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With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the essential oil-based mouthwash Listerine Cool Mint® (Listerine). Oropharyngeal swabs from 64 men who have sex with men (n = 118) from a previous study (PReGo study) were analysed (ClinicalTrials.gov, NCT03881007). These included 64 baseline and 54 samples following three months of daily use of Listerine. Inhibition was confirmed by agar overlay assay, and inhibitory bacteria isolated using replica plating and identified using MALDI-TOF. The number of inhibitory isolates were compared before and after Listerine use. Thirty-one pharyngeal samples (26%) showed inhibitory activity against N. gonorrhoeae and/or N. meningitidis, and 62 inhibitory isolates were characterised. Fourteen species belonging to the genera Streptococci and Rothia were identified. More inhibitory isolates were observed following Listerine use compared to baseline, although this effect was not statistically significant (p = 0.073). This study isolated and identified inhibitory bacteria against pathogenic Neisseria spp. and established that daily Listerine use did not decrease their prevalence. These findings could provide a new approach for the prevention and treatment of pharyngeal Neisseria infections. [ABSTRACT FROM AUTHOR]

Abstract Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation.

With increasing incidence of pathogenic Neisseria infections coupled with emerging resistance to antimicrobials, alternative approaches to limit the spread are sought. We investigated the inhibitory effect of oropharyngeal microbiota on the growth of N. gonorrhoeae and N. meningitidis and the impact of the essential oil-based mouthwash Listerine Cool Mint® (Listerine). Oropharyngeal swabs from 64 men who have sex with men (n = 118) from a previous study (PReGo study) were analysed (ClinicalTrials.gov, NCT03881007). These included 64 baseline and 54 samples following three months of daily use of Listerine. Inhibition was confirmed by agar overlay assay, and inhibitory bacteria isolated using replica plating and identified using MALDI-TOF. The number of inhibitory isolates were compared before and after Listerine use. Thirty-one pharyngeal samples (26%) showed inhibitory activity against N. gonorrhoeae and/or N. meningitidis, and 62 inhibitory isolates were characterised. Fourteen species belonging to the genera Streptococci and Rothia were identified. More inhibitory isolates were observed following Listerine use compared to baseline, although this effect was not statistically significant (p = 0.073). This study isolated and identified inhibitory bacteria against pathogenic Neisseria spp. and established that daily Listerine use did not decrease their prevalence. These findings could provide a new approach for the prevention and treatment of pharyngeal Neisseria infections.

Background: Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods: We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results: Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions: Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation. [ABSTRACT FROM AUTHOR]

Abstract The microbiota of Anopheles mosquitoes interferes with mosquito infection by Plasmodium and influences mosquito fitness, therefore affecting vectorial capacity. This natural barrier to malaria transmission has been regarded with growing interest in the last 20 years, as it may be a source of new transmission-blocking strategies. The last decade has seen tremendous progress in the functional characterisation of the tripartite interactions between the mosquito, its microbiota and Plasmodium parasites. In this review, we provide insights into the effects of the mosquito microbiota on Plasmodium infection and on mosquito physiology, and on how these aspects together influence vectorial capacity. We also discuss three current challenges in the field, namely the need for a more relevant microbiota composition in experimental mosquitoes involved in vector biology studies, for a better characterisation of the non-bacterial microbiota, and for further functional studies of the microbiota present outside the gut.

Highlights • Certain data support the assumption that imipenem exerts only a limited impact on the intestinal microbiota. • Impact of imipenem on gut microbiota versus alternatives (e.g. piperacillin/tazobactam or cephamycins) remains contentious. • These observations result from patchy studies, preventing any firm conclusions. • Comparative ecological studies are needed to support precise antimicrobial stewardship and de-escalation programmes. ABSTRACT The ongoing pandemic of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) is responsible for a global rise in carbapenem consumption that may hasten the dissemination of carbapenemase-producing Enterobacteriaceae (CPE). Hence, carbapenem sparing through the use of alternative β-lactams is increasingly considered as a potential option in patients with ESBL-E infections. However, at the individual level, this strategy implies an in-depth understanding of how carbapenems and their alternatives impair the gut microbiota, especially the anaerobic bacteria and the colonisation resistance (CR) that it confers. In this review, we sought to appraise the impact of carbapenems and their main alternatives for ESBL-E infections (namely β-lactam/β-lactamase inhibitor combinations, cephamycins and temocillin) on the gut ecosystem and the resulting hazard for acquisition of CPE. Although limited, the available evidence challenges our perception of the ecological side effects of these antimicrobials and highlights knowledge gaps regarding antibiotic-induced alterations in intestinal CR. These alterations may depend not only on anti-anaerobic properties but also on a panel of parameters with marked interindividual variability, such as baseline characteristics of the gut microbiota or the degree of biliary excretion for the considered drug. In the current context of ESBL-E dissemination and increasing opportunities for carbapenem-sparing initiatives, large, comparative, high-quality studies based on new-generation sequencing tools are more than ever warranted to better define the positioning of alternative β-lactams in antimicrobial stewardship programmes. [ABSTRACT FROM AUTHOR]

The microbiota of Anopheles mosquitoes interferes with mosquito infection by Plasmodium and influences mosquito fitness, therefore affecting vectorial capacity. This natural barrier to malaria transmission has been regarded with growing interest in the last 20 years, as it may be a source of new transmission-blocking strategies. The last decade has seen tremendous progress in the functional characterisation of the tripartite interactions between the mosquito, its microbiota and Plasmodium parasites. In this review, we provide insights into the effects of the mosquito microbiota on Plasmodium infection and on mosquito physiology, and on how these aspects together influence vectorial capacity. We also discuss three current challenges in the field, namely the need for a more relevant microbiota composition in experimental mosquitoes involved in vector biology studies, for a better characterisation of the non-bacterial microbiota, and for further functional studies of the microbiota present outside the gut. [ABSTRACT FROM AUTHOR]

Since their development over 60 years ago, antimicrobials have become an integral part of healthcare practice worldwide. Recently, this has been put in jeopardy by the emergence of widespread antimicrobial resistance, which is one of the major problems facing modern medicine. In the past, the development of new antimicrobials kept us one step ahead of the problem of resistance, but only three new classes of antimicrobials have reached the market in the last thirty years. A time is therefore approaching when we may not have effective treatment against bacterial infections, particularly for those that are caused by Gram-negative organisms. An important strategy to reduce the development of antimicrobial resistance is to use antimicrobials more appropriately, in ways that will prevent resistance. This involves a consideration of the pharmacokinetic and pharmacodynamics properties of antimicrobials, the possible use of combinations, and more appropriate choice of antimicrobials, which may include rapid diagnostic testing and antimicrobial cycling. Examples given in this review include Mycobacterium tuberculosis, Gram-negative and Gram-positive organisms. We shall summarise the current evidence for these strategies and outline areas for future development.

Sessile cultures of the skin bacteriaStaphylococcus saprophyticusandCorynebacterium xerosiswere grown using novel fine-celled foam substrata to test the outcome of challenge by methicillin-resistantStaphylococcus aureusorPseudomonas aeruginosaunder three growth medium regimens (simulated sweat, simulated serum or simulated sweat substituted with simulated serum during the microbial challenge).S. saprophyticusandC. xerosissignificantly limited MRSA andP. aeruginosaimmigration respectively, under the simulated sweat and serum medium regimes. Under the substitution medium regime however, MRSA andP. aeruginosaintegrated into pre-established biofilms to a significantly greater extent, attaining cell densities similar to the axenic controls. The outcome of challenge was influenced by the medium composition and test organism but could not be predicted based on planktonic competition assays or growth dynamics. Interactions between skin and wound isolates could be modelled using the fine-celled foam-based system. This model could be used to further investigate interactions and also in preclinical studies of antimicrobial wound care regimens. [ABSTRACT FROM AUTHOR]

A group of isolates of the genus Luteimonas was characterised, which represented a specific component of the healthy core microbiome of Fraxinus excelsior in forest districts with a high infection rate of H. fraxineus , the causal agent of ash dieback. Based on phylogenomic and phenotypic analyses, a clear differentiation from related Luteimonas species was shown. Comparisons of the overall genome relatedness indices with the closest phylogenetic neighbours resulted in values below the recommended species cut-off levels. In addition, differences in several physiological and chemotaxonomic traits allowed a clear demarcation from the type strains of closely related species. Conclusively, the strain group was considered to represent a novel species in the genus Luteimonas , for which the name Luteimonas fraxinea sp. nov. is proposed, with strain D4P002T (=DSM 113273T = LMG 32455T) as the type strain. A functional analysis of the genome revealed features particularly associated with attachment, biofilm production and motility, indicating the ability of D4P002T to effectively colonise ash leaves. In nursery trials, ash seedlings inoculated with this strain showed suppression of the pathogen over a period of three years. This effect was accompanied by a significant shift in the bacterial microbiome of the plants. Altogether, the exclusive occurrence in the microbiome of tolerant ash trees, the genetic background and the results of the inoculation experiment suggest that strain D4P002T may suppress the penetration and spreading of H. fraxineus in or on ash leaves via colonisation resistance or trigger a priming effect of plant defences against the pathogen. [ABSTRACT FROM AUTHOR]

The mouth contains both distinct mucosal (lips, cheek, tongue, palate) and, uniquely, non-shedding surfaces (teeth) for microbial colonisation. Each surface harbours a diverse but characteristic micro flora, the composition and metabolism of which is dictated by the biological properties of each site. The resident oral micro flora develops in an orderly manner via waves of microbial succession (both autogenic and allogenic). Pioneer species (many of which are sIgA protease-producing streptococci) colonise saliva-coated surfaces through specific stereo-chemical, adhesin-receptor interactions. The metabolism of these organisms modifies local environmental conditions, facilitating subsequent attachment and growth by later, and more fastidious, colonisers. Eventually, a stable bio film community develops, that plays an active role in (a) the normal development of the physiology of the habitat, and (b) the innate host defences (colonisation resistance). Thus, when considering treatment options, clinicians should be aware of the need to maintain the beneficial properties of the resident oral micro flora. [ABSTRACT FROM AUTHOR]

Abstract: An anaerobic, continuous-flow culture method has been developed to assess the effects of different levels of enrofloxacin (ENR) on the human intestinal microbiota. Chemostats containing human faecal flora were exposed to 1.25, 12.5 and 125μg/mL ENR. Before and during drug exposure, samples aspirated from culture vessels were analysed using viable cell counting and denaturing gradient gel electrophoresis (DGGE). In addition, the colonisation resistance (CR) of the microbiota to Candida albicans SC5314 was evaluated. When exposed to 1.25μg/mL ENR, total counts of aerobic bacteria, anaerobic bacteria, Lactobacillus, enterococci, Escherichia coli and Bacteroides fragilis were similar to the control group, except for Bifidobacterium; when exposed to 12.5μg/mL and 125μg/mL ENR, numbers of categorised microorganisms changed significantly, except for B. fragilis. DGGE indicated that although 1.25μg/mL ENR had little effect on the total number of microbiota, several bands representing dominant bacteria disappeared. The bands disappeared more quickly when exposed to 12.5μg/mL and 125μg/mL ENR. In addition to their influence on microbial diversity, different levels of ENR reduced the CR of the intestinal microbiota to C. albicans SC5314. [Copyright &y& Elsevier]

Abstract: Encephalitozoon spp. are the primary microsporidial pathogens of humans and domesticated animals. In this experiment, we test the efficacy of 4 commercial antimicrobials against an Encephalitozoon sp. infecting a grasshopper (Romalea microptera) host. Oral treatment with fumagillin or thiabendazole significantly reduced pathogen spore counts (93% and 88% respectively), whereas spore counts of grasshoppers fed quinine produced a non-significant 53% reduction in spores, and those fed streptomycin a non-significant 29% increase in spores, compared to the control. We observed a moderate dose–response effect for thiabendazole, whereby spore count decreased as drug consumption increased. No thiabendazole-treated animals died, whereas 27% of streptomycin-treated animals died, suggesting that thiabendazole was not toxic at the doses administered. The deaths among streptomycin-treated animals may have been caused by drug toxicity, parasite burden, or both. Although fumagillin and thiabendazole significantly reduced spore counts, in no individual was the pathogen totally eliminated. Our data confirm that microsporidia are difficult to control and that fumagillin and thiabendazole are partially effective antimicrobials against this group. Our study suggests that quinine and related alkaloids should be further examined for antimicrosporidial activity, and streptomycin should be examined as a possible enhancer of microsporidiosis. [Copyright &y& Elsevier]

The digestive microflora is characterized by a high degree of complexity and diversity. Variation in the composition of the digestive flora of an individual occurs in space and time. Two kinds of strains can be defined: transient strains in opposition to resident strains, which are repeatedly isolated from the digestive tract over a long period of time. The latter can be assumed to have colonized the digestive tract. We will present here studies on the properties of bacteria implicated in the colonisation process. Firstly, we summarize data on the role of adherence in this process, the mechanisms involved in adhesion to mucosal structures (cellular and mucus glycoproteins, extracellular matrix components) and give examples of adhesion in various intestinal bacterial groups (commensal and potentially pathogenic bacteria). Secondly, we describe the role of glucidolytic and proteolytic enzymes involved in host-bacteria interactions and implicated in colonisation and maintenance of the indigenous intestinal flora. [ABSTRACT FROM AUTHOR]

This review describes various in vivo animal models (humans; conventional animals administered antimicrobial agents and animals species used; gnotobiotic and germ-free animals), in vitro models (luminal and mucosal), and in silico and mathematical models which have been developed to study colonisation and colonisation resistance and effects of gut flora on hosts. Where applicable, the advantages and disadvantages of each model are discussed. [ABSTRACT FROM AUTHOR]

The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission. [ABSTRACT FROM AUTHOR]

The different compartments of the gastrointestinal tract are inhabited by populations of micro-organisms. By far the most important predominant populations are in the colon where a true symbiosis with the host exists that is a key for well-being and health. For such a microbiota, ‘normobiosis’ characterises a composition of the gut ‘ecosystem’ in which micro-organisms with potential health benefits predominate in number over potentially harmful ones, in contrast to ‘dysbiosis’, in which one or a few potentially harmful micro-organisms are dominant, thus creating a disease-prone situation. The present document has been written by a group of both academic and industry experts (in the ILSI Europe Prebiotic Expert Group and Prebiotic Task Force, respectively). It does not aim to propose a new definition of a prebiotic nor to identify which food products are classified as prebiotic but rather to validate and expand the original idea of the prebiotic concept (that can be translated in ‘prebiotic effects’), defined as: ‘The selective stimulation of growth and/or activity(ies) of one or a limited number of microbial genus(era)/species in the gut microbiota that confer(s) health benefits to the host.’ Thanks to the methodological and fundamental research of microbiologists, immense progress has very recently been made in our understanding of the gut microbiota. A large number of human intervention studies have been performed that have demonstrated that dietary consumption of certain food products can result in statistically significant changes in the composition of the gut microbiota in line with the prebiotic concept. Thus the prebiotic effect is now a well-established scientific fact. The more data are accumulating, the more it will be recognised that such changes in the microbiota's composition, especially increase in bifidobacteria, can be regarded as a marker of intestinal health. The review is divided in chapters that cover the major areas of nutrition research where a prebiotic effect has tentatively been investigated for potential health benefits. The prebiotic effect has been shown to associate with modulation of biomarkers and activity(ies) of the immune system. Confirming the studies in adults, it has been demonstrated that, in infant nutrition, the prebiotic effect includes a significant change of gut microbiota composition, especially an increase of faecal concentrations of bifidobacteria. This concomitantly improves stool quality (pH, SCFA, frequency and consistency), reduces the risk of gastroenteritis and infections, improves general well-being and reduces the incidence of allergic symptoms such as atopic eczema. Changes in the gut microbiota composition are classically considered as one of the many factors involved in the pathogenesis of either inflammatory bowel disease or irritable bowel syndrome. The use of particular food products with a prebiotic effect has thus been tested in clinical trials with the objective to improve the clinical activity and well-being of patients with such disorders. Promising beneficial effects have been demonstrated in some preliminary studies, including changes in gut microbiota composition (especially increase in bifidobacteria concentration). Often associated with toxic load and/or miscellaneous risk factors, colon cancer is another pathology for which a possible role of gut microbiota composition has been hypothesised. Numerous experimental studies have reported reduction in incidence of tumours and cancers after feeding specific food products with a prebiotic effect. Some of these studies (including one human trial) have also reported that, in such conditions, gut microbiota composition was modified (especially due to increased concentration of bifidobacteria). Dietary intake of particular food products with a prebiotic effect has been shown, especially in adolescents, but also tentatively in postmenopausal ... [ABSTRACT FROM PUBLISHER]