The essence of the methodology referred to lies in the use of data-driven mathematical modeling tools which extract useful information from longitudinal time-kill data collected in an optical density instrument. Implementation of this methodology entails the following elements:
We elaborate on each of the above elements next.
2.1. Longitudinal Optical Density Measurements of Bacterial Cell Suspension under Drug Exposure
In a spectrophotometer, a cell population in suspension is placed in a transparent cuvette and light is shone to it. Because cells impart turbidity (cloudiness) to the suspension as they absorb and scatter light, the intensity of transmitted light is lower than the intensity of the incident light. Comparing the two intensities provides a quantitative assessment of the number of the cells in suspension (optical density). Optical density is roughly proportional to the biomass in the cell suspension in a given range that is specific to the cell type. The simplicity and ability to generate abundant longitudinal data have made spectrophotometry the method of choice for measurements of bacterial growth in related applications. The inherent drawback of spectrophotometry, as already mentioned, is its inability to distinguish between live and dead cells, a limitation of utmost importance in time-kill experiments [
29]. Indeed, whereas in bacterial growth experiments live cells quickly far outnumber dead cells, time-kill experiments experience the reverse. In fact, bacterial populations with resistant subpopulations may exhibit interesting behavior, as depicted in
Figure 1, adapted from [
29]. This figure indicates that for successive multiples of drug concentrations the number of live cells,
, may qualitatively exhibit pure growth, delayed growth, decline followed by regrowth or delayed regrowth, and finally continued decline
Figure 1a. However, what optical density measurements will indicate is a set of curves for the total number of cells (comprising both live and dead cells),
, that never decline, as shown in
Figure 1b.
It is this inherent limitation of optical density instruments that is addressed by the integrated mathematical modeling methodology presented here, as detailed in subsequent sections.
In addition to the above inherent limitation, secondary issues with optical density instruments may arise from multiple difficulties in reliably translating optical density to number of bacterial cells. The following examples are representative of systematic error sources: To extend their dynamic range, many optical density instruments change measurement method from scattering to absorption, based on a threshold value of bacterial concentration, thus possibly introducing calibration errors [
30]; Dead cells decompose over time, thus changing the optical signature of the cell suspension and making corresponding adjustments necessary; Concentration of cells in suspension used in the instrument may not be uniform, if mixing is not adequate, thus biasing measurements; A number of antibiotics, such as fluoroquinolones, can induce morphological changes to exposed bacteria (e.g. filaments at concentrations close to the MIC) thus inadvertently changing again the optical signature observed. Nevertheless, results show remarkable robustness of the proposed mathematical modeling method based on optical density data [
29,
30]. Of course, it is also reasonable to expect that improvements in optical density instruments will help improve the applicability of the proposed method.
2.2. Kill Rate Estimation of Least Susceptible Bacteria as a Function of Drug Concentration
The study of bacterial population dynamics has a long history [
31], with a variety of mathematical models used for corresponding quantitative descriptions [
14,
32]. At the core of these models is the elementary differential equation
or its counterpart for a saturating bacterial population
, where
is the physiological growth rate and
the upper bound of the growing bacterial population [
33]. Exposure to bactericidal drugs adds a killing term
to the right-hand side of the preceding equations, where
is the kill rate, dependent on drug concentration
. A typical expression for the kill rate is
where
is the Hill exponent of sigmoidicity [
9,
34,
35,
36]. For typical time-kill experiments with time-invariant
, solution of the differential equation
is
, which corresponds to a straight line of slope
in a plot of
vs.
.
As conceptually useful as such linear plots are, most practical situations of bacterial populations exposed to drugs involve subpopulations of varying susceptibility to the drug(s), corresponding of a distribution of values of
over a bacterial population at any given drug concentration
[
9,
10]. The result is curves rather than straight lines for
, as depicted for example in
Figure 1a. For such cases it was shown [
11,
12] that the size
of a heterogeneous bacterial population exposed to one or more drugs at time-invariant concentration
is well captured by the equation
and the kill rate average and variance over time are well captured by the equations
where
is the live bacterial population size with initial value ;
is the physiological net growth rate of the entire bacterial population, common for all subpopulations;
is the kill rate induced by the antibiotic on the most resistant (least susceptible) subpopulation;
is the maximum size of a bacterial population reaching saturation under growth conditions;
is the kill rate average over the bacterial population at time ;
is the kill rate variance over the bacterial population at time ;
are constants associated with the initial decline of the average kill rate of the population, and correspond to the Poisson distributed variable ( with average and variance equal to Note that no assumptions about the mechanisms that confer bacterial resistance have been made to derive the above Equations (2)–(4).
The parameters
that appear in Equation (2) can be estimated by regression, assuming enough values of
are available. The preceding statement immediately justifies why plating methods for measurement of
are impractical for estimation of
: At least 10-20 data points would be needed for reasonable parameter estimates [
9,
10].
This limitation, posed by plating-based measurements, is overcome by the optical density-based methods discussed, which can routinely generate measurements every minute or so. However, as already mentioned, there measurements are of
rather than of
. To make measurements of
usable in parameter estimation, the following equation was derived [
29]:
when
, typical for time-kill experiments. (The full expression for
not far from
is shown in [
29].) In fact, it may be numerically simpler and conceptually insightful to use the following two differential equations (from which Equation (5) is derived for
) in parameter estimation based on measurements of
:
where
is the natural death rate of bacterial cells.
Equations (6) and (7) shed light to the nature of the parameter estimation problem:
First, estimates of can be obtained from a simple time-growth experiment () for which there is no drug-induced kill rate, i.e. and by default. Then, estimates of are reasonably well obtained from Equation (7), provided that can be estimated with reasonable accuracy. It is for this purpose that optical density-based measurements of at closely spaced points in time become crucial, as they allow a reasonably accurate estimation of , hence of via Equation (7), and finally of the parameters via standard regression using Equation (6).
Of the parameters estimated via the exercise just described, the one critical for dosing regimen design is
, the kill rate of the least susceptible (most resistant) subpopulation. (Note that in long enough time-kill experiments, Equation (3) immediately suggests that the average kill rate,
, quickly tends to
.) The importance of
stems from the fact that for complete eradication of a bacterial population exposed to a drug at concentration
it is necessary and sufficient that
i.e. the kill rate of the least susceptible bacterial subpopulation should be greater than the corresponding population growth rate (see Equation (5) and discussion in [
29]). The dependence of
on
is typically considered to follow the form of Equation (1), as shown qualitatively in
Figure 2, which depicts qualitatively a fit of Equation (1) to values of
estimated from time-kill experiments at distinct drug concentrations
It is noted that counterparts of Equation (1) can be fit to effective concentrations concerning multiple drugs, but this pharmacodynamics issue [
37,
38,
39] is beyond the scope of this paper. The outcome of fitting
to
is crucial for designing effective dosing regimens under clinically relevant pharmacokinetics, as will be discussed in the next section.
2.3. Dosing Regimen Design for Bacterial Eradication under Clinically Relevant Pharmacokinetics
The preceding discussion in
Section 2.1 and
Section 2.2 is concerned with pharmacodynamics (PD), i.e. the bactericidal effect of a drug at a certain concentration. This knowledge is one of the two fundamental components of pharmacology for antimicrobial therapy [
1]. The second fundamental component is pharmacokinetics (PK), i.e. the absorption, distribution, and metabolism / elimination of drugs. In this section we describe how pharmacodynamic information, as acquired by the approach described in the previous two sections, can be combined with related pharmacokinetics, for design of effective drug dosing regimens.
For periodic drug administration and subsequent elimination
Figure 3 shows a typical profile of drug concentration
.
The profile of
Figure 3 may produce one of the two outcomes shown in
Figure 4 for a homogeneous microbial population [
40].
It can be shown [
40] that outcome (a) of
Figure 4, i.e. elimination of a bacterial population by drug administration following the PK profile of
Figure 3, is predicted if and only if
for the least susceptible bacterial subpopulation.
Equation (9) is the main outcome of this section and can be used to
complete a dosing regimen design that ensures, with confidence, that
. It provides a direct link between PK and PD, as drugs with the same PD but different PK or with the same PK and different PD will generally result in different
, hence will require different dosing regimens to achieve similar bactericidal outcomes. A detailed investigation of this aspect is provided in [
40] and, in a broader context, in [
4]. Qualitatively, what one can expect when selecting
and
for a dosing regimen accommodating the PK of a drug with half-life
(
Figure 3) depends on all three parameters
and
of
(see Equation (1)). Of these parameters,
determines how sigmoidal
is (
Figure 5a) and ultimately whether the drug exhibits time-dependent or concentration-dependent behavior [
1]. The resulting
qualitatively follows the patterns shown in
Figure 5b,c, which provide link between PK and PD for corresponding drugs.