Purdue University Purdue e-Pubs Open Access Theses Theses and Dissertations 12-2016 Prevalence and antimicrobial resistance patterns of Salmonella isolated from poultry farms Carmen G. Velasquez Moreno Purdue University Follow this and additional works at:https://docs.lib.purdue.edu/open_access_theses Part of theFood Science Commons Recommended Citation Velasquez Moreno, Carmen G., "Prevalence and antimicrobial resistance patterns of Salmonella isolated from poultry farms" (2016). Open Access Theses. 837. https://docs.lib.purdue.edu/open_access_theses/837 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School Form 30 Updated 12/26/2015 PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared CARMEN G VELASQUEZ MORENO By Entitled PREVALENCE AND ANTIMICROBIAL RESISTANCE PATTERNS OF SALMONELLA ISOLATED FROM POULTRY FARMS Master of Science For the degree of Is approved by the final examining committee: MANPREET SINGH Chair PAUL EBNER HALEY OLIVER FERNANDA SAN MARTIN-GONZALEZ To the best of my knowledge and as understood by the student in the Thesis/Dissertation Agreement, Publication Delay, and Certification Disclaimer (Graduate School Form 32), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy of Integrity in Research” and the use of copyright material. MANPREET SINGH Approved by Major Professor(s): BRIAN E. FARKAS 11/28/2016 Approved by: Head of the Departmental Graduate Program Date i" PREVALENCE"AND"ANTIMICROBIAL"RESISTANCE"PATTERNS"OF"SALMONELLA"ISOLATED" FROM"POULTRY"FARMS" A"Thesis" Submitted"to"the"Faculty" of" Purdue"University" by" Carmen"G"Velasquez"Moreno" In"Partial"Fulfillment"of"the" Requirements"for"the"Degree" of" Master"of"Science" December"2016" Purdue"University" West"Lafayette,"Indiana" ii" " " " " "" " " " Para"mis"padres,"mis"hermanos"y"mi"mejor"amiga;"mi"hermana."Este"es"nuestro" logro,"gracias"a"su"apoyo"y"amor"incondicional."Para"Dios"por"todas"y"cada"una"de"sus" bendiciones"a"lo"largo"de"este"proceso." " " " " " " " iii" ACKNOWLEDGEMENTS" This"thesis"is"the"result"of"Dr."Manpreet"Singh’s"trust"in"me"and"my"capabilities."Thank" you"Dr."Singh"for"your"support"and"guidance"and"for"giving"me"this"opportunity."""""I"want" to"thank"my"committee"members;"Dr."Haley"Oliver,"Dr."Fernanda"SanYMartín,"and"""""""""" Dr."Paul"Ebner"for"their"help"and"suggestions."This"work"couldn’t"be"done"without"the" help"of"the"most"awesome"people"on"earth;"my"lab"team."Thank"you"for"all"your" constant"help,"advice,"and"more"importantly,"for"your"friendship."I"am"beyond"grateful" for"Rhonda"Taylor,"for"all"her"support"inside"and"outside"the"lab"and"for"Matthew"Bailey" for"all"his"mentoring"through"all"this"process."Thank"you"Jagpinder"Brar"and"Sydney" Corkran"for"all"your"help"with"this"study."Thank"you"Estefania"Novoa"for"all"your"time" and"help"and"Morgan"Redemann"for"your"friendship."I"will"walk"five"hundred"miles"for"all" of"you"guys." " " " iv" ""TABLE"OF"CONTENTS""""" """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""Page" LIST"OF"TABLES".................................................................................................................."vi" LIST"OF"FIGURES"..............................................................................................................."vii" LIST"OF"ABBREVIATIONS"..................................................................................................."viii" ABSTRACT"..........................................................................................................................."x" CHAPTER"1." INTRODUCTION"....................................................................................."1" CHAPTER"2." LITERATURE"REVIEW"............................................................................."2" 2.1" Salmonella"............................................................................................................"2" 2.2" Salmonella.in"the"poultry"industry"......................................................................."4" 2.3" Antimicrobial"resistance"......................................................................................"7" 2.3.1" Resistance"to"tetracyclines"........................................................................."11" 2.3.2" Resistance"to"macrolides"............................................................................"11" 2.3.3" Resistance"to"penicillins"............................................................................."12" 2.3.4" Resistance"to"aminoglycosides"..................................................................."12" 2.3.5" Resistance"to"sulfonamides"and"trimethoprim".........................................."12" 2.3.6" Resistance"to"fluoroquinolones".................................................................."13" 2.4" Antimicrobial"use"in"poultry"..............................................................................."14" 2.5" Antimicrobial"resistant"Salmonella"...................................................................."15" 2.6" Impact"of"antimicrobial"resistance"....................................................................."18" CHAPTER"3." PREVALENCE"AND"ANTIMICROBIAL"RESISTANCE"PATTERNS"OF" SALMONELLA.ISOLATED"FROM"POULTRY"FARMS"............................................................"22" v" 3.1" Abstract".............................................................................................................."22" 3.2" Introduction"......................................................................................................."24" 3.3" Materials"and"Methods"......................................................................................"27" 3.3.1" Sampling"Method"......................................................................................."27" 3.3.2" Reception"of"samples"and"cryopreservation".............................................."30" 3.3.3" DNA"Extraction"and"quantification"............................................................."31" 3.3.4" Polymerase"Chain"Reaction"for"Salmonella.confirmation".........................."32" 3.3.5" Serotyping".................................................................................................."34" 3.3.6" Antimicrobial"Resistance"Testing"................................................................"34" 3.3.7" Data"Analysis".............................................................................................."38" 3.4" Results"and"Discussion"......................................................................................."39" 3.4.2" Salmonella"Serotypes"................................................................................."46" 3.4.3" Antimicrobial"Resistance"............................................................................"61" 3.5" Limitations"........................................................................................................."68" CHAPTER"4." CONCLUSIONS"AND"FUTURE"WORK"...................................................."70" LIST"OF"REFERENCES.........................................................................................................72" APPENDICES" APPENDIX"A.......................................................................................................................84" APPENDIX"B.......................................................................................................................84" " vi" LIST"OF"TABLES" Table""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""Page" Table"1."Characteristics"of"each"farm"sampled"................................................................"30" Table"2."Antimicrobial"agent"classification"for"antimicrobial"class"and"minimum" inhibitory"concentration"(MIC)."........................................................................................"37" Table"3."Positive"Salmonella.isolates"in"each"farm"for"both"seasons"..............................."39" Table"4."Prevalence"of"Salmonella"by"positive"samples"at"house"level"............................"41" Table"5."Salmonella.isolates"with"antimicrobial"resistance"found"in"all"four"farms"........."61" Table"6."Antimicrobial"resistance"patterns"in"Salmonella"isolates"..................................."62" Appendix"Table""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""Page" Table"7."Presumptive"positive"Salmonella.in"samples"obtained"from"four"poultry"farms"in" two"seasons."....................................................................................................................."84" Table"8."Confirmed"Salmonella.in"samples"obtained"from"all"four"farms"in"both"seasons. .........................................................................................................................................."84" " " vii" LIST"OF"FIGURES" Figure"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""Page" Figure"1."Sensititre"Gram"Negative"NARMS"panel,"used"for"AMR"test"............................."36" Figure"2."Prevalence"of"Salmonella"among"all"four"poultry"farms"during"season"1"and"2. .........................................................................................................................................."40" Figure"3."Distribution"of"Salmonella.serotypes"found"in"all"four"poultry"farms"..............."46" Figure"4."Distribution"of"Salmonella.serotypes"found"in"farm"1"in"both"seasons"............"47" Figure"5."Distribution"of"Salmonella.serotypes"found"in"farm"2"in"both"seasons"............"49" Figure"6."Distribution"of"Salmonella.serotypes"found"in"farm"3"in"both"seasons"............"50" Figure"7."Distribution"of"Salmonella.serotypes"found"in"farm"4"in"both"seasons"............"51" Figure"8."Incidence"of"S..Enteritidis"by"sample"type"in"each"farm"for"both"seasons"........"53" Figure"9."Incidence"of"S..Berta"by"sample"type"in"each"farm"for"both"seasons"................"54" Figure"10."Incidence"of"S..Mbandaka"by"sample"type"in"each"farm"for"both"seasons"....."55" Figure"11."Incidence"of"the"least"common"serotypes"by"sample"type"............................."56" " "