Pathogens isolated from patients with community-acquired lower respiratory tract infections

The aim of the study was to assess the prevalence and antimicrobial susceptibility of pathogens in patients hospitalized in Clinic of Pneumology and Alergology University Clinical Hospital No 1 in ?od? in 2006-2008 period, due to community-acquired lower respiratory tract infections. In this samples of sputum, bronchoaspirate and BAL's were evaluated. The most frequent pathogens isolated from all examinated patients were Gram-negative rods. This bacteria were susceptible in most to imipenem (91%), ceftazydym (71%), amikacin (67%), ciprofloxacin (63%) and to amoxicillin with clavulanic acid only in 18%. This study show high prevalence of Gram-negative rods in patients hospitalized due to community-acquired lower respiratory tract infections.     

Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing

The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.     

Selective infection of lower respiratory tract by respiratory viruses in children with recurrent respiratory tract infections.

Thirty preschool children presenting with recurrent respiratory infections and their unaffected siblings were observed prospectively for a year. The index children experienced more episodes of acute respiratory infection than their siblings. Respiratory viruses were the major cause of respiratory infections. The index children had lower respiratory tract disease, predominantly wheeze, during 34% of proved respiratory virus infections compared with 11% of such infections experienced by the control children (p less than 0.02). Atopic children had an increased tendency to wheeze that did not reach significance, but atopy was not associated with increased susceptibility to respiratory infections.     

老年与中青年患者下呼吸道感染病原菌的对比分析

目的对比分析老年与中青年患者下呼吸道感染病原菌的分布规律及其耐药性特点,以指导临床合理用药。方法将研究对象分为老年(≥60岁)和中青年(20～59岁)2组;采用API系统进行菌种鉴定;采用K-B法进行药敏试验;采用纸片扩散表型确证法进行超广谱β-内酰胺酶(ESBLs)测定;采用SPSS 13.0进行χ2检验。结果老年组的真菌分离率显著高于中青年组,以白色假丝酵母菌最多;中青年组的G-杆菌分离率显著高于老年组,以铜绿假单胞菌最多;老年组主要致病菌对多数药物的耐药率比中青年组有增高趋势,但差异多无统计学意义;老年组肺炎克雷伯菌的ESBLs阳性率显著高于中青年组。结论老年与中青年患者下呼吸道感染的病原菌分布及耐药性存在一定差异。     

心功能不全合并下呼吸道感染患者病原菌分布与耐药性分析

目的分析心功能不全合并下呼吸道感染患者的病原菌分布规律及其耐药性特点,以指导临床合理用药。方法采用API系统进行菌种鉴定,采用K-B法进行药敏试验,采用纸片扩散表型确证法进行超广谱β-内酰胺酶(ESBLs)测定。结果 244株病原菌以G-杆菌最多(66.39%),主要是肺炎克雷伯菌、铜绿假单胞菌和鲍曼不动杆菌;真菌其次(28.28%),主要是白色假丝酵母菌;G+球菌较少(5.33%),主要是金黄色葡萄球菌。G-杆菌对碳青霉稀类(美罗培南)及氟喹诺酮类(环丙沙星/左氧氟沙星)抗生素较敏感,而对头孢类耐药率较高;白色假丝酵母菌对两性霉素B的耐药率最低。结论心功能不全合并下呼吸道感染患者的主要病原菌以G-杆菌、真菌为主,白色假丝酵母菌是最常见病原菌;病原菌耐药性较强,耐药监测至关重要。     

儿童下呼吸道感染病原菌分布及耐药性

目的对儿童下呼吸道感染病原菌分布情况及耐药情况进行分析。方法选取延安大学附属医院儿科2012年8月至2014年8月明确诊断的385例下呼吸道感染患儿,对其痰标本的培养结果进行统计,分析其病原菌分布及耐药情况。结果患儿痰培养阳性菌株134例,其中革兰阴性菌91株,以大肠埃希菌为主,占20.9%;革兰阳性菌40株,以金黄色葡萄球菌为主,占9.7%;真菌3株,占2.2%。对5种主要病原菌检出年度情况分析,显示大肠埃希菌、肺炎克雷伯杆菌、鲍曼不动杆菌检出率逐年增加,肺炎链球菌检出率逐年降低,而金黄色葡萄球菌三年无明显变化。婴儿组、幼儿组病原菌检出率显著高于学龄前及学龄组,病原菌检出率在年龄分布上差异有统计学意义(χ2=43.445,P0.01)。不同病原菌对常用抗菌药物呈现不同程度的耐药,革兰阴性菌对亚胺培南、美罗培南均敏感,对氨苄西林耐药率最高;金黄色葡萄球菌及肺炎链球菌对利奈唑胺及万古霉素敏感,对苄青霉素耐药率最高。结论儿童下呼吸道感染病原菌以革兰阴性菌为主,检出率在性别上无差异,婴儿、幼儿检出率高于学龄前及学龄儿童。治疗时应根据药敏试验结果,合理使用抗生素,降低耐药菌株的产生。     

神经外科颅内出血患者下呼吸道感染病原菌的耐药性监测

目的了解神经外科重症监护室（NICU）颅内出血患者下呼吸道感染病原菌的种类及耐药情况,为临床合理用药提供依据。方法对2010年1月至2011年1月颅内出血的患者,其下呼吸道感染病原菌的种类及耐药性进行回顾性分析。结果分离出的374例病原菌中以革兰阴性杆菌为主,占81．8％,革兰阳性球菌占4．0％,真菌占14．2％。分离率较高的细菌依次为鲍曼不动杆菌、铜绿假单胞菌、肺炎克雷伯菌、嗜麦芽窄食单胞菌、金黄色葡萄球菌。其中,产超广谱β-内酰胺酶（ESBLs）的肺炎克雷伯菌的检出率为50．0％;耐甲氧西林金黄色葡萄球菌（MRSA）的检出率为73．3％。鲍曼不动杆菌和铜绿假单胞菌对丁胺卡那、妥布霉素、多粘菌素B有较好的敏感性;而金黄色葡萄球菌对复方新诺明、呋喃妥因、万古霉素耐药率较低。结论NICU颅内出血患者下呼吸道感染以多重耐药的革兰阴性杆菌为主,临床应根据药敏结果合理用药,控制和减少感染的发生。     

下呼吸道感染患者病原菌分布及耐药性

目的 分析下呼吸道感染患者病原菌分布及耐药性,指导临床合理用药。方法 收集我院2013年至2015年院内感染患者痰标本进行细菌培养和药物敏感性试验。结果 3年共收集下呼吸道痰液标本21 615份,分离病原菌5 621株,阳性率为26.0%;其中革兰阴性（G－）菌4 249株,占75.6%,以铜绿假单胞菌居多（20.7%）;真菌764株,占13.6%,以白假丝酵母居多（12.6%）;革兰阳性（G+）菌608株,占10.8%,以金黄色葡萄球菌居多（9.9%）。药物敏感试验结果显示：G-杆菌对亚胺培南、美洛培南耐药率最低,对青霉素类、喹诺酮类和部分三代头孢类等抗菌药耐药率较高（>50.0%）。G+球菌对万古霉素、利奈唑胺耐药率为零,对青霉素类、喹诺酮类和红霉素等抗菌药耐药率较高（>40.0%）。结论 下呼吸道感染患者病原菌以G-杆菌为主,耐药性呈增长趋势,临床应加大病原菌分布检测及其耐药性监测力度,及时调整抗菌药物用药。     

Diagnosis methods for pneumococcal etiology determination in lower respiratory tract infections

A comparative study of etiological diagnosis in lower respiratory tract infections (LRTI), by conventional bacteriological methods and by pneumococcal antigen direct detection in sputum was performed. This work followed the establishing of rapid methods place, respectively of coagglutination (CoA), counterimmunoelectrophoresis (CIE), within the methodology of bacteriological diagnosis in lower respiratory tract infections presenting pneumococcal etiology. The results of investigations performed on 84 sputa from LRTI patients proved the utility of CoA method in determining a rapid etiological diagnosis, important for applying an emergence targetted antibiotherapy. CoA method, with the reagents in use, covering only 10 out of 83 serological types of S. pneumoniae in not capable of replacing conventional methods of bacteriological diagnosis; they complete each other, increasing the efficiency of etiological diagnosis in LRTI. CIE method is less sensitive and more difficult to perform, being less useful in rapid etiological diagnosis of LRTI.     

Rhinovirus genome variation during chronic upper and lower respiratory tract infections

Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5'UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.     

Intestinal microbiocenosis in children with thymomegaly and acute lower respiratory tract infections and regimen of its correction

57 children with thymomegaly from 3 months to 3 years of age with acute lower respiratory tract infections were studied. Disturbances of gut microflora - changes in both obligate and potentially harmful symbionts were detected in 70.2% of cases. In 47,5% of cases increased quantity of enterococci was observed. Decreased quantities of bifidobacteria and lactobacilli were observed in all and 27.5% of studied patients respectively. Most diverse gut microflora has been observed in children with pneumonia and thymomegaly of II level. During treatment of children with thymomegaly changes in gut microflora should be considered along with changes in the immune system.     

Characteristic systemic cytokine responses in children with human bocavirus‐positive lower respiratory tract infection

To investigate systemic cytokine responses in human bocavirus (HBoV)‐associated lower respiratory tract infection, serum cytokine profiles were analyzed in HBoV positive‐children (n = 14) using multiplex immunoassay. Concentrations of TNF‐α, IL‐2, IL‐5 and IL‐8 on admission were significantly different from those of respiratory syncytial virus‐positive children (n = 28). This unique cytokine response might partly explain some characteristic clinical features of HBoV‐associated respiratory infection.     

Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections

Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex II V2.0 kit and explored factors influencing its sensitivity. Nasopharyngeal swab (NPS) specimens were prospectively collected from pediatric inpatients with lower respiratory tract infections at the time of admission in the Shenzhen Children’s Hospital from May 2009 to April 2010. Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In parallel, 16 real-time TaqMan quantitative RT-PCR assays were used to quantitatively detect each virus except for RhV. Influenza and parainfluenza viral cultures were also performed. Among the total 438 NPS specimens collected during the study period, one or more viral pathogens were detected in 274 (62.6%) and 201(45.9%) specimens by monoplex TaqMan RT-PCR and multiplex ResPlex, respectively. When results from monoplex PCR or cell culture were used as the reference standard, the multiplex PCR possessed specificities of 92.9–100.0%. The sensitivity of multiplex PCR for PIV3, hMPV, PIV1 and BoV were 73.1%, 70%, 66.7% and 55.6%, respectively, while low sensitivities (11.1%–40.0%) were observed for FluA, EnV, OC43, RSV and H1N1. Among the seven viruses/genotypes detected with higher frequencies, multiplex PCR sensitivities were correlated significantly with viral loads determined by the TaqMan RT-PCR in FluA, H1N1-p and RSV (p=0.011?0.000). The Qiagen ResPlex II multiplex RT-PCR kit possesses excellent specificity for simultaneous detection of 17 viral pathogens in NPS specimens in pediatric inpatients at the time of admission. The sensitivity of multiplex RT-PCR was influenced by viral loads, specimen process methods, primer and probe design and amplification condition.     

Identification of a novel polyomavirus from patients with acute respiratory tract infections

We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus-specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen.     

小儿下呼吸道感染痰培养标本病原菌构成分析

目的了解小儿下呼吸道感染病原菌的分布及对常用抗菌药物的耐药状况。方法对2710例小儿下呼吸道感染患者痰标本进行培养,用VITEK-2Compact微生物鉴定系统鉴定菌种和药敏试验,WHO-NET5．4软件对数据进行分析。结果共分离病原菌675株,革兰阴性杆菌457株,占67．7％,主要为大肠埃希菌、肺炎克雷伯菌;革兰阳性球菌159株,占23．5％,主要为金黄色葡萄球菌、肺炎链球菌;真菌59株,占8．7％,主要为白色假丝酵母菌。结论小儿下呼吸道感染病原菌以革兰阴性杆菌为主,耐药性较为严重,应不断加强耐药性监测,合理使用抗菌药物。     

老年患者下呼吸道感染病原菌分布与耐药性分析

目的探讨老年患者下呼吸道感染常见病原菌分布及其耐药情况,为临床合理用药提供依据。方法对本院2010年1月至2013年12月老年患者下呼吸道痰标本分离的病原菌用VITEK32全自动细菌鉴定仪进行鉴定,用K-B纸片法进行体外药敏试验,用WHONET 5.4软件进行统计学分析。结果共分离出病原菌936株,其中革兰阴性菌655株(69.98%),前四位为肺炎克雷伯杆菌、大肠埃希菌、铜绿假单胞菌和鲍氏不动杆菌,占比分别为24.89%、18.38%、11.97%和8.01%;革兰阳性菌196株(20.94%),前三位为金黄色葡萄球菌、溶血葡萄球菌和肠球菌属,占比分别为10.15%、4.70%和3.10%;真菌85株(9.08%)。药敏结果显示,主要革兰阴性菌对阿米卡星、哌拉西林/他唑巴坦、头孢哌酮/舒巴坦和亚胺培南耐药率较低;主要革兰阳性菌对呋喃妥因、利福平、阿米卡星、替加环素、利奈唑胺和万古霉素耐药率较低。结论老年患者下呼吸道感染病原菌以革兰阴性杆菌为主,并出现多重耐药,临床应根据药敏结果合理选择抗菌药物。