Genotyping of Mycoplasma pneumoniae strains isolated in Japan during 2019 and 2020: spread of p1 gene type 2c and 2j variant strains

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.

Whole-genome probe capture sequencing reveals genomic diversity and characteristics of Mycoplasma pneumoniae in Nanjing, China

Mycoplasma pneumoniae (M. pneumoniae), a slow-growing, fastidious Gram-negative bacterium and a leading cause of community-acquired pneumonia globally, remains understudied and underreported across numerous geographical areas in China despite its worldwide significance. This study employed probe capture sequencing for targeted enrichment and direct sequencing of M. pneumoniae from clinical samples, combined with comparative genomic analyses of contemporary and historical global genomes. Core genome and pan-genome revealed that the M. pneumoniae genomes were classified into two distinct clades, P1-I and P1-II, each associated with a specific sequence type (ST). Most of the genomes sequenced in this study were identified as P1-I (86.96%, 20/23), contrasting with the previously reported predominance of P1-II in the area. A limited number of single-nucleotide variations were identified in the virulence-associated genes between P1-I and P1-II, leading to amino acid substitutions. The A2063G point mutation in the 23S rRNA gene was detected in all sequenced genomes (23/23), demonstrating a 100% mutation rate. This study provides the first reported application of probe capture methodology for M. pneumoniae, highlighting the critical importance of sustained surveillance efforts to monitor the evolution and epidemiology of this pathogen.

Antibiotic resistance and viral co-infection in children diagnosed with pneumonia caused by Mycoplasma pneumoniae admitted to Russian hospitals during October 2023-February 2024

BACKGROUND

Mycoplasma pneumoniae (MP) is a common bacterial respiratory infection that can cause pneumonia, particularly in children. Previously published data have highlighted the high incidence of viral co-infections and the problem of increasing macrolide resistance in MP worldwide.

AIMS

(1) to estimate the impact of viral infections circulating in a local population on the spectrum of co-infection in hospitalized children with Mycoplasma pneumoniae pneumonia (MPP), (2) to determine if there are differences in resistance mutation rate for samples from hospitals of Russia located in the European and Far East, (3) to describe genomic characteristics of MP from Russian patients during the MPP outbreaks in the fall-winter of 2023-2024.

METHODS

The carriage of viral pathogens was analyzed by real-time PCR in children with MPP from the European Part and Far East of Russian Federation and compared with the infections from two control groups. The V region of the 23S gene and the quinolone resistance-determining regions (QRDRs) of the parC and gyrA genes were sequenced to detect resistance-associated mutations in MP. Whole-genome sequencing method was used to determine the genetic relationship of a Russian MP isolate with known MP isolates.

RESULTS

The 62% of patients with MPP had a viral co-infection, with HPIV and SARS-CoV-2 predominating at 47% and 12.4%, respectively. The 15% of patients were infected with two or more viruses. In the control groups, 21% of healthy children and 43% of healthy adults were infected with Coronaviruses and Human Parainfluenza Viruses (HPIV-3 and -4), respectively. The 2063 A/G mutation of the 23S gene was found in 40.8% of patients from European Russia and in 35.7% of patients from the Far East. The result of core genes demonstrates that the sequence obtained from Russia clusters with sequences from clade 1.

CONCLUSIONS

Both HPIV and SARS-CoV-2 circulated in the population among healthy children and adults in December 2023 and they also were predominated in children with MPP. The rate of macrolide resistance was ⁓40%, which is higher than in European countries and significantly lower than in patients from Asian countries. Phylogenetic analysis showed the MP genome form Russia related to P1 type 1 (clade 1).

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.

Mycoplasma pneumoniae: not a typical respiratory pathogen

Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia among school-aged children and young adults. Infections occur throughout the year but tend to surge during winter months across Europe. A characteristic epidemic cycle, where a substantial surge in the number of infections occurs, is seen approximately every 1-4 years and hypothesized to be driven by changes in immunity and a shift in circulating variants. Once thought to be an organism of low virulence, it has now been found to possess several virulence factors, including toxin production, biofilm formation and evasion of antibody-mediated immunity. The lack of a cell wall and reduced metabolic pathways limit the options for antibiotic treatment. Acquired macrolide resistance is a growing concern, with >80% of cases in China being macrolide-resistant. Although efforts have been made to develop a vaccine, there are still substantial hurdles to overcome in relation to vaccine-enhanced disease, which results from an inappropriate immune response among vaccinated individuals.

Increased macrolide resistance rate of Mycoplasma pneumoniae correlated with epidemic in Beijing, China in 2023

We collected respiratory specimens from 128 pediatric patients diagnosed with pneumonia in Beijing in late 2023. Mycoplasma pneumoniae was detected in 77.3% (99/128) patients, with 36.4% (4/11), 82.9% (34/41), 80.3% (61/76) in children aged less than 3 years, 3-6 years, over 7 years, respectively. Mycoplasma pneumoniae (M. pneumoniae) was characterized using P1 gene typing, MLVA typing and sequencing of domain V of the 23S rRNA gene. P1 gene type 1 (P1-1; 76.1%, 54/71) and MLVA type 4-5-7-2 (73.7%, 73/99) were predominant. MLVA identified a new genotype: 3-4-6-2. Macrolide resistance-associated mutations were detected in 100% of samples, with A2063G accounting for 99% and A2064G for 1%. The positive rate of M. pneumoniae was higher compared to previous reports, especially in children less than 3 years, suggesting a M. pneumoniae epidemic showing a younger age trend occurred in late 2023 in Beijing, China. Higher proportions of macrolide-resistant M. pneumoniae, P1-1 and 4-5-7-2 genotype M. pneumoniae indicated increased macrolide resistance rate and genotyping shift phenomenon, which might be attributable to this epidemic. Additionally, complete clinical information from 73 M. pneumoniae pneumonia inpatients were analyzed. The incidence of severe M. pneumoniae pneumonia was 56.2% (41/73). Mycoplasma pneumoniae pneumonia patients exhibited longer duration of fever, with a median value of 10.0 days (IQR, 8.0-13.0), and higher incidence of complications (74.0%, 54/73). However, in this cohort, we found that the severity of M. pneumoniae pneumonia, co-infection, or complications were not associated with M. pneumoniae P1 gene or MLVA types. Clinicians should be aware that patients infected with macrolide-resistant M. pneumoniae exhibited more severe clinical presentations.

Comparison of Mycoplasma pneumoniae infection in children admitted with community acquired pneumonia before and during the COVID-19 pandemic: a retrospective study at a tertiary hospital of southwest China

PURPOSE

The COVID-19 pandemic has notably altered the infection dynamics of various pathogens. This study aimed to evaluate the pandemic's impact on the infection spectrum of Mycoplasma pneumoniae (M. pneumoniae) among children with community acquired pneumonia (CAP).

METHODS

We enrolled pediatric CAP patients admitted to a tertiary hospital in southwest China to compare the prevalence and characteristics of M. pneumoniae infections before (2018-2019) and during (2020-2022) the COVID-19 pandemic. Detection of M. pneumoniae IgM antibodies in serum were conducted using either indirect immunofluorescence or passive agglutination methods.

RESULTS

The study included 1505 M. pneumoniae-positive and 3160 M. pneumoniae-negative CAP patients. Notable findings were the higher age and frequency of pneumonia-associated symptoms in M. pneumoniae-positive patients, alongside a lower male proportion and fewer respiratory co-infections. The year 2019 saw a notable increase in M. pneumoniae infections compared to 2018, followed by a decline from 2020 to 2022. The COVID-19 pandemic period witnessed significant alterations in age distribution, male proportion, and co-infections with specific pathogens in both M. pneumoniae-positive and negative patients. The M. pneumoniae infections were predominantly seasonal, peaking in autumn and winter during 2018 and 2019. Although there was a sharp drop in February 2020, the infection still peaked in cold months of 2020 and 2021. However, the typical seasonal pattern was nearly absent in 2022.

CONCLUSIONS

The COVID-19 pandemic has markedly changed the infection landscape of M. pneumoniae in pediatric CAP patients, with shifts observed in infection rates, demographic profiles, co-infections, and seasonal patterns.