Evaluation of 16S rRNA Hypervariable Regions for Bioweapon Species Detection by Massively Parallel SequencingRead the full article
International Journal of Microbiology publishes papers on microorganisms and their interaction with hosts and the environment. The journal covers all microbes, including bacteria, fungi, viruses, archaea, and protozoa.
Chief Editor, Professor Urakawa, is currently based at Florida Gulf Coast University as Professor of Marine and Ecological Sciences and has a background in Environmental Microbiology and Microbial Ecology.
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Characterization of Streptomyces Isolates Associated with Estuarine Fish Chanos chanos and Profiling of Their Antibacterial Metabolites-Crude-Extract
Streptomyces has been reported as an essential producer of bioactive substances, including antibiotics and other types of antimicrobials. This study investigated antibacterial-producing Streptomyces isolated from the gut of estuarine fish Chanos chanos, emphasizing screening for the producer of peptide-containing antibacterial compounds. Eighteen isolates were found during preliminary screening, in which four isolates showed the best antibacterial activities. Based on the morphological, physiological, and biochemical characterization, as well as 16S rRNA partial sequencing, all of the four isolates belonged to Streptomyces. Three isolates were suspected as novel isolate candidates based on homology presentations and phylogenetic tree analysis. Disk-diffusion assay of the metabolite-crude-extract from the isolates showed broad-spectrum inhibitory activities against Staphylococcus aureus ATCC 25923, Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa InaCC B52 with minimum inhibitory concentration and minimum bactericidal concentration ranging from 2.5–10 mg/mL and 5–10 mg/mL, respectively. The highest antibacterial activity with low MIC and MBC values was shown by isolate AIA-10. Qualitative HPLC profiling revealed that the metabolic-crude-extracts showed many peaks with intensive area at 210 and 214 nm, especially from SCA-11 and AIA-10, indicating the presence of peptide groups in the structure of the constituent compound. The results also suggested that crude extracts SCA-11 and AIA-10 had higher hydrophobicity properties than the other extracts. Further characterization of the active compound was needed to find out which compounds were responsible for the antibacterial activity. The results of this study indicated that some Streptomyces isolated from new environmental niches, i.e., gut of estuarine fish Chanos chanos, produce promising peptide-containing bioactive compounds.
Possible Role for Bacteriophages in the Treatment of SARS-CoV-2 Infection
An outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan City, China, in December 2019. Since then, the outbreak has grown into a global pandemic, and neither a vaccine nor a treatment for the disease, termed coronavirus disease 2019 (COVID-19), is currently available. The slow translational progress in the field of research suggests that a large number of studies are urgently required. In this context, this review explores the impact of bacteriophages on SARS-CoV-2, especially concerning phage therapy (PT). Bacteriophages are viruses that infect and kill bacterial cells. Several studies have confirmed that in addition to their antibacterial abilities, bacteriophages also show antiviral and antifungal properties. It has also been shown that PT is effective for building immunity against viral pathogens by reducing the activation of NF kappa B; additionally, phages produce the antiviral protein phagicin. The Ganges river in India, which originates from the Himalayan range, is known to harbor a large number of bacteriophages, which are released into the river gradually by the melting permafrost. Water from this river has traditionally been considered a therapeutic agent for several diseases. In this review, we hypothesize that the Ganges river may play a therapeutic role in the treatment of COVID-19.
Genotypic Profiling of Bacillus cereus Recovered from Some Retail Foods in Ogun State, Nigeria, and Their Phylogenetic Relationship
Identifying Bacillus cereus with conventional methods is neither specific nor rapid because of the close relatedness of the B. cereus group, hence the need for molecular methods. Genotypic profiling of B. cereus isolates from food was obtained by Random Amplified Polymorphic DNA-polymerase chain reaction (RAPD-PCR) using OPR13 primer. A dendrogram was drawn with the Numerical Taxonomy System of Statistic (NTSYS) software. Thirty of the isolates were subjected to molecular identification by 16S rDNA sequencing. The thirty sequences were deposited in GenBank for accession number. Phylogenetic relationship of the 16S rDNA sequence obtained was carried out with the Multiple Alignment using Fast Fourier Transform (MAFFT) software version 7.0. The evolutionary tree was drawn using the Molecular Evolutionary Genetics Analysis (MEGA 6) software. The dendrogram generated for the RAPD profile showed that all the strains are closely related, with a similarity coefficient of 70%. The isolates were confirmed with 16S rDNA sequencing as B. cereus. The thirty sequences deposited in GenBank were given accession numbers: KX574760–KX574769, KX610811–KX610820, MT757957-MT757963, and MT772282-MT772284. By comparing the phylogenetic relationship, eleven of the strains did not cluster with the reference strains from the GenBank but form distinct clades, which means they are likely to be of different ancestors. Conventional methods rarely differentiate bacteria of the same species into clade, neither can it describe their ancestral lineage. Therefore, it is important to employ molecular methods in identifying bacteria to give detailed information about them.
Urinary Calculi: A Microbiological and Biochemical Analysis at a Tertiary Care Hospital in Eastern Nepal
Background. The occurrence of urinary tract infection in presence of urolithiasis is frequently noted; however, microbial agents of urolithiasis and their antimicrobial susceptibility patterns remain underinvestigated. This study aimed to identify the microorganisms isolated from urine and stone matrices to determine their antimicrobial susceptibility, to find the association between the pathogens of urine and stone matrices, and to perform the biochemical analysis of stones. Methods. A total of 88 cases of urolithiasis admitted for elective stone removal at Department of surgery, B.P. Koirala Institute of Health Sciences (BPKIHS), were enrolled. Preoperative urine culture and postoperative stone culture were performed. Isolation, identification, and AST were done by the standard microbiological technique. Further qualitative biochemical analysis of stones was also attempted. Result. Among 88 stone formers recruited, culture of urine, whole stone, and nidus yielded the growth of bacteria 44, 32, and 30, respectively. Bacteria isolated from urine culture correlated with those from stone matrices with a sensitivity of 90%, specificity of 79.69%, PPV of 63.64%, and NPV of 95.45%. Escherichia coli (46.7%) was the most common bacteria followed by Klebsiella pneumoniae (16.7%) and Proteus mirabilis (13.3%) from urine and stone cultures. Almost all the uropathogens isolated were susceptible to commonly used antibiotics. Calcium oxalate (84.1%) was common biochemical constituent found in stone formers followed by calcium oxalate + phosphate (8%). Conclusions. The association of microorganism isolated from urine and nidus culture was significant that can predict the source of infective stone; however, in some cases, microorganisms and the antimicrobial susceptibility pattern from urine and nidus were different. This study emphasizes the use of appropriate antimicrobial agents to prevent the regrowth of residual stones and minimize the risk of infectious complications after surgical removal of stones.
Bacterial Profile among Patients with Suspected Bloodstream Infections in Ethiopia: A Systematic Review and Meta-Analysis
Introduction. The burden of bloodstream infections (BSIs) has been warranted in Ethiopia. Globally, the emergency and raised resistance rate of bacterial antimicrobial resistance is becoming a prominent problem, and it is difficult to treat patients having sepsis. In this review, we aimed to determine the pooled prevalence of bacterial isolates among presumptive patients with bloodstream infections in Ethiopia. Methods. A systematic search was performed from PubMed/MEDLINE, Scopus, HINARI, ScienceDirect, and Google Scholar electronic databases using PRISMA guidelines. The data analysis was carried out using STATATM version 14 after the records were cleaned and sorted out. Results. A total of 26 studies with 8,958 blood specimens and 2,382 culture-positive bacterial isolates were included for systematic review and meta-analysis. The meta-analysis derived a pooled culture-positive bacterial prevalence which was 25.78% (95% CI: 21.55–30.01%). The estimated pooled prevalence of Gram-positive and Gram-negative bacterial isolates was 15.50% (95% CI: 12.84–18.15%) and 10.48 % (95% CI: 8.32–12.63%), respectively. The two common Gram-positive bacteria isolated from patients suspected of BSIs were coagulase-negative Staphylococcus with a pooled prevalence of 5.75% (95% CI: 4.58–6.92%) and S. aureus 7.04 % (95% CI: 5.37–8.72%). Similarly, the common Gram-negative bacterial isolates and their estimated pooled prevalence were E. coli 1.69% (95% CI: 1.21–2.16%), Klebsiella species 7.04 % (95% CI: 5.37–8.72%), Pseudomonas species 0.39% (95% CI: 0.08–0.70%), Salmonella species 1.09% (95% CI: 0.79–1.38%), and Streptococcus pyogenes 0.88% (95% CI: 0.54–1.22%). Conclusion. The prevalence of bacterial isolates among presumptive patients suspected to BSIs in Ethiopia remains high. Furthermore, we found a remarkable variation in the pathogen distribution across the study setting.
Morphological and Molecular Characterization of Toxigenic Aspergillus flavus from Groundnut Kernels in Kenya
Pathogenesis of Aspergillus flavus on important agricultural products is a key concern on human health due to the synthesis and secretion of the hazardous secondary metabolite, aflatoxin. This study identified and further characterized aflatoxigenic A. flavus from groundnuts sampled from sundry shops in Kenya using integrated morphological and molecular approaches. The groundnuts were plated on potato dextrose agar for isolation and morphological observation of A. flavus based on macroscopic and microscopic features. Molecular characterization was done through amplification and comparison of the partial sequence of the ITS1-5.8S-ITS2 region. The expression analysis of aflR, aflS, aflD, aflP, and aflQ genes in the aflatoxin biosynthesis pathways was conducted to confirm the positive identification of A. flavus. The gene expression also aided to delineate toxigenic isolates of A. flavus from atoxigenic ones. Morphologically, 18 isolates suspected to be A. flavus were identified. Out of these, 14 isolates successfully amplified the 500 bp ITS region of A. flavus or Aspergillus oryzae, while 4 isolates were not amplified. All the remaining 14 isolates expressed at least one of the aflatoxigenic genes but only 5 had all the genes expressed. Partial sequencing revealed that isolates 5, 11, 12, 13, and 15 had 99.2%, 97.6%, 98.4%, 97.5%, and 100% homology, respectively, to the A. flavus isolate LUOHE, ITS-5.8S-ITS2, obtained from the NCBI database. The five isolates were accurate identification of atoxigenic A. flavus. Precise identification of toxigenic strains of A. flavus will be useful in establishing control strategies of the fungus in food products.