Displaying publications 1 - 20 of 57 in total

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  1. Forde BM, Phan MD, Gawthorne JA, Ashcroft MM, Stanton-Cook M, Sarkar S, et al.
    mBio, 2015 Nov 17;6(6):e01602-15.
    PMID: 26578678 DOI: 10.1128/mBio.01602-15
    Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E. coli EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three (m6)A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for (m6)A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located.

    IMPORTANCE: DNA modification plays a crucial role in bacterial regulation. Despite several examples demonstrating the role of methyltransferase (MTase) enzymes in bacterial virulence, investigation of this phenomenon on a whole-genome scale has remained elusive until now. Here we used single-molecule real-time (SMRT) sequencing to determine the first complete methylome of a strain from the multidrug-resistant E. coli sequence type 131 (ST131) lineage. By interrogating the methylome computationally and with further SMRT sequencing of isogenic mutants representing previously uncharacterized MTase genes, we defined the target sequences of three novel ST131-specific MTases and determined the genomic distribution of all MTase target sequences. Using a large collection of 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a major factor driving diversity in DNA methylation patterns. Overall, our analysis highlights the potential for DNA methylation to dramatically influence gene regulation at the transcriptional level within a well-defined E. coli clone.

    Matched MeSH terms: Uropathogenic Escherichia coli/isolation & purification
  2. Yin W, Li H, Shen Y, Liu Z, Wang S, Shen Z, et al.
    mBio, 2017 06 27;8(3).
    PMID: 28655818 DOI: 10.1128/mBio.00543-17
    The mobile colistin resistance gene mcr-1 has attracted global attention, as it heralds the breach of polymyxins, one of the last-resort antibiotics for the treatment of severe clinical infections caused by multidrug-resistant Gram-negative bacteria. To date, six slightly different variants of mcr-1, and a second mobile colistin resistance gene, mcr-2, have been reported or annotated in the GenBank database. Here, we characterized a third mobile colistin resistance gene, mcr-3 The gene coexisted with 18 additional resistance determinants in the 261-kb IncHI2-type plasmid pWJ1 from porcine Escherichia colimcr-3 showed 45.0% and 47.0% nucleotide sequence identity to mcr-1 and mcr-2, respectively, while the deduced amino acid sequence of MCR-3 showed 99.8 to 100% and 75.6 to 94.8% identity to phosphoethanolamine transferases found in other Enterobacteriaceae species and in 10 Aeromonas species, respectively. pWJ1 was mobilized to an E. coli recipient by conjugation and contained a plasmid backbone similar to those of other mcr-1-carrying plasmids, such as pHNSHP45-2 from the original mcr-1-harboring E. coli strain. Moreover, a truncated transposon element, TnAs2, which was characterized only in Aeromonas salmonicida, was located upstream of mcr-3 in pWJ1. This ΔTnAs2-mcr-3 element was also identified in a shotgun genome sequence of a porcine E. coli isolate from Malaysia, a human Klebsiella pneumoniae isolate from Thailand, and a human Salmonella enterica serovar Typhimurium isolate from the United States. These results suggest the likelihood of a wide dissemination of the novel mobile colistin resistance gene mcr-3 among Enterobacteriaceae and aeromonads; the latter may act as a potential reservoir for mcr-3IMPORTANCE The emergence of the plasmid-mediated colistin resistance gene mcr-1 has attracted substantial attention worldwide. Here, we examined a colistin-resistant Escherichia coli isolate that was negative for both mcr-1 and mcr-2 and discovered a novel mobile colistin resistance gene, mcr-3 The amino acid sequence of MCR-3 aligned closely with phosphoethanolamine transferases from Enterobacteriaceae and Aeromonas species originating from both clinical infections and environmental samples collected in 12 countries on four continents. Due to the ubiquitous profile of aeromonads in the environment and the potential transfer of mcr-3 between Enterobacteriaceae and Aeromonas species, the wide spread of mcr-3 may be largely underestimated. As colistin has been and still is widely used in veterinary medicine and used at increasing frequencies in human medicine, the continuous monitoring of mobile colistin resistance determinants in colistin-resistant Gram-negative bacteria is imperative for understanding and tackling the dissemination of mcr genes in both the agricultural and health care sectors.
    Matched MeSH terms: Escherichia coli/isolation & purification
  3. Ujang Z, Au YL, Nagaoka H
    Water Sci Technol, 2002;46(9):109-15.
    PMID: 12448459
    This paper describes an investigation on the effect of microbial removal using IMF for high quality drinking water production. The comparison of IMF and IMF-PAC configuration was carried out in the study to highlight the importance of PAC in the system. The specific objective of this study was to study the effect of PAC adsorption in the IMF-PAC system particularly in removing microbial substances from contaminated raw water. A bench scale IMF-PAC configuration using a flat sheet microfiltration membrane was set up for experimental purposes. Experimentally, the result has shown high removal of microbial substances with the IMF-PAC system compared to IMF. The result of E. coli removal achieved was below the detectable level due to the microbial size, which is bigger than membrane pore size. The addition of PAC has shown a direct effect on total microbial removal. The adsorption of microbial onto PAC surfaces reduced the amount of smaller microbial present in permeate samples. As a conclusion, the configuration of IMF is a promising separation process in removing microbial substances, especially when the system is combined with PAC.
    Matched MeSH terms: Escherichia coli/isolation & purification
  4. Lee CW, Ng AY, Bong CW, Narayanan K, Sim EU, Ng CC
    Water Res, 2011 Feb;45(4):1561-70.
    PMID: 21146847 DOI: 10.1016/j.watres.2010.11.025
    Using the size fractionation method, we measured the decay rates of Escherichia coli, Salmonella Typhi and Vibrio parahaemolyticus in the coastal waters of Peninsular Malaysia. The size fractions were total or unfiltered, <250 μm, <20 μm, <2 μm, <0.7 μm, <0.2 μm and <0.02 μm. We also carried out abiotic (inorganic nutrients) and biotic (bacterial abundance, production and protistan bacterivory) measurements at Port Dickson, Klang and Kuantan. Klang had highest nutrient concentrations whereas both bacterial production and protistan bacterivory rates were highest at Kuantan. We observed signs of protist-bacteria coupling via the following correlations: Protistan bacterivory-Bacterial Production: r = 0.773, df = 11, p < 0.01; Protist-Bacteria: r = 0.586, df = 12, p < 0.05. However none of the bacterial decay rates were correlated with the biotic variables measured. E. coli and Salmonella decay rates were generally higher in the larger fraction (>0.7 μm) than in the smaller fraction (<0.7 μm) suggesting the more important role played by protists. E. coli and Salmonella also decreased in the <0.02 μm fraction and suggested that these non-halophilic bacteria did not survive well in seawater. In contrast, Vibrio grew well in seawater. There was usually an increase in Vibrio after one day incubation. Our results confirmed that decay or loss rates of E. coli did not match that of Vibrio, and also did not correlate with Salmonella decay rates. However E. coli showed persistence where its decay rates were generally lower than Salmonella.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  5. Gan HM, Sieo CC, Tang SG, Omar AR, Ho YW
    Virol J, 2013;10:308.
    PMID: 24134834 DOI: 10.1186/1743-422X-10-308
    Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.
    Matched MeSH terms: Escherichia coli/isolation & purification
  6. Thong KL, Lai MY, Teh C SJ, Chua KH
    Trop Biomed, 2011 Apr;28(1):21-31.
    PMID: 21602765 MyJurnal
    A PCR-based assay that can simultaneously detect and differentiate five different types of nosocomial bacterial pathogens was developed. Six pairs of selected primers targeting femA (132 bp) and mecA (310 bp) of methicillin-resistant Staphylococcus aureus, gltA (722 bp) of Acinetobacter baumannii, phoA (903 bp) of Escherichia coli, mdh (364 bp) of Klebsiella pneumoniae and oprL (504 bp) of Pseudomonas aeruginosa were used in this study. The conditions were optimized for the multiplex PCR to ensure specific amplification of the selected targets. Sensitivity and specificity tests were also carried out using a blind test approach on 50 bacterial cultures and resulted in 100% for both positive and negative predictive values.
    Matched MeSH terms: Escherichia coli/isolation & purification
  7. Jegathesan M, Wah LT, Soon LE, Su Har D, Boo Liat L
    Trop Geogr Med, 1976 Jun;28(2):91-5.
    PMID: 788266
    Three species of commonly eaten shellfish found in Malaysian coastal waters were examined for the presence of common bacterial enteropathogens. Vibrio parahaemolyticus, non-agglutinating vibrios, and various serotypes of enteropathogenic E. coli were isolated from a large proportion of them. Salmonella were isolated in two instances. High colony counts with evidence of faecal contamination indicated the strong possibility of pulltion being the cause for the presence of these enteropathogens. Methods of cooking and eating these shellfish enhance their likelihood of acting as vehicles of diarrhoeal disease.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  8. Desmarchelier P, Lew A, Caique W, Knight S, Toodayan W, Isa AR, et al.
    Trans R Soc Trop Med Hyg, 1992 7 1;86(4):448-50.
    PMID: 1440833
    The H2S water screening test and the membrane filtration faecal coliform count were compared with Escherichia coli counts for water samples collected from household water sources and domestic drinking water in rural Malaysia. Water samples were taken from 151 wells, 44 taps supplying water from the treated municipal supply and 192 domestic stored water supplies. E. coli were detected in 20% of the samples (42% of wells, 7% of tap water and 6% of drinking water). Excellent correlation (Spearman's rank correlation rs = 0.93) was found between the faecal coliform and E. coli counts for all sample types. The H2S method was poorly correlated whether read at 18 or 30 h. False positive rates were highest for well water, and false negative rates were highest for both well and drinking water samples, with low E. coli counts. The faecal coliform test was an excellent predictor of the presence of E. coli in these water samples, while the H2S test was very inadequate.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  9. Rohaya MA, Chuink BH, Aniran K
    PMID: 9656354
    Live eels and processed fish products from Malaysia are routinely checked for microbial pathogens before export to Japan. The eels and water from the ponds are screened for Vibrio cholerae and Salmonella spp, whereas the processed fish products are tested for microbial contamination (aerobic plate count), coliforms, E. coil and Vibrio cholerae. Results showed that live eels and water samples were negative for Vibrio cholerae but Salmonella spp were isolated occasionally. Various types of processed fish products had counts below 1.0 x 10(5) whilst coliforms, E. coli and Vibrio cholerae were absent. Records available showed that procedures involved in the production and transportation of live eel, preparation and processing of fish products have resulted in relatively safe food products.
    Matched MeSH terms: Escherichia coli/isolation & purification
  10. Jegathesan M, Singh RB, Kanaganayagy M, Soon LE
    PMID: 1096307
    Matched MeSH terms: Escherichia coli/isolation & purification*
  11. Rampal L, Oothuman P, Jeffery J, Daud MZ, Shekhar C, Senan P, et al.
    Med J Malaysia, 1983 Jun;38(2):104-7.
    PMID: 6353184
    Bacterial isolates were made from the intestinal tracts ofcarious species of cockroaches (Periplaneta americana, Periplaneta brunnea, Periplaneta australasiae, Neostylopyga rhombifolia, Nauphoeta cinerea) trapped from kitchens and stores (houses and hospital), Shigello, flexneri, Salmonella typhi, Escherichia coli and Salmonella sp. were some of the bacteria isolated and identified.
    Matched MeSH terms: Escherichia coli/isolation & purification
  12. Cheong YM, Jegathesan M, Ansary A, Othman M
    Med J Malaysia, 1990 Mar;45(1):42-8.
    PMID: 2152068
    The prevalence of Enterotoxigenic Escherichia coli (ETEC) in 433 stool samples from diarrhoeal cases of all ages was studied using two commercially available test kits for the detection of heat labile toxin (LT) and the infant mouse assay for the heat stable toxin (ST). 16 samples (3.7%) were positive for ETEC, of which nine were producing ST alone, six LT alone and only one was producing both LT and ST. Although the percentage of isolation rate was low, its occurrence was almost as common as the Shigella spp and Salmonella spp in the same study. Of the two test kits examined, the Phadebact ETEC-LT Test 50 (Pharmacia Diagnostics, Uppsala, Sweden) was found to be more suitable for use in a routine diagnostic laboratory. Ten out of 12 (83%) of the strains tested were resistant to one or more antibiotics.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  13. Haug NL, Davis CE, Anandan J, Lim TW
    Med J Malaya, 1969 Sep;24(1):24-31.
    PMID: 4243839
    Matched MeSH terms: Escherichia coli/isolation & purification
  14. Hara H, Yusaimi YA, Zulkeflle SNM, Sugiura N, Iwamoto K, Goto M, et al.
    J Gen Appl Microbiol, 2019 Jan 24;64(6):284-292.
    PMID: 29877296 DOI: 10.2323/jgam.2018.02.003
    The emergence of antibiotic resistance among multidrug-resistant (MDR) microbes is of growing concern, and threatens public health globally. A total of 129 Escherichia coli isolates were recovered from lowland aqueous environments near hospitals and medical service centers in the vicinity of Kuala Lumpur, Malaysia. Among the eleven antibacterial agents tested, the isolates were highly resistant to trimethoprim-sulfamethoxazole (83.7%) and nalidixic acid (71.3%) and moderately resistant to ampicillin and chloramphenicol (66.7%), tetracycline (65.1%), fosfomycin (57.4%), cefotaxime (57.4%), and ciprofloxacin (57.4%), while low resistance levels were found with aminoglycosides (kanamycin, 22.5%; gentamicin, 21.7%). The presence of relevant resistance determinants was evaluated, and the genotypic resistance determinants were as follows: sulfonamides (sulI, sulII, and sulIII), trimethoprim (dfrA1 and dfrA5), quinolones (qnrS), β-lactams (ampC and blaCTX-M), chloramphenicol (cmlA1 and cat2), tetracycline (tetA and tetM), fosfomycin (fosA and fosA3), and aminoglycosides (aphA1 and aacC2). Our data suggest that multidrug-resistant E. coli strains are ubiquitous in the aquatic systems of tropical countries and indicate that hospital wastewater may contribute to this phenomenon.
    Matched MeSH terms: Escherichia coli/isolation & purification
  15. Iyer L, Vadivelu J, Parasakthi N
    Singapore Med J, 1995 Oct;36(5):495-7.
    PMID: 8882532
    The production of heat-labile (LT) and heat-stable (ST) enterotoxins, colonisation factor antigens (CFAs) and haemagglutinins was investigated amongst 310 Escherichia coli (E. coli) isolates obtained from 62 children under the age of five, with diarrhoea. Twenty-one isolates were found to produce enterotoxins, of which fifteen (71%) isolates produced ST only, 2 (10%) produced LT only and 4 (19%) produced both LT and ST. However, none of the isolates demonstrated any of the common CFAs identified to date, but 8 out of the 21 isolates demonstrated haemagglutination with rabbit, sheep or human group A erythrocytes, suggesting the presence of putative CFAs, yet unidentified.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  16. Zainal D, Baba A
    Singapore Med J, 1994 Aug;35(4):374-5.
    PMID: 7899895
    Urinary tract infection is the most common of bacterial infections. Screening children for asymptomatic bacteriuria to prevent pyelonephritis and renal scarring is widely recommended. In Malaysia no such attempt has been made to establish the prevalence of asymptomatic bacteriuria. Bacteriuria was screened among 44,816 healthy school children from three different districts in Kelantan. There were 23,132 boys and 21,684 girls. The prevalence of bacteriuria was 0.12% after second screening. Higher prevalence was seen in other reports.
    Matched MeSH terms: Escherichia coli/isolation & purification
  17. Yuhana Ariffin E, Heng LY, Tan LL, Abd Karim NH, Hasbullah SA
    Sensors (Basel), 2020 Feb 26;20(5).
    PMID: 32111092 DOI: 10.3390/s20051279
    A novel label-free electrochemical DNA biosensor was constructed for the determination of Escherichia coli bacteria in environmental water samples. The aminated DNA probe was immobilized onto hollow silica microspheres (HSMs) functionalized with 3-aminopropyltriethoxysilane and deposited onto a screen-printed electrode (SPE) carbon paste with supported gold nanoparticles (AuNPs). The biosensor was optimized for higher specificity and sensitivity. The label-free E. coli DNA biosensor exhibited a dynamic linear response range of 1 × 10-10 µM to 1 × 10-5 µM (R2 = 0.982), with a limit of detection at 1.95 × 10-15 µM, without a redox mediator. The sensitivity of the developed DNA biosensor was comparable to the non-complementary and single-base mismatched DNA. The DNA biosensor demonstrated a stable response up to 21 days of storage at 4 ℃ and pH 7. The DNA biosensor response was regenerable over three successive regeneration and rehybridization cycles.
    Matched MeSH terms: Escherichia coli/isolation & purification*
  18. Chen SL, Ding Y, Apisarnthanarak A, Kalimuddin S, Archuleta S, Omar SFS, et al.
    Sci Rep, 2019 09 13;9(1):13245.
    PMID: 31519972 DOI: 10.1038/s41598-019-49467-5
    The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.
    Matched MeSH terms: Escherichia coli/isolation & purification
  19. Lau GL, Sieo CC, Tan WS, Hair-Bejo M, Jalila A, Ho YW
    Poult Sci, 2010 Dec;89(12):2589-96.
    PMID: 21076096 DOI: 10.3382/ps.2010-00904
    The efficacy of bacteriophage EC1, a lytic bacteriophage, against Escherichia coli O78:K80, which causes colibacillosis in poultry, was determined in the present study. A total of 480 one-day-old birds were randomly assigned to 4 treatments groups, each with 4 pens of 30 birds. Birds from the control groups (groups I and II) received PBS (pH 7.4) or 10(10) pfu of bacteriophage EC1, respectively. Group III consisted of birds challenged with 10(8) cfu of E. coli O78:K80 and treated with 10(10) pfu of bacteriophage EC1 at 2 h postinfection, whereas birds from group IV were challenged with 10(8) cfu of E. coli O78:K80 only. All the materials were introduced into the birds by intratracheal inoculation. Based on the results of the present study, the infection was found to be less severe in the treated E. coli-challenged group. Mean total viable cell counts of E. coli identified on eosin methylene blue agar (designated EMB + E. coli) in the lungs were significantly lower in treated, E. coli-challenged birds than in untreated, E. coli-challenged birds on d 1 and 2 postinfection. The EMB + E. coli isolation frequency was also lower in treated birds; no E. coli was detectable in blood samples on any sampling day, and E. coli were isolated only in the liver, heart, and spleen of treated chickens at a ratio of 2/6, 1/6, and 3/6, respectively, at d 1 postinfection. The BW of birds from the E. coli-challenged group treated with bacteriophage EC1 were not significantly different from those of birds from both control groups but were 15.4% higher than those of the untreated, E. coli-challenged group on d 21 postinfection. The total mortality rate of birds during the 3-wk experimental period decreased from 83.3% in the untreated, E. coli-challenged birds (group IV) to 13.3% in birds treated with bacteriophage EC1 (group III). These results suggest that bacteriophage EC1 is effective in vivo and could be used to treat colibacillosis in chickens.
    Matched MeSH terms: Escherichia coli/isolation & purification
  20. Noman E, Al-Gheethi A, Talip BA, Mohamed R, Kassim AH
    PLoS One, 2019;14(9):e0221522.
    PMID: 31513594 DOI: 10.1371/journal.pone.0221522
    The inactivation of antibiotic resistant Escherichia coli (Gram negative) and Staphylococcus aureus (Gram positive) seeded in greywater by bimetallic bio-nanoparticles was optimized by using response surface methodology (RSM). The bimetallic nanoparticles (Cu/Zn NPs) were synthesized in secondary metabolite of a novel fungal strain identified as Aspergillus iizukae EAN605 grown in pumpkin medium. Cu/Zn NPs were very effective for inhibiting growth of E. coli and S. aureus. The maximum inactivation was optimized with 0.028 mg mL-1 of Cu/Zn NPs, at pH 6 and after 60 min, at which the reduction of E. coli and S. aureus was 5.6 vs. 5.3 and 5.2 vs. 5.4 log reduction for actual and predicted values, respectively. The inactivation mechanism was described based on the analysis of untreated and treated bacterial cells by Field emission scanning electron microscopy (FESEM), Energy Dispersive X-Ray Spectroscopy (EDS), Atomic Force Microscopy (AFM) revealed a damage in the cell wall structure due to the effect of Cu/Zn NPs. Moreover, the Raman Spectroscopy showed that the Cu/Zn NPs led to degradation of carbohydrates and amino structures on the bacteria cell wall. The Fourier transform infrared spectroscopy (FTIR) analysis confirmed that the destruction take place in the C-C bond of the functional groups available in the bacterial cell wall. The techno economic analysis revealed that the biosynthesis Cu/Zn NPs is economically feasible. These findings demonstrated that Cu/Zn NPs can effectively inhibit pathogenic bacteria in the greywater.
    Matched MeSH terms: Escherichia coli/isolation & purification
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