The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae

Atypical pneumonia (Review)

Atypical pneumonia encompasses diverse pathogens, such as Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella species, which differ from typical bacterial pneumonia in their extrapulmonary manifestations. Clinical differentiation relies on systemic involvement rather than on standalone symptoms. Despite challenges in distinct diagnosis, syndromic approaches and weighted point systems aid in accurate presumptive diagnoses. Antibiotic treatment, often non-β-lactams due to the unique cell structures of atypical pathogens, targets intracellular processes. Macrolides, tetracyclines, quinolones and ketolides are effective due to their intracellular penetration, crucial for combating these intracellular pathogens. The prevalence of atypical pneumonia varies globally, with Europe, Asia/Africa and Latin America reporting detection rates between 20-28%. Streptococcus pneumoniae remains a primary cause of pneumonia; however, atypical pathogens contribute significantly to this disease, being more prevalent in outpatient settings and among young adults. Legionella stands out in severe hospitalized cases and is associated with higher mortality rates. Diagnosis proves challenging due to overlapping symptoms with other respiratory infections. Differentiation among pathogens, such as Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella relies on subtle clinical variations and imaging findings. Diagnostic methods include serological studies, cultures and polymerase chain reaction, each with limitations in sensitivity or specificity. Prognosis varies widely. Atypical pneumonia can progress to severe forms with fatal outcomes, causing multi-organ damage. Complications extend beyond the respiratory system, affecting the cardiovascular system, exacerbating conditions such as chronic obstructive pulmonary disease and asthma, and potentially linking to conditions such as lung cancer. Increasing antibiotic resistance poses a significant challenge, influencing treatment outcomes and prolonging illness duration.

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.

Research status and challenges of Mycoplasma pneumoniae pneumonia in children: A bibliometric and visualization analysis from 2011 to 2023

BACKGROUND

Mycoplasma pneumoniae (MP) infections occur in regional outbreaks every 3 to 7 years, lasting up to 2 years. Since this fall, there has been a significant rise in MP infections among children in China, indicating a regional epidemiological trend that imposes an increased national public health burden. To date, bibliometric methods have not been applied to studies on MP infection in children.

METHODS

We searched for all relevant English publications on MP pneumonia in children published from 2011 to 2023 using Web of Science. Analytical software tools such as Citespace and VOSviewer were employed to analyze the collected literature.

RESULTS

993 articles on MP pneumonia in children were published in 338 academic journals by 5062 authors affiliated with 1381 institutions across 75 countries/regions. China led in global productivity with 56.19%. Among the top 10 prolific organizations, 8 were Chinese institutions, with Soochow University being the most active, followed by Capital Medical University and Zhejiang University. Zhimin Chen from Zhejiang University School of Medicine exhibited the highest H-index of 32. Keyword co-occurrence network analysis revealed 7 highly relevant clusters.

CONCLUSION

The current research hotspots and frontiers in this field are primarily MP pneumonia, refractory MP pneumonia, lactate dehydrogenase, asthma, and biomarker. We anticipate that this work will provide novel insights for advancing scientific exploration and the clinical application of MP pneumonia in children.

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.

CRISPR/Cas9-based point-of-care lateral flow biosensor with improved performance for rapid and robust detection of Mycoplasma pneumonia

Screening of acute respiratory infections causes serious challenges in urgent point-of-care scenarios where conventional methods are impractical and alternative techniques suffer from low accuracy, poor robustness, and reliance on sophisticated instruments. As an improvement to this paradigm, we report a point-of-care lateral flow biosensor (LFB) based on the recognition property of clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (Cas9) and apply it to the detection of Mycoplasma pneumoniae (M. pneumoniae). The designed biosensor employs CRISPR/Cas9 for secondary recognition after preamplification of target gene using specific primer set, avoiding false positives caused by nontarget factors. The high amplification efficiency and low applicable temperatures of recombinase polymerase amplification brings the detection limit of the biosensor to 3 copies even at a preamplification temperature of 25 °C. Its practical application is further demonstrated with 100% accuracy by testing with 43 M. pneumoniae-infected specimens and 80 uninfected specimens. Additionally, the entire detection, including pretreatment, preamplification, CRISPR/Cas9 recognition, and visual analysis, can be completed in 30 min. Featured with the combination of CRISPR/Cas9 and LFB, the biosensor we developed herein ensures excellent convenience, accuracy, and robustness, which endows promising point-of-care screening potential for infectious pathogens.

The molecular characteristics, diagnosis, and treatment of macrolide-resistant Mycoplasma pneumoniae in children

The purpose of this study is to review the molecular characteristics, the diagnosis, and treatment of the widespread infection of macrolide-resistant Mycoplasma pneumoniae (M. pneumoniae; MRMP) in children, thus providing a better knowledge of this infection and presenting the associated problems. Single point mutations in the V region of the 23S rRNA gene of M. pneumoniae genome are associated with macrolide resistance. P1-1, MLVA4-5-7-2, and ST3 are usually the predominated genetic types in the M. pneumoniae epidemics. The short-term two times serological IgM (or together with IgG) test in the acute stage can be used for confirmation. Combined serological testing and PCR might be a more prudent method to reduce macrolide consumption and antibiotic selective pressure in a clinical setting. Molecular methods for the detection of single-nucleotide mutations in the V region of the 23S rRNA gene can be used for the diagnosis of MRMP. The routine use of macrolide for the treatment of macrolide-sensitive Mycoplasma pneumoniae (MSMP) infections can get good effect, but the effects are limited for severe MRMP infections. Additional corticosteroids may be required for the treatment of severe MRMP infections in children in China during the era of MRMP.

The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research

For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.

Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia

Background

Among hospitalized children suffering from community-acquired pneumonia, Mycoplasma pneumoniae (MP) is one of the most common pathogens. MP often exists as a co-infection with bacteria or viruses, which can exacerbate the clinical symptoms. We investigated the pathogen spectrum in MP-positive and MP-negative samples from hospitalized children with respiratory tract infections in Beijing, China.

Method

This study included 1038 samples of nasopharyngeal aspirates obtained between April, 2017 and March, 2018 from hospitalized children under 6 years of age with respiratory tract infections. To explore the impact of MP infection on the composition of the pathogen spectrum, 185 nasopharyngeal aspirates (83 MP-positive/102 MP-negative) were randomly selected for next-generation sequencing and comprehensive metagenomics analysis. Real-time PCR was used to detect and verify common respiratory viruses.

Results

Of the 1038 samples, 454 (43.7%) were infected with MP. In children < 6 years of age, the MP infection rate gradually increased with age, with the highest rate of 74.2% in 5–6-year-olds. The results of metagenomics analysis revealed 11 human, animal and plant virus families, and bacteriophages, including common respiratory viruses, enteroviruses and anelloviruses. The virus family with the highest number of reads in both MP-positive and MP-negative samples was the Pneumoviridae, and the number of reads for human respiratory syncytial virus (HRSV) in MP-positive samples was higher than that in MP-negative samples. Among the 83 MP-positive samples, 47 (56.63%) were co-infected with viruses, the most common of which was influenza virus (IFV). The durations of hospitalization and fever were higher in patients with MP co-infection than MP single infection, but the difference was not statistically significant.

Conclusion

The viral family with the highest number of reads in both groups was Pneumoviridae, and the number of reads matched to HRSV in MP-positive samples was much higher than MP-negative samples. Co-infection of MP and IFV infection were the most cases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01914-y.

Forty Years of Molecular Diagnostics for Infectious Diseases

Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.

Molecular Tools for Typing Mycoplasma pneumoniae and Mycoplasma genitalium

Mycoplasma pneumoniae and Mycoplasma genitalium are cell wall-less bacteria with strongly reduced genome content and close phylogenetic relatedness. In humans, the only known natural host, the microorganisms colonize the respiratory or genitourinary mucosa and may cause a broad range of clinical presentations. Besides fundamental differences in their tissue specificity, transmission route, and ability to cause prevalence peaks, both species share similarities such as the occurrence of asymptomatic carriers, preferred populations for infection, and problems with high rates of antimicrobial resistance. To further understand the epidemiology of these practically challenging bacteria, typing of strains is necessary. Since the cultivation of both pathogens is difficult and not performed outside of specialized laboratories, molecular typing methods with adequate discriminatory power, stability, and reproducibility have been developed. These include the characterization of genes containing repetitive sequences, of variable genome regions without the presence of repetitive sequences, determination of single and multi-locus variable-number tandem repeats, and detection of single nucleotide polymorphisms in different genes, respectively. The current repertoire of procedures allows reliable differentiation of strains circulating in different populations and in different time periods as well as comparison of strains occurring subsequently in individual patients. In this review, the methods for typing M. pneumoniae and M. genitalium, including the results of their application in different studies, are summarized and current knowledge regarding the association of typing data with the clinical characteristics of infections is presented.

Development of a duplex recombinase-aided amplification assay for direct detection of Mycoplasma pneumoniae and Chlamydia trachomatis in clinical samples

BACKGROUND

Pneumonia caused by Mycoplasma pneumoniae is common in the elderly and children, and pneumonia caused by Chlamydia trachomatis is prevalent in newborns. This study aimed to establish a rapid, sensitive, and simple method for the direct detection of M. pneumoniae and C. trachomatis in clinical samples without DNA extraction.

METHODS

We established a duplex recombinase-aided amplification (RAA) assay with the RNAseP gene as an internal control for detecting the P1 gene of M. pneumoniae and the ORF8 gene of C. trachomatis, respectively. The results were obtained at 39 °C within 15-20 min. A total of 130 clinical samples suspected of M. pneumoniae or C. trachomatis infection were collected and tested by duplex RAA and PCR. DNA extracted via a commercial kit or treated with a nucleic acid-releasing agent was used and compared, respectively. Standard recombinant plasmids were used to test the sensitivity of the duplex RAA assay. In addition, other similar common pathogens were used to verify the specificity of the duplex RAA assay.

RESULTS

The sensitivity of the duplex RAA assay for detecting M. pneumoniae and C. trachomatis was 10 copies/μL using recombinant plasmids. Compared with PCR, the sensitivity and specificity of duplex RAA assays for M. pneumoniae and C. trachomatis was 100% using clinical DNA samples extracted using a commercial kit and a nucleic acid-releasing agent, and the Kappa value was 1.

CONCLUSION

The advantages of this duplex RAA assay include high sensitivity and specificity, short duration, and simple extraction steps, with potential for use in the on-site detection of M. pneumoniae and C. trachomatis in resource-limited settings.

Macrolide Resistance in Mycoplasma pneumoniae, Midwestern United States, 2014 to 2021

The epidemiology of macrolide resistance in Mycoplasma (Mycoplasmoides) pneumoniae in the United States is incompletely described. Using a PCR assay targeting common mutations associated with macrolide resistance in M. pneumoniae (23S rRNA gene, A2063G/A2064G), the frequency of macrolide resistance was estimated to be 10% based on analysis of 114 samples tested from January 2014 to September 2021 at Mayo Clinic Laboratories. Seasonality data showed the highest rates of M. pneumoniae infection in the fall/early winter.

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.

Macrolide resistance and molecular typing of Mycoplasma pneumoniae infections during a 4 year period in Spain

Background

Mycoplasma pneumoniae (MP) causes community-acquired pneumonia affecting mainly children, and tends to produce cyclic outbreaks. The widespread use of macrolides is increasing resistance rates to these antibiotics. Molecular tools can help in diagnosis, typing and resistance detection, leading to better patient management.

Objectives

To assess the MP genotypes and resistance pattern circulating in our area while comparing serological and molecular diagnosis of MP.

Methods

Molecular and serological diagnosis of MP was performed in 821 samples collected in Badalona (Barcelona, Spain) from 2013 to 2017. Multiple locus variable number tandem repeat analysis (MLVA) and macrolide resistance detection by pyrosequencing were performed in those cases positive by PCR. Presence of respiratory viruses and relevant clinical data were also recorded.

Results

MP was detected in 16.8% of cases by PCR, with an overall agreement with serology of 76%. Eleven different MLVA types were identified, with 4-5-7-2 (50.1%) and 3-5-6-2 (29.2%) being the most abundant, with the latter showing a seasonal increase during the study. A total of 8% of the strains harboured a point substitution associated with macrolide resistance, corresponding mainly to an A2063G 23S rRNA mutation and directly related to previous macrolide therapy. Analysis of respiratory viruses showed viral coinfections in most cases.

Conclusions

Serological and molecular tools combined could improve MP diagnosis and the analysis of its infection patterns. Macrolide resistance is associated with previous therapy. Given that MP pneumonia usually resolves spontaneously, it should be reconsidered whether antibiotic treatment is suitable for all cases.

Evaluation of a novel immunochromatographic assay using silver amplification technology for detection of Mycoplasma pneumoniae from throat swab samples in pediatric patients

Objectives

Mycoplasma pneumoniae is one of the common causative pathogens of community-acquired respiratory tract infections mainly in children and young adults. Rapid and accurate diagnostic techniques for identifying the causative pathogen would be useful for initiating treatment with an appropriate antibiotic. The purpose of the present study was to evaluate the sensitivity and specificity of a novel immunochromatographic assay using silver amplification technology using FUJI DRI-CHEM IMMUNO AG2 and FUJI DRI-CHEM IMMUNO AG cartridge Myco (FUJIFILM Co., Tokyo, Japan) for detection of M. pneumoniae.

Methods

Throat swab samples were collected from 170 pediatric patients who were diagnosed with bronchitis or pneumonia. The silver amplification immunochromatographic (SAI) assay was performed using these samples and the results were compared with those of real-time PCR. The time required for the SAI assay is approximately 20 min (5 min for sample preparation and 15 min for waiting time after starting the assay).

Results

The sensitivity and specificity of the SAI assay for detection of M. pneumoniae were 85.2 and 99.1%, respectively, and the assay showed positive and negative predictive values of 98.1 and 92.3%, respectively, compared with the results of real-time PCR. The diagnostic accuracy was 94.1%.

Conclusions

FUJI DRI-CHEM IMMUNO AG2 and FUJI DRI-CHEM IMMUNO AG cartridge Myco are appropriate for clinical use. The optimal timing of this assay is five days or more after the onset of M. pneumoniae infection. However, PCR or other molecular methods are superior, especially with regard to sensitivity and negative predictive value.

Viral and bacterial coinfection among hospitalized children with respiratory tract infections

BACKGROUND

The epidemiology of Mycoplasma pneumoniae (MP) and local dominant etiologies of pathogens that cause respiratory tract infections (RTIs) among central China children (≤14 years old) hospitalized are poorly understood.

METHODS

A total of 10,429 specimens were analyzed, and IgM antibodies against 9 respiratory pathogens including MP were detected using indirect immunofluorescence assay from serum.

RESULTS

It showed that 59.3% of the enrolled children were positive for at least 1 pathogen; highest detection rates included those between 3 and <6 years of age (70.4%), female (63.2%), and who were hospitalized in 2014 (80.9%). The most predominant pathogen was MP (45.6%), followed by Parainfluenza viruses (PIVs) (22.6%) and influenza B viruses (IFVB) (14.7%). Coinfection was observed in 2,907 specimens (27.9%); the coinfection combination containing MP and PIVs had the highest detection rate of 15%, followed by MP and IFVB as well as IFVB and PIVs.

CONCLUSIONS

MP was the most commonly detected bacteria among hospitalized children, which should be included in the differential diagnosis for hospitalized children with RTI. These findings will contribute to the effective prevention and therapeutic approaches of pathogens among local children suffering from RTI.

Mycoplasma pneumoniae in Children With and Without Community-acquired Pneumonia. What do PCR and Serology Say?

BACKGROUND

IgM titers of Mycoplasma pneumoniae can remain high for months or years, and specific DNA can be detected in asymptomatic people.

METHODS

We compared the performance of serology and PCR in children with and without community-acquired pneumonia (CAP) for the diagnosis of M. pneumoniae.

RESULTS

In children with CAP, a positive test by M. pneumoniae (PCR and/or paired serology or both) were found in 13.9%. Of these, 10.3% were positive by multiplex PCR (Seeplex-Seegen), and 6.7% exhibited quadrupled titers (22 for IgG, 6 for IgM and 5 for both). Both tests were positive in 2.8% of cases. In the group without CAP, 3.3% were positive by PCR. Thirty-two percent of children with CAP and 38.3% of healthy children had IgM titers >11 in the acute phase.

CONCLUSIONS

The detection of IgM is not useful for diagnosing acute M. pneumoniae infection, and a positive PCR result can be due to colonization and not infection. New and better diagnostic techniques are required.

Comparison of a novel chemiluminescence immunoassay with the passive agglutination method for the diagnosis of Mycoplasma pneumoniae infection in children

OBJECTIVE

The purpose of this study was to evaluate a newly developed chemiluminescence immunoassay (CLIA) and compare it to passive agglutination (PA) for the diagnosis of pneumonia caused by Mycoplasma pneumoniae in children.

METHOD

A total of 291 children suspected of M. pneumoniae infections were enrolled. Serum samples were obtained from routine diagnostic requests, and specific antibodies were simultaneously detected by PA and CLIA. Cohen's kappa was used to assess the agreement between the PA and CLIA assays, multivariate logistic regression analysis was used to evaluate risk factors for the discordance between the PA and CLIA assays.

RESULTS

The positive rate was 62.2% (181/291) for PA and 61.2% (178/291) for CLIA (P = 0.08). The specificity, sensitivity, negative, and positive predictive values of CLIA for M. pneumoniae infection were 80.09%, 86.7%, 78.8%, and 88.2%, respectively, with the PA test considered as the diagnostic standard. The correlation of the CLIA and PA assays was 76.8%, and the Kappa coefficient was 0.80. Significant correlations were found between the PA titers and the results of MP-IgM (R = 0.88, P < .05) and MP-IgG (R = 0.84, P < .05) detected by CLIA.

CONCLUSIONS

A high degree of consistency was found between the PA and CLIA methods in detecting M. pneumoniae infections. CLIA is a reliable and rapid method and might be a promising alternative assay to PA for the diagnosis of M. pneumoniae infections.

Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010-2016

Background

Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017.

Results

The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains.

Conclusions

The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.

A comparison of genotyping tool in Treponema pallidum: Review and meta-analysis

BACKGROUND

To decipher the molecular epidemiology of the Treponema pallidum subspecies, pallidum, researchers have developed different molecular typing schemes which identify strains type from clinical specimens. However, the results of these studies show remarkable diversity.

METHODS

We searched for literature in PubMed, MEDLINE, Web of Sciences, and OVID from January 1998 to January 2019, in order to compare the efficiency of typing schemes using published evidence for systematic reviews and meta-analyses.

RESULTS

From the 43 studies included, the overall typing efficiency of Treponema pallidum was 71.4% (95% CI: 63.2-78.9%). Subgroup analyses indicated that the typing efficiency of CDC-typing (CDCT, 68.2%, 95% CI: 53.6-81.2%) was worse than those of enhanced CDC-typing (ECDCT, 72.3%, 95% CI: 60-83.1%), CDC-rspA (81.6%, 95% CI: 76.1-86.6%), multi-locus sequence typing (MLST, 67.1%, 95% CI: 61.1-72.7), and sequencing-based molecular typing (SBMT, 71.6%, 95% CI: 50-89.2%). A limitation of this review is that the studies included employed different criteria to collect and investigate samples of Treponema pallidum, which could contribute to heterogeneity.

CONCLUSIONS

This analysis suggests that CDCT is an inferior scheme in molecular typing, the discriminatory power was very similar for ECDCT and SBMT. Other factors contributing to the heterogeneity between typing studies warrants further study.

Emerging strategies for the noninvasive diagnosis of nosocomial pneumonia

Introduction: Hospital-acquired pneumonia is a common and therapeutically challenging diagnosis that can lead to severe sepsis, critical illness, and respiratory failure. In this review, we focus on efforts to enhance microbiological diagnosis of hospital-acquired pneumonia, including ventilator-associated pneumonia.

Areas covered: A systematic literature review was conducted by searching Medline from inception to December 2018, including hand-searching of the reference lists for additional studies. The search strategy comprised the following common search terms: hospital pneumonia OR nosocomial pneumonia OR noninvasive OR molecular diagnostic tests (OR point-of-care systems OR VOC [i.e. volatile organic compounds]) OR rapid (or simple or quick test), including brand names for the most common commercial tests.

Expert opinion: In recent years, the microbiological diagnosis of respiratory pathogens has improved significantly by the development and implementation of molecular diagnostic tests for pneumonia. Real-time polymerase chain reaction, hybridization, and mass spectrometry-based platforms dominate the scene, with microarray-based assays, multiplex polymerase chain reaction, and MALDI-TOF mass spectrometry capable of detecting the determinants of antimicrobial resistance (mainly β-lactamase genes). Introducing these assays into routine clinical practice for rapid identification of the causative microbes and their resistance patterns could transform the care of pneumonia, improving antimicrobial selection, de-escalation, and stewardship.

Mycoplasma hyopneumoniae variability: Current trends and proposed terminology for genomic classification

Mycoplasma hyopneumoniae (M. hyopneumoniae) is the aetiologic agent of enzootic pneumonia in swine, a prevalent chronic respiratory disease worldwide. Mycoplasma hyopneumoniae is a small, self-replicating microorganism that possesses several characteristics allowing for limited biosynthetic abilities, resulting in the fastidious, host-specific growth and unique pathogenic properties of this microorganism. Variation across several isolates of M. hyopneumoniae has been described at antigenic, proteomic, transcriptomic, pathogenic and genomic levels. The microorganism possesses a minimal number of genes that regulate the transcription process. Post-translational modifications (PTM) occur frequently in a wide range of functional proteins. The PTM by which M. hyopneumoniae regulates its surface topography could play key roles in cell adhesion, evasion and/or modulation of the host immune system. The clinical outcome of M. hyopneumoniae infections is determined by different factors, such as housing conditions, management practices, co-infections and also by virulence differences among M. hyopneumoniae isolates. Factors contributing to adherence and colonization as well as the capacity to modulate inflammatory and immune responses might be crucial. Different components of the cell membrane (i.e. proteins, glycoproteins and lipoproteins) may serve as adhesins and/or be toxic for the respiratory tract cells. Mechanisms leading to virulence are complex and more research is needed to identify markers for virulence. The utilization of typing methods and complete or partial-gene sequencing for M. hyopneumoniae characterization has increased in diagnostic laboratories as control and elimination strategies for this microorganism are attempted worldwide. A commonly employed molecular typing method for M. hyopneumoniae is Multiple-Locus Variable number tandem repeat Analysis (MLVA). The agreement of a shared terminology and classification for the various techniques, specifically MLVA, has not been described, which makes inferences across the literature unsuitable. Therefore, molecular trends for M. hyopneumoniae have been outlined and a common terminology and classification based on Variable Number Tandem Repeats (VNTR) types has been proposed.

Detection of Mycoplasma pneumoniae in Mexican children with community-acquired pneumonia: experience in a tertiary care hospital

Purpose: Mycoplasma pneumoniae is an important cause of community-acquired pneumonia (CAP). Information on the prevalence of M. pneumoniae in pediatric patients with CAP in Mexico is limited. The aim of this study was to detect M. pneumoniae in hospitalized pediatric patients with CAP. Patients and methods: We performed a descriptive study in a tertiary-level pediatric reference center, obtaining 154 respiratory samples from patients under 18 years of age and diagnosed with CAP. M. pneumoniae was detected by real-time polymerase chain reaction (PCR) targeting the p1 and CARDS genes. Complete blood cell count, measurement of C-reactive protein and detection of IgM and IgG anti-P1 were performed. Clinical, epidemiological and radiological data of the patients were analyzed. Results: M. pneumoniae was detected by real-time PCR in 26.6% of the samples. 39% of the cases occurred during the spring season. A total of 83% of the patients with M. pneumoniae had some underlying disease; renal disease, autoimmune disease and primary immunodeficiencies had a significant association with M. pneumoniae CAP. Children under 6 years of age represented 53.7% of the cases. Fever and cough were the most frequent symptoms. IgM and IgG were positive in 1.9% and 14% of the patients, respectively. In the chest X-ray, 17.1% of the patients showed multifocal alveolar infiltrates pattern. The complications in this series were 26.8%. The mortality in this study was 4.9%. Conclusion: This is the first report in Mexico about M. pneumoniae as a causal agent of CAP in a tertiary care pediatric hospital using real-time PCR and serology. M. pneumoniae was responsible for 26.6% of the cases and was frequent in children under 6 years of age. In addition, we described the clinical presentation in patients with underlying diseases.

Contagious caprine pleuropneumonia - a comprehensive review

Contagious caprine pleuropneumonia (CCPP) is a serious disease of goats, occasionally sheep and wild ruminants, caused by Mycoplasma capricolum subspecies capripneumoniae (Mccp). The disease is characterized by severe serofibrinous pleuropneumonia, very high morbidity (∼100%), and mortality (80–100%). CCPP affects goats in more than 40 countries of the world thereby posing a serious threat to goat farming around the globe. The characteristic clinical signs of CCPP are severe respiratory distress associated with sero-mucoid nasal discharge, coughing, dyspnea, pyrexia, pleurodynia, and general malaise. In later stages, severe lobar fibrinous pleuropneumonia, profuse fluid accumulation in pleural cavity, severe congestion of lungs and adhesion formation is observed. Mycoplasmal antigen interactions with host immune system and its role in CCPP pathogenesis are not clearly understood. CCPP is not a zoonotic disease. Diagnosis has overcome cumbersome and lengthy conventional tests involving culture, isolation, and identification by advanced serological (LAT, cELISA) or gene-based amplification of DNA (PCR, RFLP, and hybridization) and sequencing. The latex agglutination test (LAT) is rapid, simple, and better test for field and real-time diagnosis applicable to whole blood or serum and is more sensitive than the CFT and easier than the cELISA. Moreover, the studies on antibiotic sensitivity and exploration of novel antibiotics (fluoroquinolones, macrolides) can help in better therapeutic management besides preventing menace of antibiotic resistance. Re-visiting conventional prophylactic measures focussing on developing novel strain-based or recombinant vaccines using specific antigens (capsular or cellular) should be the most important strategy for controlling the disease worldwide.

Serological and molecular detection of Mycoplasma pneumoniae in children with community-acquired lower respiratory tract infections

This study was designed to evaluate the incidence of Mycoplasma pneumoniae infection in children with community-acquired lower respiratory tract infections (LRTIs). A total of 245 patients 6 months to 12 years of age were investigated for M. pneumoniae employing serological tests, polymerase chain reaction (PCR), nested PCR, and reverse transcription PCR (RT-PCR) on throat swab samples. Forty five (59.2%) children <5 years and 31 (40.7%) children ≥5 years age group were positive for M. pneumoniae infection, and this difference was statistically significant (P ≤ 0.01).Clinical and radiological findings across M.pneumoniae-positive and -negative cases were comparable. Serology, PCR, nested PCR, and RT-PCR together detected M. pneumoniae infection in 76 (31%) patients. Sensitivity, specificity, and positive and negative predictive values of PCR were 16.18%, 95.48%, 57.89%, and 74.78%, respectively, and those of serology were 57.89%, 74.78%, 16.18%, and 95.48%, respectively. Serological and molecular detection in combination is useful for rapid and reliable diagnosis of M. pneumoniae infections in children with LRTIs.

Evaluation of the illumigene Mycoplasma Direct DNA Amplification Assay

Mycoplasma pneumoniae is a common cause of community-acquired pneumonia. The illumigene Mycoplasma Direct (iMD) DNA amplification assay is a qualitative in vitro test utilizing loop-mediated isothermal amplification (LAMP) technology for the direct detection of M. pneumoniae DNA in respiratory specimens. The iMD assay does not require the preextraction of nucleic acids from specimens, which is a prerequisite step for the previously approved illumigene Mycoplasma (iM) assay. The aim of this prospective multicenter study was to evaluate the performance characteristics of the newly developed iMD assay, compared with the iM assay. Subjects with symptoms of upper respiratory illnesses suggesting M. pneumoniae infection were enrolled at three sites in the United States. Respiratory specimens were obtained using dual throat swabs. One swab was tested with the iMD assay at each enrollment site. Reference testing with the iM assay was performed by the manufacturer. Among 456 specimens tested, the iM reference method detected M. pneumoniae in 25 specimens (5.5%), while the iMD assay identified 34 specimens (7.5%) as M. pneumoniae positive. There were 10 false-positive results and 1 false-negative result with the iMD assay. The overall positive and negative agreement rates were 96.0% (95% confidence interval [CI], 80.5 to 99.3%) and 97.7% (95% CI, 95.8 to 98.7%), respectively. The overall agreement rate was determined to be 97.6% (95% CI, 95.7 to 98.6%). We conclude that the iMD test results were comparable to the iM assay results. The removal of the DNA extraction step for the iMD assay simplifies testing, saves time, and reduces the costs of detecting M. pneumoniae from throat swabs, compared to the iM assay.

Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques

Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.

Mycoplasma pneumoniae from the Respiratory Tract and Beyond

Mycoplasma pneumoniae is an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests for M. pneumoniae detection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms. Clinically significant acquired macrolide resistance has emerged worldwide and is now complicating treatment. In vitro susceptibility testing methods have been standardized, and several new drugs that may be effective against this organism are undergoing development. This review focuses on the many new developments that have occurred over the past several years that enhance our understanding of this microbe, which is among the smallest bacterial pathogens but one of great clinical importance.

Magnetic particles for in vitro molecular diagnosis: From sample preparation to integration into microsystems

Colloidal magnetic particles (MPs) have been developed in association with molecular diagnosis for several decades. MPs have the great advantage of easy manipulation using a magnet. In nucleic acid detection, these particles can act as a capture support for rapid and simple biomolecule separation. The surfaces of MPs can be modified by coating with various polymer materials to provide functionalization for different applications. The use of MPs enhances the sensitivity and specificity of detection due to the specific activity on the surface of the particles. Practical applications of MPs demonstrate greater efficiency than conventional methods. Beyond traditional detection, MPs have been successfully adopted as a smart carrier in microfluidic and lab-on-a-chip biosensors. The versatility of MPs has enabled their integration into small single detection units. MPs-based biosensors can facilitate rapid and highly sensitive detection of very small amounts of a sample. In this review, the application of MPs to the detection of nucleic acids, from sample preparation to analytical readout systems, is described. State-of-the-art integrated microsystems containing microfluidic and lab-on-a-chip biosensors for the nucleic acid detection are also addressed.

Evaluation of a real-time method of simultaneous amplification and testing in diagnosis of Mycoplasma pneumoniae infection in children with pneumonia

Mycoplasma pneumoniae (M. pneumoniae) infection can cause community acquired pneumonia in children. A real-time method of simultaneous amplification and testing of M. pneumoniae (SAT-MP) was developed to diagnose M. pneumoniae targeting a region of the ribosomal RNA. The SAT-MP assay can accurately identify M. pneumoniae with a detection range from 10¹ to 10⁷ CFU/ml. In this study, the specimens from 315 children with pneumonia were collected and analyzed by SAT-MP in parallel with real-time PCR method and IgM ELISA assay. The positive rates of these specimens examined by SAT-MP assay, real-time PCR method and IgM ELISA assay were 16.51%, 15.56% and 12.70% respectively. While there was statistical significance (p = 0.04) between SAT-MP assay and IgM ELISA assay, no statistical significance (p = 0.25) was found between SAT-MP assay and real-time PCR method and these two methods had high consistency (kappa value = 0.97). These findings indicate that the newly developed SAT-MP assay is a rapid, sensitive and specific method for identifying M. pneumoniae with potential clinical application in the early diagnosis of M. pneumoniae infection.

Multi-center evaluation of one commercial and 12 in-house real-time PCR assays for detection of Mycoplasma pneumoniae

Detection of Mycoplasma pneumoniae by real-time PCR is not yet standardized across laboratories. We have implemented a standardization protocol to compare the performance of thirteen commercial and in-house approaches. Despite differences on threshold values of samples, all assays were able to detect at least 20M. pneumoniae genomes per reaction.

Atypical Pneumonia: Updates on Legionella, Chlamydophila, and Mycoplasma Pneumonia

Community-acquired pneumonia (CAP) has multiple causes and is associated with illness that requires admission to the hospital and mortality. The causes of atypical CAP include Legionella species, Chlamydophila, and Mycoplasma. Atypical CAP remains a diagnostic challenge and, therefore, likely is undertreated. This article reviews the advancements in the evaluation and treatment of patients and discusses current conflicts and controversies of atypical CAP.

Inter- and intra-strain variability of tandem repeats in Mycoplasma pneumoniae based on next-generation sequencing data

AIM

To characterize inter- and intra-strain variability of variable-number tandem repeats (VNTRs) in Mycoplasma pneumoniae to determine the optimal multilocus VNTR analysis scheme for improved strain typing.

METHODS

Whole genome assemblies and next-generation sequencing data from diverse M. pneumoniae isolates were used to characterize VNTRs and their variability, and to compare the strain discriminability of new VNTR and existing markers.

RESULTS

We identified 13 VNTRs including five reported previously. These VNTRs displayed different levels of inter- and intra-strain copy number variations. All new markers showed similar or higher discriminability compared with existing VNTR markers and the P1 typing system.

CONCLUSION

Our study provides novel insights into VNTR variations and potential new multilocus VNTR analysis schemes for improved genotyping of M. pneumoniae.