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.     

Bacterial microbiota in upper respiratory tract of COVID-19 and influenza patients

The upper respiratory tract is inhabited by diverse range of commensal microbiota which plays a role in protecting the mucosal surface from pathogens. Alterations of the bacterial community from respiratory viral infections could increase the susceptibility to secondary infections and disease severities. We compared the upper respiratory bacterial profiles among Thai patients with influenza or COVID-19 by using 16S rDNA high-throughput sequencing based on MiSeq platform. The Chao1 richness was not significantly different among groups, whereas the Shannon diversity of Flu A and Flu B groups were significantly lower than Non-Flu & COVID-19 group. The beta diversity revealed that the microbial communities of influenza (Flu A and Flu B), COVID-19, and Non-Flu & COVID-19 were significantly different; however, the comparison of the community structure was similar between Flu A and Flu B groups. The bacterial classification revealed that Enterobacteriaceae was predominant in influenza patients, while Staphylococcus and Pseudomonas were significantly enriched in the COVID-19 patients. These implied that respiratory viral infections might be related to alteration of upper respiratory bacterial community and susceptibility to secondary bacterial infections. Moreover, the bacteria that observed in Non-Flu & COVID-19 patients had high abundance of Streptococcus, Prevotella, Veillonella, and Fusobacterium. This study provides the basic knowledge for further investigation of the relationship between upper respiratory microbiota and respiratory disease which might be useful for better understanding the mechanism of viral infectious diseases.     

The emerging potential of autophagy-based therapies in the treatment of cystic fibrosis lung infections

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), a channel that normally transports anions across epithelial cell membranes. The most common manifestation of CF is buildup of mucus in the airways and bacterial colonization of the lower respiratory tract, accompanied by chronic inflammation. Antibiotics are used to control CF-associated opportunistic infections, but lengthy antibiotic treatment risks the emergence of multiple-drug resistant (MDR) strains. New antimicrobial strategies are needed to prevent and treat infections in these high-risk individuals. Autophagy contributes to the control of a variety of microbial infections. For this reason, the recent discovery of functional impairment of autophagy in CF provides a new basis for understanding susceptibility to severe infections. Here, we review the role of autophagy in host defense against CF-associated bacterial and fungal pathogens, and survey pharmacologic approaches to restore normal autophagy function in these individuals. Autophagy restoration therapy may improve pathogen clearance and mitigate lung inflammation in CF airways.     

The emerging potential of autophagy-based therapies in the treatment of cystic fibrosis lung infections

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), a channel that normally transports anions across epithelial cell membranes. The most common manifestation of CF is buildup of mucus in the airways and bacterial colonization of the lower respiratory tract, accompanied by chronic inflammation. Antibiotics are used to control CF-associated opportunistic infections, but lengthy antibiotic treatment risks the emergence of multiple-drug resistant (MDR) strains. New antimicrobial strategies are needed to prevent and treat infections in these high-risk individuals. Autophagy contributes to the control of a variety of microbial infections. For this reason, the recent discovery of functional impairment of autophagy in CF provides a new basis for understanding susceptibility to severe infections. Here, we review the role of autophagy in host defense against CF-associated bacterial and fungal pathogens, and survey pharmacologic approaches to restore normal autophagy function in these individuals. Autophagy restoration therapy may improve pathogen clearance and mitigate lung inflammation in CF airways.     

Nontypeable Haemophilus influenzae: challenges in developing a vaccine.

Nontypeable Haemophilus influenzae (NTHi) is a gram-negative coccobacillus that is one of the bacteria that form the commensal flora of the upper respiratory tract in humans. This bacterium is an important human pathogen causing a broad spectrum of disease in both adults and children, including invasive and localised infections. The challenges in developing a bacterial protein antigen into an effective vaccine are, firstly, understanding what factors constitute an effective protective immune response for the host, and secondly, to design an effective delivery system that can target and induce the required immune response in humans that will prevent the variety of infections caused by NTHi.     

Specific and Selective Bacteriophages in the Fight against Multidrug-resistant Acinetobacter baumannii

Acinetobacter baumannii causes serious infections especially in immunocompromised and/or hospitalized patients. Several A. baumannii strains are multidrug resistant and infect wounds, bones, and the respiratory tract. Current studies are focused on finding new effective agents against A. baumannii. Phage therapy is a promising means to fight this bacterium and many studies on procuring and applying new phages against A. baumannii are currently being conducted. As shown in animal models, phages against multidrug-resistant A. baumannii may control bacterial infections caused by this pathogen and may be a real hope to solve this dangerous health problem.     

铜绿假单胞菌群体感应系统介导的呼吸道病原菌种间互作研究进展

细菌性慢性呼吸道感染是严重威胁人类健康和制约社会经济发展的常见疾病。呼吸道环境和结构的复杂性导致慢性感染病灶常常定植着多种病原菌,如铜绿假单胞菌Pseudomonas aeruginosa、金黄色葡萄球菌Staphylococcus aureus、大肠埃希氏菌Escherichia coli、肺炎克雷伯氏菌Klebsiella pneumoniae、鲍曼不动杆菌Acinetobacter baumannii和白色念珠菌Candida albicans等。这些病原菌在慢性呼吸道感染的发展过程中进化出了合作、竞争、共生等复杂的种间关系,通过形成相对稳定的群落系统使多种病原菌成为一个整体来应对呼吸道各种苛刻的生存条件,从而导致呼吸道感染针对性治疗的失败或病情反复。目前国际上关于病原菌种间互作关系的研究正处于起步阶段,临床证据表明铜绿假单胞菌的定植与慢性呼吸道感染的发生、发展息息相关,并且该菌可以利用群体感应系统来主导与其他病原菌的互作与共存。因此,本文围绕群体感应系统综述了铜绿假单胞菌与其他常见呼吸道感染病原菌的种间关系和互作机理,可加深人们对病原菌种间互作与慢性呼吸道感染相关疾病关联性的认识,并为进一步临床治疗方案的改进、疾病控制和新型抗感染药物的研发提供新视角、新方向。     

Sequential targeting of interferon pathways for increased host resistance to bacterial superinfection during influenza

Bacterial co-infections represent a major clinical complication of influenza. Host-derived interferon (IFN) increases susceptibility to bacterial infections following influenza, but the relative roles of type-I versus type-II IFN remain poorly understood. We have used novel mouse models of co-infection in which colonizing pneumococci were inoculated into the upper respiratory tract; subsequent sublethal influenza virus infection caused the bacteria to enter the lungs and mediate lethal disease. Compared to wild-type mice or mice deficient in only one pathway, mice lacking both IFN pathways demonstrated the least amount of lung tissue damage and mortality following pneumococcal-influenza virus superinfection. Therapeutic neutralization of both type-I and type-II IFN pathways similarly provided optimal protection to co-infected wild-type mice. The most effective treatment regimen was staggered neutralization of the type-I IFN pathway early during co-infection combined with later neutralization of type-II IFN, which was consistent with the expression and reported activities of these IFNs during superinfection. These results are the first to directly compare the activities of type-I and type-II IFN during superinfection and provide new insights into potential host-directed targets for treatment of secondary bacterial infections during influenza.     

吸烟对人体呼吸道厌氧菌的影响

目的探究吸烟对人体内的呼吸道微生态的影响。方法采用细菌鉴定及药敏分析系统鉴定健康吸烟者与非吸烟者,患下呼吸道感染吸烟与非吸烟者咽后壁分泌物的细菌密度、细菌数量及种类的改变。结果在健康吸烟者与患有下呼吸道感染患者的呼吸道中,厌氧菌明显升高,其中以韦荣菌和消化链球菌为主。结论吸烟可使人体的呼吸道微生态中细菌密度,细菌数量及种类的改变,易患呼吸系统疾病。     

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.     

Clinical complications of Mycoplasma pneumoniae disease--other organs

Although self-limited respiratory tract infections caused by Mycoplasma pneumoniae are well recognized in children and young adults, respiratory involvements and hepatic dysfunction may occur. The frequency and clinical features of these complications were investigated. Experimental studies with regard to bacterial superinfection were also carried out. The test animals which were first infected with Mycoplasma pneumoniae and then with Staphylococcus aureus showed more extensive bacteriological and pathological changes than those infected with Staphylococcus aureus only. Liver biopsies performed on three human patients showed hepatic dysfunction and the histological findings were diagnosed as non-specific reactive hepatitis in each case.     

Bordetella type III secretion modulates dendritic cell migration resulting in immunosuppression and bacterial persistence

Chronic bacterial infection reflects a balance between the host immune response and bacterial factors that promote colonization and immune evasion. Bordetella bronchiseptica uses a type III secretion system (TTSS) to persist in the lower respiratory tract of mice. We hypothesize that colonization is facilitated by bacteria-driven modulation of dendritic cells (DCs), which leads to an immunosuppressive adaptive host response. Migration of DCs to the draining lymph nodes of the respiratory tract was significantly increased in mice infected with wild-type B. bronchiseptica compared with mice infected with TTSS mutant bacteria. Reduced colonization by TTSS-deficient bacteria was evident by 7 days after infection, whereas colonization by wild-type bacteria remained high. This decrease in colonization correlated with peak IFN-gamma production by restimulated splenocytes from infected animals. Wild-type bacteria also elicited peak IFN-gamma production on day 7, but the quantity was significantly lower than that elicited by TTSS mutant bacteria. Additionally, wild-type bacteria elicited higher levels of the immunosuppressive cytokine IL-10 compared with the TTSS mutant bacteria. B. bronchiseptica colonization in IL-10(-/-) mice was significantly reduced compared with infections in wild-type mice. These findings suggest that B. bronchiseptica use the TTSS to rapidly drive respiratory DCs to secondary lymphoid tissues where these APCs stimulate an immunosuppressive response characterized by increased IL-10 and decreased IFN-gamma production that favors bacterial persistence.     

Rational antimicrobial pharmacotherapy of secondary infections in patients with pulmonary tuberculosis]

The results of 3-year (2002-2004) local microbiological monitoring of secondary infections due to opportunistic microflora that complicated the treatment of the main disease in patients of a regional (Moscow) tuberculosis hospital are presented. The monitoring revealed the leading microorganisms, the etiological agents of the secondary lower respiratory tract infection in the patients with pulmonary tuberculosis. The level of their resistance to the up-to-date antimicrobials was determined. Recommendations for optimization of antibacterial therapy of patients with pulmonary tuberculosis complicated by secondary lower respiratory tract infection due to opportunistic microorganisms were developed and validated.     

深部真菌感染临床特点分析

目的了解深部真菌感染患者的性别、年龄、感染部位、住院科室、菌种分布及真菌耐药情况,为临床防治真菌感染提供研究依据。方法收集荆州市中心医院2009年1月至2009年12月微生物实验室分离的真菌446株,采用科马嘉显色琼脂及API220C Aux鉴定系统鉴定,并使用ATMTMFUNGUS3真菌药敏卡进行体外药敏试验。结果临床真菌感染男性占72%,以老年患者为主,大于60岁者占54.9%;感染的真菌主要分布于呼吸内科和ICU,分别占35.5%、24.9%;主要感染部位为呼吸道,占91.3%;主要菌种为白假丝酵母菌、热带念株菌、近平滑假丝酵母菌、光滑念株菌和克柔念株菌,分别占64.2%、13.2%、9.6%、7.6%和5.4%;合并细菌感染的感染真菌100株,占22.2%,细菌中以革兰阴杆性菌为主,占96%;药敏试验结果显示真菌对各抗真菌药具有较好的敏感性。结论临床真菌感染已日益突出,以呼吸科及ICU患者老年男性为主,儿童真菌感染亦不容忽视,感染菌种以白假丝酵母菌和热带念株菌为主,临床应加强对这些真菌感染的预防和监测,防止真菌感染。     

Pathogenic potential of environmental Klebsiella pneumoniae isolates

Klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. K. pneumoniae infections can occur at nearly any body site; however, urinary tract infections and infections of the respiratory tract predominate. Infections are frequently preceded by gastrointestinal colonization, and the gastrointestinal tract is believed to be the most important reservoir for transmission of the bacteria. In contrast to many other bacterial pathogens, K. pneumoniae is ubiquitous in nature. Several studies have described Klebsiella isolates of environmental origin to be nearly identical to clinical isolates with respect to several phenotypic properties. However, the pathogenic potential of environmental K. pneumoniae isolates is essentially unknown. We have evaluated the virulence of K. pneumoniae strains of environmental and clinical origin directly in animal models, i.e. in urinary tract infection and intestinal colonization models. Furthermore, the ability to adhere to and invade human epithelial cell lines was examined. Although strain-to-strain differences were observed in the individual infection models, overall, strains of environmental origin were found to be as virulent as strains of clinical origin. The ubiquity of K. pneumoniae in nature and the general ability of K. pneumoniae strains to infect susceptible hosts might explain the high frequency of opportunistic infections caused by this species.     

Identifying vaccine antigens and assessing delivery systems for the prevention of bacterial infections

Bacterial infections in the respiratory tract and middle ear continue to be a major cause of morbidity and mortality despite the availability of antibiotic therapies. To assist development of vaccines for preventing these infections, animal models have been established in rodents. These models have been used effectively to evaluate different vaccination strategies. Our studies have found that for respiratory tract infections caused by Streptococcus pneumoniae, nontypeable Haemophilus influenzae (NTHI) and Moraxella catarrhalis, a primary immunisation targeted to the gut-associated lymphoid tissue was extremely effective in enhancing bacterial clearance. For the gram-negative pathogens, NTHI and M. catarrhalis, this mucosal immunisation was significantly more effective than systemic immunisation, however, for S. pneumoniae systemic immunisation was as effective. A strategy using these models has effectively been used to determine the potential of antigens from each of the pathogens to protect against infection. Antigens that demonstrate significant vaccine potential have been used to investigate delivery systems. One of the major challenges that still exists is to find mechanisms that will effectively deliver protein antigens to mucosal surfaces. Several strategies have been investigated and resulted in varying degrees of success.     

Toll-like receptor 9 acts at an early stage in host defence against pneumococcal infection

Toll-like receptor 9 (TLR9) induces an inflammatory response by recognition of unmethylated CpG dinucleotides, mainly present in prokaryotic DNA. So far, TLR9-deficient mice have been shown to be more sensitive than wild-type mice to viral, but not to bacterial infections. Here, we show that mice deficient in TLR9 but not in TLR1, TLR2, TLR4 and TLR6 or IL-1R/IL-18R are more susceptible to a respiratory tract bacterial infection caused by Streptococcus pneumoniae. Intranasal challenge studies revealed that TLR9 plays a protective role in the lungs at an early stage of infection prior to the entry of circulating inflammatory cells. Alveolar as well as bone marrow-derived macrophages deficient in either TLR9 or the myeloid adaptor differentiation protein MyD88 were impaired in pneumococcal uptake and in pneumococcal killing. Our data suggest that in the airways, pneumococcal infection triggers a TLR9 and MyD88-dependent activation of phagocytic activity from resident macrophages leading to an early clearance of bacteria from the lower respiratory tract.     

The role of antibodies in respiratory viral immunity

Antibodies protect against disease caused by viruses that infect the lower respiratory tract, and contribute to the resolution of established infection by these pathogens. The kinetics and specificities of antibodies secreted in response to respiratory virus infections are described, however the mechanisms by which antibodies prevent or resolve infection are less clear. Recent studies of virus neutralization in cell culture, the immunobiology of respiratory virus infections in animal models, and passive immunoprophylaxis of human patients are beginning to better define the role of antibodies in immunity to respiratory viruses.     

Bronchoscopic Diagnosis of Pulmonary Infections—Comparison of Protected-Specimen Brush and Cytology Brush With Lung Aspirates

In a recent study the use of a new plugged double-lumen protected-specimen brush with the flexible fiberoptic bronchoscope was advocated to isolate pathogens in lower respiratory tract infections while avoiding upper respiratory tract contamination. To compare the efficacy of this brush and a standard single-lumen cytology brush in identifying the etiologic agent in lower respiratory tract infections, we studied 18 patients with lung infections. Transthoracic lung aspiration was done in all but two patients in an attempt to identify the specific etiologic agent. In these two cases, cultures of specimens of blood or postmortem lung tissue yielded the causative organism. In 12 patients anaerobic or aerobic bacteria (or both) were identified, whereas one patient had a mixed bacterial and fungal infection. Using the cytology brush and the protected-specimen brush we identified at least one pathogen in 10 of 12 and 10 of 13 cases, whereas both brushes missed one or more causative organisms in 8 of 12 and 8 of 13 cases, respectively. Nonetiologic organisms were found in 8 of 12 cases by the cytology brush and 8 of 13 cases by the protected-specimen brush. Quantitative culture techniques improved the specificity of the brush results in infections where aerobes predominated. Our data show that bronchoscopic cultures of lower respiratory tract infections do not consistently recover the causative agent and are frequently subject to contamination by nonetiologic organisms. There was no difference between the brushes in avoiding contamination.     

白带常规联合生化快速检测方法诊断下生殖道感染

目的 调查杭州市滨江区下生殖道感染情况.方法 采用白带常规检测方法联合需氧菌阴道炎/细菌性阴道病五项联合测定技术对就诊者的阴道分泌物进行检测.结果 在500名就诊者中,检出下生殖道感染患者465例,其中单一性感染216例(46.5％),混合感染患者249例(53.6％).在249例混合感染中,主要为需氧菌引起的合并感染,占混合感染的65.9％.结论 白带常规检测方法联合需氧菌阴道炎/细菌性阴道病五项联合测定技术的检测方法可对下生殖道感染作出全面明确诊断.