Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni.

The sequencing, assembly, and analysis of bacterial genomes is central to tracking and characterizing foodborne pathogens. The bulk of bacterial genome sequencing at the US Food and Drug Administration is performed using short-read Illumina MiSeq technology, resulting in highly accurate but fragmented genomic sequences. The MinION sequencer from Oxford Nanopore is an evolving technology that produces long-read sequencing data with low equipment cost. The goal of this study was to compare Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. Two reference strains and two field isolates of C. jejuni were sequenced using MiSeq and MinION, and the sequence data were assembled using the software programs SPAdes and Canu, respectively. Hybrid genome assembly was performed using the program Unicycler. Comparison of the C. jejuni 81-176 and RM1221 genome assemblies to the PacBio reference genomes revealed that the SPAdes assemblies had the most accurate nucleotide identity, while the hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate, containing many indels and substitutions that affected downstream analyses. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements such as rRNA and tRNA genes. The full genomes of both C. jejuni field isolates were completed and circularized using hybrid sequencing, and a plasmid was detected in one isolate. Continued development of nanopore sequencing technologies will likely enhance the accuracy of hybrid genome assemblies and enable public health laboratories to routinely generate complete circularized bacterial genome sequences.

A Multiplex Quantitative Polymerase Chain Reaction Using Applied Biosystems 7500 Fast System for Simultaneous Identification of Three Campylobacter Species with Potential Applications to Food Analysis.

Consumption of Campylobacter-contaminated food is one of the most common causes of bacterial diarrhea. A previously developed quantitative polymerase chain reaction (qPCR) utilizing the SmartCycler instrument platform for identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari had to be modified to address the recent discontinuation of the SmartCycler system. In this study, a multiplex qPCR assay was optimized on the Applied Biosystems 7500 Fast (AB7500F) platform to continue using qPCR for the identification of three target Campylobacter spp. AB7500F qPCR efficiencies obtained by testing reference genomic DNA (gDNA) were 90.9%, 86.4%, and 94.6% for C. jejuni, C. coli, and C. lari, respectively, with all correlation coefficient values >0.99. The qPCR results exhibited 100% specificity by testing gDNA samples from 37 non-target reference strains and 86 target strains (50 C. jejuni, 27 C. coli, and 9 C. lari strains) in this study. The lowest detection level using gDNA was 4, 7, and 2 genome copies per reaction for C. jejuni, C. coli, and C. lari, respectively. With a 2-day enrichment procedure, the qPCR method correctly detected target species in a spiked food matrix (frog leg, an aquaculture product). The sensitivity in 25 g food matrix was 4 colony-forming units (CFUs) for C. jejuni, 3 CFUs for C. coli, and 2 CFUs for C. lari. The results suggest that this AB7500F-based qPCR has potential applications for the identification of C. jejuni, C. coli, and C. lari in contaminated food.

Anatomical study of the seminal vesicle system for transurethral seminal vesiculoscopy.

Because of a general lack of knowledge regarding the precise anatomy of the seminal vesicle system, efforts to use transurethral seminal vesiculoscopy (TSV) are currently constrained. We investigated 26 normal adult male specimens. Contrast medium was injected into the seminal vesicle system in 18 specimens and the openings of the ejaculatory ducts were examined with an operating microscope. India ink was injected into the urethra in four specimens to investigate the function of the ejaculatory duct valve. Another four specimens were examined histologically to identify the anatomical relationships of the seminal vesicle system. We found that the openings of the ejaculatory ducts were covered by the ejaculatory duct valve, which could be classified into two types and acted as a one-way valve. The apex of the seminal colliculus together with the right and left openings of the ejaculatory ducts formed a shape resembling an isosceles triangle. This could be used to locate the openings of the ejaculatory ducts during TSV. The ejaculatory ducts can be classified into two types according to their course. During surgery, efforts must be made to protect the ejaculatory duct valve. During inspection or surgery, the second segment and the angles of the ejaculatory ducts, particularly in Type Ib and Type II cases, require particular attention. Clin. Anat. 32:244-252, 2019. © 2018 Wiley Periodicals, Inc.

Whole Genome Sequencing and Multiplex qPCR Methods to Identify Campylobacter jejuni Encoding cst-II or cst-III Sialyltransferase.

Campylobacter jejuni causes more than 2 million cases of gastroenteritis annually in the United States, and is also linked to the autoimmune sequelae Guillan-Barre syndrome (GBS). GBS often results in flaccid paralysis, as the myelin sheaths of nerve cells are degraded by the adaptive immune response. Certain strains of C. jejuni modify their lipooligosaccharide (LOS) with the addition of neuraminic acid, resulting in LOS moieties that are structurally similar to gangliosides present on nerve cells. This can trigger GBS in a susceptible host, as antibodies generated against C. jejuni can cross-react with gangliosides, leading to demyelination of nerves and a loss of signal transduction. The goal of this study was to develop a quantitative PCR (qPCR) method and use whole genome sequencing data to detect the Campylobacter sialyltransferase (cst) genes responsible for the addition of neuraminic acid to LOS. The qPCR method was used to screen a library of 89 C. jejuni field samples collected by the Food and Drug Administration Pacific Northwest Lab (PNL) as well as clinical isolates transferred to PNL. In silico analysis was used to screen 827 C. jejuni genomes in the FDA GenomeTrakr SRA database. The results indicate that a majority of C. jejuni strains could produce LOS with ganglioside mimicry, as 43.8% of PNL isolates and 46.9% of the GenomeTrakr isolates lacked the cst genes. The methods described in this study can be used by public health laboratories to rapidly determine whether a C. jejuni isolate has the potential to induce GBS. Based on these results, a majority of C. jejuni in the PNL collection and submitted to GenomeTrakr have the potential to produce LOS that mimics human gangliosides.

Simultaneous Identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari with SmartCycler-Based Multiplex Quantitative Polymerase Chain Reaction.

BACKGROUND: Consumption of Campylobacter contaminated food or water is a leading cause of human acute gastroenteritis. Campylobacter jejuni, Campylobacter coli, and Campylobacter lari account for over 95% of total Campylobacter infections. A multiplex quantitative polymerase chain reaction (qPCR) for simultaneous identification of C. jejuni, C. coli, and C. lari was developed for use with the SmartCycler II system. MATERIALS AND METHODS: We evaluated and combined previously described primers and probes for Campylobacter detection, designed a new internal amplification control, and optimized the multiplex qPCR for the detection of C. jejuni, C. coli, and C. lari. RESULTS: This method was 100% specific when tested against a panel of 32 target Campylobacter strains and 31 non-Campylobacter reference strains. Furthermore, there was no cross-reactivity with seven strains from four nontarget Campylobacter species. The amplification efficiency of each target in this multiplex qPCR was over 90%, and each coefficient of linearity was greater than 0.99. With artificially mixed genomic DNA, this method detected as few as two, three, and two genome copies of C. jejuni, C. coli, and C. lari, respectively. This method was also able to detect these three Campylobacter species in artificially contaminated milk with a sensitivity of five spiked cells of each target per reaction. CONCLUSION: The three Campylobacter targets were simultaneously identified using artificially mixed genomic DNA and spiked raw milk. This SmartCycler-based multiplex qPCR is a rapid, specific, and sensitive method to identify C. jejuni, C. coli, and C. lari.

Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance.

As the most prevalent bacterial cause of human gastroenteritis, food-borne Campylobacter infections pose a serious threat to public health. Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. Here we report the WGS and annotation of a Campylobacter coli strain, FNW20G12, which was isolated from milk in the United States in 1997 and carries multidrug resistance. The draft genome of FNW20G12 (DDBJ/ENA/GenBank accession number LWIH00000000) contains 1, 855,435 bp (GC content 31.4%) with 1902 annotated coding regions, 48 RNAs and resistance to aminoglycoside, beta-lactams, tetracycline, as well as fluoroquinolones. There are very few genome reports of C. coli from dairy products with multidrug resistance. Here the draft genome of FNW20G12, a C. coli strain isolated from raw milk, is presented to aid in the epidemiology study of C. coli antimicrobial resistance and role in foodborne outbreak.

Experimental radioimmunoguided surgery for peritoneal metastases of gastric cancer using anticarcinoembryonic antigen-specific T84.66 F(ab')2.

PURPOSE: In gastric cancer, peritoneal dissemination is the most frequent cause of the noncurative resection and recurrence after curative resection. We therefore evaluated the feasibility of radioimmunoguided surgery (RIGS) in the treatment of peritoneal metastases of gastric cancer and the use of anti-CEA-specific T84.66 F(ab')2 as an efficient immune agent. METHODS: Two human gastric cancer cell lines, MKN45 and RF48, were intraperitoneally xenografted into nude mice, which were later injected with 125I-labeled T84.66 F(ab')2. Peritoneal tumors were localized by RIGS 5 days after antibody injection. The minimum number of cells detected by a gamma probe was assayed by in vitro tumor cell localization. RESULTS: We observed 37 peritoneal metastases: 8 invisible (long diameter, <1 mm), 6 small (1- < 5 mm), and 23 large (> or =5 mm) tumors. The accuracy, sensitivity and specificity of RIGS in detecting peritoneal metastasis were 82% (69/84), 76% (28/37), and 87% (41/47), respectively. RIGS accuracy did not differ with respect to tumor diameter. Mean labeling indices over minimal and maximal normal counts were 6.1+/-1.2 (mean +/- SEM) and 4.7+/-1, respectively. Mean scores of CEA immunostaining and silver grains in tumors were significantly higher than those in the nontumor-bearing peritoneum (P < 0.001). There was a close correlation among radioactivity, immunostaining and microautoradiography (P < 0.001-0.005). We observed six false-positive and nine false-negatives which may have been due to high blood background and negative radioimmune reactivity, respectively. CONCLUSIONS: 125I-labeled T84.66 F(ab')2 efficiently targeted peritoneally disseminated gastric cancer cells, suggesting that RIGS using this immune agent may accurately detect occult peritoneal metastases in patients with gastric cancer.

[Improvement of myocardial perfusion following left ventricular resection]. / A myocardialis perfusio javulása bal kamrai resectiót követóen.

Left ventricular aneurysm had detected at the 55-year-old woman after extensive anterior myocardial infarction in association with progressive ventricular dilatation and symptoms of heart failure. Coronary angiogram revealed a serious lesion in the proximal segment of the left anterior descending coronary branch with a poor run off tract. 18FDG-PET and 99mTc-MIBI-SPECT investigation were performed in order to differentiate the scarred regions from the viable myocardial segments. Taking into consideration the results an aneurysm resection was performed without revascularisation procedure. After the surgery not only the ejection fraction and the left ventricular dilatation had improved but the tissue perfusion in the segments surrounding the resected aneurysm had also showed a significant increase at the follow up MIBI-SPECT imaging.

QT dispersion in patients with end-stage renal failure and during hemodialysis.

Interlead variability of the QT interval in surface electrocardiogram (ECG), i.e., QT dispersion, reflects regional differences in ventricular recovery time, and it has been linked to the occurrence of malignant arrhythmias in different cardiac diseases. The purpose of the study was to assess the effect of hemodialysis on QT and corrected QT (QTc) interval and dispersion in chronic hemodialyzed patients. Data of 34 nondiabetic patients (male/female = 21/13; mean age, 54 +/- 15 yr) on chronic hemodialysis were studied. Polysulfone capillaries and bicarbonate dialysate containing (in mEq/L) 135 Na+, 2.0 K+, 1.5 Ca2+, and 1.0 Mg2+ were used. Simultaneous 12-lead ECG were recorded before and after hemodialysis in a standard setting. The QT intervals for each lead were measured manually on enlarged (x3) ECG by one observer using calipers. Each QT interval was corrected for patient heart rate: QTc = QT/square root of RR (in milliseconds [ms]). The average cycle intervals were 853 +/- 152 ms predialysis and 830 +/- 173 ms postdialysis; the difference was not significant. The maximal QT interval changed significantly from 449 +/- 43 to 469 +/- 41 ms (P < 0.01). The corrected maximal QT interval increased significantly from 482 +/- 42 to 519 +/- 33 ms (P < 0.01). The QT dispersion changed from 56 +/- 15 to 85 +/- 12 ms (P < 0.001) and the corrected QT interval dispersion from 62 +/- 18 to 95 +/- 17 ms (P < 0.001). During hemodialysis, the serum potassium and phosphate levels decreased from 5.5 +/- 0.8 to 3.9 +/- 0.5 (mM) and from 2.3 +/- 0.5 to 1.6 +/- 0.4 (mM), respectively, whereas calcium increased from 2.2 +/- 0.23 to 2.5 +/- 0.22 (mM). It is concluded that hemodialysis increases the QT and QTc interval and QT and QTc dispersion in patients with end-stage renal failure. Thus, it may be stated that the nonhomogeneity of regional ventricular repolarization increases during hemodialysis. Measurement of QT and QTc dispersion is a simple bedside method that can be used for analyzing ventricular repolarization during hemodialysis.

[Effect of hemodialysis on QT dispersion in chronic uremia]. / A hemodialízis hatása a QT diszperzióra krónikus uraemiás betegekben.

Interlead variability of the QT interval in surface 12-lead ECG (i.e. QT dispersion) reflects regional differences in ventricular recovery time and it has been linked to the occurrence of malignant arrhythmias in different cardiac diseases. The purpose of the study was to assess the effect of hemodialysis on QT dispersion in chronic hemodialyzed patients. The data of 34 patients (Male/Female = 21/13, mean age 54 +/- 15 years) on chronic hemodialysis were studied. Simultaneous 12 lead ECGs were recorded pre- and post-hemodialysis in a standard setting. The QT intervals for each lead were measured manually by one observer. Each QT interval was corrected for patient's heart rate: QTc = QT/square route of RR (sec). The maximal QT interval changed from 449 +/- 43 to 469 +/- 41 ms (p < 0.01). The maximal QTc interval increased from 482 +/- 42 to 519 +/- 33 ms (p < 0.01). The QT dispersion changed rom 56 +/- 15 to 85 +/- 12 ms (p < 0.001), and the QTc interval from 62 +/- 18 to 95 +/- 17 ms (p < 0.001). During hemodialysis the serum potassium and phosphate decreased from 5.5 +/- 0.8 to 3.9 +/- 0.5 (p < 0.001), and from 2.3 +/- 0.5 to 1.6 +/- 0.4, respectively, whereas calcium level increased from 2.2 +/- 0.23 to 2.5 +/- 0.22 (p < 0.001). It can be concluded that the hemodialysis increased the inhomogeneity of regional ventricular repolarization. Measurement of QT and QTc dispersion by a cheap and simple bedside method could predict the increased myocardial inhomogeneity in dialyzed patients.

[Ultrastructural study on spermatogenesis and sustentacular cell of the testes of Schistosoma japonicum].

This paper deals with the ultrastructural study of the spermatogenesis and sustentacular cell of the testes of Schistosoma japonicum by means of TEM. Albeit several papers have reported on the ultrastructural studies of the testes of male reproductive organ of S. mansoni, no systemic observation on the spermatogenesis of schistosome and ultrastructure of the testes of S. japonicum was available. The authors described the characteristics of the spermatogonium, spermatocyte and different appearance of spermatids. The latter was subdivided into 4 types, namely, Sda, Sdb, Sdc and Sdd, which could be identified by the features of nuclear shape and the density of matrix, the distribution of the mitochondria in the cytoplasm, the appearing and the formation of the acrosome-like structure, the presentation and elimination of the residual bodies, etc. The spermatids were embedded and interdigitated among the sustentacular cells, forming a complicated picture in the field of TEM. The acrosome-like structure and the inclusion of residual bodies were revealed in developing spermatids. The origin and the characteristics of these structures were discussed.