Pneumocystis, an important opportunistic fungal pathogen that parasitizes in multiple mammalian lungs, may cause life-threatening Pneumocystis pneumonia (PCP) and even death among immunocompromised individuals. With the rapid development of high-throughput sequencing and multi-omics technologies, systematic comparative analyses of genome, transcriptome, and whole-genome sequencing results demonstrate that Pneumocystis is a type of obligate biotrophic fungi, and requires obtaining nutrition from hosts. In addition, sexual reproduction is an essential process for Pneumocystis survival, production and transmission, and asexual reproduction facilitates Pneumocystis survival, which provides new insights into understanding of the whole developmental process of Pneumocystis in the host lung and inter-host transmission of Pneumocystis. This review summarizes the advances in the reproduction mode of Pneumocystis and underlying mechanisms, which provides insights into prevention and treatment of PCP, notably for the prophylaxis against nosocomial transmission of PCP.
Humans ; Lung/microbiology* ; Pneumocystis/genetics* ; Pneumonia, Pneumocystis/microbiology*

Objective: To describe the clinical characteristics of Mycoplasma pneumoniae infection and analyze the factors associated with co-infections with other pathogens in children, and provide evidence for improvement of community acquired pneumonia (CAP) prevention and control in children. Methods: Based on the surveillance of hospitalized acute respiratory infections cases conducted in Soochow University Affiliated Children's Hospital (SCH), the CAP cases aged <16 years hospitalized in SCH between 2018 and 2021 were screened. The pathogenic test results of the cases were obtained through the laboratory information system, and their basic information, underlying conditions, and clinical characteristics were collected using a standardized questionnaire. The differences in clinical characteristics between M. pneumoniae infection and bacterial or viral infection and the effect of the co-infection of M. pneumoniae with other pathogens on clinical severity in the cases were analyzed; logistic regression was used to analyze the factors associated with the co-infections with other pathogens. Results: A total of 8 274 hospitalized CAP cases met the inclusion criteria. Among them, 2 184 were positive for M. pneumoniae (26.4%). The M. pneumoniae positivity rate increased with age (P<0.001), and it was higher in girls (P<0.001) and in summer and autumn (P<0.001). There were statistically significant differences in the incidence of wheezing, shortness of breath, wheezing sounds and visible lamellar faint shadow on chest radiographs, as well as fever and hospitalization days among M. pneumoniae, bacterial, and viral infection cases (all P<0.05). In the cases aged <60 months years, co-infection cases had higher rates of wheezing, gurgling with sputum and stridor; and in the cases aged ≥60 months, co-infection cases had a higher rate of shortness of breath (all P<0.05). Multifactorial logistic regression analysis showed that being boys (aOR=1.38,95%CI:1.15-1.67), being aged <6 months (aOR=3.30,95%CI:2.25-4.89), 6-23 months (aOR=3.44,95%CI:2.63-4.51), 24-47 months (aOR=2.50,95%CI:1.90-3.30) and 48-71 months (aOR=1.77,95%CI:1.32-2.37), and history of respiratory infection within 3 months (aOR=1.28,95%CI:1.06-1.55) were factors associated with co-infections of M. pneumoniae with other pathogens. Conclusions: M. pneumoniae was the leading pathogen in children hospitalized due to CAP. M. pneumoniae infections could cause fever for longer days compared with bacterial or viral infections; M. pneumoniae was often co-detected with virus or bacteria. Being boys, being aged <72 months and history of respiratory infection within 3 months were associated factors for co-infections.
Bacteria ; Child ; Coinfection/epidemiology* ; Community-Acquired Infections/epidemiology* ; Dyspnea ; Female ; Humans ; Male ; Mycoplasma pneumoniae ; Pneumonia, Mycoplasma/microbiology* ; Respiratory Sounds ; Respiratory Tract Infections/epidemiology* ; Virus Diseases

Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R² = 0.033; P = 0.018), followed by acute kidney injury (AKI; R² = 0.032; P = 0.011) and plasma MIP-1β level (R² = 0.027; P = 0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients' lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.
Acute Kidney Injury/complications* ; Bacteria/classification* ; Chemokine CCL4/blood* ; Community-Acquired Infections/microbiology* ; Humans ; Lung ; Microbiota/genetics* ; Pneumonia, Bacterial/diagnosis* ; Prognosis ; RNA, Ribosomal, 16S/genetics*

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Air Microbiology ; Bacteria/isolation & purification* ; Child ; Child, Preschool ; China/epidemiology* ; DNA, Bacterial/analysis* ; DNA, Ribosomal/analysis* ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Pneumonia, Bacterial/microbiology* ; Risk Assessment/methods* ; Young Adult

Adult ; Anti-Bacterial Agents/therapeutic use* ; COVID-19/drug therapy* ; Catheter-Related Infections/microbiology* ; China ; Drug Resistance, Multiple, Bacterial ; Drugs, Chinese Herbal/therapeutic use* ; Humans ; Intubation, Intratracheal ; Male ; Pneumonia, Viral/drug therapy* ; Prosthesis-Related Infections/microbiology* ; SARS-CoV-2

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was found initially in Wuhan, China in early December 2019. The pandemic has spread to 216 countries and regions, infecting more than 23310 000 people and causing over 800 000 deaths globally by Aug. 24, 2020, according to World Health Organization (https://www.who.int/emergencies/diseases/ novel-coronavirus-2019). Fever, cough, and dyspnea are the three common symptoms of the condition, whereas the conventional transmission route for SARS-CoV-2 is through droplets entering the respiratory tract. To date, infection control measures for COVID-19 have been focusing on the involvement of the respiratory system. However, ignoring potential faecal transmission and the gastrointestinal involvement of SARS-CoV-2 may result in mistakes in attempts to control the pandemic.
Betacoronavirus/isolation & purification* ; COVID-19 ; China/epidemiology* ; Coronavirus Infections/virology* ; Environmental Microbiology ; Feces/virology* ; Gastrointestinal Diseases/virology* ; Humans ; Models, Biological ; Pandemics ; Pneumonia, Viral/virology* ; RNA, Viral/genetics* ; SARS-CoV-2 ; Virus Shedding

OBJECTIVE: To investigate the characteristics of gut microbiota dysbosis in patients with severe pneumonia using 16SrDNA sequencing. METHODS: A prospective observational research was conducted. The stool samples retained by natural defecation or enema within 2 days after hospital were collected from 16 patients with severe pneumonia admitted to department of intensive care unit (ICU) of General Hospital of Ningxia Medical University from June to December in 2018 and 10 persons for physical exam were enrolled as the healthy control group. The 16SrDNA sequencing technology was used to detect fecal flora and analyze biological information. RESULTS: (1) 1 015 475 effective sequences were obtained from the stool samples from the severe pneumonia group and the healthy control group. Using 16SrDNA method, it was found that the average effective length of the sample sequence was 458.35 bp and the average sequence number of the total samples was 39 056.73. (2) Analysis of α diversity of gut microbiota showed that, compared with the healthy control group, the Ace index, Chao index and the Shannon index of gut microbiota diversity in the severe pneumonia group were significantly decreased [Ace index: 167.23 (143.14, 211.26) vs. 227.71 (214.53, 247.05), Chao index: 152.38 (138.09, 182.54) vs. 228.25 (215.49, 248.95), Shannon index: 2.37 (1.68, 2.89) vs. 3.39 (3.03, 3.63), all P < 0.01], and the Simpson index was significantly increased [0.21 (0.11, 0.33) vs. 0.07 (0.06, 0.12), P < 0.01], which indicated the gut microbiota diversity of the severe pneumonia group was decreased. (3) Analysis of β diversity of gut microbiota, principal coordinate analysis (PCoA) showed that gut microbiota structural with the healthy control group was similar, while that in the severe pneumonia group was different. Adonis analysis showed that the structural of the gut microflora revealing significant differences between the severe pneumonia group and the healthy control group (R² = 0.061, P = 0.05). (4) Analysis of phylum difference gut microflora showed that, compared with the healthy control group, the proportion of Firmicutes in severe pneumonia group was decreased [27.36 (18.12, 39.28)% vs. 52.25 (38.36, 63.82)%, P = 0.02], the proportions of Actinobacterias, Synergistetes and Fusobacterias were increased [2.30 (0.30, 4.80)% vs. 0.02 (0.00, 0.06)%, 0.36 (< 0.01, 0.57)% vs. < 0.01 (< 0.01, < 0.01)%, 0.01 (< 0.01, 0.08)% vs. < 0.01 (< 0.01, < 0.01)%, all P < 0.05]. (5) Analysis of genus difference gut microflora showed that, the proportions of Bifidobacterium, Ruminococcus, Pseudobutyrivibrio, Coprococcus, Lachnospira and Prevotella in the severe pneumonia group were significantly lower than those in healthy control group [0.18 (0.01, 0.25)% vs. 3.40 (0.46, 5.78)%, 0.01 (< 0.01, 0.29)% vs. 2.26 (0.84, 4.86)%, 0.01 (< 0.01, 0.02)% vs. 2.73 (1.87, 5.74)%, 0.02 (< 0.01, 0.07)% vs. 0.80 (0.50, 2.32)%, < 0.01 (< 0.01, < 0.01)% vs. 0.88 (0.33, 2.08)%, 0.02 (< 0.01, 0.31)% vs. 7.74 (0.07, 36.27)%, all P < 0.05]; the proportions of Escherichia and Enterococcus in the severe pneumonia group were higher than those in healthy control group, but there was no difference between the two groups [2.00 (0.57, 10.23)% vs. 1.16 (0.23, 2.68)%, 0.02 (< 0.01, 0.42)% vs. < 0.01 (< 0.01, 0.04)%, both P > 0.05]; the proportions of Fusobacterium and Staphylococcus in severe pneumonia group were significantly higher than those in healthy control group [0.01 (< 0.01, 0.08)% vs. < 0.01 (< 0.01, < 0.01)%, 0.01 (< 0.01, 0.02)% vs. < 0.01 (< 0.01, < 0.01)%, both P < 0.05]. CONCLUSIONS Gut microbiota dysbiosis in patients with severe pneumonia shows that the abundance and diversity decrease, structure of intestinal flora changes, and beneficial symbiotic bacteria decrease and pathogenic bacteria increase, which may be associated with the occurrence and development of severe pneumonia.
Dysbiosis ; Feces ; Gastrointestinal Microbiome ; Humans ; Pneumonia/microbiology* ; Prospective Studies

Adolescent ; Humans ; Linezolid ; therapeutic use ; Male ; Methicillin-Resistant Staphylococcus aureus ; drug effects ; pathogenicity ; Pneumonia ; diagnostic imaging ; microbiology ; Vancomycin ; therapeutic use

ObjectiveWorldwide, community-acquired pneumonia (CAP) is a common infection that occurs in older adults, who may have pulmonary comorbidities, including chronic obstructive pulmonary disease (COPD). Although there have been clinical studies on the coexistence of CAP with COPD, there remain some controversial findings. This review presents the current status of COPD in CAP patients, including the disease burden, clinical characteristics, risk factors, microbial etiology, and antibiotic treatment.

Data SourcesA literature review included full peer-reviewed publications up to January 2018 derived from the PubMed database, using the keywords "community-acquired pneumonia" and "chronic obstructive pulmonary disease".

Study SelectionPapers in English were reviewed, with no restriction on study design.

ResultsCOPD patients who are treated with inhaled corticosteroids are at an increased risk of CAP and have a worse prognosis, but data regarding the increased mortality remains unclear. Although Streptococcus pneumoniae is still regarded as the most common bacteria isolated from patients with CAP and COPD, Pseudomonas aeruginosa is also important, and physicians should pay close attention to the occurrence of antimicrobial resistance, particularly in these two organisms.

ConclusionsCOPD is a common and important predisposing comorbidity in patients who develop CAP. COPD often aggravates the clinical symptoms of patients with CAP, complicating treatment, but generally does not appear to affect prognosis.

Community-Acquired Infections ; epidemiology ; microbiology ; mortality ; Humans ; Pneumonia ; epidemiology ; microbiology ; mortality ; Pseudomonas aeruginosa ; pathogenicity ; Pulmonary Disease, Chronic Obstructive ; epidemiology ; microbiology ; mortality ; Risk Factors ; Streptococcus pneumoniae ; pathogenicity

OBJECTIVETo investigate the association of drug resistance of Mycoplasma pneumoniae (MP) with DNA load and genotypes in children with MP pneumonia.

METHODSA total of 230 children who were hospitalized and diagnosed with MP pneumonia between January 2012 and December 2016 were enrolled. Throat swabs were collected from the 230 children, and a rapid drug sensitivity assay was used to determine the sensitivity of clinical isolates of MP to nine commonly used antibacterial agents. Quantitative real-time PCR was used to measure MP-DNA load in throat swabs. PCR sequencing was used to determine the genotype of 2063 locus of the MP 23S rRNA V domain.

RESULTSOf the 230 children, 86 (37.4%) had genotype A in 2063 locus, 134 (58.3%) had genotype G, 8 (3.5%) had genotype C, and 2 (0.9%) had genotype T. Mutant strains (genotype G+C+T) had a significantly higher MP-DNA load than wild-type strains (genotype A) (P<0.05). The strains resistant to erythromycin, azithromycin, clarithromycin, and clindamycin had a significantly higher MP-DNA load than non-resistant strains (P<0.05). MP had a high drug resistance rate to macrolide antibiotics. More than 60% of the cases with resistance to macrolides were found to have A2063G mutations. MP was rarely resistant to quinolones (less than 2%).

CONCLUSIONSMutations in 2063 locus of the MP 23S rRNA V domain may result in the resistance of MP to macrolides and the change in DNA load and can be used as a basis for selecting drugs for MP.

Child ; Child, Preschool ; DNA, Bacterial ; analysis ; Drug Resistance, Bacterial ; Female ; Genotype ; Humans ; Infant ; Male ; Mycoplasma pneumoniae ; drug effects ; genetics ; Pneumonia, Mycoplasma ; drug therapy ; microbiology