- Volume 3, Issue 9, 2021
Volume 3, Issue 9, 2021
- Editorials
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Converting Access Microbiology to an open research platform: community survey results
More LessFollowing the Microbiology Society’s successful bid for a Learned Society Curation Award from the Wellcome Trust and Howard Hughes Medical Institute, the Society is converting our sound science, open access journal, Access Microbiology, to an open research platform. As part of this, we conducted a survey of our community to gauge current attitudes towards the platform and here we present some of these results. The majority of respondents (57 %) said they would always or sometimes want to remain anonymous on their peer review report, whilst 75 % of respondents said that as an author they would be happy to make the data underlying their research open. There was a clear desire for a range of research types that are often seen with sound science publications and rigorous research. An encouraging 94 % of respondents stated that the platform is somewhere they would consider publishing, demonstrating the enthusiasm in these respondents for a new publishing platform for their community. Given this data and that from our previous focus group research, the platform will launch as outlined in the original project proposal and adopt a transparent peer review model with an open data policy.
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- Research Articles
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Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India
The phylogenetic diversity of cultivable actinobacteria isolated from sponges (Haliclona spp.) and associated intertidal zone environments along the northern parts of the western coast of India were studied using 16S rRNA gene sequences. A subset of randomly selected actinobacterial cultures were screened for three activities, namely predatory behaviour, antibacterial activity and enzyme inhibition. We recovered 237 isolates from the phylum Actinobacteria belonging to 19 families and 28 genera, which could be attributed to 95 putative species using maximum-likelihood partition and 100 putative species using Bayesian partition in Poisson tree processes. Although the trends in the discovery of actinobacterial genera isolated from sponges were consistent with previous studies from different study areas, we provide the first report of nine actinobacterial species from sponges. We observed widespread non-obligate epibiotic predatory behaviour in eight actinobacterial genera and we provide the first report of predatory activity in Brevibacterium , Glutamicibacter , Micromonospora , Nocardiopsis , Rhodococcus and Rothia . Sponge-associated actinobacteria showed significantly more predatory behaviour than environmental isolates. While antibacterial activity by actinobacterial isolates mainly affected Gram-positive target bacteria with little or no effect on Gram-negative bacteria, predation targeted both Gram-positive and Gram-negative prey with equal propensity. Actinobacterial isolates from both sponges and associated environments produced inhibitors of serine proteases and angiotensin-converting enzyme. Predatory behaviour was strongly associated with inhibition of trypsin and chymotrypsin. Our study suggests that the sponges and associated environments of the western coast of India are rich in actinobacterial diversity, with widespread predatory activity, antibacterial activity and production of enzyme inhibitors. Understanding the diversity and associations among various actinobacterial activities – with each other and the source of isolation – can provide new insights into marine microbial ecology and provide opportunities to isolate novel therapeutic agents.
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Factor H binding protein (fHbp)-mediated differential complement resistance of a serogroup C Neisseria meningitidis isolate from cerebrospinal fluid of a patient with invasive meningococcal disease
During an outbreak of invasive meningococcal disease (IMD) at the University of Southampton, UK, in 1997, two Neisseria meningitidis serogroup C isolates were retrieved from a student (‘Case’), who died of IMD, and a close contact (‘Carrier’) who, after mouth-to-mouth resuscitation on the deceased, did not contract the disease. Genomic comparison of the isolates demonstrated extensive nucleotide sequence identity, with differences identified in eight genes. Here, comparative proteomics was used to measure differential protein expression between the isolates and investigate whether the differences contributed to the clinical outcomes. A total of six proteins were differentially expressed: four proteins (methylcitrate synthase, PrpC; hypothetical integral membrane protein, Imp; fructose-1,6-bisphosphate aldolase, Fba; aldehyde dehydrogenase A, AldA) were upregulated in the Case isolate, while one protein (Type IV pilus-associated protein, PilC2) was downregulated. Peptides for factor H binding protein (fHbp), a major virulence factor and antigenic protein, were only detected in the Case, with a single base deletion (ΔT366) in the Carrier fHbp causing lack of its expression. Expression of fHbp resulted in an increased resistance of the Case isolate to complement-mediated killing in serum. Complementation of fHbp expression in the Carrier increased its serum resistance by approximately 8-fold. Moreover, a higher serum bactericidal antibody titre was seen for the Case isolate when using sera from mice immunized with Bexsero (GlaxoSmithKline), a vaccine containing fHbp as an antigenic component. This study highlights the role of fHbp in the differential complement resistance of the Case and the Carrier isolates. Expression of fHbp in the Case resulted in its increased survival in serum, possibly leading to active proliferation of the bacteria in blood and death of the student through IMD. Moreover, enhanced killing of the Case isolate by sera raised against an fHbp-containing vaccine, Bexsero, underlines the role and importance of fHbp in infection and immunity.
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- Short Communications
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Disinfection of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium and Acinetobacter baumannii using Klaran WD array system
More LessHospital-associated infections (HAIs) are a major burden in healthcare systems. In this study, UVC LEDs emitting radiation from 260 to 270 nm were evaluated for effectiveness in reducing methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium and Acinetobacter baumannii . The array has four WD LEDs, each with 70 mW placed at 7 cm from test organisms. With 11.76 mJ cm−2, the study obtained 99.99% reduction (log10 reduction factor of 4) against MRSA and VRE. For A. baumannii , 9 mJ cm−2 obtained 99.999% reduction (log10 reduction factor of 5). These results present scientific evidence on how effective UVC LEDs can be used in the fight against HAIs.
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High SARS-CoV-2 viral load is associated with a worse clinical outcome of COVID-19 disease
María Eugenia Soria, Marta Cortón, Brenda Martínez-González, Rebeca Lobo-Vega, Lucía Vázquez-Sirvent, Rosario López-Rodríguez, Berta Almoguera, Ignacio Mahillo, Pablo Mínguez, Antonio Herrero, Juan Carlos Taracido, Alicia Macías-Valcayo, Jaime Esteban, Ricardo Fernandez-Roblas, Ignacio Gadea, Javier Ruíz-Hornillos, Carmen Ayuso and Celia PeralesCOVID-19 severity and progression are determined by several host and virological factors that may influence the final outcome of SARS-CoV-2-infected patients. The objective of this work was to determine a possible association between viral load, obtained from nasopharyngeal swabs, and the severity of the infection in a cohort of 448 SARS-CoV-2-infected patients from a hospital in Madrid during the first outbreak of the pandemic in Spain. To perform this, we clinically classified patients as mild, moderate and severe COVID-19 according to a number of clinical parameters such as hospitalization requirement, need of oxygen therapy, admission to intensive care units and/or death. Also, Ct values were determined using SARS-CoV-2-specific oligonucleotides directed to ORF1ab. Here we report a statistically significant association between viral load and disease severity, a high viral load being associated with worse clinical prognosis, independently of several previously identified risk factors such as age, sex, hypertension, cardiovascular disease, diabetes, obesity and lung disease (asthma and chronic obstructive pulmonary disease). The data presented here reinforce viral load as a potential biomarker for predicting disease severity in SARS-CoV-2-infected patients. It is also an important parameter in viral evolution since it relates to the numbers and types of variant genomes present in a viral population, a potential determinant of disease progression.
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Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic
More LessReverse-transcription quantitative PCR (RT-qPCR) is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). We analysed 1927 samples collected in a local public hospital during the autumn 2020 peak of the pandemic in the Czech Republic. The tests were performed using the Seegene Allplex 2019-nCov assay, which simultaneously detects three SARS-CoV-2 genes. In all samples analysed, 44.5 % were negative for all three genes, and 37.6 % were undoubtedly positive, with all three viral genes being amplified. A high degree of correlation between C t values among the genes confirmed the internal consistency of testing. Most of the positive samples were detected between the 15th and 35th cycles. We also registered a small number of samples with only one (13.2 %) or two (4.7 %) amplified genes, which may have originated from either freshly infected or already recovering patients. In addition, we did not detect any potentially false-positive samples from low-prevalence settings. Our results document that PCR testing represents a reliable and robust method for routine diagnostic detection of SARS-CoV-2.
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- Case Reports
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Melioidosis in Bihar, India: unearthing the first of many?
Melioidosis, a disease with protean clinical manifestations, is prevalent in many parts of India, with established endemic hotspots on the southern coast of the country. However, it is still underdiagnosed in many resource-poor regions of the country. We report what is, to the best of our knowledge, the first case of melioidosis diagnosed and treated in Bihar, an economically underdeveloped state in East India. The patient, a 52-year-old diabetic male, presented to the outpatient department with a fever of insidious onset along with pain and restriction of movement in the right shoulder joint and right knee joint, and swelling and tenderness of bilateral ankle joints. Radiological features were suggestive of multiple joint and organ abscesses. A diagnosis of disseminated septicaemic melioidosis was confirmed microbiologically. The patient improved clinically following aggressive treatment with meropenem and cotrimoxazole. The case highlights the need for increased clinical suspicion of melioidosis and adequate diagnostic facilities, as well as the need for early institution of appropriate empirical antibiotics in suspected cases of melioidosis in this region of the world.
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Clostridium perfringens necrotizing pancreatitis: an unusual pathogen in pancreatic necrosis infection
Pancreatic necrosis infection (PNI) accounts for about 20–40 % of severe acute pancreatitis. PNI caused by anaerobic bacteria is unusual but when they present, Clostridium perfringens is the microorganism most commonly involved. We present a 60-year-old patient with a previous history of SARS-CoV-2, diagnosed with acute pancreatitis. During the hospitalisation he developed Clostridium perfringens bacteraemia. A CT-scan showed pancreatic gas gangrene and a surgical necrosectomy was performed. Clostridium perfringens was isolated in cultures of the pancreatic tissue and collections. The patient’s clinical status improved after surgery and the appropriate medical therapy. He was discharged 76 days after admission. Nowadays, the ‘step-up approach’ is an accepted therapeutic tool in treatment of pancreatic necrosis and peripancreatic fluid collections. However, most authors suggest that Clostridum perfringens infection requires a more aggressive approach due to the high mortality associated to clostridial infection.
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Disseminated sporotrichosis in a person with human immunodeficiency virus disease
More LessIntroduction. Disseminated sporotrichosis is an incapacitating infection caused by the dimorphic fungus Sporothrix schenckii. Because this condition may mimic the presentation of tuberculosis, syphilis and other bacterial infections, the diagnosis may be missed or delayed.
Case Presentation. We describe a case of disseminated sporotrichosis in a patient with poorly controlled human immunodeficiency virus infection. The patient was initially treated for bacterial skin infections. The differential diagnosis also included tuberculosis and syphilis. Only after appropriate specimens had been sent for microbiological and histopathological investigations was the diagnosis of disseminated sporotrichosis made and appropriate treatment started. The patient showed a good clinical response to itraconazole.
Conclusion. This report highlights the importance of having a high index of suspicion of endemic mycoses when managing immunocompromised patients. The report also demonstrates that a delay in the diagnosis of sporotrichosis increases morbidity and results in unnecessary and inappropriate treatment with associated costs and adverse effects.
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Streptococcus lutetiensis neonatal meningitis with empyema
More LessStreptococcus lutetiensis has been known to cause sepsis in adults, but only one case regarding neonatal sepsis has been reported internationally, with no sequelae. We report the first case of neonatal bacteremia and meningitis with empyema caused by S. lutetiensis in the United States.
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