Development and evaluation of a new PCR assay for detection of Pseudomonas aeruginosa D genotype

This report describes a new PCR-based assay for the detection of Pseudomonas aeruginosa genotype D in occupational saturation diving systems in the North Sea. This genotype has persisted in these systems for 11 years (1993-2003) and represents 18% of isolates from infections analysed during this period. The new PCR assay was based on sequences obtained after randomly amplified polymorphic DNA (RAPD)-PCR analysis of a group of isolates related to diving that had been identified previously by pulsed-field gel electrophoresis (PFGE). The primer set for the D genotype targets a gene that codes for a hypothetical class 4 protein in the P. aeruginosa PAO1 genome. A primer set able to detect P. aeruginosa at the species level was also designed, based on the 23S-5S rDNA spacer region. The two assays produced 382-bp and 192-bp amplicons, respectively. The PCR assay was evaluated by analysing 100 P. aeruginosa isolates related to diving, representing 28 PFGE genotypes, and 38 clinical and community P. aeruginosa isolates and strains from other species. The assay identified all of the genotype D isolates tested. Two additional diving-relevant genotypes (TP2 and TP27) were also identified, as well as three isolates of non-diving origin. It was concluded that the new PCR assay is a useful tool for early detection and prevention of infections with the D genotype.     

Distribution of prion protein in German patients with Creutzfeldt-Jakob disease is different from that in Japanese patients

We investigated the distribution of prion protein (PrP) in 14 German patients with sporadic Creutzfeldt-Jakob disease (CJD) and compared it with that observed in Japanese patients. Immunohistochemical study revealed diffuse gray matter stainings including synaptic structures in all cases. In addition, 4 patients showed plaque-type deposition which was very rarely observed among sporadic Japanese patients without known mutation of the PrP gene but with valine at codon 129. A higher incidence of PrP plaques in German sporadic CJD may be related to the racial difference in the PrP gene.     

胸苷酸合成酶基因3’-UTR多态性与晚期胃癌化疗敏感性关系的研究

目的：研究胸苷酸合成酶（TS）基因3’-UTR多态性与胃癌对5-Fu化疗敏感性的关系。方法：收集经病理学确诊的晚期胃癌106例，所有病例化疗前抽静脉血，提取白细胞DNA，用PCR-RFLP技术检测TS3’-UTR基因型。所有患者均经5-FU为基础的化疗方案治疗。以WHO实体瘤疗效评定标准和毒性评定标准评价疗效和毒性。结果：（1）106例胃癌患者中TS＋6／＋6bp、＋6／-6bp、-6／-6bp基因型频度分别为7．6％、44．3％和48．1％，化疗的总有效率为35．9％。（2）TS＋6／＋6bp、＋6／-6bp、-6／-6bp基因型组化疗的有效率分别为0％（0／8）、40．4％（19／47）和37．3％（19／51）。TS-6／-6bp基因型组和＋6／-6bp组化疗的有效率均显著高于＋6／＋6bp组（Fisher双侧精确检验，P值分别为0．0452和0．0404）。TS-6／-6bp基因型组Ⅱ度以上毒副反应的发生率高于＋6bp／＋6bp基因型组，但其差异无统计学意义。结论：TS基因3’-UTR多态性与晚期胃癌对5-FU为基础的化疗敏感性相关，TS基因型检测有助于指导晚期胃癌的化疗。     

Use of multiplexed tandem PCR to estimate the prevalence and intensity of Theileria orientalis infections in cattle

This study employed a semi-quantitative, multiplexed tandem PCR (MT-PCR) to assess the prevalence and infection intensity of four genotypes (buffeli, chitose, ikeda and type 5) of Theileria orientalis in cattle in Australia. Genomic DNA samples from blood samples (n = 448) collected from 27 to 32 dairy cows from each of 15 dairy herds with a history of recent theileriosis outbreaks (Group 1), and from blood samples available from 24 cows with or without oriental theileriosis (Group 2) were tested using MT-PCR. Results revealed that all four genotypes were present in Group 1 cattle; genotype buffeli had the highest prevalence (80.5%), followed by genotypes ikeda (71.4%), chitose (38.6%) and type 5 (20.3%). Genotype ikeda had the highest average infection intensity in the cattle (relating to 55,277 DNA copies), followed by buffeli, chitose and type 5 (6354–51,648 copies). For Group 2, results indicated that genotype ikeda had a significantly higher average intensity of infection than buffeli in symptomatic cattle (P < 0.001), and symptomatic cattle had a higher intensity of ikeda than asymptomatic cattle (P = 0.004). Future studies should assess the utility of the present MT-PCR assay as a diagnostic and epidemiological tool in other parts of Australasia and the world.     

Hepatitis C Virus Infection in a Tertiary Care Hospital in Mumbai,India: Identification of a Mixed and Novel Genotype

Purpose: Hepatitis C virus (HCV) is a leading cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma (HCC). HCV being a ribonucleic acid virus has considerable sequence variability. Assessment of viral load and genotype is necessary for designing treatment strategies and monitoring for viral resistance among HCV-infected cases. HCC is the most common form of liver cancer, often occurring in people with chronic hepatitis B or C. We undertook this study to observe genotype distribution of the virus in HCV patients from Mumbai. Materials and Methods: Between January 2017 and December 2017, the study was conducted on 120 chronic hepatitis outpatients from a tertiary care hospital, Mumbai, after obtaining ethics approval. All these diagnosed cases of HCV were subjected to molecular diagnosis in a research institute, Mumbai, by real-time polymerase chain reaction-based techniques. Results: Males were more preponderant than females with HCV infection, and the highest number of HCV-infected cases was observed in the age group of 41–50 years. Genotype 3 (n = 70; 58.3%) accounted for the highest number of cases followed by genotypes 1b (n = 29; 24.2%) and then 1a (n = 14; 11.7%). Mixed genotypes 1b + 3 and individual genotype 4 were found in two cases each (1.7%). A total of three samples (2.5%) were found with untypeable genotype. Conclusion: The major HCV genotype observed was 3 which is difficult to treat with direct-acting antivirals, owing to the more rapid progression of liver disease, increased rates of steatosis (non-alcoholic fatty liver disease), a higher risk for cancer (HCC). We believe this study is the first one to address the prevalence of mixed genotypes and untypeable genotype from India.     

Rotaviruses: Is their surveillance needed?

Rotaviruses, a major cause of gastroenteritis in children worldwide accounts for around 0.5 million deaths annually. Owing to their segmented genome and frequently evolving capability, these display a wide variation in their genotypes. In addition to commonly circulating genotypes (G1, G2, G3, G4, G9, P[4] and P[8]), a number of infrequent genotypes are being continuously reported to infect humans. These viral strains exhibit variation from one geographical setting to another in their distribution. Though the introduction of vaccines (RotaTeq and Rotarix) proved to be very effective in declining rotavirus associated morbidity and mortality, the number of infections remained same. Unusual genotypes significantly contribute to the rotavirus associated diarrhoeal burden, may reduce the efficacy of the vaccines in use and hence vaccinated individuals may not be benefited. Vaccine introduction may bring about a notable impact on the distribution and prevalence of these viruses due to selection pressure. Moreover, there is a sudden emergence of G2 and G3 in Brazil and United States, respectively, during the years 2006–2008 post-vaccination introduction; G9 and G12 became predominant during the years 1986 through 1998 before the vaccine introduction and now are commonly prevalent strains; and disparity in the predominance of strains after introduction of vaccines and their natural fluctuations poses a vital question on the impact of vaccines on rotavirus strain circulation. This interplay between vaccines and rotavirus strains is yet to be explored, but it certainly enforces the need to continuously monitor these changes in strains prevalence in a particular region. Furthermore, these fluctuations should be considered while administration or development of a vaccine, if rotavirus associated mortality is ever to be controlled.     

Burden of pediatric hepatitis C

Hepatitis C virus(HCV)is a major health burden infecting 170-210 million people worldwide.Additional 3-4millions are newly-infected annually.Prevalence of pediatric infection varies from 0.05%-0.36%in the United States and Europe;up to 1.8%-5.8%in some developing countries.The highest prevalence occurs in Egypt,sub-Saharan Africa,Amazon basin and Mongolia.HCV has been present in some populations for several centuries,notably genotypes 1 and 2 in West Africa.Parenteral anti-schistosomal therapy practiced in the 1960s until the early 1980s had spread HCV infection throughout Egypt.Parenteral acquisition of HCV remains a major route for infection among Egyptian children.Insufficient screening of transfusions,unsterilized injection equipment and re-used needles and syringes continue to be major routes of HCV transmission in developing countries,whereas vertical transmission and adolescent high-risk behaviors(e.g.,injection drug abuse)are the major routes in developed countries.The risk of vertical transmission from an infected mother to her unborn/newborn infant is approximately 5%.Early stages of HCV infection in children do not lead to marked impairment in the quality of life nor to cognitive,behavioral or emotional dysfunction;however,caregiver stress and family system strain may occur.HCV slowly progresses to serious complications as cirrhosis(1%-2%)and hepatocellular carcinoma(HCC)especially in the presence of risk factors as hemolytic anemias,obesity,treated malignancy,and concomitant human immune deficiency and/or hepatitis B virus co-infection.HCV vaccine remains elusive to date.Understanding the immune mechanisms in patients who successfully cleared the infection is essential for vaccine development.The pediatric standard of care treatment consists of pegylated interferon-α2a or b plus ribavirin for 24-48 wk.The new oral direct acting antivirals,approved for adults,need further evaluation in children.Sustained virologic response varies depending on the viral load,genotype,duration of infection,degree of am     

Current Status of Acanthamoeba in Iran: A Narrative Review Article

Background:

Free-living amoebae belonging to the genus Acanthamoeba have an environmental distribution. Amoebic keratitis due to these protozoan parasites continue to rise in Iran and worldwide. In Iran, there are various researches regarding both morphological and molecular identification of Acanthamoeba spp. in environmental and clinical samples. However, there is no thorough review about Acanthamoeba genotypes and their distribution in environmental sources such as water, dust and biofilm in Iran. Besides, according to increasing cases of Amoebic keratitis in the region awareness regarding the pathogenic potential of these sight-threatening amoebae is of utmost importance.

Methods:

We conducted a thorough review based on the database sources such as MEDLINE, PubMed and Google scholar. No restrictions were placed on study date, study design or language of publication. We searched all valuable and relevant information considering the occurrence of the Acanthamoeba in both environmental and clinical samples.

Results:

According to our thorough review Acanthamoeba belonging to T4 genotype is the most prevalent type strain in environmental and clinical samples in several regions in Iran and worldwide, however, there are reports regarding Acanthamoeba belonging to other genotypes such as T2, T3, T5, T6 and T11 and the mentioned point could leads us to more researches with the goal of presenting the real genotype dominance of Acanthamoeba and related disease in the country.

Conclusion:

Overall, the present review will focus on present status of genotypes of Acanthamoeba in Iran during recent years.     

北京地区急性呼吸道感染住院患儿腺病毒感染临床特征

目的比较北京地区急性呼吸道感染住院患儿中不同型别腺病毒感染临床特征, 明确腺病毒分型的临床必要性。方法采用横断面研究, 纳入2017年11月至2019年10月在首都儿科研究所附属儿童医院因急性呼吸道感染住院的9 022例次患儿呼吸道标本, 经直接免疫荧光(DFA)和(或)核酸检测确定为腺病毒阳性者进行五邻体、六邻体及纤维蛋白基因扩增并测序, 构建系统进化树区分腺病毒型别。收集并分析腺病毒主要型别感染患儿的实验室检查、影像学资料等临床资料, 采用t检验、U检验、χ2检验进行型别间临床特征差异的统计学分析。结果 9 022例次急性呼吸道感染住院患儿中腺病毒阳性检出率为4.34%(392例次), 成功分型205例, 其中男131例、女74例, 年龄22.6(6.7, 52.5)月龄, 3型腺病毒阳性102例(49.76%), 7型86例(41.95%), 1、2、4、6、14、21型共17例。7型与3型腺病毒感染患儿临床特征比较, 在出现喘息[10例(11.63%)比25例(24.51%)]、白细胞计数>15×109/L[4例(4.65%)比14例(13.73%)]、白细胞计数<...