Introduction

Psittacosis pneumonia is a zoonotic disease caused by Chlamydia psittaci (C. psittaci).1 Cases primarily occur in patients exposed to respiratory secretions or aerosols from infected birds.2 The clinical manifestations of psittacosis pneumonia are highly variable,3,4 often presenting as community-acquired pneumonia (CAP) with typical symptoms including high fever, dry cough, headache, myalgia, chills, and gastrointestinal disturbances. However, psittacosis accounts for less than 5% of CAP cases.5 In severe instances, the disease can progress to respiratory failure, endocarditis, jaundice, and neurological complications. More critical cases may lead to acute respiratory distress syndrome (ARDS), septic shock, or multi-organ dysfunction. In China, C. psittaci is recognized as a common pathogen of severe community-acquired pneumonia (SCAP).6

The clinical diagnosis of psittacosis pneumonia primarily relies on influenza-like atypical pneumonia symptoms and a history of poultry exposure. Suspected cases with relevant epidemiological exposure, clinical presentation, and imaging findings can be confirmed if they meet at least one of the following diagnostic criteria:7 (1) Isolation of C. psittaci from respiratory secretions, bronchoalveolar lavage fluid (BALF), or blood samples; (2) Detection of anti-C. psittaci IgM antibodies at a titer of ≥1:16 via micro-immunofluorescence (MIF); (3) A ≥4-fold increase in antibody titer between paired serum samples collected two weeks apart, tested by complement fixation or MIF; (4) Identification of C. psittaci nucleic acids in respiratory or blood samples via polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), or targeted next-generation sequencing (tNGS). Conventional culture of C. psittaci remains challenging in clinical settings due to its time-consuming nature and requirement for tissue or egg embryonation. Serological tests and PCR also exhibit low sensitivity for C. psittaci detection.8,9 The lack of highly sensitive and specific diagnostic methods poses significant limitations, contributing to historical estimates, largely derived from studies conducted before the widespread availability of molecular diagnostics and targeted therapy, suggest a mortality rate of 15%–20% in untreated or delayed-treatment cases.10–13 Contemporary cohorts with timely diagnosis and appropriate treatment generally report more favorable outcomes.

Currently, mNGS has been widely adopted to detect diverse microbial pathogens, including viruses, bacteria, fungi, and parasites.14 Notably, mNGS enables diagnosis of atypical pathogens within 24–48 hours, far surpassing the prolonged turnaround time of traditional cultures. This advancement facilitates early diagnosis and timely, effective treatment, improving clinical outcomes. For critically ill patients, mNGS has recently emerged as the most promising tool for accurate diagnosis of rare infections, particularly SCAP.15

In recent years, reported psittacosis cases have increased, with nearly all confirmed through mNGS or tNGS.16,17 A recent study analyzed 55 cases of C. psittaci pneumonia and compared severe and non-severe disease, providing valuable insights into clinical, laboratory, imaging, mNGS, and treatment characteristics. The present study differs from and extends this work in the following aspects: (i) our cohort is derived from Guangxi, a region with high poultry exposure prevalence and distinct epidemiological patterns; (ii) we provide detailed, systematic characterization of bronchoscopic findings — a feature not described in the Gao et al study — which may offer additional diagnostic information in suspected psittacosis pneumonia; and (iii) we focus specifically on features differentiating SCAP from non-SCAP cases, providing exploratory data for hypothesis generation regarding severity-associated features.18 Given the absence of routine diagnostic methods for psittacosis pneumonia, elucidating its clinical features is essential for early identification and exploration of features associated with SCAP progression. Although several case series and multicenter studies of mNGS-confirmed C. psittaci pneumonia have been reported, data from the Guangxi region — where poultry exposure is highly prevalent — remain limited. Guangxi is China’s fourth-largest poultry breeding province, with a Chlamydia psittaci infection rate of 28.20% in poultry, which exceeds the national and Asian average levels. Moreover, circulating strains in local poultry are genetically related to those isolated from human cases,19 and epidemiological data suggest higher psittacosis incidence in South China during autumn and winter months.20 Despite this significant regional disease burden, no systematic characterization of mNGS-confirmed C. psittaci pneumonia from this region has been published. Furthermore, bronchoscopic findings have rarely been systematically described in psittacosis pneumonia, and direct comparisons between SCAP and non-SCAP cases within a well-characterized cohort are lacking. However, direct population-based epidemiological evidence in this region is currently lacking.

The primary objective of this retrospective study was to systematically describe the demographic, clinical, laboratory, imaging, and bronchoscopic characteristics of 40 mNGS-confirmed C. psittaci pneumonia patients in Guangxi. The secondary objective was to explore clinical and laboratory features associated with SCAP by comparing SCAP and non-SCAP subgroups. This study does not aim to evaluate treatment efficacy or identify independent predictors of outcomes, given the observational design and limited sample size.

Early identification of patients at risk of SCAP progression is clinically important because delayed initiation of effective antimicrobial therapy is associated with worse outcomes in C. psittaci pneumonia. However, currently available severity prediction tools (eg, CURB-65, PSI) were developed for general CAP populations and have not been specifically validated in C. psittaci pneumonia. Currently, individual clinical and laboratory predictors remain limited, and larger multicenter cohorts are needed to construct robust disease prediction models for early identification of SCAP risk in psittacosis. In the present study, we provide exploratory, hypothesis-generating data that may inform the design of such future studies.

Materials and MethodsEnrolled Patients and Study Design

A retrospective analysis was conducted on 40 hospitalized CAP patients at the First Affiliated Hospital of Guangxi Medical University between September 2019 and September 2024, whose bronchoalveolar lavage fluid (BALF), or blood samples tested positive for C. psittaci via mNGS and were clinically diagnosed with psittacosis pneumonia. The inclusion criteria were as follows: (1) Detection of C. psittaci in BALF, or blood samples by mNGS; (2) Diagnosis of CAP based on the Chinese Guidelines for the Diagnosis and Treatment of Adult Community-Acquired Pneumonia (2016 Edition)21 and the 2019 joint CAP guidelines issued by the Infectious Diseases Society of America/American Thoracic Society (IDSA/ATS);22 (3) Availability of complete clinical data. The exclusion criteria included: (1) Incomplete medical records; (2) Non-CAP patients; (3) Age <18 years at admission; (4) CAP patients without C. psittaci detection on mNGS. The major diagnostic criteria for SCAP were: (1) Requirement of invasive mechanical ventilation via endotracheal intubation; (2) Septic shock necessitating vasopressor therapy despite adequate fluid resuscitation. The minor criteria were: (1) Respiratory rate ≥30 breaths/min; (2) PaO2/FiO2 ratio ≤250 mmHg (1 mmHg=0.133 kPa); (3) Multilobar infiltrates; (4) Altered mental status and/or disorientation; (5) Blood urea nitrogen ≥20 mg/dL (7.14 mmol/L); (6) Systolic blood pressure <90 mmHg requiring aggressive fluid resuscitation. Grouping was performed retrospectively based on the most abnormal clinical and laboratory values recorded within the first 24 hours of admission.

Patients meeting either 1 major criterion or ≥3 minor criteria were diagnosed with severe pneumonia, requiring close monitoring, intensive treatment, and ICU admission when feasible.

Data Collection

Clinical data were extracted from electronic medical records, including: (1) Demographics; (2) Clinical manifestations: Symptoms, vital signs, endotracheal intubation status, septic shock, duration of mechanical ventilation, and PaO2/FiO2 ratio; (3) Laboratory parameters: Inflammatory markers, arterial blood gas analysis, biochemical tests, and microbiological results; (4) Imaging features and bronchoscopic findings; (5) Antimicrobial treatment and outcomes: Vital signs, hospital length of stay, ICU admission, and ICU duration.

mNGS Analysis

Clinical specimens (39 BALF samples and 1 blood sample, blood samples were collected for mNGS testing in one patient who were unable to tolerate bronchoscopy at the time of admission) were collected following standardized operating procedures and immediately transported to WillingMed Technology (Beijing) Co, Ltd. or Hangzhou Matridx Biotechnology Co, Ltd. for mNGS testing. The samples underwent standardized processing including nucleic acid extraction and purification, library preparation, high-throughput sequencing, and bioinformatics analysis to generate pathogen reports.23,24 Sequencing was performed on the MGISEQ-200 platform (WillingMed, 50 bp single-end reads, 10–20 million reads per sample) or the Illumina NextSeq 550 platform (Matridx, 50 bp single-end reads, 10–20 million reads per sample). Human reads were subtracted by alignment to the human reference genome (GRCh38) using Bowtie2. Remaining reads were aligned to custom-curated microbial genome databases, which integrates the RefSeq complete genome database and the NCBI non-redundant nucleotide sequence database (NCBI nt), for species-level identification using Kraken2 software. Turnaround time was approximately 24–48 hours from sample receipt to report generation. Negative controls (NTC) were included in each batch to account for background microbial contamination. Published expert consensus has indicated that each testing laboratory should establish its own diagnostic thresholds for different pathogens based on its specific mNGS procedures and for different types of infections when issuing reports, and should validate these thresholds in clinical practice.25 For common bacteria, fungi, and viruses, Willingmed and Matridx have each established their own positive judgment thresholds. The pathogen determination method for Willingmed is as follows: The sequence count for each microorganism is quantified using RPTM (reads per ten million, representing the number of microorganism-specific reads per ten million total reads). A virus is considered positive if the RPTM is ≥ 3. The RPTM threshold for bacteria and fungi is ≥ 20. The pathogen determination method for Matridx is as follows: Pathogens are reported if: 1) the sequencing data pass quality control filters (library concentration > 50 pM, Q20 > 85%, Q30 > 80%); and 2) the negative control (NC) in the same sequencing run does not contain the species, or the ratio of RPM(sample) to RPM(NC) is ≥ 5. However, for special pathogens such as Chlamydia psittaci, Mycobacterium tuberculosis, and Cryptococcus, etc, both the current consensus and the thresholds set by various testing laboratories adopt the criterion that the detection of a single specific read is considered positive.

Co-detected organisms were classified by two independent clinicians as: (i) clinically confirmed co-infection (supportive clinical, radiological, and laboratory evidence); or (ii) likely colonization (detection without clinical evidence of invasive disease). Disagreements were resolved by consensus with a third reviewer.

Statistical Analysis

Statistical analyses were performed using SPSS 27.0 (IBM, USA). Continuous variables with normal distribution were expressed as mean ± standard deviation (X±SD) and compared using Student’s t-test, non-normal continuous variables were reported as median and interquartile range (IQR) and compared using the Mann–Whitney U-test. Categorical variables were presented as counts (percentages) and analyzed using chi-square or Fisher’s exact tests (when any expected cell count was < 5). A two-tailed P < 0.05 was considered statistically significant. Given the limited sample size (n=40, with 13 SCAP cases), formal multivariable logistic regression was not performed. All analyses should be considered exploratory and hypothesis-generating.

ResultsBaseline Characteristics of Patients

This retrospective study analyzed 40 patients with psittacosis pneumonia, including 27 non-SCAP and 13 SCAP cases. All patients had documented poultry exposure (birds, chickens, or ducks). Among the patients, 29 were male (72.50%). The median age was 59 years (range: 31–85), with SCAP patients had a median age of 61 years and Non-SCAP patients was 58 years, with no significant difference between groups (P = 0.823). There were 57.50% (23/40) patients with comorbidities, hypertension (n=13) was the most common. Fever was present in 97.50% (39/40) of patients, with 38 cases ≥39 C. Other common symptoms included cough (82.50%, 33/40), sputum (75.00%, 30/40), dyspnea (52.50%, 21/40), and digestive tract symptoms (including nausea, vomiting, upper abdominal discomfort, etc. 47.50%, 19/40). Less common symptoms included myalgia (5.00%, 2/40) and headache (10.00%, 4/40). SCAP patients exhibited significantly higher rates of dyspnea (76.92% vs, 40.74%, P = 0.046) and headache (30.77% vs, 0%, P=0.008) than Non-SCAP. Among the 40 patients, 12 patients had severe hypoxia (PaO2/FiO2 ≤ 250 mmHg), which was more common in SCAP patients. Compared with non-SCAP patients, the oxygenation index of SCAP patients was lower. The risk of death was evaluated according to the CURB-65 score:18,19 0–1 point: low risk; 2 points: moderate risk; 3–5 points: high risk. All 13 SCAP patients had a higher risk of death than the Non-SCAP group (Table 1). Among the 40 patients, 6 received invasive mechanical ventilation, 1 received nasal high-flow oxygen therapy, 2 received non-invasive ventilation, 23 received oxygen therapy (nasal cannula oxygen or mask oxygen), and 8 did not require oxygen therapy. All SCAP patients were admitted to the ICU, with ICU stay ranging from 3 to 74 days.

Table 1 Demographic Characteristics of Patients

Laboratory Findings in Psittacosis Pneumonia Patients

The majority of patients exhibited elevated levels of white blood cells (WBC), absolute neutrophil count (NEUT), procalcitonin (PCT), C-reactive protein (CRP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatinine (Cr), and blood urea nitrogen (BUN), while showed decreased absolute lymphocyte count (LYM). Moreover, compared to Non-SCAP patients, WBC, NEUT, CRP, PCT, and BUN levels (P < 0.05) were significantly higher in SCAP patients, while LYM and CD4⁺ counts were significantly lower (P < 0.05) (Table 2). These findings suggest that SCAP patients with C. psittaci infection have elevated inflammatory markers and are more prone to renal function impairment.

Table 2 Analysis of Differences in Clinical Indicators Between Groups

Imaging and Fiberoptic Bronchoscopy Findings

Chest CT scans revealed that 15 cases (37.50%) had single lobe pulmonary infiltration, and 25 cases (62.50%) had bilateral or multiple lobe infiltration. The most common manifestations were consolidation (72.50%, 29/40) and air bronchogram (52.50%, 21/40), followed by exudates (47.50%, 19/40) and pleural effusion (15.00%, 6/40). Compared with Non-SCAP patients, SCAP patients showed more lobe consolidation (Table 3). Representative chest CT scans from SCAP patients are presented in Figure 1. As shown in Figure 1A, bilateral lower lobe consolidation was observed. Figure 1B exhibits pulmonary infiltrates with bilateral pleural effusion. Furthermore, Figure 1C illustrates left-sided opacities and pleural effusion combined with right-sided consolidation and opacities. All patients underwent fiberoptic bronchoscopy. Results showed that congestion and edema (75%, 30/40), serous (37.50%, 15/40), mucous (20.00%, 8/40), or purulent secretions (30.00%, 12/40) were the main features. Compared with Non-SCAP patients, significantly less SCAP patients had little secretions (15.38% vs, 62.96%, P < 0.05) (Table 4).

Table 3 Pulmonary Imaging Manifestations of 40 Patients with Psittacosis Pneumonia

Table 4 Fiberoptic Bronchoscopy Manifestations of 40 Patients with Psittacosis Pneumonia

Figure 1 Chest CT imaging findings in SCAP patients. (A) Case 25, a 33-year-old male, was admitted on February 7, 2024, with a 3-day history of cough, sputum, fever, and dyspnea. mNGS was performed on February 8, and treatment was initiated on February 7. Chest CT on admission showed extensive consolidation in both lower lobes. (B) Case 1, a 69-year-old male, was admitted on September 1, 2022, with a 7-day history of cough, sputum, fever, and dyspnea. mNGS was performed on September 2, and treatment was initiated on September 1. Chest CT revealed faint ground-glass opacities in both lungs and bilateral pleural effusion in the lower lobes. (C) Case 8, an 85-year-old male, was admitted on November 14, 2024, with a 5-day history of cough, sputum, fever, dyspnea, and poor appetite. mNGS was performed on November 15, and treatment was initiated on November 14. Chest CT showed consolidation and opacities in the right lung, opacities in the left upper lobe, and pleural effusion in the left lower lobe.

mNGS Testing

All patients underwent mNGS testing, with 39 cases using BALF and 1 cases using blood samples. C. psittaci was detected in all cases. The detailed pathogen detection results and patient information for each case are presented in Supplementary Table S1. Among the 40 patients, mNGS detected a total of 22 pathogen detections classified as infection (8 in the SCAP group, 14 in the non-SCAP group) (Table 5) and 27 classified as colonization (3 in the SCAP group, 24 in the non-SCAP group) (Supplementary Table S2). In the infection category, the most frequently detected infecting organisms were Streptococcus pneumoniae (n = 3, all non-SCAP), Aspergillus fumigatus (n = 3; 2 SCAP, 1 non-SCAP), Aspergillus flavus (n = 2, all non-SCAP), and Haemophilus parainfluenzae (n = 2, all non-SCAP). No statistically significant differences in the distribution of individual pathogens were observed between SCAP and non-SCAP groups (all p > 0.05, Fisher’s exact test). In the colonization category, the most commonly colonizing organisms were Candida albicans (n = 5; 1 SCAP, 4 non-SCAP), Staphylococcus aureus (n = 3, all non-SCAP), Klebsiella pneumoniae (n = 3, all non-SCAP), Human herpesvirus 1 (HSV-1; n = 3, all non-SCAP), and Human herpesvirus 4 (EBV; n = 2, all non-SCAP). Notably, herpesvirus colonization was exclusively observed in the non-SCAP group (7 vs, 0 detections, p = 0.074).

Table 5 Spectrum of Clinically Relevant Infectious Pathogens Detected by mNGS

Treatment and Prognosis of Patients with Psittacosis Pneumonia

Among the 40 patients with psittacosis pneumonia in this study, 3 did not receive empirical anti-infective treatment but were directly treated for the identified pathogen. Two of them were treated with moxifloxacin, 1 with doxycycline. Among the 37 patients diagnosed with a specific pathogen, one patient received treatment for the pathogen alone, 25 patients received combined antibacterial treatment, one patient received combined antifungal treatment, seven patients received combined antibacterial and antifungal treatment, one patient received combined antibacterial and antiviral treatment, and two patients received combined antibacterial, antifungal, and antiviral treatment. SCAP patients were more likely to receive combined antibacterial and antifungal treatment (Table 6). After treatment, all patients in this study experienced symptom relief, improved lung imaging, and were discharged with improved conditions (Figure 2).

Table 6 Treatment and Outcomes of 40 Patients with Psittacosis Pneumonia

Figure 2 The pulmonary imaging changes of 1 case of SCAP patients. (A) The CT scan on September 10, 2022, after the patient was admitted and the pathogen was identified, showed consolidation in both lungs. Treatment with doxycycline for psittacosis began. (B) The CT scan on September 16, 2022, after 6 days of treatment for psittacosis, showed improvement with less exudate compared to the previous scan. (C) The CT scan on September 21, 2022, after 11 days of treatment for psittacosis, showed improvement with less exudate compared to the previous scan. (D) The CT scan on October 8, 2022, after 28 days of treatment for psittacosis, showed a slight exudate in both lungs, which had improved compared to the previous scan. (E) The CT scan on November 2, 2022, after 53 days of treatment for psittacosis, showed improvement with less exudate in both lungs compared to the previous scan.

Discussion

This study analyzed the clinical data of 40 patients diagnosed with C. psittaci CAP via mNGS at our hospital. We comprehensively evaluated their demographic characteristics, clinical manifestations, laboratory findings, imaging features, treatment, and outcomes to enhance understanding of psittacosis pneumonia in patients who underwent bronchoscopy, and to explore clinical features and management of C. psittaci-induced SCAP, ultimately aiming to improve patient prognosis.

All 40 patients in this study had a clear history of poultry exposure (birds, chickens, or ducks), consistent with previous reports on psittacosis transmission in humans.3,10,26 Such exposure history serves as a crucial diagnostic clue. However, some patients may present without direct contact with infected birds or poultry,11 which significantly complicates clinical diagnosis of psittacosis.

The clinical manifestations observed in our cohort were nonspecific, primarily including fever, cough, sputum production, dyspnea, gastrointestinal symptoms, myalgia, and headache. Notably, compared to non-SCAP patients, SCAP patients were more likely to demonstrate dyspnea and headache, in addition to more prominent systemic manifestations and significantly worse oxygenation (lower PaO2/FiO2 ratios). These distinct clinical patterns align with findings reported by Su et al,27 However, discrepancies exist with studies by Lu2 and Yuan,26 and a multicenter data from 116 psittacosis patients in Central-South China,17 which found no significant symptomatic differences between SCAP and non-SCAP groups, was inconsistent with our results. Given the small sample size, our study has limited statistical power, which may increase the risk of both false-negative (Type II error, missing true associations) and false-positive (Type I error) findings, particularly given the multiple unadjusted comparisons. Therefore, all reported associations should be considered exploratory and interpreted with appropriate caution. Nevertheless, our findings reinforce critical diagnostic insights: when CAP patients with avian exposure present with respiratory symptoms accompanied by extrapulmonary manifestations - particularly when paired with declining oxygenation indices - clinicians should strongly consider psittacosis pneumonia and monitor for potential SCAP progression.

Our laboratory results demonstrated that SCAP patients exhibited significantly higher levels of WBC, NEUT, CRP, and PCT compared to non-SCAP cases, suggesting a more pronounced inflammatory response in psittacosis-induced SCAP, which aligns with previous findings by Fang et al,28 It should be noted that elevated WBC, CRP, and PCT levels in SCAP compared to non-SCAP are expected findings not specific to psittacosis, as they reflect general severity markers in community-acquired pneumonia. However, lower LYM and CD4 counts in SCAP patients were associated with more severe disease, consistent with Yuan’s report.26 Whether these differences represent a cause or a consequence of disease severity remains unclear and warrants further investigation. Elevated Cr and BUN levels in SCAP cases compared to non-SCAP cases suggest that these markers are associated with SCAP progression and increased likelihood of renal dysfunction. Additionally, elevated ALT, AST, and CK levels in psittacosis patients, as observed in our study and other reports,17,29,30 indicate potential mild liver injury. Notably, CK serves as the most sensitive marker for muscle damage,31 implying possible muscular involvement in psittacosis. These findings highlight the importance of monitoring and managing hepatic and renal function in affected patients. Given the limited sample size of the present study (n=40, with only 13 SCAP cases), formal multivariate logistic regression analysis could not be performed with adequate statistical power. However, based on univariate analyses, the variables most strongly associated with SCAP included PaO2/FiO2 ratio ≤250 mmHg at admission, lymphopenia (LYM <1.0×109/L), elevated CRP (>100 mg/L), elevated BUN (>7.5 mmol/L), and multilobar consolidation on CT. These findings are exploratory and hypothesis-generating; future multicenter prospective studies with larger cohorts are needed to validate these potential SCAP-associated features through multivariate analysis and develop clinically applicable prediction models.

Segmental consolidation with air bronchograms emerged as a characteristic imaging feature of psittacosis pneumonia. While consolidation was the most common radiological finding in our cohort, it should be noted that this feature is nonspecific and may also occur in CAP caused by bacterial, viral, or fungal pathogens,32,33 complicating etiological differentiation. Previous studies have also documented that C. psittaci infection can lead to meningitis and myocarditis.16,34 Our study further revealed that SCAP cases exhibited more extensive consolidation, which maybe an indicator of severe disease. While pleural effusion has been associated with higher mortality in pneumonia patients,35,36 our study found no statistically significant difference in pleural effusion between SCAP and non-SCAP groups (P=0.075), which may be attributable to the limitation of the limited number of included cases. Nevertheless, the presence of pleural effusion should also be further investigated as a potential indicator of disease progression to severe forms.

Our systematic bronchoscopic characterization, including quantitative analysis of mucosal features and secretion types with SCAP/non-SCAP comparison, extends the limited bronchoscopic observations in the C. psittaci pneumonia literature. While Gao et al,18 briefly noted bronchial mucosal congestion and edema in their 55-case cohort without further characterization or subgroup analysis, our study provides the first detailed, quantitative description of bronchoscopic findings in psittacosis pneumonia and demonstrates that secretion abundance differs significantly between SCAP and non-SCAP patients (P < 0.05). These findings suggest that bronchoscopy may provide adjunctive information for severity assessment in suspected C. psittaci pneumonia, although prospective validation is needed.

In the current study, while elevated PCT levels have been associated with bacterial co-infection in some studies,5 in the context of severe C. psittaci pneumonia, PCT elevation may primarily reflect the magnitude of the host inflammatory response and disease severity rather than specifically indicating polymicrobial infection. Elevated PCT levels in SCAP patients should not be equated with the presence of bacterial co-infection without corroborating clinical and microbiological evidence. Our mNGS results identified additional organisms beyond C. psittaci in a substantial proportion of patients, demonstrating mNGS’s capacity for broad respiratory pathogen screening and accurate identification of C. psittaci in SCAP patients.5,37–42 Based on comprehensive clinical adjudication, detected organisms were classified as infection (Table 2) or colonization (Supplementary Table S2). Among organisms classified as infection, the most frequently detected were Streptococcus pneumoniae, Aspergillus fumigatus, Aspergillus flavus, and Haemophilus parainfluenzae (Table 2). In contrast, organisms predominantly classified as colonization included Candida albicans, Staphylococcus aureus, Klebsiella pneumoniae, human herpesvirus 1, and Epstein-Barr virus (Supplementary Table S2). Notably, Acinetobacter baumannii, Klebsiella pneumoniae, and EBV, were classified as colonization rather than infection in all cases after clinical adjudication. This distinction underscores that mNGS detection alone cannot determine the pathogenic role of an organism. It should be noted that Candida species and EBV detected by mNGS are not typically considered causative pathogens of pneumonia; their detection may reflect colonization or latent infection rather than true co-infection. Consistent with this principle, in our cohort, all EBV and the majority of Candida detections were classified as colonization, and all herpesvirus detections occurred exclusively in the non-SCAP group, further suggesting that these viral signals reflect latent viral shedding rather than clinically significant co-infection. Polymicrobial infections are well recognized to worsen clinical outcomes in severe pneumonia,5,28 potentially mediated through the observed lymphopenia and reduced CD4⁺ counts. Fu et al,43 reported that decreased CD3+ T lymphocyte percentages and CD4+/CD8+ ratios were associated with pneumonia severity in patients co-infected with influenza A virus and Mycoplasma pneumoniae. Similarly, Hao et al,44 found that dynamic decreases in lymphocyte counts significantly correlated with increased risks of ECMO-associated infections and VAP. Regarding the organisms co-detected in our cohort, those overlapping with typical VAP-associated pathogens (including Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae), were predominantly classified as colonization rather than infection. Specifically, A. baumannii was classified as colonization in the sole SCAP case in which it was detected, and K. pneumoniae and P. aeruginosa were classified as colonization in all cases where they appeared. Therefore, the detection of VAP-associated organisms in community-acquired cases without classic VAP risk factors warrants cautious interpretation and should not automatically trigger anti-VAP therapy. Critically ill patients with SCAP who require invasive mechanical ventilation are inherently at elevated risk of developing nosocomial infections, and clinicians should assess whether newly detected organisms represent true nosocomial superinfection requiring targeted treatment versus colonization or contaminant signal, based on comprehensive evaluation of the patients clinial evolution, including changes in fever pattern, sputum characteristics, radiological progression, and inflammatory marker trends. In SCAP patients with clinically suspected co-infection, individualized antimicrobial selection should be guided by comprehensive clinical assessment, local antibiograms, and antimicrobial stewardship principles rather than mNGS co-detection results alone. Broad empiric coverage of VAP-associated pathogens is not recommended for all SCAP patients without individualized risk assessment, given the risks of promoting antimicrobial resistance and unnecessary drug toxicity.

Empirical antimicrobial therapy prior to confirmed diagnosis of C. psittaci infection was often ineffective, as the pathogen is intrinsically resistant to beta-lactam antibiotics and aminoglycosides that are commonly used as first-line empirical CAP treatment.1,4 In this study, 92.5% of patients initially received empirical antibiotics, with 97.30% requiring antibiotic adjustment after definitive diagnosis (only 1 case continued original regimen). The most effective agents against psittacosis pneumonia included quinolones, macrolides, and tetracyclines, which represent first-line treatments.21 Our treatment outcomes revealed: 14 patients received doxycycline, 25 received quinolones, 3 received combination therapy with doxycycline and moxifloxacin (including 2 SCAP cases). Notably, SCAP patients showed preference for doxycycline, consistent with previous reports of this agent’s efficacy in severe psittacosis.28,45 Doxycycline should be considered as a first-line agent, consistent with existing literature and treatment guidelines. All patients achieved clinical improvement, aligning with studies demonstrating favorable outcomes with tetracycline-class antibiotics.45,46 However, the comparative effectiveness of different drug classes or monotherapy versus combination therapy cannot be determined from this uncontrolled observational study and requires further prospective evaluation.

There are several limitations in this study. First, this is a single-center retrospective study, which limits generalizability. Second, we only included 40 mNGS-confirmed C. psittaci cases and excluded clinically suspected cases without pathogen confirmation. Third, as a retrospective study relying solely on mNGS, we lacked comparator data from PCR, serology, or culture methods, preventing evaluation of mNGS sensitivity/specificity for C. psittaci detection. Fourth, the small SCAP sample size (n=13) limits statistical power and precludes multivariable modeling. Future multicenter prospective studies should incorporate multiple diagnostic modalities, evaluate utility of clinical laboratory parameters, better differentiate SCAP vs non-SCAP manifestations and optimize treatment strategies for severe cases. Fifth, since all enrolled patients underwent bronchoscopy prior to mNGS sampling, this cohort is subject to selection bias toward patients clinically deemed to require bronchoscopy — typically those with more severe or diagnostically uncertain presentations. This may account for the relatively high proportion of SCAP cases (32.5%) in our cohort compared with some population-based estimates, and limits the generalizability of our findings to the broader clinical spectrum of C. psittaci pneumonia, including milder outpatient cases. These limitations are inherent to the retrospective, single-center design and could be addressed through future multicenter prospective studies with standardized protocols and larger sample sizes. Future studies should include patients diagnosed via non-bronchoscopic sampling methods to provide a more complete clinical picture.

In conclusion, C. psittaci pneumonia should be suspected in CAP patients with poultry or bird exposure, particularly when presenting with fever, dyspnea, extrapulmonary manifestations (especially headache), lymphopenia, and compatible CT findings such as consolidation with air bronchograms. Pleural effusion on chest CT showed a trend toward higher frequency in SCAP patients but the association did not reach statistical significance in this cohort; this finding warrants further investigation in larger studies. mNGS of BALF may facilitate timely identification of C. psittaci when conventional diagnostic methods are unavailable or delayed, although this study was not designed to evaluate the diagnostic accuracy of mNGS against reference standards. Clinical improvement was observed following tetracycline- or quinolone-containing regimens. Doxycycline should be considered as a first-line agent. The comparative effectiveness of different drug classes cannot be determined from this observational study and requires prospective evaluation. This study is exploratory and hypothesis-generating; the identified severity-associated features require validation in larger, multicenter, prospective cohorts.

Data Sharing Statement

The datasets used and/or analyzed during the current study are available from the corresponding author (Yi Liang, E-mail: [email protected]) upon reasonable request.

Ethical Approval

The study was conducted in accordance with the Declaration of Helsinki. All procedures performed in the study involving human participants were in conformity to the ethical standards of the Ethics Committee of the First Affiliated Hospital of Guangxi Medical University (Approval No. 2025-E0597). The requirement for consent was waived because the study was a retrospective analysis and all data were anonymized prior to analysis.

Acknowledgments

The authors wish to thank the research staff and patients for their participation in this study.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work. Specific contributions: Tangjuan Liu and Liexiang Liao were involved in study design, data analysis, and manuscript drafting. Xiaojing Zhang and Yafeng Zheng contributed to manuscript revision and visualization. Chongxi Bao, Yujing Qi and Lu Zhu contributed to data collection and management. Yanbin Wu contributed to the revision, and funding. Yi Liang contributed to the oversight and revision of this article.

Funding

This work was supported in part by grants from Guangxi Appropriate Medical Health Technology Promotion Project (Approval No. S2024023) and a self-funded project sponsor of Guangxi Health Commission (Approval No. Z-A20240531).

Disclosure

The authors declare that they have no conflict of interest.

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