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Objective: To explore the pathogen composition and distribution characteristics of pathogens in respiratory samples from patients with fever of unknown origin. Methods: A total of 96 respiratory samples of patients with unknown cause fever with respiratory symptoms were collected from four hospitals above grade II in Shijiazhuang area (Hebei Provincial Hospital of Traditional Chinese Medicine, Luancheng District People's Hospital, Luquan District People's Hospital, Shenze County Hospital) from January to April 2020, and multiplex-fluorescent polymerase chain reaction(PCR)was used to detect influenza A virus, influenza B virus, enterovirus, parainfluenza virus I/II/III/IV, respiratory adenovirus, human metapneumovirus, respiratory syncytial virus, human rhinovirus, human bocavirus, COVID-19, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Streptococcus pneumoniae, Klebsiella pneumoniae, Group A streptococcus, Haemophilus influenzae, Staphylococcus aureus nucleic acid detection, the results were analyzed for chi-square. Results: A total of 8 pathogens were detected in the upper respiratory tract samples of 96 fever patients, including 1 kind of virus, 6 kinds of bacterias, and Mycoplasma pneumoniae. There were 12 viruses including influenza virus and parainfluenza virus, Legionella pneumophila and Chlamydia pneumoniae were not detected. The pathogen detection rates in descending order were Streptococcus pneumoniae (58/96, 60.42%), Haemophilus influenzae(38/96, 39.58%), Klebsiella pneumoniae (14/96, 14.58%), Staphylococcus aureus (10/96, 10.42%), Mycoplasma pneumoniae (8/96, 8.33%), Pseudomonas aeruginosa (6/96, 6.25%), Group A streptococcus (4/96, 4.17%) and human rhinovirus (2/96, 2.08%). The proportions of single-pathogen infection and multi-pathogen mixed infection in fever clinic patients were similar, 41.67% (40/96) and 45.83% (44/96), respectively, and 12.50% (12/96)of the cases had no pathogens detected. The infection rate of Mycoplasma pneumoniae in female patients with fever (21.43%) was higher than that in male patients with fever (2.94%) (P < 0.05). There was no statistical difference between the distribution of of other pathogens and gender and age(P > 0.05). Conclusions: The upper respiratory tract pathogens were mainly bacterial infections, and occasional human rhinovirus and Mycoplasma pneumonia infections. In clinical diagnosis and treatment, comprehensive consideration should be given to the pathogen detection.
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Objective: To describe the clinical features, causal agent and transmission mode of a fever outbreak in a school in Shanghai. Methods: Field epidemiological approaches including case definition development, searching for contacts, distribution of diseases description, environmental sampling and laboratory testing. Results: A total of 16 influenza-like cases were included, all concentrated in the one class of grade two, including 15 students and 1 teacher. Among student cases, the incidence rate was 36.59%(15/41), the average age was 7.4 years, the incidence rate was 36.84%(7/19) for boys, 36.36%(8/22) for girls. The clinical course was 5-15 days, with the median of 9 days, and 18.75%(3/16) of the cases stayed studying while sick. The nasopharyngeal swab specimens in 16 cases all tested positive for influenza B, of which 11 tested positive for mycoplasma pneumoniae and 1 case also tested positive for coronavirus OC43. Body temperature, number of mononuclear cells, and treatment time of patients infected with Influenza B and mycoplasma pneumoniae were higher than those of patients infected with influenza B alone(P < 0.05). The outbreak lasted for 12 days, all sick students were treated and discharged from hospital, with no severe cases or death, and the outbreak was effectively controlled. Conclusion: This campus cluster outbreak caused by influenza B and mycoplasma pneumoniae. Patients with influenza B with mycoplasma pneumoniae have severe symptoms and a long course of illness, suggesting the importance of early management of the epidemic.
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Bovine rhinitis virus (BRV) is an important pathogen responsible for the bovine respiratory disease complex (BRDC) and can be divided into two genotypes (BRAV and BRBV). To establish a duplex quantitative real-time RT-PCR assay for simultaneous detection of BRAV and BRBV, specific primers and TaqMan probes targeting the 5'NTR of BRAV and 3'NTR of BRBV were designed. A duplex quantitative real- time RT- PCR assay for simultaneous detecting BRAV and BRBV was preliminarily established by optimizing reaction conditions for each step. The assay specifically detects BRAV and BRBV, and no crossreaction with other common bovine respiratory pathogens, including IDV, BCoV, BVDV-1, BRSV, BPIV-3, BAdV-3, mycoplasma bovis, Pasteurella multocida, Mannheimia haemolytica, Escherichia coli, and Salmonella, was observed. In addition, the sensitivity test showed that the detection limits of this assay were 3.2x101 copies/L for both BRAV and BRBV plasmid standards. Besides, the repeatability test showed that the variation coefficients of this assay were less than 0.05 from both lot-to-lot and intra-lot. These results showed that the assay has high specificity, extreme sensitivity, and good repeatability. Moreover, a total of 43 nasal swabs of BRDC cattle were tested by our assay and four other quantitative real-time RT-PCR assays, including 3 BRAV assays and 4 BRBV assays. The results showed that the detection rates of our assay were 32.56%(14/43) for BRAV and 30.23%(13/43) for BRBV, and the detection rates of other quantitative real-time RT-PCR assays were 0(0/43), 2.33%(1/43), 23.26%(10/43) for BRAV and 27.91% (12/43), 27.91%(12/43), 27.91%(12/43), 27.91%(12/43) for BRBV, indicating that our assay has a more substantial detection capability than other assays. This study firstly established a duplex quantitative real-time RT-PCR assay for simultaneous detection of BRAV and BRBV, and the assay exhibited high specificity, sensitivity, and stability. Moreover, the study firstly confirmed the existence of BRAV in China, contributing to the prevention and control of BRDC.
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This paper describes the clinical signs and use of differential laboratory diagnostic techniques (computed tomography, cytology, histopathology, antigen/antibody detection and polymerase chain reaction) for infectious (viral, bacterial, fungal and parasitic) and non-infectious (inflammatory/immune mediated, neoplastic, cardiac, malformation, foreign body, smoke inhalation, aspiration of caustic material, non-cardiogenic, pulmonary oedema, traumativ, pneumothorax, pulmonary contusions and idiopathic) causes of respiratory diseases in cats and dogs in Ontario, Canada.
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Objective: To understand the pathogenic spectrum and epidemiological characteristics of severe acute respiratory infection (SARI) in adult inpatients in Yangpu District, Shanghai, China, in order to explore strategies for the prevention and treatment of respiratory infectious diseases. Methods: Individual cases were from adult inpatients with SARI in Yangpu District, Shanghai, China from January 2019 to July 2021. Their respiratory samples were collected for etiological pathogen testing. Results: A total of 681 SARI cases were enrolled for sampling and lab testing. Among them, 79.00% were aged 60 years and older, and 75.48% had confirmed chronic disease history. A total of 163 infection inpatients (23.94%) were positive for at least one pathogen. The pathogens identified most frequently were influenza A virus (6.75%), followed by rhinovirus/enterovirus (3.23%), parainfluenza virus (PIV) (2.79%), Mycoplasma pneumoniae (2.35%), coronavirus (CoV) (2.06%). The positive rates of adenovirus (AdV), human metapneumovirus (hMPV), respiratory syncytial virus and bocavirus were all less than 2%. Bacterial strains were identified in eleven SARI cases, including Staphylococcus aureus and Pseudomonas aeruginosa (4 strains), Klebsiella pneumoniae (3 strains). Legionella pneumophila was detected in 9 cases (1.32%) and Bordetella pertussis in 5 cases (0.73%). Two pathogens were co-detected from 11 cases, accounting for 1.62% of 163 positive cases. The most common co-detected pathogens were influenza A virus and other pathogens, accounting for 54.55% of the mixed infection. The positive rates of pathogens were not significantly different between less than 60 years old and over 60 years old groups except for Bordetella pertussis, adenovirus and Mycoplasma pneumonia(P < 0.05). Influenza virus had epidemic peak in winter and spring, but not in summer from 2019 to 2021. Conclusion: Various respiratory pathogens are detected from adult SARI cases. It is mainly influenza virus, with co-detected pathogens and rare pathogens. This study provides helpful information for targeted prevention and control measures including vaccination.
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OBJECTIVE: To investigate the diagnosis and clinical characteristics of 10 cases of clustered Chlamydia pneumoniae pneumonia during the prevention and control of the COVID-19 pandemic. METHODS: The clinical data of 10 patients with clustered Chlamydia pneumoniae infection in a college diagnosed and treated by the Third Medical Center of the PLA General Hospital from Mar. 10, 2021 to Mar. 17, 2021 were retrospectively analyzed, the clinical characteristics of Chlamydia pneumoniae infection were summarized, and the diagnosis and treatment plan was selected quickly and accurately. RESULTS: All 10 cases with Chlamydia pneumoniae pneumonia infection had no history of contact with live or dead birds, 80% of them had cough symptom, 50% of them had fever symptom. Laboratory test results showed that 80% of patients had white blood cell count in normal range, 60% of patients had increased c-reactive protein level to varying degrees, 70% of patients had creatine kinase above normal, creatinine and procalcitonin were all normal, and some coagulation function indexes were abnormal. Lung CT scan showed increased density of unilateral lung floccus, nodules or spots, with air bronchial signs and even consolidation. The results of respiratory tract five-link card showed that all 10 patients were positive for Chlamydia pneumoniae immunoglobulin M(IgM) antibody. The nucleic acid sequence of Chlamydia pneumoniae was detected by metagenomics next-generation sequencing(mNGS)in 2 patients after hospitalization. 10 patients were treated with moxifloxacin hydrochloride and sodium chloride injection and moxifloxacin hydrochloride tables in sequences, all of which were cured. After 1 month, the outpatient reexamination of lung CT showed that the inflammation was basically absorbed. CONCLUSION: Chlamydia pneumoniae infection can cause outbreak through respiratory transmission, which tend to occur in the spring. The combination of respiratory pathogen antibody detection and mNGS technology can improve the efficiency of clinical diagnosis and treatment.
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The new coronavirus reaches the cells of the lower respiratory tract, starting an inflammatory process. Considering this infection, the immune system must eliminate the pathological agents and mantein cellular homeostasis, tissue repair and generation of immunity memory. When there is a failure in this pathway, this system encounters a series of difficulties for the resumption of balance, in addition to secondary infections, leading to additional clinical complications. Thus, this study sought to address the immune response to Sars-CoV-2, and the main post-Covid secondary infections (bacterial and fungal) and antimicrobial resistance in this context. This is a literature review based on the analysis of journals from the following academic platforms: Google Scholar, Center for Biotechnology Information (PubMed), Science Direct, Scientific Electronic Library Online (SciELO) and Scopus. The research was delimited in a range from 2003 to 2021, using the keywords COVID-19 as a search tool;Immune response;Bacterial infections;Fungal infections;Resistance. The results obtained in the studies demonstrate the impact of secondary infections on mortality, thus, among the main infections, bacterial infections (84%) stand out, including mainly the agents: Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile and Mycoplasma pneumoniae. As for secondary fungal infections, Aspergillus sp. and Candida affected mainly critically ill patients. Based on the data, an evident problem was the difficulty in identifying the agent causing the secondary infection, resulting in a scenario of intense use of broad-spectrum antibiotics, contributing to the selection of resistant pathogens and, controversially, the worsening of the prognosis of the disease patient.
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Backyard poultry is evolving as a fast-growing sector in recent times across the world. Apart from providing nutritional security, and livelihood to marginalized sector, also fulfils the demand for organic and welfare meat and eggs. However, the productivity is often challenged by incidences of diseases due to poor biosecurity and lack of vaccination. In this study, systematic review and meta-analysis were performed on the global prevalence of infectious diseases in backyard chickens. A total of 22 bacterial, viral, parasitic and fungal diseases were reported from 55 publications between 2000 and 2020 worldwide. Viral diseases were the most reported followed by bacterial and parasitic diseases. 61 out of 91 studies from 55 publications investigated seven major diseases: Avian influenza (AI), Newcastle disease (ND), infectious bronchitis (IB), Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), Salmonella infection, and infectious laryngotracheitis (ILT). The overall pooled prevalence estimate for all the diseases worldwide was 33% (95% confidence interval (CI): 28-38). The pooled estimates for most reported viral diseases AI and ND were 12.5% (95% CI: 7-18) and (30% CI: 19-43), respectively. IBD (71% CI: 13-100), MS (76% CI: 67-85) and helminth infestations (72% CI: 44-93) were the highly prevalent diseases among viral, bacterial and parasitic infections, respectively. The continent wise pooled prevalence ranged from 17 to 32%. The present results will help in devising the best possible strategies to minimize the disease risk for commercial poultry and humans as well as for improving the productivity of backyard poultry farming.
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Exotic pest and disease investigations are managed and reported by the Ministry for Primary Industries' (MPI's) Diagnostic and Surveillance Directorate. This article presents a summary of investigations of suspect exotic and emerging pests and diseases in New Zealand during the period from July to September 2021.
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Objective: To understand the infection status of major respiratory pathogens in pneumonia patients in the early phase of coronavirus disease 2019 (COVID-19) epidemic (January-March, 2020) in Tongzhou district of Beijing.
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Objective: To understand the change characteristics of respiratory pathogens in hospitalized children with respiratory tract infection in Shunyi district of Beijing from 2019 to 2020, and to provide basis for the prevention and treatment of respiratory tract diseases in children.
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Objective: To understand the pathogen spectrum in the lower respiratory tracts of 100 suspected cases infected with SARS-CoV-2 in Chaoyang district of Beijing from January to March, 2020.
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Introduction - The CeGIDDs are centres of information, screening and diagnosis for HIV, viral hepatitis and bacterial sexually transmitted infections (STIs), a network of French free-to-use clinics created in 2016. This article describes the characteristics of CeGIDD visitors as well as the screening and diagnostic activities carried out by the structures for the year 2020, comparing them with 2018. Method - We present a repeated cross-sectional study, based on continuous monitoring data from the SurCeGIDD system, which relies on the secure transmission of individual visitor data according to a predefined format. The socio-demographic and behavioural data of the visitors, and their reasons for consultation, are described. The proportions of visitors tested and the positivity rates for HIV, hepatitis B (HBV) and C (HCV), syphilis, gonococcus (NG), Chlamydia trachomatis (CT) and Mycoplasma genitalium (MG) are described according to sexual practices. Results - In 2020, 336,333 consultations were reported by 50.3% of the 336 CeGIDDs identified in 2020. Attendance at CeGIDDs fell sharply in the second quarter of 2020 (-58% compared to the first quarter). In 2020, the visitors were mostly men (62.1%) and young people under 30 (64.5%). About a quarter (23.5%) of the visitors were born abroad. The proportion of men having sex with men (14.8%) and trans people (0.38%) had increased compared to 2018. The most frequent reasons for consultation remained risk exposure (60.4%) and systematic screening (43.3%). Some reasons for consultation increased between 2018 and 2020, such as initiating or monitoring a post-exposure prophylaxis. An increase in positivity rate between 2018 and 2020 is observed for HIV (from 0.37% to 0.41%), but especially for NG (from 2.8% to 4.0%), undoubtedly related to changes in visitor characteristics. At the same time, positivity rates decreased for HBV (from 1.3% to 0.93%) and HCV (from 0.94% to 0.60%). They are relatively stable for CT (7.0% in 2020), MG (6.8%) and syphilis (1.0%). Conclusion - Despite a drop in consultations in 2020 related to the COVID-19 pandemic, the CeGIDDs continued to carry out their screening/diagnostic missions in a comprehensive sexual health approach. SurCeGIDD surveillance provides elements for monitoring the national sexual health strategy, hence the need to improve the comprehensiveness and completeness of the data collected.