Sequence Type Changes Associated with Decreasing Macrolide-Resistant Mycoplasma pneumoniae, Japan

Multiplex amplicon sequencing for the comprehensive genotyping of Mycoplasma pneumoniae

Major genotyping methods used to characterize Mycoplasma pneumoniae strains are based on various experimental approaches that need to be implemented in parallel for each strain. In this study, we developed a comprehensive workflow based on amplicon sequencing using next-generation sequencing. This workflow comprised PCR amplification with seven tubes, collection into single tubes, shotgun sequencing, de novo assembly separating each target into individual contigs, and in silico genotyping. The results for p1, orf6, multilocus sequence types, 23S ribosomal RNA gene mutations conferring macrolide resistance, and single-nucleotide polymorphisms identifying the p1 type 1 lineage were obtained simultaneously. The genotyping accuracy was confirmed by comparing the sequences with the whole-genome sequences of 40 M. pneumoniae isolates collected in Tokyo, Japan. The workflow described not only enables high-throughput comprehensive data collection but also enables the detection of novel genotypes with single-nucleotide resolution.

IMPORTANCE

Genotyping plays a central role in the molecular epidemiology of pathogenic bacteria, and many methods have been developed to identify prevalent lineages, infection routes, and antimicrobial resistance. Whole-genome sequencing generally provides most of the genetic information targeted by classic PCR-based schemes and has contributed to the construction of a simplified workflow for many bacterial species. However, several issues concerning the Mycoplasma pneumoniae genome, such as the presence of repetitive elements of the p1 gene, prevent the collection of genotyping results from a single run of short-read shotgun sequencing. Herein, we describe a simplified workflow using amplicon sequencing that covers most of the major genotyping schemes for M. pneumoniae, including p1 genotyping. The workflow effectively characterized M. pneumoniae clinical isolates. This workflow could help advance research on the molecular epidemiology of M. pneumoniae and the detection of novel genotypes.

Recent Macrolide Resistance Pattern of Mycoplasma Pneumonia in the World: A Systematic Review and Meta-Analysis

Background

We aimed to systematically review and analyze the prevalence and pattern of resistance in Mycoplasma pneumoniae.

Methods

We searched authentic scientific sources and databases, and reference lists of relevant articles from Jan 1, 2017, to Jun 1, 2023.

Results

Most of the included studies were conducted in Asia (11470 patients). The overall pooled prevalence was 53% (41%-65%), I2=99.69%; P <0.001. While subgroups analyses revealed that the pooled prevalence for America (3 studies), Asia (29 studies), and Europe (3 studies) was 9% (5%-12%), 62% (52%-73%), and 6% (1%-12%), respectively. Twenty-one eligible studies for determining of A2063G and 16 for A2064G were analyzed. Global pooled prevalence was 67% (58%-76%), I2=99.65%; P<0.001, and 3% (2%-4%), I2=87.44%; P<0.001 for A2063G and A2064G, respectively. Pooled prevalence of A2063G for America, Asia and Europe was 10% (5%-16%), 77% (71%-83%) and 5% (2%-9%), respectively.

Conclusion

While the prevalence of macrolide-resistant M. pneumonia is quite low in America, it is a great dilemma in East Asia and the low prevalence in most countries could be underestimated. This study revealed an increasing trend in macrolide resistance. Indiscriminate and improper use of macrolides may be a warning in this regard.

Mycoplasma pneumoniae MLST detected in the upsurge of pneumonia during the 2023 to 2024 winter season in the Netherlands

During the winter 2023-2024, an upsurge of Mycoplasma pneumoniae (M.pneumoniae) was noted in the Netherlands. To investigate the distribution of M.pneumoniae sequence types from different patient populations and to explore genotypic macrolide resistance which is common in East Asia but not (yet) in Europe. M.pneumoniae positive throat/nasal samples from participatory respiratory surveillance, patients visiting general practitioners with an acute respiratory infection including community acquired pneumonia (CAP) and hospitalised patients with CAP were included, representing different disease severity. The M.pneumoniae were typed with multilocus sequence typing and the 23 S rRNA region was sequenced to determine macrolide resistance markers. In total, 153 M.pneumoniae were sequenced, six sequence types (STs) and only one bacterium with macrolide resistance marker were detected. No link between STs or bacterial load (PCR cycle threshold) and source population of M.pneumoniae was detected. In the Netherlands, the M.pneumoniae upsurge in 2023-2024 existed of multiple commonly found STs. No link between ST and severity of illness was detected. Macrolide resistance remained sporadic.

Epidemiological and clinical characteristics of hospitalized pediatric patients with Mycoplasma pneumoniae pneumonia before and after the COVID-19 pandemic in China: a retrospective multicenter study

BACKGROUND

In China many respiratory pathogens stayed low activities amid the COVID-19 pandemic due to strict measures and controls. We here aimed to study the epidemiological and clinical characteristics of pediatric inpatients with Mycoplasma pneumoniae pneumonia (MPP) after the mandatory COVID-19 restrictions were lifted, in comparison to those before the COVID-19 pandemic.

METHODS

We here included 4,296 pediatric patients with MPP, hospitalized by two medical centers in Jiangsu Province, China, from January 2015 to March 2024. Patients were divided into the pre-COVID (n = 1,662) and post-COVID (n = 2,634) groups. Their baseline characteristics, laboratory test results and radiological patterns were separately assessed and compared between the two groups to determine the substantial changes in the disease profile of MPP after the COVID-19 pandemic.

RESULTS

Epidemiological results suggested a higher annual incidence of MPP after the COVID-19 pandemic when the outbreak reached a peak in October, two months delayed in seasonality compared to that in the pre-COVID era. For pediatric patients with MPP, there was no difference in their median ages, gender ratios, and severe case percentages between the two groups, where most patients were younger than 14 years old. With significance, the post-COVID group had more occurrences of cough and expectoration and higher incidences of influenza A/B virus (IAV/IBV) co-infection than the pre-COVID group. Many hematological parameters and radiological features between the two groups displayed alteration, but comparatively there demonstrated no worsened severity in hospitalized children with MPP after COVID-19 pandemic. Concurrently, the post-COVID group was administered with fewer antibiotics but more corticosteroids for effective treatment than the pre-COVID group.

CONCLUSION

Through the COVID-19 pandemic, the epidemiological and clinical characteristics of pediatric patients with MPP differed, but there was no evident change in the disease severity. After the COVID-19 pandemic, the increased incidence of IAV/IBV co-infection may contribute to the differences in clinical symptoms and hematological profiles, while the adding usage of corticosteroids might treat more effectively.

CHAMP: A Centrifugal Microfluidics-Based CRISPR/Cas12b-Combined Real-Time LAMP One-Pot Method for Mycoplasma pneumoniae Infection Diagnosis

The Mycoplasma pneumoniae outbreak poses health risks to community residents. However, it still has limitations for current clinical diagnostic methods (qPCR nucleic acid assay or IgM immunoassay), including specialized handling, expensive equipment, prolonged turnaround time, and false positives and negatives, highlighting the need to improve clinical diagnostic methods. Herein, we present a novel centrifugal microfluidics-based method for rapidly diagnosing M. pneumoniae infections (CHAMP system). This user-friendly method combines CRISPR/Cas12b and real-time loop-mediated isothermal amplification (LAMP) in a one-pot reaction, offering high sensitivity, specificity, and simplicity for methodology. By adding fully automated nucleic acid magnetic bead-extracted samples to a prepackaged centrifugal microfluidics chip, 48 samples can be automated tested simultaneously within 15 to 60 min at 60 °C. 427 clinical nasopharyngeal swab specimens were used for validation, demonstrating good positive and negative predictive values and good diagnostic sensitivity, specificity, and significant time savings. This method is particularly suitable for detecting low nucleic acid copies of M. pneumoniae samples.

Expert consensus on the diagnosis and treatment of macrolide-resistant Mycoplasma pneumoniae pneumonia in children

BACKGROUND

Mycoplasma pneumoniae (M. pneumoniae) is a significant contributor to community-acquired pneumonia among children. Since 1968, when a strain of M. pneumoniae resistant to macrolide antibiotics was initially reported in Japan, macrolide-resistant M. pneumoniae (MRMP) has been documented in many countries worldwide, with varying incidence rates. MRMP infections lead to a poor response to macrolide antibiotics, frequently resulting in prolonged fever, extended antibiotic treatment, increased hospitalization, intensive care unit admissions, and a significantly higher proportion of patients receiving glucocorticoids or second-line antibiotics. Since 2000, the global incidence of MRMP has gradually increased, especially in East Asia, which has posed a serious challenge to the treatment of M. pneumoniae infections in children and attracted widespread attention from pediatricians. However, there is still no global consensus on the diagnosis and treatment of MRMP in children.

METHODS

We organized 29 Chinese experts majoring in pediatric pulmonology and epidemiology to write the world's first consensus on the diagnosis and treatment of pediatric MRMP pneumonia, based on evidence collection. The evidence searches and reviews were conducted using electronic databases, including PubMed, Embase, Web of Science, CNKI, Medline, and the Cochrane Library. We used variations in terms for "macrolide-resistant", "Mycoplasma pneumoniae", "MP", "M. pneumoniae", "pneumonia", "MRMP", "lower respiratory tract infection", "Mycoplasma pneumoniae infection", "children", and "pediatric".

RESULTS

Epidemiology, pathogenesis, clinical manifestations, early identification, laboratory examination, principles of antibiotic use, application of glucocorticoids and intravenous immunoglobulin, and precautions for bronchoscopy are highlighted. Early and rapid identification of gene mutations associated with MRMP is now available by polymerase chain reaction and fluorescent probe techniques in respiratory specimens. Although the resistance rate to macrolide remains high, it is fortunate that M. pneumoniae still maintains good in vitro sensitivity to second-line antibiotics such as tetracyclines and quinolones, making them an effective treatment option for patients with initial treatment failure caused by macrolide antibiotics.

CONCLUSIONS

This consensus, based on international and national scientific evidence, provides scientific guidance for the diagnosis and treatment of MRMP in children. Further studies on tetracycline and quinolone drugs in children are urgently needed to evaluate their effects on the growth and development. Additionally, developing an antibiotic rotation treatment strategy is necessary to reduce the prevalence of MRMP strains.

Macrolide-Resistant Mycoplasma pneumoniae Infections among Children before and during COVID-19 Pandemic, Taiwan, 2017-2023

Before the COVID-19 pandemic, Mycoplasma pneumoniae infections emerged during spring to summer yearly in Taiwan, but infections were few during the pandemic. M. pneumoniae macrolide resistance soared to 85.7% in 2020 but declined to 0% during 2022-2023. Continued molecular surveillance is necessary to monitor trends in macrolide-resistant M. pneumoniae.

Molecular epidemiology of Mycoplasma pneumoniae pneumonia in children, Wuhan, 2020-2022

BACKGROUND

Mycoplasma pneumoniae (M. pneumoniae) is an important pathogen of community-acquired pneumonia in children. The factors contributing to the severity of illness caused by M. pneumoniae infection are still under investigation. We aimed to evaluate the sensitivity of common M. pneumoniae detection methods, as well as to analyze the clinical manifestations, genotypes, macrolide resistance, respiratory microenvironment, and their relationship with the severity of illness in children with M. pneumoniae pneumonia in Wuhan.

RESULTS

Among 1,259 clinical samples, 461 samples were positive for M. pneumoniae via quantitative polymerase chain reaction (qPCR). Furthermore, we found that while serological testing is not highly sensitive in detecting M. pneumoniae infection, but it may serve as an indicator for predicting severe cases. We successfully identified the adhesin P1 (P1) genotypes of 127 samples based on metagenomic and Sanger sequencing, with P1-type 1 (113/127, 88.98%) being the dominant genotype. No significant difference in pathogenicity was observed among different genotypes. The macrolide resistance rate of M. pneumoniae isolates was 96% (48/50) and all mutations were A2063G in domain V of 23S rRNA gene. There was no significant difference between the upper respiratory microbiome of patients with mild and severe symptoms.

CONCLUSIONS

During the period of this study, the main circulating M. pneumoniae was P1-type 1, with a resistance rate of 96%. Key findings include the efficacy of qPCR in detecting M. pneumoniae, the potential of IgM titers exceeding 1:160 as indicators for illness severity, and the lack of a direct correlation between disease severity and genotypic characteristics or respiratory microenvironment. This study is the first to characterize the epidemic and genomic features of M. pneumoniae in Wuhan after the COVID-19 outbreak in 2020, which provides a scientific data basis for monitoring and infection prevention and control of M. pneumoniae in the post-pandemic era.

Recent Trend of Antimicrobial Susceptibility among Mycoplasma pneumoniae Isolated from Japanese Children

Macrolide-resistant Mycoplasma pneumoniae (MRMP) infections have become increasingly prevalent, especially in East Asia. Whereas MRMP strains have point mutations that are implicated in conferring resistance, monitoring the antibiotic susceptibility of M. pneumoniae and identifying mutations in the resistant strains is crucial for effective disease management. Therefore, we investigated antimicrobial susceptibilities among M. pneumoniae isolates obtained from Japanese children since 2011. To establish the current susceptibility trend, we analyzed the minimum inhibitory concentrations (MICs) of M. pneumoniae in recent years (2017−2020) in comparison with past data. Our observation of 122 M. pneumoniae strains suggested that 76 were macrolide-susceptible M. pneumoniae (MSMP) and 46 were macrolide-resistant. The MIC ranges (µg/mL) of clarithromycin (CAM), azithromycin (AZM), tosufloxacin (TFLX), and minocycline (MINO) to all M. pneumoniae isolates were 0.001−>128, 0.00012−>128, 0.25−0.5, and 0.125−4 µg/mL, respectively. None of the strains was resistant to TFLX or MINO. The MIC distributions of CAM and AZM to MSMP and MINO to all M. pneumoniae isolates were significantly lower, but that of TFLX was significantly higher than that reported in all previous data concordant with the amount of recent antimicrobial use. Therefore, continuation of appropriate antimicrobial use for M. pneumoniae infection is important.

Recent Trends in the Epidemiology, Diagnosis, and Treatment of Macrolide-Resistant Mycoplasma pneumoniae

Among Mycoplasma pneumoniae (MP) is one of the major pathogens causing lower respiratory tract infection. Macrolide-resistant Mycoplasma pneumoniae (MRMP) isolates have been increasing and has become a global concern, especially in East Asian countries. This affects the treatment of MP infection; that is, some patients with MRMP infections fever cannot be controlled despite macrolide therapy. Therefore, alternative therapies, including secondary antimicrobials, including tetracyclines, fluoroquinolones, or systemic corticosteroids, were introduced. However, there are insufficient data on these alternative therapies. Thus, this article provides reviews of the recent trends in the epidemiology, diagnosis, and treatment of MRMP.

Association of Tandem Repeat Number Variabilities in Subunit S of the Type I Restriction-Modification System with Macrolide Resistance in Mycoplasma pneumoniae

Mycoplasma pneumoniae is one of the major pathogens responsible for pneumonia in children. Modern molecular genetics has advanced both the management and the epidemiologic study of this disease. Despite these advancements, macrolide resistance remains a global threat in the management of M. pneumoniae infection, for which the genetic background remains unrevealed. In this study, the result of whole genome analysis of 20 sequence type 3 (ST3) M. pneumoniae strains were examined to investigate the gene(s) associated with macrolide resistance. Overall, genetic similarities within M. pneumoniae, and especially ST3, were very high (over 99.99 %). Macrolide resistant ST3 strains shared 20 single nucleotide polymorphisms, of which one gene (mpn085) was found to be associated with resistance. BLAST comparison of M. pneumoniae revealed regular tandem repeat number variabilities between macrolide-susceptible and resistant strains for genes coding the Type I restriction-modification (R-M) system of subunit S (HsdS). Of the ten known HsdS genes, macrolide resistance was determined by the unique tandem repeat of mpn085 and mpn285. In conclusion, the use of whole genome sequencing (WGS) to target macrolide resistance in M. pneumoniae indicates that the determinant of macrolide resistance is variabilities in the tandem repeat numbers of the type I R-M system in subunit S.

Integrating the Human and Animal Sides of Mycoplasmas Resistance to Antimicrobials

Mycoplasma infections are frequent in humans, as well as in a broad range of animals. However, antimicrobial treatment options are limited, partly due to the lack of a cell wall in these peculiar bacteria. Both veterinary and human medicines are facing increasing resistance prevalence for the most commonly used drugs, despite different usage practices. To date, very few reviews have integrated knowledge on resistance to antimicrobials in humans and animals, the latest dating back to 2014. To fill this gap, we examined, in parallel, antimicrobial usage, resistance mechanisms and either phenotype or genotype-based methods for antimicrobial susceptibility testing, as well as epidemiology of resistance of the most clinically relevant human and animal mycoplasma species. This review unveiled common features and differences that need to be taken into consideration in a "One Health" perspective. Lastly, two examples of critical cases of multiple drug resistance are highlighted, namely, the human M. genitalium and the animal M. bovis species, both of which can lead to the threat of untreatable infections.

Update on the Epidemiology of Macrolide-Resistant Mycoplasma pneumoniae in Europe: A Systematic Review

Macrolide-resistant Mycoplasma pneumoniae (MR-MP) infections cause upper and lower respiratory tract infections in both children and adults, and are characterized by a longer duration of symptoms. Here, we undertook a systematic review of studies on MR-MP in Europe. The review meets PRISMA guidelines. The PubMed, Scopus, and Science Direct databases were searched using suitable keywords to identify relevant studies published from 2010 to 2021; 21 studies were included. Overall, a low level of MR-MP spread was reported in Europe. MR-MP spread increased during epidemic waves registered in Europe, particularly in Italy and Scotland, where the highest MR-MP infection rates were registered during the 2010–2011 epidemic. By contrast, no MR-MP infections were reported in Finland and the Netherlands. Continued monitoring of MR-MP in Europe is needed to maintain the low rates of infection. Moreover, a coordinated and structured pan-European surveillance program adequate for public health surveillance is advisable, with the purpose of containing the spread of antimicrobial resistance.

Persistent high macrolide resistance rate and increase of macrolide-resistant ST14 strains among Mycoplasma pneumoniae in South Korea, 2019-2020

BACKGROUND

Expansion of the single sequence type 3 (ST3) was associated with a high macrolide resistance rate among Mycoplasma pneumoniae in Korea during the 2014-2016 epidemic. This study investigates the macrolide resistance rate and genetic diversity of the subsequent epidemic of M. pneumoniae pneumonia in 2019-2020.

METHODS

The culture for M. pneumoniae was developed from 1228 respiratory samples collected from children with pneumonia in four hospitals in Korea between January 2019 and January 2020. Determination of macrolide resistance and multilocus sequence typing analysis were performed on M. pneumoniae isolates. eBURST analysis was applied to estimate the relationships among strains and to assign strains to a clonal complex.

RESULTS

M. pneumoniae was cultured in 93 (7.6%) of 1228 clinical samples. The overall macrolide resistance rate of M. pneumoniae strains was 78.5% (73/93). Of the nine STs identified, three were novel. The most common ST was ST3 (66 [71.0%]) followed by ST14 (18 [19.4%]) and ST7/ST15 (2 [2.2%] each). Three STs (ST3, ST14, and ST17) exhibited macrolide resistance. The macrolide resistance rates of ST3 and ST14 were 98.5% (65 of 66) and 38.9% (7 of 18), respectively.

CONCLUSION

Compared to the previous outbreak in 2014-2016, the overall macrolide resistance remained high; however, an increasing proportion of macrolide resistance was observed within ST14 strains in 2019-2020.

Increased Macrolide Resistance Rate of M3562 Mycoplasma pneumoniae Correlated With Macrolide Usage and Genotype Shifting

To characterize Mycoplasma pneumoniae (MP) strains and to clarify the continuous high rates of macrolide resistance, 1,524 oropharyngeal swabs collected from children in Beijing Children’s Hospital infected with MP during 2016-2019 were analyzed. Among the 1,524 samples, 1,386 harbored mutations associated with macrolide resistance; 1,049 samples were successfully classified into 11 genotypes using multiple locus variable-number tandem-repeat analysis (MLVA). The proportion of the predominant type, M4572, decreased from 84.49 to 70.77% over the time period examined, while that of M3562 increased from 11.63 to 24.67%. Notably, we also found that the frequency of macrolide resistance in M3562 drastically increased, from 60% in 2016 to 93.48% in 2019. Clinical data suggested that the frequency of resistant M3562 was higher in the macrolide usage group than in the nondrug usage group (90.73 vs 53.57%, P<0.0001), while the resistance rate of M4572 was not substantially affected by previous macrolide exposure. These findings validated that antimicrobial application and clonal expansion of resistant MP strains play important roles in the high rates of macrolide resistance.

Mycoplasma pneumoniae: a pathogen with unsolved therapeutic problems

INTRODUCTION

Despite the amount of new information, the most effective approach for the diagnosis and treatment of Mycoplasma pneumoniae infections is not established. In this narrative review the pharmacological options for macrolide-resistant (ML) M. pneumoniae infections in children are discussed.

AREAS COVERED

Despite significant improvement in the diagnosis and in the definition of diseases potentially associated with this pathogen, not all the problems related to M. pneumoniae infection are solved. True epidemiology of M. pneumoniae diseases and the real role of this pathogen in extra-respiratory manifestations is still unestablished. This reflects on therapy. It is not known whether antibiotics are really needed in all the cases, independently of severity and localization. The choice of antibiotic therapy is debated as it is not known whether ML resistance has clinical relevance. Moreover, not precisely defined is the clinical importance of corticosteroids for improvement of severe cases, including those associated with ML-resistant strains.

EXPERT OPINION

Improvement in M. pneumoniae identification is mandatory to reduce antibiotics overuse , especially in the presence of ML-resistant strains. Priority for future studies includes the evaluation of the true benefit of therapeutic approaches including corticosteroids in patients with severe CAP and in those with extra-respiratory M. pneumoniae diseases.