Displaying publications 61 - 80 of 142 in total

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  1. Macrorestriction analysis and antimicrobial susceptibility profiling of Salmonella enterica at a University Teaching Hospital, Kuala Lumpur
    Tiong V, Thong KL, Yusof MY, Hanifah YA, Sam JI, Hassan H
    Jpn J Infect Dis, 2010 Sep;63(5):317-22.
    PMID: 20858996
    The genetic diversity and antimicrobial resistance rates of clinical Salmonella isolates (2007-2008) at the University of Malaya Medical Centre, Kuala Lumpur, were investigated and the genetic diversity of the isolates was determined by pulsed-field gel electrophoresis (PFGE) and repetitive extragenic palindromic (REP)-PCR. XbaI-PFGE analysis generated 57 profiles (Dice coefficient, F=0.08-1.00), whereas REP-PCR using the REP primer generated only 35 (F=0.34-1.00). PFGE was therefore the more discriminative and reproducible method for assessing the genetic diversity of salmonellae. The antibiograms of 78 Salmonella isolates were assessed against 19 antimicrobials using the disk diffusion method. Twenty serotypes were identified, with the most common being S. Enteritidis (18%) followed by S. Typhimurium (14%), S. Paratyphi B var Java (9%), S. Weltevreden (9%), and S. Corvallis (9%). A total of 38 resistant profiles were defined, with 53.8% of the isolates being resistant to three or more antimicrobials. The highest resistance rates were observed for cephalothin (55.1%), tetracycline (47.4%), and nalidixic acid (35.9%). The presence of multidrug-resistant Salmonella strains is a cause for concern as it may limit the treatment of severe salmonellosis. One multidrug-resistant S. Enteritidis strain was a putative extended-spectrum beta-lactamase producer, based on a double disk diffusion analysis, and was resistant to ceftriaxone (MIC>32 microg/mL). The data generated by this study will contribute towards epidemiological monitoring and investigations of Salmonella infections in Malaysia.
    Matched MeSH terms: Bacterial Typing Techniques/methods
  2. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment
    Lee LH, Azman AS, Zainal N, Eng SK, Fang CM, Hong K, et al.
    Int J Syst Evol Microbiol, 2014 Apr;64(Pt 4):1194-201.
    PMID: 24408529 DOI: 10.1099/ijs.0.059014-0
    A novel bacterium, strain MUSC 273(T), was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273(T) was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence of strain MUSC 273(T) showed the highest sequence similarity to those of Novosphingobium indicum H25(T) (96.8 %), N. naphthalenivorans TUT562(T) (96.4 %) and N. soli CC-TPE-1(T) (95.9 %) and lower sequence similarity to members of all other species of the genus Novosphingobium. Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273(T) formed a distinct cluster with members of the genus Novosphingobium. DNA-DNA relatedness of strain MUSC 273(T) to the type strains of the most closely related species, N. indicum MCCC 1A01080(T) and N. naphthalenivorans DSM 18518(T), was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were C18 : 1ω7c, C17 : 1ω6c, C16 : 0, C15 : 0 2-OH and C16 : 1ω7c. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273(T) represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium malaysiense sp. nov. is proposed. The type strain is MUSC 273(T) ( = DSM 27798(T) = MCCC 1A00645(T) = NBRC 109947(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  3. Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae
    Lee LH, Zainal N, Azman AS, Mutalib NA, Hong K, Chan KG
    Int J Syst Evol Microbiol, 2014 May;64(Pt 5):1461-1467.
    PMID: 24449791 DOI: 10.1099/ijs.0.058701-0
    A novel actinobacterial strain, designated MUSC 201T, was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201T represented a novel lineage within the class Actinobacteria. Strain MUSC 201T formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1%), Aeromicrobium (92.7-94.6%), Marmoricola (92.5-93.1%) and Kribbella (91.5-92.4%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3γ. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5:0.9:1.0:1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18:1ω9c (30.8%), C16:0 (24.1%), and 10-methyl C18:0 (13.9%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201T (=DSM 27763T=MCCC 1A00646T=NBRC 109973T).
    Matched MeSH terms: Bacterial Typing Techniques
  4. 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
  5. 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
  6. Antibiograms and molecular subtypes of methicillin-resistant Staphylococcus aureus in local teaching hospital, Malaysia
    Thong KL, Junnie J, Liew FY, Yusof MY, Hanifah YA
    J Microbiol Biotechnol, 2009 Oct;19(10):1265-70.
    PMID: 19884790
    The objectives of this study were to determine the antibiotypes, SCCmec subtypes, PVL carriage, and genetic diversity of MRSA strains from a tertiary hospital. Sixtysix MRSA strains were selected randomly (2003, 2004, and 2007) and tested for the Panton-Valentine leukocidin gene, mecA gene, and SCCmec type via a PCR. The antibiograms were determined using a standard disc diffusion method, and the genetic diversity of the isolates was determined by PFGE. Thirty-four antibiograms were obtained, with 55% of the 66 strains exhibiting resistance to more than 4 antimicrobials. All the isolates remained susceptible to vancomycin, and low resistance rates were noted for fusidic acid (11%), rifampicin (11%), and clindamycin acid (19%). The MRSA isolates that were multisensitive (n=12) were SCCmec type IV, whereas the rest (multiresistant) were SCCmec type III. Only two isolates (SCCmec type IV) tested positive for PVL, whereas all the isolates were mecA-positive. The PFGE was very discriminative and subtyped the 66 isolates into 55 pulsotypes (F=0.31-1.0). The multisensitive isolates were distinctly different from the multidrug-resistant MRSA. In conclusion, no vancomycin-resistant isolate was observed. The Malaysian MDR MRSA isolates were mostly SCCmec type III and negative for PVL. These strains were genetically distinct from the SCCmec type IV strains, which were sensitive to SXT, tetracycline, and erythromycin. Only two strains were SCCmec IV and PVL-positive. The infections in the hospital concerned were probably caused by multiple subtypes of MRSA.
    Matched MeSH terms: Bacterial Typing Techniques
  7. Virulotyping of Salmonella enterica subsp. enterica isolated from indigenous vegetables and poultry meat in Malaysia using multiplex-PCR
    Khoo CH, Cheah YK, Lee LH, Sim JH, Salleh NA, Sidik SM, et al.
    Antonie Van Leeuwenhoek, 2009 Nov;96(4):441-57.
    PMID: 19565351 DOI: 10.1007/s10482-009-9358-z
    The increased occurrence of Salmonella occurrence in local indigenous vegetables and poultry meat can be a potential health hazards. This study is aimed to detect the prevalence of twenty different virulence factors among Salmonella enterica strains isolated from poultry and local indigenous vegetables in Malaysia via an optimized, rapid and specific multiplex PCR assay. The assay encompasses a total of 19 Salmonella pathogenicity islands genes and a quorum sensing gene (sdiA) in three multiplex reaction sets. A total of 114 Salmonella enterica isolates belonging to 38 different serovars were tested. Each isolate in under this study was found to possess up to 70% of the virulence genes tested and exhibited variable pathogenicity gene patterns. Reproducibility of the multiplex PCR assay was found to be 100% and the detection limit of the optimized multiplex PCR was tested with lowest detectable concentration of DNA 0.8 pg microl(-1). This study demonstrated various Salmonella pathogenicity island virulence gene patterns even within the same serovar. This sets of multiplex PCR system provide a fast and reliable typing approach based on Salmonella pathogenicity islands, thus enabling an effective monitoring of emerging pathogenic Salmonella strains as an additional tool in Salmonella surveillance studies.
    Matched MeSH terms: Bacterial Typing Techniques
  8. Convenient and versatile DNA extraction using agarose plugs for ribotyping of problematic bacterial species
    Nair S, Karim R, Cardosa MJ, Ismail G, Pang T
    J Microbiol Methods, 1999 Oct;38(1-2):63-7.
    PMID: 10520586
    We describe a convenient, versatile and safe method for preparing bacterial DNA for ribotyping analysis. In this method, extraction of bacterial DNA from Salmnonella typhi and Burkholderia pseudomallei. and subsequent restriction endonuclease digestion, was performed in agarose blocks/plugs thus minimizing shearing and loss of DNA, problems commonly associated with liquid phase phenol extraction. Digested DNA in the plugs was then electrophoresed directly, transferred to nylon membranes and hybridized with labeled rDNA probes in the usual manner to provide reproducible restriction patterns. This method is particularly useful for bacterial species where standard DNA extraction in the liquid phase using phenol has been problematic (e.g. B. pseudomallei) but can be used for any bacterial species. The DNA extracted within the agarose plugs can be stored for long periods and can be used in other, widely-used typing methods such as pulsed-field gel electrophoresis (PFGE) and PCR-based techniques. Embedding live cells directly in agarose plugs also minimizes the risk of exposure to these virulent human pathogens among laboratory workers.
    Matched MeSH terms: Bacterial Typing Techniques
  9. Characterization of Burkholderia pseudomallei isolated in Thailand and Malaysia
    Radua S, Ling OW, Srimontree S, Lulitanond A, Hin WF, Yuherman, et al.
    Diagn Microbiol Infect Dis, 2000 Nov;38(3):141-5.
    PMID: 11109011
    A total of 35 Burkholderia pseudomallei isolates from Thailand (16 clinical and eight soil isolates) and Malaysia (seven animal, two isolate each from clinical and soil) were investigated by their antimicrobial resistance, plasmid profiles and were typed by randomly amplified polymorphic DNA analysis. All isolates were found to be resistant to six or more of the 12 antimicrobial agents tested. Only two small plasmids of 1.8 and 2.4 megadalton were detected in two clinical isolates from Thailand. RAPD analysis with primer GEN2-60-09 resulted in the identification of 35 RAPD-types among the 35 isolates. The constructed dendrogram differentiated the 35 isolates into two main clusters and a single isolate. The wide genetic biodiversity among the 35 isolates indicate that RAPD-PCR can be a useful method to differentiate unrelated B. pseudomallei in epidemiological investigation.
    Matched MeSH terms: Bacterial Typing Techniques
  10. Research note: Molecular subtyping of Salmonella enterica serovar Tshiongwe recently isolated in Malaysia during 2001-2002
    Thong KL, Bakeri SA, Lai KS, Koh YT, Taib MZ, Lim VK, et al.
    Southeast Asian J. Trop. Med. Public Health, 2004 Mar;35(1):92-6.
    PMID: 15272750
    Pulsed field gel electrophoresis (PFGE) and antimicrobial susceptibility analysis were undertaken on twenty-three strains of Salmonella enterica serovar Tshiongwe, an unusual serovar, which recently emerged in Malaysia. Antimicrobial susceptibility analysis showed that all the strains were sensitive to ampicilin, chloramphenicol, cotrimoxazole, and kanamycin. Twenty (87%) and 8 (3.5%) strains had resistance to tetracycline and streptomycin respectively. PFGE analysis subtyped 23 strains into 10 profiles (Dice coefficient of similarity, F = 0.7-1.0). The predominant profile, X1 was found in both clinical and environmental isolates and was widely distributed in different parts of Malaysia during the study period. In addition, isolates recovered from food, a hand-towel, apron and the surface of a table-top in one particular location had unique, indistinguishable profiles (X4/4a) and identical antibiograms. Similarly, isolates from cooked meat and a chopping board had PFGE profiles similar to some human isolates. These probably indicated cross-contamination and poor hygiene in food practices, hence contributing to Salmonellosis. Factors causing the emergence of this rare Salmonella serovar being responsible for food poisoning episodes during the study period remained unclear. The study reiterated the usefulness and versatility of PFGE in the molecular subtyping of this rare Salmonella serovar in Malaysia.
    Matched MeSH terms: Bacterial Typing Techniques
  11. Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey (Nasalis larvatus)
    Suzuki-Hashido N, Tsuchida S, Hayakawa T, Sakamoto M, Azumano A, Seino S, et al.
    Int J Syst Evol Microbiol, 2021 Apr;71(4).
    PMID: 33906706 DOI: 10.1099/ijsem.0.004787
    Three strains (YZ01T, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey (Nasalis larvatus) at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus Lactobacillus. Based on the sequence similarity of the 16S rRNA gene, Lactobacillus delbrueckii subsp. indicus JCM 15610T was the closest phylogenetic neighbour to YZ01T. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS) also indicated that the novel strains belonged to the genus Lactobacillus. The average nucleotide identity and digital DNA-DNA hybridization (dDDH) between L. delbrueckii subsp. indicus and YZ01T were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01T, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus Lactobacillus, indicating that it belonged to a new species. The DNA G+C content of strain YZ01T was 51.6 mol%. The major fatty acids were C16 : 0 and C18 : 1 ω9c. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01T, YZ02 and YZ03 represent a novel species of the genus Lactobacillus, for which the name Lactobacillus nasalidis sp. nov. is proposed with the type strain YZ01T (=JCM 33769T=DSM 110539T).
    Matched MeSH terms: Bacterial Typing Techniques
  12. Fulltext Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population
    Tay CY, Mitchell H, Dong Q, Goh KL, Dawes IW, Lan R
    BMC Microbiol, 2009;9:126.
    PMID: 19538757 DOI: 10.1186/1471-2180-9-126
    Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture.
    Matched MeSH terms: Bacterial Typing Techniques
  13. 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
  14. Pseudomonas versuta sp. nov., isolated from Antarctic soil
    See-Too WS, Salazar S, Ee R, Convey P, Chan KG, Peix Á
    Syst Appl Microbiol, 2017 Jun;40(4):191-198.
    PMID: 28501448 DOI: 10.1016/j.syapm.2017.03.002
    In this study we analysed three bacterial strains coded L10.10T, A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993T. Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10T, A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10T (LMG 29628T, DSM 101070T).
    Matched MeSH terms: Bacterial Typing Techniques
  15. Development of a species-specific PCR-RFLP targeting rpoD gene fragment for discrimination of Aeromonas species
    Puah SM, Khor WC, Kee BP, Tan JAMA, Puthucheary SD, Chua KH
    J Med Microbiol, 2018 Sep;67(9):1271-1278.
    PMID: 30024365 DOI: 10.1099/jmm.0.000796
    PURPOSE: The taxonomy of Aeromonas keeps expanding and their identification remains problematic due to their phenotypic and genotypic heterogeneity. In this study, we aimed to develop a rapid and reliable polymerase chain reaction-restriction fragment length polymorphism assay targeting the rpoD gene to enable the differentiation of aeromonads into 27 distinct species using microfluidic capillary electrophoresis.

    METHODOLOGY: A pair of degenerate primers (Aero F: 5'-YGARATCGAYATCGCCAARCGB-3' and Aero R: 5'-GRCCDATGCTCATRCGRCGGTT-3') was designed that amplified the rpoD gene of 27 Aeromonas species. Subsequently, in silico analysis enabled the differentiation of 25 species using the single restriction endonuclease AluI, while 2 species, A. sanarelli and A. taiwanensis, required an additional restriction endonuclease, HpyCH4IV. Twelve type strains (A. hydrophila ATCC7966T, A. caviae ATCC15468T, A. veronii ATCC9071T, A. media DSM4881T, A. allosaccharophila DSM11576T, A. dhakensis DSM17689T, A. enteropelogens DSM7312T, A. jandaei DSM7311T, A. rivuli DSM22539T, A. salmonicida ATCC33658T, A. taiwanensis DSM24096T and A. sanarelli DSM24094T) were randomly selected from the 27 Aeromonas species for experimental validation.Results/key findings. The twelve type strains demonstrated distinctive RFLP patterns and supported the in silico digestion. Subsequently, 60 clinical and environmental strains from our collection, comprising nine Aeromonas species, were used for screening examinations, and the results were in agreement.

    CONCLUSION: This method provides an alternative method for laboratory identification, surveillance and epidemiological investigations of clinical and environmental specimens.

    Matched MeSH terms: Bacterial Typing Techniques
  16. Fulltext Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates
    Ghazali AK, Eng SA, Khoo JS, Teoh S, Hoh CC, Nathan S
    Microb Genom, 2021 02;7(2).
    PMID: 33565959 DOI: 10.1099/mgen.0.000527
    Burkholderia pseudomallei, a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of B. pseudomallei infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across B. pseudomallei strains. We previously characterized B. pseudomallei strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical B. pseudomallei isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in B. pseudomallei and Burkholderia mallei, but not Burkholderia thailandensis. Genes encoding known B. pseudomallei virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding B. pseudomallei pathogenicity to guide the design of new therapeutics for treating melioidosis.
    Matched MeSH terms: Bacterial Typing Techniques
  17. Comparative genomic provides insight into the virulence and genetic diversity of Vibrio parahaemolyticus associated with shrimp acute hepatopancreatic necrosis disease
    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: Bacterial Typing Techniques
  18. Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia
    Dinesh B, Furusawa G, Amirul AA
    Arch Microbiol, 2017 Jan;199(1):63-67.
    PMID: 27506901 DOI: 10.1007/s00203-016-1275-8
    A Gram-staining-negative, aerobic, rod-shaped, yellow-orange-pigmented, gliding bacterium, designated as strain ST2L12(T), was isolated from estuarine mangrove sediment from Matang Mangrove Forest, Perak, Malaysia. Strain ST2L12(T) grew at 15-39 °C, pH 6-8 and in 1-6 % (w/v) NaCl. This strain was able to degrade xylan and casein. 16S rRNA gene sequence analysis showed 95.3-92.8 % similarity to members of the genera Mangrovimonas, Meridianimaribacter, Sediminibacter, Gaetbulibacter and Hoppeia. Phylogenetic analysis indicated that it belonged to the family Flavobacteriaceae. Respiratory quinone present was menaquinone-6 (MK-6), and the DNA G+C content was 38.3 mol%. The predominant fatty acids were iso-C15:0, iso-C15:1, C15:0 and iso-C17:0 3-OH. Moreover, previous genome comparison study showed that the genome of ST2L12(T) is 1.4 times larger compared to its closest relative, Mangrovimonas yunxiaonensis LYYY01(T). Phenotypic, fatty acid, 16S rRNA gene sequence and previous genome data indicate that strain ST2L12(T) represents a novel species of the genus Mangrovimonas in the family Flavobacteriaceae, for which the name Mangrovimonas xylaniphaga sp. nov. is proposed. The type strain of Mangrovimonas xylaniphaga is ST2L12(T) (=LMG 28914(T)=JCM 30880(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  19. Fulltext Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees
    Kwong WK, Moran NA
    Int J Syst Evol Microbiol, 2016 Mar;66(3):1323-1329.
    PMID: 26743158 DOI: 10.1099/ijsem.0.000882
    Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).
    Matched MeSH terms: Bacterial Typing Techniques
  20. Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.)
    Madhaiyan M, See-Too WS, Ee R, Saravanan VS, Wirth JS, Alex THH, et al.
    Int J Syst Evol Microbiol, 2020 Apr;70(4):2640-2647.
    PMID: 32202992 DOI: 10.1099/ijsem.0.004084
    A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of Burkholderiaceae revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family Burkholderiaceae. The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c /C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA-DNA hybridization clearly distinguished strain JS23T from the closely related genera Burkholderia, Caballeronia, Mycetohabitans, Mycoavidus, Pandoraea, Paraburkholderia, Robbsia and Trinickia. Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0-68.4 and 28.2-45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family Burkholderiaceae, for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).
    Matched MeSH terms: Bacterial Typing Techniques
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