Prevalence and whole genome phylogenetic analysis reveal genetic relatedness between antibiotic resistance Salmonella in hatchlings and older chickens from farms in Nigeria
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Prevalence and whole genome phylogenetic analysis reveal genetic relatedness between antibiotic resistance Salmonella in hatchlings and older chickens from farms in Nigeria. / Jibril, Abdurrahman Hassan; Okeke, Iruka N.; Dalsgaard, Anders; Olsen, John Elmerdahl.
I: Poultry Science, Bind 102, Nr. 3, 102427, 2023.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Prevalence and whole genome phylogenetic analysis reveal genetic relatedness between antibiotic resistance Salmonella in hatchlings and older chickens from farms in Nigeria
AU - Jibril, Abdurrahman Hassan
AU - Okeke, Iruka N.
AU - Dalsgaard, Anders
AU - Olsen, John Elmerdahl
N1 - Publisher Copyright: © 2022 The Authors
PY - 2023
Y1 - 2023
N2 - The presence of Salmonella in hatchlings is the single most important risk factor for the introduction of Salmonella into poultry farms, and resistant strains are particularly worrisome, as they could affect treatment outcomes in humans infected through consumption of contaminated poultry products. This study estimated Salmonella prevalence, determined resistance profiles of strains recovered from hatchlings in Nigeria, and determined genetic relatedness between hatchling strains and strains from poultry farms. In this study, 300 fecal samples were collected. Salmonella was isolated by culture and confirmed by PCR, and isolates were tested for susceptibility to antimicrobials by the disk diffusion method. Strains were pair-end sequenced, and genomes were used to obtain serotypes and antibiotic resistance genes. Whole-genome based phylogenetic analysis was used to determine genetic relatedness between these isolates and strains from previously characterized older chicken within the same geographical area. A prevalence of 10.7% was obtained belonging to 13 Salmonella serovars. Resistance to kanamycin (30/32), ciprofloxacin (22/32), nalidixic acid (22/32), and sulfonamides (22/32) were the most commonly observed phenotypic resistances. Twenty-two (68.8%) isolates showed multidrug resistance. In silico predictions identified 36 antimicrobial resistance genes. Four (12.5%) and 22 (68.8%) strains showed point mutations in gyrA and parC. Commonly observed acquired resistance genes included sul1, sul2, sul3, and tet(A) as well as a variety of aminoglycoside-modifying genes. Eleven (34.4%) isolates were predicted to have genes that confer resistance to fosfomycin (fosA7, fosB). A strain of S. Stanleyville was predicted to have optrA, which confers resistance to furazolidone. Strains of S. Kentucky, S. Muenster, and S. Menston obtained from hatchlings showed close genetic relatedness by having less than 30 SNPs difference to strains recovered from chickens at farms previously receiving hatchlings from the same sources.
AB - The presence of Salmonella in hatchlings is the single most important risk factor for the introduction of Salmonella into poultry farms, and resistant strains are particularly worrisome, as they could affect treatment outcomes in humans infected through consumption of contaminated poultry products. This study estimated Salmonella prevalence, determined resistance profiles of strains recovered from hatchlings in Nigeria, and determined genetic relatedness between hatchling strains and strains from poultry farms. In this study, 300 fecal samples were collected. Salmonella was isolated by culture and confirmed by PCR, and isolates were tested for susceptibility to antimicrobials by the disk diffusion method. Strains were pair-end sequenced, and genomes were used to obtain serotypes and antibiotic resistance genes. Whole-genome based phylogenetic analysis was used to determine genetic relatedness between these isolates and strains from previously characterized older chicken within the same geographical area. A prevalence of 10.7% was obtained belonging to 13 Salmonella serovars. Resistance to kanamycin (30/32), ciprofloxacin (22/32), nalidixic acid (22/32), and sulfonamides (22/32) were the most commonly observed phenotypic resistances. Twenty-two (68.8%) isolates showed multidrug resistance. In silico predictions identified 36 antimicrobial resistance genes. Four (12.5%) and 22 (68.8%) strains showed point mutations in gyrA and parC. Commonly observed acquired resistance genes included sul1, sul2, sul3, and tet(A) as well as a variety of aminoglycoside-modifying genes. Eleven (34.4%) isolates were predicted to have genes that confer resistance to fosfomycin (fosA7, fosB). A strain of S. Stanleyville was predicted to have optrA, which confers resistance to furazolidone. Strains of S. Kentucky, S. Muenster, and S. Menston obtained from hatchlings showed close genetic relatedness by having less than 30 SNPs difference to strains recovered from chickens at farms previously receiving hatchlings from the same sources.
KW - antibiotic resistance
KW - hatchling
KW - prevalence
KW - Salmonella
KW - whole genome
U2 - 10.1016/j.psj.2022.102427
DO - 10.1016/j.psj.2022.102427
M3 - Journal article
C2 - 36584420
AN - SCOPUS:85144923190
VL - 102
JO - Poultry Science
JF - Poultry Science
SN - 0032-5791
IS - 3
M1 - 102427
ER -
ID: 333616109