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  1. Zainol MKM, Linforth RJC, Winzor DJ, Scott DJ
    Eur Biophys J, 2021 Dec;50(8):1103-1110.
    PMID: 34611772 DOI: 10.1007/s00249-021-01572-y
    This investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ([Formula: see text]) that is a characteristic of hydrophobic interactions. The observation of enthalpy-entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy-entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA-dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.
    Matched MeSH terms: Escherichia coli Proteins*
  2. Sultana A, Tiash S
    J Control Release, 2021 04 10;332:233-244.
    PMID: 33561481 DOI: 10.1016/j.jconrel.2021.02.004
    E. coli mediated gene delivery faces a major drawback of low efficiency despite of being a safer alternative to viral vectors. This study showed a novel, simple and effective strategy to enhance invasive E. coli DH10B vector's efficiency in human epithelial cells. The bactofection efficiency of invasive E .coli vector was analyzed in nine cell lines. It demonstrated highest (16%) reporter gene (GFP) expression in cervical cells. Methods were employed to further enhance its efficiency by adding transfection reagents (trans-bactofection method) to promote entry into host cells, lysosomotropic reagents for escape from lysosomal degradation or antibiotics to lyse internalized bacteria. Increased bacterial entry, as elucidated from nil to 3% expression in liver cells, was obtained upon complexing bacteria with PULSin. Chloroquine mediated endosomal escape resulted in 7.2 folds increase whereas tetracycline addition to lyse internalized bacteria caused ≈90% of GFP in HeLa. Eventually, the combined effect of these three methods exhibited close to 100% GFP in cervical and remarkable increase of 138 folds in breast cells. This is the first study showing comparative study of vector's gene delivery ability in various epithelial cells of the human body with improving its delivery efficiency. These data demonstrated the potential of developed bactofection method to boost up the efficiency of other bacterial vectors also, which could further be used for effectual therapeutic gene delivery in human cells.
    Matched MeSH terms: Escherichia coli Proteins*
  3. Seder N, Abu Bakar MH, Abu Rayyan WS
    PMID: 33488102 DOI: 10.2147/AABC.S292143
    Introduction: Malaysian stingless bee honey (Trigona) has been aroused as a potential antimicrobial compound with antibiofilm activity. The capability of the gram-negative bacillus P. aeruginosa to sustain a fatal infection is encoded in the bacterium genome.

    Methods: In the current study, a transcriptome investigation was performed to explore the mechanism underlying the biofilm dispersal of P. aeruginosa after the exposure to Trigona honey.

    Results: Microarray analysis of the Pseudomonas biofilm treated by 20% Trigona honey has revealed a down-regulation of 3478 genes among the 6085 screened genes. Specifically, around 13.5% of the down-regulated genes were biofilm-associated genes. The mapping of the biofilm-associated pathways has shown an ultimate decrease in the expression levels of the D-GMP signaling pathway and diguanylate cyclases (DGCs) genes responsible for c-di-GMP formation.

    Conclusion: We predominantly report the lowering of c-di-GMP through the down-regulation of DGC genes as the main mechanism of biofilm inhibition by Trigona honey.

    Matched MeSH terms: Escherichia coli Proteins
  4. Wan Makhtar WR, Mohd Azlan M, Hassan NH, Aziah I, Samsurizal NH, Yusof NY
    Microbiol Resour Announc, 2020 Aug 13;9(33).
    PMID: 32817162 DOI: 10.1128/MRA.01497-19
    We describe here the draft genome sequence and basic characteristics of Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum β-lactamase-producing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9.
    Matched MeSH terms: Escherichia coli Proteins
  5. Jiemy WF, Hiew LF, Sha HX, In LLA, Hwang JS
    BMC Biotechnol, 2020 Jun 17;20(1):31.
    PMID: 32552895 DOI: 10.1186/s12896-020-00628-9
    BACKGROUND: Immunotoxin is a hybrid protein consisting of a toxin moiety that is linked to a targeting moiety for the purpose of specific elimination of target cells. Toxins used in traditional immunotoxins are practically difficult to be produced in large amount, have poor tissue penetration and a complex internalization process. We hypothesized that the smaller HALT-1, a cytolysin derived from Hydra magnipapillata, can be used as the toxin moiety in construction of a recombinant immunotoxin.

    RESULTS: In this study, pro-inflammatory macrophage was selected as the target cell due to its major roles in numerous inflammatory and autoimmune disorders. We aimed to construct macrophage-targeted recombinant immunotoxins by combining HALT-1 with anti-CD64-scFv in two orientations, and to assess whether their cytotoxic activity and binding capability could be preserved upon molecular fusion. The recombinant immunotoxins, HALT-1-scFv and scFv-HALT-1, were successfully constructed and expressed in Escherichia coli (E. coli). Our data showed that HALT-1 still exhibited significant cytotoxicity against CD64+ and CD64- cell lines upon fusion with anti-CD64 scFv, although it had half cytotoxic activity as compared to HALT-1 alone. As positioning HALT-1 at N- or C-terminus did not affect its potency, the two constructs demonstrated comparable cytotoxic activities with IC50 lower in CD64+ cell line than in CD64- cell line. In contrast, the location of targeting moieties anti-CD64 scFv at C-terminal end was crucial in maintaining the scFv binding capability.

    CONCLUSIONS: HALT-1 could be fused with anti-CD64-scFv via a fsexible polypeptide linker. Upon the successful production of this recombinant HALT-1 scFv fusion protein, HALT-1 was proven effective for killing two human cell lines. Hence, this preliminary study strongly suggested that HALT-1 holds potential as the toxin moiety in therapeutic cell targeting.

    Matched MeSH terms: Escherichia coli Proteins
  6. Ugwu IC, Lee-Ching L, Ugwu CC, Okoye JOA, Chah KF
    Iran J Vet Res, 2020;21(3):180-187.
    PMID: 33178295
    Background: Avian pathogenic Escherichia coli (APEC) strains have been associated with various disease conditions in avian species due to virulence attributes associated with the organism.

    Aims: This study was carried out to determine the in vitro pathogenic characteristics and virulence encoding genes found in E. coli strains associated with colibacillosis in chickens.

    Methods: Fifty-two stock cultures of E. coli strains isolated from chickens diagnosed of colibacillosis were tested for their ability to produce haemolysis on blood agar and take up Congo red dye. Molecular characterization was carried out by polymerase chain reaction (PCR) amplification of virulence encoding genes associated with APEC.

    Results: Eleven (22%) and 41 (71%) were positive for haemolysis on 5% sheep red blood agar and Congo red agar, respectively. Nine virulence-associated genes were detected as follows: FimH (96%), csgA (52%), iss (48%), iut (33%), tsh (21%), cva (15%), kpsII (10%), pap (2%), and felA (2%).

    Conclusion: The APEC strains exhibited virulence properties and harbored virulence encoding genes which could be a threat to the poultry population and public health. The putative virulence genes were diverse and different in almost all isolate implying that pathogenesis was multi-factorial and the infection was multi-faceted which could be a source of concern in the detection and control of APEC infections.

    Matched MeSH terms: Escherichia coli Proteins
  7. Aklilu E, Raman K
    Int J Microbiol, 2020;2020:8853582.
    PMID: 32774381 DOI: 10.1155/2020/8853582
    This study was conducted to detect the presence of colistin-resistant Escherichia coli (E. coli) in raw chicken meat and bean sprouts collected from local markets and to determine the antimicrobial resistance patterns of the E. coli isolates. A total of 100 samples, comprised of 50 raw chicken meat and 50 bean sprouts, were collected and processed. Kirby-Bauer method was used to determine the antimicrobial resistance patterns, and PCR amplification was used to detect E. coli species-specific and colistin resistance (mcr-1 and mcr-2) genes. The results showed that 52.1% (12/23) of the E. coli isolated from raw chicken meat were positive for the colistin resistance encoding gene, mcr-1, whereas all the E. coli isolates from bean sprouts were negative for colistin resistance encoding genes. The findings show that chicken meat contaminated with colistin-resistant E. coli may pose public health risk to the consumers. Hence, prudent usage of antibiotics and hygienic handling of food items helps to prevent and combat the risks of spreading of colistin-resistant E. coli and the public health risks it may pose. More comprehensive and large-scale studies focusing on all the possible sources of colistin-resistant E. coli are recommended.
    Matched MeSH terms: Escherichia coli Proteins
  8. Ngaini Z, Mortadza NA
    Nat Prod Res, 2019 Dec;33(24):3507-3514.
    PMID: 29911437 DOI: 10.1080/14786419.2018.1486310
    Chemical modification of medicines from natural product-based molecules has become of interest in recent years. In this study, a series of halogenated azo derivatives 1a-d were synthesised via coupling reaction, followed by Steglich esterification with aspirin (a natural product derivative) to form azo derivatives 2a-d. While, halogenated azo-aspirin 3a-d were synthesised via direct coupling reaction of aspirin and diazonium salt. Bacteriostatic activity was demonstrated against E. coli and S. aureus via turbidimetric kinetic method. Compound 3a-d showed excellent antibacterial activities against E. coli (MIC 75-94 ppm) and S. aureus (MIC 64-89 ppm) compared to ampicillin (MIC 93 and 124 ppm respectively), followed by 1a-d and 2a-d. The presence of reactive groups of -OH, N=N, C=O and halogens significantly contribute excellent interaction towards E. coli and S. aureus. Molecular dockings analysis of 3a against MIaC protein showed binding free energy of -7.2 kcal/mol (E. coli) and -6.6 kcal/mol (S. aureus).
    Matched MeSH terms: Escherichia coli Proteins/metabolism; Escherichia coli Proteins/chemistry
  9. Saad SM, Abdullah J, Rashid SA, Fen YW, Salam F, Yih LH
    Mikrochim Acta, 2019 11 19;186(12):804.
    PMID: 31745737 DOI: 10.1007/s00604-019-3913-8
    A fluorometric assay is described for highly sensitive quantification of Escherichia coli O157:H7. Reporter oligos were immobilized on graphene quantum dots (GQDs), and quencher oligos were immobilized on gold nanoparticles (AuNPs). Target DNA was co-hybridized with reporter oligos on the GQDs and quencher oligos on AuNPs. This triggers quenching of fluorescence (with excitation/emission peaks at 400 nm/530 nm). On introducing target into the system, fluorescence is quenched by up to 95% by 100 nM concentrations of target oligos having 20 bp. The response to the fliC gene of E. coli O157:H7 increases with the logarithm of the concentration in the range from 0.1 nM to 150 nM. The limit of detection is 1.1 ± 0.6 nM for n = 3. The selectivity and specificity of the assay was confirmed by evaluating the various oligos sequences and PCR product (fliC gene) amplified from genomic DNA of the food samples spiked with E. coli O157:H7. Graphical abstractSchematic representation of fluorometric assay for highly sensitive quantification of Escherichia coli O157:H7 based on fluorescence quenching gene assay for fliC gene of E. coli O157:H7.
    Matched MeSH terms: Escherichia coli Proteins/genetics
  10. Zaman K, Rahim F, Taha M, Wadood A, Shah SAA, Ahmed QU, et al.
    Sci Rep, 2019 11 05;9(1):16015.
    PMID: 31690793 DOI: 10.1038/s41598-019-52100-0
    Here in this study regarding the over expression of TP, which causes some physical, mental and socio problems like psoriasis, chronic inflammatory disease, tumor angiogenesis and rheumatoid arthritis etc. By this consideration, the inhibition of this enzyme is vital to secure life from serious threats. In connection with this, we have synthesized twenty derivatives of isoquinoline bearing oxadiazole (1-20), characterized through different spectroscopic techniques such as HREI-MS, 1H- NMR and 13C-NMR and evaluated for thymidine phosphorylase inhibition. All analogues showed outstanding inhibitory potential ranging in between 1.10 ± 0.05 to 54.60 ± 1.50 µM. 7-Deazaxanthine (IC50 = 38.68 ± 1.12 µM) was used as a positive control. Through limited structure activity relationships study, it has been observed that the difference in inhibitory activities of screened analogs are mainly affected by different substitutions on phenyl ring. The effective binding interactions of the most active analogs were confirmed through docking study.
    Matched MeSH terms: Escherichia coli Proteins/metabolism; Escherichia coli Proteins/chemistry
  11. Nhu NTK, Phan MD, Peters KM, Lo AW, Forde BM, Min Chong T, et al.
    mBio, 2018 08 21;9(4).
    PMID: 30131362 DOI: 10.1128/mBio.01462-18
    Curli are bacterial surface-associated amyloid fibers that bind to the dye Congo red (CR) and facilitate uropathogenic Escherichia coli (UPEC) biofilm formation and protection against host innate defenses. Here we sequenced the genome of the curli-producing UPEC pyelonephritis strain MS7163 and showed it belongs to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. MS7163 produced curli at human physiological temperature, and this correlated with biofilm growth, resistance of sessile cells to the human cationic peptide cathelicidin, and enhanced colonization of the mouse bladder. We devised a forward genetic screen using CR staining as a proxy for curli production and identified 41 genes that were required for optimal CR binding, of which 19 genes were essential for curli synthesis. Ten of these genes were novel or poorly characterized with respect to curli synthesis and included genes involved in purine de novo biosynthesis, a regulator that controls the Rcs phosphorelay system, and a novel repressor of curli production (referred to as rcpA). The involvement of these genes in curli production was confirmed by the construction of defined mutants and their complementation. The mutants did not express the curli major subunit CsgA and failed to produce curli based on CR binding. Mutation of purF (the first gene in the purine biosynthesis pathway) and rcpA also led to attenuated colonization of the mouse bladder. Overall, this work has provided new insight into the regulation of curli and the role of these amyloid fibers in UPEC biofilm formation and pathogenesis.IMPORTANCE Uropathogenic Escherichia coli (UPEC) strains are the most common cause of urinary tract infection, a disease increasingly associated with escalating antibiotic resistance. UPEC strains possess multiple surface-associated factors that enable their colonization of the urinary tract, including fimbriae, curli, and autotransporters. Curli are extracellular amyloid fibers that enhance UPEC virulence and promote biofilm formation. Here we examined the function and regulation of curli in a UPEC pyelonephritis strain belonging to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. Curli expression at human physiological temperature led to increased biofilm formation, resistance of sessile cells to the human cationic peptide LL-37, and enhanced bladder colonization. Using a comprehensive genetic screen, we identified multiple genes involved in curli production, including several that were novel or poorly characterized with respect to curli synthesis. In total, this study demonstrates an important role for curli as a UPEC virulence factor that promotes biofilm formation, resistance, and pathogenesis.
    Matched MeSH terms: Escherichia coli Proteins/genetics*; Escherichia coli Proteins/metabolism
  12. Goh KGK, Phan MD, Forde BM, Chong TM, Yin WF, Chan KG, et al.
    mBio, 2017 10 24;8(5).
    PMID: 29066548 DOI: 10.1128/mBio.01558-17
    Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract and bloodstream infections and possesses an array of virulence factors for colonization, survival, and persistence. One such factor is the polysaccharide K capsule. Among the different K capsule types, the K1 serotype is strongly associated with UPEC infection. In this study, we completely sequenced the K1 UPEC urosepsis strain PA45B and employed a novel combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon-directed insertion site sequencing (TraDIS) to identify the complement of genes required for capsule production. Our analysis identified known genes involved in capsule biosynthesis, as well as two additional regulatory genes (mprA and lrhA) that we characterized at the molecular level. Mutation of mprA resulted in protection against K1 phage-mediated killing, a phenotype restored by complementation. We also identified a significantly increased unidirectional Tn5 insertion frequency upstream of the lrhA gene and showed that strong expression of LrhA induced by a constitutive Pcl promoter led to loss of capsule production. Further analysis revealed loss of MprA or overexpression of LrhA affected the transcription of capsule biosynthesis genes in PA45B and increased sensitivity to killing in whole blood. Similar phenotypes were also observed in UPEC strains UTI89 (K1) and CFT073 (K2), demonstrating that the effects were neither strain nor capsule type specific. Overall, this study defined the genome of a UPEC urosepsis isolate and identified and characterized two new regulatory factors that affect UPEC capsule production.IMPORTANCE Urinary tract infections (UTIs) are among the most common bacterial infections in humans and are primarily caused by uropathogenic Escherichia coli (UPEC). Many UPEC strains express a polysaccharide K capsule that provides protection against host innate immune factors and contributes to survival and persistence during infection. The K1 serotype is one example of a polysaccharide capsule type and is strongly associated with UPEC strains that cause UTIs, bloodstream infections, and meningitis. The number of UTIs caused by antibiotic-resistant UPEC is steadily increasing, highlighting the need to better understand factors (e.g., the capsule) that contribute to UPEC pathogenesis. This study describes the original and novel application of lytic capsule-specific phage killing, saturated Tn5 transposon mutagenesis, and high-throughput transposon-directed insertion site sequencing to define the entire complement of genes required for capsule production in UPEC. Our comprehensive approach uncovered new genes involved in the regulation of this key virulence determinant.
    Matched MeSH terms: Escherichia coli Proteins/genetics*; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism
  13. Yu CY, Ang GY, Chong TM, Chin PS, Ngeow YF, Yin WF, et al.
    J Antimicrob Chemother, 2017 04 01;72(4):1253-1255.
    PMID: 28031273 DOI: 10.1093/jac/dkw541
    Matched MeSH terms: Escherichia coli Proteins/genetics*
  14. Hancock SJ, Phan MD, Peters KM, Forde BM, Chong TM, Yin WF, et al.
    PMID: 27872077 DOI: 10.1128/AAC.01740-16
    Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of blaNDM-positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this blaNDM-containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies.
    Matched MeSH terms: Escherichia coli Proteins/genetics
  15. Kaikabo AA, AbdulKarim SM, Abas F
    Poult Sci, 2017 Feb 01;96(2):295-302.
    PMID: 27702916 DOI: 10.3382/ps/pew255
    Disease inflicted by avian pathogenic Escherichia coli (APEC) causes economic losses and burden to the poultry industry worldwide. In this study, the efficacy of chitosan nanoparticles loaded ΦKAZ14 (C-ΦKAZ14 NPs) as an oral biological therapy for Colibacillosis was evaluated. C-ΦKAZ14 NPs containing 10(7) PFU/ml of ΦKAZ14 (Myoviridae; T4-like coliphage) bacteriophage were used to treat experimentally APEC-infected COBB 500 broiler chicks. C-ΦKAZ14 NPs and ΦKAZ14 bacteriophage were administered orally in a single dose. The clinical symptoms, mortality, and pathology in the infected birds were recorded and compared with those of control birds that did not receive C-ΦKAZ14 NPs or naked ΦKAZ14 bacteriophage. The results showed that C-ΦKAZ14 NP intervention decreased mortality from 58.33 to 16.7% with an increase in the protection rate from 42.00 to 83.33%. The bacterial colonization of the intestines of infected birds was significantly higher in the untreated control than in the C-ΦKAZ14 NP-treated group (2.30×10(9) ± 0.02 and 0.79×10(3) ± 0.10 CFU/mL, respectively) (P ≤ 0.05). Similarly, a significant difference in the fecal shedding of Escherichia coli was observed on d 7 post challenge between the untreated control and the C-ΦKAZ14 NP-treated group (2.35×10(9) ± 0.05 and 1.58×10(3) ± 0.06 CFU/mL, respectively) (P ≤ 0.05). Similar trends were observed from d 14 until d 21 when the experiment was terminated. Treatment with C-ΦKAZ14 NPs improved the body weights of the infected chicks. A difference in body weight on d 7 post challenge was observed between the untreated control and the C-ΦKAZ14 NP-treated group (140 ± 20 g and 160 ± 20 g, respectively). The increase was significant (P ≤ 0.05) on d 21 between the 2 groups (240 ± 30 g and 600 ± 80 g, respectively). Consequently, the clinical signs and symptoms were ameliorated upon treatment with C-ΦKAZ14 NPs compared with infected untreated birds. In all, based on the results, it can be concluded that the encapsulation of bacteriophage could enhance bacteriophage therapy and is a valuable approach for controlling APEC infections in poultry.
    Matched MeSH terms: Escherichia coli Proteins
  16. Afiqah RN, Paital B, Kumar S, Majeed AB, Tripathy M
    J. Mol. Recognit., 2016 11;29(11):544-554.
    PMID: 27406464 DOI: 10.1002/jmr.2554
    The inhibitory role of AgNO3 on glucose-mediated respiration in Escherichia coli has been investigated as a function of pH and temperature using Clark-type electrode, environmental scanning electron microscopy, and computational tools. In the given concentration of bacterial suspension (1 × 10(8)  CFU/ml), E. coli showed an increasing nonlinear trend of tetra-phasic respiration between 1-133 μM glucose concentration within 20 min. The glucose concentrations above 133 μM did not result any linear increment in respiration but rather showed a partial inhibition at higher glucose concentrations (266-1066 μM). In the presence of glucose, AgNO3 caused a concentration-dependent (47-1960 μM) inhibition of the respiration rate within 4 min of its addition. The respiration rate was the highest at pH 7-8 and then was decreased on either side of this pH range. The inhibitory action of AgNO3 upon bacterial respiration was the highest at 37 °C. The observations of the respiration data were well supported by the altered bacterial morphology as observed in electron microscopic study. Docking study indicated the AgNO3 binding to different amino acids of all respiratory complex enzymes in E. coli and thereby explaining its interference with the respiratory chain. Copyright © 2016 John Wiley & Sons, Ltd.
    Matched MeSH terms: Escherichia coli Proteins/metabolism; Escherichia coli Proteins/chemistry
  17. Lai YM, Zaw MT, Shamsudin SB, Lin Z
    J Infect Dev Ctries, 2016 Oct 31;10(10):1053-1058.
    PMID: 27801366 DOI: 10.3855/jidc.6944
    INTRODUCTION: Uropathogenic virulence factors have been identified by comparing the prevalence of these among urinary tract isolates and environmental strains. The uropathogenic-specific protein (USP) gene is present on the pathogenicity island (PAI) of uropathogenic Escherichia coli (UPEC) and, depending on its two diverse gene types and the sequential patterns of three open reading frame units (orfUs) following it, there is a method to characterize UPEC epidemiologically called PAIusp subtyping.
    METHODOLOGY: A total of 162 UPEC isolates from Sabah, Malaysia, were tested for the presence of the usp gene and the sequential patterns of three orfUs following it using polymerase chain reaction (PCR). In addition, by means of triplex PCR, the prevalence of the usp gene was compared with other two VFs of UPEC, namely alpha hemolysin (α-hly) and cytotoxic necrotizing factor (cnf-1) genes encoding two toxins.
    RESULTS: The results showed that the usp gene was found in 78.40% of UPEC isolates, indicating that its prevalence was comparable to that found in a previous study in Japan. The two or three orfUs were also associated with the usp gene in this study. All the PAIusp subtypes observed in Japan were present in this study, while subtype IIa was the most common in both studies. The usp gene was observed in a higher percentage of isolates when compared with α-hly and cnf-1 genes.
    CONCLUSIONS: The findings in Japan and Sabah, East Malaysia, were similar, indicating that PAIusp subtyping is applicable to the characterization of UPEC strains epidemiologically elsewhere in the world.
    Matched MeSH terms: Escherichia coli Proteins/genetics*
  18. Abuelhassan NN, Mutalib SA, Gimba FI, Yusoff WM
    Environ Sci Pollut Res Int, 2016 Sep;23(17):17553-62.
    PMID: 27234829 DOI: 10.1007/s11356-016-6954-0
    This study aimed at determining the presence and characterization of Escherichia coli and Shiga toxin-producing E. coli (STEC) from imported frozen beef meats. Seventy-four (74) frozen imported beef meat samples from two countries, India (42 samples) and Australia (32 samples), were collected and tested for E. coli. These samples were purchased from the frozen meat sections of five different supermarkets in different locations in Selangor, Malaysia, from April 2012 to October 2014. A total of 222 E. coli strains were isolated from the meat samples; 126 strains were isolated from country A (India), and 96 E. coli strains were from country of origin B (Australia), respectively. A total of 70 E. coli strains were identified and characterized. All E. coli strains were isolated into Fluorocult medium and identified using API 20E kit. All selected E. coli strains were characterized for Shiga toxin genes (stx1 and stx2). All biochemically identified E. coli in this study were further subjected to molecular detection through polymerase chain reaction (PCR) amplification and characterization using 16S ribosomal RNA (rRNA) gene of Shiga toxin-producing E. coli. Of the 70 E. coli strains, 11 strains were positive for both Shiga toxin genes (stx1 and stx2) and 11 (11/70) strains were positive for stx1 gene, while 25 (25/70) strains were positive for stx2 gene. The analysis of 16S rRNA gene of all the E. coli isolates in this study was successfully sequenced and analyzed, and based on sequence data obtained, a phylogenetic tree of the 16S rRNA gene was performed using Clustal W programme in MEGA 6.06 software. Phylogenetic tree showed that the E. coli isolates in our study cluster with the strain of E. coli isolated in other countries, which further confirm that the isolates of E. coli in this study are similar to those obtained in other studies. As a result, all the strains obtained in this study proved to be a strain of pathogenic E. coli, which may cause a serious outbreak of food-borne disease. The isolation of pathogenic E. coli strains from the imported meat samples calls for prudent management of imported meats by the relevant authorities.
    Matched MeSH terms: Escherichia coli Proteins/genetics*
  19. Mienda BS, Shamsir MS, Md Illias R
    J Biomol Struct Dyn, 2016 Aug;34(8):1705-16.
    PMID: 26513379 DOI: 10.1080/07391102.2015.1090341
    Succinic acid is an important platform chemical with a variety of applications. Model-guided metabolic engineering strategies in Escherichia coli for strain improvement to increase succinic acid production using glucose and glycerol remain largely unexplored. Herein, we report what are, to our knowledge, the first metabolic knockout of the atpE gene to have increased succinic acid production using both glucose and alternative glycerol carbon sources in E. coli. Guided by a genome-scale metabolic model, we engineered the E. coli host to enhance anaerobic production of succinic acid by deleting the atpE gene, thereby generating additional reducing equivalents by blocking H(+) conduction across the mutant cell membrane. This strategy produced 1.58 and .49 g l(-1) of succinic acid from glycerol and glucose substrate, respectively. This work further elucidates a model-guided and/or system-based metabolic engineering, involving only a single-gene deletion strategy for enhanced succinic acid production in E. coli.
    Matched MeSH terms: Escherichia coli Proteins/genetics*; Escherichia coli Proteins/metabolism*
  20. Lai YM, Zaw MT, Shamsudin SB, Lin Z
    J Microbiol Immunol Infect, 2016 Aug;49(4):591-4.
    PMID: 26212311 DOI: 10.1016/j.jmii.2015.06.002
    The putative pathogenicity island (PAI) containing the uropathogenic specific protein (usp) gene and three small open reading frames (orfU1, orfU2, and orfU3) encoding 98, 97, and 96 amino acid proteins is widely distributed among uropathogenic Escherichia coli (UPEC) strains. This PAI was designated as PAIusp. Sequencing analysis of PAIusp has revealed that the usp gene can be divided into two types - uspI and uspII - based on sequence variation at the 3' terminal region and the number and position of orfUs differ from strain to strain. Based on usp gene types and orfU sequential patterns, PAIusp can be divided into four subtypes. Subtyping of PAIusp is a useful method to characterize UPEC strains. In this study, we developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to differentiate usp gene types. This method could correctly identify the usp gene type in usp-positive UPEC strains in our laboratory.
    Matched MeSH terms: Escherichia coli Proteins/genetics*
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