- Volume 2, Issue 6, 2020
Volume 2, Issue 6, 2020
- Research Article
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Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia
Acute respiratory tract infection (ARTI) is the most common infectious disease in humans worldwide. The morbidity and mortality rates are high, especially in developing countries from Southeast Asia and Africa. While ARTI is commonly associated with viruses, there is limited data on the spectrum of viruses causing ARTI in developing countries, including Indonesia. This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In total, 98 out of 200 samples (49.0 %) tested positive for viruses. Our study confirmed 64.3 % viral etiology in children and 12.2 % in adults. Viruses that were detected were Herpesviridae (15.0 %) followed by enteroviruses (12.0 %), influenza A virus (11.5 %), respiratory syncytial virus (8.0 %), Adenoviridae (6.5 %), human metapneumovirus (3.5 %), Paramyxoviridae (2.0 %), bocavirus (1.0 %) and Coronaviridae (0.5 %). The study sheds light on the viral spectrum of ARTI in children and adults in Tabanan, Bali, Indonesia
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Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation
More LessWe used transcriptome analysis by paired-end strand-specific RNA-seq to evaluate the specific changes in gene expression associated with the transition to static biofilm growth in the rhizosphere plant growth-promoting bacterium Variovorax paradoxus EPS. Triplicate biological samples of exponential growth, stationary phase and static biofilm samples were examined. DESeq2 and Rockhopper were used to identify robust and widespread shifts in gene expression specific to each growth phase. We identified 1711 protein-coding genes (28%) using DESeq2 that had altered expression greater than twofold specifically in biofilms compared to exponential growth. Fewer genes were specifically differentially expressed in stationary-phase culture (757, 12%). A small set of genes (103/6020) were differentially expressed in opposing fashions in biofilm and stationary phase, indicating potentially substantial shifts in phenotype. Gene-ontology analysis showed that the only class of genes specifically upregulated in biofilms was associated with nutrient transport, highlighting the importance of nutrient uptake in the biofilm. The biofilm-specific genes did not overlap substantially with the loci identified by mutagenesis studies, although some were present in both sets. The most highly upregulated biofilm-specific gene is predicted to be a part of the RNA degradosome, which indicates that RNA stability is used to regulate the biofilm phenotype. Two small putative proteins, Varpa_0407 and Varpa_3832, are highly expressed specifically in biofilms and are predicted to be secreted DNA-binding proteins, which may stabilize extracellular DNA as a component of the biofilm matrix. An flp/tad type-IV pilus locus (Varpa_5148–60) is strongly downregulated specifically in biofilms, in contrast with results from other systems for these pili. Mutagenesis confirms that this locus is important in surface motility rather than biofilm formation. These experimental results suggest that V. paradoxus EPS biofilms have substantial regulatory and structural novelty.
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Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2)
Background. Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source.
Results. RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source.
Conclusions. Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.
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Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India
More LessBackground. Organisms possessing the bla NDM-1 gene (responsible for carbapenem resistance) with a class-1 integron can acquire many other antibiotic resistance genes from the community sewage pool and become multidrug-resistant superbugs. In this regard, hospital sewage, which contains a large quantity of residual antibiotics, metals and disinfectants, is being recognized as a significant cause of antimicrobial resistance (AMR) origination and spread across the major centres of the world and is thus routinely investigated as a marker for tracing the origin of drug resistance. Therefore, in this study, an attempt has been made to identify and characterize the carbapenem-resistant microbes associated with integron genes amongst the organisms isolated from the effluent treatment plant (ETP) installed in a tertiary respiratory care hospital in Delhi, India.
Methods. One hundred and thirty-eight organisms belonging to Escherichia , Klebsiella , Pseudomonas and Acinetobacter spp. were collected from the incoming and outgoing sewage lines of the ETP. Carbapenem sensitivity and characterization was performed by the imipenem and imipenem-EDTA disc diffusion method. Later DNA extraction and PCR steps were performed for the Int-1 and bla NDM-1 genes.
Results. Of the 138 organisms, 86 (62.3 %) were imipenem-resistant (P<0.05). One hundred and twenty-four (89.9 %) organisms had one or both of the genes. Overall, the bla NDM-1 gene (genotypic resistance) was present in 71 % (98/138) of organisms. 53.6 % (74/138) organisms were double gene-positive (bla NDM-1 + Int-1), of which 40 were producing the metallo-beta-lactamase enzyme, making up almost 28.9 % (40/138) of the collected organisms.
Conclusion. The current study strengthens the hypothesis that Carbapenem resistant organisms are in a high-circulation burden through the human gut and hospital ETPs are providing an environment for resistance origination and amplification.
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- Short Communication
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Does salinity affect lifestyle switching in the plant pathogen Fusarium solani?
More LessSymbiotic microbes that live within plant hosts can exhibit a range in function from mutualistic to pathogenic, but the reason for this lifestyle switching remains largely unknown. Here we tested whether environmental stress, specifically salinity, is a factor that can trigger lifestyle switching in a fungus mainly known as a pathogen, Fusarium solani. F. solani was isolated from roots of Phragmites australis (common reed) in saline coastal marshes of Louisiana, USA, and we used Oryza sativa (rice) as a model organism from wetland environments to test the symbiont lifestyle. We plated rice seeds on control plates or plates with F. solani at three levels of salinity (0, 8 and 16 p.p.t.), then assessed germination and seedling growth after 20 days. Salinity strongly reduced percentage germination, slowed the timing of germination and reduced growth of rice. F. solani slowed germination, and it also caused a minor increase in root growth at medium salinity and a minor decrease in root growth at high salinity. Overall, despite being a common pathogen in other crop species (peas, beans, potatoes and many types of cucurbits), we found little evidence that F. solani has a strong pathogenic lifestyle in rice and we found weak evidence that pathogenicity may increase slightly with elevated salinity. These results have implications for both crops and native plant health in the future as soil salinization increases worldwide.
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- Case Report
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Challenges in the veterinary microbiology diagnostic laboratory: a novel Acinetobacter species as presumptive cause for feline unilateral conjunctivitis
More LessThe present study highlights challenges in the veterinary microbiology diagnostic laboratory in the identification of bacteria responsible for infections in veterinary settings, particularly when evidence-based data is lacking. A 1.8-year-old neutered male domestic cat (FIV/FeLV negative) was presented to a veterinary practice in April 2016 with a history of left unilateral mild conjunctivitis that was empirically treated with fusidic acid and chloramphenicol. In January 2017, the same animal was presented with chronic left unilateral conjunctivitis and an eye swab was submitted for microbiological culture and susceptibility testing. Significant growth was not detected in two samples tested. Finally, in February 2017 another eye swab produced a slow growing pure culture identified by VITEK 2 as Neisseria cinerea (94 % confidence). Given the morphology and multidrug resistance profile of the isolate a 16S rRNA PCR was performed for definitive identification. The nucleotide sequence of the PCR amplicon was 99 % homologous to Acinetobacter equi sp. nov. strain 114. Veterinary microbiology diagnostic laboratories play an important role worldwide, not only in preserving animal health and welfare but also in controlling the spread of zoonotic pathogens. The lack of evidence-based information on the ocular microbiome of healthy cats and the complexity of bacterial ecosystems renders the interpretation of results difficult. A further problem for both the laboratory and the clinician is the lack of interpretive criteria for antibiotic susceptibility test results for some types of infections in animals (including those caused by Acinetobacter ) and the complete unavailability of criteria for topical antibiotic preparations.
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First case report of Schistosoma japonicum in Nepal
More LessBackground. Schistosomiasis, globally, is significant public as well as veterinary health problem as it is associated with a wide range of clinical conditions in humans and animals. Schistosomiasis is mostly caused by the following species of genus Schistosoma: Schistosoma japonicum, Schistosoma haematobium, Schistosoma mekongi, Schistosoma intercalatum Schistosoma guineensis, Schistosoma malayensis and Schistosoma mansoni. S. japonicum might be considered as the most pathogenic among these species as the clinical disease caused by this parasite ranges from mild diarrhea, nausea, Katayama fever, portal hypertension, splenomegaly and ascites to liver cirrhosis and fibrosis. S. japonicum has been commonly encountered in China, the Philippines and Indonesia. According to WHO, at least 220.8 million people required preventive treatment for schistosomiasis in 2017 but only 102.3 million people were reported to have been treated. To our knowledge, there are no cases reported from Nepal. Hence, this is the first reported case of S. japonicum in Nepal.
Case presentation. A case of acute schistosomiasis due to S. japonicum was identified in CIWEC Hospital and Travel Medicine Center, Kathmandu, Nepal. The patient arrived with gastrointestinal symptoms without any pre-existing chronic illness with no evidence of travel outside of Spain since last August, but had travelled to many other countries 2 years ago. Timely diagnosis by stool routine and microscopic examination and formal-ether concentration technique led to successful treatment of the disease.
Conclusion. As the parasite has not been reported to date in Nepal, many people are unaware of its mode of infection and pathogenesis. Many laboratory workers are heedless with the egg of the parasite due to which this parasite might be misdiagnosed or undiagnosed. This case report might help laboratory workers to be sentient about the parasite and further diagnosis in future.
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Abiotrophia defectiva endophthalmitis following routine cataract surgery: the first reported case in the United Kingdom
More LessIntroduction. Abiotrophia defectiva is a fastidious organism that has been implicated in severe infections such as endocarditis in immunocompetent patients. Modern tools are available to aid identification, but the main challenge remains clinical suspicion of A. defectiva .
Case presentation. An otherwise fit and well 65-year-old female presented with reduced vision, red eye and discomfort 2 days following routine left cataract surgery. She had visual acuity of light perception only, significant anterior chamber inflammation (including hypopyon) and limited fundal view. She was diagnosed with post-operative endophthalmitis and 0.1 ml of ceftazidime (2 mg/0.1 ml) and 0.1 ml vancomycin (2 mg/0.1 ml) were injected intravitreally after vitreous aspiration. Subconjunctival cefuroxime was also injected. A repeat injection was performed on day three of admission. Gram staining revealed Gram-positive long-chain cocci, which were identified as A. defectiva . The patient was discharged on oral ciprofloxacin 500 mg twice a day with oral prednisolone 60 mg once a day; this was tapered and stopped at 8 weeks post-discharge. The left eye received dexamethasone 0.1 % 6 times a day (again, tapered over 8 weeks), moxifloxacin 5 % 6 times a day and atropine 1 % twice a day. Vision improved to 6/12 unaided (6/9.5 with pinhole) at 9 weeks post-operatively, with a clear fundal view.
Conclusion. We present a case of A. defectiva endophthalmitis following routine cataract surgery. To our knowledge, this is the first reported case in the UK and the fourth globally, which with prompt treatment ended with a good visual outcome.
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