Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia

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.

Virulence Gene Profile, Antimicrobial Resistance and Multilocus Sequence Typing of Salmonella enterica Subsp. enterica Serovar Enteritidis from Chickens and Chicken Products

“…Many studies have observed the rate at which foodborne pathogens are acquiring resistance to tetracycline and other commonly used antimicrobials in the food chain, which is a cause for concern. In the same vein, Zakaria et al have also reported a high rate of tetracycline resistance among Salmonella isolated from poultry meat [ 8 ]. S .…”

“…It is also frequently incriminated in foodborne outbreaks [ 6 ]. In recent years, the world has been witnessing the emergence of invasive nontyphoidal Salmonella lineages with an extended multidrug-resistance range [ 7 , 8 , 9 ]. The emergence, although variable, represents a major public health concern, especially in Asia and Sub-Saharan Africa [ 10 , 11 , 12 ].…”

Antimicrobial Resistance Profiles and Genetic Typing of Salmonella Serovars from Chicken Embryos in China

“…Salmonella infection remains a major health concern that is common in poultry and is transmitted to humans through the food chain [31][32][33]. It seriously endangers the health of humans and poultry as well as the development of the poultry industry and the economy [34].…”

Retrospective Evaluation of Nosocomial Bacterial Infections and Their Antimicrobial Resistance Patterns Among Hospitalized Patients in Mogadishu, Somalia

“…The panel of antimicrobial impregnated discs (Oxoid, USA) include aminoglycosides, ansamycins, carbapenems, cephalosporins, cephalosporins+beta lactamase inhibitors, fluoroquinolones, folate pathway inhibitor, fucidanes, glycopeptides, glycylcyclines, lincosamides, nitrofuran, oxazolidinones, penicillin, penicillin+beta lactamase inhibitors, phosphonic acids, polymyxins, streptogramins, and tetracyclines to determine resistance or susceptibility of the isolates to the drugs. 21 To avoid overestimation, the isolates with the zone of inhibition within the intermediate range were susceptible. Escherichia coli ATCC 25922 was used as a control according to the CLSI standard.…”