The role of the local microbial ecosystem in respiratory health and disease

Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form—together with harmless commensal bacteria, viruses and fungi—intricate ecological networks, collectively known as the ‘microbiome’. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.     

Evolving concepts in biofilm infections

Several pathogens associated with chronic infections, including Pseudomonas aeruginosa in cystic fibrosis pneumonia, Haemophilus influenzae and Streptococcus pneumoniae in chronic otitis media, Staphylococcus aureus in chronic rhinosinusitis and enteropathogenic Escherichia coli in recurrent urinary tract infections, are linked to biofilm formation. Biofilms are usually defined as surface-associated microbial communities, surrounded by an extracellular polymeric substance (EPS) matrix. Biofilm formation has been demonstrated for numerous pathogens and is clearly an important microbial survival strategy. However, outside of dental plaques, fewer reports have investigated biofilm development in clinical samples. Typically biofilms are found in chronic diseases that resist host immune responses and antibiotic treatment and these characteristics are often cited for the ability of bacteria to persist in vivo . This review examines some recent attempts to examine the biofilm phenotype in vivo and discusses the challenges and implications for defining a biofilm phenotype.     

Can bacterial interference prevent infection?

The concept that one bacterial species can interfere with the ability of another to colonize and infect the host has at its foundation the prerequisite that bacteria must attach to biological surfaces to cause infection. Although this is an over-simplification of pathogenesis, it has led to studies aimed at creating vaccines that block adhesion events. Arguably, the use of commensal bacteria (also referred to as "normal flora", "indigenous" or "autochthonous" microorganisms) to inhibit pathogens has even greater potential than vaccine use, because these bacteria are natural competitors of pathogens and their action does not require host immune stimulation. Exogenous application of commensal organisms (probiotics) has been shown to reduce the risk of infections in the gut, urogenital tract and wound sites. To manipulate and optimize these effects, further studies are required to understand cell signaling amongst commensals and pathogens within biofilms adherent to host tissues. The potential for new therapeutic regimens using probiotics is significant and worthy of further study.     

Antibiotics in bacterial acute respiratory tract infection in children]

The data on changes in the susceptibility of the most frequent respiratory tract pathogens i.e. Pneumococcus spp. and Haemophilus influenzae within the last 15 years and Streptococcus spp., Staphylococcus spp. and Moraxella spp. at the present time as well as recommendations based on the original and some literature data on the choice of the antibacterial drugs for the initial treatment of bacterial complications of acute respiratory tract viral infections such as otitis, sinusitis and pharyngitis are presented. The necessity of decreasing the unjustified use of antibiotics in cases of uncomplicated acute respiratory tract viral infections is indicated.     

Rhizosphere pseudomonads as probiotics improving plant health

Many root‐colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health‐promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root‐colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant–probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.     

Prevalence and antimicrobial susceptibilities of bacteria isolated from blood cultures of hospitalized patients in the United States in 2002

Background

Upper respiratory tract infections (URTIs) are among the most frequent reasons for physician office visits in paediatrics. Despite their predominant viral aetiology, URTIs continue to be treated with antimicrobials. We explored general practitioners' (GPs) prescribing behaviour for antimicrobials in children (≤ 16 years) with URTIs in Trinidad, using the guidelines from the Centers for Disease Control and Prevention (CDC) as a reference.

Methods

A cross-sectional study was conducted on 92 consenting GPs from the 109 contacted in Central and East Trinidad, between January to June 2003. Using a pilot-tested questionnaire, GPs identified the 5 most frequent URTIs they see in office and reported on their antimicrobial prescribing practices for these URTIs to trained research students.

Results

The 5 most frequent URTIs presenting in children in general practice, are the common cold, pharyngitis, tonsillitis, sinusitis and acute otitis media (AOM) in rank order. GPs prescribe at least 25 different antibiotics for these URTIs with significant associations for amoxicillin, co-amoxiclav, cefaclor, cefuroxime, erythromycin, clarithromycin and azithromycin (p < 0.001). Amoxicillin alone or with clavulanate was the most frequently prescribed antibiotic for all URTIs. Prescribing variations from the CDC recommendations were observed for all URTIs except for AOM (50%), the most common condition for antibiotics. Doctors practicing for >30 years were more likely to prescribe antibiotics for the common cold (p = 0.014). Severity (95.7%) and duration of illness (82.5%) influenced doctors' prescribing and over prescribing in general practice was attributed to parent demands (75%) and concern for secondary bacterial infections (70%). Physicians do not request laboratory investigations primarily because they are unnecessary (86%) and the waiting time for results is too long (51%).

Conclusions

Antibiotics are over prescribed for paediatric URTIs in Trinidad and amoxicillin with co-amoxiclav were preferentially prescribed. Except for AOM, GPs' prescribing varied from the CDC guidelines for drug and duration. Physicians recognise antibiotics are overused and consider parents expecting antibiotics and a concern for secondary bacterial infections are prescribing pressures. Guidelines to manage URTIs, ongoing surveillance programs for antibiotic resistance, public health education on non-antibiotic strategies, and postgraduate education for rational pharmacotherapy in general practice would decrease inappropriate antibiotic use in URTIs.     

Viral and Atypical Bacterial Etiology of Acute Respiratory Infections in Children under 5 Years Old Living in a Rural Tropical Area of Madagascar

Background

In Madagascar, very little is known about the etiology and prevalence of acute respiratory infections (ARIs) in a rural tropical area. Recent data are needed to determine the viral and atypical bacterial etiologies in children with defined clinical manifestations of ARIs.

Methods

During one year, we conducted a prospective study on ARIs in children between 2 to 59 months in the community hospital of Ampasimanjeva, located in the south-east of Madagascar. Respiratory samples were analyzed by multiplex real-time RT-PCR, including 18 viruses and 2 atypical bacteria. The various episodes of ARI were grouped into four clinical manifestations with well-documented diagnosis: “Community Acquired Pneumonia”(CAP, group I), “Other acute lower respiratory infections (Other ALRIs, group II)”, “Upper respiratory tract infections with cough (URTIs with cough, group III)”and “Upper respiratory tract infections without cough (URTIs without cough, group IV)”.

Results

295 children were included in the study between February 2010 and February 2011. Viruses and/or atypical bacteria respiratory pathogens were detected in 74.6% of samples, the rate of co-infection was 27.3%. Human rhinovirus (HRV; 20.5%), metapneumovirus (HMPV A/B, 13.8%), coronaviruses (HCoV, 12.5%), parainfluenza virus (HPIV, 11.8%) and respiratory syncytial virus A and B (RSV A/B, 11.8%) were the most detected. HRV was predominantly single detected (23.8%) in all the clinical groups while HMPV A/B (23.9%) was mainly related to CAP (group I), HPIV (17.3%) to the “Other ALRIs” (group II), RSV A/B (19.5%) predominated in the group “URTIs with cough” (group III) and Adenovirus (HAdV, 17.8%) was mainly detected in the “without cough” (group IV).

Interpretation

This study describes for the first time the etiology of respiratory infections in febrile children under 5 years in a malaria rural area of Madagascar and highlights the role of respiratory viruses in a well clinically defined population of ARIs.     

Research progress on the regulation mechanism of probiotics on the microecological flora of infected intestines in livestock and poultry

The animal intestine is a complex ecosystem composed of host cells, gut microbiota and available nutrients. Gut microbiota can prevent the occurrence of intestinal diseases in animals by regulating the homeostasis of the intestinal environment. The intestinal microbiota is a complex and stable microbial community, and the homeostasis of the intestinal environment is closely related to the invasion of intestinal pathogens, which plays an important role in protecting the host from pathogen infections. Probiotics are strains of microorganisms that are beneficial to health, and their potential has recently led to a significant increase in studies on the regulation of intestinal flora. Various potential mechanisms of action have been proposed on probiotics, especially mediating the regulation mechanism of the intestinal flora on the host, mainly including competitive inhibition of pathogens, stimulation of the host's adaptive immune system and regulation of the intestinal flora. The advent of high-throughput sequencing technology has given us a clearer understanding and has facilitated the development of research methods to investigate the intestinal microecological flora. This review will focus on the regulation of probiotics on the microbial flora of intestinal infections in livestock and poultry and will depict future research directions.     

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections

Respiratory viruses such as influenza viruses, respiratory syncytial virus (RSV), and coronaviruses initiate infection at the mucosal surfaces of the upper respiratory tract (URT), where the resident respiratory microbiome has an important gatekeeper function. In contrast to gut-targeting administration of beneficial bacteria against respiratory viral disease, topical URT administration of probiotics is currently underexplored, especially for the prevention and/or treatment of viral infections. Here, we report the formulation of a throat spray with live lactobacilli exhibiting several in vitro mechanisms of action against respiratory viral infections, including induction of interferon regulatory pathways and direct inhibition of respiratory viruses. Rational selection of Lactobacillaceae strains was based on previously documented beneficial properties, up-scaling and industrial production characteristics, clinical safety parameters, and potential antiviral and immunostimulatory efficacy in the URT demonstrated in this study. Using a three-step selection strategy, three strains were selected and further tested in vitro antiviral assays and in formulations: Lacticaseibacillus casei AMBR2 as a promising endogenous candidate URT probiotic with previously reported barrier-enhancing and anti-pathogenic properties and the two well-studied model strains Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 that display immunomodulatory capacities. The three strains and their combination significantly reduced the cytopathogenic effects of RSV, influenza A/H1N1 and B viruses, and HCoV-229E coronavirus in co-culture models with bacteria, virus, and host cells. Subsequently, these strains were formulated in a throat spray and human monocytes were employed to confirm the formulation process did not reduce the interferon regulatory pathway-inducing capacity. Administration of the throat spray in healthy volunteers revealed that the lactobacilli were capable of temporary colonization of the throat in a metabolically active form. Thus, the developed spray with live lactobacilli will be further explored in the clinic as a potential broad-acting live biotherapeutic strategy against respiratory viral diseases.     

益生菌调控幼龄畜禽消化道微生物研究进展

益生菌是一类对宿主(人类或动物)有益的活性微生物,包括细菌、真菌(如酵母)等,具有促进动物生长、提高免疫力的作用,是潜在的抗生素替代品。益生菌可能通过与动物消化道微生物互作来发挥益生作用,但具体机制仍不明确。综述了基于高通量测序技术研究益生菌调控幼龄畜禽(仔猪、雏鸡、反刍动物)消化道微生物群落组成的最新进展,并提出了未来研究方向,包括益生菌如何通过与消化道微生物互作影响其功能,益生菌对于幼龄畜禽不同健康状态下肠道微生物的影响,以及宿主因素如何影响益生菌对于幼龄畜禽消化道微生物的作用效果。     

Beneficial effects of <Emphasis Type="Italic">Lactobacillus paracasei</Emphasis> subsp. <Emphasis Type="Italic">paracasei</Emphasis> NTU 101 and its fermented products

It is well-known that probiotics have a number of beneficial health effects in humans and animals, including the reduction of symptoms in lactose intolerance and enhancement of the bioavailability of nutrients. Probiotics have showed to possess antimutagenic, anticarcinogenic and hypocholesterolemic properties. Further, they were also observed to have antagonistic actions against intestinal and food-borne pathogens, to decrease the prevalence of allergies in susceptible individuals and to have immunomodulatory effects. Typically, the bacteria colonise the intestinal tract first and then reinforce the host defence systems by inducing a generalised mucosal immune response, balanced T-helper cell response, self-limited inflammatory response and secretion of polymeric IgA. Scientific reports showed that the Taiwan native lactic acid bacterium from newborn infant faeces identified as Lactobacillus paracasei subsp. paracasei NTU 101 and its fermented products proved to be effective for the management of blood cholesterol and pressure, prevention of gastric mucosal lesion development, immunomodulation and alleviation of allergies, anti-osteoporosis and inhibition the fat tissue accumulation. This review article describes that the beneficial effects of this Lactobacillus strains and derivative products may be suitable for human and animals.     

Respiratory Infections in Adults with Atopic Disease and IgE Antibodies to Common Aeroallergens

Background

Atopic diseases, including allergic rhinitis, allergic dermatitis and asthma, are common diseases with a prevalence of 30–40% worldwide and are thus of great global public health importance. Allergic inflammation may influence the immunity against infections, so atopic individuals could be susceptible to respiratory infections. No previous population-based study has addressed the relation between atopy and respiratory infections in adulthood. We assessed the relation between atopic disease, specific IgE antibodies and the occurrence of upper and lower respiratory infections in the past 12 months among working-aged adults.

Methods and Findings

A population-based cross-sectional study of 1008 atopic and non-atopic adults 21–63 years old was conducted. Information on atopic diseases, allergy tests and respiratory infections was collected by a questionnaire. Specific IgE antibodies to common aeroallergens were measured in serum. Adults with atopic disease had a significantly increased risk of lower respiratory tract infections (LRTI; including acute bronchitis and pneumonia) with an adjusted risk ratio (RR) 2.24 (95% confidence interval [CI] 1.43, 3.52) and upper respiratory tract infections (URTI; including common cold, sinusitis, tonsillitis, and otitis media) with an adjusted RR 1.55 (1.14, 2.10). The risk of LRTIs increased with increasing level of specific IgE (linear trend P = 0.059).

Conclusions

This study provides new evidence that working-aged adults with atopic disease experience significantly more LRTIs and URTIs than non-atopics. The occurrence of respiratory infections increased with increasing levels of specific IgE antibodies to common aeroallergens, showing a dose-response pattern with LRTIs. From the clinical point of view it is important to recognize that those with atopies are a risk group for respiratory infections, including more severe LRTIs.     

Biotherapeutic agents and vaginal health

Treatment of vaginal infection requires different drugs although the recurrence rate post treatment remains high due to adverse effects on the beneficial microbiota. Thus, there are clear clinical advantages for the use of biotherapeutic agents (prebiotics and/or probiotics) for treating these infections. Pre‐ and probiotic beneficial effects can be delivered topically or systemically. In general, both approaches have the potential to optimize, maintain and restore the ecology of the vaginal ecosystem. Specific carbohydrates provide a therapeutic approach for controlling infections by stimulating the growth of the indigenous lactobacilli but inhibiting the growth and adhesion of pathogens to the vaginal epithelial cells. Overall, little evidence exists to promote the prevention or treatment of vaginal disease with prebiotic carbohydrates in formulations such as pessaries, creams or douches. However, recent reports have promoted prebiotic applications in ecosystems other than the gut and include the mouth, skin and vagina. This review focuses on the utilization of pre‐ and probiotics for vaginal health.     

Evidence-based review of probiotics for antibiotic-associated diarrhea and Clostridium difficile infections

Probiotics are living microbes taken to confer a health benefit on the host. Although probiotics have a long history of use in Europe and Asia and have been on the U.S. market for over 14 years, there is still confusion about how to effectively use them. The use of probiotics for the prevention of antibiotic-associated diarrhea (AAD) and the treatment of Clostridium difficile infections (CDI) has been tested in randomized controlled clinical trials.This paper will review the evidence supporting probiotic therapy for these two diseases and also review the advantages and disadvantages of probiotics. The advantages of probiotic therapy include multiple mechanisms of action against pathogens, the ability to interact with the host's natural defense systems, survival to the target organ and a good risk to benefit ratio. Disadvantages of probiotics include lack of standardization for clinical trial designs, variations in regulatory standards, poor quality control for some products and infrequent serious adverse reactions. Overall, probiotics offer a promising strategy for the prevention and treatment for AAD and CDI     

ICU机械通气并发下呼吸道医院感染病原菌的调查分析

目的：分析ICU机械通气并发下呼吸道医院感染病原学构成及耐药情况。为临床防治提供依据。方法：对我院1996年6月-1999年6月3间ICU收住的98例机械通气合并下呼吸道医院感染患者的致病菌及药敏结果进行回顾性调查。结果：共检出致病毒128株,其中革兰阴性细菌（G^-菌）占66.4%（85株）,革兰阳性细菌（G^ 菌）占25.8%(33株）,真菌占7.8%(10株）;前四位致病菌分别为铜绿假单胞菌（24株）,革兰阳性细菌（G^ 菌）占25.8%(33株）,真菌占7.8%(10株）;前四位致病菌分别为铜绿假单胞菌（24株）,金黄色葡萄球菌（22株）,不动杆菌属（21株）,肠杆菌属（18株）,药敏结果显示这类菌株多重耐药现象严重。结论：ICU机械通气并发下呼吸道医院感染病原体构成以G^-菌为主,其药敏试验呈多重耐药,临床应重视病原学检查,开展细菌耐药性监测,合理使用抗菌药物。     

Probiotics and small bowel mucosa: Molecular aspects of their interactions

Probiotics are described as "friendly bacteria" that could improve the intestine defense by interacting with the resident microflora. There is a large body of evidence suggesting that consumption of functional food containing probiotics exerts positive effects on human health. Several clinical trials have highlighted the efficiency of probiotics in the prevention and treatment of different gastrointestinal disorders including the prevention of antibiotic associated diarrhea, the remission in patients with inflammatory bowel disease, beneficial effects against Helicobacter pylori infection, positive effects in patients affected by allergies and atopic diseases. The clinical benefits of probiotics use are mainly attributed to their antimicrobial substances production and their positive interactions with the enterocytes to reinforce the intestinal epithelial barrier. Moreover, there is evidence suggesting that probiotics stimulate both specific and non-specific host immune responses. Recently, have been published some experiments performed with the DNA microarray technology which provided a global gene screening of the complex bacteria-host interplay. Nevertheless, the molecular mechanisms by which probiotics enhance the intestinal host defense are still not completely elucidated. Here, we review the experiments and clinical studies to date on the complex mechanisms regulating the communication between probiotics and their hosts.     

Lactic acid bacteria as probiotics for the nose?

Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.     

Mechanisms of changes in immune response during bacterial coinfections of the respiratory tract

Acute diseases of the respiratory tract are often caused by viral pathogens and accompanying secondary bacterial infections. It is known that the development of such bacterial complications is caused mainly by a decreased infiltration with immune system cells and by suppressed inflammation in the lungs. There are significant advances in understanding the mechanisms of secondary infections, although many details remain unclear. This review summarizes current knowledge of the molecular and cellular changes in the host organism that can influence the course of bacterial coinfections in the respiratory tract.     

Nontypeable Haemophilus influenzae: Pathogenesis and Prevention

In this paper, we describe the ability of nontypeable Haemophilus influenzae (NTHi) to coexist with the human host and the devastating results associated with disruption of the delicate state of balanced pathogenesis, resulting in both acute and chronic respiratory tract infections. It has been seen that the strains of NTHi causing disease show a marked genetic and phenotypic diversity but that changes in the lipooligosaccharide (LOS) and protein size and antigenicity in chronically infected individuals indicate that individual strains of NTHi can remain and adapt themselves to avoid expulsion from their infective niche. The lack of reliance of NTHi on a single mechanism of attachment and its ability to interact with the host with rapid responses to its environment confirmed the success of this organism as both a colonizer and a pathogen. In vitro experiments on cell and organ cultures, combined with otitis media and pulmonary models in chinchillas, rats, and mice, have allowed investigations into individual interactions between NTHi and the mammalian host. The host-organism interaction appears to be a two-way process, with NTHi using cell surface structures to directly interact with the mammalian host and using secreted proteins and LOS to change the mammalian host in order to pave the way for colonization and invasion. Many experiments have also noted that immune system evasion through antigenic variation, secretion of enzymes and epithelial cell invasion allowed NTHi to survive for longer periods despite a specific immune response being mounted to infection. Several outer membrane proteins and LOS derivatives are discussed in relation to their efficacy in preventing pulmonary infections and otitis media in animals. General host responses with respect to age, genetic makeup, and vaccine delivery routes are considered, and a mucosal vaccine strategy is suggested.