Evaluation of Commercial Molecular Diagnostic Methods for Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae

Establishment of a microfluidic and RPA-based platform for rapid multi-sample detection of Mycoplasma pneumoniae

BACKGROUND

Mycoplasma pneumoniae (M. pneumoniae) is a major respiratory pathogen causing atypical community-acquired pneumonia. Early and rapid diagnosis and timely detection of pathogens are crucial. RPA is an emerging PCR technology that allows amplification at room temperature compared to conventional PCR technology, while combining the advantages of rapid detection and high specificity of PCR technology, enabling rapid and accurate detection of pathogens.

METHODS AND RESULTS

In this study, we established a platform for detection of M. pneumoniae based on microfluidic and RPA technologies. The RPA technology is performed in 15 to 20 minutes, and only M. pneumoniae is significantly amplified at a sensitivity of 10 copies/μL; microfluidic technology provides lean instrumentation and a convenient interactive system. Three groups negative and positive QCs and 18 clinical samples can be tested in a single run.

SIGNIFICANCE

In conclusion, we have established a microfluidic molecular assay operating system based on RPA technology, with the advantages of being simple, rapid, accurate and economical, and providing a new tool for laboratory detection of M. pneumoniae.

Molecular characteristics of macrolide-resistant Mycoplasma pneumoniae in children with community-acquired pneumonia in Urumqi, Xinjiang, China in autumn, winter, and spring 2023-2024

BACKGROUND

Following the COVID-19 pandemic, the resurgence of Mycoplasma pneumoniae (MP) infections among children in China has raised urgent concerns regarding antimicrobial drug resistance. We reveal the molecular characteristics of macrolide-resistant MP (MRMP) in children with community-acquired pneumonia (CAP) in autumn, winter, and spring 2023-2024 in Urumqi, Xinjiang, China.

METHODS

Throat samples were collected from 1446 children hospitalized for CAP between October 2023 and April 2024. The polymerase chain reaction fluorescent probe method was used to detect respiratory pathogens, and clinical data from the children were collected. Throat swab samples with positive MP nucleic acid test results were subjected to MP-23S rRNA gene sequencing, P1 genotyping, multilocus sequence typing, and 16S rRNA evolution analyses.

RESULTS

The overall positive rate for MP was 32.2 %. Among these cases, 88 % exhibited MP infection exclusively, while 12 % demonstrated mixed MP infections, with double infections being the most prevalent type of co-infection. Children aged 7-12 years had the highest infection rate, reaching 42.2 % (P < 0.05). The prevalence of macrolide-resistance mutations in MP was 99.1 %, which was predominantly due to the A2063G mutation (98.2 %). The dominant P1 genotype was P1-I (91.5 %), with a resistance mutation rate of 100 %. ST-3 was the dominant MP strain. Evolutionary analysis of 16S rRNA showed that all predominant MP strains belonged to the same evolutionary branch. The MP infection rate in children with CAP showed a significant upward trend from autumn 2023 and remained at a high level until spring 2024. During this period, the infection rate of MRMP, mainly P1-I and ST-3 types, was high. Additionally, we identified 4 MP strains classified as type P1-II, all of which belonged to CC2, and 85 MP strains were categorized as type P1-I, all belonging to CC1.

CONCLUSION

This study reveals that the MRMP epidemic was driven by near-universal macrolide-related mutations associated with clonal ST-3/P1-I strains. Our findings underscore the necessity of implementing real-time molecular surveillance and establishing treatment guidelines in post-pandemic settings.

Detection of macrolide-resistant Mycoplasma pneumoniae using the Kogene Mp-DR real-time PCR assay: A clinical validation study

Macrolide-resistant Mycoplasma pneumoniae (MRMP) requires rapid diagnosis. The Kogene Mp-DR real-time PCR assay showed 100 % sensitivity and specificity for detecting A2063G mutations in the 23S rRNA gene. Although no samples were A2064G-positive, all wild-type cases were accurately classified, highlighting the rapid diagnostic capability of this method for MRMP detection.

Establishment of a rapid detection method for Mycoplasma pneumoniae based on RPA-CRISPR-Cas12a technology

Mycoplasma pneumoniae can cause respiratory infections and pneumonia, posing a serious threat to the health of children and adolescents. Early diagnosis of Mycoplasma pneumoniae infection is crucial for clinical treatment. Currently, diagnostic methods for Mycoplasma pneumoniae infection include pathogen detection, molecular biology techniques, and bacterial culture, all of which have certain limitations. Here, we developed a rapid, simple, and accurate detection method for Mycoplasma pneumoniae that does not rely on large equipment or complex operations. This technology combines the CRISPR-Cas12a system with recombinase polymerase amplification (RPA), allowing the detection results to be observed through fluorescence curves and immunochromatographic lateral flow strips.It has been validated that RPA-CRISPR/Cas12a fluorescence analysis and RPA-CRISPR/Cas12-immunochromatographic exhibit no cross-reactivity with other common pathogens, and The established detection limit was ascertained to be as low as 102 copies/µL.Additionally, 49 clinical samples were tested and compared with fluorescence quantitative polymerase chain reaction, demonstrating a sensitivity and specificity of 100%. This platform exhibits promising clinical performance and holds significant potential for clinical application, particularly in settings with limited resources, such as clinical care points or resource-constrained areas.

Association between 25-hydroxy vitamin D, interleukin-4, and interferon-γ levels and asthma in children with Mycoplasma pneumonia infection

To explore the association between 25-hydroxy vitamin D [25-(OH)-D], interleukin-4 (IL-4), and interferon-γ (IFN-γ) in children with Mycoplasma pneumoniae (MP) infection-related asthma. Logistic analysis was conducted to compare general data in MP asthma and MP non-asthma groups. The level of 25-(OH)-D, IL-4, and IFN-γ were detected and compared between groups. Moreover, the receiver operating characteristic curve (ROC) was applied to test the predictive value of each variable. The results of logistic regression analysis demonstrated that recurrent upper respiratory tract infections and collective living are related to the incidence of MP infection whether with asthma or without asthma. IL-4 and IFN-γ in MP asthma group were significantly higher than those in MP non-asthma group and control group (p < 0. 05), whilst 25-(OH)-D and IFN-γ/IL-4 in MP asthma group were significantly lower than those in MP non-asthma group and control group (p < 0. 05). ROC curves indicated that the area under the curve (AUC) of 25-(OH)-D, IL-4, IFN-γ, IFN-γ/IL-4, and joint detection are 0.765, 0.780, 0.853, 0.638, and 0.912 in diagnosis of MP infection-related asthma, and sensitivity and specificity of joint detection are both greater than 95%. For children with MP infection-related asthma, the level of IL-4 and IFN-γ is upregulated, while 25-(OH)-D is downregulated. The joint detection of 25-(OH)-D, IL-4, IFN-γ, and IFN-γ/IL-4 may improve diagnostic capabilities of MP infection-related asthma.

A comprehensive review of Mycoplasma pneumoniae infection in chronic lung diseases: recent advances in understanding asthma, COPD, and bronchiectasis

This review summarizes the research progress over the past 30 years on the relationship between Mycoplasma pneumoniae infection and chronic respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), and bronchiectasis. Mycoplasma pneumoniae is a common cause of community-acquired pneumonia, particularly in children and young adults. Key findings from recent studies indicate that M. pneumoniae infection is associated with a higher risk of asthma exacerbations and may contribute to the development of bronchiectasis in susceptible individuals. Additionally, emerging evidence suggests that M. pneumoniae-induced immune dysregulation plays a crucial role in the pathogenesis of chronic lung diseases. This review aims to summarize the current understanding of the potential links between M. pneumoniae pneumonia and various chronic respiratory conditions, including asthma, chronic obstructive pulmonary disease (COPD), and bronchiectasis. We discuss the epidemiological data, pathogenic mechanisms, clinical manifestations, and long-term consequences of M. pneumoniae-related respiratory illnesses. Additionally, we highlight the challenges in diagnosis and treatment, as well as future research directions in this field.

An accurate and convenient method for Mycoplasma pneumoniae via one-step LAMP-CRISPR/Cas12b detection platform

INTRODUCTION

Mycoplasma pneumoniae (MP) is the major cause of respiratory infections that threaten the health of children and adolescents worldwide. Therefore, an early, simple, and accurate detection approach for MP is critical to prevent outbreaks of MP-induced community-acquired pneumonia.

METHODS

Here, we explored a simple and accurate method for MP identification that combines loop-mediated isothermal amplification (LAMP) with the CRISPR/Cas12b assay in a one-pot reaction.

RESULTS

In the current study, the whole reaction was completed within 1 h at a constant temperature of 57°C. The limit of detection of this assay was 33.7 copies per reaction. The specificity of the LAMP-CRISPR/Cas12b method was 100%, without any cross-reactivity with other pathogens. Overall, 272 clinical samples were used to evaluate the clinical performance of LAMP-CRISPR/Cas12b. Compared with the gold standard results from real-time PCR, the present method provided a sensitivity of 88.11% (126/143), specificity of 100% (129/129), and consistency of 93.75% (255/272).

DISCUSSION

Taken together, our preliminary results illustrate that the LAMP-CRISPR/Cas12b method is a simple and reliable tool for MP diagnosis that can be performed in resource-limited regions.

Comparison of Real-time Polymerase Chain Reaction and Culture for Targeting Pathogens in Pediatric Severe Community-Acquired Pneumonia

Objective

This study aims to determine the frequency of pathogen detection by real-time polymerase chain reaction (PCR), the frequency of pathogen isolation by culture; and compare the value of real-time PCR and culture of nasopharyngeal aspiration samples in patients with severe community-acquired pneumonia (sCAP).

Materials and Methods

It was a prospective and descriptive study. All pediatric patients diagnosed with sCAP were performed real-time PCR and culture of nasopharyngeal aspiration samples.

Results

A total of 336 patient samples were obtained from children with sCAP. Real-time PCR detected pathogens in 312 patients (92.9%), while culture isolated bacteria in 228 patients (67.9%). Coinfections were reported in 279 cases (83.0%) through real-time PCR. The frequency of agreement between culture and real-time PCR was quite high (P < .001).

Conclusion

Real-time PCR demonstrated more ability for detecting microorganisms than culture. This finding highlighted the value of real-time PCR for targeting pathogens in children with sCAP, particularly in cases involving complex pathogens or those requiring timely identification.

Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done

Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.

The downstream bioprocess toolbox for therapeutic viral vectors

Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and animals for sustainable agriculture. The success of viral vectors will critically depend on the availability of flexible and affordable biomanufacturing strategies that can meet the growing demand by clinics and biotech companies worldwide. In this context, a key role will be played by downstream process technology: while initially adapted from protein purification media, the purification toolbox for viral vectors is currently undergoing a rapid expansion to fit the unique biomolecular characteristics of these products. Innovation efforts are articulated on two fronts, namely (i) the discovery of affinity ligands that target adeno-associated virus, lentivirus, adenovirus, etc.; (ii) the development of adsorbents with innovative morphologies, such as membranes and 3D printed monoliths, that fit the size of viral vectors. Complementing these efforts are the design of novel process layouts that capitalize on novel ligands and adsorbents to ensure high yield and purity of the product while safeguarding its therapeutic efficacy and safety; and a growing panel of analytical methods that monitor the complex array of critical quality attributes of viral vectors and correlate them to the purification strategies. To help explore this complex and evolving environment, this study presents a comprehensive overview of the downstream bioprocess toolbox for viral vectors established in the last decade, and discusses present efforts and future directions contributing to the success of this promising class of biological medicines.

Case Report: Omadacycline in the treatment of macrolide-unresponsive Mycoplasma pneumoniae pneumonia in an adolescent patient

Omadacycline is a novel tetracycline antibiotic that exhibits good in vitro antibacterial activity against atypical pathogens such as Mycoplasma pneumoniae. It is approved for the treatment of adults with community-acquired bacterial pneumonia. However, the safety and efficacy of omadacycline in pediatric patients under 18 years of age have not yet been established. In the present paper, we report a case of pediatric community-acquired pneumonia in which initial empirical anti-infective therapy had failed. The patient received empirical anti-infective therapy with azithromycin and other antimicrobial agents upon admission but showed a poor clinical response and developed secondary tinnitus and liver dysfunction. After the confirmation of M. pneumoniae infection through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, an antibiotic switch to omadacycline was made. Thereafter, the patient's condition improved, and no adverse reactions were observed. These findings demonstrate that mNGS enables the identification of infection-causing pathogens in patients with unresponsive pneumonia. Omadacycline can be considered as an alternative option for anti-infective therapy in pediatric M. pneumoniae pneumonia, especially when the presence of bacterial resistance, adverse drug reactions, or organ failure are taken into consideration.

Absolute quantification of Mycoplasma pneumoniae in infected patients by droplet digital PCR to track disease severity and treatment efficacy

Mycoplasma pneumoniae is a common causative pathogen of community-acquired pneumonia. An accurate and sensitive detection method is important for evaluating disease severity and treatment efficacy. Digital droplet PCR (ddPCR) is a competent method enabling the absolute quantification of DNA copy number with high precision and sensitivity. We established ddPCR for M. pneumoniae detection, using clinical specimens for validation, and this showed excellent specificity for M. pneumoniae. The limit of detection of ddPCR was 2.9 copies/reaction, while that for real-time PCR was 10.8 copies/reaction. In total, 178 clinical samples were used to evaluate the ddPCR assay, which correctly identified and differentiated 80 positive samples, whereas the real-time PCR tested 79 samples as positive. One sample that tested negative in real-time PCR was positive in ddPCR, with a bacterial load of three copies/test. For samples that tested positive in both methods, the cycle threshold of real-time PCR was highly correlated with the copy number of ddPCR. Bacterial loads in patients with severe M. pneumoniae pneumonia were significantly higher than those in patients with general M. pneumoniae pneumonia. The ddPCR showed that bacterial loads were significantly decreased after macrolide treatment, which could have reflected the treatment efficacy. The proposed ddPCR assay was sensitive and specific for the detection of M. pneumoniae. Quantitative monitoring of bacterial load in clinical samples could help clinicians to evaluate treatment efficacy.

Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection

Mycoplasma pneumoniae (MP) is a one of most common pathogen in causing respiratory infection in children and adolescents. Rapid and efficient diagnostic methods are crucial for control and treatment of MP infections. Herein, we present an operationally simple, rapid and efficient molecular method for MP identification, which eliminates expensive instruments and specialized personnel. The method combines recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) 12a-based detection, with an optimal procedure less than 1 h from sample to result including DNA extraction (25 min), RPA reaction (39°C for 15-20 min), CRISPR/Cas12a detection (37°C for 10 min) and visual detection by naked eyes (2 min). This diagnostic method shows high sensitivity (two copies per reaction) and no cross-reactivity against other common pathogenic bacteria. Preliminary evaluation using 201 clinical samples shows sensitivity of 99.1% (107/108), specificity of 100% (93/93) and consistency of 99.5% (200/201), compared with real-time PCR method. The above data demonstrate that our developed method is reliable for rapid diagnosis of MP. In conclusion, the RPA-CRISPR/Cas12a has a great potential to be as a useful tool for reliable and quick diagnosis of MP infection, especially in primary hospitals with limited conditions.

Mycoplasma pneumoniae Pleural Effusion in Adults

Parapneumonic effusions often complicate Mycoplasma pneumoniae (MP) pneumonia, contrary to the notion that they are a rare feature of MP infection. Increased research and evidence on MP parapneumonic effusions (MPPE) can help elucidate its clinical significance as one of the variable manifestations of MP infection. This article aims to summarize the existing literature about the clinical characteristics of MPPE in adults and discuss its diagnostic implications from the perspective of pleural fluid analysis. Approximately 20–25% of adult patients with MP pneumonia develop MPPE, and its frequency in children and adults seems to be similar. Although the pathogenesis of MPPE remains to be elucidated, MP-induced cell-mediated immune mechanisms might be partially associated with the development of MPPE. MPPE usually shows mononuclear leukocyte predominance with elevated adenosine deaminase (ADA) activity, similar to tuberculous pleural effusion (TPE). The degree of increase in pleural fluid ADA levels and serum inflammatory biomarkers may help differentiate between MPPE and TPE. During the acute phase, a single positive IgM and positive polymerase chain reaction results allow for a precise and reliable MP infection diagnosis. The mainstay of treatment is the selection of adequate anti-mycoplasma antibiotics with or without corticosteroid, based on the local epidemiologic data on macrolide resistance.

Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction

Objectives

Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene^® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene^® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae.

Materials

Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae.

Results

Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene^® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene^® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml.

Conclusion

The Smart Gene^® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene^® system is suitable for point-of-care testing in both hospital and outpatient settings.