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  1. Fulltext Isolation of Pediococcus acidilactici Kp10 with ability to secrete bacteriocin-like inhibitory substance from milk products for applications in food industry
    Abbasiliasi S, Tan JS, Ibrahim TA, Ramanan RN, Vakhshiteh F, Mustafa S, et al.
    BMC Microbiol, 2012;12:260.
    PMID: 23153191 DOI: 10.1186/1471-2180-12-260
    Lactic acid bacteria (LAB) can be isolated from traditional milk products. LAB that secrete substances that inhibit pathogenic bacteria and are resistant to acid, bile, and pepsin but not vancomycin may have potential in food applications.
    Matched MeSH terms: Bacterial Typing Techniques
  2. Fulltext The significance of coagulase-negative staphylococci bacteremia in a low resource setting
    Abdul Rahman Z, Hamzah SH, Hassan SA, Osman S, Md Noor SS
    J Infect Dev Ctries, 2013 Jun;7(6):448-52.
    PMID: 23771288 DOI: 10.3855/jidc.2535
    INTRODUCTION: Coagulase-negative staphylococci (CoNS) are a group of micro-organisms that are increasingly implicated as a cause of significant infection and the leading cause of bloodstream infection (BSI). One important predictor of true BSI is the isolation of CoNS from multiple blood cultures, presuming that the isolates represent the same species. Thus the objective of this study was to determine the significance of repeated CoNS isolated from blood cultures.
    METHODOLOGY: This was a prospective laboratory study which was initiated in June 2007 and lasted until July 2008. CoNS isolates were obtained from patients who had two positive blood cultures within a 14-day interval. CoNS were identified to the species level using an API-Staph, and antibiotics susceptibility testing was performed according to Clinical and Laboratory Standards Institute specifications. Strain relatedness was confirmed using pulsed-field gel electrophoresis.
    RESULTS: During the study period, 202 CoNS-positive samples were isolated from 101 patients. The most common species isolated was Staphylococcus epidermidis (59.0%), and 83.2% of the patients isolated the same species of CoNS from repeated blood cultures. Among the isolates of the same species, only 40.7% had the same antibiogram. CoNS with the same species and antibiogram had 93.3% probability of belonging to the same strain. Most (65.5%) of the patients were treated with antibiotics, primarily from the glycopeptides group.
    CONCLUSION: Speciation and antibiogram of CoNS from repeated blood cultures are adequate in determining the significance of repeated CoNS isolated from blood cultures.
    Matched MeSH terms: Bacterial Typing Techniques
  3. Fulltext Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia
    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: Bacterial Typing Techniques
  4. Application of multilocus sequence analysis for molecular characterization of enterococci with virulence factors recovered from a tropical recreational beach
    Ahmad A, Dada AC, Usup G
    Southeast Asian J. Trop. Med. Public Health, 2014 May;45(3):700-18.
    PMID: 24974655
    Partial gene sequences of phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA) were evaluated for species delineation and detection of recombination among enterococci populations recovered from a bathing beach impacted by low tide river flow. At inter-species level, a maximum similarity of 86.5% and 94.8% was observed among the enterococci pheS and rpoA sequence, respectively. A superimposed plot of delimited pairwise similarity values obtained for 266 pair-wise observations revealed that while there was a harmony between species identity obtained from both genes, pheS was more discriminatory than rpoA. The difference was more pronounced for inter-species comparison. A number of putative recombination events between indigenous and non-indigenous strains was detected based on a library of aligned sequences. Virulence genes cyl, esp, gelE and asa were detected in 7, 22, 100 and 63%, respectively among river isolates but at lower proportion of 0, 20, 67 and 42%, respectively among beach water isolates. Random amplified polymorphic DNA profiling presented evidence suggesting low tide river as a source of fecal enterococci entering the recreation beach water. Multilocus sequence typing analysis of a number of Enterococcus faecalis isolates presented four sequence types, ST59, 117, 181 and 474. The presence of genetically diverse fecal enterococci with associated virulence traits and a background of recombination events in surface recreational water could present a potential public health risk.
    Matched MeSH terms: Bacterial Typing Techniques*
  5. Characteristics of community- and hospital-acquired meticillin-resistant Staphylococcus aureus strains carrying SCCmec type IV isolated in Malaysia
    Ahmad N, Ruzan IN, Abd Ghani MK, Hussin A, Nawi S, Aziz MN, et al.
    J Med Microbiol, 2009 Sep;58(Pt 9):1213-1218.
    PMID: 19528158 DOI: 10.1099/jmm.0.011353-0
    Community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) occurring among hospital isolates in Malaysia has not been reported previously. As CA-MRSA reported worldwide has been shown to carry SCCmec types IV and V, the aim of this study was to determine the SCCmec types of MRSA strains collected in Malaysia from November 2006 to June 2008. From a total of 628 MRSA isolates, 20 were SCCmec type IV, whilst the rest were type III. Further characterization of SCCmec type IV strains revealed 11 sequence types (STs), including ST22, with the majority being ST30/Panton-Valentine leukocidin positive. Eight out of nine CA-MRSA were ST30, one was ST80, and all were sensitive to co-trimoxazole and gentamicin. Five new STs designated ST1284, ST1285, ST1286, ST1287 and ST1288 were discovered, suggesting the emergence of novel clones of MRSA circulating in Malaysian hospitals. The discovery of the ST22 strain is a cause for concern because of its ability to replace existing predominant clones in certain geographical regions.
    Matched MeSH terms: Bacterial Typing Techniques
  6. Fulltext Utilization of Small RNA Genes to Distinguish Vibrio cholerae Biotypes via Multiplex Polymerase Chain Reaction
    Ahmed SA, Raabe CA, Cheah HL, Hoe CH, Rozhdestvensky TS, Tang TH
    Am J Trop Med Hyg, 2019 06;100(6):1328-1334.
    PMID: 30963989 DOI: 10.4269/ajtmh.18-0525
    The diarrheal disease "cholera" is caused by Vibrio cholerae, and is primarily confined to endemic regions, mostly in Africa and Asia. It is punctuated by outbreaks and creates severe challenges to public health. The disease-causing strains are most-often members of serogroups O1 and O139. PCR-based methods allow rapid diagnosis of these pathogens, including the identification of their biotypes. However, this necessitates the selection of specific target sequences to differentiate even the closely related biotypes of V. cholerae. Oligonucleotides for selective amplification of small RNA (sRNA) genes that are specific to these V. cholerae subtypes were designed. The resulting multiplex PCR assay was validated using V. cholerae cultures (i.e., 19 V. cholerae and 22 non-V. cholerae isolates) and spiked stool samples. The validation using V. cholerae cultures and spiked stool suspensions revealed detection limits of 10-100 pg DNA per reaction and 1.5 cells/mL suspension, respectively. The multiplex PCR assay that targets sRNA genes for amplification enables the sensitive and specific detection, as well as the differentiation of V. cholerae-O1 classical, O1 El Tor, and O139 biotypes. Most importantly, the assay enables fast and cheaper diagnosis compared with classic culture-based methods.
    Matched MeSH terms: Bacterial Typing Techniques/methods*
  7. Molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among veterinary students and personnel at a veterinary hospital in Malaysia
    Aklilu E, Zunita Z, Hassan L, Cheng CH
    Vet Microbiol, 2013 Jun 28;164(3-4):352-8.
    PMID: 23523336 DOI: 10.1016/j.vetmic.2013.02.030
    In this study, we report the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among veterinary students and personnel in Malaysia. Nasal and oral swabs were collected from 103 veterinary medicine students and 28 personnel from a veterinary hospital. Antibiotic sensitivity test (AST), minimum inhibitory concentration (MIC) test, and PCR amplifications of nucA and mecA gene were performed. Molecular characterization of the isolates was conducted using multilocus sequence typing (MLST), staphylococcal protein A gene (spa) typing, and pulsed-field gel electrophoresis (PFGE). Results from MLST show the presence of the pandemic and widespread MRSA clones, ST5 and ST59. Spa gene typing revealed spa type t267 which has a wide geographical distribution. A new spa type, t5697 was found in this study. Fingerprint analysis by using PFGE show heterogeneity of the isolates. These findings affirm the importance of MRSA in veterinary settings and underscore the need for further extensive research to devise contextual control and prevention strategies.
    Matched MeSH terms: Bacterial Typing Techniques
  8. Fulltext Using pulsed-field gel electrophoresis in the molecular investigation of an outbreak of Serratia marcescens infection in an intensive care unit
    Alfizah H, Nordiah AJ, Rozaidi WS
    Singapore Med J, 2004 May;45(5):214-8.
    PMID: 15143356
    Serratia marcescens is a well-known cause of nosocomial infections and outbreaks, particularly in immunocompromised patients with severe underlying disease. An outbreak due to S. marcescens infection was detected from 13 to 22 February 2001 at the intensive care unit (ICU) of our institution. We used pulsed-field gel electrophoresis (PFGE) typing to analyse the outbreak strains involved.
    Matched MeSH terms: Bacterial Typing Techniques
  9. Fulltext Molecular characterization of Streptococcus agalactiae strains isolated from fishes in Malaysia
    Amal MN, Zamri-Saad M, Siti-Zahrah A, Zulkafli AR, Nur-Nazifah M
    J Appl Microbiol, 2013 Jul;115(1):20-9.
    PMID: 23557382 DOI: 10.1111/jam.12210
    AIMS: The aim of this study was to characterize Streptococcus agalactiae strains that were isolated from fishes in Malaysia using random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (REP-PCR) techniques.

    METHODS AND RESULTS: A total of 181 strains of Strep. agalactiae isolated from red hybrid tilapia (Oreochromis sp.) and golden pompano (Trachinotus blochii) were characterized using RAPD and REP-PCR techniques. Both the fingerprinting techniques generated reproducible band patterns, differing in the number and molecular mass amplicons. The RAPD technique displayed greater discriminatory power by its production of more complex binding pattern and divided all the strains into 13 groups, compared to 9 by REP-PCR technique. Both techniques showed the availability to differentiate the genetic profiles of the strains according to their geographical location of origin. Three strains of Strep. agalactiae that were recovered from golden pompano showed a genetic dissimilarity from the strains isolated from red hybrid tilapia, while the strain of ATCC 27956 that recovered from bovine displayed a unique profile for both methods.

    CONCLUSIONS: Both techniques possess excellent discriminative capabilities and can be used as a rapid means of comparing Strep. agalactiae strains for future epidemiological investigation.

    SIGNIFICANCE AND IMPACT OF THE STUDY: Framework as the guideline in traceability of this disease and in the search for potential local vaccine candidates for streptococcosis in this country.

    Matched MeSH terms: Bacterial Typing Techniques/methods
  10. Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf
    Amrina RA, Furusawa G, Lau NS
    Int J Syst Evol Microbiol, 2021 Nov;71(11).
    PMID: 34752210 DOI: 10.1099/ijsem.0.005087
    A novel rod-shaped, Gram-stain-negative, strictly aerobic and alginate-degrading marine bacterium, designated CCB-QB4T, was isolated from a surface of algal turf collected from a coastal area of Penang, Malaysia. The cells showed motility by a lateral flagellum. The rod-shaped cells formed long chains end-to-end. Phylogenetic analysis based on the 16S rRNA gene sequence of strain CCB-QB4T showed 94.07, 92.69, 91.52 and 90.90 % sequence similarity to Algibacillus agarilyticus RQJ05T, Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T and Catenovulum sediminis D2T, respectively. Strain CCB-QB4T formed a cluster with A. agarilyticus RQJ05T. Strain CCB-QB4T was catalase-negative, oxidase-positive, and degraded agar, alginate, and starch. Cell growth was observed at 15-40 °C, at pH 7.0-10.0 and in the presence of 1-6 % (w/v) NaCl and glucose. The major fatty acids were summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids, an unidentified phospholipid and unidentified lipid. The major respiratory quinone was ubiquinone-8. The genomic DNA G+C content was 46.7 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain CCB-BQ4T represents a novel species in a new genus, for which the name Saccharobesus litoralis gen. nov., sp. nov. is proposed. The type strain is CCB-QB4T (=JCM 33513T=CCB-MBL 5008T).
    Matched MeSH terms: Bacterial Typing Techniques
  11. Fulltext Molecular evidence of cholera outbreak caused by a toxigenic Vibrio cholerae O1 El tor variant strain in Kelantan, Malaysia
    Ang GY, Yu CY, Balqis K, Elina HT, Azura H, Hani MH, et al.
    J Clin Microbiol, 2010 Nov;48(11):3963-9.
    PMID: 20826646 DOI: 10.1128/JCM.01086-10
    A total of 20 Vibrio cholerae isolates were recovered for investigation from a cholera outbreak in Kelantan, Malaysia, that occurred between November and December 2009. All isolates were biochemically characterized as V. cholerae serogroup O1 Ogawa of the El Tor biotype. They were found to be resistant to multiple antibiotics, including tetracycline, erythromycin, sulfamethoxazole-trimethoprim, streptomycin, penicillin G, and polymyxin B, with 35% of the isolates being resistant to ampicillin. All isolates were sensitive to ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and kanamycin. Multiplex PCR analysis confirmed the biochemical identification and revealed the presence of virulence genes, viz., ace, zot, and ctxA, in all of the isolates. Interestingly, the sequencing of the ctxB gene showed that the outbreak strain harbored the classical cholera toxin gene and therefore belongs to the newly assigned El Tor variant biotype. Clonal analysis by pulsed-field gel electrophoresis demonstrated that a single clone of a V. cholerae strain was responsible for this outbreak. Thus, we present the first molecular evidence that the toxigenic V. cholerae O1 El Tor variant has invaded Malaysia, highlighting the need for continuous monitoring to facilitate early interventions against any potential epidemic by this biotype.
    Matched MeSH terms: Bacterial Typing Techniques
  12. Fulltext Multi locus sequence typing of clinical Burkholderia pseudomallei isolates from Malaysia
    Arushothy R, Amran F, Samsuddin N, Ahmad N, Nathan S
    PLoS Negl Trop Dis, 2020 12;14(12):e0008979.
    PMID: 33370273 DOI: 10.1371/journal.pntd.0008979
    BACKGROUND: Melioidosis is a neglected tropical disease with rising global public health and clinical importance. Melioidosis is endemic in Southeast Asia and Northern Australia and is of increasing concern in Malaysia. Despite a number of reported studies from Malaysia, these reports are limited to certain parts of the country and do not provide a cohesive link between epidemiology of melioidosis cases and the nation-wide distribution of the causative agent Burkholderia pseudomallei.

    METHODOLOGY/PRINCIPLE FINDINGS: Here we report on the distribution of B. pseudomallei sequence types (STs) in Malaysia and how the STs are related to STs globally. We obtained 84 culture-confirmed B. pseudomallei from confirmed septicaemic melioidosis patients from all over Malaysia. Prior to performing Multi Locus Sequence Typing, the isolates were subjected to antimicrobial susceptibility testing and detection of the YLF/BTFC genes and BimA allele. Up to 90.5% of the isolates were sensitive to all antimicrobials tested while resistance was observed for antimicrobials typically administered during the eradication stage of treatment. YLF gene cluster and bimABp allele variant were detected in all the isolates. The epidemiological distribution patterns of the Malaysian B. pseudomallei isolates were analysed in silico using phylogenetic tools and compared to Southeast Asian and world-wide isolates. Genotyping of the 84 Malaysian B. pseudomallei isolates revealed 29 different STs of which 6 (7.1%) were novel. ST50 was identified as the group founder followed by subgroup founders ST376, ST211 and ST84. A low-level diversity is noted for the B. pseudomallei isolates described in this study while phylogenetic analysis associated the Malaysian STs to Southeast Asian isolates especially isolates from Thailand. Further analysis also showed a strong association that implicates agriculture and domestication activities as high-risk routes of infection.

    CONCLUSIONS/SIGNIFICANCE: In conclusion, MLST analysis of B. pseudomallei clinical isolates from all states in Malaysia revealed low diversity and a close association to Southeast Asian isolates.

    Matched MeSH terms: Bacterial Typing Techniques
  13. Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil
    Asem MD, Salam N, Idris H, Zhang XT, Bull AT, Li WJ, et al.
    Int J Syst Evol Microbiol, 2020 May;70(5):3210-3218.
    PMID: 32320378 DOI: 10.1099/ijsem.0.004158
    The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida, Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2-94.9 %) and in silico DNA-DNA hybridization (52.5-62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strain.
    Matched MeSH terms: Bacterial Typing Techniques
  14. Fulltext Prevalence of adhesion and regulation of biofilm-related genes in different clones of Staphylococcus aureus
    Atshan SS, Nor Shamsudin M, Sekawi Z, Lung LT, Hamat RA, Karunanidhi A, et al.
    J Biomed Biotechnol, 2012;2012:976972.
    PMID: 22701309 DOI: 10.1155/2012/976972
    Clinical information about genotypically different clones of biofilm-producing Staphylococcus aureus is largely unknown. We examined whether different clones of methicillin-sensitive and methicillin-resistant S. aureus (MSSA and MRSA) differ with respect to staphylococcal microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) in biofilm formation. The study used 60 different types of spa and determined the phenotypes, the prevalence of the 13 MSCRAMM, and biofilm genes for each clone. The current investigation was carried out using a modified Congo red agar (MCRA), a microtiter plate assay (MPA), polymerase chain reaction (PCR), and reverse transcriptase polymerase chain reaction (RT-PCR). Clones belonging to the same spa type were found to have similar properties in adheringto the polystyrene microtiter plate surface. However, their ability to produce slime on MCRA medium was different. PCR experiments showed that 60 clones of MSSA and MRSA were positive for 5 genes (out of 9 MSCRAMM genes). icaADBC genes were found to be present in all the 60 clones tested indicating a high prevalence, and these genes were equally distributed among the clones associated with MSSA and those with MRSA. The prevalence of other MSCRAMM genes among MSSA and MRSA clones was found to be variable. MRSA and MSSA gene expression (MSCRAMM and icaADBC) was confirmed by RT-PCR.
    Matched MeSH terms: Bacterial Typing Techniques
  15. Fulltext Comparative characterisation of genotypically different clones of MRSA in the production of biofilms
    Atshan SS, Shamsudin MN, Lung LT, Sekawi Z, Ghaznavi-Rad E, Pei CP
    J Biomed Biotechnol, 2012;2012:417247.
    PMID: 22529705 DOI: 10.1155/2012/417247
    The ability to adhere and produce biofilms is characteristic of enhanced virulence among isolates of methicillin-resistant Staphylococcus aureus (MRSA). The aim of the study is to find out whether these characteristics are consistently similar among isolates variations of MRSA. The study used 30 various isolates of MRSA belong to 13 spa types and 5 MLST types and determined the aggregation, the adherence, and the production of biofilms and slime for each isolate. The methods used to evaluate these characteristics were a modified Congo red agar assay (MCRA), a microtiter plate assay (MPA), high-magnification light microscopy, scanning electron microscopy (SEM), and PCR. The study found that isolates belonging to similar Spa, SCCmec, and ST types have similar abilities to produce biofilms; however, their ability to produce slime on CRA was found to be different. Moreover, isolates that have different Spa types showed high variation in their ability to produce biofilms. The results of light microscope revealed the isolates that produced strong and weak biofilms and formed similar aggregation on the glass surfaces. SEM results showed that all 30 MRSA isolates that were tested were 100% positive for biofilm formation, although to varying degrees. Further testing using PCR confirmed that 100% of the 30 isolates tested were positive for the presence of the icaADBC, fnbA, eno, ebps, clfA, and clfB genes. The prevalence of fib, cna, fnbB, and bbp in MRSA clones was 90, 93.33, 53.33, and 10%, respectively. This study indicate that differences in biofilm production capacities are caused by the differences in surface protein A (Spa) type and are not due to differences in MLST and SCCmec types.
    Matched MeSH terms: Bacterial Typing Techniques
  16. Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine
    Carlsohn MR, Groth I, Tan GYA, Schütze B, Saluz HP, Munder T, et al.
    Int J Syst Evol Microbiol, 2007 Jul;57(Pt 7):1640-1646.
    PMID: 17625209 DOI: 10.1099/ijs.0.64903-0
    Three actinomycetes isolated from the surfaces of rocks in a medieval slate mine were examined in a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics of the isolates were typical of strains of the genus Amycolatopsis. The isolates had identical 16S rRNA gene sequences and formed a distinct phyletic line towards the periphery of the Amycolatopsis mediterranei clade, being most closely related to Amycolatopsis rifamycinica. The organisms shared a wide range of genotypic and phenotypic markers that distinguished them from their closest phylogenetic neighbours. On the basis of these results, a novel species, Amycolatopsis saalfeldensis sp. nov., is proposed. The type strain is HKI 0457(T) (=DSM 44993(T)=NRRL B-24474(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  17. Actinoallomurus soli sp. nov. and Actinoallomurus rhizosphaericola sp. nov., two novel actinobacteria isolated from rhizosphere soil of Oryza rufipogon Griff
    Chantavorakit T, Muangham S, Aaron TWF, Duangmal K, Hong K
    Int J Syst Evol Microbiol, 2023 Nov;73(11).
    PMID: 37994910 DOI: 10.1099/ijsem.0.006177
    The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice (Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T. Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus, while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives. The two strains showed nearly identical 16S rRNA gene sequences (99.9 %). Strain WRP6H-15T showed 68.7 % digital DNA-DNA hybridization, 95.9 % average nucleotide identity (ANI) based on blast and 96.4 % ANI based on MUMmer to strain WRP9H-5T. A phylogenomic tree based on draft genome sequences of the strains and representative of the genus Actinoallomurus confirmed the phylogenetic relationships. The genomes sizes of strains WRP6H-15T and WRP9H-5T were 9.42 Mb and 9.68 Mb, with DNA G+C contents of 71.5 and 71.3 mol%, respectively. In silico analysis predicted that the strains contain biosynthetic gene clusters encoding for specialized metabolites. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strains WRP6H-15T and WRP9H-5T represent two novel species of the genus Actinoallomurus, for which the names Actinoallomurus soli sp. nov. (type strain WRP6H-15T=TBRC 15726T=NBRC 115556T) and Actinoallomurus rhizosphaericola sp. nov. (type strain WRP9H-5T=TBRC 15727T=NBRC 115557T) are proposed.
    Matched MeSH terms: Bacterial Typing Techniques
  18. Phenotypic and genotypic characteristics and epidemiological significance of ctx+ strains of Vibrio cholerae isolated from seafood in Malaysia
    Chen CH, Shimada T, Elhadi N, Radu S, Nishibuchi M
    Appl Environ Microbiol, 2004 Apr;70(4):1964-72.
    PMID: 15066786
    Of 97 strains of Vibrio cholerae isolated from various seafoods in Malaysia in 1998 and 1999, 20 strains carried the ctx gene and produced cholera toxin. Fourteen, one, and five of these toxigenic strains belonged to the O139, O1 Ogawa, and rough serotypes, respectively. The rough strains had the rfb gene of the O1 serotype. The toxigenic strains varied in their biochemical characteristics, the amount of cholera toxin produced, their antibiograms, and the presence or absence of the pTLC plasmid sequence. DNA fingerprinting analysis by arbitrarily primed PCR, ribotyping, and a pulsed-field gel electrophoresis method classified the toxigenic strains into 3, 7, and 10 types, respectively. The relatedness of these toxigenic strains to clinical strains isolated in other countries and from international travelers was examined by using a dendrogram constructed from the pulsed-field gel electrophoresis profiles. The results of the examination of the antibiogram and the possession of the toxin-linked cryptic plasmid were consistent with the dendrogram-based relatedness: the O139 strains isolated from Malaysian seafoods could be separated into two groups that appear to have been introduced from the Bengal area independently. The rough strains of Malaysian seafood origin formed one group and belonged to a cluster unique to the Thailand-Malaysia-Laos region, and this group may have persisted in this area for a long period. The single O1 Ogawa strain detected in Malaysian seafood appears to have an origin and route of introduction different from those of the O139 and the rough strains.
    Matched MeSH terms: Bacterial Typing Techniques
  19. Acinetobacter kookii sp. nov., isolated from soil
    Choi JY, Ko G, Jheong W, Huys G, Seifert H, Dijkshoorn L, et al.
    Int J Syst Evol Microbiol, 2013 Dec;63(Pt 12):4402-4406.
    PMID: 23950148 DOI: 10.1099/ijs.0.047969-0
    Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202(T) and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter. Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838(T) (97.9-98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963(T) and Acinetobacter bouvetii 4B02(T) (85.4-87.6 and 78.1-82.7 %, respectively). Strain 11-0202(T) displayed low DNA-DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter. The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter: summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3-27.2 %), C18 : 1ω9c (19.9-22.1 %), C16 : 0 (15.2-22.0 %) and C12 : 0 (9.2-14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202(T) ( = KCTC 32033(T) = JCM 18512(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  20. Fulltext Annotated genome sequence of Mycobacterium massiliense strain M154, belonging to the recently created taxon Mycobacterium abscessus subsp. bolletii comb. nov
    Choo SW, Wong YL, Tan JL, Ong CS, Wong GJ, Ng KP, et al.
    J Bacteriol, 2012 Sep;194(17):4778.
    PMID: 22887675 DOI: 10.1128/JB.01043-12
    Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus subsp. bolletii comb. nov. Strain M154, a clinical isolate from the bronchoalveolar lavage fluid of a Malaysian patient presenting with lower respiratory tract infection, was subjected to shotgun DNA sequencing with the Illumina sequencing technology to obtain whole-genome sequence data for comparison with other genetically related strains within the M. abscessus species complex.
    Matched MeSH terms: Bacterial Typing Techniques
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