Displaying publications 61 - 80 of 1819 in total

Abstract:
Sort:
  1. Two new species of fanged frogs from Peninsular Malaysia (Anura: Dicroglossidae)
    Matsui M, Belabut DM, Ahmad N
    Zootaxa, 2014;3881(1):75-93.
    PMID: 25543621 DOI: 10.11646/zootaxa.3881.1.6
    Taxonomic status of fanged frogs from the Peninsular Malaysia, previously assigned to Limnonectes kuhlii, is assessed using genetic and morphological approaches. Phylogenetic relationships inferred from sequences of the mitochondrial and nuclear genes revealed that the fanged frogs from the Peninsula form a monophyletic group and are clearly divergent from other species previously, or even now, assigned to L. kuhlii from Mainland Southeast Asia. In both mtDNA and nuDNA phylogeny, the Malay Peninsula clade diverges into two lineages, one from north (Larut Hill, Perak, and Hulu Terengganu, Terengganu) and another from south (Genting Highlands, Pahang, and Gombak, Selangor). These lineages are separated by large genetic distances, comparable with those observed between some other species of L. kuhlii-like frogs. Although the two lineages are very similar morphologically, they are distinguishable in several morphological traits and are considered heterospecific. We therefore describe them as L. utara sp. nov. and L. selatan sp. nov. These new species differ from all other species of kuhlii-like frogs from Mainland Southeast Asia by the surface of tibia, which is densely covered by large warts. 
    Matched MeSH terms: Phylogeny
  2. First isolation of Candida wangnamkhiaoensis from the blood of immunocompromised paediatric patient
    Tap RM, Ho Betty LS, Ramli NY, Suppiah J, Hashim R, Sabaratnam P, et al.
    Mycoses, 2016 Nov;59(11):734-741.
    PMID: 27427490 DOI: 10.1111/myc.12509
    Candida wangnamkhiaoensis is a species clustered under the Hyphopichia clade has not ever been isolated from any clinical specimens. To the best of our knowledge, this is the first report of C. wangnamkhiaoensis associated with fungaemia in immunocompromised paediatric patient. The isolate was assigned a strain name as UZ1679/14, in which the identification was confirmed by a polymerase chain reaction-sequencing of the internal transcribed spacer (ITS) and large subunit (LSU) regions of the rRNA gene. Antifungal susceptibility pattern showed that the isolate was sensitive to anidulafungin, caspofungin, fluconazole and voriconazole. The patient clinically improved after the antifungal treatment with caspofungin.
    Matched MeSH terms: Phylogeny
  3. Staphylococcal cassette chromosome mec (SCCmec) and characterization of the attachment site (attB) of methicillin resistant Staphylococcus aureus (MRSA) and methicillin susceptible Staphylococcus aureus (MSSA) isolates
    Bitrus AA, Zunita Z, Khairani-Bejo S, Othman S, Ahmad Nadzir NA
    Microb Pathog, 2018 Oct;123:323-329.
    PMID: 30053600 DOI: 10.1016/j.micpath.2018.07.033
    This study was designed to screen for SCCmec types and to characterize the attachment site (attB) and universal insertion site (orfX) of SCCmec in a collection of 27 isolates (n = 11) methicillin resistant S. aureus and (n = 16) methicillin susceptible S. aureus isolates in Malaysia. Screening of SCCmec types and characterization of the attachment site was carried out using PCR amplification and Sanger's sequencing method. The result showed that a large proportion of the MRSA isolates carried SCCmec type III 7/11 (63%). Three isolates 3/11 (27%) and 1/11 (9.0%) carried SCCmec type II and IVd respectively. Amplification of the universal insertion site of the SCCmec (orfX) and attachment site (attB) showed that all 16 S. aureus isolates were positive for the orfX gene, while only 7 were positive for the attB gene. Phylogenetic diversity showed that the isolates clustered around strains with features similar to a community acquired MRSA. In conclusion, a high carriage rate of SCCmec type III was observed. The result also showed that all the S. aureus isolates have the orfX structure; however, not all isolates possesses the attB site on the 3' end of the orfX region.
    Matched MeSH terms: Phylogeny
  4. Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer
    Venil CK, Nordin N, Zakaria ZA, Ahmad WA
    Int J Syst Evol Microbiol, 2014 Sep;64(Pt 9):3153-9.
    PMID: 24958763 DOI: 10.1099/ijs.0.063594-0
    A bacterial strain, designated UTM-3(T), isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3(T) with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus Chryseobacterium with the highest sequence similarities to Chryseobacterium lactis NCTC 11390(T), Chryseobacterium viscerum 687B-08(T), Chryseobacterium tructae 1084-08(T), Chryseobacterium arthrosphaerae CC-VM-7(T), Chryseobacterium oncorhynchi 701B-08(T), Chryseobacterium vietnamense GIMN1.005(T), Chryseobacterium bernardetii NCTC 13530(T), Chryseobacterium nakagawai NCTC 13529(T), Chryseobacterium gallinarum LMG 27808(T), Chryseobacterium culicis R4-1A(T), Chryseobacterium flavum CW-E2(T), Chryseobacterium aquifrigidense CW9(T), Chryseobacterium ureilyticum CCUG 52546(T), Chryseobacterium indologenes NBRC 14944(T), Chryseobacterium gleum CCUG 14555(T), Chryseobacterium jejuense JS17-8(T), Chryseobacterium oranimense H8(T) and Chryseobacterium joostei LMG 18212(T). The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3(T) was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium artocarpi sp. nov. is proposed. The type strain is UTM-3(T) ( = CECT 8497(T) = KCTC 32509(T)).
    Matched MeSH terms: Phylogeny*
  5. Genetic relationships among five varieties of Curcuma alismatifolia (Zingiberaceae) based on ISSR markers
    Taheri S, Abdullah TL, Abdullah NA, Ahmad Z
    Genet. Mol. Res., 2012;11(3):3069-76.
    PMID: 23007984
    The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (ISSRs) to assess genetic variation and relationships between five varieties of curcuma (Curcuma alismatifolia) cultivated in Malaysia. Sixteen ISSR primers generated 139 amplified fragments, of which 77% had high polymorphism among these varieties. These markers were used to estimate genetic similarity among the varieties using Jaccard's similarity coefficient. The similarity matrix was used to construct a dendrogram, and a principal component plot was developed to examine genetic relationships among varieties. Similarity coefficient values ranged from 0.40 to 0.58 (with a mean of 0.5) among the five varieties. The mean value of number of observed alleles, number of effective alleles, mean Nei's gene diversity, and Shannon's information index were 8.69, 1.48, 0.29, and 0.43, respectively.
    Matched MeSH terms: Phylogeny
  6. Bufavirus genotype 3 in Turkish children with severe diarrhoea
    Altay A, Yahiro T, Bozdayi G, Matsumoto T, Sahin F, Ozkan S, et al.
    Clin Microbiol Infect, 2015 Oct;21(10):965.e1-4.
    PMID: 26086570 DOI: 10.1016/j.cmi.2015.06.006
    Recently a parvovirus called bufavirus (BuV) has been implicated as a causative agent of diarrhoea. To further reveal the epidemiology and genetic characteristics of BuV, this study was performed in Turkish children with diarrhoea. BuV was detected in 1.4% (8/583) of stool samples. All stool samples from healthy children (n = 148) were negative for BuV. Diarrhoea in BuV-positive patients was severe and occurred mainly during the colder months of the year. Complete genome sequences were generated from four BuVs. Only BuV3 was found, which was genetically and phylogenetically similar to Bhutanese BuV3, indicating that BuV3 is prevalent in Asian countries.
    Matched MeSH terms: Phylogeny
  7. Fulltext The whole genome sequence data analyses of a Mycobacterium tuberculosis strain SBH321 isolated in Sabah, Malaysia, belongs to Ural family of Lineage 4
    Jani J, Mustapha ZA, Ling CK, Hui ASM, Teo R, Ahmed K
    Data Brief, 2020 Dec;33:106388.
    PMID: 33102655 DOI: 10.1016/j.dib.2020.106388
    In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).
    Matched MeSH terms: Phylogeny
  8. Fulltext Whole genome sequencing data and analysis of a rifampicin-resistant Mycobacterium tuberculosis strain SBH162 from Sabah, Malaysia
    Jani J, Mustapha ZA, Jamal NB, Stanis CS, Ling CK, Avoi R, et al.
    Data Brief, 2019 Oct;26:104445.
    PMID: 31534995 DOI: 10.1016/j.dib.2019.104445
    A Mycobacterium tuberculosis strain SBH162 was isolated from a 49-year-old male with pulmonary tuberculosis. GeneXpert MDR/RIF identified the strain as rifampicin-resistant M. tuberculosis. The whole genome sequencing was performed using Illumina HiSeq 4000 system to further investigate and verify the mutation sites of the strain through genetic analyses namely variant calling using bioinformatics tools. The de novo assembly of genome generated 100 contigs with N50 of 156,381bp. The whole genome size was 4,343,911 bp with G + C content of 65.58% and consisted of 4,306 predicted genes. The mutation site, S450L, for rifampicin resistance was detected in the rpoB gene. Based on the phylogenetic analysis using the Maximum Likelihood method, the strain was identified as belonging to the Europe America Africa lineage (Lineage 4). The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number SMOE00000000.
    Matched MeSH terms: Phylogeny
  9. Fulltext Terrestrial Animal-Derived Rabies Virus in a Juvenile Indian Flying Fox in Sri Lanka
    Matsumoto T, Nanayakkara S, Perera D, Ushijima S, Wimalaratne O, Nishizono A, et al.
    Jpn J Infect Dis, 2017 Nov 22;70(6):693-695.
    PMID: 29093322 DOI: 10.7883/yoken.JJID.2017.249
    Matched MeSH terms: Phylogeny
  10. Fulltext High incidence of asymptomatic leptospirosis among urban sanitation workers from Kota Kinabalu, Sabah, Malaysian Borneo
    Jeffree MS, Mori D, Yusof NA, Atil AB, Lukman KA, Othman R, et al.
    Sci Rep, 2020 11 10;10(1):19442.
    PMID: 33173153 DOI: 10.1038/s41598-020-76595-0
    Leptospirosis is a public health challenge in Sabah State of Malaysian Borneo. Rapid urbanization, rural-to-urban migration, and undocumented immigration in Sabah have increased the pressure on the urban garbage disposal system. Rodents and other small animals thrive under these conditions. We hypothesized that urban sanitation workers would be at risk of developing leptospirosis. In total, 303 urban sanitation workers with a mean age of 42.6 years were enrolled in this study. The serum samples collected from these workers were subjected to the microscopic agglutination test (MAT), PCR and nucleotide sequencing of the amplicons to confirm the presence of Leptospira. The phylogenetic analysis using the neighbor joining method was performed to assess whether they were pathogenic. In this study 43.8% (133/303) of the samples were MAT-seropositive and among them, 29 (21.8%) were positive by PCR. Nucleotide sequencing of the amplicons confirmed the presence of Leptospira. Phylogenetic analysis showed that our strains belonged to the pathogenic group of Leptospira. A high proportion of urban sanitation workers were seropositive for leptospirosis, and a considerable number were PCR positive for Leptospira, thereby indicating asymptomatic infections. Further research is needed to confirm whether this is a transient phenomenon or antibiotic therapy is required.
    Matched MeSH terms: Phylogeny
  11. Re-emergence of genotype G9 during a five-and-a-half-year period in Turkish children with rotavirus diarrhea
    Bozdayi G, Altay A, Yahiro T, Ahmed S, Meral M, Dogan B, et al.
    Arch Virol, 2016 Oct;161(10):2879-84.
    PMID: 27444180 DOI: 10.1007/s00705-016-2986-5
    This study was done to understand the dynamics of rotavirus genotype distribution in Turkish children. Samples were collected from January 2006 through August 2011 from children at a hospital in Ankara. Rotavirus was detected in 28 % (241/889) of the samples. Genotype G9P[8] was predominant (28 %), followed by G1P[8] (16.3 %) and G2P[8] (15.9 %). G9 was absent in the samples from 2006 and 2007 and then re-emerged in 2008 and increased gradually. Phylogenetic analysis showed that Turkish G9 rotaviruses of the present study formed a sublineage with strains from Italy and Ethiopia, possibly indicating spread of a clone in these countries.
    Matched MeSH terms: Phylogeny
  12. Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea
    Yahiro T, Takaki M, Chandrasena TGAN, Rajindrajith S, Iha H, Ahmed K
    Infect Genet Evol, 2018 11;65:170-186.
    PMID: 30055329 DOI: 10.1016/j.meegid.2018.07.014
    A human-porcine reassortant rotavirus, strain R1207, was identified from 74 group A rotaviruses detected in 197 (37.6%) stool samples collected from patients who attended a tertiary care hospital in Ragama, Sri Lanka. This is the first report of a human-porcine reassortant rotavirus in Sri Lanka. The patient was a 12-month-old boy who had been hospitalized with fever and acute diarrhea with a duration of 6 days. The family had pigs at home before the birth of this boy. However, the neighbors still practice pig farming. The genotype constellation of R1207 was G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. This is based on the assignment of all the eleven gene segments a full genome-based genotyping system. R1207 showed a 4-2-3-2 genomic electrophoretic migration pattern, which is characteristic of group A rotaviruses. Our analyses revealed that five (NSP2, NSP4, VP1, VP2, and VP7) of the 11 genes were closely related to the respective genes of porcine strains. Although the remaining six genes (NSP1, NSP3, NSP5, VP3, VP4, and VP6) were related to human strains, with the exception of the gene sequence of NSP1, all of these human strains were human-porcine reassortants. With a genogroup 1 genetic backbone, this strain was possibly formed via multiple genetic reassortments. We do not know whether this strain is circulating in pigs, as no data are available on porcine rotaviruses in Sri Lanka. Surveillance should be strengthened to determine the epidemiology of this genotype of rotavirus in Sri Lanka and to assess whether the infection was limited or sustained by ongoing human-to-human transmission.
    Matched MeSH terms: Phylogeny
  13. A novel bat-associated circovirus identified in northern Hokkaido, Japan
    Matsumoto T, Sato M, Nishizono A, Ahmed K
    Arch Virol, 2019 Aug;164(8):2179-2182.
    PMID: 31111258 DOI: 10.1007/s00705-019-04286-x
    We identified two novel circoviruses, HK02976 and HK00220, in oral swabs from bats. The size of their full genome was 2,010 nucleotides (nt). The full-genome sequence of our strains shared 96.1% nucleotide sequence identity with each other, and 39.9%-69.5% identity with bat-associated circoviruses (BatACVs)1-9. Based on the species demarcation threshold for viruses of the family Circoviridae, which is 80% genome-wide nucleotide sequence identity, we have tentatively named this group of viruses "bat-associated circovirus 10" (BatACV10).
    Matched MeSH terms: Phylogeny
  14. Fulltext High proportion of norovirus infection and predominance of GII.3 [P12] genotype among the children younger than 5 in Sabah, Malaysian Borneo
    John JL, Mori D, Amit LN, Mosiun AK, Chin AZ, Ahmed K
    J Clin Virol, 2021 10;143:104968.
    PMID: 34509928 DOI: 10.1016/j.jcv.2021.104968
    Globally, norovirus (NoV) has become one of the important causes of acute gastroenteritis (AGE) in children. It is responsible for death of children younger than 5 years in developing countries. Although there is limited information and the rate of child mortality caused by diarrhea is low in Malaysia, the burden of diarrhea is high, especially in Sabah. NoV GI, GII and GIV genogroups are known to infect humans, and GII.4 is the predominant genotype distributed worldwide. Better understanding of the etiology of NoV will help to inform policies for prevention and control. The aim of this study was to determine the burden and genotype distribution of NoV in children younger than 5 years with AGE who attended health-care facilities in Sabah, Malaysia. Diarrhea stool samples were collected from 299 children with AGE and NoV was detected by amplifying the capsid and RNA-dependent RNA polymerase gene and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Nucleotide sequencing of the amplicons was used for genotypes and phylogenetic analyses . NoV-positive stool samples were found in 17.7% (53/299) among which 13/53 (24.5%), 38/53 (71.7%), and 2/53 (3.8%) identified as NoV GI, GII and combination of GI and GII, respectively. The most common genotypes were GII.3 [P12] (80%) followed by GII.6 [P7] (13.3%), and GII.17 [P17] (6.7%). In the phylogenetic tree, all Sabahan NoV samples were shown to share ancestry with their respective genotype from predominantly East Asian countries and to some extent Australia and Europe. However, the Sabahan strains formed independent clusters with significant bootstrap values, indicating a clonal spread after the strains had entered Sabah.
    Matched MeSH terms: Phylogeny
  15. Fulltext Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia  during 2018-2019
    Amit LN, Mori D, John JL, Chin AZ, Mosiun AK, Jeffree MS, et al.
    PLoS One, 2021;16(7):e0254784.
    PMID: 34320003 DOI: 10.1371/journal.pone.0254784
    Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.
    Matched MeSH terms: Phylogeny
  16. Fulltext Surveillance of norovirus among children with diarrhea in four major hospitals in Bhutan: Replacement of GII.21 by GII.3 as a dominant genotype
    Wangchuk S, Matsumoto T, Iha H, Ahmed K
    PLoS One, 2017;12(9):e0184826.
    PMID: 28910371 DOI: 10.1371/journal.pone.0184826
    BACKGROUND: Diarrhea is a major cause of morbidity and mortality among Bhutanese children. The etiology of diarrhea is not well known due to the challenges of conducting routine surveillance with Bhutan's modest research facilities. Establishing an etiology is crucial toward generating evidence that will contribute to policy discussions on a diarrheal disease control program. Our previous study, during 2010-2012, revealed that norovirus (NoV) is an important cause of diarrhea among Bhutanese children, and that GII.21 was the major genotype circulating at that time. In other countries, GII.4 is the major genotype responsible for NoV infections. In this update report, we provide new prevalence data to describe the progression of the transformation and distribution of the NoV genotype among Bhutanese children.

    METHODS: From June 2013 through May 2014, diarrheal stool samples were collected at one national referral hospital in Thimphu, two regional referral hospitals in the eastern and central regions, and one general hospital in the western region of Bhutan. NoV was detected by reverse transcription-polymerase chain reaction (RT-PCR), by amplifying the capsid gene. The RT-PCR results were confirmed by nucleotide sequencing of the amplicons.

    RESULTS: The proportion of NoV-positive stool samples was 23.6% (147/623), of which 76.9% were NoV GII and the remainders were NoV GI. The median age of infected children was 15.5 months, with a fairly balanced female: male ratio. NoV GII was most prevalent in the colder months (late November-mid April) and NoV GI had the highest prevalence in the summer (mid April-late September). Nucleotide sequencing was successful in 99 samples of GII strains. The most common genotypes were GII.3 (42.6%), GII.4 Sydney 2012 (15.8%), and GII.4 unassigned (11.9%). No GII.21 was found in any child in the present study. Phylogenetic analysis showed that GII.3 strains in the present study belonged to an independent cluster in lineage B. These strains shared an ancestor with those from different countries and Bhutanese strains circulating during 2010.

    CONCLUSION: NoV remains an important cause of diarrhea among Bhutanese children. Genotype GII.3 from a single ancestor strain has spread, replacing the previously circulating GII.21. Current NoV genotypes are similar to the strains circulating worldwide but are primarily related to those in neighboring countries. NoV GII is prevalent during the cold season, while GI is prevalent during the summer. To develop a NoV infection control policy, further studies are needed.

    Matched MeSH terms: Phylogeny
  17. Increase in rotavirus prevalence with the emergence of genotype G9P[8] in replacement of genotype G12P[6] in Sabah, Malaysia
    Amit LN, John JL, Mori D, Chin AZ, Mosiun AK, Ahmed K
    Arch Virol, 2023 Jun 03;168(6):173.
    PMID: 37269384 DOI: 10.1007/s00705-023-05803-9
    Rotaviruses are major causative agents of acute diarrhea in children under 5 years of age in Malaysia. However, a rotavirus vaccine has not been included in the national vaccination program. To date, only two studies have been carried out in the state of Sabah, Malaysia, although children in this state are at risk of diarrheal diseases. Previous studies showed that 16%-17% of cases of diarrhea were caused by rotaviruses and that equine-like G3 rotavirus strains are predominant. Because the prevalence of rotaviruses and their genotype distribution vary over time, this study was conducted at four government healthcare facilities from September 2019 through February 2020. Our study revealed that the proportion of rotavirus diarrhea increased significantly to 37.2% (51/137) after the emergence of the G9P[8] genotype in replacement of the G12P[8] genotype. Although equine-like G3P[8] strains remain the predominant rotaviruses circulating among children, the Sabahan G9P[8] strain belonged to lineage VI and was phylogenetically related to strains from other countries. A comparison of the Sabahan G9 strains with the G9 vaccine strains used in the RotaSiil and Rotavac vaccines revealed several mismatches in neutralizing epitopes, indicating that these vaccines might not be effective in Sabahan children. However, a vaccine trial may be necessary to understand the precise effects of vaccination.
    Matched MeSH terms: Phylogeny
  18. Fulltext Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution
    Kumar N, Mariappan V, Baddam R, Lankapalli AK, Shaik S, Goh KL, et al.
    Nucleic Acids Res, 2015 Jan;43(1):324-35.
    PMID: 25452339 DOI: 10.1093/nar/gku1271
    The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host-pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner.
    Matched MeSH terms: Phylogeny
  19. Fulltext Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India
    Hussain A, Ranjan A, Nandanwar N, Babbar A, Jadhav S, Ahmed N
    Antimicrob Agents Chemother, 2014 Dec;58(12):7240-9.
    PMID: 25246402 DOI: 10.1128/AAC.03320-14
    In view of the epidemiological success of CTX-M-15-producing lineages of Escherichia coli and particularly of sequence type 131 (ST131), it is of significant interest to explore its prevalence in countries such as India and to determine if antibiotic resistance, virulence, metabolic potential, and/or the genetic architecture of the ST131 isolates differ from those of non-ST131 isolates. A collection of 126 E. coli isolates comprising 43 ST131 E. coli, 40 non-ST131 E. coli, and 43 fecal E. coli isolates collected from a tertiary care hospital in India was analyzed. These isolates were subjected to enterobacterial repetitive intergenic consensus (ERIC)-based fingerprinting, O typing, phylogenetic grouping, antibiotic sensitivity testing, and virulence and antimicrobial resistance gene (VAG) detection. Representative isolates from this collection were also analyzed by multilocus sequence typing (MLST), conjugation, metabolic profiling, biofilm production assay, and zebra fish lethality assay. All of the 43 ST131 E. coli isolates were exclusively associated with phylogenetic group B2 (100%), while most of the clinical non-ST131 and stool non-ST131 E. coli isolates were affiliated with the B2 (38%) and A (58%) phylogenetic groups, respectively. Significantly greater proportions of ST131 isolates (58%) than non-ST131 isolates (clinical and stool E. coli isolates, 5% each) were technically identified to be extraintestinal pathogenic E. coli (ExPEC). The clinical ST131, clinical non-ST131, and stool non-ST131 E. coli isolates exhibited high rates of multidrug resistance (95%, 91%, and 91%, respectively), extended-spectrum-β-lactamase (ESBL) production (86%, 83%, and 91%, respectively), and metallo-β-lactamase (MBL) production (28%, 33%, and 0%, respectively). CTX-M-15 was strongly linked with ESBL production in ST131 isolates (93%), whereas CTX-M-15 plus TEM were present in clinical and stool non-ST131 E. coli isolates. Using MLST, we confirmed the presence of two NDM-1-positive ST131 E. coli isolates. The aggregate bioscores (metabolite utilization) for ST131, clinical non-ST131, and stool non-ST131 E. coli isolates were 53%, 52%, and 49%, respectively. The ST131 isolates were moderate biofilm producers and were more highly virulent in zebra fish than non-ST131 isolates. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, and this was subsequently followed by the genetic similarity of clinical non-ST131 and stool non-ST131 E. coli strains. In conclusion, our data provide novel insights into aspects of the fitness advantage of E. coli lineage ST131 and suggest that a number of factors are likely involved in the worldwide dissemination of and infections due to ST131 E. coli isolates.
    Matched MeSH terms: Phylogeny
  20. The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey
    Abu-Bakar SB, Razali NM, Naggs F, Wade C, Mohd-Nor SA, Aileen-Tan SH
    Mol Biol Rep, 2014 Mar;41(3):1799-805.
    PMID: 24443224 DOI: 10.1007/s11033-014-3029-5
    A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
    Matched MeSH terms: Phylogeny
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links