Advanced search
Publication Cover
Infection and Drug Resistance Volume 11, 2018 - Issue
Submit an article Journal homepage
169
Views
7
CrossRef citations to date
0
Altmetric
Original Research

Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates

Fen Pan1 Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
,
Hong Zhang1 Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, ChinaCorrespondence[email protected]
,
Xiaoyan Dong2 Department of Respiratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
,
Weixing Ye3 Shanghai Personal Biotechnology Co., Ltd, Shanghai, China
,
Ping He4 Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
,
Shulin Zhang4 Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
,
Jeff Xianchao Zhu5 Zhejiang Bioruida Biotechnology co. Ltd, Zhejiang, China
&
Nanbert Zhong1 Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China;2 Department of Respiratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China;6 New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USACorrespondence[email protected]
[email protected]
 show all
Pages 659-670 | Published online: 03 May 2018

Figures & data

Table 1 Epidemiological data from S. pneumoniae strains isolated from children

Figure 1 Phylogenetic relationships of S. pneumoniae isolates based on single-nucleotide polymorphisms from whole DNA sequences.

Notes: A tree representing the isolates. The branch lengths show the evolutionary distances among the isolates. The bootstrap values of the nodes represent the reliability of a branch being formed by all isolates in this branch, and values >70% are considered to be reliable. Resistant profiles: 14LC.ER1023-25, PEN-CXM-CRO-MAC–SXT; 14LC.ER1026-28, CXM-CRO-MAC-SXT; 14LC.ER1029-31, CXM-CRO-MAC; 14LC.ER1032-34, CXM-MAC-SXT; 14LC.ER1035-37, CXM-MAC; 14LC.ER1038-40, MAC-SXT; 14LC.ER1041-43, MAC; and 14LC.ER1044-47, NONE.
Abbreviations: PEN, penicillin; CXM, cefuroxime; CRO, ceftriaxone; MAC, macrolides (erythromycin and azithromycin) and clindamycin; SXT, sulfamethoxazole–trimethoprim.
Figure 1 Phylogenetic relationships of S. pneumoniae isolates based on single-nucleotide polymorphisms from whole DNA sequences.

Figure 2 Principle component analysis of the whole genomes of 25 pneumococcal isolates.

Notes: MA, PEN-CXM-CRO-MAC–SXT; MB, CXM-CRO-MAC-SXT; MC, CXM-CRO-MAC; MD, CXM-MAC-SXT; ME, CXM-MAC; MF, MAC-SXT; MG, MAC; and CK, NONE.
Abbreviations: PEN, penicillin; CXM, cefuroxime; CRO, ceftriaxone; MAC, macrolides (erythromycin and azithromycin) and clindamycin; SXT, sulfamethoxazole–trimethoprim.
Figure 2 Principle component analysis of the whole genomes of 25 pneumococcal isolates.

Table 2 Indel changes closely associated with antibiotic resistance in S. pneumoniae

Table 3 SNP changes associated with antibiotic resistance in S. pneumoniae

Figure 3 Indel and SNP variation in the complete genome of S. pneumoniae R6 compared with 25 S. pneumoniae clinical isolates.

Notes: The distribution of nonsynonymous mutations (SNPs and indels) in the genome sequences of 25 isolates compared with the S. pneumoniae R6 reference strain is shown. Protein-coding genes on the sense and anti-sense strands are shown in rings II and III (from inside to outside). The arrow directions indicate the translational directions. The distribution of nonsynonymous mutations in the genomes of 25 isolates (from isolate 14LC-ER1023 to 14LC-ER1047) are shown from ring IV to ring XXVII. Green bars represent nonsynonymous SNPs; red bars represent nonsynonymous indels.
Abbreviation: SNP, single-nucleotide polymorphisms.
Figure 3 Indel and SNP variation in the complete genome of S. pneumoniae R6 compared with 25 S. pneumoniae clinical isolates.

Figure 4 (A) SNPs changes in PBPs associated with penicillin resistance in S. pneumoniae. (B) SNPs changes in PBPs associated with cephalosporins resistance in S. pneumoniae. (C) SNP changes associated with sulfamethoxazole–trimethoprim resistance in S. pneumonia.

Abbreviations: SNPs, single-nucleotide polymorphisms; PBPs, penicillin-binding proteins; PEN, penicillin; CXM, cefuroxime; CRO, ceftriaxone; SXT, sulfamethoxazole–trimethoprim.
Figure 4 (A) SNPs changes in PBPs associated with penicillin resistance in S. pneumoniae. (B) SNPs changes in PBPs associated with cephalosporins resistance in S. pneumoniae. (C) SNP changes associated with sulfamethoxazole–trimethoprim resistance in S. pneumonia.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.