The molecular epidemiological characteristics of the gastroenteritis outbreaks caused by norovirusin Hainan Province,2020-2022 / 安徽医科大学学报

Objective To understand the molecular epidemiological characteristics of Norovirus outbreaks and the genome evolution of Norovirus epidemic strains in Hainan Province from 2020 to 2022.Methods The information and samples have been collected from the norovirus outbreaks from 2020 to 2022.Norovirus was detected by using the real-time PCR in these samples,then the detected sequences were amplified the analyzed.The Norovirus se-quences of 8 strains had been amplified and analyzed.Results From 2020 to 2022,39 gastroenteritis outbreaks were reported,and 25 outbreaks caused by Norovirus which mainly occurred in childcare institutions and schools(20/25,80％).The Norovirus outbreaks were mainly concentrated in counties around Haikou(northeast),which including Ding'an(5 cases),Wenchang(4 cases),Chengmai(4 cases),and Lingao(3 cases);following by western regions which included Baisha(2 cases),Ledong(2 cases),and Dongfang(3 cases).1 case was in Wanning in the southeast.Among individuals aged 2-17,the positive proportion of Norovirus in males was higher than that in females.Among individuals aged over 55,the proportion of Norovirus positive in females was higher than that in males.The gender of positive samples among individuals aged 18-40 was related to their profession.According to RT-PCR typing and sequencing,GⅡ group Norovirus were classified in13 outbreaks.There were 4 genotypes detected.GⅡ.2[P1 6]was the main epidemic strain with 60％(9/13),and the other three genotypes were GⅡ.4 Sydney[P31](15.4％,2/13)GⅡ.4 Sydney[P16](7.7％,1/13)and GⅡ.3[P12](7.7％,1/13).Further genic analysis of 8 Norovirus strains showed that all of them were still in the same branch as the previ-ous strain,and all exhibited a certain amount of amino acid variation.Conclusion Norovirus is the main pathogen of gastroenteritis outbreaks in Hainan province,and the main epidemic strain is GⅡ.2[P16].It is necessary to continue to strengthen the monitoring that provides scientific evidence for the prevention and control of norovirus out-breaks in Hainan region.

Genomic analysis of endophytic Bacillus altitudinis strain VUMS1 from Kappaphycus alvarezii and its inhibitory effect against Vibrio parahaemolyticus

Aims@#Sabah’s red algae, Kappaphycus alvarezii is facing a problem whereby the production of seaweed is declining over the years due to a disease called ice-ice disease caused by Vibrio spp. Endophytic Bacillus strains have been widely studied for their potential as biocontrol agents against harmful pathogens. This study reports the genome sequence of the beneficial endophytic Bacillus strain VUMS1 isolated from the healthy K. alvarezii at Semporna Island in Sabah, attempting to determine its full biocontrol potential.@*Methodology and results @#The whole genome sequence showed that VUMS1 genome size is 3,754,982 bp with 3,854 protein-coding where 2,535 are genes with assigned functions. The analysis revealed the presence of genes that are involved in antimicrobial and antifungal activity such as fengycin, bacillibactin, bacilysin and lichenysin. The biocontrol potential of VUMS1 was evaluated against Vibrio parahaemolyticus isolated from the diseased K. alvarezii. Results showed that the inhibition zone of VUMS1 by cross-streaking method against V. parahaemolyticus was 21 ± 0.71 mm and the growth of V. parahaemolyticus treated with VUMS1 in a co-culture experiment decreased by 98% on day 5 of treatment.@*Conclusion, significance and impact of study@#The results of this work indicate that VUMS1 is affiliated as Bacillus altitudinis and it may contribute to the biocontrol activity against Vibrio spp. infection in K. alvarezii. This is the first report of endophytic Bacillus altitudinis from K. alvarezii with biocontrol properties. Future studies will determine the potential application of the B. altitudinis VUMS1 strain in biological control and growth promotion for sustainable seaweed farming.

Prevalence and antimicrobial resistance profiles of Neisseria gonorrhea and Chlamydia trachomatis isolated from individuals attending STD clinics in Kampala, Uganda

Background: Sexually transmitted diseases (STDs) management in sub-Saharan Africa is syndromic but molecular diagnostics provide quicker, sensitive diagnosis and treatment. Effective STD control hinges on identification and treatment of infected persons and sexual partner contact tracing. Objectives: This study assessed feasibility of using the Xpert CT/NG test to identify prevalent Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG) infections among STD clinic attendees and their sexual partners and tested for antimicrobial resistance for N. gonorrhea. Methods: A cross-sectional study was conducted at 4 outpatient STD clinics in Kampala, Uganda from February 2019 to October 2019. Participants received a syndromic diagnosis, were tested for NG and CT, as well as their sexual partners. Urine (men) and high vaginal swabs (women) were collected, examined using Xpert CT/NG assay. A total of 79 participants were enrolled at baseline of whom 25 had CT/NG. 21 partners of infected baseline participants and 7 partners of the 21 primary partners were enrolled. Results: The mean age of the reported sexual partners was 26 (18-43) years. The prevalence of NG was 25% at baseline and 18 % for CT. Nine (11.4%) people were dually infected. Men were more likely to have NG (p<0.001) at multivariable level. Two participants tested HIV-1 positive. On microbiological culture, 8 samples (2.5%) grew NG, and all were resistant to penicillin, ciprofloxacin. For CT, we found a preponderance of the F-serovar in this population. Conclusion: The most prevalent organism was Neisseria gonorrhea. Generally, the prevalence of CT and NG was high. Infection proportions increased among primary partners, particularly women. Etiologic testing without partner tracing and treatment may underestimate burden of CT/NG in this population and contribute to re-infection

Complete genome sequence of a rodent polyomaviruses in Hainan Island, China

Objective: Polyomavirus infection is reported in a wide range of mammalian and avian hosts, including asymptomatic infection, acute systemic disease, and tumor induction.This study aims to obtain and characterize the complete genome of rodent polyomaviruses, PyVs-HMU. The host of virus was a Rattus norvegicus in the residential areas of Hainan Island, China. Methods: The liver samples of Rattus norvegicus were collected from the residential areas of Hainan Island, and then processed with a viral particle-protected, nucleic acid purification method. The extracted RNA and DNA were amplified by sequence-independent PCR. The amplified viral nucleic acid libraries for the samples of Rattus norvegicus were then sequenced using an Illumina GAII sequencer for a single read of 100 bp in length. The raw sequence reads were then filtered using previously described criteria to obtain valid sequences. Results: We obtained the complete genome of a novel polyomaviruses, PyVs-HMU. The genomic sequence of PyVs-HMU has been submitted in GenBank under accession number MK372231. The complete genome of PyVs-HMU is 5318 nucleotides (nt) in length with a G+C content of 45.36%. The complete PyV-HMU sequences display the representative genome organization of polyomaviruses. The genome contain antigens of spliced small T (STAg), middle T (MTAg) and large T(LTAg), and a noncoding control region (NCCR) separate the late region of structural VP1, VP2, and VP3 proteins. The STAg, LTAg, VP1, VP2, VP3 and MTAg encoded proteins of 194, 776, 384, 347, 228 and 414 amino acids (aa) respectively. Phylogenetic analyses depend on LTAg amino acid sequence revealed that the PyV-HMU to be a relative lineage beside a cluster comprising RnorPyV1(KR065723). Conclusions: The discovery of PyV-HMU expands the geographic range of polyomavirus and will provide further insights into the ecology and evolution of PyVs in rodents and humans. The identification of the novel rodent PyVs will provide basic data for the control of emerging zoonotic infectious diseases.

Analysis of genomic characteristics and virulence factors of emetic-type Bacillus cereus strains isola-ted in Hangzhou / 中华微生物学和免疫学杂志

Objective To investigate the genomic characteristics and virulence factors of emetic-type Bacillus cereus strains isolated from food in Hangzhou for better understanding their pathogenic potential. Methods Real-time PCR was performed to detect the ces gene cluster ( cereulide) in 132 Bacillus cereus strains isolated from food from 2015 to 2017. Genomes of cereulide-positive strains were sequenced using Illumina MiSeq sequencing platform. Genome annotation, virulence factor detection, comparative and evolu-tionary analysis were performed after the sequences of genomes were assembled. Results Twelve strains (9. 09％) carried the ces gene. Their genome sizes ranged from 5. 35 to 5. 75 Mb and GC contents from 35. 25 to 35. 43 mol％. All of them harbored the full cereulide biosynthesis gene cluster, nonhemolytic ente-rotoxin ( NHE)-encoding gene cluster ( nheA, nheB and nheC) and hemolysinⅢ( hlyⅢ) . The average nu-cleotide identity ( ANI ) between the 12 isolates and the reference strain NC7401 ( Accession number:AP007209) was over 99. 35％. Phylogenetic analysis demonstrated these strains were clustered into the same branch with local clinical isolates and the emetic-type Bacillus cereus strains of NC7401 and AH187. Con-clusions The genomic sequences of the emetic-type Bacillus cereus strains isolated from food in Hangzhou area were highly similar to that of the reference strain NC7401. Results of the genomic analysis suggested that these isolates carried many virulence factors that were related to pathogenicity.

Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389 / Identificação e mapeamento de um novo gene de resistência a ferrugem linear na linhagem de trigo CH5389

ABSTRACT: Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.

RESUMO: A ferrugem linear causada por Puccinia striiformis é uma das doenças mais destrutivas do trigo no mundo. A linhagem CH5389 é derivada do cruzamento de trigo com Thinopyrum intermedium e confere resistência a ferrugem linear. Análises genéticas de indivíduos da população F2 e família F2:3 obtida a partir do cruzamento entre CH5389 e trigo comum suscetível revelaram que a resistência à ferrugem linear na linhagem CH5389 foi controlada por um único gene dominante, designado YrCH5389. Oito marcadores polimórficos SSR e EST-PCR no cromossomo 3AL foram identificados na população F2 de CH5389/Taichung29. O gene YrCH5389 foi delimitado pelos marcadores EST BE405348 e SSR Xwmc388 no cromossomo 3AL com distâncias genéticas de 2,2 e 4,6 cM, respectivamente. Análises genômicas comparativas demonstraram que regiões genômicas ortólogas do gene YrCH5389 compreendem 990 kb em arroz, 640 kb em braquipódio e 890 kb em sorgo. Com base nas localizações dos marcadores, o gene de resistência foi localizado no cromossomo 3AL-0.85-1.00. Como não há genes oficialmente nomeados de resistência à ferrugem linear no cromossomo 3AL, o YrCH5389 deve ser designado como um gene novo de resistência. Esses marcadores de ligação podem ser úteis para a seleção assistida de genótipos de trigo resistentes a ferrugem linear.

Genomic characterisation of Leptospira inadai serogroup Lyme isolated from captured rat in Brazil and comparative analysis with human reference strain

Leptospira inadai is classified as a species of the Leptospira intermediate group that has been poorly studied due to its apparent insignificance to human and animal health. Nevertheless, over the last two decades the species has been described in human cases in India and in carrier animals in Ecuador. Here, we present the first identification and genomic characterisation of L. inadai serogroup Lyme isolated from captured rodent in Brazil. Even though the M34/99 strain was not pathogenic for hamsters, it was able to establish renal colonisation. The M34/99 strain presented high similarity with L. inadai serogroup Lyme human reference indicating that animal strain could also infect humans, although it does not represent high risk of severe disease. An extrachromosomal sequence was also identified in M34/99 strain and presented high identity with previously described L. inadai phage LinZ_10, suggesting that phage-like extrachromosomal sequence may be another feature of this understudied species.

Genomic Analysis of Fungal Species No.11243 Mutant Strains Provides Insights into the Relationship between Mutations and High Productivity.

Aims: FR901469 is a novel antifungal antibiotic produced by fungal species No.11243. Although we have several FR901469 high-producing mutant strains, the mechanism of high productivity is unclear. This study aims to unravel the relationship between mutations and FR901469 productivity. Methodology: We performed genome sequence analysis of mutant strains and detected mutated genes. Subsequently, we classified mutated genes into functional categories and searched the categories in which mutated genes were accumulated as generations progressed. Results: We found that genome regions of two scaffolds were amplified and one of those contained putative FR901469 biosynthesis gene cluster. Moreover, we detected totally 396 mutated genes from 14 mutant strains and the genes within the “Replication, recombination and repair”, “Signal transduction mechanisms” and “Transcription” categories accumulated this mutation. Conclusion: Our study suggests that productivity improvement occurs via the following two mechanisms: the amplification of putative FR901469 biosynthesis gene cluster and mutations of genes categorized as “Replication, recombination and repair”, “Signal transduction mechanisms” and “Transcription”.

Genomic study of Argentinean Equid herpesvirus 1 strains / Estudio genómico de cepas argentinas de Herpesvirus equino 1

Equid herpesvirus 1 (EHV-1) infection has a signifcant economic impact on equine production, causing abortion, respiratory disease, neonatal death and neurological disorders. The identifcation of specifc EHV-1 genes related to virulence and pathogenicity has been the aim of several research groups. The purpose of the present study was to analyze different genomic regions of Argentinean EHV-1 strains and to determine their possible relationship with virulence or clinical signs. Twenty-fve EHV-1 Argentinean isolates recovered from different clinical cases between 1979 and 2007 and two reference strains were amplifed and sequenced. The sequence alignments were carried out using Clustal X version 1.92 and the putative amino acid sequences were deduced using Bio-Edit version 7.05. Minor changes were observed. No changes that could be involved in the different virulence in the mouse model of three EHV-1 Argentinean strains were found. No genetic variants were observed. The genomic regions analyzed are unsuitable for differentiation between abortigenic strains and those isolated from neonatal deaths.

La infección por Herpesvirus equino 1 (EHV-1) tiene un signifcativo impacto económico en la producción equina mundial al causar abortos, enfermedad respiratoria, muertes perinatales y desórdenes neurológicos. La identifcación de genes específcos relacionados con la virulencia y patogenicidad de este virus ha sido el propósito de varios grupos de investigación. En este trabajo se analizaron diferentes regiones genómicas de cepas argentinas de EHV-1 para determinar la posible relación entre la estructura genómica y la virulencia o los signos clínicos producidos. Veinticinco cepas aisladas de diferentes casos clínicos observados entre los años 1979 y 2007 y dos cepas de referencia fueron amplifcadas y secuenciadas. El alineamiento de las secuencias se realizó con el programa Clustal X versión 1.92; el programa Bio-Edit versión 7.05 permitió deducir la secuencia de aminoácidos. Solo se observaron cambios menores, no se encontraron variaciones que pudieran estar relacionadas con la diferencia de virulencia observada previamente en el modelo ratón. No se hallaron variantes genómicas. Las regiones genómicas analizadas no permitieron diferenciar cepas abortigénicas de aquellas aisladas de muertes neonatales.

Genomic analysis of Vibrio vulnificus by Infrequent Restriction Site-Polymerase Chain Reaction / 대한임상미생물학회지

BACKGROUND: Vibrio vulnificus sepsis is one of the notifiable disease(Class 3) in Korea. It is usually acquired through the consumption of raw or undercooked seafood in summer. We studied the clinical findings of V. vulnificus septicemia and the genomic patterns of V. vulnificus isolates. METHODS: Seven patients with V. vulnificus septicemia were admitted to Hanyang University hospital from 1998 to 2002. We analysed the clinical findings and the genomic patterns by infrequent restriction site-polymerase chain reaction(IRS-PCR). RESULTS: All patients were over forty years old, and five were male. The patients had underlying diseases;five with liver cirrhosis, two with DM, and four patients with heavy alcoholism. Five of seven patients had history of ingesting raw fish and four had tissue necrosis with bullae or vesicles in their extremities. Four patients who died showed disseminated intravascular coagulation symptoms. We applied IRS-PCR to 6 isolates from blood and 2 isolates from wound. The six isolates from blood showed various genomic patterns that were all different from one another, while the two isolates from wound showed IRS-PCR patterns that were identical to the blood isolates of the same patients. CONCLUSIONS: The genomic patterns of IRS-PCR are quite different in 6 cases of V. vulnificus isolates in Korea.