Amended Statement of Ownership (sc 13g/a)

SCHEDULE 13G

SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, DC 20549

Under the Securities Exchange Act of 1934
(Amendment No. 3)*

ContraFect Corporation

(Name of Issuer)

Common Stock, par value $0.0001 per share

(Title of Class of Securities)

	212326102
	(CUSIP Number)

	December 31, 2019
	(Date of Event which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

x Rule 13d-1(b)

¨ Rule 13d-1(c)

¨ Rule 13d-1(d)

*The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (the “Act”) or otherwise subject to the liabilities of that section of the Act, but shall be subject to all other provisions of the Act (however, see the Notes).

Page 1 of 10 Pages

CUSIP No. 212326102

1	NAMES OF REPORTING PERSONS Baker Bros. Advisors LP
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See Instructions)	(a) ¨ (b) ¨
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION Delaware

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER 5,553,599 (1)
	6	SHARED VOTING POWER -0-
	7	SOLE DISPOSITIVE POWER 5,553,599 (1)
	8	SHARED DISPOSITIVE POWER -0-

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,553,599 (1)
10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (See Instructions)	¨
11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 3.5% (1)(2)
12	TYPE OF REPORTING PERSON (See Instructions) IA, PN

(1)

Includes 5,553,599 shares of common stock (“Common Stock”) of ContraFect Corporation (the “Issuer”) underlying Warrants (as defined below) that are subject to the limitations on exercise described in Item 4.

(2)

Based on 153,320,667 shares of Common Stock outstanding as of December 31, 2019, as reported in the Issuer’s Proxy filed with the Securities and Exchange Commission (“SEC”) on January 6, 2020.

Page 2 of 10 Pages

CUSIP No. 212326102

1	NAMES OF REPORTING PERSONS Baker Bros. Advisors (GP) LLC
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See Instructions)	(a) ¨ (b) ¨
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION Delaware

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER 5,553,599 (1)
	6	SHARED VOTING POWER -0-
	7	SOLE DISPOSITIVE POWER 5,553,599 (1)
	8	SHARED DISPOSITIVE POWER -0-

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORING PERSON 5,553,599 (1)
10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (See Instructions)	¨
11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 3.5% (1)(2)
12	TYPE OF REPORTING PERSON (See Instructions) HC, OO

(1)

Includes 5,553,599 shares of Common Stock underlying Warrants (as defined below) that are subject to the limitations on exercise described in Item 4.

(2)

Based on 153,320,667 shares of Common Stock outstanding as of December 31, 2019, as reported in the Issuer’s Proxy filed with the SEC on January 6, 2020.

Page 3 of 10 Pages

CUSIP No. 212326102

1	NAMES OF REPORTING PERSONS Felix J. Baker
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See Instructions)	(a) ¨ (b) ¨
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION United States

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER 5,553,599 (1)
	6	SHARED VOTING POWER -0-
	7	SOLE DISPOSITIVE POWER 5,553,599 (1)
	8	SHARED DISPOSITIVE POWER -0-

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,553,599 (1)
10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (See Instructions)	¨
11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 3.5% (1)(2)
12	TYPE OF REPORTING PERSON (See Instructions) IN, HC

(1)

Includes 5,553,599 shares of Common Stock underlying Warrants (as defined below) that are subject to the limitations on exercise described in Item 4.

(2)

Based on 153,320,667 shares of Common Stock outstanding as of December 31, 2019, as reported in the Issuer’s Proxy filed with the SEC on January 6, 2020.

Page 4 of 10 Pages

CUSIP No. 212326102

1	NAMES OF REPORTING PERSONS Julian C. Baker
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (See Instructions)	(a) ¨ (b) ¨
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION United States

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER 5,553,599 (1)
	6	SHARED VOTING POWER -0-
	7	SOLE DISPOSITIVE POWER 5,553,599 (1)
	8	SHARED DISPOSITIVE POWER -0-

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,553,599 (1)
10	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES (See Instructions)	¨
11	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 3.5% (1)(2)
12	TYPE OF REPORTING PERSON (See Instructions) IN, HC

(1)

Includes 5,553,599 shares of Common Stock underlying Warrants (as defined below) that are subject to the limitations on exercise described in Item 4.

(2)

Based on 153,320,667 shares of Common Stock outstanding as of December 31, 2019, as reported in the Issuer’s Proxy filed with the SEC on January 6, 2020.

Page 5 of 10 Pages

Amendment No.3 to Schedule 13G

This Amendment No. 3 to Schedule 13G amends the previously filed Schedule 13G filed by Baker Bros. Advisors LP (the “Adviser”), Baker Bros. Advisors (GP) LLC (the “Adviser GP”), Julian C. Baker and Felix J. Baker (collectively, the “Reporting Persons”). Except as supplemented herein, such statements, as heretofore amended and supplemented, remain in full force and effect.

Item 1(a)

Name of Issuer:

ContraFect Corporation (the “Issuer”)

Item 1(b)

Address of Issuer’s Principal Executive Offices:

28 Wells Avenue, 3rd Floor

Yonkers, New York 10701

Item 2(a)

Name of Person Filing:

This Schedule 13G is being filed jointly by the Reporting Persons.

Item 2(b)

Address of Principal Business Office or, if None, Residence:

The business address of each of the Reporting Persons is:

c/o Baker Bros. Advisors LP

860 Washington Street, 3^rd Floor

New York, NY 10014

(212) 339-5690

Item 2(c)

Citizenship:

The Adviser is a limited partnership organized under the laws of the State of Delaware. The Adviser GP is a limited liability company organized under the laws of the State of Delaware. The citizenship of each of Julian C. Baker and Felix J. Baker is the United States of America.

Item 2(d)

Title of Class of Securities

Common Stock, $0.0001 par value per share (“Common Stock”)

Item 2(e)

CUSIP Number

212326102

Page 6 of 10 Pages

	Item 3.	If this statement is filed pursuant to §§240.13d-1(b) or (c), check whether the person filing is a:

		(a) ¨ Broker or dealer registered under Section 15 of the Exchange Act.

		(b) ¨ Bank as defined in section 3(a)(6) of the Exchange Act.

		(c) ¨ Insurance company as defined in section 3(a)(19) of the Exchange Act.

		(d) ¨ Investment company registered under section 8 of the Investment Company Act of 1940.

		(e) x An investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).

		(f) ¨ An employee benefit plan or endowment fund in accordance with Rule 13d-1(b)(1)(ii)(F).

		(g) x A parent holding company or control person in accordance with Rule 13d-1(b)(1)(ii)(G).

		(h) ¨ A savings association as defined in Section 3(b) of the Federal Deposit Insurance Act.

		(i) ¨ A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act of 1940.

		(j) ¨ Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

Item 4.

Ownership.

Items 5 through 9 and 11 of each of the cover pages to this Amendment No. 3 are incorporated herein reference. Set forth below is the aggregate number of shares of Common Stock of the Issuer that may be acquired by each of the 667, L.P. and Baker Brothers Life Sciences, L.P. (collectively the “Funds”), which may be deemed to be indirectly beneficially owned by the Reporting Persons, as well as shares of Common Stock that may be acquired upon exercise of the warrants expiring July 27, 2021 (“2021 Warrants”) at an exercise price of $3.00 per share and shares of Common Stock that may be acquired upon exercise of the warrants expiring July 25, 2022 (“2022 Warrants”, along with 2021 Warrants, the “Warrants”) at an exercise price of $1.55 per share, subject to the limitation on exercise described below. The 2022 Warrants are exercisable on a 2 for 1 basis into Common Stock. The information set forth below is based upon 153,320,667 shares of Common Stock outstanding as of December 31, 2019, as reported on the Issuer’s Proxy filed with the Securities and Exchange Commission (“SEC”) on January 6, 2020 and 5,553,599 shares of Common Stock underlying Warrants. Such percentage figures are calculated in accordance with Rule 13d-3 under the Securities Exchange Act of 1934, as amended.

Page 7 of 10 Pages

Name	Number of Shares of Common Stock we own or have to right to acquire within 60 days (taking account of exercise restrictions for the Warrants as described below)		Percent of Class Outstanding
667, L.P.		563,477		0.4	%
Baker Brothers Life Sciences, L.P.		4,990,122		3.1	%
Total		5,553,599		3.5	%

The Warrants are only exercisable to the extent that after giving effect to such exercise the holders thereof together with their affiliates would beneficially own, for purposes of Section 13(d) of the Securities Exchange Act of 1934, as amended, no more than 9.99% of the outstanding Common Shares of the Issuer after exercise (“Beneficial Ownership Limitation”). As a result of this restriction, the number of shares that may be issued upon exercise of the Warrants by the above holders may change depending upon changes in the outstanding shares. By written notice to the Issuer, the Funds may waive the Beneficial Ownership Limitation applicable to that Fund. Any such waiver will not be effective until the 61st day after such notice is delivered to the Issuer.

Pursuant to the management agreements, as amended, among the Adviser, the Funds and their respective general partners, the Funds’ respective general partners relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held by the Funds, and thus the Adviser has complete and unlimited discretion and authority with respect to the Funds’ investments and voting power over investments.

The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.

Item 5.

Ownership of Five Percent or Less of a Class.

If this statement is being filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five percent of the class of securities, check the following x.

Item 6.

Ownership of More than Five Percent on Behalf of Another Person.

N/A

Page 8 of 10 Pages

Item 7.

Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company or Control Person.

The information in Item 4 is incorporated herein by reference.

Item 8.

Identification and Classification of Members of the Group.

N/A

Item 9.

Notice of Dissolution of Group.

N/A

Item 10.

Certification.

By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were acquired and are held in the ordinary course of business and were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

Page 9 of 10 Pages

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

February 14, 2020