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  1. Richardson JS, Sethi G, Lee GS, Malek SN
    BMC Complement Altern Med, 2016 Oct 12;16(1):389.
    PMID: 27729078
    Cancer has been one of the leading causes of mortality in this era. Ruta angustifolia L. Pers has been traditionally used as an abortifacient, antihelmintic, emmenagogue and ophthalmic. In Malaysia and Singapore, the local Chinese community used it for the treatment of cancer.
    Matched MeSH terms: Furocoumarins/isolation & purification
  2. Jibril S, Basar N, Sirat HM, Wahab RA, Mahat NA, Nahar L, et al.
    Phytochem Anal, 2019 Jan;30(1):101-109.
    PMID: 30288828 DOI: 10.1002/pca.2795
    INTRODUCTION: Cassia singueana Del. (Fabaceae) is a rare medicinal plant used in the traditional medicine preparations to treat various ailments. The root of C. singueana is a rich source of anthraquinones that possess anticancer, antibacterial and antifungal properties.

    OBJECTIVE: The objective of this study was to develop an ultrasound-assisted extraction (UAE) method for achieving a high extraction yield of anthraquinones using the response surface methodology (RSM), Box-Behnken design (BBD), and a recycling preparative high-performance liquid chromatography (HPLC) protocol for isolation of anthraquinones from C. singueana.

    METHODOLOGY: Optimisation of UAE was performed using the Box-Behnken experimental design. Recycling preparative HPLC was employed to isolate anthraquinones from the root extract of C. singueana.

    RESULTS: The BBD was well-described by a quadratic polynomial model (R2  = 0.9751). The predicted optimal UAE conditions for a high extraction yield were obtained at: extraction time 25.00 min, temperature 50°C and solvent-sample ratio of 10 mL/g. Under the predicted conditions, the experimental value (1.65 ± 0.07%) closely agreed to the predicted yield (1.64%). The obtained crude extract of C. singueana root was subsequently purified to afford eight anthraquinones.

    CONCLUSION: The extraction protocol described here is suitable for large-scale extraction of anthraquinones from plant extracts.

    Matched MeSH terms: Anthraquinones/isolation & purification*
  3. Ninvilai P, Nonthabenjawan N, Limcharoen B, Tunterak W, Oraveerakul K, Banlunara W, et al.
    Transbound Emerg Dis, 2018 Oct;65(5):1208-1216.
    PMID: 29520997 DOI: 10.1111/tbed.12859
    Duck Tembusu virus (DTMUV), a newly emerging virus in ducks, was first reported in China in 2010. However, an unknown severe contagious disease associated with severe neurological signs and egg production losses in ducks, resembling to DTMUV infection, was observed in Thailand since 2007. To determine the presence of DTMUV in 2007, the clinical samples from affected ducks collected in 2007 were tested for DTMUV using pathological and virological analyses. Gross and histopathological lesions of affected ducks were mostly restricted to the ovary, brain and spinal cord, and correlated with the presence of flavivirus antigen in the brain and spinal cord samples. Subsequently, DTMUV was identified by RT-PCR and nucleotide sequencing of the polyprotein gene. Phylogenetic analysis of the polyprotein gene sequence revealed that the 2007 Thai DTMUV was a unique virus, belonged within DTMUV cluster 1, but distinctively separated from the Malaysian DTMUV, which was the most closely related DTMUV. It is interesting to note that the 2007 Thai DTMUV was genetically different from the currently circulating Thai and Chinese DTMUVs, which belonged to cluster 2. Our findings indicated that the 2007 Thai DTMUV emerged earlier from a common ancestor with the recently reported DTMUVs; however, it was genetically distinctive to any of the currently circulating DTMUVs. In conclusion, our data demonstrated the presence of DTMUV in the Thai ducks since 2007, prior to the first report of DTMUV in China in 2010. This study indicates that DTMUV may have circulated in the region long before 2010 and highlights high genetic diversity of DTMUVs in Asia.
    Matched MeSH terms: Flavivirus/isolation & purification*
  4. Puah SM, Tan JAMA, Chew CH, Chua KH
    J Food Sci, 2018 Sep;83(9):2337-2342.
    PMID: 30101982 DOI: 10.1111/1750-3841.14300
    Staphylococcus aureus is able to form multilayer biofilms embedded within a glycocalyx or slime layer. Biofilm formation poses food contamination risks and can subsequently increase the risk of food poisoning. Identification of food-related S. aureus strains will provide additional data on staphylococcal food poisoning involved in biofilm formation. A total of 52 S. aureus strains isolated from sushi and sashimi was investigated to study their ability for biofilm formation using crystal violet staining. The presence of accessory gene regulator (agr) groups and 15 adhesion genes was screened and their associations in biofilm formation were studied. All 52 S. aureus strains showed biofilm production on the tested hydrophobic surface with 44% (23/52) strains classified as strong, 33% (17/52) as moderate, and 23% (12/52) as weak biofilm producers. The frequency of agr-positive strains was 71% (agr group 1 = 21 strains; agr group 2 = 2 strains; agr group 3 = 12 strains; agr group 4 = 2 strains) whereas agr-negative strains were 29% (15/52). Twelve adhesion genes were detected and 98% of the S. aureus strains carried at least one adhesion gene. The ebps was significantly (p < .05) associated with strong biofilm producing strains. In addition, eno, clfA, icaAD, sasG, fnbB, cna, and sasC were significantly higher in the agr-positive group compared to the agr-negative group. The results of this study suggest that the presence of ebps, eno, clfA, icaAD, sasG, fnbB, cna, and sasC may play an important role in enhancing the stage of biofilm-related infections and warrants further investigation.

    PRACTICAL APPLICATION: This work contributes to the knowledge on the biofilm formation and the distribution of agr groups in S. aureus strains as well as microbial surface components in recognizing adherence matrix molecules of organisms isolated from ready-to-eat sushi and sashimi. The findings provide valuable information to further study the roles of specific genes in causing biofilm-related infections.

    Matched MeSH terms: Staphylococcus aureus/isolation & purification
  5. Bates SS, Hubbard KA, Lundholm N, Montresor M, Leaw CP
    Harmful Algae, 2018 11;79:3-43.
    PMID: 30420013 DOI: 10.1016/j.hal.2018.06.001
    Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be toxigenic in Tunisian waters. The known distribution of N. navis-varingica has expanded from Vietnam to Malaysia, Indonesia, the Philippines and Australia. Furthermore, 15 new species (and one new variety) of Pseudo-nitzschia have been discovered, bringing the total to 52. Seven new species were found to produce DA, bringing the total of toxigenic species to 26. We list all Pseudo-nitzschia species, their ability to produce DA, and show their global distribution. A consequence of the extended distribution and increased number of toxigenic species worldwide is that DA is now found more pervasively in the food web, contaminating new marine organisms (especially marine mammals), affecting their physiology and disrupting ecosystems. Recent findings highlight how zooplankton grazers can induce DA production in Pseudo-nitzschia and how bacteria interact with Pseudo-nitzschia. Since 2012, new discoveries have been reported on physiological controls of Pseudo-nitzschia growth and DA production, its sexual reproduction, and infection by an oomycete parasitoid. Many advances are the result of applying molecular approaches to discovering new species, and to understanding the population genetic structure of Pseudo-nitzschia and mechanisms used to cope with iron limitation. The availability of genomes from three Pseudo-nitzschia species, coupled with a comparative transcriptomic approach, has allowed advances in our understanding of the sexual reproduction of Pseudo-nitzschia, its signaling pathways, its interactions with bacteria, and genes involved in iron and vitamin B12 and B7 metabolism. Although there have been no new confirmed cases of ASP since 1987 because of monitoring efforts, new blooms have occurred. A massive toxic Pseudo-nitzschia bloom affected the entire west coast of North America during 2015-2016, and was linked to a 'warm blob' of ocean water. Other smaller toxic blooms occurred in the Gulf of Mexico and east coast of North America. Knowledge gaps remain, including how and why DA and its isomers are produced, the world distribution of potentially toxigenic Nitzschia species, the prevalence of DA isomers, and molecular markers to discriminate between toxigenic and non-toxigenic species and to discover sexually reproducing populations in the field.
    Matched MeSH terms: Kainic Acid/isolation & purification
  6. Nik Zuraina NMN, Sarimah A, Suharni M, Hasan H, Suraiya S
    J Infect Public Health, 2018 08 07;11(6):878-883.
    PMID: 30097415 DOI: 10.1016/j.jiph.2018.07.010
    BACKGROUND: Overcrowding during the annual Hajj pilgrimage has been known to increase the risk of infectious diseases transmission. Despite the high prevalence of respiratory illness among Malaysian Hajj pilgrims, knowledge about the etiologic pathogens is yet very limited. Thus, this study aimed to determine the spectrum of bacterial respiratory pathogens among the Hajj pilgrims returning to Malaysia in year 2016.

    METHODS: Expectorated sputum specimens were collected from the Hajj pilgrims with symptomatic respiratory tract infections (RTIs). Subsequently, the bacterial pathogens were identified using the standard bacteriological culture method and Vitek II system.

    RESULTS: This study indicated that 255 (87.33%) out of 292 cultured sputa were positive with at least one potential pathogenic bacteria. Out of 345 total bacterial isolates, 60% (n=207) were Haemophilus influenzae, which was associated with both single bacterium infection (132/173, 76.3%) and multiple bacterial infections (75/82, 91.5%). The other bacterial isolates included; Klebsiella pneumoniae (n=37, 10.7%), Moraxella catarrhalis (n=27, 7.8%), Haemophilus parainfluenzae (n=25, 7.2%), Streptococcus group G (n=18, 5.2%), Klebsiella spesies (n=16, 4.6%), Streptococcus pneumoniae (n=11, 3.2%) and few other organisms.

    CONCLUSION: High frequency of H. influenzae was isolated from Malaysian Hajj pilgrims, especially those with respiratory symptoms. Further study should evaluate the actual pathogenicity of the organism and the interactions between the respiratory microbiota towards developing effective prevention strategies of RTIs among the local pilgrims.

    Matched MeSH terms: Haemophilus influenzae/isolation & purification*
  7. Khairil Mokhtar NF, El Sheikha AF, Azmi NI, Mustafa S
    J Sci Food Agric, 2020 Mar 15;100(4):1687-1693.
    PMID: 31803942 DOI: 10.1002/jsfa.10183
    BACKGROUND: The growth of halal food consumption worldwide has resulted in an increase in the request for halal authentication. DNA-based detection using powerful real-time polymerase chain reaction (PCR) technique has been shown to be highly specific and sensitive authentication tool. The efficient DNA extraction method in terms of quality and quantity is a backbone step to obtain successful real-time PCR assays. In this study, different DNA extraction methods using three lysis buffers were evaluated and developed to recommend a much more efficient method as well as achieve a successful detection using real-time PCR.

    RESULTS: The lysis buffer 2 (LB2) has been shown to be the best lysis buffer for DNA extraction from both raw and processed meat samples comparing to other lysis buffers tested. Hence, the LB2 has been found to be ideal to detect meat and porcine DNAs by real-time PCR using pairs of porcine specific primers and universal primers which amplified at 119 bp fragment and 93 bp fragment, respectively. This assay allows detection as low as 0.0001 ng of DNA. Higher efficiency and sensitivity of real-time PCR via a simplified DNA extraction method using LB2 have been observed, as well as a reproducible and high correlation coefficient (R2  = 0.9979) based on the regression analysis of the standard curve have been obtained.

    CONCLUSION: This study has established a fast, simple, inexpensive and efficient DNA extraction method that is feasible for raw and processed meat products. This extraction technique allows an accurate DNA detection by real-time PCR and can also be implemented to assist the halal authentication of various meat-based products available in the market. © 2019 Society of Chemical Industry.

    Matched MeSH terms: DNA/isolation & purification*
  8. Samrot AV, Sahithya CS, Selvarani A J, Pachiyappan S, Kumar S S
    Int J Nanomedicine, 2019;14:8105-8119.
    PMID: 31632021 DOI: 10.2147/IJN.S214236
    Background: Super-paramagnetic iron oxide nanoparticles (SPIONs) are widely used metal nanoparticles for various applications for its magnetic property and biocompatibility. In recent years, pollution of our environment especially with heavy metals in waterbodies has become a major threat and has left us very minimal sources of freshwater to drink. SPIONs or surface modified SPIONs can be used to remove these heavy metals.

    Methods: SPIONs were synthesized by co-precipitation method and further coated with a biopolymer, chitosan. Chromium solution was treated with the synthesized SPIONs to study the efficiency of chromium removal by surface adsorption. Later, the adsorption was analysed by direct and indirect analysis methods using UV-VIS spectrophotometry and isotherm studies.

    Results: Stable chitosan-coated SPIONs were synthesized and they adsorbed chromium better than the uncoated SPIONs, where it was adsorbing up to 100 ppm. Adsorption was found to be increasing with decrease in pH.

    Conclusion: The surface-modified SPIONs expressed cumulative adsorption action. Even after the adsorption studies, chitosan-coated SPIONs were possessing magnetic property. Thus, the surface-modified SPIONs can become an ideal nanotechnology tool to remove the chromium from groundwater.

    Matched MeSH terms: Chromium/isolation & purification*
  9. Appaturi JN, Pulingam T, Thong KL, Muniandy S, Ahmad N, Leo BF
    Anal Biochem, 2020 01 15;589:113489.
    PMID: 31655050 DOI: 10.1016/j.ab.2019.113489
    Rapid detection of foodborne pathogens is crucial as ingestion of contaminated food products may endanger human health. Thus, the objective of this study was to develop a biosensor using reduced graphene oxide-carbon nanotubes (rGO-CNT) nanocomposite via the hydrothermal method for accurate and rapid label-free electrochemical detection of pathogenic bacteria such as Salmonella enterica. The rGO-CNT nanocomposite was characterized using Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray diffraction and transmission electron microscopy. The nanocomposite was dropped cast on the glassy carbon electrode and further modified with amino-modified DNA aptamer. The resultant ssDNA/rGO-CNT/GCE aptasensor was then used to detect bacteria by using differential pulse voltammetry (DPV) technique. Synergistic effects of aptasensor was evident through the combination of enhanced electrical properties and facile chemical functionality of both rGO and CNT for the stable interface. Under optimal experimental conditions, the aptasensor could detect S. Typhimurium in a wide linear dynamic range from 101 until 108 cfu mL-1 with a 101 cfu mL-1 of the limit of detection. This aptasensor also showed good sensitivity, selectivity and specificity for the detection of microorganisms. Furthermore, we have successfully applied the aptasensor for S. Typhimurium detection in real food samples.
    Matched MeSH terms: Salmonella typhimurium/isolation & purification*
  10. Tan LL, Ahmed SA, Ng SK, Citartan M, Raabe CA, Rozhdestvensky TS, et al.
    Food Chem, 2020 Mar 30;309:125654.
    PMID: 31678669 DOI: 10.1016/j.foodchem.2019.125654
    A specialized DNA extraction method and a SYBR Green quantitative polymerase chain reaction (SyG-qPCR) assay were combined to generate a ready-to-use kit for rapid detection of porcine admixtures in processed meat products. Our qPCR assay utilized repetitive LINE-1 elements specific to the genome of Sus scrofa domesticus (pig) as a target and incorporated internal controls. We improved the genomic DNA extraction method, and reduced extraction times to the minimum. The method was validated for specificity, sensitivity (0.001% w/w) and robustness, and values were compared with those of a commercially available kit. We also tested our method using 121 processed food products and consistently detected amplification only in samples containing pork. Due to its efficiency and cost-effectiveness, our method represents a valuable new method for detecting food adulteration with pork that is superior to existing quality control approaches.
    Matched MeSH terms: DNA/isolation & purification
  11. Ng IS, Song CP, Ooi CW, Tey BT, Lee YH, Chang YK
    Int J Biol Macromol, 2019 Aug 01;134:458-468.
    PMID: 31078593 DOI: 10.1016/j.ijbiomac.2019.05.054
    Nanofiber membrane chromatography integrates liquid membrane chromatography and nanofiber filtration into a single-step purification process. Nanofiber membrane can be functionalised with affinity ligands for promoting binding specificity of membrane. Dye molecules are a good affinity ligand for nanofiber membrane due to their low cost and high binding affinity. In this study, a dye-affinity nanofiber membrane (P-Chitosan-Dye membrane) was prepared by using polyacrylonitrile nanofiber membrane modified with chitosan molecules and immobilized with dye molecules. Reactive Orange 4, commercially known as Procion Orange MX2R, was found to be the best dye ligand for membrane chromatography. The binding capacity of P-Chitosan-Dye membrane for lysozyme was investigated under different operating conditions in batch mode. Furthermore, desorption of lysozyme using the P-Chitosan-Dye membrane was evaluated systematically. The recovery percentage of lysozyme was found to be ~100%. The optimal conditions obtained from batch-mode study were adopted to develop a purification process to separate lysozyme from chicken egg white. The process was operated continuously using the membrane chromatography and the characteristic of the breakthrough curve was evaluated. At a lower flow rate (i.e., 0.1 mL/min), the total recovery of lysozyme and purification factor of lysozyme were 98.59% and 56.89 folds, respectively.
    Matched MeSH terms: Muramidase/isolation & purification*
  12. Chang CY, Lau NLJ, Currie BJ, Podin Y
    BMC Infect Dis, 2020 Mar 06;20(1):201.
    PMID: 32143598 DOI: 10.1186/s12879-020-4937-8
    BACKGROUND: Melioidosis is a potentially life-threatening infection caused by the Gram-negative bacterium Burkholderia pseudomallei. Melioidosis is difficult to diagnose due to its diverse clinical manifestations, which often delays administration of appropriate antibiotic therapy.

    CASE PRESENTATION: Melioidosis is uncommon in pregnancy but both spontaneous abortion and neonatal melioidosis have been reported. We report a case of bacteraemic melioidosis in a young woman with a subsequent spontaneous abortion, with B. pseudomallei cultured from a high vaginal swab as well as blood.

    CONCLUSION: It remains unclear in this and previously reported cases as to whether the maternal melioidosis was sexually transmitted.

    Matched MeSH terms: Burkholderia pseudomallei/isolation & purification
  13. Davidson G, Chua TH, Cook A, Speldewinde P, Weinstein P
    Malar J, 2019 Mar 08;18(1):66.
    PMID: 30849978 DOI: 10.1186/s12936-019-2693-2
    Plasmodium knowlesi is a zoonotic malaria parasite normally residing in long-tailed and pig-tailed macaques (Macaca fascicularis and Macaca nemestrina, respectively) found throughout Southeast Asia. Recently, knowlesi malaria has become the predominant malaria affecting humans in Malaysian Borneo, being responsible for approximately 70% of reported cases. Largely as a result of anthropogenic land use changes in Borneo, vectors which transmit the parasite, along with macaque hosts, are both now frequently found in disturbed forest habitats, or at the forest fringes, thus having more frequent contact with humans. Having access to human hosts provides the parasite with the opportunity to further its adaption to the human immune system. The ecological drivers of the transmission and spread of P. knowlesi are operating over many different spatial (and, therefore, temporal) scales, from the molecular to the continental. Strategies to prevent and manage zoonoses, such as P. knowlesi malaria require interdisciplinary research exploring the impact of land use change and biodiversity loss on the evolving relationship between parasite, reservoir hosts, vectors, and humans over multiple spatial scales.
    Matched MeSH terms: Plasmodium knowlesi/isolation & purification*
  14. 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: Burkholderiaceae/isolation & purification
  15. Uti DE, Atangwho IJ, Eyong EU, Umoru GU, Egbung GE, Rotimi SO, et al.
    PMID: 31339080 DOI: 10.2174/1871530319666190724114729
    BACKGROUND: Obesity is characterized by increased body fat and involves an imbalance between the synthesis and degradation of lipids.

    OBJECTIVE: The study aimed to investigate the effect of African walnuts (Tetracarpidium conophorum) on lipids storage and the regulatory enzymes of hepatic lipid metabolism in obese rats.

    METHODS: Nuts were extracted in ethanol (WE) and further separated to obtain the ethyl-acetate fraction (ET) and the residue (RES). These were administered orally to 3 groups of monosodium glutamate- obese rats (n = 6), respectively, for 6 weeks. Other groups in the study were: normal (NC), obese control (OC) and standard control (SC) which received orlistat. Hepatic total lipids, total phospholipids, triacylglycerol (TG), total cholesterol (TCHOL), 3-hydroxyl-3-methylglutaryl-CoA (HMG-CoA) reductase and paraoxonase were studied.

    RESULTS: Total lipids, TG and TCHOL which increased in OC compared to NC group, decreased. HMG-CoA reductase activity decreased in the 3 study groups relative to OC. Paraoxonase activity which decreased in OC was up-regulated, while the magnitude of hepatic cholesterol decreased from 94.32 % in OC to 52.19, 65.43 and 47.04 % with WE, ET and RES, respectively. Flavonoids, alkaloids, glycosides, tannins and saponins were detected in the nut. GC-MS analysis revealed 16, 18 and 10 volatile components in WE, ET and RES, respectively. Unsaturated fatty acids (linolenic acids: 33.33, 47.95 and 50.93 %, and α-linolenic acids: 25, 19.66 and 26.63 %) in WE, ET and RES, respectively, are the most abundant, and likely to be responsible for the observed activity.

    CONCLUSION: African walnuts can prevent hepatic lipid accumulation through reciprocal actions on HMG-CoA reductase and paraoxonase in obesity.

    Matched MeSH terms: Plant Extracts/isolation & purification
  16. Lowbridge C, Fadhil SAM, Krishnan GD, Schimann E, Karuppan RM, Sriram N, et al.
    BMC Infect Dis, 2020 Mar 30;20(1):255.
    PMID: 32228479 DOI: 10.1186/s12879-020-04983-y
    BACKGROUND: Gastrointestinal tuberculosis (TB) is diagnostically challenging; therefore, many cases are treated presumptively. We aimed to describe features and outcomes of gastrointestinal TB, determine whether a clinical algorithm could distinguish TB from non-TB diagnoses, and calculate accuracy of diagnostic tests.

    METHODS: We conducted a prospective cohort study of hospitalized patients in Kota Kinabalu, Malaysia, with suspected gastrointestinal TB. We recorded clinical and laboratory characteristics and outcomes. Tissue samples were submitted for histology, microscopy, culture and GeneXpert MTB/RIF®. Patients were followed for up to 2 years.

    RESULTS: Among 88 patients with suspected gastrointestinal TB, 69 were included in analyses; 52 (75%) had a final diagnosis of gastrointestinal TB; 17 had a non-TB diagnosis. People with TB were younger (42.7 versus 61.5 years, p = 0.01) and more likely to have weight loss (91% versus 64%, p = 0.03). An algorithm using age  26 g/L, platelets > 340 × 109/L and immunocompromise had good specificity (96.2%) in predicting TB, but very poor sensitivity (16.0%). GeneXpert® performed very well on gastrointestinal biopsies (sensitivity 95.7% versus 35.0% for culture against a gold standard composite case definition of confirmed TB). Most patients (79%) successfully completed treatment and no treatment failure occurred, however adverse events (21%) and mortality (13%) among TB cases were high. We found no evidence that 6 months of treatment was inferior to longer courses.

    CONCLUSIONS: The prospective design provides important insights for clinicians managing gastrointestinal TB. We recommend wider implementation of high-performing diagnostic tests such as GeneXpert® on extra-pulmonary samples.

    Matched MeSH terms: Mycobacterium tuberculosis/isolation & purification
  17. Asem MD, Salam N, Idris H, Zhang XT, Bull AT, Li WJ, et al.
    Int J Syst Evol Microbiol, 2020 May;70(5):3210-3218.
    PMID: 32320378 DOI: 10.1099/ijsem.0.004158
    The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida, Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2-94.9 %) and in silico DNA-DNA hybridization (52.5-62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strain.
    Matched MeSH terms: Actinobacteria/isolation & purification
  18. Mizutani Y, Iehata S, Mori T, Oh R, Fukuzaki S, Tanaka R
    Microbiologyopen, 2019 10;8(10):e890.
    PMID: 31168933 DOI: 10.1002/mbo3.890
    Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter-specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter-specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F-positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338-positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%-100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%-94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.
    Matched MeSH terms: Arcobacter/isolation & purification*
  19. Fukuda M, Uni S, Igari T, Utsumi Y, Otsuka Y, Nakatani J, et al.
    Parasitol Int, 2019 Oct;72:101943.
    PMID: 31220633 DOI: 10.1016/j.parint.2019.101943
    A 73-year-old man living in Kawamata-machi, Fukushima Prefecture, Northeastern Honshu, Japan, visited a hospital with complaints of a subcutaneous swelling that had developed on the back of his left hand. The nodule was surgically removed from the vagina fibrosa tendinis of his left forefinger. Based on the histopathological characteristics, the causative agent of this nodule was identified as a female Onchocerca dewittei japonica (Spirurida: Onchocercidae). The species identification was confirmed by cox1 gene sequencing of the worm tissues from paraffin-embedded sections of the nodule. Although 11 cases of zoonotic onchocercosis have previously been recorded in Kyushu and Western Honshu, Japan, the present findings represent the first human case of infection with O. dewittei japonica in Northeastern Honshu, Japan.
    Matched MeSH terms: Onchocerca/isolation & purification
  20. Oulghazi S, Pédron J, Cigna J, Lau YY, Moumni M, Van Gijsegem F, et al.
    Int J Syst Evol Microbiol, 2019 Aug;69(8):2440-2444.
    PMID: 31166160 DOI: 10.1099/ijsem.0.003497
    Strains 2B12T, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947T (=CFBP 8607T) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12T (=CFBP 8650T=LMG 30903T) as the type strain.
    Matched MeSH terms: Enterobacteriaceae/isolation & purification
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