Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.

Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.

Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors.

Vibrio penaeicida (family Vibrionaceae) is an important bacterial pathogen that affects Japanese shrimp aquaculture. Only two whole-genome sequences of V. penaeicida are publicly available, which has hampered our understanding of the pathogenesis of shrimp vibriosis caused by this bacterium. To gain insight into the genetic features, evolution and pathogenicity of V. penaeicida, we sequenced five V. penaeicida strains (IFO 15640T, IFO 15641, IFO 15642, TUMSAT-OK1 and TUMSAT-OK2) and performed comparative genomic analyses. Virulence factors and mobile genetic elements were detected. Furthermore, average nucleotide identities (ANIs), clusters of orthologous groups and phylogenetic relationships were evaluated. The V. penaeicida genome consists of two circular chromosomes. Chromosome I sizes ranged from 4.1 to 4.3 Mb, the GC content ranged from 43.9 to 44.1 %, and the number of predicted protein-coding sequences (CDSs) ranged from 3620 to 3782. Chromosome II sizes ranged from 2.2 to 2.4 Mb, the GC content ranged from 43.5 to 43.8 %, and the number of predicted CDSs ranged from 1992 to 2273. All strains except IFO 15641 harboured one plasmid, having sizes that ranged from 150 to 285 kb. All five genomes had typical virulence factors, including adherence, anti-phagocytosis, flagella-related proteins and toxins (repeats-in-toxin and thermolabile haemolysin). The genomes also contained factors responsible for iron uptake and the type II, IV and VI secretion systems. The genome of strain TUMSAT-OK2 tended to encode more prophage regions than the other strains, whereas the genome of strain IFO 15640T had the highest number of regions encoding genomic islands. For comparative genome analysis, we used V. penaeicida (strain CAIM 285T) as a reference strain. ANIs between strain CAIM 285T and the five V. penaeicida strains were >95 %, which indicated that these strains belong to the same species. Orthology cluster analysis showed that strains TUMSAT-OK1 and TUMSAT-OK2 had the greatest number of shared gene clusters, followed by strains CAIM 285T and IFO 15640T. These strains were also the most closely related to each other in a phylogenetic analysis. This study presents the first comparative genome analysis of V. penaeicida and these results will be useful for understanding the pathogenesis of this bacterium.

Whole Genome 5'-Methylcytosine Level Quantification in Cirrhotic HCV-Infected Egyptian Patients with and without Hepatocellular Carcinoma.

DNA methylation is an epigenetic mechanism used by cells to control gene expression. DNA methylation is a commonly used epigenetic signaling tool that can hold genes in the "off" position. Chronic infection with hepatitis C virus (HCV) is considered a major risk for chronic liver impairment. It is the most common leading cause of HCC. The present work is aimed at studying whole genome 5'-methylcytosine levels in cirrhotic HCV-infected Egyptian patients. In the present study, 120 Egyptian adults were included. They were divided into two groups: group І (40 apparently healthy control subjects) and group ІІ (80 HCV-infected patients). Furthermore, group II was subdivided into 2 subgroups according to the presence of HCC in HCV-infected subjects. To all studied subjects, the level of 5-mC% was measured in peripheral blood. In the present study, the median of 5'-methylcytosine% in the control group (group I) was 2.5, in the HCV group (group IIa) was 2.45, and in the HCC group (group II b) was 2.25. A stepwise decrease in 5'-methylcytosine% from the control (group I) toward HCC (group IIb) was observed, taking into consideration that the stepwise global hypomethylation was not statistically significant (p = 0.811). There was a negative correlation between ALT and 5'-methylcytosine% (p = -0.029). From this study, we can conclude that global DNA 5'-methylcytosine% does not differ in HCV-infected cirrhotic patients and HCC patients when compared to normal controls. Consecutively, we had concluded that there is no impact of 5'-methylcytosine% on the development of liver cirrhosis or HCC. Moreover, the negative correlation between 5'-methylcytosine% and serum ALT level denotes a trend of decrease in 5'-methylcytosine% with more liver damage.

Identification of serum biomarker panel to differentiate malignant from benign thyroid nodules using multiplex bead assay.

BACKGROUND: The challenging target in the workup of thyroid nodule(s) is to exclude or diagnose thyroid cancer efficiently prior to surgical intervention. The present work studied a panel of eight serum biomarkers to differentiate benign from malignant thyroid nodules, aiming at reducing unnecessary thyroidectomy performed for inconclusive preoperative fine needle aspiration cytology. Serum interleukin-5 (IL-5), interleukin-8 (IL-8), hepatocyte growth factor (HGF), epidermal growth factor (EGF), angiopietin (Ang1), nonokine induced by interferon gamma (MIG), galectin (Gal-3), and vitamin D-binding protein (VDRP) were quantified by multiplex bead assay using Luminex xMAP technology. The study was conducted on 60 subjects of three groups (20 each; healthy controls, benign thyroid nodule, and malignant thyroid nodule). RESULTS: Significant increase of the following biomarkers in the malignant group compared to the benign group was found; IL-8: 29.7 vs 8.75 pg/ml, p < 0.001, EGF: 128.7 vs 6.72 pg/ml, p < 0.001, HGF: 173.2 vs 112.2 pg/ml, p = 0.012, MIG: 776.7 vs 438 pg/ml, p = 0.023, and Ang-1: 95016 vs 33327.5 pg/ml, p = 0.014. No significant differences were detected for IL-5, Gal-3, and VDBP. Serum IL-8 and EGF showed the highest diagnostic performance individually with area under the curve (AUC) 0.849 and 0.848, respectively. The combined biomarker panels of IL-8 and EGF and IL-8, EGF, and MIG have reached a sensitivity and specificity of 95% and 65%, respectively, with a negative predictive value of 92.9%. CONCLUSIONS: Serum IL-8 and EGF individually or the combined biomarker panel of IL-8, EGF, and MIG are promising tests that can help to exclude malignancy in thyroid nodule workup.

Comparison of Serum Trefoil Factor-3 to Endoscopy in Diagnosing Helicobacter Pylori Associated Gastric Ulcer.

BACKGROUND AND AIM OF THE WORK: Helicobacter pylori-associated gastric ulcer (H.pylori-GU) is a serious condition, not only because H.pylori is identified as a grade 1 carcinogen but also because GU is a precancerous condition. Identification and treatment of H.pylori-GU may prevent the sequential progression of dysplasia to carcinoma. Trefoil factor 3 (Tf3) has been implicated in gastric mucosal repair. We compared serum Tf3 to gastric endoscopy in diagnosing H.pylori-GU. SUBJECTS AND METHODS: The study included eighty patients suffering from H.pylori induced gastritis, forty of which presented with GU. Gastric endoscopy with slide urease test was used to diagnose H.pylori-GU. Serum Tf3 level was determined using an enzyme immunoassay in all patients as well as thirty healthy volunteers. RESULTS: Serum Tf3 showed a significant stepwise decrease among the studied groups. It was significantly lower in patients compared to the control group (p<0.001). Furthermore, it was lower in those with GU compared to those without GU (p=0.023). Based on a receiver operating characteristic curve generated cut off value of 2.4 ng/mL, the diagnostic performance of serum Tf3 as a biomarker of H.pylori-GU revealed a diagnostic specificity of 42.5%, sensitivity of 67.5%, positive and negative predictive values of 54% and 56.67% respectively. CONCLUSION: Although serum Tf3 showed significant variation in H.pylori-GU, further studies are warranted to confirm its role in the pathogenesis of gastric ulcers.
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Multilocus Sequence Typing (MLST) of Campylobacter jejuni Isolated From Broiler Meat in Egypt.

BACKGROUND AND OBJECTIVES: Infection with Campylobacter jejuni is one of the most common causes of bacterial gastroenteritis. Infections are mostly acquired due to consumption of raw or undercooked poultry. The aim of this pilot study is to determine the prevalence and the sequence types (STs) distribution of C. jejuni isolated from broiler meat in Egypt. MATERIALS AND METHODS: A total of 190 broiler meat samples were collected from retail chicken shops located at Mansoura, Egypt and examined bacteriologically for the presence of Campylobacter spp. The biochemically identified Campylobacter isolates were confirmed by Multiplex PCR (m-PCR). In addition, multilocus sequencing typing (MLST) was used for genotyping of C. jejuni isolates. RESULTS: Thirty two Campylobacter isolates divided into C. coli (25 isolates) and C. jejuni (7 isolates) were recovered. Multiplex PCR results found to be 100% in line with biochemical identification. Out of 7 C. jejuni isolates genotyped by MLST, 4 isolates were assigned to ST21, 2 isolates were assigned to ST48 and one isolate was assigned to ST464. CONCLUSION: This study provides valuable information concerning the prevalence of thermophilic Campylobacter spp. and sequence types distribution of C. jejuni recovered from broiler meat for the first time in Egypt. The identified sequence types from this study were frequently reported in human illnesses. Thus, the present results highlight the importance of the retail broiler meat as a significant source for human Campylobacter infection.

Possible contribution of serum activin A and IGF-1 in the development of hepatocellular carcinoma in Egyptian patients suffering from combined hepatitis C virus infection and hepatic schistosomiasis.

OBJECTIVES: The present study evaluated the role of activin A, insulin-like growth factor 1 (IGF-1) and insulin-like growth factor binding protein 3 (IGFBP-3) in Egyptian patients suffering from combined hepatitis C virus (HCV) infection and hepatic schistosomiasis. DESIGN AND METHODS: Four groups were included in the present study. Group I: 30 healthy subjects were included as controls; Group II (HCV): 30 patients with chronic liver disease due to HCV infection without evidence of schistosomiasis; Group III (SHF + HCV): 30 patients with combined disease, chronic schistosomal hepatic fibrosis (SHF) and chronic hepatitis C infection; Group IV (HCC): 30 patients with hepatocellular carcinoma associated with chronic hepatitis C virus and schistosomal infection. RESULTS: Patients with HCV, HCV + SHF and those with HCC had a significantly higher serum activin A compared with the control group (P < 0.001). Serum activin A level (mean +/- SD) was 5.7 +/- 2.76, 10.59 +/- 3.59, 15.39 +/- 4.61 and 19.93 +/- 5.43 ng/mL in controls, HCV patients, HCV + SHF patients and HCC patients, respectively. Serum IGF-1 was significantly lower in HCV patients, HCV + SHF patients and HCC patients compared to the control group (P < 0.001). Serum IGF-1 was 121.7 +/- 73.4, 76.7 +/- 23.5, 35.7 +/- 17.6 and 39.9 +/- 25.9 ng/mL in controls, HCV patients, HCV + SHF patients and HCC patients, respectively. Similarly, serum IGFBP-3 was significantly lower in HCV patients, HCV + SHF patients and HCC patients compared to the control group (P < 0.001). Furthermore, serum insulin-like growth factor binding protein 3 (IGFBP-3) was significantly lower in patients with HCC compared to patients with HCV or those with HCV + SHF (P < 0.01 and P = 0.024, respectively). The median (range) of serum IGFBP-3 was 4452 (352.2-8965), 3457 (1114-6000), 2114 (867-5901) and 1202 (576-3994) ng/mL in controls, HCV patients, HCV + SHF patients and HCC patients, respectively. Serum activin A correlated positively with Child-Pugh scoring in patients with HCV, HCV + SHF and those with HCC. The correlation coefficient was significant, at 0.001, in total cases. CONCLUSIONS: We conclude that patients with HCV, HCV + SHF and those with HCC have a significantly higher serum activin A when compared with controls. Serum activin A level was significantly higher in patients with HCV + SHF compared to those with HCV alone (P < 0.01) with a significant positive correlation between the serum activin A level and Child-Pugh scoring in patients with HCV, HCV + SHF and those with HCC. Furthermore, serum IGF-1 and IGFBP-3 levels were significantly reduced in patients with HCV, HCV + SHF and those with HCC compared to the control group. We suggest that this pattern (high activin A and low IGF-1 and its binding protein 3) may play a role in development of HCC in Egyptian patients suffering from combined hepatitis C virus infection and hepatic schistosomiasis.