Ann Lab Med.  2020 Sep;40(5):370-381. 10.3343/alm.2020.40.5.370.

Clonal Distribution of Clindamycin-Resistant Erythromycin-Susceptible (CRES) Streptococcus agalactiae in Korea Based on Whole Genome Sequences

• Takahashi T
• Maeda T
• Lee S
• Lee DH
• Kim S

• KMID: 2502567
• DOI: http://doi.org/10.3343/alm.2020.40.5.370

Abstract

Background
The clindamycin-resistant erythromycin-susceptible (CRES) phenotype is rare in Streptococcus agalactiae (group B streptococci). We aimed to determine the molecular characteristics of CRES S. agalactiae using whole genome sequencing (WGS).
Methods
Sixty-six S. agalactiae isolates obtained from blood (N=26), cerebrospinal fluid (N=10), urine (N=17), and vaginal discharge (N=13) between 2010 and 2017 in Korea were subjected to WGS. Based on the WGS data, we analyzed antimicrobial resistance (AMR) determinants, sequence types (STs), capsular polysaccharide (CPS) genotypes, and virulence gene profiles, and constructed a phylogenetic tree. We included the clindamycin-susceptible erythromycin-resistant (CSER) phenotype for comparison.
Results
We identified seven CRES S. agalactiae isolates from urine (N=5) and vaginal discharge (N=2) collected between 2010 and 2011. All CRES isolates harbored AMR determinants of lnu(B), lsa(E), and aac(6’)-aph(2’’), revealed ST19 and CPS genotype III, and had a virulence gene profile of rib-lmb-cylE. Phylogenetic tree analysis revealed that all CRES isolates belonged to the same cluster, suggesting a clonal distribution. In contrast, seven CSER isolates showed a diverse distribution and clustered separately from the CRES isolates.
Conclusions
CRES isolates collected between 2010 and 2011 showed a unique cluster with ST19 and CPS genotype III in Korea. This is the first report on WGS-based characteristics of S. agalactiae in Korea.

Keyword

Streptococcus agalactiae; Group B streptococci; Antimicrobial resistance; Whole genome sequencing; Sequence types; Clonal distribution; CRES (clindamycin-resistant erythromycin-susceptible)

Figure

• 

  Fig. 1 goeBURST diagram of the relationships among STs of 66 S. agalactiae isolates. The numbers in the circles indicate the STs, and the numbers near the lines indicate the number of differing alleles between the two connected STs. Putative CCs are identified by an outer dotted frame and correspond to the STs with the highest number of single locus variants. Abbreviations: CC, clonal complex; ST, sequence type.

• 

  Fig. 2 Phylogenetic tree of 66 S. agalactiae isolates. The phylogenetic tree was constructed using OAT, based on the OrthoANI algorithm, with S. agalactiae strain NCTC8181 (accession number UAVB00000000) as a reference. Asterisks (*) indicate CRES isolates, daggers (†) indicate CSER isolates. There was a concordance of the group distribution on the tree with the CPS genotype distribution (Ia, Ib, III, V, and VIII). Abbreviations: CPS, capsular polysaccharide; CRES, clindamycin-resistant erythromycin-susceptible; CSER, clindamycin-susceptible erythromycin-resistant; CRER, clindamycin-resistant erythromycin-resistant; CSES, clindamycin-susceptible erythromycin-susceptible; CSEI, clindamycin-susceptible erythromycin-intermediate; CREI, clindamycin-resistant erythromycin-intermediate; CIES, clindamycin-intermediate erythromycin-susceptible; OAT, Orthologous Average Nucleotide Identity Tool.

• 

  Fig. 3 Comparison of sequences of GCH61, NUBL-9601, and KMP104. Sequence of erm(B) from isolate GCH61 (accession number VYRN00000000) with the CRES phenotype contained C222T (N74N), T224C (I75T), and A299G (N100S) nucleotide (amino acid) substitutions, in addition to the insertion of an IS1216E element at nucleotide position 642, which resulted in the deletion of a segment spanning nucleotides 642–738 (97 bp). This sequence was identical to that from the CRES isolate NUBL-9601 (accession number LC430933). The sequence of erm(B) from the isolate KMP104 was used as a reference (RefSeq accession number DQ355148). Abbreviation: CRES, clindamycin-resistant erythromycin-susceptible.

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