短读全基因组测序用于确定美国当前侵袭性无乳链球菌中抗生素耐药机制和荚膜血清型。

Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA.

机构信息

National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Minnesota Department of Health, St Paul, MN, USA.

出版信息

Clin Microbiol Infect. 2017 Aug;23(8):574.e7-574.e14. doi: 10.1016/j.cmi.2017.02.021. Epub 2017 Feb 28.

DOI:10.1016/j.cmi.2017.02.021

PMID:28257899

Abstract

OBJECTIVES

Our objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS).

METHODS

For 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions with broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing β-lactams. Conventional serotyping was compared to WGS-based assignments for 302 isolates.

RESULTS

All 28 isolates with reduced susceptibility to β-lactam antibiotics harboured one of 19 rare PBP2x types. Resistances to erythromycin/clindamycin (808/1975 isolates, 41.0%), erythromycin (235/1975, 11.9%) and lincosamide/streptogramin A/pleuromutilins (56/1975, 2.8%) were predicted by the presence of erm-methylase, mef and lsa determinants, respectively (41 of 56 lsa gene-positive isolates also contained lnu, erm and/or mef genes). Presence of both erm and lsa determinants (25 isolates) predicted non-susceptibility to quinupristin/dalfopristin. Most isolates (1680/1975, 85.1%) were tet gene-positive, although 41/1565 (2.6%) tetM-positive isolates were tetracycline-susceptible. All 53 fluoroquinolone-resistant isolates contained ParC and/or GyrA substitutions. Resistances to rifampin (eight isolates), trimethoprim, chloramphenicol and vancomycin (two isolates each) were predicted by the pipeline. Resistance to macrolides/lincosamides without pipeline prediction was rare and correlated to divergent resistance genes or rRNA A2062G substitution. A selection of 267 isolates assigned WGS-based serotypes were also conventionally serotyped. Of these, 246 (92.1%) were in agreement, with the remaining 21 (7.8%) conventionally non-serotypeable. For 32 of 1975 isolates (1.6%), WGS-based serotypes could not be assigned.

CONCLUSION

The WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.

摘要

目的

我们的目的是评估和利用全基因组序列（WGS）生物信息学管道，以预测侵袭性 B 组链球菌（iGBS）的抗生素耐药性和荚膜血清型。

方法

对于 2015 年 CDC 主动细菌核心监测中回收的 1975 株 iGBS，我们将管道预测与肉汤稀释试验进行了比较。为了测试β-内酰胺，还纳入了 56 株来自早期监测的分离株。比较了 302 株分离株的常规血清型与基于 WGS 的分配。

结果

所有对β-内酰胺抗生素敏感性降低的 28 株分离株均携带 19 种罕见 PBP2x 型之一。对红霉素/克林霉素（1975 株中的 808 株，41.0%）、红霉素（1975 株中的 235 株，11.9%）和林可酰胺/链阳性菌素 A/磷霉素（1975 株中的 56 株，2.8%）的耐药性分别由 erm-甲基酶、mef 和 lsa 决定因素预测（56 株 lsa 基因阳性分离株中有 41 株也含有 lnu、erm 和/或 mef 基因）。erm 和 lsa 决定因素的存在（25 株）预测对奎奴普丁/达福普汀的不敏感性。大多数分离株（1975 株中的 1680 株，85.1%）tet 基因阳性，尽管 1565 株 tetM 阳性分离株中有 41 株对四环素敏感。所有 53 株氟喹诺酮耐药株均含有 ParC 和/或 GyrA 取代。管道预测了对利福平（8 株）、甲氧苄啶、氯霉素和万古霉素（各 2 株）的耐药性。预测到对大环内酯类/林可酰胺类的耐药性，而没有管道预测，这与不同的耐药基因或 rRNA A2062G 取代有关。还对基于 WGS 的血清型进行了常规血清分型的 267 株分离株的选择。其中，246 株（92.1%）一致，其余 21 株（7.8%）常规不可分型。对于 1975 株分离株中的 32 株（1.6%），无法基于 WGS 分配血清型。