Layer-by-layer polyelectrolyte encapsulation of Mycoplasma pneumoniae for enhanced Raman detection

Mycoplasma pneumoniae is a major cause of respiratory disease in humans and accounts for as much as 20% of all community-acquired pneumonia. Existing mycoplasma diagnosis is primarily limited by the poor success rate at culturing the bacteria from clinical samples. There is a critical need to develop a new platform for mycoplasma detection that has high sensitivity, specificity, and expediency. Here we report the layer-by-layer (LBL) encapsulation of M. pneumoniae cells with Ag nanoparticles in a matrix of the polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(styrene sulfonate) (PSS). We evaluated nanoparticle encapsulated mycoplasma cells as a platform for the differentiation of M. pneumoniae strains using surface enhanced Raman scattering (SERS) combined with multivariate statistical analysis. Three separate M. pneumoniae strains (M129, FH and II-3) were studied. Scanning electron microscopy and fluorescence imaging showed that the Ag nanoparticles were incorporated between the oppositely charged polyelectrolyte layers. SERS spectra showed that LBL encapsulation provides excellent spectral reproducibility. Multivariate statistical analysis of the Raman spectra differentiated the three M. pneumoniae strains with 97-100% specificity and sensitivity, and low (0.1-0.4) root mean square error. These results indicated that nanoparticle and polyelectrolyte encapsulation of M. pneumoniae is a potentially powerful platform for rapid and sensitive SERS-based bacterial identification.

Novel strategy for typing Mycoplasma pneumoniae isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry coupled with ClinProTools

The typing of Mycoplasma pneumoniae mainly relies on the detection of nucleic acid, which is limited by the use of a single gene target, complex operation procedures, and a lengthy assay time. Here, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and to generate a classification model based on a genetic algorithm (GA) to differentiate between type 1 and type 2 M. pneumoniae isolates. Twenty-five M. pneumoniae strains were used to construct an analysis model, and 43 Mycoplasma strains were used for validation. For the GA typing model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra and the recognition capability value, which reflects the model's ability to correctly identify its component spectra, were all 100%. This model contained 7 biomarker peaks (m/z 3,318.8, 3,215.0, 5,091.8, 5,766.8, 6,337.1, 6,431.1, and 6,979.9) used to correctly identify 31 type 1 and 7 type 2 M. pneumoniae isolates from 43 Mycoplasma strains with a sensitivity and specificity of 100%. The strain distribution map and principle component analysis based on the GA classification model also clearly showed that the type 1 and type 2 M. pneumoniae isolates can be divided into two categories based on their peptide mass fingerprints. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for M. pneumoniae typing.

Molecular characterizations of PCR-positive Mycoplasma pneumoniae specimens collected from Australia and China

Mycoplasma pneumoniae is an important cause of community-acquired pneumonia (CAP). In this study, M. pneumoniae strains in PCR-positive specimens collected from patients in Sydney, Australia (30 samples), and Beijing, China (83 samples), were characterized using multilocus variable-number tandem-repeat (VNTR) analysis (MLVA), P1-restriction fragment length polymorphism (RFLP) analysis, and sequencing of domain V of the 23S rRNA gene to compare genotype distribution and macrolide resistance rates between locations. Eighteen distinct MLVA types were identified in specimens from Sydney, of which 10 were known (types E, G, J, M, N, P, U, V, S, and X) and 8 previously unknown. Strains were equally distributed between P1-RFLP type 1 and type 2 variants. Among samples from Beijing, MLVA types E, G, J, P, U, X, and Z and four new types were identified. Most specimens belonged to P1-RFLP type 1. A nomenclature based on five VNTR loci is proposed to designate MLVA patterns. Macrolide resistance-associated mutations were identified in only 1 of 30 specimens (3.3%) from Sydney and 71 of 83 (85.5%) from Beijing (P<0.05). This study demonstrated that although multiple individual M. pneumoniae strains were circulating in Beijing, the genotypes were less diverse than those in Sydney. However, the greatest regional difference was in the incidence of macrolide resistance, which may reflect differences in antibiotic use and/or measures in resistance control.

Specific multilocus variable-number tandem-repeat analysis genotypes of Mycoplasma pneumoniae are associated with diseases severity and macrolide susceptibility

Clinical relevance of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) in patients with community-acquired pneumonia (CAP) by Mycoplasma pneumoniae (M. pneumoniae) is unknown. A multi-center, prospective study was conducted from November 2010 to April 2012. Nine hundred and fifty-four CAP patients were consecutively enrolled. M. pneumoniae clinical isolates were obtained from throat swabs. MLVA typing was applied to all isolates. Comparison of pneumonia severity index (PSI) and clinical features among patients infected with different MLVA types of M. pneumoniae were conducted. One hundred and thirty-six patients were positive with M. pneumoniae culture. The clinical isolates were clustered into 18 MLVA types. One hundred and fourteen (88.3%) isolates were resistant to macrolide, covering major MLVA types. The macrolide non-resistant rate of M. pneumoniae isolates with Mpn13-14-15-16 profile of 3-5-6-2 was significantly higher than that of other types (p≤0.001). Patients infected with types U (5-4-5-7-2) and J (3-4-5-7-2) had significantly higher PSI scores (p<0.001) and longer total duration of cough (p = 0.011). Therefore it seems that there is a correlation between certain MLVA types and clinical severity of disease and the presence of macrolide resistance.

Multiple-locus variable-number tandem-repeat analysis of mycoplasma pneumoniae clinical specimens and proposal for amendment of MLVA nomenclature

Mycoplasma pneumoniae is one of the major respiratory bacterial pathogens that cause pneumonia in humans. Multiple-locus variable-number tandem-repeat analysis (MLVA) is currently the most discriminative method for typing M. pneumoniae strains. To better understand the epidemic of M. pneumoniae-related pneumonia in pediatric patients in Beijing, China, we performed MLVA analysis on 118 specimens collected during an epidemic from 2010-2012. Eleven distinct MLVA types were identified, including four novel types. There was no obvious association of macrolide resistance with any of the genotypes. Considering the instability of VNTR locus Mpn1, we propose an amended MLVA nomenclature system based on the remaining four VNTR loci.

Multiple-locus variable-number tandem-repeat analysis of 201 Mycoplasma pneumoniae isolates from Beijing, China, from 2008 to 2011

A total of 201 Mycoplasma pneumoniae clinical isolates from Beijing, China, isolated from 2008 to 2011, were clustered into 16 multiple-locus variable-number tandem-repeat analysis (MLVA) types, of which 6 new MLVA types have never been reported previously. Type 1 isolates based on p1 gene genotyping were mainly MLVA types E, J, P, U, and X. There was no correlation between macrolide-resistant Mycoplasma pneumoniae and their MLVA type.

Mycoplasma pneumoniae large DNA repetitive elements RepMP1 show type specific organization among strains

Mycoplasma pneumoniae is the smallest self-replicating bacterium with a streamlined genome of 0.81 Mb. Complete genome analysis revealed the presence of multiple copies of four large repetitive elements (designated RepMP1, RepMP2/3, RepMP4 and RepMP5) that are implicated in creating sequence variations among individual strains. Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138). Using PCR and sequencing we analyze 28 additional M. pneumoniae strains and demonstrate the existence of S1-like sequence variants in nine strains and M129-like variants in the remaining nineteen strains. We propose a series of recombination steps that facilitates transition from M129- to S1-like sequence variants. Next we examined the remaining RepMP1-genes and observed no other rearrangements related to the repeat element. The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524. Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific. Once more our analysis confirmed existence of two highly conserved groups of M. pneumoniae strains.

Rapid effectiveness of minocycline or doxycycline against macrolide-resistant Mycoplasma pneumoniae infection in a 2011 outbreak among Japanese children

BACKGROUND

Mycoplasma pneumoniae is a major pathogen causing community-acquired pneumonia in children and young adults. Outbreaks typically occur at intervals of several years. In 2011, a widespread outbreak was associated with macrolide-resistant M. pneumoniae (MRMP) in Japanese children, often those of school age.

METHODS

Two hundred fifty-eight children were diagnosed with M. pneumoniae-associated pneumonia based on chest radiography, real-time polymerase chain reaction (PCR), and antibody titers between January and December 2011. Mycoplasma pneumoniae cultures obtained from nasopharyngeal samples using appropriate broth were subjected to real-time PCR, by which decreases in M. pneumoniae in patients treated with minocycline (MIN), doxycycline (DOX), or tosufloxacin (TFX) were calculated. Mutations of the 23S ribosomal RNA gene that confer high resistance to macrolides in M. pneumoniae were identified by DNA sequencing.

RESULTS

Among 202 M. pneumoniae isolates from M. pneumoniae-associated pneumonia patients, 176 (87.1%) were MRMP. Macrolide-resistant M. pneumoniae infection was significantly related to school age (P < .01) and initial administration of macrolides (P < .01). Minocycline or DOX (n = 125) or TFX or levofloxacin (n = 15) was used for definitive treatment of MRMP patients. Minocycline or DOX was significantly more effective than TFX (P ≤ .05) in achieving defervescence within 24 hours and in decreasing numbers of M. pneumoniae DNA copies 3 days after initiation.

CONCLUSIONS

Macrolides are inappropriate as first-choice agents against MRMP in terms of shortening the clinical course and decreasing M. pneumoniae. Control and prevention of MRMP outbreaks in children require early decreases in M. pneumoniae as well as improvement of clinical findings.

Macrolide resistance determination and molecular typing of Mycoplasma pneumoniae in respiratory specimens collected between 1997 and 2008 in The Netherlands

An important role in the treatment regimens for Mycoplasma pneumoniae infections is played by macrolide (ML) antibiotics. In the past few years, however, a steady increase has been detected in the worldwide prevalence of ML-resistant (ML(r)) M. pneumoniae strains. It is obvious that this increase necessitates a continuous monitoring of ML(r) and, when detected, modification of antibiotic treatment modalities. Previously, we developed a pyrosequencing-based assay system for the genetic determination of ML(r) as well as molecular typing of M. pneumoniae. In this study, the sensitivity of this system was improved by the inclusion of a nested-PCR protocol. The modified system was applied to 114 M. pneumoniae-positive specimens that were obtained from a collection of 4,390 samples from patients with acute respiratory tract infections. These samples were collected between 1997 and 2008 in The Netherlands. The pyrosequencing system produced reliable data in 86% of the specimens that contained >500 M. pneumoniae genome copies/ml of patient sample. Each of these samples contained DNA of the ML-sensitive genotype. While 43% of the samples were found to harbor the M. pneumoniae subtype 1 genotype, 57% contained the subtype 2 genotype. We conclude that the pyrosequencing-based assay system is a useful tool for ML(r) determination and molecular typing of M. pneumoniae in patient samples. ML(r)-associated M. pneumoniae genotypes, however, were not found in the current study population.

Complete genome sequence of Mycoplasma pneumoniae type 2a strain 309, isolated in Japan

Mycoplasma pneumoniae strain 309, a type 2a (subtype 2 variant) strain of this bacterium, has variations in the P1 protein, which is responsible for attachment of the bacterium to host cells. Here, we report the complete genome sequence of M. pneumoniae strain 309 isolated from a pneumonia patient in Japan.

Antibiotic sensitivity of 40 Mycoplasma pneumoniae isolates and molecular analysis of macrolide-resistant isolates from Beijing, China

MICs of eight antibiotics were detected with 40 Chinese Mycoplasma pneumoniae isolates. Thirty-eight isolates (95%) were macrolide resistant. Each macrolide-resistant isolate harbored an A2063G or A2064G point mutation in the 23S rRNA gene. All 40 isolates (100%) were type I strains, but they might have originated from different clones.

Sequence analysis of the p1 adhesin gene of Mycoplasma pneumoniae in clinical isolates collected in Beijing in 2008 to 2009

The p1 genes of 60 Mycoplasma pneumoniae clinical isolates were sequenced and compared to previously reported p1 gene sequences. An AGT trinucleotide variable-number tandem repeat was identified that ranged in copy number from 5 to 14 among the isolates. In addition, a novel p1 gene variant named 2c was identified in 6 of the isolates.

Emergence of macrolide-resistant strains during an outbreak of Mycoplasma pneumoniae infections in children

OBJECTIVES

Mycoplasma pneumoniae is a frequent cause of human lower respiratory tract infections (LRTIs) for which macrolides are the treatment of choice. The aim of this study was to determine the rate of macrolide resistance and to subtype M. pneumoniae strains in Italy.

PATIENTS AND METHODS

During an outbreak of M. pneumoniae infections in southern Italy in 2010, 48 clinical specimens from 43 paediatric patients hospitalized for LRTIs were analysed for macrolide resistance. The mutations associated with resistance (A2063G and A2064G) and M. pneumoniae subtypes were detected by sequencing the targeted domain V region of the 23S rRNA gene and a region in the MPN528a gene, respectively.

RESULTS

Macrolide resistance genotypes were detected in 11 (26%) of the 43 M. pneumoniae-positive children. The A2063G mutation was identified in seven patients and the A2064G mutation was identified in the remaining four. Upon admission, the isolates from three patients showed a susceptible genotype but subsequently acquired the A2063G mutation. Genotyping revealed M. pneumoniae subtype 1 in 33 of 40 sequenced strains and subtype 2 in the remaining 7. There was no association between macrolide resistance or susceptibility and the M. pneumoniae subtypes.

CONCLUSIONS

This is the first report of macrolide resistance among M. pneumoniae strains in Italy. Our findings indicate an unexpected high prevalence of macrolide resistance genotypes in children, and so macrolide resistance should be carefully considered in patients who do not respond appropriately to antibiotic treatment. The epidemiological monitoring of macrolide resistance has become necessary in Italy and in the rest of Europe.

Detection of Mycoplasma pneumoniae in simulated and true clinical throat swab specimens by nanorod array-surface-enhanced Raman spectroscopy

The prokaryote Mycoplasma pneumoniae is a major cause of respiratory disease in humans, accounting for 20% of all community-acquired pneumonia and the leading cause of pneumonia in older children and young adults. The limitations of existing options for mycoplasma diagnosis highlight a critical need for a new detection platform with high sensitivity, specificity, and expediency. Here we evaluated silver nanorod arrays (NA) as a biosensing platform for detection and differentiation of M. pneumoniae in culture and in spiked and true clinical throat swab samples by surface-enhanced Raman spectroscopy (SERS). Three M. pneumoniae strains were reproducibly differentiated by NA-SERS with 95%-100% specificity and 94-100% sensitivity, and with a lower detection limit exceeding standard PCR. Analysis of throat swab samples spiked with M. pneumoniae yielded detection in a complex, clinically relevant background with >90% accuracy and high sensitivity. In addition, NA-SERS correctly classified with >97% accuracy, ten true clinical throat swab samples previously established by real-time PCR and culture to be positive or negative for M. pneumoniae. Our findings suggest that the unique biochemical specificity of Raman spectroscopy, combined with reproducible spectral enhancement by silver NA, holds great promise as a superior platform for rapid and sensitive detection and identification of M. pneumoniae, with potential for point-of-care application.

Identification of P1 types and variants of Mycoplasma pneumoniae during an epidemic in Chile

This study was conducted to determine the types of M. pneumoniae prevalent in adults presenting with community-acquired pneumonia during an epidemic period, and to scrutinize a variable region of the RepMP4 element for the detection of P1 variants. All 23 clinical specimens PCR-positive for M. pneumoniae obtained in two hospitals in Santiago, Chile, from 2005 to 2006 were typed by a multiplex PCR directly and then the RepMP4 fragment of 18 specimens was sequenced. A predominance of M. pneumoniae type 2 was found, 18 (78.3 %) specimens being grouped as type 2 and 5 (21.7 %) as type 1. Co-infection of M. pneumoniae with other respiratory pathogens was found in 10/23 (43.4 %) patients, but their frequency was not related to the M. pneumoniae type. Sequence analysis revealed a single nucleotide polymorphism, a transition mutation, in 50 % of amplicons belonging to type 1 and in 71.4 % of amplicons of type 2. The nucleotide changes were synonymous in each P1 variant. In conclusion, during the 2005–2006 epidemic in Santiago, both types of M. pneumoniae circulated. Although the analysed area in the RepMP4 was small, we detected the existence of P1 variants in the two types of this organism.

Subtypes and variants ofMycoplasma pneumoniae: local and temporal changes in Germany 2003–2006 and absence of a correlation between the genotype in the respiratory tract and the occurrence of genotype-specific antibodies in the sera of infected patients

Mycoplasma pneumoniaeis a frequent cause of community-acquired pneumonia. Three subtypes and three variants ofM. pneumoniaehave been described showing sequence differences in the main P1 adhesin. Between 2003 and 2006 we collected respiratory tract samples of adult outpatients with symptoms of pneumonia in a German nationwide network and detectedM. pneumoniaeby real-time PCR in 140 specimens. The strains were typed by sequencing and demonstrated the circulation of subtypes 1 and 2 and variants 2a and 2b. The overall number of isolates belonging to the two variant genotypes increased during the investigation period but the relationship of subtypes and variants within the participating local centres varied strongly. ELISA experiments using sera of acute-phase patients with a knownM. pneumoniaetype in the respiratory tract resulted in no correlation of IgA and IgG antibodies to subtype- and variant-specific regions of theP1gene with the genotype of theM. pneumoniaestrain causing the actual infection.

Clinical severity of Mycoplasma pneumoniae (MP) infection is associated with bacterial load in oropharyngeal secretions but not with MP genotype

BACKGROUND

Disease severity in Mycoplasma pneumoniae (MP) infection could potentially be related to bacterial factors such as MP genotype (MP1 or MP2; distinguished by different adhesions proteins) or bacterial load in airway secretions. We have compared these parameters in patients who were hospitalized for MP pneumonia, with outpatients with mild MP disease.

METHODS

MP bacterial load was measured by real-time PCR in 45 in- and outpatients ("clinical study group") in whom MP DNA had been detected in oropharyngeal secretions by PCR. In addition, genotype and phylogenetic relationships were determined. The phylogenetical assessment was done by partial DNA sequencing of the P1 gene on isolates from 33 patients in the clinical study-group where sufficient DNA was available. The assessment was further extended to isolates from 13 MP-positive family members and 37 unselected MP positive patients from the two subsequent years and two different geographical locations. In total 83 strains were molecular characterized.

RESULTS

Mean MP loads were significantly higher in 24 hospitalized patients than in 21 outpatients (1600 vs. 170 genomic equivalents/microL, p = 0.009). This difference remained significant after adjustment for age and days between disease onset and sampling. Hospitalized patients also had higher C-reactive protein levels. Mean levels were 188 vs 20 mg/L (p = 0,001). The genotype assessment showed MP genotype 1 in 17 of the 33 sequenced strains from the clinical study-group, and type 2 in 16 of these patients. Within each genotype, sequence differences were minimal. No association between disease severity and MP genotype was observed. In the extended genotype assessment, MP1 was found in similar proportions. In family contacts it was found in 53% and among patients from the two subsequent years 53% and 40%.

CONCLUSIONS

A higher MP bacterial load in throat secretions at diagnosis was associated with more advanced respiratory disease in patients, but MP genotype did not influence disease severity. Both MP genotypes co-circulated during recent outbreaks in Sweden.

Analysis identifying common and distinct sequences among Texas clinical strains of Mycoplasma genitalium

Mycoplasma genitalium is a human bacterial pathogen linked to urethritis and other sexually transmitted diseases. Here, we assessed the incidence of M. genitalium infection in patients attending a sexually transmitted disease clinic in San Antonio, TX, by use of diagnostic real-time PCR. Overall, 16.8% of women and 15.1% of men were found M. genitalium positive. Regions of the mgpB gene, which encodes the MgPa adhesin, were amplified from positive clinical specimens and evaluated for sequence variability, which demonstrated transmission of the pathogen between sexual partners. Follow-up analysis of a subset of patient specimens revealed reinfection by a different strain of M. genitalium, indicating the absence of protective immunity. Eighteen DNA sequence variants were obtained and compared with all other available clinical sequences. Detailed analysis revealed silent mutations of six amino acid residues within the encoded region of the MgPa adhesin in numerous clinical strains. In addition, missense mutations of limited numbers of amino acids were observed. Alignment of putative amino acid sequences revealed the simultaneous occurrence of several mutations and the existence of identical or similar protein variants in strains from different locations.

Comparison of commercial and in-house real-time PCR assays used for detection of Mycoplasma pneumoniae

We tested two commercial and three in-house PCR assays under standardized conditions to detect Mycoplasma pneumoniae. All five procedures were able to demonstrate M. pneumoniae DNA in a concentration comparable to 1 CFU/microl, but the mean crossing points resulted in differences in the concentration of the genome copies of a factor of 20.

Epidemiology, clinical manifestations, pathogenesis and laboratory detection of Mycoplasma pneumoniae infections

Since its initial description in the 1940s and eventual elucidation as a highly evolved pathogenic bacterium, Mycoplasma pneumoniae has come to be recognized as a worldwide cause of primary atypical pneumonia. Beyond its ability to cause severe lower respiratory illness and milder upper respiratory symptoms it has become apparent that a wide array of extrapulmonary infectious and postinfectious events may accompany the infections in humans caused by this organism. Autoimmune disorders and chronic diseases such as asthma and arthritis are increasingly being associated with this mycoplasma, which frequently persists in individuals for prolonged periods. The reductive evolutionary process that has led to the minimal genome of M. pneumoniae suggests that it exists as a highly specialized parasitic bacterium capable of residing in an intracellular state within the respiratory tissues, occasionally emerging to produce symptoms. This review includes discussion of some of the newer aspects of our knowledge on this pathogen, characteristics of clinical infections, how it causes disease, the recent emergence of macrolide resistance, and the status of laboratory diagnostic methods.