| Objective: The incidence data of scarlet fever in Shenzhen from 2010 to 2020 were analyzed to explore the epidemic trend of scarlet fever in Shenzhen;In addition,group A Streptococcus(GAS)isolated from scarlet fever patients in Shenzhen was studied,and the antibiotic susceptibility profiles and genomic characteristics of the strains were discussed,so as to reveal the reasons for the high incidence of scarlet fever in Shenzhen and provide evidence for the treatment and prevention of scarlet fever.Methods: The incidence data of scarlet fever were collected,and the distributions of scarlet fever cases in Shenzhen were described using descriptive epidemiological methods.488 GAS strains isolated from scarlet fever patients were collected from various hospitals in Shenzhen.Antibiotic susceptibility tests were performed on the collected strains,including tests for 20 antibiotics.Whole-genome sequencing of the strains was carried out,and based on the data of whole-genome sequencing,the molecular typing of the strains,the analysis of the genetic evolution of the strains,the analysis of the virulence level and the resistance mechanism were performed.Results: Shenzhen,with the largest number of reported scarlet fever cases in Guangdong Province,showed an upward trend from 2010 to 2017,and a downward trend from 2017 to 2020,but the incidence was still much higher than that in 2010.The affected population is mainly children aged1-11 years,and most of them are male children.Longgang and Guangming District are the areas with the highest incidence of scarlet fever in Shenzhen.The emm type of GAS in Shenzhen was mainly emm12 and emm1,and the MLST type was mainly ST36 and ST28.There were 3 clonal clusters with no SNP differences,and the onset time of the patients was concentrated.The epidemic strains(emm12 and emm1)were closely related to other cities in China,and far from the British strains.The isolates were highly resistant to erythromycin,azithromycin,clindamycin and tetracycline,especially the epidemic strains.We discovered three novel Integrative and Conjugative Element(ICE)variants carrying resistance genes,which we named ICE-SZ1,ICE-SZ2 and ICE-SZ3.Combining the antibiotic susceptibility results and the carrying situation of antibiotic resistance genes and ICE,the resistance of epidemic strains to erythromycin,azithromycin,clindamycin and tetracycline is caused by the erm(B)and tet(M)genes carried by ICE.Different emm strains have different superantigen gene profiles,and the epidemic strains carryΦHKU.vir rate of 98.7%,while non-epidemic strains do not carryΦHKU.vir..The number of virulence genes carried by emm1 type is much higher than that of other emm types,and the number of virulence genes of emm12 type is higher than that of non-epidemic strains.Pan-genome analysis found that there were specific genes in the epidemic strains,but the gene functions were unknown.Conclusions: The incidence of scarlet fever in Shenzhen decreased from2017 to 2020,but compared with before 2011,the scarlet fever epidemic situation remains severe.GAS from scarlet fever patients in Shenzhen is dominated by emm12 and emm1 strains.Based on genomic epidemiological analysis,community outbreaks of scarlet fever were inferred in the population from which the isolates were derived.Three new antibiotic-resistant ICE variants were identified.The resistance of the strains to macrolides,clindamycin and tetracycline was acquired by the transfer of ICE carrying the resistance genes erm(B)and tet(M)in bacterial populations.Epidemic strains have higher virulence levels than nonepidemic strains.The spread of antibiotic-resistant ICE and the high virulence of the epidemic strains may be the reasons driving the high incidence of scarlet fever in Shenzhen. |
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