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The 10 clinical M. pneumoniae isolates analysed in this study all showed resistance to macrolide antibiotics based on the CLSI criteria (MIC > 1 μg/mL), and all harboured A2063G mutations in the domain V of the 23S rRNA gene (correspond to A2058G in E. coli numbering). M. pneumoniae reference strain FH was susceptible to all antibiotics tested (MIC < 1 μg/mL) (Table 1).
Table 1. Minimal Inhibitory Concentrations and the Effect of Efflux Pump Inhibitors on 10 Clinical Strains of M. pneumoniae Isolated in Beijing
Strain No. Minimal Inhibitory Concentration (μg/mL) Erythromycin Azithromycin Medemycin ERY2 alone +RSP3 +CCCP4 +RSP +CCCP5 AZM6alone +RSP +CCCP +RSP +CCCP MED7 alone +RSP +CCCP +RSP +CCCP FH (ATCC15531) < 1 / / / < 1 / / / < 1 / / / 1CIP10349 64 64 32 8 32 32 4 1 2 2 < 1 < 1 CIP10361 64 64 32 4 64 64 8 2 2 2 1 < 1 CIP12206 512 512 128 64 512 512 64 64 8 8 4 1 CIP12235 64 64 16 < 1 256 256 4 < 1 4 4 4 < 1 CIP12261 128 128 64 32 256 256 16 8 4 4 2 1 CIP12265 128 128 128 128 512 512 64 64 64 64 4 4 CIP12267 128 128 128 64 256 256 8 8 16 16 2 1 CIP12311 64 64 64 32 > 512 > 512 32 16 8 8 4 2 CIP12355 64 64 64 8 128 64 8 < 1 4 4 1 < 1 CIP12357 32 32 16 2 > 512 256 8 2 8 8 8 1 Note. 1CIP: Capital Institute of Pediatrics; 2ERY: Erythromycin tested alone; 3RSP: Reserpine and agent tested in combination with 20 μg/mL reserpine; 4CCCP: Carbonyl cyanide m-chlorophenyl-hydrazone and agent tested in combination with 7.5 μg/mL CCCP; 5(+RSP+CCCP): Agent tested in combination with 20 μg/mL reserpine and 7.5 μg/mL CCCP; 6AZM: Azithromycin tested alone; 7MED: medemycin tested alone. -
The basic whole genome sequencing statistics are shown in Table 2. The mapped depth ranged between 70 × and 730 ×, and the percent of the reference genome covered was 99.97%-99.99%. Genome sequence analysis of the 10 clinical strains revealed that the draft genome sequences of eight clinical M. pneumoniae strains isolated in 2012 were similar in size (800, 977 to 807, 092 bp); however, the strains isolated in 2010 had smaller genomes (777, 576 bp for CIP10349 and 778, 884 bp for CIP10361). The minimal sequencing depth was 137 × among the 10 clinical isolates, and all isolates had a G + C content of 39%. The PCR results of some target DNA fragments showed that the levels of identity were 99.7%.
Table 2. Sequencing Statistics for the M. pneumoniae Isolates
Strain Read Length (bp) Paired Read Number Raw Data (M) Mapping to Reference M129 2SNP Percent (%) Depth (X) 1CIP 12265 116 2994424 1, 011 99.98 730 336 CIP 12311 116 483739 112 99.97 70 335 CIP10349 110 722615 159 99.97 100 330 CIP10361 110 764851 168 99.98 100 350 CIP 12357 116 706950 164 99.99 190 346 CIP 12206 116 1285328 298 99.98 330 356 CIP 12235 116 1161819 270 99.99 310 350 CIP 12261 116 628844 146 99.99 170 351 CIP 12267 116 1124693 261 99.99 310 362 CIP 12355 116 633894 147 99.97 170 352 Note.1CIP: Capital Institute of Pediatrics; 2SNP: single nucleotide polymorphism. Comparative genomic analyses were performed using the genome sequence of reference strains M129 and FH (International standard sensitive strains). The numbers of SNPs in each of the clinical isolates ranged between 330 and 362 when compared with reference strain M129. Gene function predictions based on M129 gene annotation showed that SNPs located within hypothetical proteins and intergenic regions were the most common variations. Other mutations included those located within genes encoding: type Ⅰ restriction enzyme EcoKI specificity protein, cytadherence protein, the membrane export protein family protein, ABC transporters, amino acid permease and cell division protein FtsH (Figure 1). Of the SNPs identified, 56 were shared by 10 clinical isolates but were absent from the M129 and FH reference strains. Of the 56 SNPs, 19 were synonymous mutations, 30 were non-synonymous mutations, and seven were located within non-coding sequences. Among 30 non-synonymous SNPs, there were 4 SNPs clustered in the gene encoding a macrolide-specific efflux pump protein of the ATP-binding cassette (ABC) transporter family (Table S1, available in BES online, www.besjournal.com).
Figure 1. SNP density map constructed using circos. Red bars indicate the regions of high SNP density, these include the genes encoding: hypothetical proteins, intergenic regions, type Ⅰ restriction enzyme EcoKI specificity protein, cytadherence protein, the membrane export protein family protein, ABC transporter, amino acid permease and cell division protein FtsH.
Table Table S1. Fifty-six Mutations in All 10 Clinical Isolates which were Different from the M129 and FH Reference Strains
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To identify new mutations associated with drug resistance, coding genes were identified in all isolates. BLAST searches against the ARDB showed that a total of seven different resistance profiles were found: polymyxin, bacitracin, trimethoprim, kasugamycin, macrolide, tetracycline, and thiostrepton. However, only macrolide antibiotics were investigated further as they are clinically relevant in treating M. pneumoniae pneumonia in children. BLAST analysis against the ARDB showed that SNPs associated with drug resistance were focused on the macb gene which belongs to resistance-nodulation-cell division transporter system and multidrug resistance efflux pump and macrolide-specific efflux system gene encoding a macrolide ABC transporter ATP-binding protein.
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The MIC values for macrolides tested in the presence and absence of efflux pump inhibitors are presented in Table 1. The efflux pump inhibitor RSP produced little or no change in susceptibility. In only two of the 10 strains, the MIC value for AZM was decreased two-fold by RSP (CIP12355 from 128 to 64 μg/mL and CIP12357 from > 512 to 256 μg/mL). However, unlike RSP, CCCP produced a strong decrease in the macrolide MIC values, with the exception of strains CIP12265, CIP12267, CIP12311, and CIP12355 to erythromycin and strains CIP12235 and CIP12357 to midecamycin (Table 1). Surprisingly, on combining CCCP and RSP, the MIC values showed a greater decrease than for CCCP alone, with strains CIP10349, CIP10361, CIP12355, and CIP12235 even becoming susceptible ( < 1 μg/mL) to between one and three types of macrolides (Table 1).
doi: 10.3967/bes2017.045
Whole Genome Analysis Reveals New Insights into Macrolide Resistance in Mycoplasma pneumoniae
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Abstract:
Objective Mutations in 23S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae (M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. Methods The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina HiSeq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone (CCCP). Results A total of 56 single nucleotide polymorphisms (SNPs) were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene macB encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations (MIC) of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains. Conclusion Our study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23S rRNA gene. 注释:1) AUTHOR CONTRIBUTIONS: -
Figure 1. SNP density map constructed using circos. Red bars indicate the regions of high SNP density, these include the genes encoding: hypothetical proteins, intergenic regions, type Ⅰ restriction enzyme EcoKI specificity protein, cytadherence protein, the membrane export protein family protein, ABC transporter, amino acid permease and cell division protein FtsH.
Table 1. Minimal Inhibitory Concentrations and the Effect of Efflux Pump Inhibitors on 10 Clinical Strains of M. pneumoniae Isolated in Beijing
Strain No. Minimal Inhibitory Concentration (μg/mL) Erythromycin Azithromycin Medemycin ERY2 alone +RSP3 +CCCP4 +RSP +CCCP5 AZM6alone +RSP +CCCP +RSP +CCCP MED7 alone +RSP +CCCP +RSP +CCCP FH (ATCC15531) < 1 / / / < 1 / / / < 1 / / / 1CIP10349 64 64 32 8 32 32 4 1 2 2 < 1 < 1 CIP10361 64 64 32 4 64 64 8 2 2 2 1 < 1 CIP12206 512 512 128 64 512 512 64 64 8 8 4 1 CIP12235 64 64 16 < 1 256 256 4 < 1 4 4 4 < 1 CIP12261 128 128 64 32 256 256 16 8 4 4 2 1 CIP12265 128 128 128 128 512 512 64 64 64 64 4 4 CIP12267 128 128 128 64 256 256 8 8 16 16 2 1 CIP12311 64 64 64 32 > 512 > 512 32 16 8 8 4 2 CIP12355 64 64 64 8 128 64 8 < 1 4 4 1 < 1 CIP12357 32 32 16 2 > 512 256 8 2 8 8 8 1 Note. 1CIP: Capital Institute of Pediatrics; 2ERY: Erythromycin tested alone; 3RSP: Reserpine and agent tested in combination with 20 μg/mL reserpine; 4CCCP: Carbonyl cyanide m-chlorophenyl-hydrazone and agent tested in combination with 7.5 μg/mL CCCP; 5(+RSP+CCCP): Agent tested in combination with 20 μg/mL reserpine and 7.5 μg/mL CCCP; 6AZM: Azithromycin tested alone; 7MED: medemycin tested alone. Table 2. Sequencing Statistics for the M. pneumoniae Isolates
Strain Read Length (bp) Paired Read Number Raw Data (M) Mapping to Reference M129 2SNP Percent (%) Depth (X) 1CIP 12265 116 2994424 1, 011 99.98 730 336 CIP 12311 116 483739 112 99.97 70 335 CIP10349 110 722615 159 99.97 100 330 CIP10361 110 764851 168 99.98 100 350 CIP 12357 116 706950 164 99.99 190 346 CIP 12206 116 1285328 298 99.98 330 356 CIP 12235 116 1161819 270 99.99 310 350 CIP 12261 116 628844 146 99.99 170 351 CIP 12267 116 1124693 261 99.99 310 362 CIP 12355 116 633894 147 99.97 170 352 Note.1CIP: Capital Institute of Pediatrics; 2SNP: single nucleotide polymorphism. Table S1. Fifty-six Mutations in All 10 Clinical Isolates which were Different from the M129 and FH Reference Strains
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