Controlled Human Infection Model Challenge/Rechallenge: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Controlled Human Infection Model Challenge/Rechallenge (NCT04992520), a non-randomized phase 1 study. The primary outcome is Percentage of Participants With Shigellosis Following Shigella Challenge.

2. Clinical Question

The study was designed to investigate Shigella immunity and cross-protection in a controlled challenge setting. It included sequences in which participants first received S. sonnei 53G and later could receive S. flexneri 2a 2457T, and sequences in the opposite order. Comparisons of veterans with naïve participants address whether prior exposure is associated with different illness rates after a later challenge. They do not, by themselves, establish that prior exposure caused any difference: prior exposure was not randomly assigned, and the comparison groups may differ in other ways.

3. Trial Design

The registry identifies this as a Phase 1, completed, non-randomized study with no masking and a crossover model. Its title describes a controlled human infection model challenge/rechallenge study. Enrollment was 46. The sponsor was PATH. The recorded study start was 2022-04-26 and primary completion was 2023-08-29.

Two challenge strains were used: S. sonnei 53G and S. flexneri 2a 2457T. The arm descriptions outline two directions of challenge sequence. In one, naïve participants received S. sonnei 53G; participants could later receive S. flexneri 2a 2457T. In the other, naïve participants received S. flexneri 2a 2457T; participants could later receive S. sonnei 53G. The described interval before the second challenge was at least 3 months. The challenge dose described for each strain was 1500 CFU.

The record also distinguishes veterans, who had received the other serotype first, from naïve participants. It describes newly recruited naïve participants in the later challenge groups as well as veteran participants undergoing rechallenge. These groups allow comparison of observed illness after challenge by prior challenge history, but the groups were not formed by random allocation. Differences in outcomes could therefore reflect group characteristics or study conduct as well as prior exposure.

The study was not masked. The record states that outcome data were evaluated by an independent, blinded adjudication board, which is a feature of endpoint assessment and does not make the overall study masked. The registry record does not report the rationale for the sample size, detailed recruitment procedures, or whether the crossover designation involved any additional design features beyond the described challenge sequences.

4. Participant Flow and Accounting

The registry reports how participants moved through each stage of the study. All counts below are exactly as posted; missing counts are not inferred from other stages.

Before assignment: Naive participants were challenged with either Shigella sonnei strain 53G (Group 1A) or Shigella flexneri 2a strain 2457T (Group 2A). Approximately 3 months later, participants who continued to meet eligibility criteria received a 2nd challenge with the other Shigella strain ("Veterans"). Additional naive volunteers were enrolled alongside the veteran participants receiving their 2nd challenge; both received the same challenge agent to allow a comparison of shigellosis rates across the groups.

Part A: First Challenge

Reasons for not completing this period:

Part B: 3 Months Later/Second Challenge

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: Per-Protocol Population included participants who received the challenge dose and had no major protocol violations that were determined to potentially interfere with the clinical assessment.

5. Baseline Characteristics

The table reproduces the baseline characteristics posted in the registry, which describe the participants analysed at baseline and help show whether the randomized groups were comparable.

Population: Baseline data for veteran participants who received a 2nd challenge (Groups 1B and 2B Veterans) are included in the relevant first challenge reporting group (1A or 2A).

Only the first 6 of 7 groups are shown.

6. Primary Endpoint

The registry lists the primary outcome as Percentage of Participants With Shigellosis Following Shigella Challenge, measured over 8 days after challenge administration (Days 1-8 and Days 90-97 for challenge 2).

The primary endpoint was the percentage of participants with shigellosis following a Shigella challenge. It was assessed during the 8 days after challenge administration: Days 1-8 for the initial challenge and Days 90-97 for challenge 2. The endpoint was defined using clinical criteria that combined stool frequency or stool weight, symptoms, fever, vomiting, and dysentery. Severe diarrhea could qualify on its own; moderate diarrhea or dysentery required specified accompanying symptoms or signs. The record also defines stool grades and states that an independent, blinded adjudication board evaluated outcome data.

This kind of composite endpoint is intended to capture clinically defined illness rather than a laboratory finding alone. Combining stool characteristics with symptoms and fever creates a prespecified rule for classifying shigellosis, which can make comparisons more consistent than relying on a broad, subjective impression of illness. The specific threshold rules matter: participants who do not meet the definition are not counted as cases for this primary outcome, even if they experience some symptoms. Secondary outcomes separately address features such as diarrhea severity, stool volume or weight, symptoms, dysentery, and time to diarrhea onset.

The primary outcome population was the Per-Protocol Population, defined as participants who received the challenge dose and had no major protocol violations that could potentially interfere with clinical assessment. The primary endpoint estimate, its confidence interval, and the analysis denominator are not reported in the registry record. Without those results, the posted record does not show the observed shigellosis rate for either challenge history.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

What does the primary percentage represent?

A percentage of participants with an event expresses how often the defined event occurred in a group, using the group’s relevant analysis population as the denominator. In this study, the event was shigellosis according to the clinical definition in the registry. A group percentage would need to be read alongside its denominator and the endpoint assessment window. Neither the primary group percentages nor their analysis denominators are reported in the registry record, so they cannot be interpreted or compared.

Why is the confidence interval important?

A confidence interval communicates uncertainty around an estimated quantity. In general, it helps distinguish a precise estimate from one compatible with a broad range of possible values. For a percentage or a difference between percentages, the interval should be considered alongside the estimate itself; it is not a guarantee about where the true value lies. The registry lists a 95% Confidence Interval for the primary endpoint, but does not report an interval or an estimate. Consequently, the precision of the primary comparison is not available.

Why does the non-randomized design matter?

Random allocation is a way to make comparison groups more similar, on average, with respect to factors known and unknown at the time of assignment. Here, allocation was non-randomized. The veteran groups had previously received the alternate strain, while naïve comparison participants had not previously been exposed to Shigella challenge; some naïve participants were newly recruited. Differences in age, prior health, study participation history, or other characteristics could be related to both group membership and outcome. The registry record does not report baseline characteristics or adjusted analyses, so the extent to which groups were comparable cannot be assessed.

General statistical principle: when treatment or exposure assignment is not random, an unadjusted difference between groups can reflect both the exposure of interest and pre-existing group differences. Adjustment can address measured factors if appropriate data and a justified model are available, but it cannot ensure control of unmeasured factors. The registry record reports 0 analyses, so no adjusted primary estimate is available to examine.

What does crossover mean in this study?

The registry labels the model crossover and describes two challenge sequences. Participants in one sequence could receive S. sonnei 53G first and S. flexneri 2a 2457T later; the opposite sequence began with S. flexneri 2a 2457T and could be followed by S. sonnei 53G. The interval described before a second challenge was at least 3 months. This design allows observation after a later challenge in participants with a prior challenge history. It also means that challenge order and prior exposure are relevant to interpretation. The registry record does not report a statistical model for repeated observations or a method for accounting for challenge order.

General statistical principle: repeated measurements on the same participant are usually related rather than independent. An analysis should account for that relationship when estimating uncertainty. The record does not report whether or how such dependence was handled, and no outcome analysis is posted.

How should the challenge endpoint be understood?

The endpoint is a binary classification: each participant either meets the registry definition of shigellosis in the stated assessment window or does not. Its definition combines stool frequency and weight criteria with associated symptoms, fever, vomiting, or dysentery criteria. An independent, blinded adjudication board evaluated outcome data. Blinded adjudication can help apply an endpoint rule without knowledge of relevant group information, although it does not change the non-randomized allocation or the open-label status of the study overall.

General statistical principle: a composite endpoint can capture several clinically relevant ways an event occurs, but interpretation depends on the components and thresholds. Two groups might have the same overall composite percentage while differing in the types of symptoms that led participants to meet the definition. The registry lists secondary outcomes that separately describe several illness characteristics, but their analysis results are not reported in the registry record.

What do the planning illustrations mean?

The registry describes planning illustrations based on the observed effect, with a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. The stated effect to detect is a fraction of the observed effect. These are planning illustrations, not observed power, and they are not the trial’s own design justification. In general, sample-size planning asks how many participants per arm would be needed under specified assumptions to detect a chosen effect with a chosen probability. Such an illustration depends on the effect assumption, variability or event rate, significance level, allocation, and analysis method. The registry record does not report the trial’s sample-size justification, and the primary observed effect is not reported, so the planning assumptions cannot be independently appraised from the outcome data.

General statistical principle: when the event is binary, the precision of a percentage depends in part on how many participants contribute outcome information and how frequently the event occurs. A planned sample size is not evidence that an effect was observed or that a study had a particular power after completion. The actual endpoint estimates and confidence intervals remain necessary for judging what the data show.

10. Exact Estimates for Each Arm

No two-arm comparison is shown for this trial, but each arm's result can still be summarized with exact interval estimates computed from the posted counts. The Clopper-Pearson interval is exact and conservative; the Wilson interval is a common closer-to-nominal alternative; the Bayesian credible interval uses a uniform Beta(1, 1) prior. For small groups the three can differ noticeably.

R code and output

arm    <- c("Group 1A: S. Sonnei 53G", "Group 1B: S. Flexneri 2a (Naive)", "Group 1B: S. Flexneri 2a (Veteran)", "Group 2A: S. Flexneri 2a", "Group 2B: S. Sonnei 53G (Naive)", "Group 2B: S. Sonnei 53G (Veteran)")
n      <- c(22, 5, 19, 12, 6, 10)
events <- c(13, 4, 3, 7, 5, 5)
for (i in seq_along(n)) {
  ci <- binom.test(events[i], n[i])$conf.int          # Clopper-Pearson exact interval
  cr <- qbeta(c(0.025, 0.975), 1 + events[i], 1 + n[i] - events[i])   # Bayesian, uniform Beta(1,1) prior
  wi <- (function(x, n) { p <- x / n; z <- qnorm(0.975); d <- 1 + z^2 / n
    c((p + z^2 / (2 * n) - z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d, (p + z^2 / (2 * n) + z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d) })(events[i], n[i])
  cat(sprintf("ARM|%s|%d|%d|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f\n", arm[i], n[i], events[i], 100 * events[i] / n[i],
              100 * ci[1], 100 * ci[2], 100 * wi[1], 100 * wi[2], 100 * cr[1], 100 * cr[2]))
}

ARM  Group 1A: S. Sonnei 53G  22  13  59.1  36.4  79.3  38.7  76.7  38.5  76.8
ARM  Group 1B: S. Flexneri 2a (Naive)  5  4  80.0  28.4  99.5  37.6  96.4  35.9  95.7
ARM  Group 1B: S. Flexneri 2a (Veteran)  19  3  15.8  3.4  39.6  5.5  37.6  5.7  37.9
ARM  Group 2A: S. Flexneri 2a  12  7  58.3  27.7  84.8  32.0  80.7  31.6  80.8
ARM  Group 2B: S. Sonnei 53G (Naive)  6  5  83.3  35.9  99.6  43.6  97.0  42.1  96.3
ARM  Group 2B: S. Sonnei 53G (Veteran)  10  5  50.0  18.7  81.3  23.7  76.3  23.4  76.6

11. Multiplicity, Missing Data and Analysis Populations

The registry lists 12 outcome measures, including the primary shigellosis endpoint and secondary outcomes related to stool volume and weight, diarrhea severity, symptoms, dysentery, and time to onset. It reports 0 analyses. Primary and secondary outcome estimates, statistical tests, confidence intervals, and analysis results are not reported in the registry record.

When a study assesses multiple outcomes, the chance of obtaining at least one apparently noteworthy result can increase if many tests are conducted. Statistical methods can address multiplicity through a prespecified hierarchy, adjustment, or other strategy. Whether any such strategy was planned or used is not reported in the registry record. The registry also does not report a testing hierarchy or identify which secondary outcomes were intended to support confirmatory conclusions. Without that information and without results, the relative evidential weight of any outcome cannot be evaluated.

The primary population is described as per-protocol: participants had to receive the challenge dose and have no major protocol violations judged potentially to interfere with clinical assessment. This defines the intended population for the primary endpoint, but the registry record does not report the number included in each endpoint analysis, exclusions, or the handling of participants with incomplete outcome data. Missing-data methods, imputation, and sensitivity analyses are not reported in the registry record.

These details matter because exclusions or missing outcomes can affect the observed percentage, especially if missingness or protocol violations are related to illness or group assignment. The record does not report interim analyses, stopping rules, or the statistical plan used for the primary comparison. They should not be inferred from the registry’s listing of outcome measures or planning assumptions.

12. Safety Results

The registry reports serious adverse events as affected participants divided by participants at risk.

Deaths

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 0% reporting threshold.

Most frequent non-serious adverse event terms

The registry reports serious adverse events as zero affected participants in each of the six listed groups, with zero deaths in each group. The numbers at risk were 22 in Group 1A: S. Sonnei 53G; 5 in Group 1B: S. Flexneri 2a (Naive); 19 in Group 1B: S. Flexneri 2a (Veteran); 13 in Group 2A: S. Flexneri 2a; 6 in Group 2B: S. Sonnei 53G (Naive); and 10 in Group 2B: S. Sonnei 53G (Veteran). The registry also lists 0 serious adverse events in each of those groups.

For other adverse events, the registry lists 22 affected participants among 22 at risk in Group 1A; 5 among 5 in Group 1B (Naive); 19 among 19 in Group 1B (Veteran); 10 among 13 in Group 2A; 5 among 6 in Group 2B (Naive); and 9 among 10 in Group 2B (Veteran). These are the registry’s group-level counts, not the primary shigellosis endpoint results. The top serious adverse event terms are not reported in the registry record. A zero serious-event count in these groups does not establish that no non-serious events occurred, and the other-event counts should not be read as a measure of severity or as a comparison adjusted for group differences.

13. What the Result Does, and Does Not, Mean

The registry record establishes that this completed Phase 1 study used two Shigella challenge strains and examined challenge sequences involving naïve and previously challenged participants. It specifies a primary endpoint based on the percentage meeting a clinical shigellosis definition during a stated follow-up window. It also provides group-level adverse event counts. However, the primary endpoint results and analyses are not reported in the registry record.

As a result, the posted results do not show whether the shigellosis rate was higher, lower, or similar among veteran participants compared with naïve participants. They do not quantify any association between prior challenge and subsequent illness, and they do not show how precise such an estimate would be. No conclusion about cross-protection can be drawn from the listed design and safety counts alone. The absence of a reported primary analysis is not evidence that there was no difference; it means the primary comparison cannot be evaluated from the record.

Even with results, the study’s non-randomized allocation would limit causal interpretation. A difference between veterans and naïve participants could be associated with prior challenge, but could also reflect differences between the groups. The registry does not report baseline characteristics or adjusted outcome analyses. The lack of masking applies to the study, while the independent, blinded adjudication board evaluated outcome data; that assessment feature cannot eliminate all possible bias.

In general, an estimate and its confidence interval are needed to understand both the size and the uncertainty of a comparison. Counts of serious adverse events address a separate safety classification and cannot substitute for the primary endpoint. The registry’s study setting is a controlled challenge in healthy adults in the United States; the record alone does not support conclusions about other populations or settings.

14. Why This Trial Matters Statistically

This study addresses a statistical question that is more specific than whether participants became ill after challenge: whether illness frequency differs according to prior challenge with another Shigella serotype. The two challenge sequences make prior exposure and challenge order central features of the comparison. Clear definitions of the veteran and naïve groups, the challenge strains, and the assessment window are therefore essential to interpreting any eventual estimate.

The primary outcome is a clinically defined binary event, with rules based on stool characteristics and accompanying symptoms. Such definitions turn a complex illness presentation into a reproducible classification for analysis. The independent, blinded adjudication board is relevant because consistent endpoint classification matters when comparing groups. At the same time, outcome definition and adjudication do not resolve the statistical limitations created by non-randomized allocation.

The record illustrates why results and design information must be read together. A group contrast would need its denominators, effect estimate, and confidence interval to convey both magnitude and precision. It would also need an analysis approach suited to the challenge sequence and any repeated observations. The registry reports 0 analyses, so these elements are not available for the primary endpoint. The posted record therefore documents a question and design, but does not provide the outcome evidence needed to answer that question.

Statistically, the most informative next step for readers would be a report of group-specific primary endpoint counts and estimates, with uncertainty intervals and a transparent account of the analyzed populations, missing data, and any adjustment or multiplicity strategy. Those details are not reported in the registry record. Their absence prevents a quantitative appraisal of cross-serotype differences, regardless of the study’s completed status.

15. Limitations

• The posted summary statistics are the only data these results rest on; patient-level data, full protocols and statistical analysis plans are not available.
• Recalculated results are simple, unadjusted calculations from posted summaries. They do not replace the sponsor's prespecified analysis.

The main limitation for interpreting the registry results is that the primary endpoint analysis is not reported. The record gives no shigellosis counts or percentages by group, no comparison estimate, and no confidence interval. Although the study is marked completed, completion status does not supply the missing outcome results.

Allocation was non-randomized, and masking was none. Veteran participants and naïve participants may therefore differ in ways that are related to outcome. The record does not report baseline characteristics, an adjusted analysis, or methods for accounting for those differences. Newly recruited naïve participants are also described, so the veteran and naïve groups are not necessarily directly comparable in study history or recruitment.

The challenge sequences involve two serotypes and a later challenge at least 3 months after the first. The registry does not report an analysis method for challenge order, repeated observations, or dependence between outcomes from the same participant. The endpoint uses a clinical composite definition, but the registry does not report component-level primary results that would show which criteria contributed to any cases.

The record lists 12 outcome measures but reports 0 analyses. It does not report a multiplicity strategy, handling of missing outcomes, interim analyses, or the statistical plan. The primary population is described as per-protocol, but analysis denominators and exclusions are not reported in the registry record. Finally, the study concerns healthy adults in the United States in a controlled challenge setting. The registry record does not establish how findings would apply beyond that setting, and, without the primary results, such generalization cannot be assessed.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Controlled Human Infection Model Challenge/Rechallenge — NCT04992520.
• Registry record last updated 2025-01-31; status last verified 2024-12.
• Results first posted 2025-01-31.
• Data retrieved from ClinicalTrials.gov on 2026-11-09.
• Group sizes, means, event counts and sponsor-reported p-values are reproduced as posted. Effect estimates, confidence intervals and p-values not attributed to the sponsor are independently calculated from the posted summary statistics.

19. Record Summary

NCT04992520 is a completed Phase 1, non-randomized, unmasked controlled human infection model study sponsored by PATH. Enrollment was 46. The study examined challenge and rechallenge with S. sonnei 53G and S. flexneri 2a 2457T, including veteran and naïve groups. A second challenge was described as occurring at least 3 months after the first.

The primary endpoint was the percentage of participants meeting the registry’s clinical definition of shigellosis during the stated post-challenge window. The outcome population was per-protocol, and outcome data were evaluated by an independent, blinded adjudication board. The registry lists 12 outcome measures and 0 analyses. Primary endpoint results and their confidence interval are not reported in the registry record. Serious adverse events and deaths were listed as zero in each group; other adverse event counts were also reported by group. The record supports describing the design and listed safety counts, but not estimating or interpreting the primary cross-serotype comparison.