<PAGE>

                                                                   Exhibit 4.3.2
                                                                   -------------



                          WAIVER AND SECOND AMENDMENT

                                      TO

                         $15,000,000 CREDIT AGREEMENT

                                     AMONG

                            SYNBIOTICS CORPORATION,

                            THE BANKS NAMED THEREIN

                                      AND

                                   PARIBAS,
                                   AS AGENT



                               JANUARY 12, 1999
<PAGE>

                WAIVER AND SECOND AMENDMENT TO CREDIT AGREEMENT


This Waiver and Second Amendment to Credit Agreement (this "Agreement") is
entered into as of January 12, 1999, by and among Synbiotics Corporation, a
California corporation ("Synbiotics"), the banks referred to in the Credit
Agreement (as defined below) (collectively, the "Banks") and Paribas, as agent
(the "Agent").  For all purposes of this Agreement, capitalized terms used
herein shall have the respective meanings set forth in the Credit Agreement,
dated as of July 9, 1997, among Synbiotics, the Banks and the Agent, as amended
as of March 6, 1998 (the "Credit Agreement").


                                   RECITALS
                                   --------

     A.   Synbiotics and Barnes-Jewish Hospital (the "Hospital"), a Missouri
not-for-profit corporation with headquarters in St. Louis, Missouri, have
entered into a Settlement Agreement, Stipulation to Settlement Order Under Seal,
Release and License (the "BJH Settlement") effective as of July 28, 1998,
whereby Synbiotics and the Hospital have agreed to fully and finally settle all
of the controversies between them as described in Schedule 4.4 of the Credit
Agreement.

     B.   In connection with and pursuant to the BJH Settlement, Synbiotics has
issued to the Hospital two promissory notes (collectively, the "BJH Notes").

     C.   Synbiotics and Prisma Acquisition Corp., a Delaware corporation
("Prisma") have combined into a single company through the statutory merger of
Prisma with and into Synbiotics (the "Merger").

     D.   In connection with the Merger, Synbiotics has sold and issued to
BioQuest Venture Leasing Partnership, L.P., a limited partnership organized
under the laws of the State of Delaware ("BioQuest") a $1,000,000 convertible
promissory note (the "BioQuest Note") in exchange for 482 shares of common stock
of Prisma.

     E.   The Agent and the Banks hereby desire to (i) waive any default under
the Credit Agreement that may result from the transactions contemplated by the
BJH Settlement, the Merger and the other transactions referred to in this
Agreement and (ii) amend the Credit Agreement as set forth herein.


                                   AGREEMENT
                                   ---------

NOW, THEREFORE, in consideration of the mutual promises and agreements contained
in this Agreement and other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, the parties hereto hereby agree to
the above Recitals and as follows:

     1.   Conditions Precedent.  This Agreement shall not become effective
          --------------------
until, and shall become effective when, each of the following conditions
precedent (the "Conditions Precedent") have been satisfied, to the Agent's and
each of the Banks, satisfaction (the date such Conditions Precedent are
satisfied, the "Closing Date"):

          1.1.  Confirmation of Covenants and Representations and Warranties.
                -------------------------------------------------------------
All of the covenants, representations, and warranties of Synbiotics contained in
the Loan Documents (except as expressly modified by this Agreement) and this
Agreement remain true and correct and enforceable in all respects and shall
remain true and correct and enforceable in all respects after giving effect to
this Agreement.

          1.2.  Closing Documents.  Synbiotics shall have delivered the
                -----------------
following documentation to each Bank and the Agent:

                                       2
<PAGE>

          (a)   in order to perfect the Agent's and Banks, security interest in
certain licensed patents of Synbiotics as a result of the BJH Settlement, an
amendment to the Patent Security Agreement (as defined in the Security
Agreement), naming the Agent as secured party with respect to all such licensed
patents of Synbiotics, to be filed in the Patent and Trademark Office; and

          (b)   copies of (i) the February 9, 1998 amendments to Synbiotics' by-
laws, (ii) the August 4, 1998 amendments to Synbiotics, articles of
incorporation and (iii) the certificate of determination, and any amendments to
the certificates of determination, with respect to Synbiotics' preferred stock,
if any, which shall, in each case (i), (ii) and (iii), be reasonably
satisfactory to the Agent and the Banks.

          1.3.  Fees and Expenses. (a) The Agent shall have received a working
                -----------------
fee in connection with the negotiation, preparation, approval, execution and
delivery of this Amendment equal to $40,000 for the account of the Agent.

     2.   Waiver.  The Agent and the Banks hereby waive any default by
          ------
Synbiotics of the following provisions of the Credit Agreement:

          2.1.  BJH Settlement.  Sections 4.5, 4.71 4.14, 4.15, 4.18, and 4.21
                --------------
of the Credit Agreement solely to the extent such default would be caused by the
terms of the BJH Settlement or the preceding litigation or the contingent
liability that existed before the BJH Settlement in relation to such preceding
litigation.

          2.2.  Plans.  The first sentence of Section 4.12 of the Credit
Agreement solely to the extent such default would be caused by the existence of
Plans not previously disclosed to the Agent and the Banks.  Synbiotics hereby
represents and warrants that all Plans have been in compliance with the
provisions of Section 4.12 since the Closing Date.

          2.3.  Ownership of Property.  Section 4.19 of the Credit Agreement
                ---------------------
solely to the extent such default would be caused by the failure of Synbiotics
to amend Schedule 4.19 to set forth Synbiotics' leasehold interest in certain
real property in Rome, New York.

          2.4.  Amended Provisions.  Any other provision of the Credit Agreement
                ------------------
which is expressly amended by this Agreement solely to the extent such default
would be caused by the failure of Synbiotics to amend such provision as
contemplated by this Agreement prior to such default.

     3.   Amendments.
          ----------

          3.1   Definitions. (a) The following shall be added as new definitions
                -----------
in alphabetical order to Section 1.1 of the Credit Agreement:

          "BJH Settlement" shall mean the Settlement Agreement, Stipulation to
Settlement Order Under Seal, Release and License, effective as of July 28, 1998,
whereby Synbiotics and the Hospital have agreed to fully and finally settle all
of the controversies between them as described in Schedule 4.4 of the Credit
Agreement.  The terms and conditions of the BJH Settlement shall not be amended
without the consent of the Agent as long as either Paribas or Imperial Bank are
Banks.

          "BioQuest Note" shall mean the $1,000,000 promissory note issued by
Synbiotics to BioQuest Venture Leasing Partnership, L.P., dated as of March 6,
1998, which is convertible, at the option of Synbiotics, into the common stock
of Synbiotics.

          "BJH Notes" shall mean, collectively, the two promissory notes issued
by Synbiotics to the Hospital in connection with and pursuant to the BJH
Settlement.

                                       3
<PAGE>

          "Date-Sensitive Data" means any data of any type that includes date
information or which is otherwise derived from or dependent on date information.

          "Date-Sensitive System" means any software or hardware system or
component, including any electronic or electronically controlled system, that
processes any Date-Sensitive Data and that is installed, in development or on
order.

          "Hospital" shall mean Barnes-Jewish Hospital, a Missouri not-for-
profit corporation with headquarters in St. Louis, Missouri.

          "SL Guaranty" shall mean the guaranty by the Borrower of the
obligations of Serge Leterme, an employee of the Borrower, to Imperial Bank
under that certain short term home purchase loan dated September 14, 1998.

          "SL Loan" shall mean the $75,000 loan made by the Borrower to Serge
Leterme, an employee of the Borrower, in order to cover his relocation expenses
to San Diego, California.

          (b)  The defined term "Consolidated EBITDA" shall be and is hereby
amended by replacing the word "and" in the seventh line thereof with 11,11 and
by inserting the following language at the end thereof:

     "and (iv) with respect to the Borrower, the costs and expenses incurred by
     the Borrower in connection with the BJH Settlement (including without
     limitation the issuance of the BJH Notes) in an amount not to exceed
     $4,746,000; provided, however, that any loans and advances made after
                 -----------------
     October 31, 1998 by the Borrower and its Subsidiaries to their employees in
     accordance with Section 6.8(c) shall be deducted from Consolidated EBITDA
     for purposes of Section 6.1."

          (c)  The defined term "Consolidated Net Income" shall be and is hereby
amended by inserting the following language at the end thereof:

     "For purposes of Section 6.1(e)(ii)(b) only, the $4,746,000 in costs and
     expenses incurred by the Borrower in connection with the BJH Settlement
     shall not be deducted for purposes of determining Consolidated Net Income."

          (d)  The defined term "Consolidated Tangible Net Worth" shall be and
is hereby amended by inserting the following language at the end thereof:

     "For purposes of Section 6.1(e) only, (i) the amounts outstanding under the
     BioQuest Note shall constitute Consolidated Tangible Net Worth and (ii) the
     after-tax effect of the $4,746,000 costs and expenses at the time incurred
     by the Borrower in connection with the BJH Settlement shall be added to
     Consolidated Tangible Net Worth."

          (e)  The defined term "Eligible Accounts Receivable" shall be and is
hereby amended by inserting the following language at the end of clause (p)
thereof:

     "; provided, however, that accounts from RM, an Affiliate of the Borrower,
     shall be considered to be Eligible Accounts Receivable to the extent
     provided for in clause (1) above.

          (f)  The defined term "Indebtedness" shall be and is hereby amended by
inserting the following language at the end thereof:

     "provided, however, that the amounts outstanding under the BioQuest Note
      -----------------
     and the BJH Notes shall not constitute Indebtedness for purposes of Section
     6.1"

                                       4
<PAGE>

          3.2  Section 4.16.
               ------------

          (a)  Section 4.16 of the Credit Agreement shall be and is hereby
amended by inserting the following after the word "Subsidiary" in the sixth line
thereof:

     ", as of the Closing Date.  Schedule 4.16(b) hereto sets forth the number
     of authorized and issued shares of capital stock of the Borrower and each
     of its Subsidiaries and the registered owner(s) of each such Subsidiary, as
     of October 30, 1998."

          (b)  Section 4.16 of the Credit Agreement shall be and is hereby
further amended by replacing the word "and" on the twenty-first line thereof
with "," and adding the following at the end thereof:

     ", and (iv) preferred stock purchase rights issued pursuant to any
     shareholder rights plan previously approved by the Agent."

          3.3  Schedule 4.19.  Schedule 4.19 of the Credit Agreement shall be
               -------------
and is hereby amended by deleting item number 4 in its entirety and inserting
the following in replacement thereof:

     "4.  1721 Black River Road;        C.A. Kaplan Real Estate
          Rome, NY 13440                1300 Floyd Avenue
          315-337-6014                  Rome, NY 13440"

          3.4  Section 6.16. The following shall be added as a new Section 6.16
               ------------
to the Credit Agreement:

          "Section 6.16 Conversion of BioQuest Note.  The Borrower shall not
                        ---------------------------
repay the BioQuest Note and shall instead convert such note into the common
stock of Borrower in accordance with the terms thereof."

          3.5  Section 6.1. Section 6.1(d) shall be and is hereby amended by
               -----------
deleting such section in its entirety and inserting the following in replacement
therefor:

               "(d) Capital Expenditures.  Other than with respect to Prisma
                    --------------------
     Capital Expenditures, which are covered by the following sentence, the
     Borrower shall not make or incur (or commit to make or incur) and shall not
     permit any of its Subsidiaries to make or incur (or commit to make or
     incur) Capital Expenditures (i) in the 1998 fiscal year which exceed, in
     the aggregate, $1,000,000, (ii) in the 1999 fiscal year which exceed, in
     the aggregate, $1,000,000 in connection with the Borrower's Date-Sensitive
     System (the "DSS Capex") and $1,000,000 in connection with any other
     Capital Expenditures (the "Other Capex"), and (iii) in the 2000 fiscal year
     and any fiscal year thereafter which exceed, in the aggregate, $1,000,000
     for such fiscal year; provided that if the maximum amount set forth above
                           --------
     for any period in clauses (ii) and (iii) exceeds the aggregate amount of
     Capital Expenditures made or incurred (or committed to be made or incurred)
     during such period (such excess, the "CE Excess"), then the maximum amount
     set forth above for the following period (but not any subsequent periods)
     shall be increased by the amount of CE Excess; provided further, that
                                                    ----------------
     calculations of CE Excess during the 1999 fiscal year shall only be made
     with respect to Other Capex and not DSS Capex.  The Borrower shall not make
     or incur (or commit to make or incur) and shall not permit any of its
     Subsidiaries to make or incur (or commit to make or incur) Prisma Capital
     Expenditures other than Prisma Capital Expenditures which do not exceed, in
     the aggregate, $250,000 in each of the Borrower's 1998 and 1999 fiscal
     years; provided, however, that Prisma Capital Expenditures in the 2000
            --------
     fiscal year and any fiscal year thereafter shall be applied against the
     limitation set forth in clause (iii) ."

          3.5  Section 6.2. (a) Section 6.2(f) of the Credit Agreement shall be
               -----------
and is hereby (i) re-lettered as Section 6.2(i) and (ii) amended by replacing
"(e)" with "(h)".

                                       5
<PAGE>

          (b)  The following shall be added as new Sections 6.2(f), (g), and (h)
of the Credit Agreement:

          "(f) Indebtedness under the BioQuest Note;

          (g)  Indebtedness under the BJH Notes;

          (h)  Indebtedness under the SL Guaranty, provided such guaranty shall
terminate on or prior to November 13, 1998;"

          3.6  Section 6.4.
               -----------

          (a)  Section 6.4(b) of the Credit Agreement shall be and is hereby
amended by adding the following language at the end thereof:

     "provided, however, this Section 6.4(b) shall not apply to the Borrower's
      -----------------
     acquisition of a nonexclusive license to certain patents of the Hospital,
     as more fully described in attachment 1 to the Second Amendment to Patent
     Security Agreement, dated as of October 23, 1998, between the Agent and the
     Borrower"

          (b)  Section 6.4(c) of the Credit Agreement shall be and is hereby
amended by inserting the following language at the end thereof:

     "except for the amendments to the Borrower's (i) bylaws of February 9,
     1998, (ii) articles of incorporation of August 4, 1998 and (iii)
     certificates of determination with respect to the Borrower's preferred
     stock"

          3.7  Section 6.5.  Section 6.5 of the Credit Agreement shall be and is
               -----------
hereby amended by inserting the following language at the end thereof:

     "and (iii) sales of contract rights in connection with the transaction with
     Merial LLC allowing Merial LLC to use certain distribution channels and to
     receive the benefits of the Borrower's strategic position in the supply of
     feline leukemia virus vaccine in North America and Central America"

          3.8  Section 6.6. The introductory paragraph of Section 6.6 of the
               -----------
Credit Agreement shall be and is hereby amended by replacing "6.2(f)" with
"6.2(h) or (i)".

          3.9  Section 6.7. Section 6.7 of the Credit Agreement shall be and is
               -----------
hereby amended by inserting the following language at the end thereof:

     "and (iii) the Borrower may distribute and/or redeem shares of its common
     stock or other equity interests (or rights to acquire other equity
     interests) in the Borrower pursuant to any shareholder rights plan
     previously approved by the Agent."

          3.10 Section 6.8. (a) Section 6.8(c) of the Credit Agreement shall be
               -----------
and is hereby amended by deleting such section in its entirety and inserting the
following in replacement therefor:

     "(c) loans and advances by the Borrower and its Subsidiaries to their
     employees for the purpose of providing for relocation expenses."

          (b)  The following shall be added as new Sections 6.8(e) and (f) of
the Credit Agreement:

          "(e) subsequent to October 31, 1998 or as otherwise agreed to by the
          Lenders, loans and advances by the Borrower and its Subsidiaries to
          their employees in the ordinary course of its business not exceeding
          $1,000 per employee at any one time outstanding; and

                                       6
<PAGE>

          (f)  the issuance of the BJH Notes and the BioQuest Note and the
          acquisition of Prisma Acquisition Corp., a Delaware corporation."

          3.11 Section 6.10. Section 6.10 of the Credit Agreement shall be and
               ------------
is hereby amended by inserting the following sentence at the end thereof:

     "The foregoing shall not apply to the conversion of the BioQuest Note into
     common stock of the Borrower or to the scheduled complete or partial
     forgiveness, based on time of continued service, of the SL Loan or of any
     other loans and advances by the Borrower and its Subsidiaries to their
     employees for the purpose of providing for relocation expenses."

          3.12 Section 6.11. Section 6.11 of the Credit Agreement shall be and
               ------------
is hereby amended by inserting the following language at the end thereof:

     "with the exception of the veterinary diagnostics instrumentation business
     of Prisma Acquisition Corp., a Delaware corporation, acquired by the
     Borrower"

          3.13 Schedule 4.16(b). Schedule 4.16 of the Credit Agreement shall be
               ----------------
and is hereby amended to include the schedule entitled "Schedule 4.16(b)", which
is attached hereto as an additional schedule to the Credit Agreement.

     4.   Representations, Warranties and Covenants of Synbiotics.  In addition
          -------------------------------------------- ----------
to the representations and warranties contained in the Loan Documents,
Synbiotics makes the following undertakings, representations and warranties to
the Agent and the Banks, which undertakings, representations and warranties
shall survive the execution of this Agreement and shall continue in full force
and effect until the full and final satisfaction and discharge of all
obligations of Synbiotics under this Agreement and under the other Loan
Documents:

          4.1  No Further Modifications.  Synbiotics expressly acknowledges and
               ------------------------
agrees that neither the Agent nor any Bank shall have any obligation, and have
made no commitment, to further waive, modify or amend the Credit Agreement or
other Loan Documents, except as expressly set forth in this Agreement.  Except
as otherwise provided in this Agreement or pursuant to the Credit Agreement,
Synbiotics will not sell, assign, pledge, exchange or dispose of any of the
Collateral in any manner whatsoever or attempt to do any of the foregoing or
agree to any modification or cancellation of, or substitution for, any of the
Collateral.

          4.2  No Default.  No Default or Event of Default under the Loan
               ----------
Documents has occurred and is continuing or will occur by giving effect hereto
and the execution of this Agreement will not result in any Default, Event of
Default or in any breach of any of the terms, conditions or provisions of or
constitute a default under any indenture, mortgage, deed of trust or other
agreement or instrument to which Synbiotics is a party or by which it or its
property is bound or any order of any court or administrative agency entered in
any proceeding to which Synbiotics is a party or by which it or its property may
be bound or to which it or its property may be subject.

     5.   Miscellaneous.
          -------------

          5.1. Notices, etc.  Any and all notices, requests, certificates and
               ------------
other instruments executed and delivered after the execution and delivery of
this Agreement may refer to the Credit Agreement without making specific
reference to this Agreement but nevertheless all such references shall include
this Agreement unless the context otherwise requires.

          5.2. Headings.  The descriptive headings of the various Sections or
               --------
parts of this Agreement are for convenience only and shall not affect the
meaning or construction of any of the provisions hereof.

                                       7
<PAGE>

          5.3.  Governing Law.  This Agreement shall be governed by and
                -------------
construed in accordance with the laws of California.

          5.4.  Counterparts.  The execution hereof by the parties hereto shall
                ------------
constitute a contract between the parties heretofore the uses and purposes
hereinabove set forth, and this Agreement may be executed in any number of
counterparts, each executed counterpart constituting an original, but all
together only one agreement.

                                       8
<PAGE>

IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be duly
executed as of the day and the year first written.


                                         SYNBIOTICS CORPORATION


                                         By:  /s/ Michael Green
                                              ----------------------
                                         Name:  Michael Green
                                         Title:  V.P. Finance


(signatures continued on next page)

                                      S-1
<PAGE>

                                         PARIBAS,
                                         as Agent and as a Bank


                                         By:  /s/ John W. Kopcha
                                              -----------------------
                                         Name:  John W. Kopcha
                                         Title:  Vice President


                                         By:  /s/ Marc A. Preiser
                                              -----------------------
                                         Name:  Marc A. Preiser
                                         Title:  Assistant Vice President

(signatures continued on next page)

                                      S-2
<PAGE>

                                         IMPERIAL BANK, as a Bank


                                         By:  /s/ Leila Ghoroghchi
                                              ------------------------
                                         Name:  Leila Ghoroghchi
                                         Title: Vice President

                                      S-3
<PAGE>

                                Schedule 4.16b

                      Corporate Structure; Capitalization
                      -----------------------------------
                                 (at 10/31/98)


                                Authorized             Issued
                                -----------            ------

1. Pre-Acquisition
   ---------------

Synbiotics Corporation            24,800,000            7,393,000
Common Stock

2. Post-Acquisition
   ----------------

Synbiotics Corporation            24,800,000            9,005,420
Common Stock

Synbiotics Corporation            25,000,000                  -0-
Preferred Stock

Synbiotics Europe                 47,500,000 FF        47,500,000 FF
(R.M. - Diagnostics S.A.S.)
Common Stock.