http://www.microbiologyresearch.org/content/journal/jmm?TRACK=RSS Please follow the links to view the content. http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001597?TRACK=RSS Staphylococcus epidermidis is the most abundant commensal bacterium of human skin. Despite protecting us from foreign invaders, S. epidermidis itself exploits human vulnerability when given the opportunity. Such opportunities arise when patients are immunocompromised or when biomedical implants present an opportunity to colonize the surface and form biofilms. S. epidermidis is one of the most frequently isolated organisms from implanted devices and from bloodstream infections. However, S. epidermidis infections are often recalcitrant to antibiotics because of biofilm-associated antibiotic tolerance. Furthermore, the emergence and spread of nearly pan-resistant strains is a considerable health concern. Symptoms can be subclinical, making diagnosis challenging, and treatment with antibiotics is inefficient. For now, infection prevention remains the best strategy available. Sandra Maria Skovdal, Nis Pedersen Jørgensen and Rikke Louise Meyer 2022-10-28T15:33:25Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001566?TRACK=RSS Rifampicin (also known as rifampin) inhibits RNA synthesis, and is used to treat tuberculosis, leprosy, staphylococcal infections and legionnaires’ disease. It can also protect at-risk populations from   Haemophilus influenzae   type b and   Neisseria meningitidis  . It is a polyketide antibiotic and is on the World Health Organization (WHO) list of essential medicines due to its critical importance to human medicine. The adverse effect of liver toxicity is controlled by testing during prolonged treatment regimes. Rifampicin’s red–orange colour can result in the colouration of sweat, tears and urine. Resistance to rifampicin arises from mutation of the target RNA polymerase or ADP ribosylation of the antibiotic or efflux. Mycobacteria may become singularly resistant to rifampicin or as part of multidrug or extensive drug resistance. Kim R. Hardie and Samuel Jacob Fenn 2022-08-05T15:30:00Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001940?TRACK=RSS Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time. Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus. Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus. Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2. Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx. Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus. Samuel González-García, Aida Hamdan-Partida, Julia Pérez-Ramos, José Félix Aguirre-Garrido, Anaíd Bustos-Hamdan and Jaime Bustos-Martínez 2024-12-04T12:30:43Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001939?TRACK=RSS Diagnosis of Clostridioides difficile infection (CDI) remains challenging as it involves in the first instance recognition (clinical awareness) of the patients’ symptoms for clinical suspicion of CDI to warrant testing, and secondly, different laboratory tests have been described for CDI. Due to the overwhelming amount of information in the literature on CDI tests and their performance, with separately published guidelines, this review aims to provide a comprehensive but concise summary of the current state of CDI diagnostic testing. Current knowledge and the impact of using different laboratory diagnostic procedures for CDI, including the most recommended approach as a two-step algorithm and the concept of diagnostic stewardship, are being discussed. This review provides an updated overview and valuable take-home messages in the field of CDI laboratory testing and highlights that timely diagnosis is important for the clinical management of CDI and that the recommended testing procedures are increasingly becoming more widely accepted. Virginie F. Viprey, Emma Clark and Kerrie A. Davies 2024-12-03T15:42:00Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001232?TRACK=RSS Given the increased reporting of multi-resistant bacteria and the shortage of newly approved medicines, researchers have been looking towards extreme and unusual environments as a new source of antibiotics. Streptomyces currently provides many of the world’s clinical antibiotics, so it comes as no surprise that these bacteria have recently been isolated from traditional medicine. Given the wide array of traditional medicines, it is hoped that these discoveries can provide the much sought after core structure diversity that will be required of a new generation of antibiotics. This review discusses the contribution of Streptomyces to antibiotics and the potential of newly discovered species in traditional medicine. We also explore how knowledge of traditional medicines can aid current initiatives in sourcing new and chemically diverse antibiotics. Gerry A. Quinn, Aiya M. Banat, Alyaa M. Abdelhameed and Ibrahim M. Banat 2020-07-21T15:51:25Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001435?TRACK=RSS Alteration in the composition of the gut microbiota can lead to a number of chronic clinical diseases. Akkermansia muciniphila is an anaerobic bacteria constituting 3–5% of the gut microbial community in healthy adults. This bacterium is responsible for degenerating mucin in the gut; its scarcity leads to diverse clinical disorders. In this review, we focus on the role of A. muciniphila in diabetes, obesity and atherosclerosis, as well as the use of this bacterium as a next-generation probiotic. In regard to obesity and diabetes, human and animal trials have shown that A. muciniphila controls the essential regulatory system of glucose and energy metabolism. However, the underlying mechanisms by which A. muciniphila alleviates the complications of obesity, diabetes and atherosclerosis are unclear. At the same time, its abundance suggests improved metabolic disorders, such as metabolic endotoxemia, adiposity insulin resistance and glucose tolerance. The role of A. muciniphila is implicated in declining aortic lesions and atherosclerosis. Well-characterized virulence factors, antigens and cell wall extracts of A. muciniphila may act as effector molecules in these diseases. These molecules may provide novel mechanisms and strategies by which this bacterium could be used as a probiotic for the treatment of obesity, diabetes and atherosclerosis. Alka Hasani, Saba Ebrahimzadeh, Fatemeh Hemmati, Aytak Khabbaz, Akbar Hasani and Pourya Gholizadeh 2021-10-08T11:56:09Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001910?TRACK=RSS Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia among school-aged children and young adults. Infections occur throughout the year but tend to surge during winter months across Europe. A characteristic epidemic cycle, where a substantial surge in the number of infections occurs, is seen approximately every 1–4 years and hypothesized to be driven by changes in immunity and a shift in circulating variants. Once thought to be an organism of low virulence, it has now been found to possess several virulence factors, including toxin production, biofilm formation and evasion of antibody-mediated immunity. The lack of a cell wall and reduced metabolic pathways limit the options for antibiotic treatment. Acquired macrolide resistance is a growing concern, with >80% of cases in China being macrolide-resistant. Although efforts have been made to develop a vaccine, there are still substantial hurdles to overcome in relation to vaccine-enhanced disease, which results from an inappropriate immune response among vaccinated individuals. Richard S. Rowlands, Patrick M. Meyer Sauteur, Michael L. Beeton and On behalf of the ESCMID Study Group for Mycoplasma and Chlamydia Infections (ESGMAC) 2024-10-30T12:29:00Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001833?TRACK=RSS Background. Dengue is an important arboviral infection of considerable public health significance. It occurs in a wide global belt within a variety of tropical regions. The timely laboratory diagnosis of Dengue infection is critical to inform both clinical management and an appropriate public health response. Vaccination against Dengue virus is being introduced in some areas. Discussion. Appropriate diagnostic strategies will vary between laboratories depending on the available resources and skills. Diagnostic methods available include viral culture, the serological detection of Dengue-specific antibodies in using enzyme immunoassays (EIAs), microsphere immunoassays, haemagglutination inhibition or in lateral flow point of care tests. The results of antibody tests may be influenced by prior vaccination and exposure to other flaviviruses. The detection of non-structural protein 1 in serum (NS1) has improved the early diagnosis of Dengue and is available in point-of-care assays in addition to EIAs. Direct detection of viral RNA from blood by PCR is more sensitive than NS1 antigen detection but requires molecular skills and resources. An increasing variety of isothermal nucleic acid detection methods are in development. Timing of specimen collection and choice of test is critical to optimize diagnostic accuracy. Metagenomics and the direct detection by sequencing of viral RNA from blood offers the ability to rapidly type isolates for epidemiologic purposes. Conclusion. The impact of vaccination on immune response must be recognized as it will impact test interpretation and diagnostic algorithms. Jaimie L. Frazer and Robert Norton 2024-05-09T14:34:39Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001206?TRACK=RSS Ticks are the most important vectors of human pathogens, leading to increased public health burdens worldwide. Tick-borne pathogens include viruses (e.g. tick-borne encephalitis and Powassan); bacteria, such as the causative agents of Lyme disease, spotted fever rickettsiosis and human anaplasmosis; and malaria-like protozoan parasites causing babesiosis. Tick-borne diseases are emerging due to the geographical expansion of their tick vectors, especially in the northern hemisphere. Two examples of this phenomenon are Ixodes scapularis and Amblyomma americanum, which have expanded their ranges in the USA in recent decades and are responsible for the continuous emergence of Lyme disease and human ehrlichiosis, respectively. This phenomenon is also occurring worldwide and is reflected by the increasing number of tick-borne encephalitis and haemorrhagic fever cases in Europe and Asia. In this review, we provide a concise synopsis of the most medically important tick-borne pathogen worldwide, with a particular emphasis on emerging public health threats. Ilia Rochlin and Alvaro Toledo 2020-06-01T15:10:34Z http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001912?TRACK=RSS Introduction. Antibiotic tolerance corresponds to the bacterial ability to survive a transient exposure to antibiotics and is often associated with treatment failure. Current methods of identifying tolerance based on bacterial growth are time-consuming. This study explores the use of a growth-independent method utilizing nanomotion technology to detect antibiotic-tolerant bacteria. Hypothesis. The nanomotion signal obtained from a nanomechanical sensor measures real-time metabolic activity and cellular processes and could provide valuable information about the tolerance of bacteria to antibiotics that cannot be detected by standard antibiotic susceptibility tests. Aim. The aim of this study is to investigate the potential of nanomotion technology to record antibiotic-tolerant bacteria. Methodology. We generated a slow-growing Escherichia coli strain by manipulating mazF expression levels and confirmed its viability by several standard methods. We subsequently measured its nanomotion and the nanomotion of the WT E. coli in the presence or absence of antibiotics. Supervised machine learning was employed to distinguish slow-growing from exponentially growing bacteria. Observations for bacterial nanomotions were confirmed by standard kill curves. Results. We distinguished slow-growing from exponentially growing bacteria using specific features from the nanomotion signal. Furthermore, the exposition of both growth phenotypes to polymyxin decreased the nanomotion signal indicating cell death. Similarly, when exponentially growing cells were exposed to ampicillin, an antibiotic whose efficacy depends on the growth rate, the nanomotion signal also decreased. In contrast, the nanomotion signal remained unchanged for slow-growing bacteria upon exposure to ampicillin. In addition, antibiotic exposure can cause bacterial elongation, in which the biomass of a cell increases without cell division. By overexpressing sulA, we mimicked antibiotic-induced elongation. Differences in the nanomotion signal were observed when comparing elongating and non-elongating phenotypes. Conclusion. This work shows that nanomotion signals entail information about the reaction to antibiotics that standard MIC-based antibiotic susceptibility tests cannot detect. In the future, nanomotion-based antibiotic tolerance tests could be developed for clinical use in chronic or relapsing infections. Christèle Aubry, Carole Kebbi-Beghdadi, Amanda Luraschi-Eggemann, Gino Cathomen, Danuta Cichocka, Alexander Sturm, Gilbert Greub and The ERADIAMR Consortium§ 2024-11-08T13:34:48Z