methodologies for the detection of Erysipelothrix spp. were evaluated. Twenty-one Erysipelothrix spp. were isolated from 52 seafood parts. Primary isolation of Erysipelothrix spp. was most efficiently achieved with brain heart infusion broth enrichment followed by subculture onto a selective brain heart infusion agar containing kanamycin, neomycin, and vancomycin after 48 h of incubation. Selective tryptic soy broth, with 48 h of incubation, was the best culture method for the detection of Erysipelothrix spp. with PCR. PCR detection was 50% more sensitive than culture. E. rhusiopathiae was isolated from a variety of different fish, cephalopods, and crustaceans, including a Western rock lobster (Panulirus cygnus). There was no significant correlation between the origin of the seafoods tested and the distribution of E. rhusiopathiae. An organism indistinguishable from Erysipelothrix tonsillarum was isolated for the first time from an Australian oyster and a silver bream. Overall, Erysipelothrix spp. were widely distributed in Australasian seafoods, illustrating the potential for erysipeloid-like infections in fishermen.     

3种小球藻DNA提取方法的比较

单细胞真核藻类小球藻已成为藻类分子生物学研究的热点,但其特殊的细胞壁组分给DNA的提取带来了一定的困难。文章比较了3种从小球藻中提取DNA的方法,即纤维素酶法、作者改进的CATB法和目前单细胞藻类常用的裂解法。通过所提取的DNA进行浓度、纯度分析,认为CTAB法是一种简单、快速和高效的适合于小球藻的DNA提取方法。     

Method for the Detection of Injured Vibrio parahaemolyticus in Seafoods

The sensitivity of Vibrio parahaemolyticus cells to refrigeration and frozen storage and the development of a method for detecting injured and uninjured V. parahaemolyticus cells were studied. Cell suspensions in different kinds of seafood homogenates were either regrigerated (4°C) or frozen (−20°C), stored, and examined for cell survival during storage. V. parahaemolyticus cells were sensitive to both storage temperatures. Many cells died, and many survivors were sublethally injured. In general, refrigeration storage appeared to be more injurious than frozen storage. The initial recovery of the sublethally injured cells was highest in a nutritionally rich, nonselective liquid medium such as Trypticase soy broth, whereas maximum cell multiplication was observed in Trypticase soy broth containing 3% NaCl. The sublethally injured V. parahaemolyticus cells demonstrated sensitivity to the selective enrichment medium, glucose salt teepol broth. From these findings, a new method (designated as the “repair-detection” method) was developed for the isolation and enumeration of V. parahaemolyticus. Comparative studies between the recommended and the repair-detection methods showed that injured V. parahaemolyticus cells were present in commercial seafoods and that the repair-detection method was definitely more effective for the detection of total numbers of V. parahaemolyticus cells.     

Dynamics and Distribution of Cyanophages and Their Effect on Marine Synechococcus spp.

Cyanophages infecting marine Synechococcus cells were frequently very abundant and were found in every seawater sample along a transect in the western Gulf of Mexico and during a 28-month period in Aransas Pass, Tex. In Aransas Pass their abundance varied seasonally, with the lowest concentrations coincident with cooler water and lower salinity. Along the transect, viruses infecting Synechococcus strains DC2 and SYN48 ranged in concentration from a few hundred per milliliter at 97 m deep and 83 km offshore to ca. 4 × 10⁵ ml^-1 near the surface at stations within 18 km of the coast. The highest concentrations occurred at the surface, where salinity decreased from ca. 35.5 to 34 ppt and Synechococcus concentrations were greatest. Viruses infecting strains SNC1, SNC2, and 838BG were distributed in a similar manner but were much less abundant (<10 to >5 × 10³ ml^-1). When Synechococcus concentrations exceeded ca. 10³ ml^-1, cyanophage concentrations increased markedly (ca. 10² to > 10⁵ ml^-1), suggesting that a minimum host density was required for efficient viral propagation. Data on the decay rate of viral infectivity d (per day), as a function of solar irradiance I (millimoles of quanta per square meter per second), were used to develop a relationship (d = 0.2610I - 0.00718; r² = 0.69) for conservatively estimating the destruction of infectious viruses in the mixed layer of two offshore stations. Assuming that virus production balances losses and that the burst size is 250, ca. 5 to 7% of Synechococcus cells would be infected daily by viruses. Calculations based on contact rates between Synechococcus cells and infectious viruses produce similar results (5 to 14%). Moreover, balancing estimates of viral production with contact rates for the farthest offshore station required that most Synechococcus cells be susceptible to infection, that most contacts result in infection, and that the burst size be about 324 viruses per lytic event. In contrast, in nearshore waters, where ca. 80% of Synechococcus cells would be contacted daily by infectious cyanophages, only ca. 1% of the contacts would have to result in infection to balance the estimated virus removal rates. These results indicate that cyanophages are an abundant and dynamic component of marine planktonic communities and are probably responsible for lysing a small but significant portion of the Synechococcus population on a daily basis.     

Sensitive Real-Time PCR Detection of Pathogenic Leptospira spp. and a Comparison of Nucleic Acid Amplification Methods for the Diagnosis of Leptospirosis

Background

Bacteria of the genus Leptospira, the causative agents of leptospirosis, are categorized into pathogenic and non-pathogenic species. However, the benefit of using a clinical diagnostic that is specific for pathogenic species remains unclear. In this study, we present the development of a real-time PCR (rtPCR) for the detection of pathogenic Leptospira (the pathogenic rtPCR), and we perform a comparison of the pathogenic rtPCR with a published assay that detects all Leptospira species [the undifferentiated febrile illness (UFI) assay] and a reference 16S Leptospira rtPCR, which was originally designed to detect pathogenic species.

Methodology/Principal Findings

For the pathogenic rtPCR, a new hydrolysis probe was designed for use with primers from the UFI assay, which targets the 16S gene. The pathogenic rtPCR detected Leptospira DNA in 37/37 cultured isolates from 5 pathogenic and one intermediate species. Two strains of the non-pathogenic L. biflexa produced no signal. Clinical samples from 65 patients with suspected leptospirosis were then tested using the pathogenic rtPCR and a reference Leptospira 16S rtPCR. All 65 samples had tested positive for Leptospira using the UFI assay; 62 (95.4%) samples tested positive using the pathogenic rtPCR (p = 0.24). Only 24 (36.9%) samples tested positive in the reference 16S rtPCR (p<0.0001 for comparison with the pathogenic rtPCR and UFI assays). Amplicon sequencing confirmed the detection of pathogenic Leptospira species in 49/50 cases, including 3 cases that were only detected using the UFI assay.

Conclusions/Significance

The pathogenic rtPCR displayed similar sensitivity to the UFI assay when testing clinical specimens with no difference in specificity. Both assays proved significantly more sensitive than a real-time molecular test used for comparison. Future studies are needed to investigate the clinical and epidemiologic significance of more sensitive Leptospira detection using these tests.     

Comparison of Method 1623 and Cell Culture-PCR for Detection of Cryptosporidium spp. in Source Waters

Analysis of Cryptosporidium occurrence in six watersheds by method 1623 and the integrated cell culture-PCR (CC-PCR) technique provided an opportunity to evaluate these two methods. The average recovery efficiencies were 58.5% for the CC-PCR technique and 72% for method 1623, but the values were not significantly different (P = 0.06). Cryptosporidium oocysts were detected in 60 of 593 samples (10.1%) by method 1623. Infectious oocysts were detected in 22 of 560 samples (3.9%) by the CC-PCR technique. There was 87% agreement between the total numbers of samples positive as determined by method 1623 and CC-PCR for four of the sites. The other two sites had 16.3 and 24% correspondence between the methods. Infectious oocysts were detected in all of the watersheds. Overall, approximately 37% of the Cryptosporidium oocysts detected by the immunofluorescence method were viable and infectious. DNA sequence analysis of the Cryptosporidium parvum isolates detected by CC-PCR showed the presence of both the bovine and human genotypes. More than 90% of the C. parvum isolates were identified as having the bovine or bovine-like genotype. The estimates of the concentrations of infectious Cryptosporidium and the resulting daily and annual risks of infection compared well for the two methods. The results suggest that most surface water systems would require, on average, a 3-log reduction in source water Cryptosporidium levels to meet potable water goals.     

芽胞杆菌菌体蛋白提取方法的比较

目的：比较不同破碎方法下3种芽胞杆菌菌体蛋白的提取效果。方法：以菊酯类农药降解菌巨大芽胞杆菌、球形芽胞杆菌、弯曲芽胞杆菌为研究对象,以裂解液为提取介质,分别采用超声波破碎法、水煮法和机械破碎法提取芽胞杆菌蛋白,并通过革兰染色电镜观察菌株破碎程度,用SDS-PAGE和Bradford法测定蛋白浓度。结果：革兰染色电镜观察发现玻璃珠机械破碎法对3种芽孢杆菌的细胞壁破碎程度最明显,其次为超声波破碎法,水煮法破碎效果不明显。SDS-PAGE和Bradford法测定结果表明,巨大芽胞杆菌、球形芽胞杆菌、弯曲芽胞杆菌经玻璃珠机械破碎后,提取的蛋白图谱条带清晰,丰度高,重复性好,含量分别为20.247、19.902和18.893 mg/mL;经超声波破碎提取的蛋白图谱条带较清晰,丰度一般,重复性不好,含量分别为10.572、9.438和10.424 mg/mL;经沸水浴破碎提取的蛋白图谱条带模糊,丰度低,重复性差,含量分别为1.366、1.119和1.136 mg/mL。结论：玻璃珠机械破碎法是破碎3种芽胞杆菌的最优方法,破碎后提取的蛋白含量高,条带清晰,重复性好。     

The detection and recovery of Erysipelothrix spp. in meat and abattoir samples in Western Australia

AIMS: To investigate the occurrence of Erysipelothrix rhusiopathiae and other Erysipelothrix spp. in abattoir and meat samples in Western Australia. METHODS AND RESULTS: Samples were collected from various parts of pig and sheep carcasses, as well as different sections of slaughtering line, pen soil and effluent. Previously evaluated culture methods were applied for the isolation of Erysipelothrix spp., in conjunction with phenotypic and genotypic detection and identification procedures. Of 109 samples from the two abattoirs, 35 (32.1%) were Erysipelothrix genus-specific PCR-positive. These came from swabs of animal exterior surfaces and joints, slaughtering areas, pig pen soil and abattoir effluent. Four samples (3.7%) from sheep arthritic joints and pig abattoir effluent were also E. rhusiopathiae species-specific PCR-positive. Of 123 carcass washing samples, 12 (9.8%) were genus-specific PCR-positive, and these came from all five kinds of meat samples tested, including beef, lamb, mutton, pork and chicken. Four of them (3.3%) were also species-specific PCR-positive. A total of 25 isolates was recovered from the samples, of which seven were identified as E. rhusiopathiae, seven were consistent with E. tonsillarum, and the remaining 11 were other species of Erysipelothrix. CONCLUSIONS: Erysipelothrix spp. can still be isolated and identified from specimens of animal origin with relative ease, provided that appropriate cultural and molecular procedures are used. Clinical microbiology laboratories may need to improve their diagnostic protocols. SIGNIFICANCE AND IMPACT OF THE STUDY: This study confirms that E. rhusiopathiae and other species of Erysipelothrix continue to colonize and contaminate farmed animals and animal products. Erysipelothrix infection still poses a potential threat to the economy of the farmed animal industry, as well as being a potential human public health hazard.     

Genotyping of Brazilian Erysipelothrix spp. strains by amplified fragment length polymorphism

One hundred and fifty-one Erysipelothrix spp. isolates from diseased and carrier swine from Brazil were identified by PCR, submitted to serotyping and analyzed by amplified fragment length polymorphism with a single enzyme (AFLP).Reference strains from Australia and the United Kingdom were also examined. The 151 strains were classified into 18 different serotypes (1a, 1b, 2a, 2b, 4, 5, 6, 7, 8, 10, 11, 12, 15, 17, 19, 21, 24 and 25), being serotype 2b the most frequent (39.7%). By associating serotyping and PCR results, it was possible to identify 146 strains as E. rhusiopathiae and five strains as E. tonsillarum. Despite the fact that for this genus AFLP did not cluster all isolates according to serotype, origin, disease or isolation data, the execution of the technique was easy and fast, demonstrating high discriminatory power. The results produced by the AFLP analysis of Erysipelothrix spp. could also support its use as a discriminatory tool for E. rhusiopathiae and E. tonsillarum species.     

PCR for Detection of Shigella spp. in Mayonnaise

The use of PCR to amplify a specific virA gene fragment serves as a highly specific and sensitive method to detect virulent bacteria of the genus Shigella and enteroinvasive Escherichia coli. Amplification of a 215-bp DNA band was obtained by using isolated genomic DNA of Shigella, individual cells of Shigella dysenteriae, and mayonnaise contaminated with S. dysenteriae. Moreover, a multiplex PCR with specific (virA) and bacterium-restricted (16S ribosomal DNA) primers generated an amplification product of approximately 755 bp for all bacteria tested and an additional 215-bp product for Shigella and enteroinvasive E. coli.     

Dynamics and Distribution of Cyanophages and Their Effect on Marine Synechococcus spp

Cyanophages infecting marine Synechococcus cells were frequently very abundant and were found in every seawater sample along a transect in the western Gulf of Mexico and during a 28-month period in Aransas Pass, Tex. In Aransas Pass their abundance varied seasonally, with the lowest concentrations coincident with cooler water and lower salinity. Along the transect, viruses infecting Synechococcus strains DC2 and SYN48 ranged in concentration from a few hundred per milliliter at 97 m deep and 83 km offshore to ca. 4 x 10 ml near the surface at stations within 18 km of the coast. The highest concentrations occurred at the surface, where salinity decreased from ca. 35.5 to 34 ppt and Synechococcus concentrations were greatest. Viruses infecting strains SNC1, SNC2, and 838BG were distributed in a similar manner but were much less abundant (<10 to >5 x 10 ml). When Synechococcus concentrations exceeded ca. 10 ml, cyanophage concentrations increased markedly (ca. 10 to > 10 ml), suggesting that a minimum host density was required for efficient viral propagation. Data on the decay rate of viral infectivity d (per day), as a function of solar irradiance I (millimoles of quanta per square meter per second), were used to develop a relationship (d = 0.2610I - 0.00718; r = 0.69) for conservatively estimating the destruction of infectious viruses in the mixed layer of two offshore stations. Assuming that virus production balances losses and that the burst size is 250, ca. 5 to 7% of Synechococcus cells would be infected daily by viruses. Calculations based on contact rates between Synechococcus cells and infectious viruses produce similar results (5 to 14%). Moreover, balancing estimates of viral production with contact rates for the farthest offshore station required that most Synechococcus cells be susceptible to infection, that most contacts result in infection, and that the burst size be about 324 viruses per lytic event. In contrast, in nearshore waters, where ca. 80% of Synechococcus cells would be contacted daily by infectious cyanophages, only ca. 1% of the contacts would have to result in infection to balance the estimated virus removal rates. These results indicate that cyanophages are an abundant and dynamic component of marine planktonic communities and are probably responsible for lysing a small but significant portion of the Synechococcus population on a daily basis.     

新城疫病毒3种检测方法的研究比较

目的:利用3种方法对新城疫(Newcastle disease virus, NDV)病毒进行检测并对这3种检测方法的优缺点做出比较。方法:分别将NDV强毒F48E9和弱毒Lasota接种SPF鸡胚后,获取尿囊液。利用双抗夹心ELISA法、悬液芯片系统以及RT-PCR进行检测。通过对制备的针对新城疫病毒的抗体4D9和6C4蛋白浓度测定后,选择6C4进行生物素标记,将4D9作为固相捕获抗体,利用生物素-链霉亲和素放大系统构建双抗夹心检测体系。通过对Genebank上已发表的新城疫强弱毒F基因进行电脑分析后,设计一组针对NDV强弱毒的通用型引物,分别对强弱毒进行RT-PCR并检测其检出限。结果:ELISA法对NDV强弱毒尿囊液的检出灵敏度为1:160,但操作繁琐,耗时长;液相芯片对强弱毒尿囊液的检出限为1:160和1:320,然而和ELISA相比,操作较为方便,但仪器设备昂贵。RT-PCR对强弱毒RNA检出限分别为259pg和14pg,与前两种方法相比,PR-PCR在核酸水平上对病毒进行检测,理论上灵敏度较高,但是所需试剂、设备昂贵,且实验人员还需一定的技能培训。     

志贺菌毒力检测的常用方法

志贺菌属的细菌以人类为特异性宿主,感染人类肠上皮细胞,多导致痉挛性腹痛、腹泻、发烧等症状,是细菌性痢疾最为常见的病原菌。志贺菌的致病机理主要由其Ⅲ型分泌系统调节。志贺菌侵袭力的高低及毒力强弱决定了其致病性的强弱。我们简要介绍志贺菌属细菌的毒力检测方法。     

Mass Spectrometry-Based Strategy for Direct Detection and Quantification of Some Mycotoxins Produced by Stachybotrys and Aspergillus spp. in Indoor Environments

Dampness in buildings has been linked to adverse health effects, but the specific causative agents are unknown. Mycotoxins are secondary metabolites produced by molds and toxic to higher vertebrates. In this study, mass spectrometry was used to demonstrate the presence of mycotoxins predominantly produced by Aspergillus spp. and Stachybotrys spp. in buildings with either ongoing dampness or a history of water damage. Verrucarol and trichodermol, hydrolysis products of macrocyclic trichothecenes (including satratoxins), and trichodermin, predominately produced by Stachybotrys chartarum, were analyzed by gas chromatography-tandem mass spectrometry, whereas sterigmatocystin (mainly produced by Aspergillus versicolor), satratoxin G, and satratoxin H were analyzed by high-performance liquid chromatography-tandem mass spectrometry. These mycotoxin analytes were demonstrated in 45 of 62 building material samples studied, in three of eight settled dust samples, and in five of eight cultures of airborne dust samples. This is the first report on the use of tandem mass spectrometry for demonstrating mycotoxins in dust settled on surfaces above floor level in damp buildings. The direct detection of the highly toxic sterigmatocystin and macrocyclic trichothecene mycotoxins in indoor environments is important due to their potential health impacts.     

Adaptive Methods of Trend Detection and Their Application in Analysing Biosignals

In the study estimations of the linear trend and its slope of discrete deterministic and stochastic signals are introduced, which are based on adaptive methods of mean estimation. Because of its simple recursive nature both the trend and the slope estimation may be realized in real time and thus they may be used for on-line procedures e.g. in monitoring systems of intensive care units. The adaptive estimation functions are self-learning, that means they are able to adapt automatically to the new conditions after structure changes of the time series and thus may be also used for detecting points of structure fracture. The properties of the adaptive trend- and slope estimations are demonstrated by some characteristic simulation examples and the possibilities of their applications for analysing biological signals are investigated in three different medical cases.     

Comparison of Some Plant DNA Extraction Methods

DNA isolation is a routine procedure when performed in laboratory environment, yet in the field it may still remain problematic. This is especially true of some crop species bred for useful metabolites that may also hinder DNA extraction. Here we compare the efficiency of DNA extraction protocols and commercial DNA isolation kits when used on samples from Helianthus and Allium. Since extraction of DNA is known to be compromised by co-extraction of PCR-inhibiting metabolites, the isolation of DNA was followed by PCR as a testing procedure for the isolation step. The MagnoPrime Fact and MagnoPrime Uni DNA isolation kits were better suited for field work due to faster processing times and smaller required amount of starting material (20 mg fresh/0.5 mg dry). In all cases the subsequent PCR managed to amplify the DNA fragments of interest well enough to be useful in further research.     

Comparison of Rapid Quantitative PCR-Based and Conventional Culture-Based Methods for Enumeration of Enterococcus spp. and Escherichia coli in Recreational Waters

Recreational water quality is currently monitored using culture-based methods that require 18 to 96 h for results. Quantitative PCR (QPCR) methods that can be completed in less than 2 h have been developed, but they could yield different results than the conventional methods. We present two studies in which samples were processed simultaneously for Enterococcus spp. and Escherichia coli using two culture-based methods (EPA method 1600 and Enterolert/Colilert-18) and QPCR. The proprietary QPCR assays targeted the 23S rRNA (Enterococcus spp.) and uidA (E. coli) genes and were conducted using lyophilized beads containing all reagents. In the first study, the QPCR method developers processed 54 blind samples that were inoculated with sewage or pure cultures or were ambient beach samples. The second study involved 163 samples processed by water quality personnel. The correlation between results of QPCR and EPA 1600 during the first study (r²) was 0.69 for Enterococcus spp., which was less than that observed between the culture-based methods (r², 0.87). During the second study, the correlations were similar. No false positives occurred in either study when QPCR-based assays were used with blank samples. Levels of reproducibility measured through coefficients of variation were similar for results by Enterococcus QPCR and culture-based methods during both studies but were higher for E. coli QPCR results in the first study. Regarding the concentration at which beach management decisions are issued in the State of California, the agreement between results of Enterococcus QPCR and EPA method 1600 was 88%, compared to 94% agreement between EPA method 1600 and Enterolert. The beach management decision agreement between E. coli QPCR and Colilert-18 was 94%. The samples showing disagreement suggested an underestimation bias for QPCR.Fecal indicator bacteria (FIB) are presently measured to assess recreational water quality using one of three U.S. Environmental Protection Agency (EPA)-approved method classes: membrane filtration, multiple-tube fermentation, or defined-substrate technology (DST). The membrane filtration approach is based on passing water through a filter that is placed on a medium selective for the bacterial group of interest. Multiple-tube fermentation relies on quantification via most-probable number (MPN) using serial dilutions within replicate tubes incubated with selective media. The DST methods are also typically used in an MPN approach, where water samples are incubated with specific media in a tray with replicate wells. These methods are detailed by the American Public Health Association (1, 2) and in the U.S. Federal Register (29). These culture-based methods are widely accepted because of their relative ease of use, low cost, and demonstrated relationship to health risk (6, 7, 9, 11). However, the time required for sample processing ranges from 18 to 96 h, with confirmation and verification steps taking even longer.Advances in technology provide new opportunities to measure bacterial water quality more rapidly (4, 16, 19). While currently used methods rely on bacterial growth and metabolic activity, these new methods directly measure DNA, RNA, or surface immunological properties. This is important because FIB concentrations have been shown to change substantially on a time scale of hours (3). Thus, contaminated beaches remain open during the laboratory processing period, but the contamination event has often passed by the time warnings are posted (20). By eliminating the need for a lengthy incubation step, results from rapid methods are available in several hours, enabling managers to take action to protect public health (i.e., post warnings or close beaches) on the same day that water samples are collected. Rapid quantitative PCR (QPCR) methods, such as the Enterococcus sp. assay developed by Haugland et al. (16), have also exhibited significant relationships with the risk of gastrointestinal illness in beachgoers (31, 32).While QPCR-based methods are promising, their results may differ from those of the conventional culture-based methods that they are intended to replace. Since QPCR measures genetic material rather than the viable cells quantified by culture-based methods, it may overestimate FIB concentrations because of the inclusion of target DNA from dead or dying cells in the measurement. Differences may also be related to chemical inhibition of the amplification, assay design, or challenges in technology transfer to personnel with little or no molecular biology-based experience. Acceptance of new methods by water quality professionals with a long history of using culture-based methods will depend on understanding the frequency and the underlying causes of these differences. Whereas a number of studies have assessed the relative performance of the three most commonly used culture-based methods (13, 25, 30), there have been few comparisons of QPCR- and culture-based method performance, especially with marine beach samples. Here, quantification of FIB by Enterococcus species QPCR (here referred to as simply Enterococcus QPCR) and Escherichia coli QPCR is compared to that by their respective culture-based assays. We also quantify the effect of two different QPCR sample processing approaches and assess the ability of personnel from a state-certified water quality laboratory to implement the rapid QPCR-based methods.