Rapid Classification of Multilocus Sequence Subtype for Group B Streptococcus Based on MALDI-TOF Mass Spectrometry and Statistical Models

Lianfen Huang,Zixian Li,Yongqiang Xie,Huamin Zhong,Chien-Yi Chang,Qiulian Deng,Guanglian Chen,David J Mciver,Wenjing Ji,Xiaoshan Guan,Kankan Gao,Haiying Liu

doi:10.3389/fcimb.2020.577031

Abstract

Group B Streptococcus (GBS) is an important etiological agent of maternal and neonatal infections as well as postpartum women and individuals with impaired immunity. We developed and evaluated a rapid classification method for sequence types (STs) of GBS based on statistic models with Matrix-Assisted Laser Desorption/Ionization Time-of Flight Mass Spectrometry (MALDI-TOF/MS). Whole-cell lysates MALDI-TOF/MS analysis was performed on 235 well-characterized GBS isolates from neonatal invasive infections in a multi-center study in China between 2015 and 2017. Mass spectra belonging to major STs (ST10, ST12, ST17, ST19, ST23) were selected for model generation and validation. Recognition and cross validation values were calculated by Genetic Algorithm-K Nearest Neighbor (GA-KNN), Supervised Neural Network (SNN), QuickClassifier (QC) to select models with the best performance for validation of diagnostic efficiency. Informative peaks were further screened through peak statistical analysis, ST subtyping MSP peak data and mass spectrum visualization. For major STs, the ML models generated by GA-KNN algorithms attained highest cross validation values in comparison to SNN and QC algorithms. GA-KNN models of ST10, ST17, and ST12/ST19 had good diagnostic efficiency, with high sensitivity (95–100%), specificity (91.46%–99.23%), accuracy (92.79–99.29%), positive prediction value (PPV, 80%–92.68%), negative prediction value (NPV, 94.32%–99.23%). Peak markers were firstly identified for ST10 (m/z 6250, 3125, 6891) and ST17 strains (m/z 2956, 5912, 7735, 5218). Statistical models for rapid GBS ST subtyping using MALDI-TOF/MS spectrometry contributes to easier epidemical molecular monitoring of GBS infection diseases.

Highlights

Group B Streptococcus (GBS), a gram-positive coccus commonly colonizing in the female lower genital tract or rectum, is one of the most common causes of sepsis, meningitis and pneumonia in neonates and fetal injury, preterm birth, spontaneous abortion in pregnant women (Lamagni et al, 2013; Nanduri et al, 2019), or invasive infections in postpartum women and individuals with impaired immune systems (Tevdorashvili et al, 2015), leaving poor prognosis such as neonatal death, severe neutral system sequelae, etc
Sequence type allelic profile of seven housekeeping genes of the 235 GBS isolates was generated by STRAT2 software (Jolley et al, 2001) (Figure S1), which was based on the unweightedpair group method using average (UPGMA) linkages and represented as a dendritic tree showing the genetic relationships among 31 sequence types (STs) subtypes
No MALDI-TOF/MS based statistical classification methodology has been reported for rapid GBS ST typing and peak biomarkers discovery yet

Summary

Introduction

Group B Streptococcus (GBS), a gram-positive coccus commonly colonizing in the female lower genital tract or rectum, is one of the most common causes of sepsis, meningitis and pneumonia in neonates and fetal injury, preterm birth, spontaneous abortion in pregnant women (Lamagni et al, 2013; Nanduri et al, 2019), or invasive infections in postpartum women (endometritis) and individuals with impaired immune systems (Tevdorashvili et al, 2015), leaving poor prognosis such as neonatal death, severe neutral system sequelae, etc. GBS colonization in pregnant women is a major risk factor for neonatal and infant infections (Burcham et al, 2019). The most common epidemiological analysis of GBS infections is the latex agglutination (LA) assay using the specific surface capsular polysaccharide (CPS) antibodies for serologic typing (El et al, 2019). The commercial LA kits sometimes are unable to serotype the GBS isolates with low expression of CPS, methods for genoserotyping with both serotyping and PCR amplification of the capsular gene was developed (Poyart et al, 2007; Imperi et al, 2010). GBS strains belonging to identical capsular serotype III or Ib have shown significant differential characteristics in phenotype and genotype (Arias et al, 2019; Wu et al, 2019; Zheng et al, 2020). Ribotyping is not widely applied for determination of rDNA RFLP patterns, it can be used as a typing system only in conjunction with serotyping (Huet et al, 1993), and this methods is not always comparable among different laboratories

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Conclusion