Study on Identification of Non-Tuberculosis Mycobacteria Based on Single-Cell Raman Spectroscopy

Zhen RUAN; Peng-fei ZHU; Lei ZHANG; Rong-ze CHEN; Xun-rong LI; Xiao-ting FU; Zheng-gu HUANG; Gang ZHOU; Yue-tong JI; Pu LIAO

doi:10.3964/j.issn.1000-0593(2021)11-3468-06

Journals >Spectroscopy and Spectral Analysis >Volume 41 >Issue 11 >Page 3468 > Article

Spectroscopy and Spectral Analysis
Vol. 41, Issue 11, 3468 (2021)

Study on Identification of Non-Tuberculosis Mycobacteria Based on Single-Cell Raman Spectroscopy

Zhen RUAN^1、1;, Peng-fei ZHU^3、3;, Lei ZHANG^3、3;, Rong-ze CHEN^3、3;, Xun-rong LI^3、3;, Xiao-ting FU^3、3;, Zheng-gu HUANG^4、4;, Gang ZHOU^4、4;, Yue-tong JI^5、5;, and Pu LIAO^{1、1; 2; *;}

Author Affiliations

¹1. Key Laboratory of Diagnostic Medicine, Ministry of Education; School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China

³3. Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China

⁴4. Center Lab, Chongqing Public Health Medical Center, Chongqing 400036, China

⁵5. Qingdao Single-Cell Biotechnology Co., Ltd., Qingdao 266101, China

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DOI: 10.3964/j.issn.1000-0593(2021)11-3468-06 Cite this Article

Zhen RUAN, Peng-fei ZHU, Lei ZHANG, Rong-ze CHEN, Xun-rong LI, Xiao-ting FU, Zheng-gu HUANG, Gang ZHOU, Yue-tong JI, Pu LIAO. Study on Identification of Non-Tuberculosis Mycobacteria Based on Single-Cell Raman Spectroscopy[J]. Spectroscopy and Spectral Analysis, 2021, 41(11): 3468 Copy Citation Text

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Fig. 1. Original average Raman spectra and difference peaks of six NTMs

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Fig. 2. Pretreatment average Raman spectra of six NTMs

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Fig. 3. t-SNE results of six NTMs SCRS

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细菌名称	光谱数
脓肿分枝杆菌Mycobacterium abscessus	92
戈登分枝杆菌Mycobacterium gordonae	99
偶发分枝杆菌Mycobacterium fortuitum	67
土分枝杆菌Mycobacterium terrae	73
鸟分枝杆菌Mycobacterium avium	68
堪萨斯分枝杆菌Mycobacterium kansasii	154

Table 1. List of species and the number of Raman spectra from single cells

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Peak position /cm^-1	Proteins	Lipids	Nucleic acids	Carbohydrates
644.126	C—S stretching & C—C twisting of proteins
726.371		Characteristic for phospholipids
783.39			U, T, C
829.318			tyrosine (proteins), O—P—O stretch DNA
854.267				C—O—C skeletal mode of α-anomers
1 004.49	Phenylalanine ring breath
1 030.24				ν(CO), ν(CC), ν(CCO)
1 084.69		Typical phospholipids
1 128.03				C—O stretching
1 153.82	C—C/C—N stretching
1 172.2	C—H in-plane bending mode of tyrosine, (CH) phenylalanine
1 211.05	ν(C-C₆H₅), tryptophan, phenylalanine
1 248.78	Amide Ⅲ
1 340.43			CH stretching of adenine
1 449.47		CH₂ bending and scissoring modes of phospholipids
1 518.22				v(C=C) diagnostic for the presence of a carotenoid structure, most likely a cellular pigment v(C=C) carotenoid
1 574.87	Phenylalanine
1 604.68	Phenylalanine, tyrosine, C=C
1 669.75		Allyl C=C stretches

Table 2. Molecular structure and composition of Raman peaks

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Model	Test dataset
Model	Sample	Correct	Accuracy/%
SVM	164	163	99.4
K-NN	164	113	69.1
PLS-DA	164	139	85.0
RF	164	156	95.2
LDA	164	162	98.8
XGB	164	143	87.3

Table 3. Results of six identification models

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SVM	Prediction
SVM	M. abscessus	M. gordonae	M. fortuitum	M. terrae	M. avium	M. kansasii
M. abscessus	23	0	0	0	0	0
M. gordonae	0	27	0	0	0	0
M. fortuitum	0	0	16	0	0	0
M. terrae	0	0	0	29	0	0
M. avium	0	0	0	0	21	0
M. kansasii	0	0	0	1	0	48

Table 4. Prediction results of SVM confusion matrix

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LDA	Prediction
LDA	M. abscessus	M. gordonae	M. fortuitum	M. terrae	M. avium	M. kansasii
M. abscessus	22	0	1	0	0	0
M. gordonae	0	26	0	1	0	0
M. fortuitum	0	0	16	0	0	0
M. terrae	0	0	0	29	0	0
M. avium	0	0	0	0	21	0
M. kansasii	0	0	0	0	0	49

Table 5. Prediction results of LDA confusion matrix

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