Displaying publications 41 - 60 of 87 in total

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  1. Ali H, Muhammad A, Bala NS, Wang G, Chen Z, Peng Z, et al.
    Mol Phylogenet Evol, 2018 10;127:1000-1009.
    PMID: 29981933 DOI: 10.1016/j.ympev.2018.07.003
    Wolbachia pipientis is a diverse, ubiquitous and most prevalent intracellular bacterial group of alpha-Proteobacteria that is concerned with many biological processes in arthropods. The coconut hispine beetle (CHB), Brontispa longissima (Gestro) is an economically important pest of palm cultivation worldwide. In the present study, we comprehensively surveyed the Wolbachia-infection prevalence and mitochondrial DNA (mtDNA) polymorphism in CHB from five different geographical locations, including China's Mainland and Taiwan, Vietnam, Thailand, Malaysia and Indonesia. A total of 540 sequences were screened in this study through three different genes, i.e., cytochrome oxidase subunit I (COI), Wolbachia outer surface protein (wsp) and multilocus sequencing type (MLST) genes. The COI genetic divergence ranges from 0.08% to 0.67%, and likewise, a significant genetic diversity (π = 0.00082; P = 0.049) was noted within and between all analyzed samples. In the meantime, ten different haplotypes (H) were characterized (haplotype diversity = 0.4379) from 21 different locations, and among them, H6 (46 individuals) have shown a maximum number of population clusters than others. Subsequently, Wolbachia-prevalence results indicated that all tested specimens of CHB were found positive (100%), which suggested that CHB was naturally infected with Wolbachia. Wolbachia sequence results (wsp gene) revealed a high level of nucleotide diversity (π = 0.00047) under Tajima's D test (P = 0.049). Meanwhile, the same trend of nucleotide diversity (π = 0.00041) was observed in Wolbachia concatenated MLST locus. Furthermore, phylogenetic analysis (wsp and concatenated MLST genes) revealed that all collected samples of CHB attributed to same Wolbachia B-supergroup. Our results strongly suggest that Wolbachia bacteria and mtDNA were highly concordant with each other and Wolbachia can affect the genetic structure and diversity within the CHB populations.
    Matched MeSH terms: Multilocus Sequence Typing
  2. Vasconcelos TNC, Proença CEB, Ahmad B, Aguilar DS, Aguilar R, Amorim BS, et al.
    Mol Phylogenet Evol, 2017 04;109:113-137.
    PMID: 28069533 DOI: 10.1016/j.ympev.2017.01.002
    Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the relative position of Myrtus communis, the placement of the Blepharocalyx group, the absence of generic endemism in the Caribbean, and the paraphyletism of the former Pimenta group. Distinct calibration approaches affect biogeography interpretation, increasing the number of necessary long distance dispersal events in the topology with older nodes. It is hypothesised that biological intrinsic factors such as modifications of embryo type and polyploidy might have played a role in accelerating shifts of diversification rates in Neotropical lineages. Future perspectives include formal subtribal classification, standardization of fossil calibration approaches and better links between diversification shifts and trait evolution.
    Matched MeSH terms: Multilocus Sequence Typing
  3. Lemlem M, Aklilu E, Mohammed M, Kamaruzzaman F, Zakaria Z, Harun A, et al.
    PLoS One, 2023;18(5):e0285743.
    PMID: 37205716 DOI: 10.1371/journal.pone.0285743
    Antimicrobial resistance is one of the major public health threats globally. This challenge has been aggravated with the overuse and misuse of antibiotics in food animals and humans. The present study aimed to investigate the prevalence of Extended-Spectrum β-lactamase (ESBL) genes in Escherichia coli (E. coli) isolated from broiler chickens in Kelantan, Malaysia. A total of 320 cloacal swabs were collected from farms in different districts of Kelantan and were analyzed using routine bacteriology, antimicrobial susceptibility test, and molecular techniques for further identification and characterization of ESBL encoding genes. Based on PCR detection for the E. coli species-specific Pho gene, 30.3% (97/320) of isolates were confirmed as E. coli, and 84.5% (82/97) of the isolates were positive for at least one ESBL gene. Majority of the isolates, 62.9% (61/97) were harboring blaCTX-M followed by 45.4% (44/97) of blaTEM genes, while 16.5% (16/97) of the isolates were positive for both mcr-1 and ESBL genes. Overall, 93.8% (90/97) of the E. coli were resistant to three or more antimicrobials; indicating that the isolates were multi-drug resistance. 90.7% of multiple antibiotic resistance (MAR) index value greater than 0.2, would also suggest the isolates were from high-risk sources of contamination. The MLST result shows that the isolates are widely diverse. Our findings provide insight into the alarmingly high distribution of antimicrobial resistant bacteria, mainly ESBL producing E. coli in apparently healthy chickens indicating the role of food animals in the emergence and spread of antimicrobial resistance, and the potential public health threats it may pose.
    Matched MeSH terms: Multilocus Sequence Typing
  4. Abidin N, Ismail SI, Vadamalai G, Yusof MT, Hakiman M, Karam DS, et al.
    PLoS One, 2020;15(6):e0234350.
    PMID: 32530926 DOI: 10.1371/journal.pone.0234350
    Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.
    Matched MeSH terms: Multilocus Sequence Typing
  5. Chua HS, Soh YH, Ibrahim S, Abdullah NH, Che Mat Seri NAA, AbuBakar S, et al.
    Trop Biomed, 2024 Jun 01;41(2):220-223.
    PMID: 39154277 DOI: 10.47665/tb.41.2.014
    Vibrio vulnificus infection is associated with high morbidity and mortality in high-risk patients. Poor prognoses could lead to >50% mortality rate. The present report describes a case of V. vulnificus bacteremia in a cirrhotic patient with underlying hepatitis C. He presented with generalised abdominal pain associated with distention and could not ambulate for one week. He also complained of fever for six days and pruritus for 10 days. Tea-coloured urine was noted in continuous bag drainage. The abdomen was distended but soft, with mild tenderness palpated over the left lumbar and iliac region. Blood investigation indicated ongoing infection and inflammation. The aerobic blood culture was identified using the matrix-assisted laser desorption/ionisation-time of flight mass spectrometry and confirmed via 16S rDNA sequencing as V. vulnificus. Multilocus sequence typing of the isolated V. vulnificus revealed a novel sequence type, ST540. The patient responded well to the intravenous cefoperazone and was then discharged with a four day-course of oral ciprofloxacin, 500 mg twice daily after completing the intravenous cefoperazone for 10 days. Clinical history and physical examination are important for early antibiotic therapy initiation and appropriate surgical intervention. Furthermore, bacterial strain typing is also essential for epidemiological surveillance and potentially anticipating the pathogen's virulence traits, which are vital in controlling and preventing the spread of infection.
    Matched MeSH terms: Multilocus Sequence Typing
  6. Divis PC, Lin LC, Rovie-Ryan JJ, Kadir KA, Anderios F, Hisam S, et al.
    Emerg Infect Dis, 2017 04;23(4):616-624.
    PMID: 28322705 DOI: 10.3201/eid2304.161738
    Multilocus microsatellite genotyping of Plasmodium knowlesi isolates previously indicated 2 divergent parasite subpopulations in humans on the island of Borneo, each associated with a different macaque reservoir host species. Geographic divergence was also apparent, and independent sequence data have indicated particularly deep divergence between parasites from mainland Southeast Asia and Borneo. To resolve the overall population structure, multilocus microsatellite genotyping was conducted on a new sample of 182 P. knowlesi infections (obtained from 134 humans and 48 wild macaques) from diverse areas of Malaysia, first analyzed separately and then in combination with previous data. All analyses confirmed 2 divergent clusters of human cases in Malaysian Borneo, associated with long-tailed macaques and pig-tailed macaques, and a third cluster in humans and most macaques in peninsular Malaysia. High levels of pairwise divergence between each of these sympatric and allopatric subpopulations have implications for the epidemiology and control of this zoonotic species.
    Matched MeSH terms: Multilocus Sequence Typing
  7. William T, Thevarajah B, Lee SF, Suleiman M, Jeffree MS, Menon J, et al.
    Emerg Infect Dis, 2015 Jan;21(1):142-5.
    PMID: 25531078 DOI: 10.3201/eid2101.141092
    Of the ≈400 cases of avian influenza (H7N9) diagnosed in China since 2003, the only travel-related cases have been in Hong Kong and Taiwan. Detection of a case in a Chinese tourist in Sabah, Malaysia, highlights the ease with which emerging viral respiratory infections can travel globally.
    Matched MeSH terms: Multilocus Sequence Typing
  8. Al-Hamidhi S, Mahdy MA, Idris MA, Bin Dajem SM, Al-Sheikh AA, Al-Qahtani A, et al.
    Infect Genet Evol, 2014 Oct;27:25-31.
    PMID: 24981966 DOI: 10.1016/j.meegid.2014.06.015
    In the Arabian Peninsula malaria control is progressing steadily, backed by adequate logistic and political support. As a result, transmission has been interrupted throughout the region, with exception of limited sites in Yemen and Saudi Arabia. Here we examined Plasmodium falciparum parasites in these sites to assess if the above success has limited diversity and gene flow.
    Matched MeSH terms: Multilocus Sequence Typing
  9. Jeevajothi Nathan J, Mohd Desa MN, Thong KL, Clarke SC, Masri SN, Md Yasin R, et al.
    Infect Genet Evol, 2014 Jan;21:391-4.
    PMID: 24342879 DOI: 10.1016/j.meegid.2013.11.026
    Streptococcus pneumoniae is an epidemiologically important bacterial pathogen. Recently, we reported the antibiotic susceptibility patterns of a limited collection of pneumococcal isolates in Malaysia with a high prevalence of erythromycin resistant strains. In the present study, 55 of the pneumococcal isolates of serotype 19F were further analysed by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The generated genotypic patterns were then correlated with the antibiograms previously reported. Forty-seven different PFGE profiles (PTs) were obtained, showing that the isolates were genetically diverse. MLST identified 16 sequence types (STs) with ST-236 being predominant (58.2%), followed by ST-81 (10.3%). Among the ST-236 isolates, 22 were erythromycin resistant S. pneumoniae (ERSP) and 15 were trimethoprim/sulfamethoxazole (TMP/SMX) resistant, while among ST-81, four isolates were ERSP and two were TMP/SMX resistant. The high prevalence of erythromycin resistant serotype 19F isolates of ST-236 in this study has also been reported in other North and South East Asian countries.
    Matched MeSH terms: Multilocus Sequence Typing
  10. Ngoi ST, Thong KL
    Diagn Microbiol Infect Dis, 2013 Dec;77(4):304-11.
    PMID: 24139970 DOI: 10.1016/j.diagmicrobio.2013.09.004
    Salmonella enterica serovar Enteritidis (S. Enteritidis) is the most common causative agent of non-typhoidal salmonellosis in Malaysia. We aimed to characterize S. Enteritidis isolated from humans and animals by analyzing their antimicrobial resistance profiles and genotypes. A total of 111 strains were characterized using multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and antimicrobial susceptibility testing. Both typing methods revealed that genetically similar S. Enteritidis strains had persisted among human and animal populations within the period of study (2003-2008). Only 39% of the strains were multi-drug resistant (i.e., resistant to 3 or more classes of antimicrobial agents), with a majority (73%) of these in low-risk phase (multiple antibiotic resistant index <0.20). Limited genetic diversity among clinical and zoonotic S. Enteritidis suggested that animals are possible sources of human salmonellosis. The degree of multi-drug resistance among the strains was generally low during the study period.
    Matched MeSH terms: Multilocus Sequence Typing
  11. Alreshidi MA, Alsalamah AA, Hamat RA, Neela V, Alshrari AS, Atshan SS, et al.
    Eur J Clin Microbiol Infect Dis, 2013 Jun;32(6):755-61.
    PMID: 23318757 DOI: 10.1007/s10096-012-1801-9
    One hundred and twenty methicillin-resistant Staphylococcus aureus (MRSA) isolated from cancer and non-cancer patients in Saudi Arabia were investigated for antibiotic resistance, virulence determinants and genotypes. The majority of MRSA isolates from cancer (n = 44, 73.3 %) and non-cancer patients (n = 34, 56.7 %) were multi-resistant to more than four classes of antibiotics. Virulence gene profiling showed that all strains were commonly positive for adhesin genes, except ebps and bbp genes, which were not detected in any isolate. Although the presence of adhesin genes varied slightly among MRSA isolates from cancer and non-cancer patients, these variations were not found to be statistically significant. In contrast, the presence of the toxin genes seb, sec, seg and sei was significantly elevated in MRSA strains isolated from cancer patients. Multilocus sequence typing (MLST) detected six and nine sequence types (STs) among isolates from cancer and non-cancer patients, respectively. Using spa typing, 12 and 25 types were detected, including four new types. The ability of different MRSA clones to become multi-resistant and their ability to acquire different virulence factors may contribute to their success as pathogens in individual groups of patients.
    Matched MeSH terms: Multilocus Sequence Typing
  12. Yan CZY, Austin CM, Ayub Q, Rahman S, Gan HM
    FEMS Microbiol Lett, 2019 09 01;366(17).
    PMID: 31589302 DOI: 10.1093/femsle/fnz211
    The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
    Matched MeSH terms: Multilocus Sequence Typing
  13. Lim KT, Yeo CC, Suhaili Z, Thong KL
    Jpn J Infect Dis, 2012;65(6):502-9.
    PMID: 23183202
    Staphylococcus aureus is a persistent human pathogen responsible for a variety of infections ranging from soft-tissue infections to bacteremia. The objective of this study was to determine genetic relatedness between methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) strains. We isolated 35 MRSA and 21 MSSA strains from sporadic cases at the main tertiary hospital in Terengganu, Malaysia, screening them for the presence of virulence genes. Their genetic relatedness was determined by accessory gene regulator (agr) types, PCR-restriction fragment length polymorphism (RFLP) of the coa gene, pulsed-field gel electrophoresis (PFGE), S. aureus protein A (spa), and multilocus-sequence typing (MLST). We found that 57% of MRSA and 43% of MSSA strains harbored enterotoxin genes. The majority (87.5%) of the strains were agr type I. PCR-RFLP and PFGE genotyping of the coa gene revealed that MRSA strains were genetically related, whereas MSSA strains had higher heterogeneity. The combined genotype, MLST-spa type ST239-t037, was shared among MRSA and MSSA strains, indicating that MRSA strains could have evolved from MSSA strains. Two combined MLST-spa types were present in MRSA strains, whereas 7 different MLST-spa types were detected in MSSA strains, including 2 combined types (ST779-t878 and ST1179-t267) that have not been reported in Malaysia. In conclusion, enterotoxin genes were more prevalent in MRSA than in MSSA strains in the Terengganu hospital. The MSSA strains were genetically more diverse than the MRSA strains.
    Matched MeSH terms: Multilocus Sequence Typing
  14. Testamenti VA, Surya M, Saepuloh U, Iskandriati D, Tandang MV, Kristina L, et al.
    Vet World, 2020 Nov;13(11):2459-2468.
    PMID: 33363342 DOI: 10.14202/vetworld.2020.2459-2468
    Background and Aim: Melioidosis is a potentially fatal disease affecting humans and a wide range of animal species; it is often underdiagnosed and underreported in veterinary medicine in Indonesia. This study aimed to characterize morphological and molecular features of Burkholderia pseudomallei, the causative agent of melioidosis which caused the death of a Bornean orangutan.

    Materials and Methods: Pulmonary abscess samples were cultured on several types of media, including Ashdown agar, Ashdown broth, and MacConkey agar. Type three secretion system orf 2 real-time polymerase chain reaction (PCR) and latex agglutination tests were performed to identify the bacteria. Morphological characteristics were compared to all previously published morphotypes. Subsequently, the bacteria were characterized by multilocus sequence typing (MLST) and Yersinia-like flagellum/Burkholderia thailandensis-like flagellum and chemotaxis PCR. The results of the genotyping were afterward compared to all genotypes from Southeast Asia.

    Results: Multiple morphotypes of B. pseudomallei were perceived during the growth on Ashdown agar. Furthermore, it was identified by MLST that the Type I and Type II morphotypes observed in this study were clones of a single ST, ST54, which is predominantly found in humans and the environment in Malaysia and Thailand, although a very limited number of reports was published in association with animals. Moreover, the E-BURST analysis showed that the ST is grouped together with isolates from Southeast Asian countries, including Malaysia, Thailand, Singapore, and Cambodia. ST54 was predicted to be the founding genotype of several STs from those regions.

    Conclusion: B. pseudomallei ST54 that caused the death of a Bornean orangutan has a distant genetic relationship with other STs which were previously reported in Indonesia, implying a vast genetic diversity in Indonesia that has not been discovered yet.

    Matched MeSH terms: Multilocus Sequence Typing
  15. Liew SM, Rajasekaram G, Puthucheary SD, Chua KH
    J Glob Antimicrob Resist, 2018 06;13:271-273.
    PMID: 29432937 DOI: 10.1016/j.jgar.2018.01.026
    OBJECTIVES: The increasing incidence of carbapenem-resistant Pseudomonas aeruginosa along with the discovery of novel metallo-β-lactamases (MBLs) is of concern. In this study, the isolation of MBL-producing P. aeruginosa clinical strains in Malaysia was investigated.

    METHODS: A total of 53 P. aeruginosa clinical strains were isolated from different patients in Sultanah Aminah Hospital (Johor Bahru, Malaysia) in 2015. Antimicrobial susceptibility testing was performed, and minimum inhibitory concentrations (MICs) of imipenem and meropenem were determined by Etest. Carbapenem-resistant strains were screened for MBL production by the imipenem-ethylene diamine tetra-acetic acid (IMP-EDTA) double-disk synergy test, MBL imipenem/imipenem-inhibitor (IP/IPI) Etest and PCR. Multilocus sequence typing (MLST) analysis was performed for genotyping of the isolates.

    RESULTS: Among the 53 clinical strains, 3 (5.7%) were identified as MBL-producers. Multidrug resistance was observed in all three strains, and two were resistant to all of the antimicrobials tested. Sequencing analysis confirmed that the three strains harboured carbapenemase genes (blaIMP-1, blaVIM-2 and blaNDM-1 in one isolate each). These multidrug-resistant strains were identified as sequence type 235 (ST235) and ST308.

    CONCLUSIONS: The blaIMP-1 and blaNDM-1 genes have not previously been reported in Malaysian P. aeruginosa isolates. The emergence of imipenemase 1 (IMP-1)- and New Delhi metallo-β-lactamase 1 (NDM-1)-producing P. aeruginosa in Malaysia maybe travel-associated.

    Matched MeSH terms: Multilocus Sequence Typing
  16. Yu LH, Teh CSJ, Yap KP, Ung EH, Thong KL
    Infect Genet Evol, 2020 09;83:104347.
    PMID: 32360538 DOI: 10.1016/j.meegid.2020.104347
    Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp disease of economic importance which causes mass mortality of cultivated penaeid shrimps in Southeast Asian countries, Mexico and South America. This disease was originally caused by Vibrio parahaemolyticus (VPAHPND) which is reported to harbour a transferable plasmid carrying the virulent PirAB-like toxin genes (pirABvp). However, little is known about the pathogenicity of VPAHPND. To extend our understanding, comparative genomic analyses was performed in this study to identify the genetic differences and to understand the phylogenetic relationship of VPAHPND strains. Seven Vibrio parahaemolyticus strains (five VPAHPND strains and two non-VPAHPND strains) were sequenced and 31 draft genomes of V. parahaemolyticus were retrieved from NCBI database and incorporated into the genomic comparison to elucidate their genomic diversity. The study showed that the genome sizes of the VPAHPND strains were approximately 5 Mbp. Ten sequence types (STs) were identified among the VPAHPND strains using in silico-Multilocus Sequence Typing analysis (MLST) and ST 970 was the predominant ST. Phylogenetic analysis based on MLST and single nucleotide polymorphisms (SNP) showed that the VPAHPND strains were genetically diverse. Based on the comparative genomic analysis, several functional proteins were identified from diiferent categories associated with virulence-related proteins, secretory proteins, conserved domain proteins, transporter proteins, and phage proteins. The CRISPR analysis showed that VPAHPND strains contained less number of CRISPRs elements than non-VPAHPND strains while six prophages regions were identified in the genomes, suggested the lack of CRISPR might promote prophage insertion. The genomic information in this study provide improved understanding of the virulence of these VPAHPND strains.
    Matched MeSH terms: Multilocus Sequence Typing
  17. Asis A, Shahriar SA, Naher L, Saallah S, Fatihah HNN, Kumar V, et al.
    Mol Biol Rep, 2021 Apr;48(4):3285-3301.
    PMID: 33880673 DOI: 10.1007/s11033-021-06321-0
    Trichoderma is a genus of soil-borne fungus with an abundance of reports of its economic importance in the agriculture industry. Thus, the correct identification of Trichoderma species is necessary for its commercial purposes. Globally, Trichoderma species are routinely identified from micro-morphological descriptions which can be tedious and prone to errors. Thus, we emphasize that the accurate identification of Trichoderma strains requires a three-pronged approach i.e. based on its morphological characteristics, multilocus gene sequences of the rDNA [internal transcribed spacer (ITS) 1 and 2 regions], translation elongation factor 1-α (TEF-1α), Calmodulin (CAL) and its lignocellulolytic activities. We used this approach to identify a total of 53 Trichoderma strains which were isolated from a wet paddy field located at Tuaran, Sabah, Malaysia. The 53 strains were positively identified as belonging to three Trichoderma species, namely T. asperellum (43 strains), T. harzianum (9 strains), and T. reesei (one strain) on the basis of its morphological characteristics and multilocus gene sequences. Phylogenetic trees constructed based on the UPGMA method of the ITS 1 and 2 regions of the rDNA, TEF-1α and CAL revealed three distinct groups with the T. asperellum, T. harzianum and T. reesei strains placed under the section of Trichoderma, Pachybasium and Longibrachiatum, respectively. In addition, the lignocellulolytic activities of the isolates were measured based on the diameters of the halo zones produced when degrading cellulose, lignin, and starch, respectively. This diagnostic assay can be used to identify Trichoderma as it produces polyphenol oxidase when Tannic Acid Media is used for the lignin test, endoglucanases when Jensen media is used for cellulose, and it hydrolyzes starch to glucose when the modified Melin-Nokrans media is used for the starch test. Accurate identification of Trichoderma species is needed as these strains can potentially be used as a biocontrol agent to prevent diseases and to increase yield in agriculture crops.
    Matched MeSH terms: Multilocus Sequence Typing
  18. Toh YF, Yew SM, Chan CL, Na SL, Lee KW, Hoh CC, et al.
    PLoS One, 2016;11(9):e0162095.
    PMID: 27626635 DOI: 10.1371/journal.pone.0162095
    Pyrenochaeta unguis-hominis is a rare human pathogen that causes infection in human skin and nail. P. unguis-hominis has received little attention, and thus, the basic biology and pathogenicity of this fungus is not fully understood. In this study, we performed in-depth analysis of the P. unguis-hominis UM 256 genome that was isolated from the skin scraping of a dermatitis patient. The isolate was identified to species level using a comprehensive multilocus phylogenetic analysis of the genus Pyrenochaeta. The assembled UM 256 genome has a size of 35.5 Mb and encodes 12,545 putative genes, and 0.34% of the assembled genome is predicted transposable elements. Its genomic features propose that the fungus is a heterothallic fungus that encodes a wide array of plant cell wall degrading enzymes, peptidases, and secondary metabolite biosynthetic enzymes. Antifungal drug resistance genes including MDR, CDR, and ERG11/CYP51 were identified in P. unguis-hominis UM 256, which may confer resistance to this fungus. The genome analysis of P. unguis-hominis provides an insight into molecular and genetic basis of the fungal lifestyles, understanding the unrevealed biology of antifungal resistance in this fungus.
    Matched MeSH terms: Multilocus Sequence Typing
  19. Kim SY, Ko KS
    Microb Drug Resist, 2019 Mar;25(2):227-232.
    PMID: 30212274 DOI: 10.1089/mdr.2018.0020
    To reveal whether an increase of CTX-M-15-producing Klebsiella pneumoniae ST11 isolates is due to clonal dissemination across the countries, plasmids (pHK02-026, pM16-13, pIN03-01, and pTH02-34) were extracted from four K. pneumoniae isolates collected in Hong Kong, Malaysia, Thailand, and Indonesia, respectively. Complete sequencing of blaCTX-M-15-carrying plasmids was performed. In addition to the four plasmids, a previously sequenced plasmid (pKP12226) of a K. pneumoniae ST11 isolate from Korea was included in the analysis. While pIN03-01 and pTH02-34, which belonged to the incompatibility group IncX3, showed nearly the same structure, the others of IncF1A or IncFII exhibited very different structures. The number and kinds of antibiotic genes found in the plasmids were also different from each other. Cryptic prophage genes were identified in all five blaCTX-M-15-harboring plasmids from the ST11 isolates; P1-like region in pKP12226, CPZ-55 prophage region in pHK02-026, phage shock operon pspFABCD in pM16-13, and SPBc2 prophage yokD in pIN03-01 and pTH02-34. The plasmids with blaCTX-M-15 in the prevailing K. pneumoniae ST11 isolates in Asian countries might emerge from diverse origins by recombination. The prevalence of CTX-M-15-producing K. pneumoniae ST11 clone in Asian countries is not mainly due to the dissemination of a single strain.
    Matched MeSH terms: Multilocus Sequence Typing
  20. Lia Natasha Amit, John DV, Fong SM
    Staphylococcus aureus aregram positive cocci which colonizethe skin and mucous membranes particularly the anterior nares. Prevalence of nosocomial infections associated with methicillin resistant S. aureus have been reported in hospitals (HA-MRSA) for over five decades. Recently,community-acquired MRSA (CA-MRSA) has emerged as a cause of skin and soft tissue infections in healthy individuals. These strains are sensitive to antimicrobials, carry genes for Panton-Valentine leukocidin (PVL) toxin and belong to the staphylococcal cassette chromosome (SCC) mec type IV or V. The suspected mode of transmission involves close contact with carriers leading to skin or nasal colonization that resultin subsequent active infection. Molecular typing is used to determine the mode of transmission of CA-MRSA in the community.General typing methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and specific methods for Staphylococci such as SCCmec typing and spa typing have the capability to characterize bacterial chromosomes and mobile genetic elements. Combination of these molecular typing methods is necessary as each method has its own advantages with respect to discriminatory power, rapidity, cost effectiveness, reproducibility, and ease of performance.
    Matched MeSH terms: Multilocus Sequence Typing
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