Isolates In Hainan Research Articles

Complete Genomic Sequence Analysis of a Sugarcane Streak Mosaic Virus Isolate from Yunnan Province of China.

In recent years, the sugarcane streak mosaic virus (SCSMV) has been the primary pathogen of sugarcane mosaic disease in southern China. In this study, the complete genome of a sugarcane mosaic sample (named YN-21) from Kaiyuan City, Yunnan Province, was amplified and sequenced. By comparing the amino acid sequences of YN-21 and 15 other SCSMV isolates from the NCBI database, the protease recognition site of SCSMV was determined. YN-21 had the highest nucleotide and amino acid identities of 97.66% and 99.30%, respectively, in comparison with the SCSMV isolate (JF488066). The P1 had the highest variability of 83.38-99.72% in the amino acid sequence, and 6K2 was the most conserved, with 97.92-100% amino acid sequence identity. A phylogenetic analysis of nucleotide and amino acid sequences clustered the 16 SCSMV isolates into two groups. All the Chinese isolates were clustered into the same group, and YN-21 was closely related to the Yunnan and Hainan isolates in China. Recombination analysis showed no major recombination sites in YN-21. Selective pressure analysis showed that the dN/dS values of 11 proteins of SCSMV were less than 1, all of which were undergoing negative selection. These results can provide practical guidance for monitoring SCSMV epidemics and genetics.

Comparative analyses of the mitochondrial genomes of the cattle tick Rhipicephalus microplus clades A and B from China.

The cattle tick (Rhipicephalus microplus) is one of the most common ticks parasitizing livestock, causing diseases as the vector of pathogens. In this study, we amplified and sequenced the complete mitochondrial (mt) genome of R. microplus from Hainan province of China and compared it with that of R. microplus from Guizhou province of China. The mt genome sequence of R. microplus from Hainan isolate was 15,163bp in size, which was significantly longer (299bp) than R. microplus from Guizhou isolate. Nucleotide sequence difference in the entire mt genome except for non-coding region was 5.6% between R. microplus from Hainan and Guizhou isolates. For the 13 protein-coding genes, this comparison revealed the sequence differences of nucleotide (3.8-10.1%) and amino acid (1.2-17.3%). Phylogenetic analysis of R. microplus indicated that R. microplus from Hainan isolate clustered in clade A, and R. microplus from Guizhou isolate clustered in clade B. Taken together, the findings support the recent proposal the existence of two lineages (clades A and B) of R. microplus in China.

Novel Streptococcus uberis sequence types causing bovine subclinical mastitis in Hainan, China.

To determine the molecular epidemiology, genotypes and phenotypes of the major species of Streptococcus associated with bovine subclinical mastitis in Hainan, China. In total, 150 subclinical mastitis milk samples were collected from two large dairy farms in Hainan. On the basis of biochemical tests and 16S rDNA sequencing, 39samples were Streptococcus positive and the most frequently isolated species was Streptococcus uberis (n=29, 74.4%). According to multilocus sequence typing (MLST), and assays of biofilm formation, antimicrobial susceptibility, resistance and virulence genes, the S. uberis isolates were clustered into nine new sequence types (STs; ST986-ST994) but were not merged into a clonal group (except for ST991 [CC143]). All isolates produced biofilm, but most weakly. The dominant virulence pattern was hasABC+sua+gapC+oppF+pauA+mtuA+cfu (27/29, 91.1%), based on the 11 virulence genes tested. The majority of isolates (88.46%) carried at least one resistance gene, and more than half (58.62%) were multidrug-resistant. The main resistance genes were linB (65.5%), ermB (37.9%) and tetS (34.5%), among the six antibiotic resistance genes and 11 antimicrobials tested. Environmental S. uberis is important in bovine subclinical mastitis in Hainan. Streptococcus uberis isolates in Hainan, China, show distinct MLST, virulence and antibiotic resistance characteristics.

Founder Effects Contribute to the Population Genetic Structure of the Major Dermatophytosis Pathogen Trichophyton rubrum on Hainan Island, China.

BackgroundFounder events have been observed among numerous plants and animal species living on oceanic islands due to the geographic separation of these islands and the small amount of original life they harbor. However, there has been little research on the ecological characteristics of pathogenic microorganisms on islands. Trichophyton rubrum ranks the most common isolated dermatophyte causing dermatophytosis in clinic and has become an epidemic strain worldwide in recent decades.ObjectiveTo study the phylogenetic characteristics and the distribution pattern of genetic polymorphism of T. rubrum in China, which further provide theoretical basis for the prevention and control of T. rubrum.MethodsIn the present study, we sequenced and analyzed the genetic characteristics of 204 T. rubrum isolates from Hainan Island and other sites in China. Phylogenetic analysis and genetic polymorphisms were studied based on a total of 41,409 high-quality whole-genome SNPs.ResultsThe majority of the isolates from Hainan Island clustered together. Mixed T. rubrum population differentiation was observed among the strains of different geographical origins. In addition, the genetic diversity (π) of the Hainan isolates was low and showed no significant difference from that of isolates from other sites.ConclusionThis study is the first to discuss general ecological and evolutionary principles related to pathogenic fungi. Our findings reveal a founder effect during the origination of T. rubrum on Hainan Island and provide guidance regarding prevention and treatment strategies.

Genetic diversity analysis of papaya leaf distortion mosaic virus isolates infecting transgenic papaya "Huanong No. 1" in South China.

The commercialized genetically modified papaya “Huanong No. 1” has been utilized to successfully control the destructive virus‐papaya ringspot virus (PRSV) in South China since 2006. However, another new emerging virus, papaya leaf distortion mosaic virus (PLDMV), was found in some PRSV‐resistant transgenic plants in Guangdong and Hainan provinces of South China through a field investigation from 2012 to 2019. The survey results showed that “Huanong No. 1” papaya plants are susceptible to PLDMV, and the disease prevalence in Hainan Province is generally higher than that in Guangdong Province. Twenty representative isolates were selected to inoculate “Huanong No. 1,” and all of the inoculated plants showed obvious disease symptoms similar to those in the field, indicating that PLDMV is a new threat to widely cultivated transgenic papaya in South China. Phylogenetic analysis of 111 PLDMV isolates in Guangdong and Hainan based on the coat protein nucleotide sequences showed that PLDMV isolates can be divided into two groups. The Japan and Taiwan China isolates belong to group I, whereas the Guangdong and Hainan isolates belong to group II and can be further divided into two subgroups. The Guangdong and Hainan isolates are far different from the Japan and Taiwan China isolates and belong to a new lineage. Further analysis showed that the Guangdong and Hainan isolates had a high degree of genetic differentiation, and no recombination was found. These isolates deviated from neutral evolution and experienced population expansion events in the past, which might still be unstable. The results of this study provide a theoretical basis for clarifying the evolutionary mechanism and population genetics of the virus and for preventing and controlling the viral disease.

Molecular characteristics and virulence gene profiles of Staphylococcus aureus isolates in Hainan, China

BackgroundThere have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus (S. aureus) from Hainan, the southernmost province of China.MethodsTwo hundred twenty-seven S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013–2014 and 2018–2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes.ResultsForty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A (spa) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013 to 2014 (5.5%, 5/91) to 2018–2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCCmec) typing. SCCmec-IVa was the predominant SCCmec type, and specifically, ST45-SCCmec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S. aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin (pvl) and eta, were determined, and the frequency of eta and pvl were found to be 57.3 and 47.6%. Such high prevalence has never been seen in mainland China before.ConclusionS. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.

Geographic Distribution and Genetic Diversity of Rice Stripe Mosaic Virus in Southern China

Rice stripe mosaic virus (RSMV) transmitted by the leafhopper Recilia dorsalis is a tentative new species in the genus Cytorhabdovirus identified recently in South China. To explore its geographic distribution and genetic diversity, field investigation and viral whole-genome sequencing were conducted in this study. The results indicated that RSMV was present in the rice samples collected across southern China. Twelve representative samples from different geographical regions were selected for viral whole-genome sequencing and the viral genome variation was analyzed in combination with a previously reported RSMV isolate. Identity analysis showed that the genome sequences of 13 RSMV isolates were highly conserved with nucleotide identities over 99.4%. There was a strong negative selection pressure during the evolution of RSMV with more transitions (72.08%) than transversions (27.92%) found between the RSMV isolates. Among the seven genes encoded by RSMV, the P gene was the most variable, followed by N, M, L, and G; the P3 and P6 amino acid sequences were not found to be mutated and no mutations were found in the non-coding region. A phylogenetic tree based on the RSMV whole-genome nucleotide sequences revealed that all RSMV isolates clustered in two groups based on geographical origin. Notably, the L proteins of the Guangxi and Hainan isolates had five and one specific amino acid sites, respectively, suggesting that the L gene has undergone environmental adaptive variation during the dispersal of RSMV.

Use of RNAi technology to develop a PRSV-resistant transgenic papaya

Papaya ringspot virus (PRSV) seriously limits papaya (Carica papaya L.) production in tropical and subtropical areas throughout the world. Coat protein (CP)- transgenic papaya lines resistant to PRSV isolates in the sequence-homology-dependent manner have been developed in the U.S.A. and Taiwan. A previous investigation revealed that genetic divergence among Hainan isolates of PRSV has allowed the virus to overcome the CP-mediated transgenic resistance. In this study, we designed a comprehensive RNAi strategy targeting the conserved domain of the PRSV CP gene to develop a broader-spectrum transgenic resistance to the Hainan PRSV isolates. We used an optimized particle-bombardment transformation system to produce RNAi-CP-transgenic papaya lines. Southern blot analysis and Droplet Digital PCR revealed that line 474 contained a single transgene insert. Challenging this line with different viruses (PRSV I, II and III subgroup) under greenhouse conditions validated the transgenic resistance of line 474 to the Hainan isolates. Northern blot analysis detected the siRNAs products in virus-free transgenic papaya tissue culture seedlings. The siRNAs also accumulated in PRSV infected transgenic papaya lines. Our results indicated that this transgenic papaya line has a useful application against PRSV in the major growing area of Hainan, China.

Molecular epidemiological study on rubella virus strains isolated in Zhejiang province, China, 2005-2010

To analyze the molecular epidemiological characteristic of rubella virus strains isolated in Zhejiang province from 2005 to 2010, to provide basic data for rubella prevention and control. Rubella virus strains were isolated on Vero cells from the suspected patients' specimens collected in Zhejiang province during 2005 to 2010. Partial fragments of the structural gene of Zhejiang rubella strains were amplified, using nested reverse transcription-polymerase chain reaction (RT-PCR). The amplified products were sequences and analyzed. In total, 7 rubella strains were isolated from 52 clinical specimens, of which six were classified as genotype 1E and only one was characterized as genotype 2B. In the phylogenetic tree, the Zhejiang 1E genotype rubella strains were located in the same branches with Hongkong or Hainan isolates respectively, but the Zhejiang 2B genotype strain were located in the same branch with oversea strain BuenosAires. ARG/46.08. Through p-distance analysis, results also showed that the Zhejiang 2B genotype strain was closer to the 2B strains isolated from overseas (0.011) than those strains from other provinces of China (0.023). Compared with Chinese vaccine strain BRD II, the homology on three structural genes was C > E2 > E1, but the homology of deduced amino acid sequence was E1 > C > E2, with corresponding 3, 11 and 23 amino acid mutations. There was only one amino acid on E1 gene with entropy value higher than 0.600, but seven sites on E2 gene with entropy value appeared higher than 0.600 and one with entropy value higher than 1.000. Two genotypes of rubella virus had circulated in Zhejiang province during 2005 to 2010. Genotype 1E appeared to be the predominant genotype and 2B being an imported one. Amino acid sequence of E1 gene from Zhejiang rubella strains was comparatively conserved, but E2 gene was hypervariable. Study on rubella virus E2 and C gene should be conducted in the epidemiological surveillance program of rubella.

Molecular subtyping of Vibrio cholerae isolates from outbreaks of cholera by pulsed-field gel electrophoresis in Hainan in 2008

To analyze the molecular characteristics and genetic correlations of Vibrio cholerae isolates in Hainan in 2008, so as to provide pathogenic proof to diagnose the plague. Seventy six cholera strains were isolated from this cholera epidemic.69 strains were obtained from patients, 7 were isolated from external environment, among which, one was from patient's toilet, one from water sample, three were isolated from fish pond near patient's home, one came from swab of the patient vomit on the ground of health center and one from swab of kitchen knife from Hainan University canteen respectively. With conventional aetiological methods, pulse-field gel electrophoresis was conducted and the patterns of the 76 isolates were analyzed. The PFGE image was analyzed using BioNumerics (Version4.0, Applied Maths BVBA, Belium). Image bands were identified and similarity coefficient was automatically generated. Seventy six strains were isolated from Vibrio cholerae outbreaks in Hainan in 2008.5 PFGE patterns of patient's isolates in June were the same, sharing a similarity coefficient of 100%. 70 PFGE patterns of patients and water in October and November were completely same, the similarity coefficient being 100%. But they were not same as that of June. 1 PFGE pattern of isolate from the sample in Hainan University was different, only sharing a similarity coefficient of 79.7%, which showed no correlation with the outbreak. Different outbreaks of Vibrio cholera occurred in Hainan in 2008. The epidemic in October and November at different counties was one outbreak. The pollution of water in environment was an important factor for outbreak.

Oral yeast flora and its ITS sequence diversity among a large cohort of medical students in Hainan, China

The most prevalent fungal infection of humans is candidiasis which is caused by species of Candida that are typical members of the commensal microbial flora of the oral mucosa and other body surfaces. Since species of Candida differ in virulence properties and susceptibilities to anti-fungal drugs, understanding the human commensal yeast flora will have a significant impact on designing treatment and prevention strategies against yeast infections. However, although there is a global interest in Candida species, the global distributions of Candida species remain largely unknown, especially among healthy hosts. Here we report the oral yeast flora from the surveys of over 1,000 medical students in China. Our results showed that this population had a yeast carriage rate (4.5%) much lower than other population samples reported previously from Mainland China (40-70%). In addition, C. albicans was isolated at a much higher frequency than those from other Chinese samples, with a frequency (80.9%) more similar to those in developed regions such as North America. The oral yeast carriage rates and yeast species compositions were similar between male and female students and between the hosts borne and raised on Hainan Island and those borne and raised on Mainland China. Furthermore, the sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster was analyzed for strains of the dominant species, C. albicans. Our analysis identified 14 ITS types among the 41 Hainan isolates of C. albicans. However, only four of the 14 ITS types were identical to those in reference strains from Europe and North America. Taken together, our analyses suggest that the oral yeast flora among host populations in China is highly heterogeneous and that there is a high ITS sequence diversity in the Hainan population of C. albicans.