Comparison of pyrosequencing, Sanger sequencing, and melting curve analysis for detection of low-frequency macrolide-resistant mycoplasma pneumoniae quasispecies in respiratory specimens

Novel Knowledge of Macrolide Resistance in Mycoplasma pneumoniae by Azithromycin Exposure

The rise of macrolide-resistant Mycoplasma pneumoniae (MRMP), marked by point mutations in the 23S rRNA gene, poses a growing global concern since its initial detection in 2001. The prominence of the A2063G mutation during this emergence remains unexplained. This study aimed to clarify the possibility of detecting MRMP from recent clinical macrolide-susceptible M. pneumoniae through exposure to azithromycin (AZM), which has a long half-life and was launched immediately before the first MRMP detection. Six strains isolated from Japanese children in 2019 and reference strain (FH), all belonging to the recent dominant P1 genotype, two, or two subtype, were cultivated in a medium containing slightly higher concentrations than the originated minimum inhibitory concentration (MIC) of AZM and underwent sequencing if they grew. Four out of the seven strains grew after exposure to AZM, and C2617G and C2617A were detected, with no mutation in two strains. After another cultivation and sequencing, two of four strains grew, one was changed from C2617G to A2063G, and the other remained C2617A. The MIC of AZM in A2063G strains was 128 mg/mL; for C2617A, it was 0.0156 mg/mL. This is the first study to detect the strains with A2063G mutation from recent macrolide-susceptible M. pneumoniae using AZM exposure.

Pyrosequencing analysis for rapid and accurate detection of clarithromycin resistance-associated mutations in Iranian Helicobacter pylori isolates

BACKGROUND

Treatment of Helicobacter pylori (H. pylori) infection has become challenging following the development of primary antibiotic resistance. A primary therapeutic regimen for H. pylori eradication includes clarithromycin; however, the presence of point mutations within the 23S rRNA sequence of H. pylori contributes to clarithromycin resistance and eradication failure. Thus, we aimed to develop a rapid and precise method to determine clarithromycin resistance-related point mutations using the pyrosequencing method.

METHODS AND RESULTS

H. pylori was isolated from 82 gastric biopsy samples and minimal inhibitory concentration (MIC) was evaluated using the agar dilution method. Clarithromycin resistance-associated point mutations were detected by Sanger sequencing, from which 11 isolates were chosen for pyrosequencing. Our results demonstrated a 43.9% (36/82) prevalence in resistance to clarithromycin. The A2143G mutation was detected in 8.3% (4/48) of H. pylori isolates followed by A2142G (6.2%), C2195T (4.1%), T2182C (4.1%), and C2288T (2%). Although the C2195T mutation was only detected by Sanger sequencing, the overall results from pyrosequencing and Sanger sequencing platforms were comparable.

CONCLUSIONS

Pyrosequencing could be used as a rapid and practical platform in clinical laboratories to determine the susceptibility profile of H. pylori isolates. This might pave the way for efficient H. pylori eradication upon detection.

Somatic mosaicism in inborn errors of immunity: Current knowledge, challenges, and future perspectives

Inborn errors of immunity (IEI) are a diverse group of monogenic disorders of the immune system due to germline variants in genes important for the immune response. Over the past decade there has been increasing recognition that acquired somatic variants present in a subset of cells can also lead to immune disorders or 'phenocopies' of IEI. Discovery of somatic mosaicism causing IEI has largely arisen from investigation of seemingly sporadic cases of IEI with predominant symptoms of autoinflammation and/or autoimmunity in which germline disease-causing variants are not detected. Disease-causing somatic mosaicism has been identified in genes that also cause germline IEI, such as FAS, and in genes without significant corresponding germline disease, such as UBA1 and TLR8. There are challenges in detecting low-level somatic variants, and it is likely that the extent of the somatic mosaicism causing IEI is largely uncharted. Here we review the field of somatic mosaicism leading to IEI and discuss challenges and methods for somatic variant detection, including diagnostic approaches for molecular diagnoses of patients.

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.

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.

Rapid screening method for the detection of SARS-CoV-2 variants of concern

Background

Comprehensive and up-to-date monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) is crucial as these are characterized by their increased transmissibility, immune evasion and virulence.

Objectives

To describe the wide-scale implementation of a reverse transcriptase polymerase chain reaction (RT-PCR) multiple variants assay with melting curve analysis as a routine procedure.

Study design

We prospectively performed multiple variants RT-PCR on consecutive SARS-CoV-2 RT-PCR positive samples from patients, healthcare workers and nursing home residents from our hospital catchment area. This technique was implemented in our automated Roche FLOW system with a turn-around time of 6 h.

Results

Between February 1 and May 2, 2021, 989 samples were tested by the variant RT-PCR. Our method was validated by comparison of variant RT-PCR to whole genome sequencing testing. We observed an increase over time in the proportion of UK variant that became the dominant variant, and the concurrent emergence of the South-African and Brazilian variants. Prompt public health responses for infection control were possible because of this rapid screening method, resulting in early detection and reduction of unnoticed spread of VOC as early as possible.

Conclusion

A variant RT-PCR with additional melting curve analyses is a feasible, rapid and efficient screening strategy that can be implemented in routine microbiological laboratories.

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.

Allele-specific real-time PCR testing for minor macrolide-resistant Mycoplasma Pneumoniae

Background

The point mutations in 23S rRNA gene of Mycoplasma pneumoniae (M. pneumoniae) can lead to high-level resistance to macrolides. This study aimed to evaluate allele-specific real-time PCR (ASPCR) to detect the resistance-related mutations located at positions A2063G and A2064G of 23S rRNA gene.

Methods

We detected 178 pharyngeal swab specimens and calculated the proportions of resistant and sensitive quasispecies using ASPCR assays. ASPCR assays can detect down to 10 copies of 23S rRNA gene and achieved sensitivities of < 0.1% for A2063G and A2064G. We also compared the findings of ASPCR with the results of nested PCR with sequencing.

Results

Of 178 samples, 164 were found to have M. pneumoniae including 90.85% (149/164) samples with macrolide-resistant M. pneumoniae (MRMP) quasispecies by ASPCR, while 153 were found to be M. pneumoniae-positive including 71.90% (110/153) samples with MRMP quasispecies by nested PCR with sequencing. Of the 164 M. pneumoniae-positive samples, 61.59% (101/164) had the mixed population of wild-type and mutant M. pneumoniae, and 56.44% (57/101) of the latter contained the mutations at low frequency (≤50%).

Conclusion

ASPCR indicated that sensitive and resistant quasispecies coexisted in most of the M. pneumoniae positive samples. The ASPCR was a highly sensitive, accurate and rapid method for detecting the macrolide resistance-associated mutations and it could provide earlier and more drug-resistant information for M. pneumoniae research and the clinical therapy.

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.

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

Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Emergence of Macrolide-Resistant Mycoplasma pneumoniae in Hong Kong Is Linked to Increasing Macrolide Resistance in Multilocus Variable-Number Tandem-Repeat Analysis Type 4-5-7-2

Macrolide-resistant Mycoplasma pneumoniae (MRMP) is rapidly emerging in Asia, but information on the temporal relationship between the increase in macrolide resistance and changes in strain types is scarce. Between 2011 and 2014, M. pneumoniae infection was diagnosed by PCR as part of routine care in a health care region in Hong Kong. Testing was initiated by clinicians, mainly in patients with suspected M. pneumoniae pneumonia. Specimens positive for M. pneumoniae were retrospectively investigated by macrolide resistance genotyping and a four-locus (Mpn13 to -16) multilocus variable-number tandem-repeat analysis (MLVA) scheme. The overall percentage of M. pneumoniae-positive specimens was 17.9%, with annual rates ranging from 9.8% to 27.2%. The prevalence of MRMP had rapidly increased from 13.6% in 2011 to 30.7% in 2012, 36.6% in 2013, and 47.1% in 2014 (P = 0.038). Two major MLVA types, 4-5-7-2 and 3-5-6-2, accounted for 75% to 85% of the infections each year. MLVA types 4-5-7-2 and 3-5-6-2 predominated among macrolide-resistant and macrolide-sensitive groups, respectively. The increase in MRMP was mainly caused by increasing macrolide resistance in the prevalent MLVA type 4-5-7-2, changing from 25.0% in 2011 to 59.1% in 2012, to 89.7% in 2013, and to 100% in 2014 (P < 0.001). In conclusion, increasing MRMP in Hong Kong was linked to a single MLVA type, which was both prevalent and increasingly resistant to macrolides.

Viral lung infections: epidemiology, virology, clinical features, and management of avian influenza A(H7N9)

PURPOSE OF REVIEW

The avian influenza A(H7N9) virus has jumped species barrier and caused severe human infections. Here, we present the virological features relevant to clinical practice, and summarize the epidemiology, clinical findings, diagnosis, treatment, and preventive strategies of A(H7N9) infection.

RECENT FINDINGS

As of 18 February 2014, A(H7N9) virus has caused 354 infections in mainland China, Taiwan, and Hong Kong with a case-fatality rate of 32%. Elderly men were most affected. Most patients acquired the infection from direct contact with poultry or from a contaminated environment, although person-to-person transmission has likely occurred. A(H7N9) infection has usually presented with severe pneumonia, often complicated by acute respiratory distress syndrome and multiorgan failure. Mild infections have been reported in children and young adults. Nasopharyngeal aspirate and sputum samples should be collected for diagnosis, preferably using reverse transcriptase-PCR. Early treatment with neuraminidase inhibitors improved survival, but the efficacy of antivirals was hampered by resistant mutants. The closure of live poultry markets in affected areas has significantly contributed to the decline in the incidence of human cases.

SUMMARY

The emergence of A(H7N9) virus represents a significant health threat. High vigilance is necessary so that appropriate treatment can be instituted for the patient and preventive measures can be implemented.

A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds

Chlamydophila psittaci is found worldwide, but is particularly common among psittacine birds in tropical and subtropical regions. While investigating a human psittacosis outbreak that was associated with avian chlamydiosis in Hong Kong, we identified a novel adenovirus in epidemiologically linked Mealy Parrots, which was not present in healthy birds unrelated to the outbreak or in other animals. The novel adenovirus (tentatively named Psittacine adenovirus HKU1) was most closely related to Duck adenovirus A in the Atadenovirus genus. Sequencing showed that the Psittacine adenovirus HKU1 genome consists of 31,735 nucleotides. Comparative genome analysis showed that the Psittacine adenovirus HKU1 genome contains 23 open reading frames (ORFs) with sequence similarity to known adenoviral genes, and six additional ORFs at the 3' end of the genome. Similar to Duck adenovirus A, the novel adenovirus lacks LH1, LH2 and LH3, which distinguishes it from other viruses in the Atadenovirus genus. Notably, fiber-2 protein, which is present in Aviadenovirus but not Atadenovirus, is also present in Psittacine adenovirus HKU1. Psittacine adenovirus HKU1 had pairwise amino acid sequence identities of 50.3-54.0% for the DNA polymerase, 64.6-70.7% for the penton protein, and 66.1-74.0% for the hexon protein with other Atadenovirus. The C. psittaci bacterial load was positively correlated with adenovirus viral load in the lung. Immunostaining for fiber protein expression was positive in lung and liver tissue cells of affected parrots, confirming active viral replication. No other viruses were found. This is the first documentation of an adenovirus-C. psittaci co-infection in an avian species that was associated with a human outbreak of psittacosis. Viral-bacterial co-infection often increases disease severity in both humans and animals. The role of viral-bacterial co-infection in animal-to-human transmission of infectious agents has not received sufficient attention and should be emphasized in the investigation of disease outbreaks in human and animals.

Severe macrolide-resistant Mycoplasma pneumoniae pneumonia associated with macrolide failure

We investigated differences in outcomes between 68 children hospitalized with macrolide-sensitive Mycoplasma pneumoniae pneumonia (MSMP group) and 25 children hospitalized with macrolide-resistant M. pneumoniae pneumonia (MRMP group). In the MRMP group, 19 children received macrolides and clinical failure occurred in six of which five had pneumonia progression during therapy.

Typical or atypical pneumonia and severe acute respiratory symptoms in PICU

Background and Aims

Mycoplasma pneumoniae (MP) is a common childhood pathogen associated with atypical pneumonia (AP). It is often a mild disease and seldom results in paediatric intensive care (PICU) admission. In 2003, World Health Organization (WHO) coined the word SARS (severe acute respiratory syndrome) in patients with severe acute respiratory symptoms (sars) for an outbreak of AP in Hong Kong due to a novel coronavirus. In 2012, another outbreak of coronavirus AP occurred in the Middle East. Confusing case definitions such as MERS (Middle East respiratory syndrome) and SARI (severe acute respiratory infections) were coined. This paper aims to present a case of MP with sars, ARDS, pneumonia and pleural effusion during the MERS epidemics, and review the incidence and mortality of severe AP with MP.

Methods

We presented a case of MP with sars, acute respiratory distress syndrome (ARDS), pneumonia and pleural effusion during the MERS epidemics, and performed a literature review on the incidence and mortality of severe AP with MP requiring PICU care.

Results

In early 2013, an 11‐year‐old girl presented with sars, ARDS (acute respiratory distress syndrome), right‐sided pneumonia and pleural effusion. She was treated with multiple antibiotics. Streptococcus pneumoniae was not isolated in this girl with ‘typical’ pneumonia by symptomatology and chest radiography, but tracheal aspirate identified MP instead. The respiratory equations are computed with PaO₂/FiO₂ consistent with severe lung injury. Literature on the incidence and mortality of severe AP with MP requiring PICU care is reviewed. Six, 165 and 293 articles were found when PubMed (a service of the U.S. National Library of Medicine) was searched for the terms ‘mycoplasma’ and ‘ICU’, ‘mycoplasma’ and ‘mortality’, and ‘mycoplasma' and ‘severe’. Mortality and PICU admission associated with MP is general low and rarely reported. Experimental and clinical studies have suggested that the pathogenesis of lung injuries in MP infection is associated with a cell‐mediated immune reaction, and high responsiveness to corticosteroid therapy has been reported especially for severe disease. Management of severe mycoplasma infection in the PICU includes general cardiopulmonary support and specific antimicrobial treatment. Macrolide resistance genotypes have been detected.

Conclusion

We urge health organizations to refrain from the temptation of coining unnecessary new terminology to describe essentially the same conditions each and every time when outbreaks of AP occur.

Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong

Objective

Human infections caused by avian influenza virus A(H7N9) re-emerged in late 2013. We reported the first Hong Kong patient without risk factors for severe A(H7N9) disease.

Methods

Direct sequencing was performed on the endotracheal aspirate collected from a 36-year-old female with history of poultry contact. Bioinformatic analysis was performed to compare the current strain and previous A(H7N9) isolates.

Results

The influenza A/Hong Kong/470129/2013 virus strain was detected in a patient with acute respiratory distress syndrome, deranged liver function and coagulation profile, cytopenia, and rhabdomyolysis. The HA, NA and MP genes of A/Hong Kong/470129/2013 cluster with those of other human A(H7N9) strains. The PB1, PB2 and NS genes are most closely related to those of A/Guangdong/1/2013 strain identified in August 2013, but are distinct from those of other human and avian A(H7N9) strains. The other internal genes NP and PA genes are more closely related to those of non-A(H7N9) avian influenza A viruses. A unique PA L336M mutation, associated with increased polymerase activity, was found. The patient required salvage by extracorporeal membrane oxygenation.

Conclusions

The A/Hong Kong/470129/2013 virus is a novel reassortant derived from A/Guangdong/1/2013 virus. The unique mutation PA L336M may enhance viral replication and therefore disease severity.