The Hibiscus sabdariffa var. UMKL (Roselle) investigated here may potentially be used as an alternative fibre source. To
the best of our knowledge, there was no study focusing on the genetics underlying the cellulose biosynthesis machinery
in Roselle thus far. This paper presents the results of the first isolation of the cellulose synthase gene, HsCesA1 from this
plant, which is fundamental for working towards understanding the functions of CesA genes in the cellulose biosynthesis
of Roselle. A full-length HsCesA1 cDNA of 3528 bp in length (accession no: KJ608192) encoding a polypeptide of 974
amino acid was isolated. The full-length HsCesA1 gene of 5489 bp length (accession no: KJ661223) with 11-introns
and a promoter region of 737 bp was further isolated. Important and conserved characteristics of a CesA protein were
identified in the HsCesA1 deduced amino acid sequence, which strengthened the prediction that the isolated gene being
a cellulose synthase belonging to the processive class of the 2-glycosyltransferase family 2A. Relative gene expression
analysis by semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) on young leaf and stem tissues
found that HsCesA1 had similar levels of gene expression in both tissues. Phylogenetic and Blast analyses also supported
the prediction that the isolated HsCesA1 may play roles in the cell wall depositions in both leaf and stem tissues.
Actinobacteria from underexplored and unusual environments have gained significant attention for their capability in producing novel bioactive molecules of diverse chemical entities. Streptomyces is the most prolific Actinobacteria in producing useful molecules. Rapid decline effectiveness of existing antibiotics in the treatment of infections are caused by the emergence of multidrug-resistant pathogens. Intensive efforts are urgently required in isolating non-Streptomyces or rare Actinobacteria and understanding of their distribution in the harsh environment for new drug discovery. In this study, pretreatment of soil samples with 1.5% phenol was used for the selective isolation of Actinobacteria from Dee Island and Greenwich Island. A high number of non-Streptomyces (69.4%) or rare Actinobacteria was significantly recovered despite the Streptomyces (30.6%), including the genera Micromonospora, Micrococcus, Kocuria, Dermacoccus, Brachybacterium, Brevibacterium, Rhodococcus, Microbacterium and Rothia. Reduced diversity and shift of distribution were observed at the elevated level of soil pH. The members of genera Streptomyces, Micromonospora and Micrococcus were found to distribute and tolerate to a relatively high pH level of soil (pH 9.4-9.5), and could potentially be alkaliphilic Actinobacteria. The phylogenetic analysis had revealed some potentially new taxa members of the genera Micromonospora, Micrococcus and Rhodococcus. Principal Component Analysis of soil samples was used to uncover the factors that underlie the diversity of culturable Actinobacteria. Water availability in soil was examined as the principal factor that shaped the diversity of the Actinobacteria, by providing a dynamic source for microbial interactions and elevated diversity of Actinobacteria.
The JC polyomavirus (JCV) is ubiquitous in humans infecting children asymptomatically, then persisting in renal tissue. Since JCV DNA can be readily isolated from urine, it should be a useful tool with which to study the evolution of DNA viruses in humans. We showed that JCV DNA from the urine of Japanese, Taiwanese, Dutch and German patients can be classified into A and B types, based upon restriction fragment length polymorphisms (RFLPs). This work was extended in the present study. We established multiple JCV DNA clones from the UK, Spain, Italy, Sweden, South Korea, People's Republic of China, Malaysia, Indonesia, Mongolia, India, Sri Lanka, Saudi Arabia, Ethiopia, Kenya, Zambia, South Africa and Ghana. Using type-specific RFLPs, most clones except the four clones from Ghana were classified as either type A or B. We constructed a molecular phylogenetic tree for the Ghanaian clones and several representative type A and B clones. According to the phylogenetic tree, the Ghanaian clones constituted a major new group, tentatively named type C. From the findings presented here and elsewhere, the following conclusions were drawn: (i) type A is prevalent only in Europe; (ii) type B is found mainly in Asia and Africa; and (iii) type C is localized to part of Africa. Our findings should help to clarify how JCV evolved in humans.
This overview of the Luciolinae addresses the fauna of S. E. Asia including India, Sri Lanka, China, Japan, Malaysia, Thailand, Laos, Cambodia, Vietnam, Indonesia, the Philippines, the Republic of Palau, Federated States of Micronesia, and the Australopacific area of Australia, Papua New Guinea, Solomon Islands, New Caledonia, Vanuatu and Fiji.Of the 28 genera now recognised in the Luciolinae we address 27 genera from the study area as defined above, including three new genera which are described herein, and 222 species including 13 species newly described herein. Photuroluciola Pic from Madagascar is the only Luciolinae genus not addressed here. A key to genera is presented. Keys to species are either included here or referenced in existing literature. Twelve genera have had no new taxonomic decisions made nor are any new species records listed, and are addressed in an abbreviated fashion, with short diagnoses and plates of features of life stages: Aquatica Fu et al. 2010, Australoluciola Ballantyne 2013, Convexa Ballantyne 2009, Emeia Fu et al. 2012a, Inflata Boontop 2015, Lloydiella Ballantyne 2009, Missimia Ballantyne 2009, Pteroptyx Olivier 1902, Pyrophanes Olivier 1885, Sclerotia Ballantyne 2016, Triangulara Pimpasalee 2016, and Trisinuata Ballantyne 2013. Abscondita Ballantyne 2013 contains 8 species, and includes new records for Abs. anceyi (Olivier 1883), Abs. chinensis (L.) (which is newly synonymised with Luciola succincta Bourgeois), Abs. terminalis (Olivier 1883) including a first record from both Laos and Thailand, and Abs. perplexa (Walker 1858). Luciola pallescens Gorham 1880 is transferred to Abscondita and the pronotal colour range is addressed from a wide range of localities. Abs. berembun Nada sp. nov. and Abs. jerangau Nada sp. nov. are described from Malaysia. Hooked bursa plates are described for pallescens and berembun. Aquilonia Ballantyne 2009 is expanded to include 3 species. Gilvainsula Ballantyne 2009, represented by two species from the south eastern coast of New Guinea is synonymised under Aquilonia Ballantyne 2009, which is briefly redescribed and keyed from: Aquil. costata (Lea) from northern Australia, including many new records, Aquil. messoria (Ballantyne) comb. nov. and Aquil. similismessoria (Ballantyne) comb. nov. Asymmetricata Ballantyne 2009 now includes 4 species. As. bicoloripes (Pic 1927) comb. nov. and As. humeralis (Walker 1858) comb. nov. are transferred from Luciola, with L. doriae Olivier 1885, L. impressa Olivier 1910b and L. notatipennis Olivier 1909a newly synonymised with As. humeralis. Luciola aemula Olivier 1891 is synonymised with As. ovalis (Hope 1831). The variation in the extent of the anterior median emargination of the light organ in ventrite 7, and the possibility of a bipartite light organ in males of As. circumdata (Motsch. 1854) is explored. Females of both As. circumdata and As. ovalis (Hope 1831) are without bursa plates and the distinctively shaped median oviduct plate in each is described. Records from Thailand are recorded for both As. circumdata and As. ovalis. Atyphella Olliff 1890 now contains 28 species with 4 transferred from other genera, and one new species: Aty. abdominalis (Olivier 1886) comb. nov. and Aty. striata (Fabricius 1801) comb. nov. are transferred from Luciola, with Aty. carolinae Olivier 1911b and Aty. rennellia (Ballantyne 2009) comb. nov. transferred from Magnalata Ballantyne 2009. Atyphella telokdalam Ballantyne sp. nov. from Indonesia is described herein. Atyphella is now known from records in the Philippines and Indonesia as well as Australia and New Guinea. Colophotia Motschulsky 1853 is considered here from seven species for which intact types can be located for three. An abbreviated revision based on the United States National Museum collection only is presented, with specimens of C. bakeri Pic 1924, C. brevis Olivier 1903a, C. plagiata (Erichson 1834) and C. praeusta (Eschscholtz 1822) redescribed, using where possible features of males, females and larvae. Colophotia particulariventris Pic 1938 is newly synonymised with C. praeusta. Colophotia miranda Olivier 1886 and L. truncata Olivier 1886 are treated as species incertae sedis. Curtos Motschulsky 1845 includes 19 species with suggestions made, but not yet formalised, for the possible transfer of the following seven species from Luciola: Luciola complanata Gorham 1895, L. costata Pic 1929, L. delauneyi Bourgeois 1890, L. deplanata Pic 1929, L. extricans Walker 1858, L. multicostulata Pic 1927 and L. nigripes Gorham 1903. Curtos is not revised here. Emarginata Ballantyne gen nov. is described for E. trilucida (Jeng et al. 2003b) comb. nov., transferred from Luciola and characterised by the emarginated elytral apex. An extended range of specimens from Thailand is listed. Kuantana Ballantyne gen. nov. from Selangor, Malaysia is described from K. menayah gen. et sp. nov. having bipartite light organs in ventrite 7 and an asymmetrical tergite 8 which is not emarginated on its left side. Female has no bursa plates. Luciola Laporte 1833 s. stricto as defined by a population of the type species Luciola italica (L. 1767) from Pisa, Italy, is further expanded and considered to comprise the following19 species: L. antipodum (Bourgeois 1884), L. aquilaclara Ballantyne 2013, L. chapaensis Pic 1923 which is synonymised with L. atripes Pic 1929, L. curtithorax Pic 1928, L. filiformis Olivier 1913c, L. horni Bourgeois 1905, L. hypocrita Olivier 1888, L. italica (L. 1767), L. kagiana Matsumura 1928, L. oculofissa Ballantyne 2013, L. pallidipes Pic 1928 which is synonymised with L. fletcheri Pic 1935, L. parvula Kiesenwetter 1874, L. satoi Jeng Yang 2003, L. tuberculata Yiu 2017, and two species treated as near L. laticollis Gorham 1883, and near L. nicollieri Bugnion 1922. The following are described as new: L. niah Jusoh sp. nov., L. jengai Nada sp. nov. and L. tiomana Ballantyne sp. nov. Luciola niah sp. nov. female has two wide bursa plates on each side of the bursa. Luciola s. lato (as defined here) consists of 36 species. Twenty-seven species formerly standing under Luciola have been assigned to other genera or synonymised. Seven species are recommended for transfer to Curtos, and 32 species now stand under species incertae sedis. Magnalata Ballantyne is reduced to the type species M. limbata and redescribed. Medeopteryx Ballantyne 2013 is expanded to 20 species with the addition of two new combinations, Med. semimarginata (Olivier 1883) comb. nov. and Med. timida (Olivier 1883) comb. nov., both transferred from Luciola, and one new species, Med. fraseri Nada sp. nov. from Malaysia. The range of this genus now extends from Australia and the island of New Guinea to SE Asia. Medeopteryx semimarginata females have wide paired bursa plates. Pygoluciola Wittmer 1939 now includes 19 species with 5 new species: P. bangladeshi Ballantyne sp. nov., P. dunguna Nada 2018, P. matalangao Ballantyne sp. nov. (scored by the code name 'Jeng Matalanga' in Ballantyne Lambkin 2013), P. phupan Ballantyne sp. nov. and P. tamarat Jusoh sp. nov. Six species are transferred from Luciola: P. abscondita (Olivier 1891) comb. nov., P. ambita (Olivier 1896) comb. nov., P. calceata (Olivier 1905) comb. nov., P. insularis (Olivier 1883) comb. nov., P. nitescens (Olivier 1903b) comb. nov. and P. vitalisi (Pic 1934) comb. nov., and redescribed from males, and includes female reproductive anatomy for P. nitescens comb. nov. and P. dunguna, both of which have hooked bursa plates. Serratia Ballantyne gen. nov. is erected for S. subuyania gen. et sp. nov. and characterised by the serrate nature of certain antennal flagellar segments in the male. The following 37 species listed under species incertae sedis are further explored: Colophotia miranda Olivier 1886, Lampyris serraticornis Boisduval 1835, Luciola angusticollis Olivier 1886, L. antennalis Bourgeois 1905, L. antica (Boisduval 1835), L. apicalis (Eschscholtz 1822), L. aurantiaca Pic 1927, L. bicoloriceps Pic 1924, L. binhana Pic 1927, L. bourgeoisi Olivier 1895, L. dilatata Pic 1929, L. exigua (Gyllenhall 1817), L. exstincta Olivier 1886, L. fissicollis Fairmaire 1891, L. flava Pic 1929, L. flavescens (Boisduval 1835), L. fukiensis Pic 1955, L. immarginata Bourgeois 1890, L. incerta (Boisduval 1835), L. infuscata (Erichson 1834), L. intricata (Walker 1858), L. japonica (Thunberg 1784), L. klapperichi Pic 1955, L. lata Olivier 1883, L. limbalis Fairmaire 1889, L. marginipennis (Boisduval 1835), L. melancholica Olivier 1913a, L. robusticeps Pic 1928, L. ruficollis (Boisduval 1835), L. spectralis Gorham 1880, L. stigmaticollis Fairmaire 1887, L. tincticollis Gorham 1895, L. trivandrensis Raj 1947, L. truncata Olivier 1886, L. vittata (Laporte 1833) Pteroptyx atripennis Pic 1923 and P. curticollis Pic 1923. While phylogenetic analyses indicate their distinctiveness, no further taxonomic action is taken with Luciola cruciata Motschulsky 1854 and L. owadai Sâtô et Kimura 1994 from Japan given the importance of the former as a national icon. Analyses also indicate that Lampyroidea syriaca Costa 1875 belongs in Luciola s. str. A much wider taxonomic analysis of this genus including all the species is necessary before any further action can be taken.
Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).
The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation.
The coronavirus disease 2019 (COVID-19) pandemic and related public health intervention measures have been reported to have resulted in the reduction of infections caused by influenza viruses and other common respiratory viruses. However, the influence may be varied in areas that have different ecological, economic, and social conditions. This study investigated the changing epidemiology of 8 common respiratory pathogens, including Influenza A (IFVA), Influenza B (IFVB), Respiratory syncytial virus (HRSV), rhinovirus (RV), Human metapneumovirus Adenovirus, Human bocavirus, and Mycoplasma pneumoniae, among hospitalized children during spring and early summer in 2019-2021 in two hospitals in Hainan Island, China, in the COVID-19 pandemic era. The results revealed a significant reduction in the prevalence of IFVA and IFVB in 2020 and 2021 than in 2019, whereas the prevalence of HRSV increased, and it became the dominant viral pathogen in 2021. RV was one of the leading pathogens in the 3 year period, where no significant difference was observed. Phylogenetic analysis revealed close relationships among the circulating respiratory viruses. Large scale studies are needed to study the changing epidemiology of seasonal respiratory viruses to inform responses to future respiratory virus pandemics.
Chitinases in terrestrial plants have been reported these are involved in heavy metal tolerance/detoxification. This is the first attempt to reveal chitinase gene (AcCHI I) and its function on metal detoxification in mangroves Aegiceras corniculatum. RT-PCR and RACE techniques were used to clone AcCHI I, while real-time quantitative PCR was employed to assess AcCHI I mRNA expressions in response to Cadmium (Cd). The deduced AcCHI I protein consists of 316 amino acids, including a signal peptide region, a chitin-binding domain (CBD) and a catalytic domain. Protein homology modeling was performed to identify potential features in AcCHI I. The CBD structure of AcCHI I might be critical for metal tolerance/homeostasis of the plant. Clear tissue-specific differences in AcCHI I expression were detected, with higher transcript levels detected in leaves. Results demonstrated that a short duration of Cd exposure (e.g., 3 days) promoted AcCHI I expression in roots. Upregulated expression was also detected in leaves under 10 mg/kg Cd concentration stress. The present study demonstrates that AcCHI I may play an important role in Cd tolerance/homeostasis in the plant. Further studies of the AcCHI I protein, gene overexpression, the promoter and upstream regulation will be necessary for clarifying the functions of AcCHI I.
Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.
The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA-DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).
Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants. An interesting genetic feature seen in majority of A. baumannii genomes analyzed is the presence of small plasmids that usually ranged from 2 to 10 kb in size, some of which harbor antibiotic resistance genes and homologs of plasmid mobilization genes. These plasmids are often overlooked when compared to their larger, conjugative counterparts that harbor multiple antibiotic resistance genes and transposable elements. In this mini-review, we will examine our current knowledge of these small A. baumannii plasmids and look into their genetic diversity and phylogenetic relationships. Some of these plasmids, such as the Rep-3 superfamily group and the pRAY-type, which has no recognizable replicase genes, are quite widespread among diverse A. baumannii clinical isolates worldwide, hinting at their usefulness to the lifestyle of this pathogen. Other small plasmids especially those from the Rep-1 superfamily are truly enigmatic, encoding only hypothetical proteins of unknown function, leading to the question of whether these small plasmids are "good" or "bad" to their host A. baumannii.
OBJECTIVES: To analyse the genome sequences of four archival Acinetobacter nosocomialis clinical isolates (designated AC13, AC15, AC21 and AC25) obtained from Terengganu, Malaysia in 2011 to determine their genetic relatedness and basis of antimicrobial resistance.
METHODS: Antimicrobial susceptibility profiles of the A. nosocomialis isolates were determined by disk diffusion. Genome sequencing was performed using the Illumina NextSeq platform.
RESULTS: The four A. nosocomialis isolates were cefotaxime resistant whereas three isolates (namely, AC13, AC15 and AC25) were tetracycline resistant. The carriage of the blaADC-255-encoded cephalosporinase gene is likely responsible for cefotaxime resistance in all four isolates. Phylogenetic analysis indicated that the three tetracycline-resistant isolates were closely related, with an average nucleotide identity of 99.9%, suggestive of nosocomial spread, whereas AC21 had an average nucleotide identity of 97.9% when compared to these three isolates. The tetracycline-resistant isolates harboured two plasmids: a 13476 bp Rep3-family plasmid of the GR17 group designated pAC13-1, which encodes the tetA(39) tetracycline-resistance gene, and pAC13-2, a 4872 bp cryptic PriCT-1-family plasmid of a new Acinetobacter plasmid group, GR60. The tetA(39) gene was in a 2 001 bp fragment flanked by XerC/XerD recombination sites characteristic of a mobile pdif module. Both plasmids also harboured mobilisation/transfer-related genes.
CONCLUSIONS: Genome sequencing of A. nosocomialis isolates led to the discovery of two novel plasmids, one of which encodes the tetA(39) tetracycline-resistant gene in a mobile pdif module. The high degree of genetic relatedness among the three tetracycline-resistant A. nosocomialis isolates is indicative of nosocomial transmission.
Despite the importance of methicillin-resistant Staphylococcus aureus (MRSA) as a priority nosocomial pathogen, the genome sequences of Malaysian MRSA isolates are currently limited to a small pool of samples. Here, we present the genome sequence analyses of 88 clinical MRSA isolates obtained from the main tertiary hospital in Terengganu, Malaysia in 2016-2020, to obtain in-depth insights into their characteristics. The EMRSA-15 (ST22-SCCmec IV) clone of the clonal complex 22 (CC22) lineage was predominant with a total of 61 (69.3%) isolates. Earlier reports from other Malaysian hospitals indicated the predominance of the ST239 clone, but only two (2.3%) isolates were identified in this study. Two Indian-origin clones, the Bengal Bay clone ST772-SCCmec V (n = 2) and ST672 (n = 10) were also detected, with most of the ST672 isolates obtained in 2020 (n = 7). Two new STs were found, with one isolate each, and were designated ST7879 and ST7883. From the core genome phylogenetic tree, the HSNZ MRSA isolates could be grouped into seven clades. Antimicrobial phenotype-genotype concordance was high (> 95%), indicating the accuracy of WGS in predicting most resistances. Majority of the MRSA isolates were found to harbor more than 10 virulence genes, demonstrating their pathogenic nature.
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.
This retrospective study examined the G/P type of rotavirus in RNA samples that have previously been e-typed by RNA-PAGE in 1996. The results were then compared to 2007 samples to ascertain the extent of changes that may have occurred in this 11-years time interval. The G and P genotypes were determined by hemi-nested PCR and further analysed by phylogenetic study. In 1996, the G/P combination G1P[8], G(UT)P[8] and G1P(UT) prevalence rate were 81%, 9% and 7%, respectively. As expected, the G9 genotype which has already emerged worldwide was identified in 42% of the 2007 samples with the remaining 33% G1P[8] and 25% G1P(UT) Analysis of the RNA pattern showed that majority of the isolates were long e-type in both series, nevertheless minor differences within electropherotypes were observed. Genetic diversity in some strains of the human group A rotaviruses was analysed by phylogenetic methods. These findings will help in the decision to introduce rotavirus vaccines within the next decade.
Amelogenin paralogs on Chromosome X (AMELX) and Y (AMELY) are commonly used sexing markers. Interstitial deletion of Yp involving the AMELY locus has previously been reported. The combined frequency of the AMELY null allele in Singapore and Malaysia populations is 2.7%, 0.6% in Indian and Malay ethnic groups respectively. It is absent among 541 Chinese screened. The null allele in this study belongs to 3 Y haplogroups; J2e1 (85.7%), F* (9.5%) and D* (4.8%). Low and high-resolution STS mapping, followed by sequence analysis of breakpoint junction confirmed a large deletion of 3 to 3.7-Mb located at the Yp11.2 region. Both breakpoints were located in TSPY repeat arrays, suggesting a non-allelic homologous recombination (NAHR) mechanism of deletion. All regional null samples shared identical breakpoint sequences according to their haplogroup affiliation, providing molecular evidence of a common ancestry origin for each haplogroup, and at least 3 independent deletion events recurred in history. The estimated ages based on Y-SNP and STR analysis were approximately 13.5 +/- 3.1 kyears and approximately 0.9 +/- 0.9 kyears for the J2e1 and F* mutations, respectively. A novel polymorphism G > A at Y-GATA-H4 locus in complete linkage disequilibrium with J2e1 null mutations is a more recent event. This work re-emphasizes the need to include other sexing markers for gender determination in certain regional populations. The frequency difference among global populations suggests it constitutes another structural variation locus of human chromosome Y. The breakpoint sequences provide further information to a better understanding of the NAHR mechanism and DNA rearrangements due to higher order genomic architecture.
To isolate and identify the pathogen of Dengue fever from Shenzhen city in 2005 - 2006, and to analyze the molecular characteristics of the isolated Dengue virus strain as well as to explore its possible origin.
Three new and one previously described species of Physalacria (Physalacriaceae, Agaricales) are reported from China. Specimens of two additional species described from Malaysia and North America were studied for comparison. Placements of these species were corroborated based on morphological observations and molecular evidence from partial sequences of the nuc rDNA internal transcribed spacer regions (ITS) and the 28S D1-D3 region, and genes for translation elongation factor 1-α (tef1α) and the second largest subunit of RNA polymerase II (rpb2). These new species of Physalacria distributed in subtropical China were found on rotten wood of broadleaf trees or bamboo and possess stipitate-capitate basidiomata with four-spored basidia, clamp connections and smooth, inamyloid basidiospores. To facilitate studies of the genus in Asia, a key is provided for all Physalacria species reported from this region.
Some Amanita specimens collected from Malaysia are critically investigated by morphological examination and molecular analysis of two gene fragments, the nuc rDNA partial 28S (28S) gene and the internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) regions. Six phylogenetic species of Amanita section Caesareae are recognized among the studied collections. One of them is described as new, A. malayensis. Four of the phylogenetic species correspond with existing morphology-based taxa: A. aporema, A. javanica, A. princeps, and A. similis. The remaining species is not described because of the paucity of material. Detailed descriptions and the distribution of these southeastern Asian species are provided, along with a key to the species of section Caesareae from Malaysia.