Phenotypic and genetic antimicrobial resistance of the intestinal microbiota isolated from two alpacas (Vicugna pacos) post mortem

Antimicrobial resistance pattern of miscellaneous isolates from two alpacas’ intestinal swabs and faeces

Species	Sample source (animal)	Antimicrobial resistance profile
Moraxella osloensis	small intestine (2)	PG-ERY
Leuconostoc citreum	rectum (2)	PG
Corynebacterium diphtheriae	colon (1)	PG-DOX-OXY-ERY-SXT
Corynebacterium stationis	colon (1)	PG-DOX-OXY-ERY-SXT
Stenotrophomonas maltophilia	colon (1)	DOX-OXY-SXT

Antimicrobial resistance pattern of Gram-negative Yersiniaceae isolates from two alpacas’ intestinal swabs and faeces

Yersiniaceae rods	Sample source (animal)	Antimicrobial resistance profile	Antimicrobial resistance gene
Serratia liquefaciens	colon (2)	AMO-AMC-CLE-CF-COL-PB-DOX-TET-FLO	tetA
Serratia liquefaciens	small intestine (2)	CLE-CF-COL-PB-FLO	-
Serratia odorifera	faeces (2)	AMO-AMC-CLE-CF-COL-PB-FLO	-
Serratia odorifera	rectum (2)	CLE-CF-COL-PB-FLO	-
Serratia marcescens	faeces (1)	AMO-AMC-CF-COL-PB-DOX-TET-FLO	tetB

Antimicrobial resistance pattern of Bacillus spp_ isolates from alpaca 2’s intestinal swabs and faeces

Bacillus species	Sample source (animal)	Antimicrobial resistance profile
Bacillus altitudinis	small intestine	PG-ERY-SXT
Bacillus licheniformis	small intestine	PG-DOX-OXY-ERY-SXT
Bacillus licheniformis	small intestine	PG-SXT
Bacillus cereus	colon	PG-ERY-SXT
Bacillus cereus	colon	PG-ERY-SXT
Bacillus cecembensis	colon	PG-SXT
Bacillus flexus	colon	PG-ERY-SXT
Bacillus licheniformis	colon	PG-GEN-SXT
Bacillus licheniformis	colon	PG-ERY-SXT
Bacillus pumilus	colon	PG-ERY-SXT
Bacillus pumilus	colon	PG-ERY-SXT
Bacillus pumilus	colon	PG-ERY-SXT
Bacillus subtilis	colon	PG-ERY-SXT
Bacillus subtilis	colon	PG-ERY-SXT
Bacillus licheniformis	rectum	PG-DOX-OXY-ERY-SXT
Bacillus aeolinus	rectum	PG-DOX-OXY-ERY-SXT
Bacillus cereus	rectum	PG-SXT

Antimicrobial resistance pattern of Gram-positive cocci isolates from two alpacas’ intestinal swabs and faeces

Gram-positive cocci species	Sample source (animal)	Antimicrobial resistance profile	(T)ECOFF*
Enterococcus faecium	small intestine (1)	PG-BEN-NOR-DOX-TET	GEN-NEO-STR
Enterococcus hirae	small intestine (1)	PG-BEN-NOR-ERY	GEN-NEO-STR
Enterococcus hirae	colon (2)	PG-BEN-NOR-ERY-DOX-TET-FLO	GEN-NEO-STR
Enterococcus hirae	rectum (2)	PG-BEN-NOR-ERY-DOX-TET-FLO	GEN-NEO-STR
Enterococcus casseliflavus	colon (2)	PG-BEN-ERY-FLO	-
Enterococcus casseliflavus	rectum (2)	PG-BEN-ERY-FLO	-
Enterococcus gallinarum	rectum (1)	PG-BEN-DOX-TET-NOR-ERY	GEN-NEO-STR
Staphylococcus aureus	colon (1)	AMO-ENR	NEO-STR
Staphylococcus aureus	rectum (1)	AMO-ENR	NEO-STR
Staphylococcus pseudintermedius	rectum (2)	AMO-PG-BEN-ERY	TYL
Staphylococcus sciuri	colon (1)	AMO-PG-BEN	-
Staphylococcus sciuri	small intestine (2)	PG-BEN	-
Micrococcus luteus	rectum (2)	PG-BEN-ERY-CLI	-

Antimicrobial resistance pattern of Gram-negative Enterobacteriaceae isolates from two alpacas’ intestinal swabs and faeces

Enterobacteriaceae rods	Sample source (animal)	Antimicrobial resistance profile	Antimicrobial resistance gene
Citrobacter freundii	rectum (1)	AMP-AMO-AMC-CLE-CF-DOX-TET-FLO-SXT-ENR-NOR	tetA, sul1, floR
Citrobacter freundii	rectum (1)	AMP-AMO-AMC-CLE-CF-DOX-TET-FLO-SXT-ENR-NOR	tetA, sul1, floR
Citrobacter freundii	faeces (1)	AMP-AMO-AMC-CLE-CF-DOX-TET-FLO-SXT-ENR-NOR	tetA, sul1, floR
Citrobacter freundii	faeces (2)	AMP-AMO-AMC-CLE-CF-DOX-TET-FLO-SXT-NOR	aadA, tetA, sul1
Citrobacter braakii	small intestine (1)	DOX-TET-FLO-SXT	floR
Enterobacter cloacae	colon (1)	AMP-AMO-CF-FLO-SXT	sul1, sul2, floR
Enterobacter cloacae	colon (1)	AMP-AMO-CF-FLO-SXT	sul1, sul2, floR
Enterobacter cloacae	colon (1)	AMO-CF-DOX-TET-ENR-NOR	tetA
Enterobacter cloacae	rectum (2)	AMP-AMO-CF-ENR-NOR	-
Enterobacter cloacae	faeces (2)	AMP-AMO-AMC-CLE-CF-SXT	sul1
Enterobacter gergoviae	small intestine (2)	AMP-AMO-AMC-CLE-FLO	-
Enterobacter hormaechei	colon (2)	AMP-AMO-CLE-CF-FLO-SXT	sul1, dfrA1
Enterobacter ludwigii	rectum (1)	AMP-AMO-AMC-CLE-CF-FLO	-
E. coli	colon (1)	AMP-AMO-AMC-CF-STR	aadA, strA/strB