Detection of Borrelia Bacteria in Early Stage Lyme Borreliosis Using the T2Lyme Panel
Phase: NA
Conditions: Lyme Disease
Sponsor: T2 Biosystems

 
 
 
 
 
PRO-00879A Sample Collection Protocol 
Detection of Borrelia Bacteria in Early Stage Lyme Borreliosis 
 using the T2Lyme Panel 
 
 
 
 
 
 
 
 
 
 
Sponsor: 
 
T2 Biosystems, Inc. 
 
 
 
101 Hartwell Avenue 
 
 
 
Lexington, MA 02421 
 
Study Monitor: 
MDC Associates 
 
 
 
180 Cabot Street 
 
 
 
Beverly, MA 01915 
 
 
CONFIDENTIAL 
 
 
 
 
 

 
 
Document: PRO-00879A 
Revision #: 4.1 
 
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Protocol Title: 
Sample Collection Protocol for the Detection of Borrelia Bacteria in Early 
Stage Lyme Borreliosis using the T2Lyme Panel 
Protocol Number: 
PRO-00879A 
Revision Number: 
4.1 
Revision Date: 
October 1, 2018 
Sponsor: 
T2 Biosystems, Inc. 
 
101 Hartwell Avenue 
 
Lexington, MA 02421 
Study Monitor: 
MDC Associates, LLC 
 
180 Cabot Street 
 
Beverly, MA 01915 
 
Contact: Fran White 
 
Phone: (978) 927 3808 
 
Fax:      (978) 927 1308 
 
Email:   regulatory@mdcassoc.com 
 
 
 
FOR INVESTIGATIONAL USE ONLY 
Results obtained with this protocol are for use by T2Biosystems, Inc. Any other use, including 
publication, requires mutual consent of T2Biosystems, Inc. and the Investigator. The confidential 
information contained in this document is provided to you as an investigator, potential 
investigator, or consultant for review by you, your staff, and applicable institutional review 
committee. By accepting this document, you agree that the information contained herein will 
not be disclosed to others without written authorization from T2 Biosystems, Inc., except to the 
extent necessary to obtain informed consent from those persons who may be enrolled in the 
study. All information obtained during the course of this study will be regarded as confidential. 
 
 
 
 

 
 
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Table of Contents 
I. 
Study Overview 
 
 
 
 
 
 
 
4 
II. 
Intended Use 
 
 
 
 
 
 
 
4 
III. 
Study Timeframe  
 
 
 
 
 
 
4 
IV. 
Study Sites 
 
 
 
 
 
 
 
4 
V. 
Study Design 
 
 
 
 
 
 
 
5 
VI. 
Institutional Review Board (IRB) Approval 
 
 
 
8 
VII. 
Sample Collection Protocol 
 
 
 
 
 
8 
VIII. 
Data Collection 
 
 
 
 
 
 
 
11 
IX. 
Shipping  
 
 
 
 
 
 
 
12 
X. 
Withdrawn Samples 
 
 
 
 
 
 
12 
XI. 
Site File/Data Record Storage 
 
 
 
 
 
13 
XII. 
Risk/Benefit Analysis 
 
 
 
 
 
 
13 
XIII. 
Study Oversight 
 
 
 
 
 
 
 
13 
XIV. 
Confidentiality 
 
 
 
 
 
 
 
14 
XV. 
Protocol Departure 
 
 
 
 
 
 
14 
XVI. 
Protocol Approval  
 
 
 
 
 
 
14 
XVII. 
Protocol Revision History  
 
 
 
 
 
15 
 
Appendix I 
Sample Shipping Procedure 
16 
 
 
 
 
 
 
 
 
 
 

 
 
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I. 
Study Overview 
The objective of this study is to demonstrate the clinical performance of the T2Lyme 
Panel on the T2Dx instrument. The assay will be compared to Borrelia culture from 
erythema migrans (EM) biopsy and/or detection of the C6 antigen in serum collected 
prospectively from patients suspected of early Lyme disease demonstrated by EM 
lesion or constitutional abnormalities consistent with a tick bite and sickness from a 
tick bite. The data from this study will be used to support a de novo application for 
the T2Lyme Panel to the U.S. Food and Drug Administration (FDA) for product 
approval.  
 
The T2Lyme Panel is an investigational use in vitro diagnostic (IVD) designed to 
qualitatively detect and identify the major causative agents of Lyme disease (Borrelia 
burgdorferi, Borrelia afzelii, Borrelia garinii, as well as an inclusive Borrelia spp. 
detection channel) from K2EDTA human whole blood samples. 
 
This protocol (PRO-00897A) outlines subject enrollment, sample collection and 
shipping procedures. Samples collected will be shipped to defined laboratories for 
reference testing and sample storage.  
 
II. 
Intended Use 
The T2Lyme Panel is a qualitative T2 Magnetic Resonance (T2MR®) assay for the 
direct detection of bacteria species from EDTA human whole blood of patients with 
signs, symptoms and clinical history consistent with early Lyme disease. The T2Lyme 
Panel detects Borrelia spp., and specifically differentiates Borrelia burgdorferi, 
Borrelia afzelii, and Borrelia garinii. The T2Lyme Panel is used as an aid in the 
diagnosis of early stage Lyme disease. 
 
III. 
Study Timeframe 
The goal is to collect and test as many patients as possible in the initial Lyme season 
of 2018. If needed, study will continue into the 2019 season. 
 
IV. 
Study Sites 
Point-of-care site(s) including, but not limited to, physician’s offices, urgent care 
centers, hospital clinics/ER in areas endemic to Lyme disease will be contracted to 
collect required study samples. Sites will be contracted to recruit individuals 
suspected of having early Lyme disease in accordance with protocol defined 

 
 
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inclusion criteria. Trained collection site staff members or technicians will consent 
and enroll eligible patients prior to obtaining required samples.  
 
- Arm 1 
o The five (5) K2EDTA  tubes, single serum tube, and tissue samples collected 
at the study sites will be delivered by overnight express delivery to a single, 
defined laboratory for T2Lyme, serology and culture of tissue biopsy.  The 
reference laboratory will receive and document receipt of each sample.   
- Arm 2 
o Three (3) K2EDTA tubes and the single serum tube of blood collected at the 
study sites will be delivered by overnight express delivery to a single, defined 
laboratory for T2Lyme, serology and PCR testing. The remaining five (5) 
K2EDTA tubes collected will be delivered by overnight express delivery to T2 
Biosystems for blood culture studies. 
 
Sponsor may add additional sites as needed to complete study within needed 
timelines. All study staff members will be trained on study protocol, processes and 
study forms. Training will be documented. 
 
V. 
Study Design 
Patients meeting eligibility criteria will be consented for the study prior to collecting 
samples.  The study will consist of two arms; one in which subjects have a clinician-
documented erythema migrans (EM) lesion and a second arm where subjects do not 
have an EM, but present with an appropriate epidemiologic history and clinical signs 
and symptoms consistent with early Lyme disease.   
Arm I – Early Lyme disease with EM lesion 
All patients must be diagnosed by a clinician as having an EM lesion.   
PATIENTS MUST NOT HAVE RECEIVED ANY TREATMENT FOR LYME DISEASE WITHIN 
30 DAYS PRIOR TO STUDY PARTICIPATION.   
After obtaining informed consent, a trained staff member/phlebotomist will collect 
the following samples: 
- Five (5) 4mL K2EDTA vacutainer tubes 
- One (1) serum separator tube 
- Two (2) 2mm punch biopsies from the leading edge of the largest EM lesion 
NOTE: Every effort must be made to obtain two (2) 2mm punch biopsies. However, if only 
one (1) punch biopsy is available, participant will still be included in the study. 

 
 
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The collected samples will be sent to the reference lab for T2Lyme, culturing of 
tissue biopsy, PCR testing from tissue culture, and serology testing. 
Arm II – Early Lyme disease Without EM lesion 
All patients must be diagnosed by a clinician as having an appropriate epidemiologic 
history and signs/symptoms (excluding EM) of early Lyme disease  
PATIENTS MUST NOT HAVE RECEIVED ANY TREATMENT FOR LYME DISEASE WITHIN 
30 DAYS PRIOR TO STUDY PARTICIPATION.   
A trained staff member/phlebotomist will collect the following samples: 
- Eight (8) 4mL K2EDTA vacutainer tubes (three (3) additional tubes will be 
used for blood culture testing) 
- One (1) 5 mL serum separator tube 
Five (5) of the 4mL K2EDTA tubes will be sent to T2 Biosystems for blood culture. The 
remaining blood samples (3 K2EDTA tubes and one serum separator tube) will be 
forwarded to the reference lab for T2Lyme, PCR testing from whole blood, and 
serology testing. 
All Patients (Arm 1 and 2) 
After approximately 45-60 days, patients will return to the site to donate a 
convalescent serum sample.  Blood will be collected in one (1) 5 mL serum separator 
tube.  The blood sample will then be forwarded to the reference laboratory for 
serology testing. Appointment for this follow-up visit will be set and documented 
during the initial visit. 
All samples will be shipped in accordance with provided instructions to a single, 
defined reference laboratory for T2Lyme Panel and reference testing, with the 
exception of samples for blood culture, which will be forwarded to T2Biosystems.  
Sponsor may add additional sites as needed.  
An estimated 300 patients are expected to be enrolled with the goal of obtaining at 
least 40 samples from early Lyme disease patients with a culture-positive tissue 
biopsy sample or without EM that seroconvert appropriately. 
Each sample will be de-identified and assigned a specific study number that will 
designate which arm of the study they are enrolled in. Study numbers and labels will 
be provided to collection site(s) by the sponsor/study monitor. Study-associated test 
results will not be made available to patients. 

 
 
 
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See workflow below. 

 
 
 
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VI. 
Institutional Review Board (IRB) Approval 
The Principal Investigator (PI) at each study site will obtain IRB approval for the 
study protocol, consent form, and study-related documents. IRB approval will be 
received prior to beginning the study. 
 
VII. 
Sample Collection Protocol 
The collection site technician must review all eligibility criteria prior to enrolling 
subjects. The screening process will be documented.  The technician will review all 
relevant study information with the patient and answer questions. Informed consent 
(either by the subject or the subject’s legal representative) will be documented for 
every study subject. 
 
Arm 1:  
 
Initial Visit 
Subjects diagnosed with early Lyme disease by clinician documentation of an EM 
lesion.  NOTE: Subjects must have the rash confirmed as EM by a clinician.  
Examples of EM presentation include: 
 
 
- Red welts, sometimes with purple or blistered areas in the center 
- Gradually expanding lesion 
 
 
- Circular, sometimes with a bulls-eye shape 
 
 
- Central clearing 
 
Inclusion Criteria 
Presence of a single or multiple erythematous skin lesion(s), consistent with EM 
(Erythema migrans) is required for all patients in Arm 1. 
Subject is age 18 or older 
Subject or subject’s legal representative can read, comprehend and sign the study-
specific informed consent form (ICF) after the specifics of the study have been 
explained. 
Exclusion Criteria 
Subject has a bleeding disorder 
Subject is currently on antibiotics or has taken antibiotics in the past 30 days 
Subject has an EM located on the face or neck 
Subject is unable to provide informed consent 
 
 
 

 
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Collection of Punch Biopsies  
NOTE: Clinicians must make every effort to obtain two (2) 2mm punch biopsies from 
the leading edge of the EM according to standard laboratory practices. At least one 
(1) 2mm punch biopsy must be provided for inclusion in the study.  
1. Select the area to be biopsied.  The punch biopsies must be taken from 
the leading edge of the EM, including both derma and sub-derma.   
2. Take a focused, initial photograph of the EM. Any digital camera can be 
used, provided the photograph is clear and can be shared with the study 
monitor/sponsor. Include a subject ID label in the image. 
3. Sterilize the area and anesthetize according to standard laboratory 
practices. 
4. Stretch the skin surrounding the biopsy site with the thumb and index 
finger of the non-dominant hand. 
5. Holding the punch biopsy instrument vertically over the skin with the 
dominant hand, rotate downwards using a twirling motion. 
6. Once the instrument has penetrated the dermis, remove and transfer the 
biopsy sample  and place in pre-labeled tube containing culture medium 
(provided).    
7. Every effort must be made to collect a second 2mm punch biopsy. 
Identify a second site on the leading edge of the same EM, and follow 
steps 3-5. 
8. Take a second photograph of the EM post-biopsy. Include a subject ID 
label in the frame. 
9. Samples can be stored at room temperature, but must be shipped 
overnight to reference laboratory within 24 hours of collection.  
 
Collection of Blood Samples 
NOTE: Blood must be obtained by a trained phlebotomist. 
1. Pre-label five (5) (Arm I) 4 mL K2EDTA vacutainers and one (1) 5 mL serum 
separator tube with subject’s de-identified study ID. 
2. Disinfect the injection site and perform venous blood draw in accordance 
with institutional laboratory practices. 
3. Fill every vacutainer to the recommended amount. 
4. Invert the K2EDTA tubes 8-10 times to fully mix the anticoagulant with 
the blood. 

 
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5. Store blood samples 2-8°C until shipment to reference laboratory. 
Samples must be shipped overnight, on ice, within 24 hours of collection. 
 
Arm 2:  
Initial visit 
Subjects suspected with early Lyme disease by clinician documentation of 
appropriate epidemiologic history and clinical signs and symptoms (no EM) 
consistent with early Lyme disease.  
Inclusion Criteria 
Clinician documentation of appropriate epidemiologic history and clinical signs and 
symptoms (no EM) consistent with early Lyme disease. 
Subject is age 18 or older 
Subject or subject’s legal representative is able to read, comprehend and sign the 
study-specific informed consent form (ICF) after the specifics of the study have been 
fully explained. 
Exclusion Criteria 
Subject has a bleeding disorder 
Subject is currently on antibiotics or has taken antibiotics in the past 30 days 
Subject is unable to provide informed consent 
 
 
Collection of Blood Samples 
 
NOTE: Blood must be obtained by a trained phlebotomist. 
6. Pre-label eight (8) (Arm 2) 4 mL K2EDTA vacutainers and one (1) 5 mL 
serum separator tube with subject’s de-identified study ID. 
7. Disinfect the injection site and perform venous blood draw in accordance 
with institutional laboratory practices. 
8. Fill every vacutainer to the recommended amount. 
9. Invert the K2EDTA tubes 8-10 times to fully mix the anticoagulant with 
the blood. 
10. Store blood samples 2-8°C until shipment to T2 Biosystems and reference 
laboratory. Samples must be shipped overnight, on ice, within 24 hours 
of collection. 
 
 
 
 

 
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Follow-Up Visit (Arms 1 and 2) 
Collection of Blood Sample 
NOTE: Blood must be obtained by a trained phlebotomist, 
1. Pre-label one (1) 5 mL serum separator tube with the de-identified study 
ID. 
2. Disinfect the site, and perform venous blood draw in accordance with 
institutional laboratory practices. 
3. Fill vacutainer entirely. 
4. Document date/time of sample collection on data form. 
Store at 2-8°C until preparation for shipment to reference laboratory. 
Sample must be shipped overnight, on ice, within 24 hours of collection.  
VIII. Data Collection 
NOTE: All documentation on provided data forms will be sent to the study monitor. 
Data will be submitted in accordance with an agreed upon schedule (between study 
site, study monitor, and sponsor) and instructions provided. Any shipments 
processed will be documented.  Study monitor will provide sites with information 
specific to any errors or protocol deviations. These will be documented and 
corrected in a timely manner. 
Initial Visit (Arm 1 and 2) 
Prior to collecting specific case-related information or study samples, each subject 
will be assigned a subject ID number specific to the arm of the study.  Collection site 
staff will maintain a patient log linking the patient’s Medical Record Number (MRN) 
to the assigned study ID. This information will not be made available to the study 
monitor/sponsor. 
The study monitor/sponsor will provide labels to affix to all patient-related 
documentation.  Patient demographic information and medical history will be 
obtained. Information collected may include, but will not be limited to: 
 
Demographic and epidemiologic data such as: 
- Age/Date of Birth 
- Gender 
- Antibiotic history (within past 30 days) 
- Previous Lyme diagnosis 

 
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- Was a tick observed at time of potential Lyme exposure? 
Clinical signs and symptoms such as: 
 
 Fever > 100.4°F 
 Chills 
 Headache 
 Fatigue 
 Myalgia (Muscle aches) 
 
 Anthralgia (Joint aches) 
 
 Swollen lymph nodes 
 EM lesion 
 Neck Pain 
 
 Follow-up Visit (Arm 1 and 2) 
After approximately 45-60 days, the subjects will return to the collection site, where 
the following information will be documented: 
- Resolution or persistence of EM (if subject presented with an EM at initial 
visit) 
- Any remaining Lyme disease-related symptoms/complaints 
- Any ongoing constitutional symptoms (including, but not limited to: weight 
loss, fever, chills, dyspnea, pain, fatigue, decreased appetite) 
- Adherence to prescribed treatment(s) related to Lyme disease 
  
IX. 
Shipping 
Samples will be shipping according to provided instructions (see Appendix 1).   
   
X. 
Withdrawn Samples 
Subjects may withdraw from participation at any point in the study. The principal 
investigator (or designee) may also determine that withdrawal from the study is in 
the best interest of the subject. 
If a blood sample cannot be obtained from the patient’s arm/hand after three (3) 
blood draw attempts at the initial visit, patient will be withdrawn from study.  For 
subjects that present with an EM at the initial visit, if only the convalescent sample 
cannot be obtained, participant data will be maintained in the study.  For subjects 
that do not present with an EM at the initial visit, subjects will be withdrawn if the 
convalescent sample cannot be collected.  Subjects that do not provide two biopsies 
(or biopsy is unattainable) may also be withdrawn if an EM is present. Patients will 
be compensated by the sponsor for their involvement in the study. 

 
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A patient with an EM who consents to the initial visit but fails to present at follow-up 
visit will still be considered enrolled in the study, unless specifically requesting to 
withdraw from the study. 
Samples may also be withdrawn from the study if sample volume is insufficient for 
testing (blood is clotted in all K2EDTA tubes or tissue biopsy received is not of 
sufficient volume). In the event of shipment errors (leakage or delays that render 
samples unstable), samples will be evaluated and withdrawn, as necessary.  
For every withdrawn subject, reason for withdrawal will be documented. However, 
based on subject agreement, any data or blood samples collected prior to study 
withdrawal will be analyzed and included in the study database. A patient who 
consents to the initial visit but fails to present at follow-up visit will still be 
considered as enrolled in the study, unless specifically requesting to withdraw from 
the study. 
XI. 
Site File/Data Record Storage 
The study site will maintain all study documentation for a minimum of three (3) 
years. 
 
XII. 
Risk/Benefit Analysis 
This method comparison presents no risk or benefits to patients.  Results will not be 
used for diagnostic or clinical purposes. The benefit of this method comparison is to 
expand laboratory options for early Lyme disease diagnosis. 
 
All patient identifiers will be removed. Results will be identified only by a unique 
study identification number.  
 
XIII. Study Oversight 
At the discretion of the Sponsor, this protocol may be prematurely terminated.  
Reasons may include but are not limited to: assay and/or instrument performance, 
new regulatory pathway information, business and/or market information. 
 
This study may be subject to and will be made available for monitoring, auditing, IRB 
review and regulatory inspection as deemed necessary by providing direct access to 
study related source data. 
 
 
 

 
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XIV. Confidentiality 
Samples enrolled in this study will be de-identified, therefore confidentiality of 
records identifying the subject is not a concern. Demographic information requested 
are not requirements and, if not readily known by the laboratory requisition form, 
do not need to be sought via a medical record review. Subjects will not be provided 
the study test results, nor will the results be included in their medical records. 
 
The FDA may inspect all records related to this study. As this study does not require 
nor request a medical record review, the IRB and/or other regulatory authorities will 
not have access to study-related medical records. 
 
XV. 
Protocol Departure 
The protocol described for this study will only be changed or altered on the written 
approval of the PIs, study monitor, sponsor and IRBs.  In instances of protocol 
deviation, notify the study monitor immediately. 
 
XVI. Protocol Approval 
I/We agree to perform this study according to the requirements listed in this 
revision of the protocol. 
 
Sponsor Approval 
 
 
_______________________________   _______________________________   ____ / ____ / ______ 
              Sponsor Printed Name                                 Sponsor Signature                              Date Signed 
 
Principal Investigator (PI) Approval 
 
 
_______________________________   _______________________________   ____ / ____ / ______ 
                     PI Printed Name                                           PI Signature                                    Date Signed 
 
Study Monitor Approval 
 
 
_______________________________   _______________________________   ____ / ____ / ______ 
          Study Monitor Printed Name                      Study Monitor Signature                        Date Signed 
 
 

 
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XVII. Protocol Revision History 
Revision Number 
Revision Date 
Description of Changes 
1 
March 27, 2018 
Initial Release 
2 
March 30, 2018 
Clarification of convalescent serum sample 
collection protocol. 
3 
June 8, 2018 
Added procedures for Arm 2 of sample 
collection without presence of EM. 
4 
September 6, 2018 
Updates for clarification of procedure and 
alignment with testing protocol. 
4.1 
October 1, 2018 
Minor updates to language. 
 
 
 
 

 
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APPENDIX I 
Sample Shipping Procedure 
Samples that need to be shipped to Gundersen should be packaged using the following procedures: 
1. Obtain the following material 
a. T2Biosystems insulated shipping box provided by T2 Biosystems (Image 1)  
b. One (1) frozen gel pack provided by T2Biosystems (Image 2) 
c. Two (2) tri-fold cardboard inserts provided by T2Biosystems (Image 3) 
d. Two (2) strips of bubble wrap  
e. Two Biohazard Transport bags (Image 4) 
2. Place the frozen gel pack at the bottom of the Styrofoam box 
3. Take one of the tri-fold cardboard inserts and fold the flaps over so they are facing the same 
direction. 
4. Place the divider over the frozen gel pack so that the flat side sits atop the gel pack and the flaps 
are directed towards the bottom of the Styrofoam box. 
5. Place the blood samples into the biohazard transport bags and seal.  
6. Wrap the blood samples in bubble wrap.  
7. Using a piece of tape, tape the wrapped samples to the cardboard divider. 
8. Fold the second tri-fold cardboard insert and place this atop of the blood samples so that the 
flaps are directed towards top of the Styrofoam box. 
9. Place the tissue samples (if collected) into a biohazard transport bag and seal. 
10. Wrap the tissue sample in bubble wrap. 
11. Using a piece of tape secure the wrapped tissue sample to the flat side of the cardboard insert.  
12. Close the Styrofoam container. 
13. Seal the outer cardboard box closed using packing tape. 
14. Ensure that the UN3373, Biological Substance Category B label is on package. 
15. Affix shipping label with the following address: 
Gundersen Health System 
Microbiology Research Laboratory 
Health Science Center 
1300 Badger Street 
Room 5032 
La Crosse, WI 54601 
 
Samples that need to be shipped to T2 Biosystems should be packaged using the following procedures: 
 
1. Obtain the following material 
a. T2Biosystems insulated shipping box provided by T2 Biosystems (Image 1)  
b. A tri-fold cardboard insert provided by T2Biosystems (Image 3) 
c. Strip of bubble wrap  
d. Biohazard Transport bag (Image 4) 
2. Place the blood samples into the biohazard transport bag and seal.  
3. Wrap the blood samples in bubble wrap.  
4. Using a piece of tape, tape the wrapped samples to the bottom of the container. 

 
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5. Fold a tri-fold cardboard insert and place this atop of the blood samples so that the flaps are 
directed towards bottom of the Styrofoam box. 
6. Close the Styrofoam container. 
7. Seal the outer cardboard box closed using packing tape. 
8. Ensure that the UN3373, Biological Substance Category B label is on package. 
9. Affix shipping label with the following address: 
T2 Biosystems 
Attention: Roger Smith 
101 Hartwell Ave. 
Lexington, MA  02421