Clinical application the loop-mediated isothermal amplification assay for the identification of pathogens in lower respiratory tract infections

doi:10.3877/cma.j.issn.1674-6902.2022.04.005

Abstract

Abstract:

Objective

To more accurately evaluate the performance of loop-mediated isothermal amplification (LAMP) assay for the identification of pathogens in lower respiratory tract infections(LRTIs).

Methods

The pathogen identification results of 1092 bronchoalveolar lavage fluid (BALF) samples from presumptive LRTI patients admitted to the Tangdu Hospital from January 2018 to September 2018 were analyzed retrospectively. Taking the bacterial culture as the gold standard, the sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio and negative likelihood ratio of LAMP for detecting 8 common lower respiratory tract infection pathogens were calculated.

Results

The sensitivity of LAMP for detecting 8 pathogens were quite different, with the highest sensitivity to Staphylococcus aureus (100%) and the lowest sensitivity to Escherichia coli (40%). The specificity of LAMP for detecting 8 pathogens were higher than 94%. The positive predictive value of the LAMP test results for 8 pathogens were lower than 65%, the negative predictive value were higher than 98%, the positive likelihood were higher than 13. The negative likelihood ratio of the LAMP test results for 8 pathogens were quite different, with the lowest negative likelihood ratio to Staphylococcus aureus (0.00) and the highest negative likelihood ratio to Escherichia coli (0.60).

Conclusion

The LAMP has high accuracy in detecting pathogens of lower respiratory tract infections, which is helpful for early diagnosis and precise treatment of lower respiratory tract infections.

Key words: Lower respiratory infections, Loop-mediated isothermal amplification assay, Pathogens, Bacterial culture

Yanyan Qiao, Luyao Han, Zaiqiang Wang, Yanzhen Feng, Chan Li, Yujuan Li, Faguang Jin, Enqing Fu. Clinical application the loop-mediated isothermal amplification assay for the identification of pathogens in lower respiratory tract infections[J]. Chinese Journal of Lung Diseases(Electronic Edition), 2022, 15(04): 477-480.

/ / Recommend

Add to citation manager EndNote|Ris|BibTeX

URL: https://zhfbjbzz.cma-cmc.com.cn/EN/10.3877/cma.j.issn.1674-6902.2022.04.005

https://zhfbjbzz.cma-cmc.com.cn/EN/Y2022/V15/I04/477

Figures/Tables 2

References 31

1	GBD 2013 Mortality and Causes of Death Collaborators.Global, regional，and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013[J]. Lancet, 2015, 385(9963): 117-171.
2	Troeger C, Forouzanfar M, Rao PC, et al. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in 195 countries: a systematic analysis for the Global Burden of Disease Study 2015[J]. Lancet Infect Dis, 2017, 17(11): 1133-1161.
3	Gadsby NJ, McHugh MP, Russell CD, et al. Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections[J]. Clin Microbiol Infect, 2015, 21(8): 781-788.
4	Notomi T, Mori Y, Tomita N, et al. Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects[J]. J Microbiol, 2015, 53(1): 1-5.
5	陈愉生，王大璇，李鸿茹，等. 环介导等温扩增技术在下呼吸道感染常见病原体检测中的应用[J]. 中华结核和呼吸杂志，2014, 37(4): 270-273.
6	Si Y, Zhang T, Chen N, et al. A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections[J]. J Microbiol Methods, 2021, 190: 106339.
7	van den Munckhof E, de Koning M, Quint W, et al. Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections[J]. Eur J Clin Microbiol Infect Dis, 2019, 38(4): 747-754.
8	Zhang L, Huang W, Zhang S, et al. Rapid detection of bacterial pathogens and antimicrobial resistance genes in clinical urine samples with urinary tract infection by metagenomic nanopore sequencing[J]. Front Microbiol, 2022, 13: 858777.
9	Saragih R, Yanni GN. Correlation between platelet profile (mean platelet volume, platelet volume distribution width and plateletcrit) with procalcitonin and C-reactive protein in critically Ⅲ children[J]. Prague Med Rep, 2022, 123(2): 82-87.
10	Hou J, Wu H, Zeng X, et al. Clinical evaluation of the loop-mediated isothermal amplification assay for the detection of common lower respiratory pathogens in patients with respiratory symptoms[J]. Medicine (Baltimore), 2018, 97(51): e13660.
11	Kang Y, Deng R, Wang C, et al. Etiologic diagnosis of lower respiratory tract bacterial infections using sputum samples and quantitative loop-mediated isothermal amplification[J]. PLoS One, 2012, 7(6): e38743.
12	熊丽丽，段京京，宁永忠，等. 支气管肺泡灌洗液细菌学和真菌学分析[J]. 中华检验医学杂志，2014, 37(10): 784-786.
13	Loens K, Van Heirstraeten L, Malhotra-Kumar S, et al. Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections[J]. J Clin Microbiol, 2009, 47: 21-31.
14	崔立慧，姚　欣，陈名霞. 环介导恒温扩增芯片技术在医院获得性肺炎病原菌检测中的应用[J]. 中国临床研究，2022, 35(4): 451-455.
15	Liu Z, Pan J, Zhang T, et al. Application of isothermal amplification chip method in lower respiratory tract pathogens detection[J]. Lab Med Clinic, 2017, 8: 1052-1053.
16	Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA[J]. Nucleic Acids Res, 2000, 28(12): e63.
17	Kim CK, Cho EA, Shin DM, et al. Comparative evaluation of the loop-mediated isothermal amplification assay for detecting pulmonary tuberculosis[J]. Ann Lab Med, 2018, 38: 119-124.
18	李　美，陈飘飘，应斌武. 基于环介导等温扩增技术的即时检测在检验医学中的应用[J]. 中华检验医学杂志，2021, 44(9): 776-780.
19	Lim KT, Teh CS, Thong KL. Loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus[J]. Biomed Res Int, 2013, 2013: 895816.
20	Ishiguro N, Koseki N, Kaiho M, et al. Sensitivity and specificity of a loop-mediated isothermal amplification assay for the detection of mycoplasma pneumonia from nasopharyngeal swab samples compared with those of realtime PCR[J]. Clin Lab, 2015, 61: 603-606.
21	吴阳升，罗淑萍. 一种新的高效快速核酸恒温扩增方法——LAMP法[J]. 生物技术，2004, 14(4): 76-89.
22	石　磊，王　曼，时国强，等. 环介导等温扩增技术研究进展[J]. 河北大学学报：自然科学版，2021, 41(5): 565-571.
23	李玉姣，程小刚，钱　飞，等. 健康成人口腔微生物组成及功能的宏基因组学研究[J]. 口腔疾病防治，2022, 30(8): 533-541.
24	Kolenbrander PE. Oral microbial communities: biofilms, interactions，and genetic systems[J]. Annu Rev Microbiol, 2000, 54: 413-437.
25	Tuganbaev T, Yoshida K, Honda K. The effects of oral microbiota on health[J]. Science, 2022, 376(6596): 934-936.
26	蔡　甜，陈振华，牛英波，等. 恒温扩增芯片法对下呼吸道标本细菌检测中的临床应用价值[J/CD]. 心电图杂志(电子版), 2019, 8(2): 89-92.
27	Kirst ME, Baker D, Li E, et al. Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation[J]. PLoS One, 2019, 14(9): e222323.
28	Leeflang MM, Rutjes AW, Reitsma JB, et al. Variation of a test′s sensitivity and specificity with disease prevalence[J]. CMAJ, 2013, 185(11): e537-e544.
29	Akobeng AK. Understanding diagnostic tests 1: sensitivity, specificity and predictive values[J]. Acta Paediatr, 2007, 96(3): 338-341.
30	Rehling M. Visualizing the impact of prevalence on a diagnostic test[J]. Scand J Clin Lab Invest, 2010, 70(6): 458-461.
31	Akobeng AK. Understanding diagnostic tests 2: likelihood ratios, pre- and post-test probabilities and their use in clinical practice[J]. Acta Paediatr, 2007, 96(4): 487-491.

病原体	LAMP		细菌培养
病原体	阳性	阳性率	阳性	阳性率
肺炎链球菌	59	5.40	12	1.10
金黄色葡萄球菌	17	1.56	3	0.27
大肠埃希菌	10	0.92	5	0.46
肺炎克雷伯菌	38	3.48	7	0.64
铜绿假单胞菌	40	3.66	30	2.75
鲍曼不动杆菌	60	5.49	51	4.67
嗜麦芽窄食单胞菌	24	2.20	11	1.01
流感嗜血杆菌	63	5.77	7	0.64

病原体	LAMP		细菌培养
病原体	阳性	阳性率	阳性	阳性率
肺炎链球菌	59	5.40	12	1.10
金黄色葡萄球菌	17	1.56	3	0.27
大肠埃希菌	10	0.92	5	0.46
肺炎克雷伯菌	38	3.48	7	0.64
铜绿假单胞菌	40	3.66	30	2.75
鲍曼不动杆菌	60	5.49	51	4.67
嗜麦芽窄食单胞菌	24	2.20	11	1.01
流感嗜血杆菌	63	5.77	7	0.64

病原体	LAMP	培养法		灵敏度(%)	特异度(%)	阳性预测值(%)	阴性预测值(%)	阳性似然比	阴性似然比
病原体	LAMP	阳性	阴性	灵敏度(%)	特异度(%)	阳性预测值(%)	阴性预测值(%)	阳性似然比	阴性似然比
肺炎链球菌	阳性	10	49	83.33	95.46	16.95	99.81	18.37	0.17
	阴性	2	1 031
金黄色葡萄球菌	阳性	3	14	100.00	98.71	17.65	100.00	77.79	0.00
	阴性	0	1 075
大肠埃希菌	阳性	2	8	40.00	99.26	20.00	99.72	54.35	0.60
	阴性	3	1 079
肺炎克雷伯菌	阳性	6	32	85.71	97.05	15.79	99.91	29.06	0.15
	阴性	1	1 053
铜绿假单胞菌	阳性	26	14	86.67	98.68	65.00	99.62	65.74	0.14
	阴性	4	1 048
鲍曼不动杆菌	阳性	39	21	76.47	97.98	65.00	98.84	37.91	0.24
	阴性	12	1 020
嗜麦芽窄食单胞菌	阳性	7	17	63.64	98.43	29.17	99.63	40.47	0.37
	阴性	4	1 064
流感嗜血杆菌	阳性	5	58	71.43	94.65	7.94	99.81	13.36	0.30
	阴性	2	1 027

病原体	LAMP	培养法		灵敏度(%)	特异度(%)	阳性预测值(%)	阴性预测值(%)	阳性似然比	阴性似然比
病原体	LAMP	阳性	阴性	灵敏度(%)	特异度(%)	阳性预测值(%)	阴性预测值(%)	阳性似然比	阴性似然比
肺炎链球菌	阳性	10	49	83.33	95.46	16.95	99.81	18.37	0.17
	阴性	2	1 031
金黄色葡萄球菌	阳性	3	14	100.00	98.71	17.65	100.00	77.79	0.00
	阴性	0	1 075
大肠埃希菌	阳性	2	8	40.00	99.26	20.00	99.72	54.35	0.60
	阴性	3	1 079
肺炎克雷伯菌	阳性	6	32	85.71	97.05	15.79	99.91	29.06	0.15
	阴性	1	1 053
铜绿假单胞菌	阳性	26	14	86.67	98.68	65.00	99.62	65.74	0.14
	阴性	4	1 048
鲍曼不动杆菌	阳性	39	21	76.47	97.98	65.00	98.84	37.91	0.24
	阴性	12	1 020
嗜麦芽窄食单胞菌	阳性	7	17	63.64	98.43	29.17	99.63	40.47	0.37
	阴性	4	1 064
流感嗜血杆菌	阳性	5	58	71.43	94.65	7.94	99.81	13.36	0.30
	阴性	2	1 027

[1]	Tingting Yang, Jun Wang. Influencing factors of ventilator-associated pneumonia in neonates with the treament of mechanical ventilation [J]. Chinese Journal of Obstetrics & Gynecology and Pediatrics(Electronic Edition), 2022, 18(02): 234-239.
[2]	Yufei Zhao, Hanmin Liu. Chest radiography imaging manifestations of children with community-acquired pneumonia caused by common pathogens [J]. Chinese Journal of Obstetrics & Gynecology and Pediatrics(Electronic Edition), 2022, 18(01): 7-14.
[3]	Yuehe Lu, Xiaoyan Gao. Early diagnosis of neonatal infectious brain injury [J]. Chinese Journal of Obstetrics & Gynecology and Pediatrics(Electronic Edition), 2021, 17(04): 380-386.
[4]	Haijin Zhang, Zengguo Wang, Huijun Cai, Bingtong Zhao. Distribution and drug resistance of pathogenic bacteria in neonates from 2020 to 2022 in Xi’an Children’s Hospital [J]. Chinese Journal of Experimental and Clinical Infectious Diseases(Electronic Edition), 2023, 17(04): 222-229.
[5]	Fei Li, Dawei Zhang, Yulei Liu, Jiang Xie, Guangfa Zhu. Inflammation indicators and pathogenic bacteria in puerperium patients complicated with bloodstream infection [J]. Chinese Journal of Experimental and Clinical Infectious Diseases(Electronic Edition), 2021, 15(04): 243-249.
[6]	Xiaojing Zhuang, Haiyan Ding, Xiaorong Lin. Clinical characteristics and distribution of pathogens in patients with type 2 diabetes complicated with bloodstream infection [J]. Chinese Journal of Experimental and Clinical Infectious Diseases(Electronic Edition), 2019, 13(04): 328-333.
[7]	Siyuan Yang, Huimin Zhang, Hongyan Gu, Chengjie Ma, Yunxia Tang, Fengting Yu, Lin Pang, Linghang Wang. Laboratory detection and clinical characteristics of children infected with Bordetella pertussis and respiratory virus [J]. Chinese Journal of Experimental and Clinical Infectious Diseases(Electronic Edition), 2019, 13(02): 152-157.
[8]	Shuting Yang, Jing Tang, Changchang Ye. Research progress on probiotics for the prevention and treatment of periodontal disease and peri-implant disease [J]. Chinese Journal of Stomatological Research(Electronic Edition), 2022, 16(01): 55-58.
[9]	Cunquan Li, Lei Cui, Kejun Liu, Zhengquan Li, Junhao Liu, Yang Bu. Risk factors and pathogen composition of complicated intra-abdominal infection after pancreaticoduodenectomy [J]. Chinese Archives of General Surgery(Electronic Edition), 2022, 16(06): 417-421.
[10]	Meishan Zhao, Jian Zhang, Yichen Zhu, Jun Lin, Ye Tian. Clinical analysis of postoperative infections in kidney transplant recipients [J]. Chinese Journal of Transplantation(Electronic Edition), 2020, 14(03): 168-171.
[11]	Min Yang, Jijian Xie, Wei Chen. Pathogenicity and drug resistance changes of common pathogens of infant community acquired pneumonia in Shiyan area [J]. Chinese Journal of Lung Diseases(Electronic Edition), 2020, 13(06): 737-741.
[12]	Yuanzhe Li, Debin Yang, Beibei Huo, Wenjie Hu, Xianfei Ding. Characteristics of respiratory pathogen detection in children with pneumonia and correlation with PM2.5 concentration [J]. Chinese Journal of Clinicians(Electronic Edition), 2022, 16(10): 959-964.
[13]	Yin Tong, Jianping Yan, Fangjun Zheng, Nianguo Shu, Jianjun Yang, Bolin Wang. Effect of lidocaine glue on bacterial culture of urine and double-J stent after double-J stent indwelling [J]. Chinese Journal of Clinicians(Electronic Edition), 2019, 13(04): 277-280.
[14]	Lihua Feng, Yun Xia, Honghui Dang, Hang Li, Xiaodong Jia, Jianchun Chen. Clinical application of loop-mediated isothermal amplification in the detection of pathogenic bacteria in children's lower respiratory tract [J]. Chinese Journal of Clinical Laboratory Management(Electronic Edition), 2020, 08(02): 82-86.
[15]	Jiajia Yu, Xuxia Zhang, Chuanyou Li, Yi Liu, Shenjie Tang. The application and progress of clustered regularly interspaced short palindromic repeats and associated proteins gene editing technology in the diagnosis of infectious diseases [J]. Chinese Journal of Diagnostics(Electronic Edition), 2021, 09(01): 62-66.

Please choose a citation manager

Content to export