Etiologic diagnosis of lower respiratory tract bacterial infections using sputum samples and quantitative loop-mediated isothermal amplification.
Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship.


BACKGROUND
ClinicalTrials.gov NCT00567827.
Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China.
Yu
Y
Kang
Rui
R
Deng
Can
C
Wang
Tao
T
Deng
Peichao
P
Peng
Xiaoxing
X
Cheng
Guoqing
G
Wang
Minping
M
Qian
Huafang
H
Gao
Bei
B
Han
Yusheng
Y
Chen
Yinghui
Y
Hu
Rong
R
Geng
Chengping
C
Hu
Wei
W
Zhang
Jingping
J
Yang
Huanying
H
Wan
Qin
Q
Yu
Liping
L
Wei
Jiashu
J
Li
Guizhen
G
Tian
Qiuyue
Q
Wang
Ke
K
Hu
Siqin
S
Wang
Ruiqin
R
Wang
Juan
J
Du
Bei
B
He
Jianjun
J
Ma
Xiaoning
X
Zhong
Lan
L
Mu
Shaoxi
S
Cai
Xiangdong
X
Zhu
Wanli
W
Xing
Jun
J
Yu
Minghua
M
Deng
Zhancheng
Z
Gao
D001424:Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology; D006801:Humans; D011336:Probability; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000382:microbiology; D013183:Sputum / Q000382:microbiology*