Abstract
Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016–2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6′)-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens.
Highlights
Salmonella is a very important zoonotic pathogen that has been reported to cause over 200 million human clinical infections with an estimated mortality of 3 million annually (Coburn et al, 2007; Graham et al, 2018; Moussa et al, 2021)
93% of the serotype prediction according to the Kauffmann White Scheme was concordant with the in silico WGS prediction, six isolates were found to conflict as they were predicted to be Brancaster (S6-human), Mbandaka (S18-human), Ohio (S72-poultry), Weltevreden (S77-poultry), and Kentucky (S81-poultry), while S63 was found to be either Albany or Duesseldorf because they share the same antigenic formula (8: z4, z24)
The antimicrobial susceptibility assay, according to the Clinical and Laboratory Standards Institute (CLSI) standards (Patel et al, 2016), showed that thirty (30) isolates were resistant to at least one of the tested antimicrobial drugs, while twenty-four (24) were resistant to multiple drugs tested (MDR: resistance to three or more antimicrobial classes), and the remaining isolates were all susceptible to the tested antimicrobials
Summary
Salmonella is a very important zoonotic pathogen that has been reported to cause over 200 million human clinical infections with an estimated mortality of 3 million annually (Coburn et al, 2007; Graham et al, 2018; Moussa et al, 2021). The emergence of antimicrobial-resistant Salmonella enterica subspecies enterica serovar Enteritidis constitutes a serious global health problem (Pan et al, 2018). This phenomenon is believed to be due to the unregulated use and abuse of antimicrobials especially veterinary drugs including the World Health Organization’s critically important antimicrobials for prophylaxis, during the management of diseases or as growth promoters (Azmi et al, 2018; Sharma et al, 2018; Yu et al, 2021). The sustained and undetected presence of these bacteria in food-producing animals makes it possible to cause prolonged epidemics globally, especially where the consumption of poorly cooked poultry egg and meat is common (Salihu et al, 2015; Judd et al, 2019)
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