scholarly journals Molecular Diversity of Bacillus thuringiensis and Bioinformatics Analysis of Local Isolate of Auky Island, Padaido District in Biak Numfor Papua as a Control of Anopheles Mosquito Larvae

2021 ◽  
Author(s):  
Daniel Lantang ◽  
Arsyam Mawardi
Keyword(s):  
Molecular Diversity ◽  
Bioinformatics Analysis ◽  
Anopheles Mosquito ◽  
Mosquito Larvae ◽  
Sequencing Analysis ◽  
E Coli ◽  
16S Gene ◽  
Tree Construction ◽  
Pcr Product ◽  
Plasmid Isolation

This research aims to analyze the level of similarity and diversity among local isolates of B. thuringiensis Auky Island Padaido District in Biak Numfor Regency with NCBI gene bank base, the basis of which is to obtain B. thuringiensis isolates from jayapura local isolates that can act as controllers of Anopheles mosquito larvae. Several steps in the research are 16s gene amplification, PCR product purification, cloning using pTA2 vectors and transformation into competent E. coli Zymo 5α cells, confirmation with PCR colonies, recombinant plasmid isolation, sequencing analysis and phylogenetic tree construction. The isolates of ABNP8, ABNP9, ABNP11, ABNP12 and ABNP18 have been detected as local isolates from in Auky Island Padaido District in Biak Numfor Papua Regency that have great potential as bioinsecticides, and capable of controlling and killing Anopheles mosquito larvae. Of the five isolates, ABNP8 isolates had unique diversity and characteristics and were different from the four other isolates. Based on the similarity analysis in the MEGA7 program, the similarity rate reached 84%. Its diversity can be seen from the uniqueness of the sequence and its position in different branching dendrograms.

scholarly journals Kloning dan Analisis Bioinformatika Gen MSP1 Plasmodium falciparum Isolat Kota Jayapura

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Arsyam Mawardi ◽  
Leonardo E. Aisoi ◽  
Paula N. Lefaan
Keyword(s):  
Plasmodium Falciparum ◽  
Heat Shock ◽  
Phylogenetic Tree ◽  
Recombinant Plasmid ◽  
Bioinformatics Analysis ◽  
Competent Cell ◽  
E Coli ◽  
Competent Cells ◽  
Plasmid Isolation ◽  
Msp1 Gene

Cloning gene involves the construction of a recombinant plasmid that inserted in a competent cell. On the other hand, genetic engineering requires bioinformatic analysis to be converted into tabulation and data interpretation. The study, titled "cloning block 2 MSP1 gene of Plasmodium falciparum isolate Jayapura city and bioinformatics analysis" is aimed to improve the technique of cloning the MSP1 gene of P. falciparum, initiated the creation of DH5α competent cells, ligations and transformations, plasmid isolation, confirmation the recombinant plasmid and able to perform bioinformatics analysis and construct phylogenetic tree. This study began with the manufacture of E. coli DH5α competent cells, MSP1 gene ligation in pJET1.2/blunt vector and transformation by using the heat shock transformation method, plasmid isolation of alkali lysis method, then plasmid confirmed by PCR and sequencing method, further sequence analysis and phylogenetic tree construction. The results showed that confirmation of MSP1 gene presence in pJET1.2/blunt with PCR was successful. From a total of 4 positive colonies grown in liquid culture, then isolated plasmid and confirmed with PCR obtained electroferogram bands with a size about 1049 bp indicates the presence of MSP1 gene in plasmid. Based on the results, cloning of MSP1 gene using pJET1.2/blunt cloning vector and competent cell E. coli DH5α has been successfully performed. Bioinformatics analysis of sequencing result and phylogenetic tree were constructed successfully with 2 clusters isolate of malaria patients from Jayapura city. Key words: Bioinformatics, cloning gene, heat shock transformation, MSP1, P. falciparum.

scholarly journals 16S rDNA Sequencing analysis in identification of some multidrug resistant (MDR) bacterial isolates from clinical specimens

2020 ◽  
Vol 36 (2) ◽  
pp. 158-166
Author(s):  
M.Y. Iliyasu ◽  
R.A. Bamanga ◽  
A.F. Umar ◽  
E.B. Agbo ◽  
A. Uba
Keyword(s):  
16S Rdna ◽  
Gene Sequencing ◽  
Enterobacter Cloacae ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Sequencing Analysis ◽  
Clinical Specimens ◽  
E Coli ◽  
16S Gene ◽  
16S Rdna Pcr

Accurate identification of bacterial pathogens from clinical specimens and Multidrug Resistant (MDR) characterization is a key to empirical therapy.  Twelve (12) bacteria isolates from blood, urine and faecal samples were selected based on the ability to grow on Luria Bertani (LB) agar medium containing 100μg/ml ampicillin, identified by 16S rDNA PCR and sequencing. Identified isolates tagged; U01, U02, U03, U04, S08, U10 and U11 were  from urine specimens, S05, S06, S07 and S12 from stool, while B09 was from blood. The isolates were screened for MDR pattern according to Kirby-Bauer disc diffusion method. Conventional biochemical tests revealed that all the isolates are Escherichia coli. The 16S gene sequencing results confirmed that, ten (10) isolates had high similar sequence alignment with identified E. coli strains, while two are Enterobacter cloacae and P. aeruginosa. The antimicrobial susceptibility pattern shows that, most of the isolates (83.3%) were MDR. All the 12 isolates (100%) are resistant to Ampicillin, Cephalothin, Erythromycin, Fusidic acid, Novobiocin and Oxacillin, but sensitive to Colistin sulphate and Imipenem. Eleven isolates (91.7%) are resistant to Chloramphenicol, Cotrimoxazole, Streptomycin, Sulphatriad and Tetracycline. Eight of the 12 isolates (66.7%) are resistant to Ciprofloxacin and Ceftriaxone. Seven (58.3%) are resistant to Cefotaxime, Cefuroxime and Gentamycin. Nine (75%) are sensitive and three isolates (25%) are resistant to Augmentin. The high resistance to these antibacterial agents in this study was due to the indiscriminate use of first-line  common antibiotics like ampicillin in the study area, which is now substituted with Augmentin. Routine biochemical identification tests should always be confirmed with genotypic methods such as 16S gene sequencing, to avoid misdiagnosis, as variations do exist among some bacterial strains. Keywords: Multidrug resistance, sequencing, 16S rDNA, E. coli, Enterobacter cloacae, P. aeruginosa.

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals 166. Activity of a Novel β-lactamase Inhibitor QPX7728 Combined With β-lactams Against st258 klebsiella Pneumoniae and st131 escherchia Coli Isolates Producing β-lactamases

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S212-S213
Author(s):  
Mariana Castanheira ◽  
Jill Lindley ◽  
Timothy B Doyle ◽  
Andrew P Davis ◽  
Olga Lomovskaya
Keyword(s):  
Multidrug Resistant ◽  
Chemical Diversity ◽  
Sequencing Analysis ◽  
E Coli ◽  
Escherchia Coli ◽  
Global Spread ◽  
Encoding Genes ◽  
Center Research ◽  
Lactamase Inhibitor ◽  
Research Grant

Abstract Background ST258 K. pneumoniae and ST131 E. coli clones are considered vectors for the global spread of multidrug resistance. We evaluated the activity of β-lactams in combination with QPX7728, a novel β-lactamase inhibitor active against all β-lactamase classes, against a collection of 210 isolates belonging to these clones collected from a worldwide surveillance study. Methods A total of 118 ST258 K. pneumoniae and 92 ST131 E. coli (single loci variant also included) were susceptibility tested by reference broth microdilution against various β-lactams ± QPX7728 and comparator agents. All isolates were screened for β-lactamases using whole genome sequencing analysis. Results All β-lactam agents had limited activity against 118 ST258 K. pneumoniae (1.7–7.6% susceptible). Among these, 104 carried carbapenemase-encoding genes: 66 KPC variants, 20 NDM and 17 OXA-48-like. One isolate carried 2 carbapenemases. The addition of QPX7728 at 4 mg/L or 8 mg/L lowered the MICs for cefepime (MIC50/90, 0.25/1 mg/L and MIC50/90, 0.12/0.5 mg/L), ceftolozane (MIC50/90, 0.5/ > 32 mg/L and MIC50/90, 0.25/16 mg/L), ertapenem (MIC50/90, 0.12/2 mg/L and MIC50/90, 0.06/0.5 mg/L), and meropenem (MIC50/90, 0.06/0.5 mg/L and MIC50/90, 0.03/0.12 mg/L; Table). QPX7728 at 4 mg/L reduced the ceftibuten (MIC50/90, 0.25/8 mg/L) or tebipenem (MIC50/90, 0.12/2 mg/L) MICs for ST258 isolates. E. coli ST131 carried mainly CTX-M variant (85 isolates), but 6 isolates harbored carbapenemases. Carbapenems were the only β-lactams displaying > 80.0% activity against ST131 E. coli, followed by piperacillin-tazobactam (79.3% susceptible). Only 5.4%and 41.3% ST131 isolates were susceptible to cefepime and ceftibuten, respectively. MIC50/MIC90 values for these agents with QPX7728 were ≤ 0.015/≤ 0.015 mg/L for cefepime and ≤ 0.015/0.06 mg/L for ceftolozane with the inhibitor at 8 mg/L and ≤ 0.015/0.03 mg/L for ceftibuten with the inhibitor at 4 mg/L. Conclusion QPX7728 lowered the MICs for all agents tested to clinically achievable levels when tested against isolates multidrug resistant belonging to important clones responsible to the dissemination of KPC, CTX variants, and metallo-β-lactamases. The development of this broad β-lactamase inhibitor should be pursued. Table 1 Disclosures Mariana Castanheira, PhD, 1928 Diagnostics (Research Grant or Support)A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Amplyx Pharmaceuticals (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Fox Chase Chemical Diversity Center (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Paratek Pharma, LLC (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support) Jill Lindley, Allergan (Research Grant or Support)Qpex Biopharma (Research Grant or Support) Timothy B. Doyle, Allergan (Research Grant or Support)Allergan (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support) Olga Lomovskaya, PhD, Qpex Biopharma (Employee)

scholarly journals A PCR-Based Method of Detection and Differentiation of K88+ Adhesive Escherichia Coli

1996 ◽  
Vol 8 (4) ◽  
pp. 460-463 ◽  
Author(s):  
Mark A. Franklin ◽  
David H. Francis ◽  
Diane Baker ◽  
Alan G. Mathew
Keyword(s):  
Escherichia Coli ◽  
Enzyme Linked Immunosorbent Assay ◽  
Antigenic Variant ◽  
Variable Regions ◽  
E Coli ◽  
Clinical Assay ◽  
Pcr Product ◽  
Structural Subunit ◽  
Pcr Products ◽  
Polymerase Chain

The objective of this study was to develop a polymerase chain reaction (PCR)-based method to detect and differentiate among Escherichia coli strains containing genes for the expression of 3 antigenic variants of the fimbrial adhesin K88 (K88ab, K88ac, and K88ad). Five primers were designed that allowed detection of K88+ E. coli, regardless of antigenic variant, and the separate detection of the ab, ac, and ad variants. Primers AM005 and AM006 are 21 base pair (bp) oligomers that correspond to a region of the K88 operon that is common to all 3 antigenic variants. Primers MF007, MF008, and MF009 are 24-bp oligomers that matched variable regions specific to ab, ac, and ad, respectively. Using primers AM005 and AM006, a PCR product was obtained that corresponds to a 764-bp region within the large structural subunit of the K88 operon common to all 3 antigenic variants. Primer AM005 used with MF007, MF008, or MF009 produced PCR products approximately 500-bp in length from within the large structural subunit of the K88 operon of the 3 respective antigenic variants. Fragments were identified by rates of migration on a 1% agarose gel relative to each other as well as to BstEII-digested lambda fragments. This PCR-based method was comparable to the enzyme-linked immunosorbent assay and western blot test in the ability to differentiate between the antigenic variants. K88+ E. coli were differentiated from among laboratory strains and detected in ileal samples taken from cannulated pigs challenged with a known K88+ variant. K88+ E. coli were also detected from fecal swabs taken from newly weaned pigs, thus confirming that this PCR-based test could provide a convenient clinical assay for the detection of K88+ E. coli. Detection and differentiation of K88+ E. coli using general and specific primers was successful. PCR methods of detection should permit identification of K88+ antigenic variants regardless of the level of expression of the antigen.

scholarly journals LARVICIDAL ACTIVITY OFTITHONIA DIVERSIFOLIALEAF EXTRACT ONPERI-URBAN MOSQUITO LARVEA INABAKALIKI; ALTERNATIVE TO INSECTICIDE DEVELOPMENT.

2015 ◽  
Vol 7 (1) ◽  
pp. 1225-1228
Author(s):  
UHUO CA ◽  
OKEREKE CN ◽  
NWELE ED ◽  
OGBONNA S.U ◽  
NWANCHOR K.C ◽  
...  
Keyword(s):  
Mortality Rate ◽  
Adverse Effects ◽  
Bioactive Compounds ◽  
Larvicidal Activity ◽  
Urban Areas ◽  
Insect Pests ◽  
Anopheles Mosquito ◽  
Mosquito Population ◽  
Mosquito Larvae ◽  
Dose Dependent

The bioassay activitiesofTithonia diversifolia leave extract was conducted on the larvae of Anopheles mosquito collected at peri-urban areas of Abakaliki Ebonyi State, using the concentrations of the extract in dilutions at 50/100ml, 40/100ml, 30/100ml and 20/100ml introduced with 10 Anopheles mosquito larvae each in four replicates and allowed for 3hrs. Mean mortality rate of the larvae were observed after the first hour, thus 30%, 10%, 05% and 0% respectively while in the 2nd hour were 60%, 40%, 20% and 10% and in the 3rd hour were 80%, 60%, 50% & 30% respectively. The result thus revealed that the treatment is dose dependent and that the studied specie has some bioactive compounds that can be exploited for insect pests control hence observed to be sensitive in anopheles mosquito larvae. Therefore Tithonia diversifolialeaf extract could be used as a bioassay for the control of mosquito due to its active properties as this has exhibited adverse effects on the larvae thereby reducing the mosquito population and thus reducing the malarious infection associated with the bite of mosquito.

scholarly journals Integron Expression in Multidrug-Resistant Escherichia coli Isolated from House Flies within the Hospital

2018 ◽  
Vol 16 (5) ◽  
pp. 319-327
Author(s):  
Atchariya YOSBOONRUANG ◽  
Anong KIDDEE ◽  
Chatsuda BOONDUANG ◽  
Phannarai PIBALPAKDEE
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Hospital Environment ◽  
Sequencing Analysis ◽  
Class 1 Integron ◽  
House Flies ◽  
E Coli ◽  
Class 1 Integrons ◽  
Class 1

Escherichia coli is a serious cause of a variety of hospital-acquired infections and commonly contributes to the environment by house flies. Integrons, particularly class 1 integrons, are the genetic elements that play an important role in the horizontal transfer of antimicrobial resistance mechanism. This mechanism is commonly found in Enterobacteriaceae, especially E. coli. In this study, we aim to investigate the occurrence and antimicrobial resistance patterns of E. coli isolated from the house flies in Phayao hospital and to determine the gene expression of class 1 integrons in those isolates of E. coli. Totally, 70 isolates of E. coli were isolated from 60 house flies collected from the hospital. Fifty-seven of the isolates (81.43 %) were multidrug resistance (MDR) and highly resistant to b-lactams, tetracyclines, and sulfonamides. Of 57 isolates of MDR-E. coli, 20 isolates (35 %) were found to carry class 1 integron genes. Fifteen patterns of antimicrobial resistance occurred in the isolates of integron-positive E. coli. Most integron-positive E. coli isolates were resistant to 7 antimicrobials. Two isolates of these bacteria (10 %) were able to resist 13 out of 14 tested antimicrobials. Using PCR and sequencing analysis, an investigation showed that dfrA17-aadA5, dfrA12-aadA2 gene cassette was the most prevalent cassette (n = 10; 50 %) among the integron-positive E. coli isolates. Our results indicated that the presences of multidrug resistance and class 1 integrons were common in E. coli isolated from the houseflies in hospital. Therefore, screening for integron-positive E. coli from the hospital environment might be necessary for prevention of nosocomial infections.

scholarly journals A Study of the Essential Oils of Four Sudanese Accessions of Basil (Ocimum basilicum L.) Against Anopheles Mosquito Larvae

2009 ◽  
Vol 6 (7) ◽  
pp. 1359-1363 ◽  
Author(s):  
Azhari H. Nour ◽  
Salah A. Elhusse ◽  
Nour A. Osman ◽  
Abduelrahman H. Nour ◽  
Mashitah M. Yusoff
Keyword(s):  
Essential Oils ◽  
Ocimum Basilicum ◽  
Anopheles Mosquito ◽  
Mosquito Larvae

scholarly journals Staphylococcus aureus MazF Specifically Cleaves a Pentad Sequence, UACAU, Which Is Unusually Abundant in the mRNA for Pathogenic Adhesive Factor SraP

2009 ◽  
Vol 191 (10) ◽  
pp. 3248-3255 ◽  
Author(s):  
Ling Zhu ◽  
Koichi Inoue ◽  
Satoshi Yoshizumi ◽  
Hiroshi Kobayashi ◽  
Yonglong Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Cell Growth ◽  
Bioinformatics Analysis ◽  
Human Tissues ◽  
Regulatory Relationship ◽  
E Coli ◽  
Pathogenic Factors ◽  
Inhibit Cell Growth ◽  
Adhesive Factor

ABSTRACT Escherichia coli mRNA interferases, such as MazF and ChpBK, are sequence-specific endoribonucleases encoded by toxin-antitoxin (TA) systems present in its genome. A MazF homologue in Staphylococcus aureus (MazFSa) has been shown to inhibit cell growth when induced in E. coli. Here, we determined the cleavage site for MazFSa with the use of phage MS2 RNA as a substrate and CspA, an RNA chaperone, which prevents the formation of secondary structures in the RNA substrate. MazFSa specifically cleaves the RNA at a pentad sequence, U↓ACAU. Bioinformatics analysis revealed that this pentad sequence is significantly abundant in several genes, including the sraP gene in the S. aureus N315 strain. This gene encodes a serine-rich protein, which is known to play an important role in adhesion of the pathogen to human tissues and thus in endovascular infection. We demonstrated that the sraP mRNA became extremely unstable in comparison with the ompA mRNA only when MazFSa was induced in E. coli. Further bioinformatics analysis indicated that the pentad sequence is also significantly abundant in the mRNAs for all the pathogenic factors in S. aureus. This observation suggests a possible regulatory relationship between the MazEFSa TA module and the pathogenicity in S. aureus.

Molecular diversity survey on diarrheagenic Escherichia coli isolates among children with gastroenteritis in Fars, Iran

2021 ◽  
Author(s):  
Amir Emami ◽  
Neda Pirbonyeh ◽  
Fatemeh Javanmardi ◽  
Abdollah Bazargani ◽  
Afagh Moattari ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Diversity ◽  
Pediatric Patients ◽  
Watery Diarrhea ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Clinical Laboratories ◽  
Health Burden ◽  
Stool Specimens ◽  
Encoding Genes

Aim: To differentiate Escherichia coli isolates from diarrheal pediatric patients in clinical laboratories. Materials & methods: Patients with watery diarrhea were selected for sampling and tested for Diarrheagenic E. coli (DEC) by API kit. DEC isolates were tested for phylotyping, pathotyping and presence of determined virulence-encoding genes by specific molecular methods. Results: About 50% of isolates were detected as DECs (>55 and >31% were categorized B2 and D phylotypes respectively). Enterotoxigenic E. coli was the most and Enteroinvasive E. coli was the lowest prevalent pathotypes. csg and fim genes were the most present virulence factors. Conclusion: Typing of E. coli isolates from stool specimens will help to determine the diversity of diarrheal pathogens and take proper decisions to reduce the health burden of diarrheal diseases.

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