Correlations among Resistances to Different Antimicrobial Compounds in Salmonella Strains from Hen Eggshells

Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database

Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.

Effects of antibiotic-induced resistance on the growth, survival ability and virulence of Salmonella enterica

Salmonella enterica is an important foodborne pathogen that constitutes a major health hazard. The emergence and aggravation of antibiotic-resistant Salmonella has drawn attention widely around the world. Conducting a risk assessment of antibiotic-resistant foodborne pathogens throughout the food chain is a pressing requirement for ensuring food safety. The growth, survival capability, and virulence of antibiotic-resistant Salmonella represent crucial biological characteristics that play an important role in microbial risk assessment. In this study, eight antibiotic-sensitive S. enterica strains were induced by Ampicillin (Amp) and Ciprofloxacin (CIP), respectively, and AMP-resistant and CIP-resistant mutants were obtained. The growth characteristics under different temperatures (25, 30, 35 °C), viability after exposure to heat (55, 57.5, 60 °C) and acid (HCl, pH = 3.0), the virulence potential (adhesion and invasion to Caco-2 cells, biofilm formation and motility) and the lethality in a model species (Galleria mellonella) were evaluated and compared for S. enterica strains before and after antibiotic exposure. The induction by AMP and CIP are likely to promote cross-antibiotic resistance to their antibiotic classes, β-lactams and quinolones, as well as some compound antibiotics. It was observed that generally the antibiotic-induction-resistant strains showed decreased growth ability and lower heat resistance, although the differences were not significant at all the conditions tested. The AMP-resistant strains were significantly less acid resistance than the sensitive and the CIP-resistant ones, while exhibiting increased biofilm formation ability. In general, the antibiotic-induced resistance did not significantly affect the motility, adherence, or invasion ability of Caco-2 cells. However, CIP-resistant strains displayed lower lethality in G. mellonella infection, whereas AMP-resistant strains did not, and even two strains improved lethality. The study of the biological characteristics of antibiotic-resistant S. enterica is essential in better understanding the microbial risks to both the food chain and human health, thereby facilitating a more accurate risk assessment.

Towards a Harmonized Terminology: A Glossary for Biocide Susceptibility Testing

Disinfection is a key strategy to reduce the burden of infections. The contact of bacteria to biocides-the active substances of disinfectants-has been linked to bacterial adaptation and the development of antimicrobial resistance. Currently, there is no scientific consensus on whether the excessive use of biocides contributes to the emergence and spread of multidrug resistant bacteria. The comprehensive analysis of available data remains a challenge because neither uniform test procedures nor standardized interpretive criteria nor harmonized terms are available to describe altered bacterial susceptibility to biocides. In our review, we investigated the variety of criteria and the diversity of terms applied to interpret findings in original studies performing biocide susceptibility testing (BST) of field isolates. An additional analysis of reviews summarizing the knowledge of individual studies on altered biocide susceptibility provided insights into currently available broader concepts for data interpretation. Both approaches pointed out the urgent need for standardization. We, therefore, propose that the well-established and approved concepts for interpretation of antimicrobial susceptibility testing data should serve as a role model to evaluate biocide resistance mechanisms on a single cell level. Furthermore, we emphasize the adaptations necessary to acknowledge the specific needs for the evaluation of BST data. Our approach might help to increase scientific awareness and acceptance.

Untargeted Metabolomics Approach of Cross-Adaptation in Salmonella Enterica Induced by Major Compounds of Essential Oils

Cross-adaptation phenomena in bacterial populations, induced by sublethal doses of antibacterial solutions, are a major problem in the field of food safety. In this regard, essential oils and their major compounds appear as an effective alternative to common sanitizers in food industry environments. The present study aimed to evaluate the untargeted metabolomics perturbations of Salmonella enterica serovar Enteritidis that has been previously exposed to the sublethal doses of the major components of essential oils: cinnamaldehyde, citral, and linalool (CIN, CIT, and LIN, respectively). Cinnamaldehyde appeared to be the most efficient compound in the assays evaluating the inhibitory effects [0.06% (v/v) as MBC]. Also, preliminary tests exhibited a phenotype of adaptation in planktonic and sessile cells of S. Enteritidis when exposed to sublethal doses of linalool, resulting in tolerance to previously lethal concentrations of citral. A metabolomics approach on S. Enteritidis provided an important insight into the phenomenon of cross-adaptation induced by sublethal doses of major compounds of some essential oils. In addition, according to the results obtained, when single molecules were used, many pathways may be involved in bacterial tolerance, which could be different from the findings revealed in previous studies regarding the use of phytocomplex of essential oils. Orthogonal projection to latent structures (OPLS) proved to be an interesting predictive model to demonstrate the adaptation events in pathogenic bacteria because of the global engagement to prevent and control foodborne outbreaks.

Salmonella from Farm to Table: Isolation, Characterization, and Antimicrobial Resistance of Salmonella from Commercial Broiler Supply Chain and Its Environment

Antimicrobial resistance (AMR) in poultry production chain is one of the major food safety concerns due to indiscriminate usage of antibiotics and the presence of pathogens such as Salmonella which causes infections in various stages of production. In the present study, 182 samples were collected from commercial broiler supply chain, viz., three hatcheries (n = 29), three commercial broiler farms (CBF; n = 99), and three retail meat shops (RMS; n = 54), and used for isolation and identification of Salmonella using three different selective agar media and a selective enrichment medium followed by PCR confirmation targeting the hilA gene. The overall prevalence of Salmonella was 47/182 (25.82%), and a significantly higher (P < 0.05) prevalence was observed in retail meat shops (46.29%), CBF (19.19%), and hatcheries (10.34%). Comparison of three agar media for isolation of Salmonella revealed that all the media were equally selective. However, PCR amplification of hilA gene fragment was significantly higher (P < 0.01) in selective enrichment culture tetrathionate brilliant green bile broth (TTB) as compared to all solid (agar-based) media. Susceptibility pattern against most frequently used antibiotics revealed that 100% of the isolates were resistant to at least one antibiotic. High resistance was observed for doxycycline (94.34%), followed by cefpodoxime (84.91%), ciprofloxacin (72.64%), gentamicin (65.09%), enrofloxacin (61.32%), colistin sulphate (40.42%), amikacin (34.91%), ampicillin (33.96%), neomycin (33.02), cefotaxime (30.19%), ceftazidime (29.25%), trimethoprim-sulfamethoxazole (23.58%), amoxicillin+clavulanic acid (21.70%), and chloramphenicol (12.26%); 16.98% of the isolates were ex-tended spectrum β-lactamase (ESBL) producers, and 76.41% were multidrug resistant (MDR). MDR Salmonella were significantly higher (P < 0.01) in RMS (91.66%) followed by CBF (82.75%), whereas no MDR isolates were present in the isolates from hatcheries. The results indicated a higher prevalence of Salmonella and AMR for commonly used antibiotics in the complete broiler supply chain, especially RMS and CBF. Also, this study idicated that TTB enrichment followed by PCR and colony PCR was found to be rapid, specific and time-saving method.

Antimicrobial resistance associated with the use of antimicrobial processing aids during poultry processing operations: cause for concern?

Antimicrobial resistance has become a global issue and a threat to human and animal health. Contamination of poultry carcasses with meat-borne pathogens represents both an economic and a public health concern. The use of antimicrobial processing aids (APA) during poultry processing has contributed to an improvement in the microbiological quality of poultry carcasses. However, the extensive use of these decontaminants has raised concerns about their possible role in the co-selection of antibiotic-resistant bacteria. This topic is presented in the current review to provide an update on the information related to bacterial adaptation to APA used in poultry processing establishments, and to discuss the relationship between APA bacterial adaptation and the acquisition of a new resistance phenotype to therapeutic antimicrobials by bacteria. Common mechanisms such as active efflux and changes in membrane fluidity are the most documented mechanisms responsible for bacterial cross-resistance to APA and antimicrobials. Although most studies reported a bacterial resistance to antibiotics not reaching a clinical level, the under-exposure of bacteria to APA remains a concern in the poultry industry. Further research is needed to determine if APA used during poultry processing and therapeutic antimicrobials share common sites of action in bacteria and encounter similar mechanisms of resistance.

Exploitation of plant extracts and phytochemicals against resistant Salmonella spp. in biofilms

Salmonella is one of the most frequent causes of foodborne outbreaks throughout the world. In the last years, the resistance of this and other pathogenic bacteria to antimicrobials has become a prime concern towards their successful control. In addition, the tolerance and virulence of pathogenic bacteria, such as Salmonella, are commonly related to their ability to form biofilms, which are sessile structures encountered on various surfaces and whose development is considered as a universal stress response mechanism. Indeed, the ability of Salmonella to form a biofilm seems to significantly contribute to its persistence in food production areas and clinical settings. Plant extracts and phytochemicals appear as promising sources of novel antimicrobials due to their cost-effectiveness, eco-friendliness, great structural diversity, and lower possibility of antimicrobial resistance development in comparison to synthetic chemicals. Research on these agents mainly attributes their antimicrobial activity to a diverse array of secondary metabolites. Bacterial cells are usually killed by the rupture of their cell envelope and in parallel the disruption of their energy metabolism when treated with such molecules, while their use at sub-inhibitory concentrations may also disrupt intracellular communication. The purpose of this article is to review the current available knowledge related to antimicrobial resistance of Salmonella in biofilms, together with the antibiofilm properties of plant extracts and phytochemicals against these detrimental bacteria towards their future application to control these in food production and clinical environments.

Understanding Antimicrobial Resistance (AMR) Profiles of Salmonella Biofilm and Planktonic Bacteria Challenged with Disinfectants Commonly Used During Poultry Processing

Foodborne pathogens such as Salmonella that survive cleaning and disinfection during poultry processing are a public health concern because pathogens that survive disinfectants have greater potential to exhibit resistance to antibiotics and disinfectants after their initial disinfectant challenge. While the mechanisms conferring antimicrobial resistance (AMR) after exposure to disinfectants is complex, understanding the effects of disinfectants on Salmonella in both their planktonic and biofilm states is becoming increasingly important, as AMR and disinfectant tolerant bacteria are becoming more prevalent in the food chain. This review examines the modes of action of various types of disinfectants commonly used during poultry processing (quaternary ammonium, organic acids, chlorine, alkaline detergents) and the mechanisms that may confer tolerance to disinfectants and cross-protection to antibiotics. The goal of this review article is to characterize the AMR profiles of Salmonella in both their planktonic and biofilm state that have been challenged with hexadecylpyridinium chloride (HDP), peracetic acid (PAA), sodium hypochlorite (SHY) and trisodium phosphate (TSP) in order to understand the risk of these disinfectants inducing AMR in surviving bacteria that may enter the food chain.

Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid

The application of RNA sequencing in commercial poultry could facilitate a novel approach toward food safety with respect to identifying conditions in food production that mitigate transcription of genes associated with virulence and survivability. In this study, we evaluated the effects of disinfectant exposure on the transcriptomes of two field isolates of Salmonella Heidelberg (SH) isolated from a commercial broiler processing plant in 1992 and 2014. The isolates were each exposed separately to the following disinfectants commonly used in poultry processing: cetylpyridinium chloride (CPC), acidified calcium hypochlorite (aCH), and peroxyacetic acid (PAA). Exposure times were 8 s with CPC to simulate a poultry processing dipping station or 90 min with aCH and PAA to simulate the chiller tank in a poultry processing plant at 4°C. Based on comparison with a publicly available annotated SH reference genome with 5,088 genes, 90 genes were identified as associated with virulence, pathogenicity, and resistance (VPR). Of these 90 VPR genes, 9 (10.0%), 28 (31.1%), and 1 (1.1%) gene were upregulated in SH 2014 and 21 (23.3%), 26 (28.9%), and 2 (2.2%) genes were upregulated in SH 2014 challenged with CPC, aCH, and PAA, respectively. This information and previously reported MICs for the three disinfectants with both SH isolates allow researchers to make more accurate recommendations regarding control methods of SH and public health considerations related to SH in food production facilities where SH has been isolated. For example, the MICs revealed that aCH is ineffective for SH inhibition at regulatory levels allowed for poultry processing and that aCH was ineffective for inhibiting SH growth and caused an upregulation of VPR genes.