The percentage of bacteria identified as definite (dark blue) and possible (light blue) causative agents in LRTI patients (for the full bacterial names see the legend of

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038743#pone-0038743-g002" target="_blank"><b>Figure 2</b></a><b>).</b> The patients are classified as: children, ≤14 yr; middle-aged adult, >14 yr but <70 yr; aged, ≥70 yr; AB, acute bronchitis; CAP, community acquired pneumonia; AECOPD, acute exacerbation of COPD; and AEBX, acute exacerbation of bronchiectasis.</p

Data Summary of qLAMP and culture assays.

<p>Note: The Abbreviations are: Ab, <i>A. baumannii</i>; Ec, <i>E. coli</i>; Hi, <i>H. influenzae</i>; Kp, <i>K. pneumoniae</i>; Pa, <i>P. aeruginosa</i>; Sa, <i>S. aureus</i>; Sm, <i>S. maltophilia</i>; and Sp, <i>S. pneumonia</i>.</p>*<p>indicates the number of patients whose positive culture was confirmed by one of the 4 culture-based tests.</p>**<p>indicate confirmation rate of the positive cultures by one of the 4 culture-based tests.</p>***<p>indicate the bacterial mortality due to refrigeration, storage, and transportation.</p

Relatedness between qLAMP and culture assays and cutoffs in different subgroups.

<p>Note: We only used the data from the three-time culture to test the consistency between qLAMP and culture assays. N and BX stand for not found and bronchiectasis, respectively.</p>*<p>In the piecewise linear regression of <i>S. pneumoniae</i> for child patients, all the detected titers were PCs (pathogen candidates), and no breakpoint was found. Therefore, the lowest titer detected in this subgroup is deemed as the upper cutoff.</p

The qLAMP-based diagnostic rates in LRTI patients and different subgroups.

<p>The qLAMP-based diagnostic rates in LRTI patients and different subgroups.</p

qLAMP and culture result from LRTI patients.

<p>(A) The positive rates (the right vertical axis) of one-time culture (brown bar), three-time culture (blue bar), and quantitative LAMP (yellow bar) for the eight species in the panel (from the left: Ab, <i>A. baumannii</i>; <i>Ec, E. coli;</i> Hi, <i>H. influenzae;</i> Kp, <i>K. pneumoniae;</i> Pa, <i>P. aeruginosa;</i> Sa, <i>S. aureus</i>; Sm, <i>S. maltophilia;</i> and Sp, <i>S. pneumoniae</i>) detected from the number of patients (the left vertical axis). (B) The number of patients (the left vertical axis) who were tested positive for at least one bacterium in one-time culture, three-time culture, and qLAMP. Each bar is the sum of patient with single (blue bar) and multiple (yellow bar) species detected.</p

Examples of <i>S. pneumonia</i> showing the relationship between qLAMP and culture results (logistic regression) and cutoff determination based on competitive relationship (piece-wise linear regression).

<p>The horizontal axis displays the bacterial natural logarithmic titer in sputum sample. (A) Logistic regression curve (green line). Solid circles indicate patients; they are placed at the top of the chart when being test as positive and at the bottom of the chart when being tested as negative in the culture assays. The height and width of the bars display the frequency and the number of patients being tested positive in cultures, respectively. (B) Piecewise linear regression (black lines) of <i>S. pneumonia</i> in COPD patients. Open circles indicate patients; they are placed at the top of the chart when being PC (Pathogen Candidate) and at the bottom of the chart when NOT being PC.</p