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Princeton University Undergraduate Senior Theses, 1924-2023

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Catalog of Princeton University Senior Theses

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List of theses starting in 1926 written by seniors at Princeton University. Not all departments are represented. Princeton University network connected patrons may view most 2014 to current theses. 

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Senior Thesis

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Through their Senior Thesis, majors learn to identify interesting economics questions, survey the existing academic literature and demonstrate command of theoretical, empirical, and/or experimental methods needed to critically analyze their chosen topic.

All seniors are encouraged to browse the Senior Thesis Database for examples of past work.

To see examples of papers that won Senior Thesis Prizes, see this article about the Class of ’22 student winners.

Senior Thesis Coordinator Professor Alessandro Lizzeri [email protected]

Key Resources for Seniors

Senior Thesis Handbook Senior Thesis At-a-Glance Senior Thesis Advisors and Their Advising Interests Senior Thesis Proposal/Advisor Request Form Senior Thesis Advisor Assignments Senior Thesis Grading Rubric Exit form: Senior Thesis Research Integrity Form Exit form: Senior Thesis Advisor Evaluation Exit form: Departmental Survey

Senior Prizes

At the end of senior year, the department awards several prizes to acknowledge the best Senior Thesis projects from each class. Available awards are listed below.

• John Glover Wilson Memorial Award: Awarded to the best thesis on international economics or politics.
• Walter C. Sauer ’28 Prize (joint eligibility with Politics, SPIA): Awarded to the student whose thesis or research project on any aspect of United States foreign trade is judged to be the most creative.
• The Griswold Center for Economic Policy Studies Prize: Awarded annually to the best five policy-relevant theses.
• Burton G. Malkiel ’64 Senior Thesis Prize in Finance: Awarded for the most outstanding thesis in the field of finance.
• Elizabeth Bogan Prize in Economics: Awarded for the best thesis in health, education, or welfare.
• Daniel L. Rubinfeld ’67 Prize in Empirical Economics: Awarded for the best thesis in empirical economics.
• Hugo Sonnenschein Prize in Economic Theory: Awarded for the best thesis on economic theory.
• Wolf Balleisen Memorial Prize: Awarded for the best thesis on an economics subject, written by an economics major.
• Halbert White ’72 Prize in Economics: Awarded to the most outstanding senior economics major, as evidenced by excellence in departmental coursework and creativity in the Junior Paper and Senior Thesis.

Senior Thesis Advisor Selection Guide

Students should use this to identify thesis advisors who match their interests and possible thesis topics. This tool is organized by faculty issue and regional expertise.

Narrow your search for an advisor by selecting a policy area or region.

7 Princeton Traditions in My Last Semester

May 16, 2024, amélie lemay.

As a follow-up to my sophomore blog post about 7 traditions in my first on-campus semester , I now present to you 7 traditions from my final semester. 

1. Taking 3 courses + thesis

In the final semester, seniors generally take a lighter course load to have additional time to focus on the thesis. This spring I only took 3 courses plus the thesis (which counts as a course), giving me more time to focus on my project than when I have a typical 4-5 course load. This also gave me time for graduate school interviews, student visit days, and other tasks associated with planning for life post-Princeton.

2. Choosing a grad school program

Come March, I was notified of my acceptances to the different graduate school programs I'd applied to. In the fall, I'll be starting a doctoral program in Civil and Environmental Engineering at MIT working with Dr. Desirée Plata! Being able to share this news with my professors and letter of recommendation writers was exciting and rewarding.

3. Printing and binding my thesis

In mid-April, my thesis was wrapping up, and it was time for official printing and binding. Printing your thesis is optional, but it's traditional to present a leather-bound copy to your advisor. I chose to print my thesis and was incredibly proud to present the culmination of my project to Dr. Bourg.

4. Stepping into the Fountain of Freedom post-thesis submission

Following submission of the thesis, seniors will step into the Fountain of Freedom to officially mark the beginning of the mythical "PTL" (post-thesis life). The water wasn't very warm on the day after my department's thesis submission date (April 15), but I still honored the tradition by stepping into the water.

5. Wearing my class jacket

Formerly known as a " beer jacket ," to be worn by seniors at the Nassau Inn to protect their day clothes, the class jacket is now the de facto uniform for Reunions. The jacket prominently displays your class year, making it easy to spot your classmates among the masses of orange and black that flock to campus for Reunions each May. Our class voted on the design in the fall, and I'm really pleased with the final design.

6. Taking photos by the bronze tigers

Our class government offered free sessions with a pro photographer by the bronze tigers, and I also took photos of my friends myself. We brought numerous graduation props (thesis, class jacket, cap) to the session.

7. Walking through FitzRandolph Gate

At Commencement, I'll walk through FitzRandolph Gate for the first time since the class of 2024 Pre-Rade in my first on-campus semester. Legend has it that students who walk through the gates between the Pre-Rade and Commencement won't graduate in four years. All appears to be on track for me to officially receive my diploma on May 28, but I certainly won't be taking any chances between now and then.

And with that, my undergraduate experience at Princeton has come to a close! I've truly loved my time here, and I'll forever be grateful to Old Nassau.

Related Articles

Commencement commences, amor fati: embracing my path through princeton, plasa’s inaugural latine history series.

7 Princeton Traditions in My Last Semester

May 16, 2024, amélie lemay.

As a follow-up to my sophomore blog post about 7 traditions in my first on-campus semester , I now present to you 7 traditions from my final semester. 

1. Taking 3 courses + thesis

In the final semester, seniors generally take a lighter course load to have additional time to focus on the thesis. This spring I only took 3 courses plus the thesis (which counts as a course), giving me more time to focus on my project than when I have a typical 4-5 course load. This also gave me time for graduate school interviews, student visit days, and other tasks associated with planning for life post-Princeton.

2. Choosing a grad school program

Come March, I was notified of my acceptances to the different graduate school programs I'd applied to. In the fall, I'll be starting a doctoral program in Civil and Environmental Engineering at MIT working with Dr. Desirée Plata! Being able to share this news with my professors and letter of recommendation writers was exciting and rewarding.

3. Printing and binding my thesis

In mid-April, my thesis was wrapping up, and it was time for official printing and binding. Printing your thesis is optional, but it's traditional to present a leather-bound copy to your advisor. I chose to print my thesis and was incredibly proud to present the culmination of my project to Dr. Bourg.

4. Stepping into the Fountain of Freedom post-thesis submission

Following submission of the thesis, seniors will step into the Fountain of Freedom to officially mark the beginning of the mythical "PTL" (post-thesis life). The water wasn't very warm on the day after my department's thesis submission date (April 15), but I still honored the tradition by stepping into the water.

5. Wearing my class jacket

Formerly known as a " beer jacket ," to be worn by seniors at the Nassau Inn to protect their day clothes, the class jacket is now the de facto uniform for Reunions. The jacket prominently displays your class year, making it easy to spot your classmates among the masses of orange and black that flock to campus for Reunions each May. Our class voted on the design in the fall, and I'm really pleased with the final design.

6. Taking photos by the bronze tigers

Our class government offered free sessions with a pro photographer by the bronze tigers, and I also took photos of my friends myself. We brought numerous graduation props (thesis, class jacket, cap) to the session.

7. Walking through FitzRandolph Gate

At Commencement, I'll walk through FitzRandolph Gate for the first time since the class of 2024 Pre-Rade in my first on-campus semester. Legend has it that students who walk through the gates between the Pre-Rade and Commencement won't graduate in four years. All appears to be on track for me to officially receive my diploma on May 28, but I certainly won't be taking any chances between now and then.

And with that, my undergraduate experience at Princeton has come to a close! I've truly loved my time here, and I'll forever be grateful to Old Nassau.

Related Articles

Commencement commences, amor fati: embracing my path through princeton, plasa’s inaugural latine history series.

What Six Senior Music Majors’ Say About Their Theses

As the Spring semester concludes and in anticipation for the Class of 2024’s graduation, the Music Department asked six Senior Music Majors to expand on their creative theses and offer advice to future students preparing their own. The Music Department is proud to share the results of each Music Major’s cumulative work at Princeton, which highlights scholarly research and true mastery of their disciplines. 

Jared Bozinko

Thesis: SIN PHONY for two soprano clarinets, two auxiliary clarinets, two saxophones, and two horns

Jared:  In the process of writing  SIN PHONY , I found inspiration in seemingly twee places. Poulenc’s  Sonata for horn, trumpet and trombone,  Prokofiev’s  Romeo and Juliet , a 1995 clarinet quartet by Met Opera clarinetist Sean Osborn, and Ligeti’s  Six Bagatelles , a quirky wind quintet version of his  Musica ricercata .  SIN PHONY  is a chamber piece, technically an octet, for clarinets, saxes, and horns. My advisor, Dr. Dmitri Tymoczko, has been indispensable to the process, guiding me all fall semester in writing short chamber music sketches, which became the basis of the material that makes up my thesis. The process was so smooth and, at points, genuinely fun, and it was a great challenge as a composer to blend disparate thematic material from sketches written completely separately into cohesive, compelling music that had cohesion and let my compositional voice shine through.

Tanaka Dunbar Ngwara

Thesis: Paivapo ’76: A New Musical 

Tanaka:  My thesis was an original musical entitled Paivapo ’76 and set in Domboshava Zimbabwe in 1976, during the Zimbabwean Liberation War. The show deals with the conflict between traditional practice/spirituality and Christianity, and explores themes of community, first love and grief. I received the Alex Adam ’07 Award to conduct research for this project over the summer and since the musical also served as independent work for my theater and music theater certificates, I was able to premiere the piece on May 3rd, 4th and 5th in the Wallace Theater in the Lewis Center Complex. 

Thesis: Flung Into Space: A Collection of Songs

Nina:   My thesis is a collection of six songs titled  Flung Into Space . It consists of three story heavy songs about my life, along with an electronic counterpart for each which explores the same topic from a new perspective. 

Rupert Peacock

Thesis: John Farrant’s “O Lord Allmighty (ca. 1570):  The English Anthem at Ely Cathedral With Critical Edition

Rupert:  My thesis is a critical edition and history surrounding a piece of unpublished English choral music. The piece is called “O Lord Almighty” by John Farrant. I went to the library at Cambridge University and looked through manuscripts from Ely cathedral, which is about 10 minutes from where I live in the UK. I found lots of great and famous choral works, but stumbled across this piece by Farrant almost by accident. Professor Wendy Heller taught me everything I needed to know to get this done. She’s an expert in critical editions and this kind of research. I couldn’t have done it without her.

Molly Trueman

Thesis: Angels & Aliens: The Making of an Album

Molly:  For my thesis, I wrote and recorded my debut full-length album entitled  Angels & Aliens . Based around acoustic guitar and vocals, the album has an alternative indie-folk feel. This is a milestone I’ve been working towards for a few years now, so I’m incredibly grateful that this album ended up being my thesis.

Gabriela Veciana

Thesis: Breaking the Sound Barrier: Investigating Latine Racial Bias Through Reggaetón Music

Gabriela:  For my thesis, I researched colorism within Latine communities through reggaetón music. I knew I was interested in looking at identity and Latin music, but it wasn’t until I heard my advisor, Lisa Margulis, present her work in music cognition that I saw a potential connection with psychology fields. 

If you were to describe your thesis in one word, what would it be?

Jared :  Darksided (hehe)

Tanaka:  Fusion

Nina:  Honest

Rupert:  Difficult!

Molly:  Extraterrestrial

Gabriela:  Interdisciplinary!

What advice would you give to future seniors on creating a successful thesis?

Jared:  Don’t be afraid that your thesis isn’t going to materialize in time, instead, always try to remember just why you chose this amazing department, and to remember your likely lifelong personal devotion to music. There’s a lot to love about being able to share your art as the capstone of your work at Princeton. 

Tanaka:  If you can, use the thesis as an opportunity to work on something that you’ve always wanted to do, but never had the time to do! It’s amazing to have the excuse of a thesis project to give you the drive and space to complete it. 

Nina:  Try to start without judgement. The hardest part of writing my thesis was my own expectations of what my thesis should look like. 

Rupert:  It has to be something you care about and/or are passionate about. It got to the point where I was actually looking forward to the next steps in my thesis and enjoyed working on it. That was crucial for motivation!

Molly:  In terms of creating a thesis, my biggest piece of advice is to find a topic that you’re truly passionate about. Don’t settle for something you don’t care about.

Gabriela:  You don’t always have to have a topic and then find an advisor, you can start by finding an advisor you are interested in working with and craft your topic from there.

What are your plans after graduation?

Jared:  Still figuring it out, though I’m certain I want music to be a core component of my everyday life. I am trying to move to Philadelphia and get involved with their variety of music scenes, from DIY punk basement shows to chamber orchestras to early music groups. I also want to continue composing and am eager to hone my craft even further wherever I go. 

Tanaka:  I’m going to attend the Royal Academy of Music for Music Theater vocal performance! I’m very excited to be in a new city, and get to do another music degree in a conservatory.

Nina:  I’m moving to Nashville, TN and pursuing a career as a performing musician. I’ll also be releasing music soon as a part of the band Upwhirl, as well as later this year releasing my thesis. 

Rupert:  I am going to split my time between singing and construction!

Molly:  After graduation, I’m going to McGill University to study in the Sound Recording program.

Gabriela:  I hope to work in theater administration in New York!

In Other News

Student Perspectives: The Musical Odyssey of Princeton’s Adrian Thananopavarn

Jan 18, 2024

Adrian P. Thananopavarn ’24, Math major with certificates in Computer Science and Music Composition, premieres “March of Dusk” with Princeton University Sinfonia

How 3 Princeton Students Spend a Monday at the Royal College of Music

Dec 7, 2023

Dorothy Junginger ’25, Kyle Tsai ’25, and Audrey Yang ’25 are currently participating in Princeton’s immersive abroad program this semester at the Royal College of Music in London.

Music Major Kasey Shao Named 2024 Gilmore Young Artist

Sep 18, 2023

The Department of Music congratulates Kasey Shao (Class of 2025), a Music Major who is pursuing Minors in Piano Performance and Engineering Biology, who was one of two students named 2024 Gilmore Young Artists. We caught up with Kasey this summer following the official announcement to discuss how she found out she’d been selected, what she has planned for her 2024 Gilmore recitals and piano commission, and what’s on the docket for her final two years at Princeton.

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Inbox thesis memories and a missed opportunity.

I'm sure others will also point out that the photo on page 36 shows a machine for micro film , not micro fiche  (as indicated by the photo caption). Although I will acknowledge that when working on my thesis, I did look at some materials on a microfiche machine in Firestone. (Editor’s note: PAW has updated the caption above.)

To the extent I can remember it, like those quoted in the article, I recall working on my senior thesis as a history major as a rewarding experience (at least once it came to an end, following a short extension provided by the college after a problem at the computer center the day before they were due). What I wonder about, though, is what might have been if I had pursued a different topic.

At the beginning of senior year, I went to Professor James McPherson, who had not yet published Battle Cry of Freedom , about a research idea I had based on a project I had worked on the previous summer in the Firestone rare book room, organizing papers of a family that included a Civil War admiral — possibly the only member of the Virginia Lee family to have served on the Union side. But I had not taken any courses in Civil War-era history at Princeton, so he discouraged me from pursuing it.

If I had planned differently, I might have been able to engage with a topic that allowed for more in-depth work directly with conveniently located primary sources, possibly one of the first to work with those sources in any detail. But I was able to complete the work, got a decent grade and graduated, which is what mattered at that point in time.

Meanwhile, all the extra copies I made of my senior thesis for various family members have been coming back to me after the family members have passed on, so I now have several reminders of how I spent my senior year.

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An Integrated Approach to Rapid Diagnosis of Tuberculosis and Multidrug Resistance Using Liquid Culture and Molecular Methods in Russia

Yanina balabanova.

1 National Mycobacterium Reference Laboratory, Institute of Cell and Molecular Sciences, Queen Mary College, Barts and the London School of Medicine, University of London, London, United Kingdom

2 Samara Oblast Tuberculosis Dispensary, Samara, Russia

Francis Drobniewski

Vladyslav nikolayevskyy, annika kruuner, nadezhda malomanova, tatyana simak, nailya ilyina, svetlana zakharova.

3 Samara City Tuberculosis Service, Samara, Russia

Natalya Lebedeva

Heather l. alexander.

4 Foundation for Innovative New Diagnostic, Cointrin/Geneva, Switzerland

5 US Centers for Disease Control and Prevention, Division of TB Elimination, Atlanta, Georgia, United States of America

Rick O'Brien

Hojoon sohn, anastasia shakhmistova, ivan fedorin.

Conceived and designed the experiments: YB FD VN AK NM SZ NL HLA RO HS IF. Performed the experiments: YB FD VN AK NM TS NI SZ NL HLA HS. Analyzed the data: YB FD VN TS RO HS AS. Contributed reagents/materials/analysis tools: YB VN AK NM HLA RO HS IF. Wrote the paper: YB FD HLA RO.

To analyse the feasibility, cost and performance of rapid tuberculosis (TB) molecular and culture systems, in a high multidrug-resistant TB (MDR TB) middle-income region (Samara, Russia) and provide evidence for WHO policy change.

Performance and cost evaluation was conducted to compare the BACTEC™ MGIT™ 960 system for culture and drug susceptibility testing (DST) and molecular systems for TB diagnosis, resistance to isoniazid and rifampin, and MDR TB identification compared to conventional Lowenstein-Jensen culture assays.

698 consecutive patients (2487 sputum samples) with risk factors for drug-resistant tuberculosis were recruited. Overall M. tuberculosis complex culture positivity rates were 31.6% (787/2487) in MGIT and 27.1% (675/2487) in LJ (90.5% and 83.2% for smear-positive specimens). In total, 809 cultures of M. tuberculosis complex were isolated by any method. Median time to detection was 14 days for MGIT and 36 days for LJ (10 and 33 days for smear positive specimens) and indirect DST in MGIT took 9 days compared to 21 days on LJ. There was good concordance between DST on LJ and MGIT (96.8% for rifampin and 95.6% for isoniazid). Both molecular hybridization assay results correlated well with MGIT DST results, although molecular assays generally yielded higher rates of resistance (by approximately 3% for both isoniazid and rifampin).

With effective planning and logistics, the MGIT 960 and molecular based methodologies can be successfully introduced into a reference laboratory setting in a middle incidence country. High rates of MDR TB in the Russian Federation make the introduction of such assays particularly useful.

Introduction

Tuberculosis (TB) remains one of the leading causes of morbidity and mortality globally, focused principally, but not exclusively, in the non-industrialized world.

Timely diagnosis and prompt treatment of infectious cases are the key elements of the international effort to combat TB, providing cure of an individual patient and reducing the spread of TB by rendering infectious cases non-infectious.

Multidrug-resistant TB (MDR TB), i.e. resistance to at least isoniazid (Inh) and rifampin (Rif), and extensively drug-resistant TB (XDR TB), i.e. MDR plus resistance to amikacin, kanamycin or capreomycin and a fluoroquinolone, are the most problematic forms of resistance because treatment options are limited and the second-line drugs used for therapy are more toxic, less effective, more expensive, and must be administered for a longer period of time than standard first-line drug therapy [1] .

The highest rates of MDR TB in the world (approximately 10% in new and 25% in re-treatment cases), have been reported from the Baltic region and countries of the former Soviet Union [2] – [11] .

Conventional culture and DST on solid media is a slow process, and in high income, low-incidence countries these systems have been supplemented (or replaced) by automated liquid culture systems such as the Becton Dickinson BACTEC™ MGIT™ 960 system. Decreased time to detection, greater sensitivity than Lowenstein-Jensen (LJ) solid media, comparable sensitivity to the radiometric Bactec 460 system in detecting Mycobacteria in clinical specimens, and good concordance with both LJ and Bactec 460 DST for first-line drugs (FLD) have been demonstrated in several studies [12] – [16] .

Rapid molecular methods, including commercial or in-house DNA hybridisation or amplification methods [17] allow detection of TB and rifampin resistance (and, for some, assays isoniazid resistance as well) in clinical samples within 1–2 days [18] – [25] . Despite the demonstrated advantages, the limited data on the performance, role and value of rapid culture, DST and molecular detection systems, together with concerns of increased cost and contamination rates relative to conventional culture on solid media, have dampened interest and progress in implementing these systems in low to middle income settings. However, this situation is changing in response to the growing MDR TB epidemic and the recent WHO recommendations on the use of liquid culture and DST and line probe assays (LPAs) [26] , [27] .

This study describes the feasibility of introduction, diagnostic accuracy and costs of the MGIT rapid culture system for primary specimens and FLD DST, coupled with rapid molecular systems for TB culture identification and detection of resistance to isoniazid and rifampin in Samara, Russia, a middle income region with a high burden of MDR TB [5] , [9] , [28] . The project was undertaken with the intention (achieved) of producing evidence for the implementation of global health policy changes relating to TB diagnosis by the WHO.

Materials and Methods

Ethics statement.

The study was approved by the Samara Medical University Ethics Committee. The study received a waiver of informed consent because the study used samples that were routinely collected for use in approved routine tests on LJ media. The tests on the MGIT 960 system were performed in parallel with the approved routine tests on LJ media. All aspects related to culture and phenotypic DST were reviewed and approved by the U.S. Centers for Disease Control and Prevention as non-human subjects research which does not require informed consent.

Setting and Design

A programmatic intervention and evaluation was conducted to compare the feasibility, utility and performance characteristics (recovery rates, time-to-detection) of the MGIT culture and DST system (Becton Dickinson, Sparks, MD) and rapid molecular systems to conventional standard reference LJ-based assays in patients at high risk of MDR TB in the central TB laboratory of Samara Region (Category 3 level facility), Russia Federation. The study was preceded by development of an agreed customer support plan that included installation and maintenance of the BACTEC™ machine as well as an uninterrupted supply of reagents needed based on reduced pricing policy offered for Samara. Principles outlined by the Standards for the Reporting of Diagnostic accuracy studies (STARD) for diagnostic accuracy studies were followed.

Prior to implementation into routine practice, MGIT and molecular methods were quality controlled and validated by the Health Protection Agency National Mycobacterium Reference Unit (HPA NMRL) according to the WHO/IUATLD Supranational Reference Laboratory (SRL) proficiency testing criteria [29] using a panel of defined M. tuberculosis cultures provided through the WHO SRL mechanism. Once the laboratory achieved pre-determined minimum standard efficiency levels based on WHO/IUATLD Supranational Reference Laboratory proficiency testing criteria for performance [29] of 80% (E and S), 89% (Inh), and 95% (Rif) in performing MGIT DST, MGIT and LJ culture and FLD DST were performed in parallel and all results were made available to clinicians. All staff was formally trained in bacteriological and molecular methods. Staff performing molecular assays was blinded to culture results and both were blinded to epidemiological data. This study also evaluated the detailed costs associated with the introduction of MGIT for TB culture diagnosis and DST in comparison with conventional methods on solid LJ media.

Patient Population

Patients were enrolled from 8 TB clinics in Samara Oblast that are part of a specialised service which provides diagnostics and treatment for TB patients only. The clinics verify the diagnosis for patients referred by the general health care sector after initial screening with a high suspicion for TB. All confirmed or suspected pulmonary TB patients who were sputum smear-positive and/or at high risk for MDR TB (individuals with prior TB treatment, persistent smear-positivity after 3 months treatment and/or poor clinical improvement, relapse, default, repeated treatment interruptions, contacts of patients with confirmed MDR TB, homeless persons and former prisoners) were included.

Patients were excluded if they were currently receiving TB treatment and smear-converted or remained smear-negative, were known to be infected with an MDR TB strain, or were suspected of having extra-pulmonary TB without pulmonary involvement.

Enrolment commenced in April 2006 and continued through April 2008.

Specimen preparation and primary culture

At least three routine sputum samples were collected from each patient into 50 ml screw-cap centrifuge tubes (Falcon, Becton Dickenson, USA) prior to treatment initiation as well as during treatment as follow-up control samples. Sputum samples were sent daily from the clinics to the laboratory; specimens were stored at 4°C until processed.

Specimens were processed using the NaOH-NALC method [30] employing the Becton Dickinson MycoPrep™ kit as described by the manufacturer. The final concentration of NaOH (1.0% w/v) was determined during the validation phase to maintain contamination rates below 8–10%. Concentrated specimens were stained for the presence of acid-fast bacilli (AFB) according to the Ziehl-Nielsen method [31] .

All processed specimens were immediately inoculated on both MGIT (0.5 ml inoculum) and LJ media (0.2 ml inoculum).

The MGIT 960 was checked daily for positive and negative cultures and LJ cultures were checked at least weekly. Although this standard approach carried an observation bias for time to detection of positive cultures, it followed the accepted practice of periodic visual scanning of LJ slopes reported in all previous published studies of the MGIT and comparable systems and LJ culture. Tubes flagged as positive by the MGIT 960 instrument were examined visually for potential mycobacterial growth and growth was inoculated onto a blood agar plate, subcultured on an LJ slant and MGIT for DST, and an AFB smear was prepared.

Isolate identification

Cultures were identified as M. tuberculosis complex (MTC) according to colony morphology, microscopic appearance, and standard biochemical assays, as specified in the Russian Federal guidelines [31] .

Molecular tests also were used to decrease the time to identification of MTC. Previous studies suggested that liquid culture systems would increase the isolation of non-tuberculous mycobacteria (NTM) as well as M. tuberculosis [32] . Therefore, 327 consecutive mycobacterial cultures initially isolated on the MGIT 960 system were identified to species level using the GenoType® CM assay (Hain Lifesciences GmbH, Nehren, Germany).

First Line drug susceptibility (DST)

The drug concentrations used in the MGIT system were (µg/ml): streptomycin (S): 1.0; isoniazid (Inh): 0.1; rifampin (Rif): 1.0; ethambutol (E): 5.0; pyrazinamide (Z): 100.0 [31] , [33] . DST on LJ was performed according to the absolute concentration method, utilizing the following drug concentrations (µg/ml): S: 10.0; Inh: 1.0; Rif: 40.0; E: 2.0 [31] . Sensitivity to pyrazinamide is not routinely tested on LJ media according to Russian Federal guidelines [31] .

As the majority of isolates were MTC (see Results ), subsequent cultures were identified using an in-house macroarray, as described elsewhere [34] and/or a commercial “line probe” assay system for MTC identification and rifampin and isoniazid resistance (GenoType® MTBDR plus , Hain Lifesciences GmbH, Germany). Both systems employed the same basic principles i.e. polymerase chain reaction (PCR) amplification of relevant regions of genes including the katG and rpoB genes and inhA promoter region, followed by reverse phase hybridisation to probes immobilised on a solid phase membrane.

Cost analysis

All laboratory procedures for both LJ and MGIT culture and DST were broken down into their component parts and a detailed time-and-motion study was conducted [35] – [37] . Total salaries, consumables costs, and capital (including equipment) infrastructure costs, maintenance, administrative and overhead costs of the laboratory, as well as transport costs were included in the final analysis.

Prices were converted into US dollars (USD) for this analysis. International pricings for all relevant laboratory resources and consumables for our study were based on published manufacturer suggested retail prices (MSRP) in developed countries such as the US. For local price analysis, procurement pricings specific to Samara with exceptions to MGIT instrumentation and consumables (for which we used the FIND-Becton Dickinson (BD) negotiated price available in 2006) were used. The usage of equipment, reagents, and laboratory space were quantified as minute used per square meter of space and minutes used. Overhead costs were calculated and allocated based on time-observation data particular to building space and staff utilization for each laboratory procedures included in our cost analysis.

Statistical analysis

All data were obtained from records collected by the clinical and laboratory staff and entered in a password protected stand-alone database to maintain confidentiality.

Statistical analysis was performed using the SPSS version 15 package (SPSS, http://www.spss.com ). The difference between rates among different groups was assessed using chi-test (χ 2 ).

In total, 698 consecutive patients were recruited into the study and 2545 sputum samples were subjected to bacteriological examination on both LJ and MGIT media.

Initially, the MGIT 960 system yielded increased rates of culture contamination but rates were quickly lowered to 3.4% by meticulous adherence to the manufacturer's manual and protocols, and with rapid transport and/or refrigeration of samples. The samples collected from patients were immediately refrigerated and stored at +4 for a maximum time of 48 hours prior to decontamination and culture. All samples from participating study sites were transported in cool bags. Sterility checks of water, buffer and NALC solutions and disposables consumables (such as washes from sputum containers, cryovials and laboratory tubes used) were regularly run using blood agar plates. Negative controls of each batch of MGIT tubes and daily logs of all ready-made solutions were used to monitor any potential manufacturer's contamination. In order for any increased culture speed to be valuable, a rapid molecular identification method was essential to identify culture growth in 1 day; this also permitted TB identification in bacterially-contaminated cultures (data not shown). A proportion of cultures was also spoligotyped to exclude cross-contamination within the laboratory.

Of the first 327 consecutive patients with positive mycobacterial isolates, the applied GenoType® Mycobacterium CM assay demonstrated that the vast majority (96.6%) of isolates were M. tuberculosis complex ( Figure 1 ). Subsequently, molecular methods were used to test all subsequent isolates simply for the presence or absence of MTC. Since very few NTMs were isolated, this paper presents results for MTC only. The overall MTC culture positivity rate for MGIT and LJ was 31.6% and 27.1% respectively (χ 2  =  11.9, p = 0.001); for smear positive specimens it was 90.5% and 83.2% (χ 2  =  8.6, p = 0.003) and for smear negative specimens, 20.4% and 16.4% respectively (χ 2  =  10.7, p = 0.001) ( Table 1 ).

The overall proportion of the total MTC isolates (number confirmed positive cultures by MGIT or LJ/total number positive cultures by either method) which were positive by MGIT was 97.2% (786/809) compared to 81.1% (656/809) for LJ. Of all culture positive specimens, 99.2% of smear-positive and 95.5% of smear-negative specimens were positive by MGIT while LJ recovery rates were 90.9% for smear-positives and 73.2% for smear-negative specimens. The concordance of results between the two systems was high for isolating MTC (92.7%) ( Table 2 ).

(+) positive test, (−) negative test.

Among culture positives, the overall median time to detection of M. tuberculosis complex was 14 days and 36 days for MGIT and LJ, respectively. Indirect DST from isolates took an additional 9 days in MGIT and 21 days on LJ. Therefore, providing a rapid molecular identification method is available that takes 1–2 days to perform as in the case of the GenoType® MTBDR plus method and comparable methods such as in house in situ hybridisation methods [34] , [38] the overall turn-around time can be as short as 25 days for MGIT vs approximately 60 days for LJ ( Figure 2 ).

Comparative phenotypic DST data for both methods ( Table 3 ) on all bacteriologically confirmed TB strains demonstrate approximately 63%, 50%, 27%, 60%, and 10% of the patients were resistant to isoniazid, rifampin, ethambutol, streptomycin, and pyrazinamide, respectively. Approximately 50% of cultures were MDR TB and nearly all rifampin-resistant isolates (98.7% and 100% detected by LJ and MGIT, respectively) were MDR TB. There was good concordance between the results obtained by the LJ and MGIT methods ( Table 4 ) with agreement of 96.8% for rifampin, 95.6% for isoniazid but only 91.9% for ethambutol and for 89.5% for streptomycin.

* for cultures, on which DST results were available from both methods; 11 MGIT and 9 LJ subcultures were contaminated across all four drugs.

The overall Inh, Rif and MDR resistance rates in the population as determined by the in-house macroarray (65.7%, 54.6% and 51.0% respectively) and the Hain methods (66.6%, 54.8% and 53.2% respectively) were comparable.

There was good concordance for isoniazid and rifampin resistance between the commercial and in-house low-density array-based methods (88.5% and 80.7% for macroarray and 87.3% and 77.9% for Hain; 87.6% and 84.9% for macroarray and 84.4% and 82.2% for Hain respectively) compared with the MGIT culture or LJ systems The sensitivity and specificity of both methods when compared to either culture system were high: almost 93% and 94% for detection of isoniazid and approximately 87% and 94% for detection of rifampicin resistance against the MGIT system; approximately 92% and 93% for isoniazid and 90% and 93% for rifampicin against the LJ system respectively ( Tables 5 – 6 ).

MA-macroarray method; Hain - GenoType® MTBDR plus method (Hain Lifesciences GmbH, Germany).

Where R-resistant and S-sensitive, 1 – by the test method (Hain or Macroarray), 2 – by the reference method (MGIT).

Where R-resistant and S-sensitive, 1 – by the test method (Hain or Macroarray), 2 – by the reference method (LJ).

Compared to the LJ method, MGIT culture was consistently more expensive than LJ regardless of pricing levels but the difference was small ( Table 7 ). However, the FIND-BD pricing agreement brings about a 40% reduction in overall costs for screening one specimen for full first line DST with MGIT at $32 as compared to $56 for full catalogue pricing. LJ methodology costs ranged from $17 to $20 in Samara and international prices; if only isoniazid and rifampin resistance was tested the equivalent costs for Samara and internationally were $13 and $15 for LJ and $17 and $28 for the MGIT system.

≠ Macroarray steps include all steps from DNA extraction to reading/reporting of the results.

Int'L – international prices.

NA – not applicable.

The cost of performing the in-house method (macroarray) in Samara was calculated based on local wages and overhead costs: the overall average unit cost of the macroarray test was at about $15 per specimen. The total chemical and reagent components of the test was between $5–6 per specimen ( Table 6 ). The test-strips used for this method were produced at the HPA MRU, London; more detailed assessment of the total assay costs when produced in Russia is needed and is subject of another on-going study.

The costs of the GenoType® MTBDR plus assay were not assessed within this project.

This study describes the performance characteristics of rapid liquid culture (MGIT 960) and molecular assays for the identification of MTC, rifampin, isoniazid and MDR TB as well as costs of the MGIT 960 system when introduced into Samara, a region within the Russian Federation with high rates of drug resistance and MDR TB [11] .

The MGIT 960 method was quickly taken up by the staff and successfully introduced into practice in an escalating manner from primary culture to DST. An initially high contamination rate was lowered to 3.4% within a month of initiation of the project by meticulous adherence to manufacturer's instructions, use of standard protocols as well as a well-developed system of rapid sample collection and transport logistics. Coupled with high recovery rates, it demonstrates that decontamination procedure was not overly harsh and permitted adequate growth of mycobacteria while ensuring low contamination rates. A preliminary analysis presented here found that over 96% of positive cultures were M. tuberculosis complex, suggesting that frequent NTM isolation (as reported elsewhere [32] ) was unlikely to be a significant problem in this study population. This was probably due to the high proportion of smear-positivity and drug resistant TB among enrolled patients, lower HIV-positivity rates compared to African countries, and dominance of the Beijing family TB strains in the area. This strain family has been actively transmitted in the area and has a strong association with drug resistance [5] . Subsequent culture growth was identified using a second commercial rapid identification system and a non-commercial in house system for MTC, isoniazid and rifampin resistance which both employed the same principle of PCR amplification coupled with a reverse phase hybridisation detection system.

As reported in high-resource, low-TB incidence settings, a greater proportion of positive cultures from primary specimens grew in the MGIT system primarily due to increased culture sensitivity for smear-negative specimens.

The median time for culture isolation was significantly faster for the MGIT 960 compared to LJ at 14 days versus 36 days for all specimens in agreement with other international studies mainly from low incidence [32] , [39] – [42] .

The proportion of drug resistance was very high in the studied population – almost half of the isolates were MDR TB. Mono –resistance to rifampicin was very rarely seen and nearly all rifampin-resistant isolates were MDR TB suggesting that rifampin resistance may serve as a reliable surrogate marker for MDR TB in this population. The median time to obtain DST results from positive cultures was faster with the MGIT system at 9 versus 21 days for LJ based methods in line with previously published works mainly from countries with lower levels of drug resistance [43] . Therefore introduction of the MGIT method can significantly decrease the overall turn-around time to 25 days comparable to data reported elsewhere [44] ). However, within the project framework the turn-around-time for positive cultures and DST ranged from 13 to 87 days with a median of 38 days for the MGIT. Delays occurred due to logistical problems during the introduction of the MGIT system into routine use (e.g. reagents supply), training of additional personnel, contamination and delays between receiving a culture and subculturing for DST. One of the advantages of using the MGIT system was an opportunity to reliably determine sensitivity to pyrazinamide. This test is not routinely performed on LJ media in Russia due to the lack of standard protocols and variable standardization recommended on the national level.Although the MGIT system generated all FLD DST results more rapidly than the LJ methodology, the molecular methods provided results for isoniazid and rifampin resistance within one day. Another study performed in the same setting of the Samara Regional Tuberculosis Laboratory presented evidence for efficient use of molecular assays (GenoType® MTBDRplus) directly on smear-positive sputum samples [45] . The current study demonstrated that concordance of the commercial and in-house molecular methods for isoniazid and rifampin resistance was high, with very close but not complete agreement for isoniazid and rifampin resistance between the molecular and MGIT defined DST results. These methods could be implemented as an initial screen for MDR TB (directly on smear-positive samples or on mycobacterial cultures isolated from smear-negative samples), permitting the institution of infection control measures at an earlier stage, as well as more rapid provision of appropriate treatment in line with recent WHO recommendations that were developed with the support of the Samara project data [26] . The presence of mutations indicating resistance could be used as an indicator for simultaneously initiating first- and second-line resistance testing in MGIT, which could significantly reduce the delay in administering an appropriate drug regimen to an MDR TB (or XDR TB) case.

The economic analysis demonstrated that although the MGIT culture system was slightly more expensive than the LJ method ($12 versus $11 respectively), it would permit earlier diagnosis of TB and prompt treatment initiation (a reduction in median culture time of 22 days).

Similarly MGIT FLD DST was more expensive than LJ FLD DST ($56 versus $20 using international prices) but the difference allowed a significant decrease in diagnostic turn-around time resulting in earlier identification of drug resistance, including MDR TB, especially when FLD and SLD DST are set up simultaneously for isolates which were diagnosed as having mutations to rifampicin and isoniazid by molecular methods. Coupled with molecular systems for rapid identification and drug resistance detection, this would have a significant impact on a timely administration of an adequate treatment regimen and potentially improve treatment outcomes. Administration of timely therapy will render an individual non-infectious and interrupt transmission; molecular methods and/or MGIT based DST identify the many patients who have MDR TB (who will not be rendered non-infectious by standard TB therapy and so will continue to transmit MDR TB) and culture –based phenotypic methods are the only way of reliably identifying the antimicrobials that are able to render MDR TB individuals non-infectious.

This demonstration project provided much of the evidence underpinning the diagnostic policy changes relating to bacteriological culture adopted by the WHO in 2007-8. Currently WHO recommend the routine use of TB liquid culture and DST even in resource-limited settings to improve diagnosis of TB in general, MDR TB and smear-negative pulmonary TB including application of a rapid method of species identification [27] . The higher cost of the automated liquid culture media systems is currently being addressed by the manufacturers by introducing changes into the pricing policy for the public sector in lower income countries. This project showed that it is possible to successfully introduce this technology into resource-constrained settings but that to achieve satisfactory implementation and performance of the MGIT system (which is more prone to bacterial contamination due to the greater sensitivity of liquid media for culture of mycobacteria as well as other microorganisms compared with solid culture and for DST which is more complex to perform that using solid culture) key issues needed to be resolved. These include: (1) availability of appropriate Category 3 level laboratory infrastructure including an agreed maintenance plan for the BACTEC system; (2) repetitive on-site training of laboratory personnel in MGIT methodology (using detailed SOPs and the system manual) and molecular methods to create a multi-skilled cadre of staff; (3) initial expert observation of the performance and implementation of internal and external quality control of laboratory work; (4) development of effective logistics for timely collection, storage and transport of fresh sputum samples to the laboratory as well as the reporting of results; (5) the creation of algorithms for laboratory work flow and computerized laboratory record keeping; (6) timely maintenance of equipment and ensuring a safe continuous supply of reagents by establishing a commercial contract with a manufacturer and (7) introduction of a robust stock control system.

For these diagnostic culture systems to have a maximum therapeutic impact there must be rapid identification of cultures with the ability to analyse first and second-line DST phenotypically when molecular tests demonstrate the presence of mutations encoding rifampin (and possibly isoniazid) resistance in the original patient specimen or the resulting culture. This will significantly reduce the time between sputum collection and full susceptibility testing for MDR TB cases. Addressing timeliness in technological improvement should go in tandem with minimizing organizational delay. Clinicians need to make prompt therapeutic changes following rapid DST analysis.

With effective planning and logistics, an adequate decontamination protocol and careful training, the MGIT 960 and molecular-based methodologies can be successfully introduced into a reference laboratory setting in a middle TB incidence country. The high rates of MDR TB in the Russian Federation make the introduction of such assays particularly useful and are likely to translate to other settings with a high level of drug resistance or where the additional speed of diagnosis and increased diagnostic sensitivity are of value as in HIV associated tuberculosis.

Acknowledgments

The project was a close collaboration between the Samara TB service, the UK Health Protection Agency and Barts and the London Medical School, University of London, Hain Lifescience Gmbh and the Foundation for Innovative New Diagnostics (FIND).

We would like to thank Dr Olga Kurkina for help with participants' recruitment, Mrs Marina Korobova for performing a proportion of bacteriological work, Ms Olga Ignat'yeva and Ms Svetlana Mironova for performing molecular work on a proportion of isolates.

Competing Interests: The authors have declared that no competing interests exist.

Funding: The work was jointly funded by Foundation of Innovative New Diagnostics (FIND), Queen Mary College, University of London and Hain Lifesciences GmbH, Nehren, Germany. Neither Becton Dickenson Diagnostic Systems nor Hain Lifesciences GmbH had a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.