Antimicrobial Resistance of Non-Typhoid Salmonella in Meat and Meat Products

Analysis on Foodborne Pathogen Contamination of Food Samples in Longnan City from 2013 to 2022

The objective was to determine the prevalence of foodborne pathogens in food in Longnan City, Gansu Province, China. In this research, we conducted tests on baked foods, catering foods, meat, and fruits and vegetables sold in supermarkets, farmers' markets, restaurants, retail stores, street stalls, and school canteens from 2013 to 2022. We analyzed the variety of foodborne pathogens (Salmonella, Staphylococcus aureus, Listeria monocytogenes, Bacillus cereus, and diarrheagenic Escherichia coli) in different sites and food types. Once foodborne pathogens were detected in the sample, it was deemed unqualified. The total detection rates of foodborne pathogens were 1.559%, 3.349%, 1.980%, 1.040%, 3.383%, and 1.303% in food from supermarkets, farmers' markets, restaurants, retail stores, street stalls, and school canteens, respectively. No pathogenic bacteria were detected in baked foods. Salmonella, S. aureus, L. monocytogenes, B. cereus, and diarrheagenic E. coli were detected in catering foods, among which B. cereus had the highest detection rate. Salmonella was the most common pathogenic bacteria detected in meat, while the detection rate of pathogenic bacteria in fruits and vegetables was low, with only one positive sample for diarrheagenic E. coli. Among the six sites, street stalls (3.382%) and farmers' markets (3.349%) had higher detection rates of pathogens. In general, the detection rate of pathogens from 2013 to 2022 was not high, but there were also some hidden dangers. Catering food is vulnerable to pathogen contamination, and street stalls and farmers' markets are the main sites of pollution. According to the above findings, the regulatory authorities should continue to strengthen supervision, guarantee food safety through early warning, and reduce the risk of food contamination.

Virulence potential of Salmonella 1,4, [5],12:i:- strains isolated during decades from different sources in the Southeast region of Brazil

Salmonella 1,4, [5],12:i:- is one of the most prevalent serovars associated with gastroenteritis in several countries, including Brazil. However, few studies have analyzed the virulence potential of this variant in this country. Therefore, this study aimed to characterize S. 1,4, [5],12:i:- strains isolated in Southeast Brazil. To this end, 113 S. 1,4, [5],12:i:- strains isolated from different sources between 1983 and 2020 were analyzed. For all strains, the frequencies of 11 virulence genes were investigated using PCR and the molecular typing was performed using pulsed-field gel electrophoresis (PFGE). Furthermore, 40 strains isolated from human and non-human sources were characterized by survival under acid and oxidative stress, and virulence analysis in Galleria mellonella was performed for 20 selected strains. All virulence genes were detected in more than 91% of the strains. The studied strains were grouped into four clusters using PFGE. Most strains were present in one cluster, named PFGE-A, with a genetic similarity of ≥ 79.5%. All 40 strains survived acid stress after 10 min and 1 h of exposure. Under oxidative stress, all 40 strains survived after 10 min, and 36 survived after 1 h of exposure. In the G. mellonella assay, nine isolates from non-human sources and six isolates from human showed high-to-intermediate virulence profiles. In conclusion, the pathogenic potential of the strains studied was corroborated by the high frequency of all the virulence genes identified. The PFGE results suggested that most strains belonged to one main cluster that has been prevailing in the São Paulo State, Brazil. The S. 1,4, [5],12:i:- strains isolated from human and non-human sources successfully survived the unfavorable conditions in the human gastrointestinal tract. Finally, strains isolated from non-human sources showed a higher proportion of isolates with high to intermediate virulence profiles in G. mellonella than in human isolates, suggesting a possible difference between isolates from different origins.

Detection of Cyclomodulin CNF-1 Toxin-Producing Strains of Escherichia coli in Pig Kidneys at a Slaughterhouse

Food is often contaminated with Escherichia coli (E. coli) bacteria strains, which have been associated with different diseases, including urinary tract infections. The consumption of meat by humans is a potential route of transmission of antimicrobial resistance, and food-producing animals have been associated as a major reservoir of resistant bacterial strains. The aim of this study was to determine the presence of the E. coli strains producing the CNF-1 toxin in pig kidneys. Pig kidneys were collected from a Mexican slaughterhouse and classified according to their coloration into reddish kidneys (RK) and yellowish kidneys (YK). A tissue sample from each kidney was processed for histological analysis, the presence of E. coli was determined by conventional PCR assay, and the CNF-1 toxin was detected by both conventional PCR and Western blotting. Herein, an inflammatory cell infiltrate was found in all collected kidneys, regardless of macroscopic differences. Surprisingly, E. coli and the CNF-1 toxin were detected in all kidney samples. We clearly demonstrate contamination by CNF-1 toxin-producing E. coli in pork kidneys from a slaughterhouse, even in those without apparent damage. This suggests that pork may serve as a reservoir for pathogens, representing an important risk to human health.

Isolation, susceptibility profiles and genomic analysis of a colistin-resistant Salmonella enterica serovar Kentucky strain COL-R

Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03559-2.

Comparative Analysis between Salmonella enterica Isolated from Imported and Chinese Native Chicken Breeds

Salmonella enterica is considered a significant threat to the global poultry industry and public health. In recent decades, antimicrobial resistance in Salmonella enterica has attracted increasing concern throughout the world. However, limited information is available on Salmonella enterica among different breeds of breeder chickens. Thus, this study aimed to compare the prevalence, serotype distribution, emergence of extended-spectrum beta-lactamases (ESBLs), antimicrobial resistance, and genetic resistance mechanisms in Salmonella enterica among different breeds of breeder chickens. A total of 693 samples (dead embryos, cloacal swabs, water, feed, environmental swabs, and meconium of newly hatched chicks) were selected and cultured for Salmonella from four breeder chicken farms in Shandong province, China, representing one imported and three native breeds, and the isolates were further serotyped. Of the Salmonella isolates, susceptibility to 11 antimicrobials of 5 classes, ESBL screening, and the presence of 21 antimicrobial resistance genes were determined in the present study. Overall, 94 (13.6%) isolates were recovered, which were divided into 3 serotypes (Salmonella Pullorum (n = 36), Salmonella Thompson (n = 32), and Salmonella Enteritidis (n = 26)). The results showed that the prevalence of Salmonella enterica isolates from the imported breeds was higher compared with the three domestic breeds. Eight of the ninety-four isolates were ESBL-positive strains, which were recovered from a domestic breed chicken farm. These eight ESBL-producing isolates were serotyped to Pullorum. Surprisingly, Salmonella Enteritidis (S. enteritidis) and S. pullorum were simultaneously isolated from a single dead embryo observed among one native breed. Meanwhile, among the Salmonella isolates, 53.2% (50/94) were multidrug-resistant strains, and 44.7% (42/94) of the isolates presented resistance to at least five antibiotics. Nearly all of the isolates (97.9%, 92/94) were resistant to at least one antimicrobial; one isolate of S. Thompson was resistant to seven antimicrobial agents belonging to four different classes. The carriage rate of three resistance genes (tetA, tetB, and sul1) among isolates from the imported breeds (87%, 70%, and 65.2%) was higher than that in those from domestic breeds (35.2%, 36.6, and 14.1%). To our knowledge, this is the first report of ESBLs-producing Salmonella isolated from a Chinese native breed of breeder chickens. Our results also highlight that a high prevalence of multidrug-resistant Salmonella enterica contamination is widespread among different breeds of breeder chickens, which is a major risk of food-borne diseases and public health.

Antimicrobial resistance and molecular typing of Salmonella in the chicken production chain in Hubei Province, China

Salmonella is a significant foodborne zoonotic pathogen that endangers both human and animal health. The goal of this research is to gain a preliminary understanding of Salmonella contamination and antimicrobial resistance in the chicken production chain in Hubei Province, China. 1149 animal and environmental samples were collected from chicken farms, slaughterhouses, and retail markets in six cities across Hubei Province in China from 2019 to 2020, yielding Salmonella isolation rates of 4.68% (28/598), 12.21% (47/385), and 9.64% (16/166), respectively. Seventeen distinct serotypes were detected among 53 non-clonal Salmonella strains, of which Meleagridis (26.42%, 14/53) was the dominant serotype. Almost half of the strains (49.06%, 26/53) were multi-drug resistant (MDR). Whole-genome sequencing (WGS) showed that 10 resistance genes (tetA, blaTEM, parC, qnrS1, floR, aac(6′)-Iy, aph(6)-Id, aph(3″)-Ib, aac(6′)-Iaa and sul2) and 7 categories of virulence genes were present in all three links in 22 non-clonal dominant serotype strains. It was shown that Salmonella in the chicken production chain in Hubei Province had a high resistance rate to Tetracycline (TET, 73.58%), Ofloxacin (OFL, 69.81%), Florfenicol (FFC, 60.38%) and Ampicillin (AMP, 39.62%) which was consistent with the widespread use of these drugs in the husbandry industry in China. Salmonella ST types determined by MLST and serotypes determined by WGS had a one-to-one correlation. Minimum spanning tree analysis revealed that there was cross contamination of Salmonella in farms and slaughterhouses, slaughterhouses and markets, animal samples and environmental samples. This work provides useful information for the prevention and control of contamination and antimicrobial resistance of Salmonella in the chicken production chain, as well as demonstrating the dependable role of WGS in Salmonella molecular typing.

Antimicrobial Resistant E. coli in Pork and Wild Boar Meat: A Risk to Consumers

Antimicrobial-resistant foodborne microorganisms may be transmitted from food producing animals to humans through the consumption of meat products. In this study, meat that was derived from farmed pigs and wild boars was analyzed and compared. Escherichia coli (E. coli) were isolated and tested phenotypically and genotypically for their resistance to quinolones, aminoglycosides and carbapenems. The co-presence of AMR-associated plasmid genes was also evaluated. A quinolone AMR phenotypic analysis showed 41.9% and 36.1% of resistant E. coli derived from pork and wild boars meat, respectively. A resistance to aminoglycosides was detected in the 6.6% of E. coli that was isolated from pork and in 1.8% of the wild boar meat isolates. No resistant profiles were detected for the carbapenems. The quinolone resistance genes were found in 58.3% of the phenotypically resistant pork E. coli and in 17.5% of the wild boar, thus showing low genotypic confirmation rates. The co-presence of the plasmid-related genes was observed only for the quinolones and aminoglycosides, but not for the carbapenems. Wild boar E. coli were the most capable to perform biofilm production when they were compared to pork E. coli. In conclusion, the contamination of pork and wild boar meat by AMR microorganisms could be a threat for consumers, especially if biofilm-producing strains colonize the surfaces and equipment that are used in the food industry.

Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance Are Incompatible with Available Surveillance Data

ABSTRACT

Foodborne antimicrobial-resistant (AMR) microorganisms are a global food safety concern. Antimicrobial drug use (AMU) in livestock may increase the risk of resistant foodborne bacterial infections in humans via contaminated animal products. Consequently, countries have implemented different livestock AMU restriction policies, opening the potential for trade disputes. AMR risk equivalence between countries with different AMU policies must be established by using scientifically justified risk assessments. The Codex Alimentarius Commission's Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance (AMR Codex) recommends an approach that requires quantification of detailed information, for which, in many instances, little to no data exist. Using AMR Salmonella exposure from beef consumption as an example, we demonstrate the difficulty of implementing the AMR Codex by comparing key regionally specific parameters within the United States and European Union, two regions with substantial beef production and consumption, robust foodborne pathogen sampling and surveillance systems, and different AMU policies. Currently, neither region fully captures data for key regional variables to populate a detailed risk assessment as outlined in the AMR Codex, nor are they able to adequately link AMU in livestock to AMR infections in humans. Therefore, the AMR Codex guidelines are currently aspirational and not a viable option to assess the impact of livestock AMU reductions on the human health risk of AMR salmonellosis from beef or produce regionally comparable estimates of risk. More flexible risk assessment guidelines that more directly link livestock AMU to human health risk and are amenable to currently available data are needed to allow for country variations and to calculate comparable regional risk estimates, which can be used to guide international trade policy.

HIGHLIGHTS

New Advances in Lateral Flow Immunoassay (LFI) Technology for Food Safety Detection

With the continuous development of China’s economy and society, people and the government have higher and higher requirements for food safety. Testing for food dopants and toxins can prevent the occurrence of various adverse health phenomena in the world’s population. By deploying new and powerful sensors that enable rapid sensing processes, the food industry can help detect trace adulteration and toxic substances. At present, as a common food safety detection method, lateral flow immunochromatography (LFI) is widely used in food safety testing, environmental testing and clinical medical treatment because of its advantages of simplicity, speed, specificity and low cost, and plays a pivotal role in ensuring food safety. This paper mainly focuses on the application of lateral flow immunochromatography and new technologies combined with test strips in food safety detection, such as aptamers, surface-enhanced Raman spectroscopy, quantum dots, electrochemical test strip detection technology, biosensor test strip detection, etc. In addition, sensing principles such as fluorescence resonance energy transfer can also more effective. Different methods have different characteristics. The following is a review of the application of these technologies in food safety detection.

Resistance and Pathogenicity of Salmonella Thompson Isolated from Incubation End of a Poultry Farm

Simple Summary

Non-typhoid Salmonella is the general term of Salmonella other than typhoid and paratyphoid, which often causes foodborne gastroenteritis in humans, but some serotypes have been proved to be pathogenic to poultry. Salmonella Enterica and Salmonella Typhimurium are the common serotypes pathogenic to poultry and have been systematically studied, but other serotypes have rarely been studied. During Salmonella surveillance in farms, we discovered by chance that Salmonella Thompson, a common non-typhoid Salmonella, is also pathogenic to avian embryos. Therefore, this study aimed to explore antimicrobial resistance and pathogenicity of clinical S. Thompson. Firstly, we found that the core-genome multilocus sequence typing of 14 clinical S. Thompson was consistent with two strains of S. Thompson from humans in China. Secondly, the antimicrobial resistance gene analysis demonstrated that all strains carried the polymyxin resistance gene mcr-9, which had not appeared resistance phenotype. Meanwhile, many essential virulence genes were also found in each S. Thompson isolate. Finally, the bacterial inoculation experiment revealed that clinical S. Thompson was highly pathogenic to newborn chicks after yolk sac inoculation. This study suggests that Salmonella Thompson can circulate between humans and poultry farms and transmit drug resistance genes and demonstrated that Salmonella Thompson is highly pathogenic to chicks and should be guarded against in the hatching stage of poultry farms.

Abstract

Salmonella Thompson, an important foodborne pathogen, is rarely found to be pathogenic to poultry. Accidentally, S. Thompson was found to be pathogenic to embryos of white feather broiler at a poultry farm in China. Therefore, this study aimed to explore antimicrobial resistance and pathogenicity of clinical S. Thompson isolated from dead poultry embryos. The phylogenetic tree based on 16S rRNA and seven housekeeping genes showed that the 14 clinical S. Thompson were closely related. The core-genome multilocus sequence typing of 14 clinical S. Thompson based on whole-genome sequencing was cgST-12774, consistent with the only two strains of S. Thompson from humans in China as reported in the NCBI database. The antimicrobial resistance gene analysis demonstrated that all strains carried aac(6′)-Iaa and the polymyxin resistance gene mcr-9. Antimicrobial sensitivity tests for 18 antibiotics showed that S. Thompson isolates displayed resistance against streptomycin (100%), ampicillin (35.7%), and doxycycline (14.3%), but sensitivity to polymyxin B, proving that the mcr-9 gene had not appeared resistance phenotype. Virulence genes Salmonella pathogenicity island (SPI) SPI1-5, type I fimbriae gene (fimA), flagellar assembly genes (bcfC, flhD, fliA, fliC, fljB, flgK, and lpfC), and other virulence genes (iroN, pagC, and cigR) were found in each S. Thompson isolate. Additionally, the bacterial inoculation experiment with 1-day-old chicks revealed that clinical S. Thompson was highly pathogenic to newborn chicks after yolk sac inoculation. This study highlighted that the S. Thompson isolated from poultry embryos and the S. Thompson causing human foodborne diarrhea in some parts of China belong to the same cgMLST typology (cgST-12774) and showed the pathogenicity of this clinical S. Thompson to chicks.

Impact of Antibiotics as Waste, Physical, Chemical, and Enzymatical Degradation: Use of Laccases

The first traces of Tetracycline (TE) were detected in human skeletons from Sudan and Egypt, finding that it may be related to the diet of the time, the use of some dyes, and the use of soils loaded with microorganisms, such as Streptomyces spp., among other microorganisms capable of producing antibiotics. However, most people only recognise authors dating between 1904 and 1940, such as Ehrlich, Domagk, and Fleming. Antibiotics are the therapeutic option for countless infections treatment; unfortunately, they are the second most common group of drugs in wastewaters worldwide due to failures in industrial waste treatments (pharmaceutics, hospitals, senior residences) and their irrational use in humans and animals. The main antibiotics problem lies in delivered and non-prescribed human use, use in livestock as growth promoters, and crop cultivation as biocides (regulated activities that have not complied in some places). This practice has led to the toxicity of the environment as antibiotics generate eutrophication, water pollution, nutrient imbalance, and press antibiotic resistance. In addition, the removal of antibiotics is not a required process in global wastewater treatment standards. This review aims to raise awareness of the negative impact of antibiotics as residues and physical, chemical, and biological treatments for their degradation. We discuss the high cost of physical and chemical treatments, the risk of using chemicals that worsen the situation, and the fact that each antibiotic class can be transformed differently with each of these treatments and generate new compounds that could be more toxic than the original ones; also, we discuss the use of enzymes for antibiotic degradation, with emphasis on laccases.