The Open Microbiology Journal
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Published By Bentham Science

1874-2858

2021 ◽  
Vol 15 (1) ◽  
pp. 159-167
Author(s):  
Gitanjali Dass ◽  
Vrishty Sharma ◽  
Muneer Ahmad Malla ◽  
Sally Lukose ◽  
Rajesh Kumar Kori

Background: Microbes play a significant role in the degradation of biological evidence collected for forensic analysis. The present study is aimed to isolate and identify the microbes present inside the empty container used for the biological evidence collection. Methods: Bacterial isolation from the selected containers was done by cotton swab over the inner surface of the containers. Streaking was done on the surface of the three different culture plates as a Blood agar plate, Nutrient plate and MacConkey plate. The plates were placed in an incubator shaker at 37ºC for 48 hours. The colonies grown on the surface of the media were counted on and used for further study. Various biochemical assays were performed to characterize isolated bacteria. Results: Staining results suggested that the presence of Gram-positive stain (Staphylococcus, Bacillus, Corynebacterium, Clostridium) and Gram negative stain (E. coli, Enterobacteriaceae, Pseudomonas, Salmonella, Shigella, Stenotrophomonas, Bdellovibrio, Acetic acid bacteria). The Catalase and Coagulase test suggested the presence of Staphylococcus aureus, S. epidermis and S. sapropyticus. Moreover, the indole test suggested the presence of Citrobacter koseri, Kebsiella oxytoca, Proteus vulgaris etc. Some of the bacteria were urea metabolizing, including Proteus spp, Helicobacter pylori, Cryptococcus spp, Corynebacterium spp. Conclusion: This study recommends that there should be proper maintenance of the chain of custody from the collection to analysis so that evidence properly prevents degradation or contamination in the biological evidence. Extra care is needed for the collection and packing of biological evidence from the crime scene. Moreover, the collection containers, if left wide open, lead to contamination and degradation of biological evidence.


2021 ◽  
Vol 15 (1) ◽  
pp. 177-187
Author(s):  
Vrishty Sharma ◽  
Muneer Ahmad Malla ◽  
Rajesh Kumar Kori ◽  
Rajesh Singh Yadav ◽  
Zaffar Azam

Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.


2021 ◽  
Vol 15 (1) ◽  
pp. 152-157
Author(s):  
Tirasak Pasharawipas

After exposure to SARS-CoV-2, varying symptoms of COVID-19 ranging from asymptomatic symptoms to morbidity and mortality have been exhibited in each individual. SARS-CoV-2 requires various cellular molecules for penetration into a target host cell. Angiotensin-converting enzyme2 (ACE2) acts as the viral receptor molecule. After attachment, SARS-CoV-2 also requires the transmembrane protease serine-2 (TMPRSS-2) and furin molecules, which serve as co-receptors for penetration into the target cell and for subsequent replication. In the meantime, a major histocompatibility complex (MHC) is required for the induction of adaptive immune cells, especially cytotoxic T cells and helper T cells, to clear the virally infected cells. This perspective review article proposes different aspects to explain the varying symptoms of the individuals who have been exposed to SARS-CoV-2, which relates to the polymorphisms of these involved molecules.


2021 ◽  
Vol 15 (1) ◽  
pp. 168-176
Author(s):  
Uraisha Ramlucken ◽  
Krishna Suresh Babu Naidu ◽  
Patrick Govender

Background: Human Immunodeficiency Virus 1 (HIV-1) subtype C is responsible for the majority of infections of patients in Southern Africa. The HIV protease is a primary target for the development of highly efficient anti-retroviral pharmaceuticals because of its pivotal role in the maturation of the virus in the host cell. For target validation of novel HIV protease inhibitors, there is a need for the availability of an abundance of this protease. Objective: This study reports an optimized method to produce HIV-1 protease derived from HIV-1 subtype C. Methods: It involves the use of a transgenic E. coli strain that overexpresses the native form of the enzyme via inclusion bodies. A stringent method for the isolation, purification, and renaturation resulted in the production of highly pure active HIV-1 protease. In order to facilitate an increase in protease yields, an optimized growth strategy was developed. In this regard, a chemically defined medium with lower glucose content and devoid of essential amino acids of the TCA cycle was used as an alternative to the widely used nutrient-rich Luria Bertani (LB) medium. Results: Results indicated an increase in protease yield up to twice the amount, thereby making this medium an attractive alternative for increasing biomass and HIV protease production for future research. Conclusion: An optimized method for HIV-1 protease derived from HIV-1 subtype C production using chemically defined media was established. This was achieved using a known method to isolate and purify the enzyme with the use of a specialized feeding strategy.


2021 ◽  
Vol 15 (1) ◽  
pp. 188-197
Author(s):  
Anamika Dubey ◽  
Ashwani Kumar ◽  
Mohammed Latif Khan ◽  
Devendra Kumar Payasi

Background: Applications of bioinoculants for improving crop productivity may be an eco-friendly alternative to chemical fertilizers. Rhizosphere or soil-inhabiting beneficial microbes can enhance plant growth and productivity through direct and indirect mechanisms, i.e., phosphate solubilization, nutrient acquisition, phytohormone production, etc. Objective: This study is based on the hypothesis that diseases resistant plants can act as a source of potential microbes that can have good plant growth-promoting traits and bio-control potential. Methods: In this study, we have isolated the rhizobacterial strains (AKAD 2-1, AKAD 2-10, AKAD 3-5, AKAD 3-9) from the rhizosphere of a disease-resistant variety of soybean (JS-20-34) (Glycine max (L.) Merr.). These bacterial strains were further screened for various plant growth-promoting traits (phosphate solubilization, indole acetic acid (IAA), ammonia, biofilm, HCN, Exopolysaccharide (EPS), and enzyme production activity (catalase, cellulase, and chitinase)). Results: Among four, only bacterial strain AKAD 3-5 has shown plant-growth-promoting and biocontrol (98%) activity against Fusarium oxysporum. Morphological, biochemical, and molecular characterization (16S rRNA) revealed that this rhizobacterial isolate AKAD 3-5 closely resembles Micrococcus luteus (Gene bank accession: MH304279). Conclusion: Here, we conclude that this strain can be utilized to promote soybean growth under varied soil stress conditions.


2021 ◽  
Vol 15 (1) ◽  
pp. 145-151
Author(s):  
Abdulrahman A. Al-Sultan

Background: Acinetobacter baumannii strains resistant to carbapenems are a global public health problem. Objectives: The aim of the present study is to evaluate the prevalence of genetic fingerprints associated with Metallo β-lactamases in A. baumannii in addition to the clonal diversity of A. baumannii in Makkah and Al-Madinah regions of Saudi Arabia, which receive a high number of international visitors. Methods: Multi-antibiotic resistant A. baumannii isolates were investigated. Bacterial isolation was conducted employing a basic bacteriological technique after confirming the ID of isolates. The antimicrobial susceptibility test was carried out using the Vitek 2 compact system. The molecular clonal diversity of the isolates was determined by Pulse Field Gel Electrophoresis (PFGE). Clusters were analyzed with BioNumerics software version 6.5. Dice coefficient was used for calculating the similarities. Results: The results indicated resistance in 82.5% of A. baumannii isolates against the carbapenems. All the isolates were found to be sensitive to colistin, while 5% of isolates were resistant to tigecycline. The screening of carbapenem-resistant A. baumannii isolates showed that the dissemination of imipenem and meropenem resistance was 81 and 84%, respectively, while the majority of the strains were susceptible to tigecycline and colistin. The blaOXA and blaVIM were the most encountered genes in A. baumannii isolates, while ISAba1 was the prominent insertion sequence. The genetic fingerprinting results (PFGE) revealed two types of epidemic clones: monoclonal and polyclonal models of 17 clusters. Conclusion: The current investigation indicates the diversity in genetic fingerprints of carbapenem-resistant A. baumannii in Makkah and Al-Madinah region of Saudi Arabia, and that two types of epidemic clones are present. It has also been demonstrated that such clones create serious infection dissemination to other parts of the world as heavy pilgrimage traffic is received throughout the year in Makkah and Al-Madinah, especially in the Haj season.


2021 ◽  
Vol 15 (1) ◽  
pp. 139-144
Author(s):  
Maysaa El Sayed Zaki ◽  
Abd ElRahman Eid ◽  
Samah Sabry El-Kazzaz ◽  
Amr Mohamed El-Sabbagh

Background: There are insufficient data about the presence of E. albertii as a causative organism in urinary tract infection in pediatric patients. Objective: The present study aimed to detect E. albertii by polymerase chain reaction (PCR) for detection of uidA, mdh, and lysP genes among isolated E.coli from children with urinary tract infection. Methods: The present study was a cross-sectional retrograde study which was carried out on 100 isolates of phenotypically confirmed E.coli detected in urine samples of children suffering from urinary tract infection. The isolates were subjected to molecular identification by PCR for uidA, mdh, and lysP genes. Results: E. albertii was identified by PCR in 7% of the isolates and E.coli was identified in 93% of the isolates. Two mdh and lysP genes were detected for E. albertii and the uidA gene for E. coli. E. albertii isolates had marked resistance to gentamicin (71.4%), followed by resistance to ciprofloxacin (57.1%), meropenem and imipenem (42.9% each) and ESBL activity by double discs method was reported in 57.1% of the isolates. However, none of the isolates had shown resistance to nalidixic acid and only one isolate had resistance to norfloxacin. There was a statistically insignificant difference between resistance to the used antibiotics such as aztreonam (P=0.083), ampicillin/clavulanate (P=0.5), ciprofloxacin (P=0.69), gentamicin (P=0.3) and ceftazidime (P=1.00). Conclusion: The present study highlights the emergence of E. albertii as a pathogen associated with urinary tract infections in children. There is marked antibiotic resistance of this pathogen, especially toward extended spectrum beta-lactams antibiotics. The identification method depends mainly on genetic studies. Further longitudinal studies with large number of patients are required to verify the accurate prevalence of this bacterium.


2021 ◽  
Vol 15 (1) ◽  
pp. 129-138
Author(s):  
Raegan S. Hoefler ◽  
Indira T. Kudva

Background: Differences between Escherichia coli O157 (O157) strains are well-established with some of these strains being associated with major outbreaks in the US. EDL933 is one such O157 strain that caused a multistate outbreak in 1982 and has since been used as a prototype in various O157-related experiments. Objective: As O157 can readily acquire genetic mutations, we sought to determine if the genetic and phenotypic profiles of EDL933 strains from different sources would be consistent. Methods: We evaluated wild-type O157 strains stocked as EDL933 from three different laboratories, in the strain typing Polymorphic Amplified Typing Sequence (PATS) and the bovine rectal-anal junction squamous epithelial (RSE) cell- and HEp-2 cell- adherence assays. In addition, we also verified if Shiga toxins (Stx), the Locus of Enterocyte Effacement (LEE) or curli fimbriae contributed to the adherence phenotypes observed using mutant and wild-type EDL933 isolates. Results: Our results showed differences in PATS profiles and RSE cell-adherence phenotype, with no influence from the Stx or LEE genes, between EDL933 from different sources. Interestingly, the EDL933 strain that demonstrated the most contrasting diffuse adherence phenotype on RSE cells, EDL933-T, had decreased curli production that may have contributed to this phenotype. Conclusion: Our observations suggest that a comprehensive characterization of bacterial isolates, even if assigned to the same strain type prior to use in experiments, is warranted to ensure consistency and reproducibility of results.


2021 ◽  
Vol 15 (1) ◽  
pp. 120-128
Author(s):  
Izabela Chudzicka-Strugała ◽  
Iwona Gołębiewska ◽  
Grzegorz P. Brudecki ◽  
Barbara Zwoździak

The aim of this study was to draw attention to the possible consequences of improper, unhygienic use of mouth and nose covers in the context of prophylaxis against the spread of COVID-19 from the point of view of a family physician and focus on the risk of respiratory infections and skin lesions in patients, in different age groups. The use of protective masks may reduce the likelihood of infection but will not eliminate the risk of infection. However, it should be remembered that any mask, no matter how effective the filtration is or how well it seals, will have little effect if not used in conjunction with other preventive measures, including isolation of infected people, immunization, proper respiratory culture, regular, frequent replacement of masks, and hand hygiene. Additionally, certain risks associated with this form of prophylaxis should be taken into account, which, unfortunately, may also aggravate or even constitute a source of serious respiratory infections and lead to the development and aggravation of skin problems. Moreover, educating society not only on hand hygiene but also on the topic of the value of nose and mouth covers, as well as the frequency of their replacement and/or disinfection, is becoming a significant issue.


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