About

Brooke Nichols, PhD, MSc, is an infectious disease mathematical modeller and health economist specializing in transmission dynamics, implementation modeling, and optimal resource allocation for pathogens including HIV, tuberculosis, SARS-CoV-2, and other pathogens of pandemic potential. Her work seeks to minimize the health and economic impact of infectious diseases through innovative quantitative approaches. Dr. Nichols leads a multi-continental research team of quantitative scientists and modellers who integrate insights from clinical science, epidemiology, health economics, and mathematical modeling to develop actionable, evidence-based strategies. Her team advances novel quantitative methods and adapts existing frameworks to design cost-effective, scalable interventions aimed at reducing transmission, morbidity, and mortality. Their work has significantly influenced national and global health policies across critical public health domains, including contributing to evidence and normative guidance on HIV prevention and care, informing global strategies for diagnostics during the SARS-CoV-2 pandemic, and guiding the development of WHO’s Target Product Profiles for diagnostics.

Research topics

• Medicine
• Biology
• Geography
• Virology
• Demography
• Family medicine
• Psychology
• Environmental health
• Medical physics

Selected publications

• Global solidarity in genomic surveillance improves early detection of acute respiratory virus threats

  Nature Communications · 2026-01-13

  articleOpen access

  As genomic surveillance is key to detecting novel respiratory viruses or variants, the highly unequal global distribution of respiratory virus sequencing infrastructure raises concerns about preparedness for future threats. Using mathematical models and global epidemic simulations, we demonstrate that attaining a global minimum sequencing capacity of two sequences per million people per week at fortnightly sequencing regularity could reduce the time to first detection of novel respiratory (variant) viruses by weeks to months compared to global sequencing efforts during the COVID-19 pandemic, even with a substantially reduced number of viruses sequenced globally. Establishing this minimum global capacity could increase the time between the virus’ first global detection and the first domestic case in all countries, universally improving prospects for mitigation of potential public health impacts. Importantly, these benefits cannot be attained by siloed expansion in countries that already possess strong capacity. Our results show that operationalizing global health solidarity is key to guiding investment in health security. Respiratory virus genomic surveillance output is unevenly distributed globally. Here, the authors show that addressing this imbalance could substantially reduce the time to first detection of novel (variant) viruses, enhancing surveillance effectiveness and efficiency.

  PublisherOA PDFDOI

• Defining the potential impact and cost-effectiveness of a non-invasive diagnostic for malaria: a modeling study

  medRxiv · 2026-04-01

  articleOpen accessSenior author

  Abstract Background Malaria rapid diagnostic tests (RDTs) are widely used to detect and treat malaria infections, yet a diagnostic gap remains. With turnaround times of ∼15 minutes, RDTs may be too slow to enable broad-scale implementation in certain contexts. Novel non-invasive diagnostics (NIDs) have potential to provide faster (<5 minutes), sensitive (90% for symptomatic, 65% for asymptomatic carriage), and cost-effective alternatives, which may increase testing throughput, enhance case detection, guide appropriate antimicrobial use, and reduce waste by using fewer consumables. Their potential impact has yet to be investigated. Methods We modeled a country-agnostic population of 10 million individuals to assess the impact of population-level scale-up of four malaria testing strategies for active case-finding: 1) current practice (50% syndromic diagnosis and 50% RDTs), 2) full RDT scale-up, 3) full NID implementation, and 4) NID screening plus confirmatory RDT, using a decision-tree model of the malaria diagnostic and care cascade. We varied prevalence (0.02–0.25) and proportion of cases with symptoms (0.05–0.60) to evaluate strategy performance across epidemiological contexts. We investigated case detection rates, antimicrobial use, incremental cost-effectiveness ratios (ICERs) per disability adjusted life year (DALY) averted, net positive treatment outcomes, and threshold performance levels at which an NID would outperform RDTs. Results Full NID implementation (strategy 3) yielded the highest case detection rates (up to 85%), followed by strategies 2, 4, and 1 (45%, 38%, 36% respectively). NID-based methods (strategies 3 and 4) saved costs and RDT scale-up was cost-effective at averting DALYs compared to current practice (ICERs: $60–1,270). Despite high case detection, universal NID testing spiked unnecessary antimicrobial use. Overall, our results suggest that an NID with 55% asymptomatic sensitivity and 84% specificity, followed by RDT confirmation (strategy 4), could simultaneously improve case detection, reduce antimicrobial overuse, and limit costs. Conclusions This modeling analysis suggests that NIDs can sustainably optimize malaria case detection in symptomatic and asymptomatic cases and reduce costs, potentially making them a valuable addition to the diagnostic toolbox. When paired with confirmatory RDTs, they could help reduce inappropriate antimicrobial use, supporting drug efficacy amid rising resistance. Further research should assess their real-world utility, feasibility, and scalability for malaria surveillance and elimination efforts.

  PublisherOA PDFDOI

• Economic value of resistance-guided gonorrhea treatment: cost-neutrality thresholds for resistance test pricing in the United States

  medRxiv · 2026-04-07

  articleOpen access1st authorCorresponding

  ABSTRACT Background Rising antimicrobial resistance in Neisseria gonorrhoeae threatens the effectiveness of existing therapies. Resistance-guided treatment (RGT) may reduce treatment failures, complications, and inappropriate use of last-line agents while slowing resistance emergence. Methods and Findings We developed an individual-level stochastic simulation model of gonorrhea diagnosis and treatment in the United States, incorporating infection prevalence, symptom status, diagnostic accuracy, resistance profiles, treatment pathways, and partner management (costs in 2025 USD). We evaluated three resistance testing strategies, ciprofloxacin-only, ciprofloxacin+ceftriaxone, and triple-target (including a novel drug A), across a wide range of resistance scenarios. We quantified economic value across three dimensions: (1) per-episode direct medical cost savings, (2) system-level costs attributable to ceftriaxone resistance emergence among MSM, and (3) avoided costs of new antibiotic development, estimating the maximum per-test price at which RGT remains cost-neutral. Per-episode cost-neutrality thresholds ranged from near $0 when ceftriaxone resistance was absent to up to $45/test at 15% ceftriaxone resistance. At 50% ciprofloxacin and 5% ceftriaxone resistance, the population-weighted threshold was $4 (95% UI:$3-$8) for a CIP-only test and $11 (95% UI:$5-$14) for a triple-target test. Among MSM, incorporating system-level resistance emergence costs and avoided antibiotic development costs increased the total per-test value to $35–$145 for a single-target test and $84–$128 for a triple-target test, depending on whether prescribing practices shift when ceftriaxone resistance reaches 5%. Conclusions Resistance-guided therapy offers economic benefits across multiple dimensions even at relatively high diagnostic prices, supporting investment in gonorrhea resistance testing to improve partner outcomes, delay resistance emergence, and enhance the long-term cost-efficiency of gonorrhea management.

  PublisherOA PDFDOI

• Cost-effectiveness of Targeted Next Generation Sequencing for TB drug-resistance testing as an alternative to the standard of care in South Africa

  medRxiv · 2025-03-14

  preprintOpen accessSenior author

  Abstract Background South Africa faces emerging resistance to key TB drugs, including bedaquiline. Phenotypic drug susceptibility testing (pDST), the current reference standard for bedaquiline DST, while accurate has long turnaround times. Targeted next-generation sequencing (tNGS) offers a comprehensive alternative to pDST, potentially delivering faster results. However, its advantages must be weighed against differences in implementation cost and test accuracy. Methods We used a decision tree model to evaluate the cost-effectiveness of tNGS against the standard of care (SOC) in South Africa at different levels of tNGS decentralization (1, 3, 4, or 6 sites). Key outcomes considered were survival rates, time to a correct resistance profile, duration of infectiousness, and disability-adjusted life years (DALYs). Sensitivity analyses assessed the impact of drug resistance prevalence, tNGS sensitivity, and improved DST access on DALYs and incremental cost per DALY averted. Results tNGS averted 408 DALYs and returned a greater number of correct resistance profiles (90.7%) as compared to the SOC (87.7%). Based on model and scenario assumptions for South Africa, tNGS returned results with a reduced turnaround time and averted 96 years of infectious time. Centralized tNGS was determined to be cost-saving relative to the SOC, however decentralization of tNGS resulted in higher incremental costs per DALY averted ($671-$2,454). tNGS performance relative to the SOC improved at higher bedaquiline resistance prevalence and when tNGS sensitivity increased. Access gains through tNGS increased the number of DALYs averted and decreased the respective incremental cost per DALY averted for decentralized scenarios. Conclusions Centralized tNGS testing is likely to be cost-saving in South Africa and decentralised tNGS would result in higher costs but could be cost-effective under current assumptions. Additionally, tNGS has the potential to reduce DALYs, shorten result turnaround times, and decrease infectious duration while improving the percentage of individuals receiving correct DST results.

  PublisherOA PDFDOI

• National scale-up of etiological testing for <i>N. gonorrhoeae</i> and <i>C. trachomatis</i> in South Africa: a health economic modelling analysis

  medRxiv · 2025-10-13

  preprintOpen accessSenior author

  Abstract Background Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) remain highly prevalent in South Africa, where syndromic management is the standard-of-care (SOC) for sexually transmitted infections (STIs). However, syndromic management lacks diagnostic precision leading to both under-treatment and excess antibiotic use, which contributes to antimicrobial resistance (AMR). With a novel lateral flow assay (LFA) for NG approaching market entry and an extensive existing GeneXpert network in South Africa, there is an opportunity to shift towards etiology-informed management of STIs. Methods We developed a static cohort model to evaluate the health and economic outcomes of scaling up testing for NG/CT across symptomatic and opportunistic screening pathways in South Africa. Scenarios included syndromic management, GeneXpert testing, and hypothetical NG/CT point-of-care tests (POCTs). Outcomes assessed included cases treated, quality-adjusted life years (QALYs) gained, excess antibiotic use, and cost-effectiveness. Results Syndromic management produced the poorest health outcomes and highest antibiotic overuse. POCTs achieved the best health outcomes and were cost-effective compared to SOC, with an incremental cost-effectiveness ratio (CER) of US$1,083–$3,497 per QALY gained. GeneXpert, though dominated overall, could be considered cost-effective for testing of symptomatic women (Average CER: US$5,073). Diagnostic testing had the greatest benefit among women due to poor sensitivity of syndromic management. Opportunistic screening using a NG-only POCT during antenatal care, family planning clinics or HIV-related services was also found to be cost-effective. Conclusion Despite higher costs, etiological testing offers significant benefits over syndromic management— particularly for women—by improving diagnostic accuracy, reducing unnecessary antibiotic use, and supporting antibiotic stewardship. As South Africa considers introducing new treatments like zoliflodacin, investment in diagnostic testing is essential to preserve treatment efficacy and reduce long-term STI burden.

  PublisherOA PDFDOI

• Integrated multi‐month dispensing for HIV and hypertension in South Africa: A model of epidemiological impact and cost‐effectiveness

  Journal of the International AIDS Society · 2025-02-01 · 5 citations

  articleOpen access

  INTRODUCTION: In the current era of universal antiretroviral treatment (ART), health systems have the dual challenge of a growing number of people living with HIV and on ART who are also receiving chronic, life-long treatment for non-communicable diseases. Current evidence suggests that 6-month multi-month dispensing (6MMD) can maintain at least equivalent clinical outcomes to conventional care and reduce costs, but little is known when integrating 6MMD for multiple conditions. We examined the cost-effectiveness of integrated multi-month drug dispensing for people living with HIV and hypertension. METHODS: Using an age- and sex-specific hybrid decision tree and Markov state-transition model, we constructed a 100,000-person simulated population cohort who may develop HIV and hypertension and initiate treatment at clinics in South Africa over a 10-year time horizon. We assessed the incremental costs and effectiveness of 6MMD versus conventional care from a health system perspective under different conditions of care-seeking, eligibility and uptake of 6MMD for clinically stable patients. Model inputs were sourced from previously published literature. 6MMD was defined as reducing the frequency of clinic visits by increasing the number of medications dispensed to stable patients at each visit from 3 to 6 months. For the integrated 6MMD, we assumed that comorbid patients receive both HIV and hypertension drugs at the same facility on the same day. RESULTS: Our study demonstrates that integrated 6MMD for HIV and hypertension in South Africa can avert between 0.8 and 1 DALYs and increase health systems costs between $24 and $49 per patient per year, compared to the status quo. One-way sensitivity analysis showed that HTN drug cost and prevalence of HIVHTN and HIV were key drivers in the cost per DALYs averted. Overall, integrated 6MMD with a greater proportion of well-controlled patients and lower mortality rates led to greater cost savings or better cost-effectiveness (less than $50 per DALY averted) across a wide range of loss-to-follow-up (LTFU) factor variation. CONCLUSIONS: By better controlling disease among patients already in care, integrated 6MMD can be more beneficial than the status quo treatment by resulting in fewer cases of LTFU and fewer deaths through high-quality care.

  PublisherOA PDFDOI

• Prior antiretroviral therapy exposure among clients presenting for HIV treatment initiation in South Africa: an exploratory mixed-methods study using multiple indicators of exposure

  BMC Infectious Diseases · 2025-07-26 · 1 citations

  articleOpen access

  BACKGROUND: The era of universal treatment for HIV has seen high rates of disengagement from antiretroviral therapy (ART) programs and re-engagement after interruptions, with modeled estimates of non-naïve initiators > 50% in many places. Most re-engagers are reluctant to admit prior antiretroviral exposure, and non-self-reported data on proportions reinitiating are scarce. We conducted a sequential, mixed-methods study to explore the proportion of people who present for initiation with evidence of prior ART use and understand why many are reluctant to admit prior exposure in South Africa. METHODS: We enrolled a sequential sample of adults presenting to initiate ART or re-initiate ART after an interruption > 3 months and collected (1) self-reported previous treatment experience; (2) electronic medical record (EMR) evidence of prior ART clinic visits; (3) baseline blood tests for metabolites of tenofovir diphosphate; and (4) laboratory records indicating prior ART-related tests. Interviews were conducted with clients who self-reported no prior ART use but had evidence of metabolites. RESULTS: Among 89 enrolled participants (median age 32.5, 62% female), 21 (24%) self-reported previously taking ART > 3 months prior to enrolment. An additional 19 (21%) who did not self-report prior exposure had EMR or laboratory evidence of prior ART use, for a total of 40 (45%) clients with known prior treatment exposure at initiation. Sensitivity of self-report was 40% (95% CI: 25-57%), EMR 43% (27-59%), metabolite testing 45% (29-62%), and laboratory records 73% (56-87%). Interviewees (n = 11) reported opting to present as naïve because they perceived that disclosure of prior disengagement would cause delays accessing treatment, require additional documentation, and elicit negative responses from healthcare workers. Study limitations included short duration of metabolite detectability, inability to link individuals within the EMR to discern ART experience at other facilities, and lack of baseline viral load testing. CONCLUSIONS: At least 45% of clients initiating ART in South Africa have prior treatment experience, but only a third of re-initiators voluntarily reveal this. Laboratory records yielded the most accurate results for ascertaining prior treatment exposure. As numbers re-engaging in HIV care after a treatment interruption increase, understanding reluctance to self-report ART experience and exploring opportunities to overcome barriers are critical for preventing repeated interruptions. REGISTRATION: The protocol was registered on July 12, 2022 on clinicaltrials.gov (NCT05454839).

  PublisherOA PDFDOI

• Assessing feasibility and effectiveness of point-of-care limited HPV genotype tests in cervical cancer screening: a modelling study

  medRxiv · 2025-03-13 · 1 citations

  preprintOpen access

  Abstract Background Cervical cancer (CaCx) remains a significant cause of morbidity and mortality, especially among women in sub-Saharan Africa, where only 15% of women have undergone screening. To address these substantial screening gaps, the WHO recommends human papillomavirus (HPV) DNA detection as the primary screening method. One strategy to improve screening coverage is the use of limited HPV genotype target tests which can be offered as true point-of-care (POC) tests. However, understanding the conditions under which limited-genotype tests can compete with existing full genotype testing remains a barrier to their development and adoption. We explored the trade-offs between accessibility, retention, costs, and test performance to inform the development of new POC limited-genotype tests. Methods We developed a once-off HPV screening model to investigate the potential use-cases and required specifications of limited-target POC tests. We estimated the proportion of cases of cervical intraepithelial neoplasia grade 2+ (CIN2+) and the testing costs per case identified for three scenarios: (1) limited-genotype tests alone, (2) full-genotype tests, and (3) limited-genotype rule-in tests followed by full-genotype testing for those screening negative. We compared screening program performance across ranges of screening coverage, genotype target capture, loss to follow-up, and test price to identify the conditions where limited-genotype screening was non-inferior to full-genotype screening. Results When coverage and retention following full-genotype screening were high, limited-genotype tests were only competitive at a very low cost. However, with either modest increases (≥5%) in screening coverage or higher loss to follow-up after full-genotype screening (≥19.8%), an 8-target limited-genotype test could identify the same number of CIN2+ cases as full-genotype screening, but must cost &lt;US$8.50 to be cost-equivalent. Adding full-genotype testing following a rule-in 4-target test would be as effective as full-genotype screening in the number of CIN2+ cases identified; the limited-genotype test must cost &lt;US$2.20 to be cost-equivalent. Conclusions Our modeling supports screening with an 8-target limited-genotype HPV POC test priced at &lt;US$8.50 for cost-equivalence with full-genotype screening. A rule-in 4-target test will be cost-equivalent if priced at &lt;US$2.20. These insights can enhance CaCx screening access and support the goal of eliminating CaCx in sub-Saharan Africa.

  PublisherOA PDFDOI

• Patterns of engagement in care during clients’ first 12 months after HIV treatment initiation in Zambia: a retrospective cohort analysis using routinely collected data

  BMJ Global Health · 2025-08-01 · 3 citations

  articleOpen access

  BACKGROUND: The first year after HIV treatment initiation or re-initiation is the period of highest risk of a treatment interruption or disengagement, yet little is known about the timing, patterns and effects of interruptions in the early treatment period. METHODS: Using routinely collected electronic medical record data from 543 Zambian facilities from 2018 to 2023, we described patterns of engagement during the first year of HIV treatment. We defined engagement patterns for months 0-6 and months 7-12 after initiation or reinitiation as (1) continuous (attended all scheduled clinic and medication pickup visits as planned; (2) cyclical (attended ≥1 visits late >28 days but returned to and remained in care) or (3) disengaged (missed a scheduled visit by >28 days and had no evidence of return). RESULTS: Our sample population comprised 159 429 adult participants (61% female, median age 33). Of the 513 322 interactions observed ≤12 months after initiation, 53% occurred as planned, 22% were late ≤28 days late, 9% were >28 days late, and 17% were scheduled but never attended. In 0-6 months after initiation, 51% clients were continuously engaged, 12% cyclically engaged and 33% disengaged. Two-thirds of disengagers (21% of cohort) did not return after the initiation visit. During months 7-12, most clients who had been continuously engaged in months 0-6 (54%) remained continuous, while 18% moved to cyclical engagement. Among cyclical engagers in months 0-6, nearly half (47%) moved to being continuously engaged by month 12. Only 34% of the study population remained engaged continuously by the end of the 12-month period. CONCLUSIONS: Fewer than 60% of clients initiating antiretroviral therapy care between 2018 and 2022 at Zambian facilities remained continuously engaged at month 6 and 34% at month 12. Cyclical engagement and frequent interruptions should be accepted as the norm and models of service delivery designed to accommodate them.

  PublisherOA PDFDOI

• Evaluating the impact of differentiated service delivery (DSD) on retention in care and HIV viral suppression in South Africa: A target trial emulation using routine healthcare data

  PLoS Medicine · 2025-08-26 · 2 citations

  articleOpen accessCorresponding

  BACKGROUND: Replacing conventional, facility-based HIV treatment with less intensive differentiated service delivery (DSD) models could benefit DSD clients and the health system, but its value depends on maintaining or improving clinical outcomes. We compared retention and viral suppression between antiretroviral therapy (ART) clients enrolled in DSD models to those eligible for but not enrolled in DSD models in South Africa. METHODS AND FINDINGS: We applied a target trial emulation (TTE) methodology to data from South Africa's electronic medical record system (TIER.Net) for 24 public-sector health facilities across three provinces and estimated retention in care (attended facility visit within 12 months) and viral suppression (<400 copies/ml3) at 12, 24, and 36 months after follow-up start date, defined as DSD enrollment date for the intervention arm and the first trial enrollment period facility visit for the comparison arm. Clients were eligible for DSD models if they were ≥18 years old, on ART ≥12 months, and had two suppressed viral load (VL) measurements, per prevailing national guidelines. For the TTE, we designated eight 6-month target trial enrollment periods between 1 July 2017 and 1 July 2021. For each period, we estimated the risk differences for retention in care and viral suppression by comparing those enrolled in DSD models to those not enrolled, using a Poisson distribution with an identity link function. We report adjusted and unadjusted risk differences for clients enrolled in DSD models and for DSD-eligible clients not enrolled in a DSD model. Estimates were adjusted for age, sex, urban/rural facility setting, province, WHO stage at ART initiation, and years on ART at trial enrollment. 49,595 unique individuals were eligible for DSD enrollment over eight target trials, contributing to a total of 148,943 trial-clients, of whom 17% (25,775) were enrolled in DSD models. The pooled adjusted risk difference for retention in care between clients enrolled in DSD and those not enrolled in DSD was 3.2% (95% confidence interval (CI) [1.6%,4.7%]) at 12 months, 4.2% (95% CI [2.4%,6.0%]) at 24 months, and 4.4% (95% CI [2.0%,6.8%]) at 36 months. For viral suppression, the adjusted risk difference comparing DSD to non-DSD was estimated to be 1.4% (95% CI [-0.5%,3.2%]) at 12 months, 1.7% (95% CI [-0.5%,4.0%]) at 24 months, and 1.4% (95% CI [-0.6%,4.4%]) at 36 months. Results remained consistent across target trials. Clients who were younger, received care from a facility in an urban settings, or had less ART experience at trial enrollment had lower retention. Study limitations include reliance on routinely collected medical records and the likely presence of residual confounding. CONCLUSIONS: Clients enrolled in DSD models in South Africa had slightly better retention in care and similar viral suppression to those who were eligible for but not enrolled in DSD. With better or equivalent outcomes, DSD models can be assessed on the basis of non-clinic costs and benefits, such as changes in quality of care and resource utilization. TRIAL REGISTRATION: Clinicaltrials.gov NCT04149782.

  PublisherOA PDFDOI

Frequent coauthors

• Gesine Meyer‐Rath

  Boston University

  153 shared

• Lise Jamieson

  University of the Witwatersrand

  145 shared

• Sydney Rosen

  Boston University

  127 shared

• Colin A. Russell

  University of Amsterdam

  121 shared

• Lawrence Long

  Boston University

  105 shared

• Sheetal Silal

  University of Cape Town

  89 shared

• Alvin X. Han

  University of Amsterdam

  82 shared

• Sarah Girdwood

  Foundation for Innovative New Diagnostics

  75 shared

Education

• Ph.D., Viroscience

  Erasmus MC

  2015

• M.S., Epidemiology

  University of Massachusetts Amherst

  2010

• B.A., International Relations

  Mount Holyoke College

  2008