Multi-Drug Resistance to Salmonella spp. When Isolated from Raw Meat Products

Does Salmonella diarizonae 58:r:z53 Isolated from a Mallard Duck Pose a Threat to Human Health?

Salmonella diarizonae (IIIb) is frequently isolated from reptiles and less frequently from birds and mammals. However, its isolation from invasive human infections has not been widely reported. Migratory mallard ducks are excellent bioindicators of pathogen presence and pathogen antibiotic resistance (AMR). We present the first isolation from a mallard duck in central Europe of the antibiotic-resistant Salmonella enterica subsp. diarizonae with the unique antigenic pattern 58:r:z53 and report its whole-genome sequencing, serosequencing, and genotyping, which enabled the prediction of its pathogenicity and comparison with phenotypic AMR. The isolated strain was highly similar to S. diarizonae isolated from humans and food. Twenty-four AMR genes were detected, including those encoding aminoglycoside, fluoroquinolone, macrolide, carbapenem, tetracycline, cephalosporin, nitroimidazole, peptide antibiotic, and disinfecting agent/antiseptic resistance. Six Salmonella pathogenicity islands were found (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, and SPI-13). An iron transport system was detected in SPI-1 centisome C63PI. Plasmid profile analyses showed three to be present. Sequence mutations in the invA and invF genes were noted, which truncated and elongated the proteins, respectively. The strain also harbored genes encoding type-III secretion-system effector proteins and many virulence factors found in S. diarizonae associated with human infections. This study aims to elucidate the AMR and virulence genes in S. enterica subsp. diarizonae that may most seriously threaten human health.

Antimicrobial resistance and genetic relatedness of Salmonella serotypes isolated from food, asymptomatic carriers, and clinical cases in Shiyan, China

Salmonella is a primary cause of foodborne diseases globally. Despite food contamination and clinical infections garnering substantial attention and research, asymptomatic Salmonella carriers, potential sources of infection, have been comparatively overlooked. In this study, we conducted a comparative analysis of serotype distribution, antimicrobial resistance phenotypes, and genetic profiles of archived Salmonella strains isolated from food (26), asymptomatic carriers (41), and clinical cases (47) in Shiyan City, China. Among the 114 Salmonella strains identified, representing 31 serotypes and 34 Sequence Types (STs), the most prevalent serovars included Typhimurium, Derby, Enteritidis, Thompson, and London, with the most predominant STs being ST11, ST40, ST26, ST34, and ST155. Antimicrobial resistance testing revealed that all strains were only sensitive to meropenem, with 74.6% showing antimicrobial resistance (AMR) and 53.5% demonstrating multidrug resistance (MDR). Strains resistant to five and six classes of antibiotics were the most common. Pearson's chi-square test showed no statistically significant difference in the occurrence of AMR (p = 0.105) or MDR (p = 0.326) among Salmonella isolates from the three sources. Our findings underscore associations and diversities among Salmonella strains isolated from food, asymptomatic carriers, and clinical patients, emphasizing the need for increased vigilance towards asymptomatic Salmonella carriers by authorities.

In Situ Cas12a-Based Allele-Specific PCR for Imaging Single-Nucleotide Variations in Foodborne Pathogenic Bacteria

In situ profiling of single-nucleotide variations (SNVs) can elucidate drug-resistant genotypes with single-cell resolution. The capacity to directly "see" genetic information is crucial for investigating the relationship between mutated genes and phenotypes. Fluorescence in situ hybridization serves as a canonical tool for genetic imaging; however, it cannot detect subtle sequence alteration including SNVs. Herein, we develop an in situ Cas12a-based amplification refractory mutation system-PCR (ARMS-PCR) method that allows the visualization of SNVs related to quinolone resistance inside cells. The capacity of discriminating SNVs is enhanced by incorporating optimized mismatched bases in the allele-specific primers, thus allowing to specifically amplify quinolone-resistant related genes. After in situ ARMS-PCR, we employed a modified Cas12a/CRISPR RNA to tag the amplicon, thereby enabling specific binding of fluorophore-labeled DNA probes. The method allows to precisely quantify quinolone-resistant Salmonella enterica in the bacterial mixture. Utilizing this method, we investigated the survival competition capacity of quinolone-resistant and quinolone-sensitive bacteria toward antimicrobial peptides and indicated the enrichment of quinolone-resistant bacteria under colistin sulfate stress. The in situ Cas12a-based ARMS-PCR method holds the potential for profiling cellular phenotypes and gene regulation with single-nucleotide resolution at the single-cell level.

Molecular docking-based virtual screening, drug-likeness, and pharmacokinetic profiling of some anti-Salmonella typhimurium cephalosporin derivatives

Objective

The rising cases of resistance to existing antibiotic therapies in Salmonella typhimurium has made it necessary to search for novel drug candidates. The present study employed the molecular docking technique to screen a set of antibacterial cephalosporin analogues against penicillin-binding protein 1a (PBP1a) of the bacterium. This is the first study to screen cephalosporin analogues against PBP1a, a protein central to peptidoglycan synthesis in S. typhimurium.

Methods

Some cephalosporin analogues were retrieved from a drug repository. The structures of the molecules were optimized using the semi-empirical method of Spartan 14 software and were subsequently docked against the active sites of PBP1a using AutoDock vina software. The most potent ligands were chosen as the most promising leads and subsequently subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling using the SwissADME online server and DataWarrior chemoinformatics program. The CABSflex 2.0 server was used to carry out molecular dynamics (MD) simulation on the most stable ligand-protein complex.

Results

Compounds 3, 23, and 28 with binding affinity (ΔG) values of -9.2, -8.7, and -8.9 kcal/mol, respectively, were selected as the most promising leads. The ligands bound to the active sites of PBP1a via hydrophobic bonds, hydrogen bonds, and electrostatic interactions. Furthermore, ADMET analyses of the ligands revealed that they exhibited sound pharmacokinetic and toxicity profiles. In addition, an MD study revealed that the most active ligand bound favorably and dynamically to the target protein.

Conclusion

The findings of this research could provide an excellent platform for the discovery and rational design of novel antibiotics against S. typhimurium. Additional in vitro and in vivo studies should be carried out on the drug candidates to validate the findings of this study.

Optimisation of Three Essential Oils against Salmonella spp. and Escherichia coli by Mixture Designa

The aim of this work is to optimise the antibacterial activity of essential oils (EOs) from Eucalyptus camaldulensis (ECEO), Mentha pulegium (MPEO) and Rosmarinus officinalis (ROEO) plants against Salmonella spp. and Escherichia coli. The qualitative antimicrobial effect was assessed using the disc diffusion method, the broth microdilution method was used to determine the minimum inhibitory concentrations (MIC). Polynomial models were created using an augmented centroid simplex mixture design to highlight the synergy of EOs. The results show a significant antibacterial effect of ECEO and MPEO against both bacterial strains, with inhibition zones (IZs) of 13 and 12 mm respectively against E. coli, and 13 and 11 mm against Salmonella spp. The latter strain showed a MIC of 0.625 % (v : v) by the ECEO, while E. coli exhibited a MIC of 0.0781 % (v : v). The binary combinations of essential oils display a synergistic effect, the proportions of the optimum EOs in the mixture giving the lowest MICm were of the order of 50.51 % ECEO and 49.49 % ROEO against Salmonella spp. and around 50 % MPEO and 50 % ECEO against E. coli. These results indicate the effectiveness of binary combinations EOs against resistant bacterial strains and suggest their importance in bacterial infections treatment.

Antibiotic Resistance and Plasmid Replicon Types of Non-Typhoidal Salmonella Serovars Isolated From Food Animals and Humans in Lagos, Nigeria

Multidrug resistance and invasiveness of non-typhoidal Salmonella (NTS) serovars have in recent times brought to the fore the public health risk associated with salmonellosis. This study was aimed at profiling NTS serovars isolated from food animals and humans for their susceptibility to antibiotics and plasmid replicon types. Forty seven NTS serovars were profiled for their susceptibility to antibiotics using the disk diffusion method. Polymerase chain reaction based replicon typing assay was used for profiling plasmid replicon types detected in Salmonella isolates. High rate of resistance were found for amoxicillin/clavulanic acid (40/47; 85.1%), cefuroxime (38/47; 80.9%) and ceftazidime (30/47; 63.8%). Thirty one (65.9%) and 33 (70.2%) showed intermediate resistance to ofloxacin and ciprofloxacin respectively. Plasmids of sizes ranging from 14.3 to 16.7 kb were detected in 24 (51.1%) of Salmonella isolates with some serovars harbouring multiple plasmids. FIA, FIB, Frep and W plasmid replicon types were detected in 11, 4, 2 and 1 of the Salmonella isolates respectively. Three of the isolates harboured both FIA and FIB replicon types. The high rate of resistance to β-lactams observed in Salmonella serovars harbouring different plasmid replicon types in this study highlight potential public health threat and the need for prudent use of antibiotics in human and veterinary medicine.

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk

Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.

In Vitro Assessment of Antimicrobial Activity of Phytobiotics Composition towards of Avian Pathogenic Escherichia coli (APEC) and Other E. coli Strains Isolated from Broiler Chickens

Escherichia coli infections (including APEC) in broiler chickens are not only a health and economic problem of the flock, but also a significant health threat to poultry meat consumers. The prophylactic and therapeutic effects of the phytobiotic composition on E. coli in broiler chickens were previously described. However, most of the data were related to the reference strains (for both in vitro and in vivo models). Based on the previous studies in human and animals, E. coli strains seem to be multidrug resistance. This, in turn, makes it necessary to develop effective alternative methods of treating this type of infection already at the stage of poultry production. In the present study, the antibacterial activity against various strains of E. coli (including APEC) was assessed for two innovative phytobiotics mixtures: H1, containing thymol, menthol, linalool, trans-anethole, methyl salicylate, 1,8-cineol, and p-cymene; H2, in addition to compounds from H1, containing terpinen-4-ol and γ-terpinene. The unique mixtures of phytobiotics used in the experiment were effective against various strains of E. coli, also against APEC, isolated from broiler chickens from traditional industrial breeding, as well as against those showing colistin resistance. The minimum inhibitory concentration (MIC) values for these unique mixtures were: For H1 1:512 for APEC and non-APEC E. coli strains isolated from day old chicks (DOCs), 1:512 for non-APEC, and 1:1024 for non-APEC isolated from broilers sample. For mixture H2, MIC for APEC from both type of samples (DOCs and broilers) was 1:1024 and for non-APEC (DOCs and broilers) was 1:512. The results suggest that phytobiotic compositions used in this study can be successfully used as a natural alternative to antibiotics in the treatment of E. coli infections in broiler chickens. The promising results may be a crucial point for further analyses in broiler flocks exposed to E. coli infections and where it is necessary to reduce the level of antibiotics or completely eliminate them, thus reducing the risk of foodborne infections.

Phage Therapy vs. the Use of Antibiotics in the Treatment of Salmonella-Infected Chickens: Comparison of Effects on Hematological Parameters and Selected Biochemical Markers

Previous studies indicated that the use of a phage cocktail, composed of bacteriophages vB_SenM-2 and vB_Sen-TO17, is effective in killing cells of Salmonella enterica serovars Typhimurium and Enteritidis in vitro and in the Galleria mellonella animal model as efficiently as antibiotics (enrofloxacin or colistin) and induced fewer deleterious changes in immune responses. Here, we investigated the effects of this phage cocktail on the hematological parameters and selected biochemical markers in chickens infected with S. enterica serovar Typhimurium, in comparison to those caused by enrofloxacin or colistin. We found that treatment with antibiotics (especially with enrofloxacin) caused nonbeneficial effects on red blood cell parameters, including hematocrit, MCV, MCH, and MCHC. However, Salmonella-induced changes in the aforementioned parameters were normalized by the use of the phage cocktail. Importantly, hepatotoxicity was suggested to be induced by both antibiotics on the basis of increased alanine transaminase (ALT) and aspartate aminotransferase (AST) activities, in contrast to the phage cocktail, which did not influence these enzymes. We conclude that phage therapy with the cocktail of vB_SenM-2 and vB_Sen-TO17 in Salmonella-infected chickens is not only as effective as antibiotics but also significantly safer for the birds than enrofloxacin and colistin.

Bacterial Pathogens in the Food Industry: Antibiotic Resistance and Virulence Factors of Salmonella enterica Strains Isolated from Food Chain Links

Salmonella is one of the most important foodborne pathogens. Fifty-three strains of Salmonella deposited in the Culture Collection of Industrial Microorganisms-Microbiological Resources Center (IAFB) were identified using molecular and proteomic analyses. Moreover, the genetic similarity of the tested strains was determined using the PFGE method. Main virulence genes were identified, and phenotypical antibiotic susceptibility profiles and prevalence of resistance genes were analyzed. Subsequently, the occurrence of the main mechanisms of β-lactam resistance was determined. Virulence genes, invA, fimA, and stn were identified in all tested strains. Phenotypic tests, including 28 antibiotics, showed that 50.9% of the strains were MDR. The tet genes associated with tetracyclines resistance were the most frequently identified genes. Concerning the genes associated with ESBL-producing Salmonella, no resistance to the TEM and CTX-M type was identified, and only two strains (KKP 1597 and KKP 1610) showed resistance to SHV. No strains exhibited AmpC-type resistance but for six Salmonella strains, the efflux-related resistance of PSE-1 was presented. The high number of resistant strains in combination with multiple ARGs in Salmonella indicates the possible overuse of antibiotics. Our results showed that it is necessary to monitor antimicrobial resistance profiles in all food chain links constantly and to implement a policy of proper antibiotic stewardship to contain or at least significantly limit the further acquisition of antibiotic resistance among Salmonella strains.

Concerning Increase in Antimicrobial Resistance Patterns of Pathogenic Strains of Salmonella Isolated in Poultry Meat Products

Salmonella is considered to be one of the major foodborne pathogens associated with the consumption of contaminated poultry meat products. To the best of our knowledge this is the first extended research performed on a number of Salmonella strains isolated during 2011-2021 from poultry meat products in Romania. The aim of this study was to characterize the prevalence of pathogenic Salmonella serovars, antimicrobial susceptibility, and antimicrobial resistance genes in 112 Salmonella isolates recovered from raw poultry meat products. The results showed that Salmonella enterica serovars Enteritidis and Typhimurium were the common serotypes (56%; 25%). Overall, the majority of the isolates were resistant to at least three tested antimicrobials. High resistance was observed for tetracycline (84%), nalidixic acid (78%), and ampicillin (78%) in pathogenic Salmonella isolated during the period 2016-2021. All the pathogenic Salmonella isolated during 2016-2021 tested positive to at least one resistance gene encoding for tetracycline resistance, with the tetA gene being the most prevalent (62%). In addition, 64% (24/37) of the Salmonella isolates carried at least one of the genes (blaCMY-2, blaSHV1, blaTEM1) that code for β-Lactams resistance. The findings in this study showed a high prevalence of multi-drug resistant (MDR) Salmonella serovars in poultry meat products and a concerning increase of resistance patterns. The continuous occurrence of more resistant strains implies that effective measures should be strictly applied in this particular food chain in order to prevent their spread and guarantee microbial safety.

Pet Reptiles in Poland as a Potential Source of Transmission of Salmonella

Reptiles are considered a potential source of Salmonella transmission to humans. The aim of this research was to determine the incidence of Salmonella in pet reptiles in Poland and to examine Salmonella isolates with regard to their biochemical characteristics, serotype, antimicrobial susceptibility, and pathogenic and zoonotic potential. The research material consisted of 67 reptile faeces samples. The taxonomic affiliation of the Salmonella isolates was determined by MALDI-TOF mass spectrometry, biochemical analyses, and serotyping; whole genome sequencing (WGS) analysis was performed on three isolates whose serotype could not be determined by agglutination. The antimicrobial susceptibility of the Salmonella isolates was determined by the broth dilution method, and in the case of some antimicrobials by the disk diffusion method. The pathogenic and zoonotic potential of the identified serotypes was estimated based on available reports and case studies. The presence of Salmonella was confirmed in 71.6% of faecal samples, with the highest incidence (87.1%) recorded for snakes, followed by lizards (77.8%) and turtles (38.9%). All isolates (n = 51) belonged to the species S. enterica, predominantly to subspecies I (66.7%) and IIIb (25.5%). Among these, 25 serotypes were identified, including 10 that had previously been confirmed to cause reptile-associated salmonellosis (RAS). Salmonella isolates were susceptible to all antimicrobial substances used except streptomycin, to which 9.8% of the strains showed resistance. None of the strains contained corresponding resistance genes. The study demonstrates that pet reptiles kept in Poland are a significant reservoir of Salmonella and contribute to knowledge of the characteristics of reptilian Salmonella strains. Due to the risk of salmonellosis, contact with these animals requires special hygiene rules.

Antibiotic Resistance in Bacteria—A Review

Background: A global problem of multi-drug resistance (MDR) among bacteria is the cause of hundreds of thousands of deaths every year. In response to the significant increase of MDR bacteria, legislative measures have widely been taken to limit or eliminate the use of antibiotics, including in the form of feed additives for livestock, but also in metaphylaxis and its treatment, which was the subject of EU Regulation in 2019/6. Numerous studies have documented that bacteria use both phenotypis and gentic strategies enabling a natural defence against antibiotics and the induction of mechanisms in increasing resistance to the used antibacterial chemicals. The mechanisms presented in this review developed by the bacteria have a significant impact on reducing the ability to combat bacterial infections in humans and animals. Moreover, the high prevalence of multi-resistant strains in the environment and the ease of transmission of drug-resistance genes between the different bacterial species including commensal flora and pathogenic like foodborne pathogens (E. coli, Campylobacter spp., Enterococcus spp., Salmonella spp., Listeria spp., Staphylococcus spp.) favor the rapid spread of multi-resistance among bacteria in humans and animals. Given the global threat posed by the widespread phenomenon of multi-drug resistance among bacteria which are dangerous for humans and animals, the subject of this study is the presentation of the mechanisms of resistance in most frequent bacteria called as “foodborne pathoges” isolated from human and animals. In order to present the significance of the global problem related to multi-drug resistance among selected pathogens, especially those danger to humans, the publication also presents statistical data on the percentage range of occurrence of drug resistance among selected bacteria in various regions of the world. In addition to the phenotypic characteristics of pathogen resistance, this review also presents detailed information on the detection of drug resistance genes for specific groups of antibiotics. It should be emphasized that the manuscript also presents the results of own research i.e., Campylobacter spp., E. coli or Enetrococcus spp. This subject and the presentation of data on the risks of drug resistance among bacteria will contribute to initiating research in implementing the prevention of drug resistance and the development of alternatives for antimicrobials methods of controlling bacteria.