Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform

Epidemiological changes in Chlamydia pneumoniae molecular detections before, during and after the COVID-19 pandemic in 27 European sites and Taiwan, 2018 to 2023

BackgroundDuring the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) such as social distancing, lockdowns and enhanced hygiene led to a decrease in respiratory pathogens. However, as NPIs were relaxed, a resurgence in several respiratory pathogens was observed including one local Chlamydia pneumoniae outbreak in Switzerland, prompting the need for a better understanding of C. pneumoniae epidemiology.AimTo assess temporal and geographical variations in C. pneumoniae detection before, during and after the COVID-19 pandemic.MethodsData on C. pneumoniae PCR detection ratios (number of positive tests/ total number of tests) across pre-pandemic (2018-2019), pandemic (2020-2022) and post-pandemic (2023) periods were collected via a global survey disseminated through various professional networks.ResultsC. pneumoniae detection ratios were analysed across 28 sites (27 in Europe, one in Taiwan) in 2023 (Dataset A, n = 172,223 tests) and 20 sites from 2018 to 2023 (Dataset B, n = 693,106 tests). Twenty-seven sites were laboratories (hospital or clinical) and one a surveillance system (Denmark). A significant decrease in detection ratios was observed during the pandemic period (from 1.05% to 0.23%, p < 0.001). In 2023, detection ratios increased to 0.28% (p < 0.002). Notable regional variations were found, with statistically significant increases in detection ratios at six sites located in Switzerland and Slovenia, where ratios ranged from 0.52% to 3.25%.DiscussionThe study highlights how NPIs influenced C. pneumoniae epidemiology, with reduced detection during the pandemic and partial resurgence afterwards. Regional variations suggest differing NPI impacts and underscore the need for continued surveillance.

From coughs to complications: the story of Chlamydia pneumoniae

Chlamydia pneumoniae is an obligate intracellular bacterium and a significant cause of respiratory infections. It is associated with upper and lower respiratory tract diseases, including bronchitis and pneumonia. The pathogen employs specific virulence factors, such as the Type III Secretion System (T3SS) and Inc proteins, to invade and subvert host cell machinery during its peculiar developmental life cycle. Chronic infections have been linked to asthma and, more controversially, to atherosclerosis and neurodegenerative diseases. Diagnosis primarily relies on PCR-based molecular assays, while treatment includes macrolides, tetracyclines or fluoroquinolones. Despite its clinical relevance, research on C. pneumoniae has declined in recent years, highlighting the need for renewed scientific focus.

Chlamydia pneumoniae Upsurge at Tertiary Hospital, Lausanne, Switzerland

Chlamydia pneumoniae infection cases have usually accounted for <1.5% of community-acquired respiratory tract infections. Currently, Lausanne, Switzerland is experiencing a notable upsurge in cases, with 28 reported within a span of a few months. This upsurge in cases highlights the need for heightened awareness among clinicians.

Recent advances and public health implications for environmental exposure to Chlamydia abortus: from enzootic to zoonotic disease

Environmental transmission of Chlamydia abortus as a result of enzootic disease or disease outbreaks and the threats posed by this pathogen has been previously reported, however a state-of-the-science review of these reports and the identification of future research priorities in this area is still lacking. This study provides an overview of the current knowledge of host–pathogen–environment interactions, addressing public health risks and identifying critical questions and research gaps. We performed a systematic PubMed and Web of Science search for publications related to Chlamydia abortus in the past four decades, and we reviewed and combined the evidence critically discussing and commenting the results. A total of 182 studies, 5 chapters of specific books and the “OIE terrestrial manual” were included in this review. There were substantial variations between the studies in topic addressed and experimental design. Overall, the literature largely supports the crucial role played by environmental exposure on the acquisition of zoonotic disease caused by Chlamydia abortus. We also identify the paucity of information related to interspecies transmission and pathogen adaptation in relation to environmental dissemination and zoonotic risk. This analysis further highlights the need for additional research given that environmental transmission represents a serious risk not only to susceptible patients (pregnant women and immunocompromised individuals), but also for other species including wildlife.

Utility of Polymerase Chain Reaction in Nasopharyngeal Swabs for Identifying Respiratory Bacteria Causing Community-Acquired Pneumonia

Timely identification of a pathogen in lower respiratory tract infections (LRTI) can support appropriate antibiotics use. The difficulty of obtaining lower respiratory tract (LRT) samples limits the utility of point-of-care syndromic molecular assays. We assessed the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in nasopharyngeal (NP) swab for detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Patients in the study included retrospectively consenting adults who attended the emergency department of Lausanne University Hospital between February 2019 and August 2020 for a community-acquired LRTI, with available NP swab and a high-quality LRT sample. These samples were tested with the FilmArray PP (cutoff of ≥10⁴ copies/mL). Positive (PPA) and negative percent agreement (NPA) of FilmArray PP in NP swab were calculated, using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. To assess the performance of a lower detection cutoff, NP samples were also tested with an in-house PCR (cutoff of ≥10 copies/mL) for S. pneumoniae and H. influenzae. Overall, 118 patients were included. FilmArray PP in LRT sample and standard microbiology tests detected S. pneumoniae in 19/118 and 12/118, H. influenzae in 44/118 and 19/118, and M. catarrhalis in 14/118 and 0/118, respectively. Using LRT FilmArray PP as reference, PPA and NPA of FilmArray PP on NP were 58% and 100% for S. pneumoniae, 61% and 100% for H. influenzae, and 57% and 99% for M. catarrhalis. Using standard diagnostic tests as reference, PPA and NPA were 58% and 96% for S. pneumoniae, 74% and 87% for H. influenzae, and indefinite and 92% for M. catarrhalis. Using a lower cutoff on NP (≥10² copies/mL), PPA was 68% for S. pneumoniae and 77% for H. influenzae with LRT FilmArray PP as reference. FilmArray PP in NP swabs has a limited PPA for identifying the most common etiologies of community-acquired LRTI irrespective of the reference standard, preventing its use for withholding antibiotics. The PCR detection cutoff does not explain the low PPA. The excellent NPA suggests the use of NP PCR results for rapidly targeted antimicrobial therapy.

IMPORTANCE Timely identification of a pathogen in patients with lower respiratory tract infections is of paramount importance to avoid inappropriate antibiotic prescription. We aimed to evaluate the performance of a rapid syndromic molecular assay in nasopharyngeal swabs for identifying the most common bacterial causes of lower respiratory tract infections in adults (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis). Our data show that nasopharyngeal molecular assay has a good concordance with lower respiratory tract sample when positive but not when negative. A positive result is therefore concordant with a lower respiratory tract infection and can be used to target antibiotics. Nevertheless, a negative result does not have a good concordance, so it cannot be used to withhold antibiotics. Our findings illustrate the potential utility of these easily collected samples for the management of patients with lower respiratory tract infections.

Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples

OBJECTIVES

In order to cope with the rapid spread of the COVID-19 pandemic, we introduced on our in-house high-throughput molecular diagnostic platform (MDx Platform) a real-time reverse transcriptase PCR (RT-PCR) to detect the SARS-CoV-2 from any clinical specimens. The aim of this study was to compare the RT-PCR results obtain with the MDx Platform and the commercial assay cobas SARS-CoV-2 (Roche) on nasopharyngeal swab and other clinical specimens including sputum, bronchial aspirate, bronchoalveolar lavage and anal swabs.

METHODS

Samples received in our laboratory from patients suspected of COVID-19 (n = 262) were tested in parallel with our MDx platform SARS-CoV-2 PCR and with the cobas SARS-CoV-2 test.

RESULTS

The overall agreement between the two tests for all samples tested was 99.24% (260/262), which corresponded to agreements of 100% (178/178) on nasopharyngeal swabs, 95.45% (42/44) on lower respiratory tract specimen with discordant resultS obtained for very high cycle threshold (Ct) value and 100% (40/40) on anorectal swabs. The Ct values for nasopharyngeal swabs displayed an excellent correlation (R2 > 96%) between both tests.

CONCLUSIONS

The high agreements between the cobas SARS-CoV-2 test and the MDx platform supports the use of both methods for the diagnostic of COVID-19 on various clinical samples. Very few discrepant results may occur at very low viral load.

Human psittacosis: a review with emphasis on surveillance in Belgium

Chlamydia psittaci causes psittacosis in humans, mainly in persons in contact with birds in either the setting of occupational or companion bird exposure. Infection is associated with a range of clinical manifestations from asymptomatic infection to severe atypical pneumonia and systemic disease. This paper reviews new knowledge on psittacosis, its legal and regulatory aspects and presents epidemiological data on psittacosis in Belgium. In Belgium, the number of reported positive laboratory results increased slowly since 2010, and in 2017, the number almost doubled compared to the two previous years. The number of psittacosis cases in Belgium, as in other countries, is probably highly underestimated, because of underdiagnoses and underreporting. Over the 3-year period, the mandatory notification system registered 24% only of all reported positive laboratory result. Therefore, increased awareness among general and occupational physicians, clinicians and the public is needed. Policies aimed at reducing psittacosis disease burden are justified, nevertheless national health authorities should provide more legal and financial support to implement more adequate C. psittaci diagnostic tools.

Analysis of humoral immune responses to recombinant Chlamydia pneumoniae antigens

OBJECTIVES

Chlamydia pneumoniae is a difficult to diagnose respiratory pathogen. This study was performed to systematically characterize humoral immune responses to selected C. pneumoniae antigens in order to provide novel serodiagnostic perspectives for clinical and epidemiological issues.

METHODS

Based on a literature search, gene library screening, and serological proteome analysis, 15 immunogenic surface-associated, virulence-associated, and hypothetical C. pneumoniae antigens were selected, recombinantly expressed, and lined on a nitrocellulose strip. Specific IgM and IgG reactivity was measured in a total of 172 PCR- and micro-immunofluorescence testing (MIF)-characterized serum samples from patients with respiratory infections. A theoretical model was conceived to approximate a putative course of C. pneumoniae antigen expression and assess the potential of early and late antigens.

RESULTS

While surface antigens performed poorly, the virulence-associated TARP was a reliable antigen for IgM detection, with a sensitivity of 80.0% and a diagnostic specificity of 90.2%. The hypothetical protein YwbM proved powerful for IgG detection with MIF-correlative sensitivities of up to 94.4% and a diagnostic specificity of 95.1%.

CONCLUSIONS

This study provides new insights into antibody profiles to immunogenic proteins in C. pneumoniae infection. The study findings offer antigen candidates for more reliable and standardized serological investigations of C. pneumoniae infections, including studies on seroprevalence and epidemiology.

First Report of Chlamydia Seroprevalence in Slaughter Pigs in Shandong Province, Eastern China

Chlamydia, a kind of obligate intracellular Gram-negative bacteria, can infect humans and animals worldwide, including pigs. However, the information on Chlamydia infection is unavailable in pigs in Shandong province, eastern China. To assess the seroprevalence and risk factors of Chlamydia infection in pigs in Shandong province, eastern China, a total of 2108 serum samples of slaughter pigs were collected between January 2017 and December 2018, and specific antibodies against Chlamydia were detected by the indirect hemagglutination assay. The overall Chlamydia seroprevalence was 24.15% (509/2108, 95% confidence interval: 22.32-25.97). Species, sampling regions, and rearing systems of pigs were considered as risk factors for Chlamydia infection through statistical analysis by SAS analysis (p < 0.05). These results indicated that Chlamydia is highly prevalent in slaughter pigs in Shandong province, eastern China, and may pose a potential risk for human health. To our knowledge, this is the first investigation of Chlamydia seroprevalence in slaughter pigs in Shandong province, eastern China. Moreover, this is the first report to compare the Chlamydia seroprevalence between domestic pigs and farmed wild boars in a same study, which may provide important data for preventing and controlling Chlamydia infection in pigs in China.

A Bird's-Eye View of Chronic Unilateral Conjunctivitis: Remember about Chlamydia psittaci

Chlamydia psittaci causes psittacosis in humans, mainly in people in contact with birds in either the setting of occupational or companion bird exposure. Infection is associated with a range of clinical manifestations from asymptomatic infection to severe atypical pneumonia and systemic disease. C. psittaci has also been associated with ocular adnexal lymphoma in human patients. The current paper describes successful doxycycline treatment of a male patient suffering from C. psittaci chronic unilateral conjunctivitis, most probably linked to the visit of a South African wildlife reserve. Increased awareness among general and occupational physicians, ophthalmologists, clinicians, and the public on the potential of C. psittaci to cause ocular infection is needed.

Seroprevalence and Risk Factors of Chlamydia abortus Infection in Goats in Hunan Province, Subtropical China

Chlamydia abortus is an obligate intracellular Gram-negative bacteria, which can infect animals and human, including goats. However, little information on C. abortus infection is available in goats in Hunan province, subtropical China. To investigate the seroprevalence and risk factors of C. abortus infection in goats in Hunan province, China, a total of 911 goat blood samples were collected randomly from 14 herds having number of goats ranging from 1000 to 3000 from March 2014 to December 2015. Seropositive animals were found in 11 out of 14 (78.57%) goat herds with seroprevalence ranging from 0.00% to 29.94% in individual herds. Overall, the seroprevalence of C. abortus infection was different among regions (southern Hunan: 1.78%; northeast Hunan: 5.47%; and west Hunan: 15.29%), gender (male: 4.58% and female: 9.10%), seasons (spring: 5.97%; summer: 2.61%; autumn: 16.88%; and winter: 10.94%), and ages (year ≤1: 2.39%; 1 < year ≤2: 9.58%; 2 < year ≤3: 9.16%; and year >3: 17.57%). Risk factors for C. abortus infection were associated with region, season, and age in this study. To our knowledge, this is the first document to demonstrate the existence of C. abortus infection in goats, and the seroprevalence was 8.45% out of 911 goats in Hunan province.