Whole genome analysis of a multidrug-resistant Streptococcus pneumoniae isolate from a patient with invasive
Yasuo Ohkoshi1, Toyotaka Sato2, Takayuki Wada3
1Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Clinical Laboratory, NTT East Sapporo Hospital, Sapporo, Japan.
Abstract:
Multidrug-resistant Streptococcus pneumoniae strains were isolated from blood and sputum of a patient with disseminated intravascular coagulation in Sapporo city, Japan. These antibiograms were only susceptible to vancomycin, linezolid, daptomycin, some carbapenems, and some fluoroquinolones. Identical antibiograms, serotypes (19F), and sequence types (ST10017) suggested a shared origin of these isolates. Only one ST10017 strain has been isolated in the same city in Japan previously (2014), and the 2014 isolate is still susceptible to macrolides. The whole genome of the blood-derived isolate was sequenced. The strain harbored resistance mutations in parC, gyrA, pbp1a, pbp2a, pbp2b, and pbp2x, and harbored the resistance genes, ermB and tetM. The nucleotide sequences of parC and pbp2x genes of strain MDRSPN001 were clearly different from those of other S. pneumoniae strains and were similar to those of oral streptococci strains. These findings suggest that strain MDRSPN001 has been rapidly and drastically evolving multidrug resistance by gene replacement and accumulation of genes originating from other strains, such as oral streptococci, Streptococcus mitis.
Insights
Multidrug-resistant Streptococcus pneumoniae strains exhibiting novel resistance mechanisms were identified in Japan. These strains rapidly evolved resistance through gene acquisition from other bacteria, posing a significant public health threat.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Emergence of multidrug-resistant (MDR) Streptococcus pneumoniae poses a global health challenge.
- Streptococcus pneumoniae is a leading cause of bacterial pneumonia, meningitis, and sepsis.
Observation:
- MDR Streptococcus pneumoniae strains with unique resistance profiles were isolated from a patient in Sapporo, Japan.
- These isolates showed resistance to multiple antibiotics, including vancomycin, linezolid, daptomycin, carbapenems, and fluoroquinolones.
- Genomic analysis revealed mutations in key resistance genes (parC, gyrA, pbp1a, pbp2a, pbp2b, pbp2x) and the presence of ermB and tetM resistance genes.
Findings:
- The MDR Streptococcus pneumoniae strain (MDRSPN001) exhibited significant genetic divergence, with parC and pbp2x sequences resembling those of oral streptococci.
- Evidence suggests rapid evolution of multidrug resistance through horizontal gene transfer and gene replacement, potentially involving Streptococcus mitis.
- Identical serotypes (19F) and sequence types (ST10017) indicated a common origin for the isolated strains, with one previous isolate from 2014 showing macrolide susceptibility.
Implications:
- The findings highlight the potential for rapid and drastic evolution of antibiotic resistance in Streptococcus pneumoniae through interspecies gene transfer.
- Understanding these evolutionary mechanisms is crucial for developing effective strategies to combat MDR bacterial infections.
- This study underscores the importance of continuous genomic surveillance for emerging resistance patterns in clinically significant pathogens.
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