- Volume 2, Issue 11, 2020
Volume 2, Issue 11, 2020
- Short Communication
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Identification of a SARS-like bat coronavirus that shares structural features with the spike glycoprotein receptor-binding domain of SARS-CoV-2
More LessSARS-CoV-2 is a recently emerged coronavirus that binds angiotensin-converting enzyme 2 (ACE2) for cell entry via its receptor-binding domain (RBD) on a surface-expressed spike glycoprotein. Studies show that despite its similarities to severe acute respiratory syndrome (SARS) coronavirus, there are critical differences in key RBD residues when compared to SARS-CoV-2. Here we present a short in silico study, showing that SARS-like bat coronavirus Rs3367 shares a high conservation with SARS-CoV-2 in important RBD residues for ACE2 binding: SARS-CoV-2’s Phe486, Thr500, Asn501 and Tyr505; implicated in receptor-binding strength and host-range determination. These features were not shared with other studied bat coronaviruses belonging to the betacoronavirus genus, including RaTG13, the closest reported bat coronavirus to SARS-CoV-2’s spike protein. Sequence and phylogeny analyses were followed by the computation of a reliable model of the RBD of SARS-like bat coronavirus Rs3367, which allowed structural insight of the conserved residues. Superimposition of this model on the SARS-CoV-2 ACE2-RBD complex revealed critical ACE2 contacts are also maintained. In addition, residue Asn488Rs3367 interacted with a previously defined pocket on ACE2 composed of Tyr41, Lys353 and Asp355. When compared to available SARS-CoV-2 crystal structure data, Asn501SARS-CoV-2 showed a different interaction with the ACE2 pocket. Taken together, this study offers molecular insights on RBD-receptor interactions with implications for vaccine design.
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Shewanella algae and Microbulbifer elongatus from marine macro-algae – isolation and characterization of agar-hydrolysing bacteria
Macro-algae are a good source of agar oligosaccharides, which can be obtained through bacterial enzymatic hydrolysis. The agarase enzyme secreted by the micro-organisms cleaves the cell wall of the algae and releases agar oligosaccharides as degradation products with various applications. Agarolytic bacteria were isolated from the marine algae Kappaphycus sp., and Sargassum sp., and studied for their agar-degrading properties. Among the 70 isolates, 2 isolates (A13 and Sg8) showed agarase activity in in vitro assays. The maximum agarolytic index was recorded in the isolate Sg8 (3.75 mm and 4.29 µg ml−1 agarase activity), followed by the isolate A13 (2.53 mm and 2.6 µg ml−1 agarase activity). Optimum agarase production of isolate Sg8 was observed at pH7 and at a temperature of 25 °C in 24–48 h, whereas for isolate A13 the optimum production was at pH7 and at a temperature of 37 °C in 48 h. The identities of the agarolytic isolates (Sg8 and A13) were confirmed based on microscopy, morphological, biochemical and molecular analysis as Shewanella algae [National Center for Biotechnology Information (NCBI) GenBank accession number MK121204.1] and Microbulbifer elongatus [NCBI GenBank accession number MK825484.1], respectively.
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- Research Article
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Evaluation of LAMP for detection of Shigella from stool samples in children
Background. To assess the diagnostic accuracy of loop-mediated isothermal amplification (LAMP) for the detection of Shigella from stool samples from children.
Methods. Consecutive stool samples from children aged <13 years old who presented with acute watery diarrhoea or dysentery to the Department of Paediatrics were collected and processed in the Department of Microbiology. All the stool samples were subjected to culture, conventional PCR and LAMP. Genomic sequencing was performed for samples that were positive by LAMP but negative by both culture and conventional PCR. The LAMP results were compared to those from culture and to a composite reference standard based on culture and conventional PCR.
Results. Amongst the 374 stool samples tested, 291 samples were positive by LAMP and 213 were positive by the composite reference standard. The sensitivity of LAMP was 100 % (98.3–100 %) and its specificity was 51.6 % (43.6–59.5 %) with a disease prevalence of 57 %. The sensitivity and specificity of LAMP improved to 99.3 % (94.2–100) and 98.2 % (94.5–99.9), respectively, using latent class analysis, while assuming that genomic sequencing has perfect specificity.
Discussion. The authors have standardized the LAMP procedure for direct application to clinical stool samples. LAMP is a sensitive and specific method for the diagnosis of Shigella from stool samples of children as compared to both culture and conventional PCR.
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- Case Report
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Emerging source of infection – Mycobacterium tuberculosis in rescue dogs: a case report
Rescue dog activity is a heavily increasing form of dog charity. Imported homeless dogs represent a reservoir of zoonotic diseases putting owners, veterinarians and pathologists repeatedly at risk. The clinical signs of tuberculosis in a dog are non-specific and diagnosis is often delayed or dismissed. We present a case of 9 months of possible exposure at home and definite exposure at laparotomy and autopsy to intestinal tuberculosis in a family dog imported from Romania to Finland. Persistent gastrointestinal symptoms started 2 years after the import. Abdominal pain, diarrhoea and vomiting proceeded and led to spontaneous death. Mycobacterium tuberculosis was identified in the liver, lymph nodes and intestine at autopsy. Exposed persons were notified and follow-up was provided, and no further infections were identified within 12 months of follow-up. The heavily increasing import of companion animals presents unexpected public health risks, such as prolonged exposure to tuberculosis, of which the general public is not aware. The dramatic consequences and high costs of tuberculosis could be reduced through accessible information of the risks of imported animals to both the general public and veterinarians, in addition to availability of rapid diagnostics and proper personal protection.
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Endogenous Klebsiella endophthalmitis as the presentation of both Klebsiella liver abscess and underlying anti-IFN-3 autoimmunity
More LessThis case study is one of the first ever reported examples of infection in a patient with anti-IFN-3 autoimmunity and demonstrates how overwhelming infection can sometimes present with visual symptoms. We report the case of a previously fit middle-aged patient presenting with painless loss of vision and loss of appetite. Examination showed choroidal abscess and a pan-uveitis, leading to admission for vitreous biopsy. Klebsiella pneumoniae was isolated both in the vitreous and in blood cultures. Subsequent investigation discovered a liver abscess which was treated with percutaneous drainage. Despite the administration of intravitreal antibiotics from the time of presentation, intravenous antibiotics and vitrectomy on the same day, the patient proceeded to need enucleation 19 days later, and now has only light perception in the remaining eye. The strong association between K. pneumoniae endophthalmitis and underlying liver abscess leads to a significant mortality rate. Early diagnosis is essential, with prompt aggressive treatment with antibiotics, but sadly the visual prognosis remains poor. In cases of suspected choroidal abscess, initiation of sepsis screen and immediate empirical treatment is vital to improve this prognosis. This patient had no significant past medical history, no known immunocompromise, was not diabetic and had no recent significant foreign travel. However, further immunological analysis demonstrated the presence of anti-IFN-3 antibodies, a hitherto under-reported potential cause of increased susceptibility to infection, and so cases of sepsis in previously healthy individuals should be considered for further immunology assessment.
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Mycobacterium mucogenicum meningitis due to external ventricular drain
More LessIntroduction. Mycobacterium mucogenicum is a rare non-tuberculous organism associated with catheter-related infections when pathogenic in humans. We present the first case of an external ventricular drain (EVD)-associated M. mucogenicum meningitis.
Case presentation. A 55-year-old woman had EVD placement for obstructive hydrocephalus following traumatic subarachnoid haemorrhage. Cerebrospinal fluid (CSF) was obtained 5 days later for fever and neurological changes. M. mucogenicum was ultimately isolated from the CSF and the patient was placed on appropriate antibiotics. Her management included replacement of the EVD and a prolonged course of anti-mycobacterial antibiotics. CSF findings showed her response to therapy and neurological exam improved after 6 weeks.
Conclusion. M. mucogenicum infections are very rare and existing reports indicate that it may be a device- or catheter-related pathogen. This microorganism has not been previously associated with an EVD. Ours may be the first documented report of EVD-related M. mucogenicum infection.
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